diff --git a/src/ASPHERE/atom_vec_ellipsoid.cpp b/src/ASPHERE/atom_vec_ellipsoid.cpp
index e48e7ae30..5d85e01ef 100755
--- a/src/ASPHERE/atom_vec_ellipsoid.cpp
+++ b/src/ASPHERE/atom_vec_ellipsoid.cpp
@@ -1,850 +1,850 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "stdlib.h"
#include "atom_vec_ellipsoid.h"
-#include "lmptype.h"
#include "math_extra.h"
#include "atom.h"
#include "force.h"
#include "domain.h"
#include "modify.h"
#include "fix.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define DELTA 10000
/* ---------------------------------------------------------------------- */
AtomVecEllipsoid::AtomVecEllipsoid(LAMMPS *lmp, int narg, char **arg) :
AtomVec(lmp, narg, arg)
{
molecular = 0;
mass_type = 1;
shape_type = 1;
comm_x_only = comm_f_only = 0;
size_forward = 7;
size_reverse = 6;
size_border = 10;
size_velocity = 6;
size_data_atom = 9;
size_data_vel = 7;
xcol_data = 3;
atom->angmom_flag = atom->torque_flag = atom->quat_flag = 1;
}
/* ----------------------------------------------------------------------
grow atom arrays
n = 0 grows arrays by DELTA
n > 0 allocates arrays to size n
------------------------------------------------------------------------- */
void AtomVecEllipsoid::grow(int n)
{
if (n == 0) nmax += DELTA;
else nmax = n;
atom->nmax = nmax;
if (nmax < 0 || nmax > MAXSMALLINT)
error->one("Per-processor system is too big");
tag = atom->tag = (int *)
memory->srealloc(atom->tag,nmax*sizeof(int),"atom:tag");
type = atom->type = (int *)
memory->srealloc(atom->type,nmax*sizeof(int),"atom:type");
mask = atom->mask = (int *)
memory->srealloc(atom->mask,nmax*sizeof(int),"atom:mask");
image = atom->image = (int *)
memory->srealloc(atom->image,nmax*sizeof(int),"atom:image");
x = atom->x = memory->grow_2d_double_array(atom->x,nmax,3,"atom:x");
v = atom->v = memory->grow_2d_double_array(atom->v,nmax,3,"atom:v");
f = atom->f = memory->grow_2d_double_array(atom->f,nmax,3,"atom:f");
quat = atom->quat =
memory->grow_2d_double_array(atom->quat,nmax,4,"atom:quat");
angmom = atom->angmom =
memory->grow_2d_double_array(atom->angmom,nmax,3,"atom:angmom");
torque = atom->torque =
memory->grow_2d_double_array(atom->torque,nmax,3,"atom:torque");
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
}
/* ----------------------------------------------------------------------
reset local array ptrs
------------------------------------------------------------------------- */
void AtomVecEllipsoid::grow_reset()
{
tag = atom->tag; type = atom->type;
mask = atom->mask; image = atom->image;
x = atom->x; v = atom->v; f = atom->f;
quat = atom->quat; angmom = atom->angmom; torque = atom->torque;
}
/* ---------------------------------------------------------------------- */
void AtomVecEllipsoid::copy(int i, int j)
{
tag[j] = tag[i];
type[j] = type[i];
mask[j] = mask[i];
image[j] = image[i];
x[j][0] = x[i][0];
x[j][1] = x[i][1];
x[j][2] = x[i][2];
v[j][0] = v[i][0];
v[j][1] = v[i][1];
v[j][2] = v[i][2];
quat[j][0] = quat[i][0];
quat[j][1] = quat[i][1];
quat[j][2] = quat[i][2];
quat[j][3] = quat[i][3];
angmom[j][0] = angmom[i][0];
angmom[j][1] = angmom[i][1];
angmom[j][2] = angmom[i][2];
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j);
}
/* ---------------------------------------------------------------------- */
int AtomVecEllipsoid::pack_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = quat[j][0];
buf[m++] = quat[j][1];
buf[m++] = quat[j][2];
buf[m++] = quat[j][3];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
dz = pbc[2]*domain->zprd;
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = quat[j][0];
buf[m++] = quat[j][1];
buf[m++] = quat[j][2];
buf[m++] = quat[j][3];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecEllipsoid::pack_comm_vel(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = quat[j][0];
buf[m++] = quat[j][1];
buf[m++] = quat[j][2];
buf[m++] = quat[j][3];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
buf[m++] = angmom[j][0];
buf[m++] = angmom[j][1];
buf[m++] = angmom[j][2];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
dz = pbc[2]*domain->zprd;
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = quat[j][0];
buf[m++] = quat[j][1];
buf[m++] = quat[j][2];
buf[m++] = quat[j][3];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
buf[m++] = angmom[j][0];
buf[m++] = angmom[j][1];
buf[m++] = angmom[j][2];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecEllipsoid::pack_comm_one(int i, double *buf)
{
buf[0] = quat[i][0];
buf[1] = quat[i][1];
buf[2] = quat[i][2];
buf[3] = quat[i][3];
return 4;
}
/* ---------------------------------------------------------------------- */
void AtomVecEllipsoid::unpack_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
quat[i][0] = buf[m++];
quat[i][1] = buf[m++];
quat[i][2] = buf[m++];
quat[i][3] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
void AtomVecEllipsoid::unpack_comm_vel(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
quat[i][0] = buf[m++];
quat[i][1] = buf[m++];
quat[i][2] = buf[m++];
quat[i][3] = buf[m++];
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
angmom[i][0] = buf[m++];
angmom[i][1] = buf[m++];
angmom[i][2] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecEllipsoid::unpack_comm_one(int i, double *buf)
{
quat[i][0] = buf[0];
quat[i][1] = buf[1];
quat[i][2] = buf[2];
quat[i][3] = buf[3];
return 4;
}
/* ---------------------------------------------------------------------- */
int AtomVecEllipsoid::pack_reverse(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
buf[m++] = f[i][0];
buf[m++] = f[i][1];
buf[m++] = f[i][2];
buf[m++] = torque[i][0];
buf[m++] = torque[i][1];
buf[m++] = torque[i][2];
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecEllipsoid::pack_reverse_one(int i, double *buf)
{
buf[0] = torque[i][0];
buf[1] = torque[i][1];
buf[2] = torque[i][2];
return 3;
}
/* ---------------------------------------------------------------------- */
void AtomVecEllipsoid::unpack_reverse(int n, int *list, double *buf)
{
int i,j,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
f[j][0] += buf[m++];
f[j][1] += buf[m++];
f[j][2] += buf[m++];
torque[j][0] += buf[m++];
torque[j][1] += buf[m++];
torque[j][2] += buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecEllipsoid::unpack_reverse_one(int i, double *buf)
{
torque[i][0] += buf[0];
torque[i][1] += buf[1];
torque[i][2] += buf[2];
return 3;
}
/* ---------------------------------------------------------------------- */
int AtomVecEllipsoid::pack_border(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = quat[j][0];
buf[m++] = quat[j][1];
buf[m++] = quat[j][2];
buf[m++] = quat[j][3];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0];
dy = pbc[1];
dz = pbc[2];
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = quat[j][0];
buf[m++] = quat[j][1];
buf[m++] = quat[j][2];
buf[m++] = quat[j][3];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecEllipsoid::pack_border_vel(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = quat[j][0];
buf[m++] = quat[j][1];
buf[m++] = quat[j][2];
buf[m++] = quat[j][3];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
buf[m++] = angmom[j][0];
buf[m++] = angmom[j][1];
buf[m++] = angmom[j][2];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0];
dy = pbc[1];
dz = pbc[2];
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = quat[j][0];
buf[m++] = quat[j][1];
buf[m++] = quat[j][2];
buf[m++] = quat[j][3];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
buf[m++] = angmom[j][0];
buf[m++] = angmom[j][1];
buf[m++] = angmom[j][2];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecEllipsoid::pack_border_one(int i, double *buf)
{
buf[0] = quat[i][0];
buf[1] = quat[i][1];
buf[2] = quat[i][2];
buf[3] = quat[i][3];
return 4;
}
/* ---------------------------------------------------------------------- */
void AtomVecEllipsoid::unpack_border(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
if (i == nmax) grow(0);
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
tag[i] = static_cast<int> (buf[m++]);
type[i] = static_cast<int> (buf[m++]);
mask[i] = static_cast<int> (buf[m++]);
quat[i][0] = buf[m++];
quat[i][1] = buf[m++];
quat[i][2] = buf[m++];
quat[i][3] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
void AtomVecEllipsoid::unpack_border_vel(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
if (i == nmax) grow(0);
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
tag[i] = static_cast<int> (buf[m++]);
type[i] = static_cast<int> (buf[m++]);
mask[i] = static_cast<int> (buf[m++]);
quat[i][0] = buf[m++];
quat[i][1] = buf[m++];
quat[i][2] = buf[m++];
quat[i][3] = buf[m++];
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
angmom[i][0] = buf[m++];
angmom[i][1] = buf[m++];
angmom[i][2] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecEllipsoid::unpack_border_one(int i, double *buf)
{
quat[i][0] = buf[0];
quat[i][1] = buf[1];
quat[i][2] = buf[2];
quat[i][3] = buf[3];
return 4;
}
/* ----------------------------------------------------------------------
pack data for atom I for sending to another proc
xyz must be 1st 3 values, so comm::exchange() can test on them
------------------------------------------------------------------------- */
int AtomVecEllipsoid::pack_exchange(int i, double *buf)
{
int m = 1;
buf[m++] = x[i][0];
buf[m++] = x[i][1];
buf[m++] = x[i][2];
buf[m++] = v[i][0];
buf[m++] = v[i][1];
buf[m++] = v[i][2];
buf[m++] = tag[i];
buf[m++] = type[i];
buf[m++] = mask[i];
buf[m++] = image[i];
buf[m++] = quat[i][0];
buf[m++] = quat[i][1];
buf[m++] = quat[i][2];
buf[m++] = quat[i][3];
buf[m++] = angmom[i][0];
buf[m++] = angmom[i][1];
buf[m++] = angmom[i][2];
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]);
buf[0] = m;
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecEllipsoid::unpack_exchange(double *buf)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
int m = 1;
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
x[nlocal][2] = buf[m++];
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
tag[nlocal] = static_cast<int> (buf[m++]);
type[nlocal] = static_cast<int> (buf[m++]);
mask[nlocal] = static_cast<int> (buf[m++]);
image[nlocal] = static_cast<int> (buf[m++]);
quat[nlocal][0] = buf[m++];
quat[nlocal][1] = buf[m++];
quat[nlocal][2] = buf[m++];
quat[nlocal][3] = buf[m++];
angmom[nlocal][0] = buf[m++];
angmom[nlocal][1] = buf[m++];
angmom[nlocal][2] = buf[m++];
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->
unpack_exchange(nlocal,&buf[m]);
atom->nlocal++;
return m;
}
/* ----------------------------------------------------------------------
size of restart data for all atoms owned by this proc
include extra data stored by fixes
------------------------------------------------------------------------- */
int AtomVecEllipsoid::size_restart()
{
int i;
int nlocal = atom->nlocal;
int n = 18 * nlocal;
if (atom->nextra_restart)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
for (i = 0; i < nlocal; i++)
n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
return n;
}
/* ----------------------------------------------------------------------
pack atom I's data for restart file including extra quantities
xyz must be 1st 3 values, so that read_restart can test on them
molecular types may be negative, but write as positive
------------------------------------------------------------------------- */
int AtomVecEllipsoid::pack_restart(int i, double *buf)
{
int m = 1;
buf[m++] = x[i][0];
buf[m++] = x[i][1];
buf[m++] = x[i][2];
buf[m++] = tag[i];
buf[m++] = type[i];
buf[m++] = mask[i];
buf[m++] = image[i];
buf[m++] = v[i][0];
buf[m++] = v[i][1];
buf[m++] = v[i][2];
buf[m++] = quat[i][0];
buf[m++] = quat[i][1];
buf[m++] = quat[i][2];
buf[m++] = quat[i][3];
buf[m++] = angmom[i][0];
buf[m++] = angmom[i][1];
buf[m++] = angmom[i][2];
if (atom->nextra_restart)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]);
buf[0] = m;
return m;
}
/* ----------------------------------------------------------------------
unpack data for one atom from restart file including extra quantities
------------------------------------------------------------------------- */
int AtomVecEllipsoid::unpack_restart(double *buf)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) {
grow(0);
if (atom->nextra_store)
atom->extra = memory->grow_2d_double_array(atom->extra,nmax,
atom->nextra_store,
"atom:extra");
}
int m = 1;
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
x[nlocal][2] = buf[m++];
tag[nlocal] = static_cast<int> (buf[m++]);
type[nlocal] = static_cast<int> (buf[m++]);
mask[nlocal] = static_cast<int> (buf[m++]);
image[nlocal] = static_cast<int> (buf[m++]);
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
quat[nlocal][0] = buf[m++];
quat[nlocal][1] = buf[m++];
quat[nlocal][2] = buf[m++];
quat[nlocal][3] = buf[m++];
angmom[nlocal][0] = buf[m++];
angmom[nlocal][1] = buf[m++];
angmom[nlocal][2] = buf[m++];
double **extra = atom->extra;
if (atom->nextra_store) {
int size = static_cast<int> (buf[0]) - m;
for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++];
}
atom->nlocal++;
return m;
}
/* ----------------------------------------------------------------------
create one atom of itype at coord
set other values to defaults
------------------------------------------------------------------------- */
void AtomVecEllipsoid::create_atom(int itype, double *coord)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
tag[nlocal] = 0;
type[nlocal] = itype;
x[nlocal][0] = coord[0];
x[nlocal][1] = coord[1];
x[nlocal][2] = coord[2];
mask[nlocal] = 1;
image[nlocal] = (512 << 20) | (512 << 10) | 512;
v[nlocal][0] = 0.0;
v[nlocal][1] = 0.0;
v[nlocal][2] = 0.0;
quat[nlocal][0] = 1.0;
quat[nlocal][1] = 0.0;
quat[nlocal][2] = 0.0;
quat[nlocal][3] = 0.0;
angmom[nlocal][0] = 0.0;
angmom[nlocal][1] = 0.0;
angmom[nlocal][2] = 0.0;
atom->nlocal++;
}
/* ----------------------------------------------------------------------
unpack one line from Atoms section of data file
initialize other atom quantities
------------------------------------------------------------------------- */
void AtomVecEllipsoid::data_atom(double *coord, int imagetmp, char **values)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
tag[nlocal] = atoi(values[0]);
if (tag[nlocal] <= 0)
error->one("Invalid atom ID in Atoms section of data file");
type[nlocal] = atoi(values[1]);
if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
error->one("Invalid atom type in Atoms section of data file");
x[nlocal][0] = coord[0];
x[nlocal][1] = coord[1];
x[nlocal][2] = coord[2];
quat[nlocal][0] = atof(values[5]);
quat[nlocal][1] = atof(values[6]);
quat[nlocal][2] = atof(values[7]);
quat[nlocal][3] = atof(values[8]);
MathExtra::normalize4(quat[nlocal]);
image[nlocal] = imagetmp;
mask[nlocal] = 1;
v[nlocal][0] = 0.0;
v[nlocal][1] = 0.0;
v[nlocal][2] = 0.0;
angmom[nlocal][0] = 0.0;
angmom[nlocal][1] = 0.0;
angmom[nlocal][2] = 0.0;
atom->nlocal++;
}
/* ----------------------------------------------------------------------
unpack hybrid quantities from one line in Atoms section of data file
initialize other atom quantities for this sub-style
------------------------------------------------------------------------- */
int AtomVecEllipsoid::data_atom_hybrid(int nlocal, char **values)
{
quat[nlocal][0] = atof(values[0]);
quat[nlocal][1] = atof(values[1]);
quat[nlocal][2] = atof(values[2]);
quat[nlocal][3] = atof(values[3]);
MathExtra::normalize4(quat[nlocal]);
return 4;
}
/* ----------------------------------------------------------------------
unpack one line from Velocities section of data file
------------------------------------------------------------------------- */
void AtomVecEllipsoid::data_vel(int m, char **values)
{
v[m][0] = atof(values[0]);
v[m][1] = atof(values[1]);
v[m][2] = atof(values[2]);
angmom[m][0] = atof(values[3]);
angmom[m][1] = atof(values[4]);
angmom[m][2] = atof(values[5]);
}
/* ----------------------------------------------------------------------
unpack hybrid quantities from one line in Velocities section of data file
------------------------------------------------------------------------- */
int AtomVecEllipsoid::data_vel_hybrid(int m, char **values)
{
angmom[m][0] = atof(values[0]);
angmom[m][1] = atof(values[1]);
angmom[m][2] = atof(values[2]);
return 3;
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
------------------------------------------------------------------------- */
double AtomVecEllipsoid::memory_usage()
{
double bytes = 0.0;
if (atom->memcheck("tag")) bytes += nmax * sizeof(int);
if (atom->memcheck("type")) bytes += nmax * sizeof(int);
if (atom->memcheck("mask")) bytes += nmax * sizeof(int);
if (atom->memcheck("image")) bytes += nmax * sizeof(int);
if (atom->memcheck("x")) bytes += nmax*3 * sizeof(double);
if (atom->memcheck("v")) bytes += nmax*3 * sizeof(double);
if (atom->memcheck("f")) bytes += nmax*3 * sizeof(double);
if (atom->memcheck("quat")) bytes += nmax*4 * sizeof(double);
if (atom->memcheck("angmom")) bytes += nmax*3 * sizeof(double);
if (atom->memcheck("torque")) bytes += nmax*3 * sizeof(double);
return bytes;
}
diff --git a/src/CLASS2/dihedral_class2.cpp b/src/CLASS2/dihedral_class2.cpp
index 9b43673da..df80d249a 100644
--- a/src/CLASS2/dihedral_class2.cpp
+++ b/src/CLASS2/dihedral_class2.cpp
@@ -1,938 +1,938 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Eric Simon (Cray)
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "math.h"
#include "string.h"
#include "stdlib.h"
#include "dihedral_class2.h"
-#include "lmptype.h"
#include "atom.h"
#include "neighbor.h"
#include "update.h"
#include "domain.h"
#include "comm.h"
#include "force.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MIN(A,B) ((A) < (B)) ? (A) : (B)
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
#define TOLERANCE 0.05
#define SMALL 0.0000001
/* ---------------------------------------------------------------------- */
DihedralClass2::DihedralClass2(LAMMPS *lmp) : Dihedral(lmp)
{
PI = 4.0*atan(1.0);
}
/* ---------------------------------------------------------------------- */
DihedralClass2::~DihedralClass2()
{
if (allocated) {
memory->sfree(setflag);
memory->sfree(setflag_d);
memory->sfree(setflag_mbt);
memory->sfree(setflag_ebt);
memory->sfree(setflag_at);
memory->sfree(setflag_aat);
memory->sfree(setflag_bb13t);
memory->sfree(k1);
memory->sfree(k2);
memory->sfree(k3);
memory->sfree(phi1);
memory->sfree(phi2);
memory->sfree(phi3);
memory->sfree(mbt_f1);
memory->sfree(mbt_f2);
memory->sfree(mbt_f3);
memory->sfree(mbt_r0);
memory->sfree(ebt_f1_1);
memory->sfree(ebt_f2_1);
memory->sfree(ebt_f3_1);
memory->sfree(ebt_r0_1);
memory->sfree(ebt_f1_2);
memory->sfree(ebt_f2_2);
memory->sfree(ebt_f3_2);
memory->sfree(ebt_r0_2);
memory->sfree(at_f1_1);
memory->sfree(at_f2_1);
memory->sfree(at_f3_1);
memory->sfree(at_theta0_1);
memory->sfree(at_f1_2);
memory->sfree(at_f2_2);
memory->sfree(at_f3_2);
memory->sfree(at_theta0_2);
memory->sfree(aat_k);
memory->sfree(aat_theta0_1);
memory->sfree(aat_theta0_2);
memory->sfree(bb13t_k);
memory->sfree(bb13t_r10);
memory->sfree(bb13t_r30);
}
}
/* ---------------------------------------------------------------------- */
void DihedralClass2::compute(int eflag, int vflag)
{
int i1,i2,i3,i4,i,j,k,n,type;
double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm;
double edihedral;
double r1mag2,r1,r2mag2,r2,r3mag2,r3;
double sb1,rb1,sb2,rb2,sb3,rb3,c0,r12c1;
double r12c2,costh12,costh13,costh23,sc1,sc2,s1,s2,c;
double cosphi,phi,sinphi,a11,a22,a33,a12,a13,a23,sx1,sx2;
double sx12,sy1,sy2,sy12,sz1,sz2,sz12,dphi1,dphi2,dphi3;
double de_dihedral,t1,t2,t3,t4,cos2phi,cos3phi,bt1,bt2;
double bt3,sumbte,db,sumbtf,at1,at2,at3,da,da1,da2,r1_0;
double r3_0,dr1,dr2,tk1,tk2,s12,sin2;
double dcosphidr[4][3],dphidr[4][3],dbonddr[3][4][3],dthetadr[2][4][3];
double fabcd[4][3];
edihedral = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = 0;
double **x = atom->x;
double **f = atom->f;
int **dihedrallist = neighbor->dihedrallist;
int ndihedrallist = neighbor->ndihedrallist;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
for (n = 0; n < ndihedrallist; n++) {
i1 = dihedrallist[n][0];
i2 = dihedrallist[n][1];
i3 = dihedrallist[n][2];
i4 = dihedrallist[n][3];
type = dihedrallist[n][4];
// 1st bond
vb1x = x[i1][0] - x[i2][0];
vb1y = x[i1][1] - x[i2][1];
vb1z = x[i1][2] - x[i2][2];
domain->minimum_image(vb1x,vb1y,vb1z);
// 2nd bond
vb2x = x[i3][0] - x[i2][0];
vb2y = x[i3][1] - x[i2][1];
vb2z = x[i3][2] - x[i2][2];
domain->minimum_image(vb2x,vb2y,vb2z);
vb2xm = -vb2x;
vb2ym = -vb2y;
vb2zm = -vb2z;
domain->minimum_image(vb2xm,vb2ym,vb2zm);
// 3rd bond
vb3x = x[i4][0] - x[i3][0];
vb3y = x[i4][1] - x[i3][1];
vb3z = x[i4][2] - x[i3][2];
domain->minimum_image(vb3x,vb3y,vb3z);
// distances
r1mag2 = vb1x*vb1x + vb1y*vb1y + vb1z*vb1z;
r1 = sqrt(r1mag2);
r2mag2 = vb2x*vb2x + vb2y*vb2y + vb2z*vb2z;
r2 = sqrt(r2mag2);
r3mag2 = vb3x*vb3x + vb3y*vb3y + vb3z*vb3z;
r3 = sqrt(r3mag2);
sb1 = 1.0/r1mag2;
rb1 = 1.0/r1;
sb2 = 1.0/r2mag2;
rb2 = 1.0/r2;
sb3 = 1.0/r3mag2;
rb3 = 1.0/r3;
c0 = (vb1x*vb3x + vb1y*vb3y + vb1z*vb3z) * rb1*rb3;
// angles
r12c1 = rb1*rb2;
r12c2 = rb2*rb3;
costh12 = (vb1x*vb2x + vb1y*vb2y + vb1z*vb2z) * r12c1;
costh13 = c0;
costh23 = (vb2xm*vb3x + vb2ym*vb3y + vb2zm*vb3z) * r12c2;
// cos and sin of 2 angles and final c
sin2 = MAX(1.0 - costh12*costh12,0.0);
sc1 = sqrt(sin2);
if (sc1 < SMALL) sc1 = SMALL;
sc1 = 1.0/sc1;
sin2 = MAX(1.0 - costh23*costh23,0.0);
sc2 = sqrt(sin2);
if (sc2 < SMALL) sc2 = SMALL;
sc2 = 1.0/sc2;
s1 = sc1 * sc1;
s2 = sc2 * sc2;
s12 = sc1 * sc2;
c = (c0 + costh12*costh23) * s12;
// error check
if (c > 1.0 + TOLERANCE || c < (-1.0 - TOLERANCE)) {
int me;
MPI_Comm_rank(world,&me);
if (screen) {
char str[128];
sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " %d %d %d %d",
me,update->ntimestep,
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
error->warning(str,0);
fprintf(screen," 1st atom: %d %g %g %g\n",
me,x[i1][0],x[i1][1],x[i1][2]);
fprintf(screen," 2nd atom: %d %g %g %g\n",
me,x[i2][0],x[i2][1],x[i2][2]);
fprintf(screen," 3rd atom: %d %g %g %g\n",
me,x[i3][0],x[i3][1],x[i3][2]);
fprintf(screen," 4th atom: %d %g %g %g\n",
me,x[i4][0],x[i4][1],x[i4][2]);
}
}
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
cosphi = c;
phi = acos(c);
sinphi = sqrt(1.0 - c*c);
sinphi = MAX(sinphi,SMALL);
a11 = -c*sb1*s1;
a22 = sb2 * (2.0*costh13*s12 - c*(s1+s2));
a33 = -c*sb3*s2;
a12 = r12c1 * (costh12*c*s1 + costh23*s12);
a13 = rb1*rb3*s12;
a23 = r12c2 * (-costh23*c*s2 - costh12*s12);
sx1 = a11*vb1x + a12*vb2x + a13*vb3x;
sx2 = a12*vb1x + a22*vb2x + a23*vb3x;
sx12 = a13*vb1x + a23*vb2x + a33*vb3x;
sy1 = a11*vb1y + a12*vb2y + a13*vb3y;
sy2 = a12*vb1y + a22*vb2y + a23*vb3y;
sy12 = a13*vb1y + a23*vb2y + a33*vb3y;
sz1 = a11*vb1z + a12*vb2z + a13*vb3z;
sz2 = a12*vb1z + a22*vb2z + a23*vb3z;
sz12 = a13*vb1z + a23*vb2z + a33*vb3z;
// set up d(cos(phi))/d(r) and dphi/dr arrays
dcosphidr[0][0] = -sx1;
dcosphidr[0][1] = -sy1;
dcosphidr[0][2] = -sz1;
dcosphidr[1][0] = sx2 + sx1;
dcosphidr[1][1] = sy2 + sy1;
dcosphidr[1][2] = sz2 + sz1;
dcosphidr[2][0] = sx12 - sx2;
dcosphidr[2][1] = sy12 - sy2;
dcosphidr[2][2] = sz12 - sz2;
dcosphidr[3][0] = -sx12;
dcosphidr[3][1] = -sy12;
dcosphidr[3][2] = -sz12;
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
dphidr[i][j] = -dcosphidr[i][j] / sinphi;
// energy
dphi1 = phi - phi1[type];
dphi2 = 2.0*phi - phi2[type];
dphi3 = 3.0*phi - phi3[type];
if (eflag) edihedral = k1[type]*(1.0 - cos(dphi1)) +
k2[type]*(1.0 - cos(dphi2)) +
k3[type]*(1.0 - cos(dphi3));
de_dihedral = k1[type]*sin(dphi1) + 2.0*k2[type]*sin(dphi2) +
3.0*k3[type]*sin(dphi3);
// torsion forces on all 4 atoms
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
fabcd[i][j] = de_dihedral*dphidr[i][j];
// set up d(bond)/d(r) array
// dbonddr(i,j,k) = bond i, atom j, coordinate k
for (i = 0; i < 3; i++)
for (j = 0; j < 4; j++)
for (k = 0; k < 3; k++)
dbonddr[i][j][k] = 0.0;
// bond1
dbonddr[0][0][0] = vb1x / r1;
dbonddr[0][0][1] = vb1y / r1;
dbonddr[0][0][2] = vb1z / r1;
dbonddr[0][1][0] = -vb1x / r1;
dbonddr[0][1][1] = -vb1y / r1;
dbonddr[0][1][2] = -vb1z / r1;
// bond2
dbonddr[1][1][0] = vb2x / r2;
dbonddr[1][1][1] = vb2y / r2;
dbonddr[1][1][2] = vb2z / r2;
dbonddr[1][2][0] = -vb2x / r2;
dbonddr[1][2][1] = -vb2y / r2;
dbonddr[1][2][2] = -vb2z / r2;
// bond3
dbonddr[2][2][0] = vb3x / r3;
dbonddr[2][2][1] = vb3y / r3;
dbonddr[2][2][2] = vb3z / r3;
dbonddr[2][3][0] = -vb3x / r3;
dbonddr[2][3][1] = -vb3y / r3;
dbonddr[2][3][2] = -vb3z / r3;
// set up d(theta)/d(r) array
// dthetadr(i,j,k) = angle i, atom j, coordinate k
for (i = 0; i < 2; i++)
for (j = 0; j < 4; j++)
for (k = 0; k < 3; k++)
dthetadr[i][j][k] = 0.0;
t1 = costh12 / r1mag2;
t2 = costh23 / r2mag2;
t3 = costh12 / r2mag2;
t4 = costh23 / r3mag2;
// angle12
dthetadr[0][0][0] = sc1 * ((t1 * vb1x) - (vb2x * r12c1));
dthetadr[0][0][1] = sc1 * ((t1 * vb1y) - (vb2y * r12c1));
dthetadr[0][0][2] = sc1 * ((t1 * vb1z) - (vb2z * r12c1));
dthetadr[0][1][0] = sc1 * ((-t1 * vb1x) + (vb2x * r12c1) +
(-t3 * vb2x) + (vb1x * r12c1));
dthetadr[0][1][1] = sc1 * ((-t1 * vb1y) + (vb2y * r12c1) +
(-t3 * vb2y) + (vb1y * r12c1));
dthetadr[0][1][2] = sc1 * ((-t1 * vb1z) + (vb2z * r12c1) +
(-t3 * vb2z) + (vb1z * r12c1));
dthetadr[0][2][0] = sc1 * ((t3 * vb2x) - (vb1x * r12c1));
dthetadr[0][2][1] = sc1 * ((t3 * vb2y) - (vb1y * r12c1));
dthetadr[0][2][2] = sc1 * ((t3 * vb2z) - (vb1z * r12c1));
// angle23
dthetadr[1][1][0] = sc2 * ((t2 * vb2x) + (vb3x * r12c2));
dthetadr[1][1][1] = sc2 * ((t2 * vb2y) + (vb3y * r12c2));
dthetadr[1][1][2] = sc2 * ((t2 * vb2z) + (vb3z * r12c2));
dthetadr[1][2][0] = sc2 * ((-t2 * vb2x) - (vb3x * r12c2) +
(t4 * vb3x) + (vb2x * r12c2));
dthetadr[1][2][1] = sc2 * ((-t2 * vb2y) - (vb3y * r12c2) +
(t4 * vb3y) + (vb2y * r12c2));
dthetadr[1][2][2] = sc2 * ((-t2 * vb2z) - (vb3z * r12c2) +
(t4 * vb3z) + (vb2z * r12c2));
dthetadr[1][3][0] = -sc2 * ((t4 * vb3x) + (vb2x * r12c2));
dthetadr[1][3][1] = -sc2 * ((t4 * vb3y) + (vb2y * r12c2));
dthetadr[1][3][2] = -sc2 * ((t4 * vb3z) + (vb2z * r12c2));
// mid-bond/torsion coupling
// energy on bond2 (middle bond)
cos2phi = cos(2.0*phi);
cos3phi = cos(3.0*phi);
bt1 = mbt_f1[type] * cosphi;
bt2 = mbt_f2[type] * cos2phi;
bt3 = mbt_f3[type] * cos3phi;
sumbte = bt1 + bt2 + bt3;
db = r2 - mbt_r0[type];
if (eflag) edihedral += db * sumbte;
// force on bond2
bt1 = -mbt_f1[type] * sinphi;
bt2 = -2.0 * mbt_f2[type] * sin(2.0*phi);
bt3 = -3.0 * mbt_f3[type] * sin(3.0*phi);
sumbtf = bt1 + bt2 + bt3;
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
fabcd[i][j] += db*sumbtf*dphidr[i][j] + sumbte*dbonddr[1][i][j];
// end-bond/torsion coupling
// energy on bond1 (first bond)
bt1 = ebt_f1_1[type] * cosphi;
bt2 = ebt_f2_1[type] * cos2phi;
bt3 = ebt_f3_1[type] * cos3phi;
sumbte = bt1 + bt2 + bt3;
db = r1 - ebt_r0_1[type];
if (eflag) edihedral += db * (bt1+bt2+bt3);
// force on bond1
bt1 = ebt_f1_1[type] * sinphi;
bt2 = 2.0 * ebt_f2_1[type] * sin(2.0*phi);
bt3 = 3.0 * ebt_f3_1[type] * sin(3.0*phi);
sumbtf = bt1 + bt2 + bt3;
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
fabcd[i][j] -= db*sumbtf*dphidr[i][j] + sumbte*dbonddr[0][i][j];
// end-bond/torsion coupling
// energy on bond3 (last bond)
bt1 = ebt_f1_2[type] * cosphi;
bt2 = ebt_f2_2[type] * cos2phi;
bt3 = ebt_f3_2[type] * cos3phi;
sumbte = bt1 + bt2 + bt3;
db = r3 - ebt_r0_2[type];
if (eflag) edihedral += db * (bt1+bt2+bt3);
// force on bond3
bt1 = -ebt_f1_2[type] * sinphi;
bt2 = -2.0 * ebt_f2_2[type] * sin(2.0*phi);
bt3 = -3.0 * ebt_f3_2[type] * sin(3.0*phi);
sumbtf = bt1 + bt2 + bt3;
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
fabcd[i][j] += db*sumbtf*dphidr[i][j] + sumbte*dbonddr[2][i][j];
// angle/torsion coupling
// energy on angle1
at1 = at_f1_1[type] * cosphi;
at2 = at_f2_1[type] * cos2phi;
at3 = at_f3_1[type] * cos3phi;
sumbte = at1 + at2 + at3;
da = acos(costh12) - at_theta0_1[type];
if (eflag) edihedral += da * (at1+at2+at3);
// force on angle1
bt1 = at_f1_1[type] * sinphi;
bt2 = 2.0 * at_f2_1[type] * sin(2.0*phi);
bt3 = 3.0 * at_f3_1[type] * sin(3.0*phi);
sumbtf = bt1 + bt2 + bt3;
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
fabcd[i][j] -= da*sumbtf*dphidr[i][j] + sumbte*dthetadr[0][i][j];
// energy on angle2
at1 = at_f1_2[type] * cosphi;
at2 = at_f2_2[type] * cos2phi;
at3 = at_f3_2[type] * cos3phi;
sumbte = at1 + at2 + at3;
da = acos(costh23) - at_theta0_2[type];
if (eflag) edihedral += da * (at1+at2+at3);
// force on angle2
bt1 = -at_f1_2[type] * sinphi;
bt2 = -2.0 * at_f2_2[type] * sin(2.0*phi);
bt3 = -3.0 * at_f3_2[type] * sin(3.0*phi);
sumbtf = bt1 + bt2 + bt3;
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
fabcd[i][j] += da*sumbtf*dphidr[i][j] + sumbte*dthetadr[1][i][j];
// angle/angle/torsion coupling
da1 = acos(costh12) - aat_theta0_1[type];
da2 = acos(costh23) - aat_theta0_2[type];
if (eflag) edihedral += aat_k[type]*da1*da2*cosphi;
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
fabcd[i][j] -= aat_k[type] *
(cosphi * (da2*dthetadr[0][i][j] - da1*dthetadr[1][i][j]) +
sinphi * da1*da2*dphidr[i][j]);
// bond1/bond3 coupling
if (fabs(bb13t_k[type]) > SMALL) {
r1_0 = bb13t_r10[type];
r3_0 = bb13t_r30[type];
dr1 = r1 - r1_0;
dr2 = r3 - r3_0;
tk1 = -bb13t_k[type] * dr1 / r3;
tk2 = -bb13t_k[type] * dr2 / r1;
if (eflag) edihedral += bb13t_k[type]*dr1*dr2;
fabcd[0][0] += tk2 * vb1x;
fabcd[0][1] += tk2 * vb1y;
fabcd[0][2] += tk2 * vb1z;
fabcd[1][0] -= tk2 * vb1x;
fabcd[1][1] -= tk2 * vb1y;
fabcd[1][2] -= tk2 * vb1z;
fabcd[2][0] -= tk1 * vb3x;
fabcd[2][1] -= tk1 * vb3y;
fabcd[2][2] -= tk1 * vb3z;
fabcd[3][0] += tk1 * vb3x;
fabcd[3][1] += tk1 * vb3y;
fabcd[3][2] += tk1 * vb3z;
}
// apply force to each of 4 atoms
if (newton_bond || i1 < nlocal) {
f[i1][0] += fabcd[0][0];
f[i1][1] += fabcd[0][1];
f[i1][2] += fabcd[0][2];
}
if (newton_bond || i2 < nlocal) {
f[i2][0] += fabcd[1][0];
f[i2][1] += fabcd[1][1];
f[i2][2] += fabcd[1][2];
}
if (newton_bond || i3 < nlocal) {
f[i3][0] += fabcd[2][0];
f[i3][1] += fabcd[2][1];
f[i3][2] += fabcd[2][2];
}
if (newton_bond || i4 < nlocal) {
f[i4][0] += fabcd[3][0];
f[i4][1] += fabcd[3][1];
f[i4][2] += fabcd[3][2];
}
if (evflag)
ev_tally(i1,i2,i3,i4,nlocal,newton_bond,edihedral,
fabcd[0],fabcd[2],fabcd[3],
vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
}
}
/* ---------------------------------------------------------------------- */
void DihedralClass2::allocate()
{
allocated = 1;
int n = atom->ndihedraltypes;
k1 = (double *) memory->smalloc((n+1)*sizeof(double),"dihedral:k1");
k2 = (double *) memory->smalloc((n+1)*sizeof(double),"dihedral:k2");
k3 = (double *) memory->smalloc((n+1)*sizeof(double),"dihedral:k3");
phi1 = (double *) memory->smalloc((n+1)*sizeof(double),"dihedral:phi1");
phi2 = (double *) memory->smalloc((n+1)*sizeof(double),"dihedral:phi2");
phi3 = (double *) memory->smalloc((n+1)*sizeof(double),"dihedral:phi3");
mbt_f1 = (double *) memory->smalloc((n+1)*sizeof(double),"dihedral:mbt_f1");
mbt_f2 = (double *) memory->smalloc((n+1)*sizeof(double),"dihedral:mbt_f2");
mbt_f3 = (double *) memory->smalloc((n+1)*sizeof(double),"dihedral:mbt_f3");
mbt_r0 = (double *) memory->smalloc((n+1)*sizeof(double),"dihedral:mbt_r0");
ebt_f1_1 = (double *)
memory->smalloc((n+1)*sizeof(double),"dihedral:ebt_f1_1");
ebt_f2_1 = (double *)
memory->smalloc((n+1)*sizeof(double),"dihedral:ebt_f2_1");
ebt_f3_1 = (double *)
memory->smalloc((n+1)*sizeof(double),"dihedral:ebt_f3_1");
ebt_r0_1 = (double *)
memory->smalloc((n+1)*sizeof(double),"dihedral:ebt_r0_1");
ebt_f1_2 = (double *)
memory->smalloc((n+1)*sizeof(double),"dihedral:ebt_f1_2");
ebt_f2_2 = (double *)
memory->smalloc((n+1)*sizeof(double),"dihedral:ebt_f2_2");
ebt_f3_2 = (double *)
memory->smalloc((n+1)*sizeof(double),"dihedral:ebt_f3_2");
ebt_r0_2 = (double *)
memory->smalloc((n+1)*sizeof(double),"dihedral:ebt_r0_2");
at_f1_1 = (double *)
memory->smalloc((n+1)*sizeof(double),"dihedral:at_f1_1");
at_f2_1 = (double *)
memory->smalloc((n+1)*sizeof(double),"dihedral:at_f2_1");
at_f3_1 = (double *)
memory->smalloc((n+1)*sizeof(double),"dihedral:at_f3_1");
at_theta0_1 = (double *)
memory->smalloc((n+1)*sizeof(double),"dihedral:at_theta0_1");
at_f1_2 = (double *)
memory->smalloc((n+1)*sizeof(double),"dihedral:at_f1_2");
at_f2_2 = (double *)
memory->smalloc((n+1)*sizeof(double),"dihedral:at_f2_2");
at_f3_2 = (double *)
memory->smalloc((n+1)*sizeof(double),"dihedral:at_f3_2");
at_theta0_2 = (double *)
memory->smalloc((n+1)*sizeof(double),"dihedral:at_theta0_2");
aat_k = (double *) memory->smalloc((n+1)*sizeof(double),"dihedral:aat_k");
aat_theta0_1 = (double *)
memory->smalloc((n+1)*sizeof(double),"dihedral:aat_theta0_1");
aat_theta0_2 = (double *)
memory->smalloc((n+1)*sizeof(double),"dihedral:aat_theta0_2");
bb13t_k = (double *)
memory->smalloc((n+1)*sizeof(double),"dihedral:bb13t_k");
bb13t_r10 = (double *)
memory->smalloc((n+1)*sizeof(double),"dihedral:bb13t_r10");
bb13t_r30 = (double *)
memory->smalloc((n+1)*sizeof(double),"dihedral:bb13t_r30");
setflag = (int *) memory->smalloc((n+1)*sizeof(int),"dihedral:setflag");
setflag_d = (int *)
memory->smalloc((n+1)*sizeof(int),"dihedral:setflag_d");
setflag_mbt = (int *)
memory->smalloc((n+1)*sizeof(int),"dihedral:setflag_mbt");
setflag_ebt = (int *)
memory->smalloc((n+1)*sizeof(int),"dihedral:setflag_ebt");
setflag_at = (int *)
memory->smalloc((n+1)*sizeof(int),"dihedral:setflag_at");
setflag_aat = (int *)
memory->smalloc((n+1)*sizeof(int),"dihedral:setflag_aat");
setflag_bb13t = (int *)
memory->smalloc((n+1)*sizeof(int),"dihedral:setflag_bb13t");
for (int i = 1; i <= n; i++)
setflag[i] = setflag_d[i] = setflag_mbt[i] = setflag_ebt[i] =
setflag_at[i] = setflag_aat[i] = setflag_bb13t[i] = 0;
}
/* ----------------------------------------------------------------------
set coeffs for one or more types
arg1 = "mbt" -> MiddleBondTorsion coeffs
arg1 = "ebt" -> EndBondTorsion coeffs
arg1 = "at" -> AngleTorsion coeffs
arg1 = "aat" -> AngleAngleTorsion coeffs
arg1 = "bb13" -> BondBond13Torsion coeffs
arg1 -> Dihedral coeffs
------------------------------------------------------------------------- */
void DihedralClass2::coeff(int narg, char **arg)
{
if (narg < 2) error->all("Invalid coeffs for this dihedral style");
if (!allocated) allocate();
int ilo,ihi;
force->bounds(arg[0],atom->ndihedraltypes,ilo,ihi);
int count = 0;
if (strcmp(arg[1],"mbt") == 0) {
if (narg != 6) error->all("Incorrect args for dihedral coefficients");
double f1_one = force->numeric(arg[2]);
double f2_one = force->numeric(arg[3]);
double f3_one = force->numeric(arg[4]);
double r0_one = force->numeric(arg[5]);
for (int i = ilo; i <= ihi; i++) {
mbt_f1[i] = f1_one;
mbt_f2[i] = f2_one;
mbt_f3[i] = f3_one;
mbt_r0[i] = r0_one;
setflag_mbt[i] = 1;
count++;
}
} else if (strcmp(arg[1],"ebt") == 0) {
if (narg != 10) error->all("Incorrect args for dihedral coefficients");
double f1_1_one = force->numeric(arg[2]);
double f2_1_one = force->numeric(arg[3]);
double f3_1_one = force->numeric(arg[4]);
double f1_2_one = force->numeric(arg[5]);
double f2_2_one = force->numeric(arg[6]);
double f3_2_one = force->numeric(arg[7]);
double r0_1_one = force->numeric(arg[8]);
double r0_2_one = force->numeric(arg[9]);
for (int i = ilo; i <= ihi; i++) {
ebt_f1_1[i] = f1_1_one;
ebt_f2_1[i] = f2_1_one;
ebt_f3_1[i] = f3_1_one;
ebt_f1_2[i] = f1_2_one;
ebt_f2_2[i] = f2_2_one;
ebt_f3_2[i] = f3_2_one;
ebt_r0_1[i] = r0_1_one;
ebt_r0_2[i] = r0_2_one;
setflag_ebt[i] = 1;
count++;
}
} else if (strcmp(arg[1],"at") == 0) {
if (narg != 10) error->all("Incorrect args for dihedral coefficients");
double f1_1_one = force->numeric(arg[2]);
double f2_1_one = force->numeric(arg[3]);
double f3_1_one = force->numeric(arg[4]);
double f1_2_one = force->numeric(arg[5]);
double f2_2_one = force->numeric(arg[6]);
double f3_2_one = force->numeric(arg[7]);
double theta0_1_one = force->numeric(arg[8]);
double theta0_2_one = force->numeric(arg[9]);
// convert theta0's from degrees to radians
for (int i = ilo; i <= ihi; i++) {
at_f1_1[i] = f1_1_one;
at_f2_1[i] = f2_1_one;
at_f3_1[i] = f3_1_one;
at_f1_2[i] = f1_2_one;
at_f2_2[i] = f2_2_one;
at_f3_2[i] = f3_2_one;
at_theta0_1[i] = theta0_1_one/180.0 * PI;
at_theta0_2[i] = theta0_2_one/180.0 * PI;
setflag_at[i] = 1;
count++;
}
} else if (strcmp(arg[1],"aat") == 0) {
if (narg != 5) error->all("Incorrect args for dihedral coefficients");
double k_one = force->numeric(arg[2]);
double theta0_1_one = force->numeric(arg[3]);
double theta0_2_one = force->numeric(arg[4]);
// convert theta0's from degrees to radians
for (int i = ilo; i <= ihi; i++) {
aat_k[i] = k_one;
aat_theta0_1[i] = theta0_1_one/180.0 * PI;
aat_theta0_2[i] = theta0_2_one/180.0 * PI;
setflag_aat[i] = 1;
count++;
}
} else if (strcmp(arg[1],"bb13") == 0) {
if (narg != 5) error->all("Incorrect args for dihedral coefficients");
double k_one = force->numeric(arg[2]);
double r10_one = force->numeric(arg[3]);
double r30_one = force->numeric(arg[4]);
for (int i = ilo; i <= ihi; i++) {
bb13t_k[i] = k_one;
bb13t_r10[i] = r10_one;
bb13t_r30[i] = r30_one;
setflag_bb13t[i] = 1;
count++;
}
} else {
if (narg != 7) error->all("Incorrect args for dihedral coefficients");
double k1_one = force->numeric(arg[1]);
double phi1_one = force->numeric(arg[2]);
double k2_one = force->numeric(arg[3]);
double phi2_one = force->numeric(arg[4]);
double k3_one = force->numeric(arg[5]);
double phi3_one = force->numeric(arg[6]);
// convert phi's from degrees to radians
for (int i = ilo; i <= ihi; i++) {
k1[i] = k1_one;
phi1[i] = phi1_one/180.0 * PI;
k2[i] = k2_one;
phi2[i] = phi2_one/180.0 * PI;
k3[i] = k3_one;
phi3[i] = phi3_one/180.0 * PI;
setflag_d[i] = 1;
count++;
}
}
if (count == 0) error->all("Incorrect args for dihedral coefficients");
for (int i = ilo; i <= ihi; i++)
if (setflag_d[i] == 1 && setflag_mbt[i] == 1 && setflag_ebt[i] == 1 &&
setflag_at[i] == 1 && setflag_aat[i] == 1 && setflag_bb13t[i] == 1)
setflag[i] = 1;
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void DihedralClass2::write_restart(FILE *fp)
{
fwrite(&k1[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&k2[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&k3[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&phi1[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&phi2[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&phi3[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&mbt_f1[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&mbt_f2[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&mbt_f3[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&mbt_r0[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&ebt_f1_1[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&ebt_f2_1[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&ebt_f3_1[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&ebt_r0_1[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&ebt_f1_2[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&ebt_f2_2[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&ebt_f3_2[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&ebt_r0_2[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&at_f1_1[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&at_f2_1[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&at_f3_1[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&at_theta0_1[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&at_f1_2[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&at_f2_2[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&at_f3_2[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&at_theta0_2[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&aat_k[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&aat_theta0_1[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&aat_theta0_2[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&bb13t_k[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&bb13t_r10[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&bb13t_r30[1],sizeof(double),atom->ndihedraltypes,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void DihedralClass2::read_restart(FILE *fp)
{
allocate();
if (comm->me == 0) {
fread(&k1[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&k2[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&k3[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&phi1[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&phi2[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&phi3[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&mbt_f1[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&mbt_f2[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&mbt_f3[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&mbt_r0[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&ebt_f1_1[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&ebt_f2_1[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&ebt_f3_1[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&ebt_r0_1[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&ebt_f1_2[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&ebt_f2_2[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&ebt_f3_2[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&ebt_r0_2[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&at_f1_1[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&at_f2_1[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&at_f3_1[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&at_theta0_1[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&at_f1_2[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&at_f2_2[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&at_f3_2[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&at_theta0_2[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&aat_k[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&aat_theta0_1[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&aat_theta0_2[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&bb13t_k[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&bb13t_r10[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&bb13t_r30[1],sizeof(double),atom->ndihedraltypes,fp);
}
MPI_Bcast(&k1[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&k2[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&k3[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&phi1[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&phi2[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&phi3[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&mbt_f1[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&mbt_f2[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&mbt_f3[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&mbt_r0[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&ebt_f1_1[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&ebt_f2_1[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&ebt_f3_1[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&ebt_r0_1[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&ebt_f1_2[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&ebt_f2_2[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&ebt_f3_2[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&ebt_r0_2[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&at_f1_1[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&at_f2_1[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&at_f3_1[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&at_theta0_1[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&at_f1_2[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&at_f2_2[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&at_f3_2[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&at_theta0_2[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&aat_k[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&aat_theta0_1[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&aat_theta0_2[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&bb13t_k[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&bb13t_r10[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&bb13t_r30[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
for (int i = 1; i <= atom->ndihedraltypes; i++) setflag[i] = 1;
}
diff --git a/src/CLASS2/improper_class2.cpp b/src/CLASS2/improper_class2.cpp
index 7f0f31bc1..57ada4cfc 100644
--- a/src/CLASS2/improper_class2.cpp
+++ b/src/CLASS2/improper_class2.cpp
@@ -1,850 +1,850 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Eric Simon (Cray)
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "math.h"
#include "string.h"
#include "stdlib.h"
#include "improper_class2.h"
-#include "lmptype.h"
#include "atom.h"
#include "neighbor.h"
#include "update.h"
#include "domain.h"
#include "comm.h"
#include "force.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define SMALL 0.001
/* ---------------------------------------------------------------------- */
ImproperClass2::ImproperClass2(LAMMPS *lmp) : Improper(lmp)
{
PI = 4.0*atan(1.0);
}
/* ---------------------------------------------------------------------- */
ImproperClass2::~ImproperClass2()
{
if (allocated) {
memory->sfree(setflag);
memory->sfree(setflag_i);
memory->sfree(setflag_aa);
memory->sfree(k0);
memory->sfree(chi0);
memory->sfree(aa_k1);
memory->sfree(aa_k2);
memory->sfree(aa_k3);
memory->sfree(aa_theta0_1);
memory->sfree(aa_theta0_2);
memory->sfree(aa_theta0_3);
}
}
/* ---------------------------------------------------------------------- */
void ImproperClass2::compute(int eflag, int vflag)
{
int i1,i2,i3,i4,i,j,k,n,type;
double eimproper;
double delr[3][3],rmag[3],rinvmag[3],rmag2[3];
double theta[3],costheta[3],sintheta[3];
double cossqtheta[3],sinsqtheta[3],invstheta[3];
double rABxrCB[3],rDBxrAB[3],rCBxrDB[3];
double ddelr[3][4],dr[3][4][3],dinvr[3][4][3];
double dthetadr[3][4][3],dinvsth[3][4][3];
double dinv3r[4][3],dinvs3r[3][4][3];
double drCBxrDB[3],rCBxdrDB[3],drDBxrAB[3],rDBxdrAB[3];
double drABxrCB[3],rABxdrCB[3];
double dot1,dot2,dd[3];
double fdot[3][4][3],ftmp,invs3r[3],inv3r;
double t,tt1,tt3,sc1;
double dotCBDBAB,dotDBABCB,dotABCBDB;
double chi,deltachi,d2chi,cossin2;
double drAB[3][4][3],drCB[3][4][3],drDB[3][4][3];
double dchi[3][4][3],dtotalchi[4][3];
double schiABCD,chiABCD,schiCBDA,chiCBDA,schiDBAC,chiDBAC;
double fabcd[4][3];
eimproper = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = 0;
for (i = 0; i < 3; i++)
for (j = 0; j < 4; j++)
for (k = 0; k < 3; k++) {
dthetadr[i][j][k] = 0.0;
drAB[i][j][k] = 0.0;
drCB[i][j][k] = 0.0;
drDB[i][j][k] = 0.0;
}
double **x = atom->x;
double **f = atom->f;
int **improperlist = neighbor->improperlist;
int nimproperlist = neighbor->nimproperlist;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
for (n = 0; n < nimproperlist; n++) {
i1 = improperlist[n][0];
i2 = improperlist[n][1];
i3 = improperlist[n][2];
i4 = improperlist[n][3];
type = improperlist[n][4];
if (k0[type] == 0.0) continue;
// difference vectors
delr[0][0] = x[i1][0] - x[i2][0];
delr[0][1] = x[i1][1] - x[i2][1];
delr[0][2] = x[i1][2] - x[i2][2];
domain->minimum_image(delr[0]);
delr[1][0] = x[i3][0] - x[i2][0];
delr[1][1] = x[i3][1] - x[i2][1];
delr[1][2] = x[i3][2] - x[i2][2];
domain->minimum_image(delr[1]);
delr[2][0] = x[i4][0] - x[i2][0];
delr[2][1] = x[i4][1] - x[i2][1];
delr[2][2] = x[i4][2] - x[i2][2];
domain->minimum_image(delr[2]);
// bond lengths and associated values
for (i = 0; i < 3; i++) {
rmag2[i] = delr[i][0]*delr[i][0] + delr[i][1]*delr[i][1] +
delr[i][2]*delr[i][2];
rmag[i] = sqrt(rmag2[i]);
rinvmag[i] = 1.0/rmag[i];
}
// angle ABC, CBD, ABD
costheta[0] = (delr[0][0]*delr[1][0] + delr[0][1]*delr[1][1] +
delr[0][2]*delr[1][2]) / (rmag[0]*rmag[1]);
costheta[1] = (delr[1][0]*delr[2][0] + delr[1][1]*delr[2][1] +
delr[1][2]*delr[2][2]) / (rmag[1]*rmag[2]);
costheta[2] = (delr[0][0]*delr[2][0] + delr[0][1]*delr[2][1] +
delr[0][2]*delr[2][2]) / (rmag[0]*rmag[2]);
// angle error check
for (i = 0; i < 3; i++) {
if (costheta[i] == -1.0) {
int me;
MPI_Comm_rank(world,&me);
if (screen) {
char str[128];
sprintf(str,
"Improper problem: %d " BIGINT_FORMAT " %d %d %d %d",
me,update->ntimestep,
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
error->warning(str,0);
fprintf(screen," 1st atom: %d %g %g %g\n",
me,x[i1][0],x[i1][1],x[i1][2]);
fprintf(screen," 2nd atom: %d %g %g %g\n",
me,x[i2][0],x[i2][1],x[i2][2]);
fprintf(screen," 3rd atom: %d %g %g %g\n",
me,x[i3][0],x[i3][1],x[i3][2]);
fprintf(screen," 4th atom: %d %g %g %g\n",
me,x[i4][0],x[i4][1],x[i4][2]);
}
}
}
for (i = 0; i < 3; i++) {
if (costheta[i] > 1.0) costheta[i] = 1.0;
if (costheta[i] < -1.0) costheta[i] = -1.0;
theta[i] = acos(costheta[i]);
cossqtheta[i] = costheta[i]*costheta[i];
sintheta[i] = sin(theta[i]);
invstheta[i] = 1.0/sintheta[i];
sinsqtheta[i] = sintheta[i]*sintheta[i];
}
// cross & dot products
cross(delr[0],delr[1],rABxrCB);
cross(delr[2],delr[0],rDBxrAB);
cross(delr[1],delr[2],rCBxrDB);
dotCBDBAB = dot(rCBxrDB,delr[0]);
dotDBABCB = dot(rDBxrAB,delr[1]);
dotABCBDB = dot(rABxrCB,delr[2]);
t = rmag[0] * rmag[1] * rmag[2];
inv3r = 1.0/t;
invs3r[0] = invstheta[1] * inv3r;
invs3r[1] = invstheta[2] * inv3r;
invs3r[2] = invstheta[0] * inv3r;
// chi ABCD, CBDA, DBAC
// final chi is average of three
schiABCD = dotCBDBAB * invs3r[0];
chiABCD = asin(schiABCD);
schiCBDA = dotDBABCB * invs3r[1];
chiCBDA = asin(schiCBDA);
schiDBAC = dotABCBDB * invs3r[2];
chiDBAC = asin(schiDBAC);
chi = (chiABCD + chiCBDA + chiDBAC) / 3.0;
deltachi = chi - chi0[type];
d2chi = deltachi * deltachi;
// energy
if (eflag) eimproper = k0[type]*d2chi;
// forces
// define d(delr)
// i = bond AB/CB/DB, j = atom A/B/C/D
for (i = 0; i < 3; i++)
for (j = 0; j < 4; j++)
ddelr[i][j] = 0.0;
ddelr[0][0] = 1.0;
ddelr[0][1] = -1.0;
ddelr[1][1] = -1.0;
ddelr[1][2] = 1.0;
ddelr[2][1] = -1.0;
ddelr[2][3] = 1.0;
// compute d(|r|)/dr and d(1/|r|)/dr for each direction, bond and atom
// define d(r) for each r
// i = bond AB/CB/DB, j = atom A/B/C/D, k = X/Y/Z
for (i = 0; i < 3; i++)
for (j = 0; j < 4; j++)
for (k = 0; k < 3; k++) {
dr[i][j][k] = delr[i][k] * ddelr[i][j] / rmag[i];
dinvr[i][j][k] = -dr[i][j][k] / rmag2[i];
}
// compute d(1 / (|r_AB| * |r_CB| * |r_DB|) / dr
// i = atom A/B/C/D, j = X/Y/Z
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
dinv3r[i][j] = rinvmag[1] * (rinvmag[2] * dinvr[0][i][j] +
rinvmag[0] * dinvr[2][i][j]) +
rinvmag[2] * rinvmag[0] * dinvr[1][i][j];
// compute d(theta)/d(r) for 3 angles
// angleABC
tt1 = costheta[0] / rmag2[0];
tt3 = costheta[0] / rmag2[1];
sc1 = 1.0 / sqrt(1.0 - cossqtheta[0]);
dthetadr[0][0][0] = sc1 * ((tt1 * delr[0][0]) -
(delr[1][0] * rinvmag[0] * rinvmag[1]));
dthetadr[0][0][1] = sc1 * ((tt1 * delr[0][1]) -
(delr[1][1] * rinvmag[0] * rinvmag[1]));
dthetadr[0][0][2] = sc1 * ((tt1 * delr[0][2]) -
(delr[1][2] * rinvmag[0] * rinvmag[1]));
dthetadr[0][1][0] = -sc1 * ((tt1 * delr[0][0]) -
(delr[1][0] * rinvmag[0] * rinvmag[1]) +
(tt3 * delr[1][0]) -
(delr[0][0] * rinvmag[0] * rinvmag[1]));
dthetadr[0][1][1] = -sc1 * ((tt1 * delr[0][1]) -
(delr[1][1] * rinvmag[0] * rinvmag[1]) +
(tt3 * delr[1][1]) -
(delr[0][1] * rinvmag[0] * rinvmag[1]));
dthetadr[0][1][2] = -sc1 * ((tt1 * delr[0][2]) -
(delr[1][2] * rinvmag[0] * rinvmag[1]) +
(tt3 * delr[1][2]) -
(delr[0][2] * rinvmag[0] * rinvmag[1]));
dthetadr[0][2][0] = sc1 * ((tt3 * delr[1][0]) -
(delr[0][0] * rinvmag[0] * rinvmag[1]));
dthetadr[0][2][1] = sc1 * ((tt3 * delr[1][1]) -
(delr[0][1] * rinvmag[0] * rinvmag[1]));
dthetadr[0][2][2] = sc1 * ((tt3 * delr[1][2]) -
(delr[0][2] * rinvmag[0] * rinvmag[1]));
// angleCBD
tt1 = costheta[1] / rmag2[1];
tt3 = costheta[1] / rmag2[2];
sc1 = 1.0 / sqrt(1.0 - cossqtheta[1]);
dthetadr[1][2][0] = sc1 * ((tt1 * delr[1][0]) -
(delr[2][0] * rinvmag[1] * rinvmag[2]));
dthetadr[1][2][1] = sc1 * ((tt1 * delr[1][1]) -
(delr[2][1] * rinvmag[1] * rinvmag[2]));
dthetadr[1][2][2] = sc1 * ((tt1 * delr[1][2]) -
(delr[2][2] * rinvmag[1] * rinvmag[2]));
dthetadr[1][1][0] = -sc1 * ((tt1 * delr[1][0]) -
(delr[2][0] * rinvmag[1] * rinvmag[2]) +
(tt3 * delr[2][0]) -
(delr[1][0] * rinvmag[2] * rinvmag[1]));
dthetadr[1][1][1] = -sc1 * ((tt1 * delr[1][1]) -
(delr[2][1] * rinvmag[1] * rinvmag[2]) +
(tt3 * delr[2][1]) -
(delr[1][1] * rinvmag[2] * rinvmag[1]));
dthetadr[1][1][2] = -sc1 * ((tt1 * delr[1][2]) -
(delr[2][2] * rinvmag[1] * rinvmag[2]) +
(tt3 * delr[2][2]) -
(delr[1][2] * rinvmag[2] * rinvmag[1]));
dthetadr[1][3][0] = sc1 * ((tt3 * delr[2][0]) -
(delr[1][0] * rinvmag[2] * rinvmag[1]));
dthetadr[1][3][1] = sc1 * ((tt3 * delr[2][1]) -
(delr[1][1] * rinvmag[2] * rinvmag[1]));
dthetadr[1][3][2] = sc1 * ((tt3 * delr[2][2]) -
(delr[1][2] * rinvmag[2] * rinvmag[1]));
// angleABD
tt1 = costheta[2] / rmag2[0];
tt3 = costheta[2] / rmag2[2];
sc1 = 1.0 / sqrt(1.0 - cossqtheta[2]);
dthetadr[2][0][0] = sc1 * ((tt1 * delr[0][0]) -
(delr[2][0] * rinvmag[0] * rinvmag[2]));
dthetadr[2][0][1] = sc1 * ((tt1 * delr[0][1]) -
(delr[2][1] * rinvmag[0] * rinvmag[2]));
dthetadr[2][0][2] = sc1 * ((tt1 * delr[0][2]) -
(delr[2][2] * rinvmag[0] * rinvmag[2]));
dthetadr[2][1][0] = -sc1 * ((tt1 * delr[0][0]) -
(delr[2][0] * rinvmag[0] * rinvmag[2]) +
(tt3 * delr[2][0]) -
(delr[0][0] * rinvmag[2] * rinvmag[0]));
dthetadr[2][1][1] = -sc1 * ((tt1 * delr[0][1]) -
(delr[2][1] * rinvmag[0] * rinvmag[2]) +
(tt3 * delr[2][1]) -
(delr[0][1] * rinvmag[2] * rinvmag[0]));
dthetadr[2][1][2] = -sc1 * ((tt1 * delr[0][2]) -
(delr[2][2] * rinvmag[0] * rinvmag[2]) +
(tt3 * delr[2][2]) -
(delr[0][2] * rinvmag[2] * rinvmag[0]));
dthetadr[2][3][0] = sc1 * ((tt3 * delr[2][0]) -
(delr[0][0] * rinvmag[2] * rinvmag[0]));
dthetadr[2][3][1] = sc1 * ((tt3 * delr[2][1]) -
(delr[0][1] * rinvmag[2] * rinvmag[0]));
dthetadr[2][3][2] = sc1 * ((tt3 * delr[2][2]) -
(delr[0][2] * rinvmag[2] * rinvmag[0]));
// compute d( 1 / sin(theta))/dr
// i = angle, j = atom, k = direction
for (i = 0; i < 3; i++) {
cossin2 = -costheta[i] / sinsqtheta[i];
for (j = 0; j < 4; j++)
for (k = 0; k < 3; k++)
dinvsth[i][j][k] = cossin2 * dthetadr[i][j][k];
}
// compute d(1 / sin(theta) * |r_AB| * |r_CB| * |r_DB|)/dr
// i = angle, j = atom
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++) {
dinvs3r[0][i][j] = (invstheta[1] * dinv3r[i][j]) +
(inv3r * dinvsth[1][i][j]);
dinvs3r[1][i][j] = (invstheta[2] * dinv3r[i][j]) +
(inv3r * dinvsth[2][i][j]);
dinvs3r[2][i][j] = (invstheta[0] * dinv3r[i][j]) +
(inv3r * dinvsth[0][i][j]);
}
// drCB(i,j,k), etc
// i = vector X'/Y'/Z', j = atom A/B/C/D, k = direction X/Y/Z
for (i = 0; i < 3; i++) {
drCB[i][1][i] = -1.0;
drAB[i][1][i] = -1.0;
drDB[i][1][i] = -1.0;
drDB[i][3][i] = 1.0;
drCB[i][2][i] = 1.0;
drAB[i][0][i] = 1.0;
}
// d((r_CB x r_DB) dot r_AB)
// r_CB x d(r_DB)
// d(r_CB) x r_DB
// (r_CB x d(r_DB)) + (d(r_CB) x r_DB)
// (r_CB x d(r_DB)) + (d(r_CB) x r_DB) dot r_AB
// d(r_AB) dot (r_CB x r_DB)
for (i = 0; i < 3; i++)
for (j = 0; j < 4; j++) {
cross(delr[1],drDB[i][j],rCBxdrDB);
cross(drCB[i][j],delr[2],drCBxrDB);
for (k = 0; k < 3; k++) dd[k] = rCBxdrDB[k] + drCBxrDB[k];
dot1 = dot(dd,delr[0]);
dot2 = dot(rCBxrDB,drAB[i][j]);
fdot[0][j][i] = dot1 + dot2;
}
// d((r_DB x r_AB) dot r_CB)
// r_DB x d(r_AB)
// d(r_DB) x r_AB
// (r_DB x d(r_AB)) + (d(r_DB) x r_AB)
// (r_DB x d(r_AB)) + (d(r_DB) x r_AB) dot r_CB
// d(r_CB) dot (r_DB x r_AB)
for (i = 0; i < 3; i++)
for (j = 0; j < 4; j++) {
cross(delr[2],drAB[i][j],rDBxdrAB);
cross(drDB[i][j],delr[0],drDBxrAB);
for (k = 0; k < 3; k++) dd[k] = rDBxdrAB[k] + drDBxrAB[k];
dot1 = dot(dd,delr[1]);
dot2 = dot(rDBxrAB,drCB[i][j]);
fdot[1][j][i] = dot1 + dot2;
}
// d((r_AB x r_CB) dot r_DB)
// r_AB x d(r_CB)
// d(r_AB) x r_CB
// (r_AB x d(r_CB)) + (d(r_AB) x r_CB)
// (r_AB x d(r_CB)) + (d(r_AB) x r_CB) dot r_DB
// d(r_DB) dot (r_AB x r_CB)
for (i = 0; i < 3; i++)
for (j = 0; j < 4; j++) {
cross(delr[0],drCB[i][j],rABxdrCB);
cross(drAB[i][j],delr[1],drABxrCB);
for (k = 0; k < 3; k++) dd[k] = rABxdrCB[k] + drABxrCB[k];
dot1 = dot(dd,delr[2]);
dot2 = dot(rABxrCB,drDB[i][j]);
fdot[2][j][i] = dot1 + dot2;
}
// force on each atom
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++) {
ftmp = (fdot[0][i][j] * invs3r[0]) +
(dinvs3r[0][i][j] * dotCBDBAB);
dchi[0][i][j] = ftmp / cos(chiABCD);
ftmp = (fdot[1][i][j] * invs3r[1]) +
(dinvs3r[1][i][j] * dotDBABCB);
dchi[1][i][j] = ftmp / cos(chiCBDA);
ftmp = (fdot[2][i][j] * invs3r[2]) +
(dinvs3r[2][i][j] * dotABCBDB);
dchi[2][i][j] = ftmp / cos(chiDBAC);
dtotalchi[i][j] = (dchi[0][i][j]+dchi[1][i][j]+dchi[2][i][j]) / 3.0;
}
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
fabcd[i][j] = -2.0*k0[type] * deltachi*dtotalchi[i][j];
// apply force to each of 4 atoms
if (newton_bond || i1 < nlocal) {
f[i1][0] += fabcd[0][0];
f[i1][1] += fabcd[0][1];
f[i1][2] += fabcd[0][2];
}
if (newton_bond || i2 < nlocal) {
f[i2][0] += fabcd[1][0];
f[i2][1] += fabcd[1][1];
f[i2][2] += fabcd[1][2];
}
if (newton_bond || i3 < nlocal) {
f[i3][0] += fabcd[2][0];
f[i3][1] += fabcd[2][1];
f[i3][2] += fabcd[2][2];
}
if (newton_bond || i4 < nlocal) {
f[i4][0] += fabcd[3][0];
f[i4][1] += fabcd[3][1];
f[i4][2] += fabcd[3][2];
}
if (evflag)
ev_tally(i1,i2,i3,i4,nlocal,newton_bond,eimproper,
fabcd[0],fabcd[2],fabcd[3],
delr[0][0],delr[0][1],delr[0][2],
delr[1][0],delr[1][1],delr[1][2],
delr[2][0]-delr[1][0],delr[2][1]-delr[1][1],
delr[2][2]-delr[1][2]);
}
// compute angle-angle interactions
angleangle(eflag,vflag);
}
/* ---------------------------------------------------------------------- */
void ImproperClass2::allocate()
{
allocated = 1;
int n = atom->nimpropertypes;
k0 = (double *) memory->smalloc((n+1)*sizeof(double),"improper:k0");
chi0 = (double *) memory->smalloc((n+1)*sizeof(double),"improper:chi0");
aa_k1 = (double *) memory->smalloc((n+1)*sizeof(double),"improper:aa_k1");
aa_k2 = (double *) memory->smalloc((n+1)*sizeof(double),"improper:aa_k2");
aa_k3 = (double *) memory->smalloc((n+1)*sizeof(double),"improper:aa_k3");
aa_theta0_1 = (double *)
memory->smalloc((n+1)*sizeof(double),"improper:aa_theta0_1");
aa_theta0_2 = (double *)
memory->smalloc((n+1)*sizeof(double),"improper:aa_theta0_2");
aa_theta0_3 = (double *)
memory->smalloc((n+1)*sizeof(double),"improper:aa_theta0_3");
setflag = (int *) memory->smalloc((n+1)*sizeof(int),"improper:setflag");
setflag_i = (int *)
memory->smalloc((n+1)*sizeof(int),"improper:setflag_i");
setflag_aa = (int *)
memory->smalloc((n+1)*sizeof(int),"improper:setflag_aa");
for (int i = 1; i <= n; i++)
setflag[i] = setflag_i[i] = setflag_aa[i] = 0;
}
/* ----------------------------------------------------------------------
set coeffs for one or more types
arg1 = "aa" -> AngleAngle coeffs
else arg1 -> improper coeffs
------------------------------------------------------------------------- */
void ImproperClass2::coeff(int narg, char **arg)
{
if (narg < 2) error->all("Incorrect args for improper coefficients");
if (!allocated) allocate();
int ilo,ihi;
force->bounds(arg[0],atom->nimpropertypes,ilo,ihi);
int count = 0;
if (strcmp(arg[1],"aa") == 0) {
if (narg != 8) error->all("Incorrect args for improper coefficients");
double k1_one = force->numeric(arg[2]);
double k2_one = force->numeric(arg[3]);
double k3_one = force->numeric(arg[4]);
double theta0_1_one = force->numeric(arg[5]);
double theta0_2_one = force->numeric(arg[6]);
double theta0_3_one = force->numeric(arg[7]);
// convert theta0's from degrees to radians
for (int i = ilo; i <= ihi; i++) {
aa_k1[i] = k1_one;
aa_k2[i] = k2_one;
aa_k3[i] = k3_one;
aa_theta0_1[i] = theta0_1_one/180.0 * PI;
aa_theta0_2[i] = theta0_2_one/180.0 * PI;
aa_theta0_3[i] = theta0_3_one/180.0 * PI;
setflag_aa[i] = 1;
count++;
}
} else {
if (narg != 3) error->all("Incorrect args for improper coefficients");
double k0_one = force->numeric(arg[1]);
double chi0_one = force->numeric(arg[2]);
// convert chi0 from degrees to radians
for (int i = ilo; i <= ihi; i++) {
k0[i] = k0_one;
chi0[i] = chi0_one/180.0 * PI;
setflag_i[i] = 1;
count++;
}
}
if (count == 0) error->all("Incorrect args for improper coefficients");
for (int i = ilo; i <= ihi; i++)
if (setflag_i[i] == 1 && setflag_aa[i] == 1) setflag[i] = 1;
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void ImproperClass2::write_restart(FILE *fp)
{
fwrite(&k0[1],sizeof(double),atom->nimpropertypes,fp);
fwrite(&chi0[1],sizeof(double),atom->nimpropertypes,fp);
fwrite(&aa_k1[1],sizeof(double),atom->nimpropertypes,fp);
fwrite(&aa_k2[1],sizeof(double),atom->nimpropertypes,fp);
fwrite(&aa_k3[1],sizeof(double),atom->nimpropertypes,fp);
fwrite(&aa_theta0_1[1],sizeof(double),atom->nimpropertypes,fp);
fwrite(&aa_theta0_2[1],sizeof(double),atom->nimpropertypes,fp);
fwrite(&aa_theta0_3[1],sizeof(double),atom->nimpropertypes,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void ImproperClass2::read_restart(FILE *fp)
{
allocate();
if (comm->me == 0) {
fread(&k0[1],sizeof(double),atom->nimpropertypes,fp);
fread(&chi0[1],sizeof(double),atom->nimpropertypes,fp);
fread(&aa_k1[1],sizeof(double),atom->nimpropertypes,fp);
fread(&aa_k2[1],sizeof(double),atom->nimpropertypes,fp);
fread(&aa_k3[1],sizeof(double),atom->nimpropertypes,fp);
fread(&aa_theta0_1[1],sizeof(double),atom->nimpropertypes,fp);
fread(&aa_theta0_2[1],sizeof(double),atom->nimpropertypes,fp);
fread(&aa_theta0_3[1],sizeof(double),atom->nimpropertypes,fp);
}
MPI_Bcast(&k0[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
MPI_Bcast(&chi0[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
MPI_Bcast(&aa_k1[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
MPI_Bcast(&aa_k2[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
MPI_Bcast(&aa_k3[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
MPI_Bcast(&aa_theta0_1[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
MPI_Bcast(&aa_theta0_2[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
MPI_Bcast(&aa_theta0_3[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
for (int i = 1; i <= atom->nimpropertypes; i++) setflag[i] = 1;
}
/* ----------------------------------------------------------------------
angle-angle interactions within improper
------------------------------------------------------------------------- */
void ImproperClass2::angleangle(int eflag, int vflag)
{
int i1,i2,i3,i4,i,j,k,n,type;
double eimproper;
double delxAB,delyAB,delzAB,rABmag2,rAB;
double delxBC,delyBC,delzBC,rBCmag2,rBC;
double delxBD,delyBD,delzBD,rBDmag2,rBD;
double costhABC,thetaABC,costhABD;
double thetaABD,costhCBD,thetaCBD,dthABC,dthCBD,dthABD;
double sc1,t1,t3,r12;
double dthetadr[3][4][3],fabcd[4][3];
double **x = atom->x;
double **f = atom->f;
int **improperlist = neighbor->improperlist;
int nimproperlist = neighbor->nimproperlist;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
for (n = 0; n < nimproperlist; n++) {
i1 = improperlist[n][0];
i2 = improperlist[n][1];
i3 = improperlist[n][2];
i4 = improperlist[n][3];
type = improperlist[n][4];
// difference vectors
delxAB = x[i1][0] - x[i2][0];
delyAB = x[i1][1] - x[i2][1];
delzAB = x[i1][2] - x[i2][2];
domain->minimum_image(delxAB,delyAB,delzAB);
delxBC = x[i3][0] - x[i2][0];
delyBC = x[i3][1] - x[i2][1];
delzBC = x[i3][2] - x[i2][2];
domain->minimum_image(delxBC,delyBC,delzBC);
delxBD = x[i4][0] - x[i2][0];
delyBD = x[i4][1] - x[i2][1];
delzBD = x[i4][2] - x[i2][2];
domain->minimum_image(delxBD,delyBD,delzBD);
// bond lengths
rABmag2 = delxAB*delxAB + delyAB*delyAB + delzAB*delzAB;
rAB = sqrt(rABmag2);
rBCmag2 = delxBC*delxBC + delyBC*delyBC + delzBC*delzBC;
rBC = sqrt(rBCmag2);
rBDmag2 = delxBD*delxBD + delyBD*delyBD + delzBD*delzBD;
rBD = sqrt(rBDmag2);
// angle ABC, ABD, CBD
costhABC = (delxAB*delxBC + delyAB*delyBC + delzAB*delzBC) / (rAB * rBC);
if (costhABC > 1.0) costhABC = 1.0;
if (costhABC < -1.0) costhABC = -1.0;
thetaABC = acos(costhABC);
costhABD = (delxAB*delxBD + delyAB*delyBD + delzAB*delzBD) / (rAB * rBD);
if (costhABD > 1.0) costhABD = 1.0;
if (costhABD < -1.0) costhABD = -1.0;
thetaABD = acos(costhABD);
costhCBD = (delxBC*delxBD + delyBC*delyBD + delzBC*delzBD) /(rBC * rBD);
if (costhCBD > 1.0) costhCBD = 1.0;
if (costhCBD < -1.0) costhCBD = -1.0;
thetaCBD = acos(costhCBD);
dthABC = thetaABC - aa_theta0_1[type];
dthCBD = thetaCBD - aa_theta0_2[type];
dthABD = thetaABD - aa_theta0_3[type];
// energy
if (eflag) eimproper = aa_k2[type] * dthABC * dthABD +
aa_k1[type] * dthABC * dthCBD +
aa_k3[type] * dthABD * dthCBD;
// d(theta)/d(r) array
// angle i, atom j, coordinate k
for (i = 0; i < 3; i++)
for (j = 0; j < 4; j++)
for (k = 0; k < 3; k++)
dthetadr[i][j][k] = 0.0;
// angle ABC
sc1 = sqrt(1.0/(1.0 - costhABC*costhABC));
t1 = costhABC / rABmag2;
t3 = costhABC / rBCmag2;
r12 = 1.0 / (rAB * rBC);
dthetadr[0][0][0] = sc1 * ((t1 * delxAB) - (delxBC * r12));
dthetadr[0][0][1] = sc1 * ((t1 * delyAB) - (delyBC * r12));
dthetadr[0][0][2] = sc1 * ((t1 * delzAB) - (delzBC * r12));
dthetadr[0][1][0] = sc1 * ((-t1 * delxAB) + (delxBC * r12) +
(-t3 * delxBC) + (delxAB * r12));
dthetadr[0][1][1] = sc1 * ((-t1 * delyAB) + (delyBC * r12) +
(-t3 * delyBC) + (delyAB * r12));
dthetadr[0][1][2] = sc1 * ((-t1 * delzAB) + (delzBC * r12) +
(-t3 * delzBC) + (delzAB * r12));
dthetadr[0][2][0] = sc1 * ((t3 * delxBC) - (delxAB * r12));
dthetadr[0][2][1] = sc1 * ((t3 * delyBC) - (delyAB * r12));
dthetadr[0][2][2] = sc1 * ((t3 * delzBC) - (delzAB * r12));
// angle CBD
sc1 = sqrt(1.0/(1.0 - costhCBD*costhCBD));
t1 = costhCBD / rBCmag2;
t3 = costhCBD / rBDmag2;
r12 = 1.0 / (rBC * rBD);
dthetadr[1][2][0] = sc1 * ((t1 * delxBC) - (delxBD * r12));
dthetadr[1][2][1] = sc1 * ((t1 * delyBC) - (delyBD * r12));
dthetadr[1][2][2] = sc1 * ((t1 * delzBC) - (delzBD * r12));
dthetadr[1][1][0] = sc1 * ((-t1 * delxBC) + (delxBD * r12) +
(-t3 * delxBD) + (delxBC * r12));
dthetadr[1][1][1] = sc1 * ((-t1 * delyBC) + (delyBD * r12) +
(-t3 * delyBD) + (delyBC * r12));
dthetadr[1][1][2] = sc1 * ((-t1 * delzBC) + (delzBD * r12) +
(-t3 * delzBD) + (delzBC * r12));
dthetadr[1][3][0] = sc1 * ((t3 * delxBD) - (delxBC * r12));
dthetadr[1][3][1] = sc1 * ((t3 * delyBD) - (delyBC * r12));
dthetadr[1][3][2] = sc1 * ((t3 * delzBD) - (delzBC * r12));
// angle ABD
sc1 = sqrt(1.0/(1.0 - costhABD*costhABD));
t1 = costhABD / rABmag2;
t3 = costhABD / rBDmag2;
r12 = 1.0 / (rAB * rBD);
dthetadr[2][0][0] = sc1 * ((t1 * delxAB) - (delxBD * r12));
dthetadr[2][0][1] = sc1 * ((t1 * delyAB) - (delyBD * r12));
dthetadr[2][0][2] = sc1 * ((t1 * delzAB) - (delzBD * r12));
dthetadr[2][1][0] = sc1 * ((-t1 * delxAB) + (delxBD * r12) +
(-t3 * delxBD) + (delxAB * r12));
dthetadr[2][1][1] = sc1 * ((-t1 * delyAB) + (delyBD * r12) +
(-t3 * delyBD) + (delyAB * r12));
dthetadr[2][1][2] = sc1 * ((-t1 * delzAB) + (delzBD * r12) +
(-t3 * delzBD) + (delzAB * r12));
dthetadr[2][3][0] = sc1 * ((t3 * delxBD) - (delxAB * r12));
dthetadr[2][3][1] = sc1 * ((t3 * delyBD) - (delyAB * r12));
dthetadr[2][3][2] = sc1 * ((t3 * delzBD) - (delzAB * r12));
// angleangle forces
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
fabcd[i][j] = -
((aa_k1[type] *
(dthABC*dthetadr[1][i][j] + dthCBD*dthetadr[0][i][j])) +
(aa_k2[type] *
(dthABC*dthetadr[2][i][j] + dthABD*dthetadr[0][i][j])) +
(aa_k3[type] *
(dthABD*dthetadr[1][i][j] + dthCBD*dthetadr[2][i][j])));
// apply force to each of 4 atoms
if (newton_bond || i1 < nlocal) {
f[i1][0] += fabcd[0][0];
f[i1][1] += fabcd[0][1];
f[i1][2] += fabcd[0][2];
}
if (newton_bond || i2 < nlocal) {
f[i2][0] += fabcd[1][0];
f[i2][1] += fabcd[1][1];
f[i2][2] += fabcd[1][2];
}
if (newton_bond || i3 < nlocal) {
f[i3][0] += fabcd[2][0];
f[i3][1] += fabcd[2][1];
f[i3][2] += fabcd[2][2];
}
if (newton_bond || i4 < nlocal) {
f[i4][0] += fabcd[3][0];
f[i4][1] += fabcd[3][1];
f[i4][2] += fabcd[3][2];
}
if (evflag)
ev_tally(i1,i2,i3,i4,nlocal,newton_bond,eimproper,
fabcd[0],fabcd[2],fabcd[3],
delxAB,delyAB,delzAB,delxBC,delyBC,delzBC,delxBD,delyBD,delzBD);
}
}
/* ----------------------------------------------------------------------
cross product: c = a x b
------------------------------------------------------------------------- */
void ImproperClass2::cross(double *a, double *b, double *c)
{
c[0] = a[1]*b[2] - a[2]*b[1];
c[1] = a[2]*b[0] - a[0]*b[2];
c[2] = a[0]*b[1] - a[1]*b[0];
}
/* ----------------------------------------------------------------------
dot product of a dot b
------------------------------------------------------------------------- */
double ImproperClass2::dot(double *a, double *b)
{
return (a[0]*b[0] + a[1]*b[1] + a[2]*b[2]);
}
diff --git a/src/COLLOID/atom_vec_colloid.cpp b/src/COLLOID/atom_vec_colloid.cpp
index 0ba21a735..d35bfe7de 100644
--- a/src/COLLOID/atom_vec_colloid.cpp
+++ b/src/COLLOID/atom_vec_colloid.cpp
@@ -1,706 +1,706 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "stdlib.h"
#include "atom_vec_colloid.h"
-#include "lmptype.h"
#include "atom.h"
#include "force.h"
#include "domain.h"
#include "modify.h"
#include "fix.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define DELTA 10000
/* ---------------------------------------------------------------------- */
AtomVecColloid::AtomVecColloid(LAMMPS *lmp, int narg, char **arg) :
AtomVec(lmp, narg, arg)
{
molecular = 0;
mass_type = 1;
shape_type = 1;
comm_x_only = 1;
comm_f_only = 0;
size_forward = 3;
size_reverse = 6;
size_border = 6;
size_velocity = 6;
size_data_atom = 5;
size_data_vel = 7;
xcol_data = 3;
atom->omega_flag = atom->torque_flag = 1;
}
/* ----------------------------------------------------------------------
grow atom arrays
n = 0 grows arrays by DELTA
n > 0 allocates arrays to size n
------------------------------------------------------------------------- */
void AtomVecColloid::grow(int n)
{
if (n == 0) nmax += DELTA;
else nmax = n;
atom->nmax = nmax;
if (nmax < 0 || nmax > MAXSMALLINT)
error->one("Per-processor system is too big");
tag = atom->tag = (int *)
memory->srealloc(atom->tag,nmax*sizeof(int),"atom:tag");
type = atom->type = (int *)
memory->srealloc(atom->type,nmax*sizeof(int),"atom:type");
mask = atom->mask = (int *)
memory->srealloc(atom->mask,nmax*sizeof(int),"atom:mask");
image = atom->image = (int *)
memory->srealloc(atom->image,nmax*sizeof(int),"atom:image");
x = atom->x = memory->grow_2d_double_array(atom->x,nmax,3,"atom:x");
v = atom->v = memory->grow_2d_double_array(atom->v,nmax,3,"atom:v");
f = atom->f = memory->grow_2d_double_array(atom->f,nmax,3,"atom:f");
omega = atom->omega =
memory->grow_2d_double_array(atom->omega,nmax,3,"atom:omega");
torque = atom->torque =
memory->grow_2d_double_array(atom->torque,nmax,3,"atom:torque");
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
}
/* ----------------------------------------------------------------------
reset local array ptrs
------------------------------------------------------------------------- */
void AtomVecColloid::grow_reset()
{
tag = atom->tag; type = atom->type;
mask = atom->mask; image = atom->image;
x = atom->x; v = atom->v; f = atom->f;
omega = atom->omega; torque = atom->torque;
}
/* ---------------------------------------------------------------------- */
void AtomVecColloid::copy(int i, int j)
{
tag[j] = tag[i];
type[j] = type[i];
mask[j] = mask[i];
image[j] = image[i];
x[j][0] = x[i][0];
x[j][1] = x[i][1];
x[j][2] = x[i][2];
v[j][0] = v[i][0];
v[j][1] = v[i][1];
v[j][2] = v[i][2];
omega[j][0] = omega[i][0];
omega[j][1] = omega[i][1];
omega[j][2] = omega[i][2];
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j);
}
/* ---------------------------------------------------------------------- */
int AtomVecColloid::pack_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
dz = pbc[2]*domain->zprd;
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecColloid::pack_comm_vel(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
buf[m++] = omega[j][0];
buf[m++] = omega[j][1];
buf[m++] = omega[j][2];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
dz = pbc[2]*domain->zprd;
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
buf[m++] = omega[j][0];
buf[m++] = omega[j][1];
buf[m++] = omega[j][2];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecColloid::unpack_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
void AtomVecColloid::unpack_comm_vel(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
omega[i][0] = buf[m++];
omega[i][1] = buf[m++];
omega[i][2] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecColloid::pack_reverse(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
buf[m++] = f[i][0];
buf[m++] = f[i][1];
buf[m++] = f[i][2];
buf[m++] = torque[i][0];
buf[m++] = torque[i][1];
buf[m++] = torque[i][2];
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecColloid::pack_reverse_one(int i, double *buf)
{
buf[0] = torque[i][0];
buf[1] = torque[i][1];
buf[2] = torque[i][2];
return 3;
}
/* ---------------------------------------------------------------------- */
void AtomVecColloid::unpack_reverse(int n, int *list, double *buf)
{
int i,j,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
f[j][0] += buf[m++];
f[j][1] += buf[m++];
f[j][2] += buf[m++];
torque[j][0] += buf[m++];
torque[j][1] += buf[m++];
torque[j][2] += buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecColloid::unpack_reverse_one(int i, double *buf)
{
torque[i][0] += buf[0];
torque[i][1] += buf[1];
torque[i][2] += buf[2];
return 3;
}
/* ---------------------------------------------------------------------- */
int AtomVecColloid::pack_border(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0];
dy = pbc[1];
dz = pbc[2];
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecColloid::pack_border_vel(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
buf[m++] = omega[j][0];
buf[m++] = omega[j][1];
buf[m++] = omega[j][2];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0];
dy = pbc[1];
dz = pbc[2];
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
buf[m++] = omega[j][0];
buf[m++] = omega[j][1];
buf[m++] = omega[j][2];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecColloid::unpack_border(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
if (i == nmax) grow(0);
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
tag[i] = static_cast<int> (buf[m++]);
type[i] = static_cast<int> (buf[m++]);
mask[i] = static_cast<int> (buf[m++]);
}
}
/* ---------------------------------------------------------------------- */
void AtomVecColloid::unpack_border_vel(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
if (i == nmax) grow(0);
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
tag[i] = static_cast<int> (buf[m++]);
type[i] = static_cast<int> (buf[m++]);
mask[i] = static_cast<int> (buf[m++]);
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
omega[i][0] = buf[m++];
omega[i][1] = buf[m++];
omega[i][2] = buf[m++];
}
}
/* ----------------------------------------------------------------------
pack data for atom I for sending to another proc
xyz must be 1st 3 values, so comm::exchange() can test on them
------------------------------------------------------------------------- */
int AtomVecColloid::pack_exchange(int i, double *buf)
{
int m = 1;
buf[m++] = x[i][0];
buf[m++] = x[i][1];
buf[m++] = x[i][2];
buf[m++] = v[i][0];
buf[m++] = v[i][1];
buf[m++] = v[i][2];
buf[m++] = tag[i];
buf[m++] = type[i];
buf[m++] = mask[i];
buf[m++] = image[i];
buf[m++] = omega[i][0];
buf[m++] = omega[i][1];
buf[m++] = omega[i][2];
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]);
buf[0] = m;
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecColloid::unpack_exchange(double *buf)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
int m = 1;
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
x[nlocal][2] = buf[m++];
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
tag[nlocal] = static_cast<int> (buf[m++]);
type[nlocal] = static_cast<int> (buf[m++]);
mask[nlocal] = static_cast<int> (buf[m++]);
image[nlocal] = static_cast<int> (buf[m++]);
omega[nlocal][0] = buf[m++];
omega[nlocal][1] = buf[m++];
omega[nlocal][2] = buf[m++];
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->
unpack_exchange(nlocal,&buf[m]);
atom->nlocal++;
return m;
}
/* ----------------------------------------------------------------------
size of restart data for all atoms owned by this proc
include extra data stored by fixes
------------------------------------------------------------------------- */
int AtomVecColloid::size_restart()
{
int i;
int nlocal = atom->nlocal;
int n = 14 * nlocal;
if (atom->nextra_restart)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
for (i = 0; i < nlocal; i++)
n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
return n;
}
/* ----------------------------------------------------------------------
pack atom I's data for restart file including extra quantities
xyz must be 1st 3 values, so that read_restart can test on them
molecular types may be negative, but write as positive
------------------------------------------------------------------------- */
int AtomVecColloid::pack_restart(int i, double *buf)
{
int m = 1;
buf[m++] = x[i][0];
buf[m++] = x[i][1];
buf[m++] = x[i][2];
buf[m++] = tag[i];
buf[m++] = type[i];
buf[m++] = mask[i];
buf[m++] = image[i];
buf[m++] = v[i][0];
buf[m++] = v[i][1];
buf[m++] = v[i][2];
buf[m++] = omega[i][0];
buf[m++] = omega[i][1];
buf[m++] = omega[i][2];
if (atom->nextra_restart)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]);
buf[0] = m;
return m;
}
/* ----------------------------------------------------------------------
unpack data for one atom from restart file including extra quantities
------------------------------------------------------------------------- */
int AtomVecColloid::unpack_restart(double *buf)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) {
grow(0);
if (atom->nextra_store)
atom->extra = memory->grow_2d_double_array(atom->extra,nmax,
atom->nextra_store,
"atom:extra");
}
int m = 1;
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
x[nlocal][2] = buf[m++];
tag[nlocal] = static_cast<int> (buf[m++]);
type[nlocal] = static_cast<int> (buf[m++]);
mask[nlocal] = static_cast<int> (buf[m++]);
image[nlocal] = static_cast<int> (buf[m++]);
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
omega[nlocal][0] = buf[m++];
omega[nlocal][1] = buf[m++];
omega[nlocal][2] = buf[m++];
double **extra = atom->extra;
if (atom->nextra_store) {
int size = static_cast<int> (buf[0]) - m;
for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++];
}
atom->nlocal++;
return m;
}
/* ----------------------------------------------------------------------
create one atom of itype at coord
set other values to defaults
------------------------------------------------------------------------- */
void AtomVecColloid::create_atom(int itype, double *coord)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
tag[nlocal] = 0;
type[nlocal] = itype;
x[nlocal][0] = coord[0];
x[nlocal][1] = coord[1];
x[nlocal][2] = coord[2];
mask[nlocal] = 1;
image[nlocal] = (512 << 20) | (512 << 10) | 512;
v[nlocal][0] = 0.0;
v[nlocal][1] = 0.0;
v[nlocal][2] = 0.0;
omega[nlocal][0] = 0.0;
omega[nlocal][1] = 0.0;
omega[nlocal][2] = 0.0;
atom->nlocal++;
}
/* ----------------------------------------------------------------------
unpack one line from Atoms section of data file
initialize other atom quantities
------------------------------------------------------------------------- */
void AtomVecColloid::data_atom(double *coord, int imagetmp, char **values)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
tag[nlocal] = atoi(values[0]);
if (tag[nlocal] <= 0)
error->one("Invalid atom ID in Atoms section of data file");
type[nlocal] = atoi(values[1]);
if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
error->one("Invalid atom type in Atoms section of data file");
x[nlocal][0] = coord[0];
x[nlocal][1] = coord[1];
x[nlocal][2] = coord[2];
image[nlocal] = imagetmp;
mask[nlocal] = 1;
v[nlocal][0] = 0.0;
v[nlocal][1] = 0.0;
v[nlocal][2] = 0.0;
omega[nlocal][0] = 0.0;
omega[nlocal][1] = 0.0;
omega[nlocal][2] = 0.0;
atom->nlocal++;
}
/* ----------------------------------------------------------------------
unpack one line from Velocities section of data file
------------------------------------------------------------------------- */
void AtomVecColloid::data_vel(int m, char **values)
{
v[m][0] = atof(values[0]);
v[m][1] = atof(values[1]);
v[m][2] = atof(values[2]);
omega[m][0] = atof(values[3]);
omega[m][1] = atof(values[4]);
omega[m][2] = atof(values[5]);
}
/* ----------------------------------------------------------------------
unpack hybrid quantities from one line in Velocities section of data file
------------------------------------------------------------------------- */
int AtomVecColloid::data_vel_hybrid(int m, char **values)
{
omega[m][0] = atof(values[0]);
omega[m][1] = atof(values[1]);
omega[m][2] = atof(values[2]);
return 3;
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
------------------------------------------------------------------------- */
double AtomVecColloid::memory_usage()
{
double bytes = 0.0;
if (atom->memcheck("tag")) bytes += nmax * sizeof(int);
if (atom->memcheck("type")) bytes += nmax * sizeof(int);
if (atom->memcheck("mask")) bytes += nmax * sizeof(int);
if (atom->memcheck("image")) bytes += nmax * sizeof(int);
if (atom->memcheck("x")) bytes += nmax*3 * sizeof(double);
if (atom->memcheck("v")) bytes += nmax*3 * sizeof(double);
if (atom->memcheck("f")) bytes += nmax*3 * sizeof(double);
if (atom->memcheck("omega")) bytes += nmax*3 * sizeof(double);
if (atom->memcheck("torque")) bytes += nmax*3 * sizeof(double);
return bytes;
}
diff --git a/src/DIPOLE/atom_vec_dipole.cpp b/src/DIPOLE/atom_vec_dipole.cpp
index cc81711b4..bc254cbb6 100644
--- a/src/DIPOLE/atom_vec_dipole.cpp
+++ b/src/DIPOLE/atom_vec_dipole.cpp
@@ -1,840 +1,840 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "stdlib.h"
#include "atom_vec_dipole.h"
-#include "lmptype.h"
#include "atom.h"
#include "domain.h"
#include "modify.h"
#include "fix.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define DELTA 10000
/* ---------------------------------------------------------------------- */
AtomVecDipole::AtomVecDipole(LAMMPS *lmp, int narg, char **arg) :
AtomVec(lmp, narg, arg)
{
molecular = 0;
mass_type = 1;
shape_type = 1;
dipole_type = 1;
comm_x_only = comm_f_only = 0;
size_forward = 6;
size_reverse = 6;
size_border = 10;
size_velocity = 6;
size_data_atom = 9;
size_data_vel = 7;
xcol_data = 4;
atom->q_flag = atom->mu_flag = atom->omega_flag = atom->torque_flag = 1;
}
/* ----------------------------------------------------------------------
grow atom arrays
n = 0 grows arrays by DELTA
n > 0 allocates arrays to size n
------------------------------------------------------------------------- */
void AtomVecDipole::grow(int n)
{
if (n == 0) nmax += DELTA;
else nmax = n;
atom->nmax = nmax;
if (nmax < 0 || nmax > MAXSMALLINT)
error->one("Per-processor system is too big");
tag = atom->tag = (int *)
memory->srealloc(atom->tag,nmax*sizeof(int),"atom:tag");
type = atom->type = (int *)
memory->srealloc(atom->type,nmax*sizeof(int),"atom:type");
mask = atom->mask = (int *)
memory->srealloc(atom->mask,nmax*sizeof(int),"atom:mask");
image = atom->image = (int *)
memory->srealloc(atom->image,nmax*sizeof(int),"atom:image");
x = atom->x = memory->grow_2d_double_array(atom->x,nmax,3,"atom:x");
v = atom->v = memory->grow_2d_double_array(atom->v,nmax,3,"atom:v");
f = atom->f = memory->grow_2d_double_array(atom->f,nmax,3,"atom:f");
q = atom->q = (double *)
memory->srealloc(atom->q,nmax*sizeof(double),"atom:q");
mu = atom->mu =
memory->grow_2d_double_array(atom->mu,nmax,3,"atom:mu");
omega = atom->omega =
memory->grow_2d_double_array(atom->omega,nmax,3,"atom:omega");
torque = atom->torque =
memory->grow_2d_double_array(atom->torque,nmax,3,"atom:torque");
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
}
/* ----------------------------------------------------------------------
reset local array ptrs
------------------------------------------------------------------------- */
void AtomVecDipole::grow_reset()
{
tag = atom->tag; type = atom->type;
mask = atom->mask; image = atom->image;
x = atom->x; v = atom->v; f = atom->f;
q = atom->q; mu = atom->mu;
omega = atom->omega; torque = atom->torque;
}
/* ---------------------------------------------------------------------- */
void AtomVecDipole::copy(int i, int j)
{
tag[j] = tag[i];
type[j] = type[i];
mask[j] = mask[i];
image[j] = image[i];
x[j][0] = x[i][0];
x[j][1] = x[i][1];
x[j][2] = x[i][2];
v[j][0] = v[i][0];
v[j][1] = v[i][1];
v[j][2] = v[i][2];
q[j] = q[i];
mu[j][0] = mu[i][0];
mu[j][1] = mu[i][1];
mu[j][2] = mu[i][2];
omega[j][0] = omega[i][0];
omega[j][1] = omega[i][1];
omega[j][2] = omega[i][2];
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j);
}
/* ---------------------------------------------------------------------- */
int AtomVecDipole::pack_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = mu[j][0];
buf[m++] = mu[j][1];
buf[m++] = mu[j][2];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
dz = pbc[2]*domain->zprd;
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = mu[j][0];
buf[m++] = mu[j][1];
buf[m++] = mu[j][2];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecDipole::pack_comm_vel(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = mu[j][0];
buf[m++] = mu[j][1];
buf[m++] = mu[j][2];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
buf[m++] = omega[j][0];
buf[m++] = omega[j][1];
buf[m++] = omega[j][2];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
dz = pbc[2]*domain->zprd;
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = mu[j][0];
buf[m++] = mu[j][1];
buf[m++] = mu[j][2];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
buf[m++] = omega[j][0];
buf[m++] = omega[j][1];
buf[m++] = omega[j][2];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecDipole::pack_comm_one(int i, double *buf)
{
buf[0] = mu[i][0];
buf[1] = mu[i][1];
buf[2] = mu[i][2];
return 3;
}
/* ---------------------------------------------------------------------- */
void AtomVecDipole::unpack_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
mu[i][0] = buf[m++];
mu[i][1] = buf[m++];
mu[i][2] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
void AtomVecDipole::unpack_comm_vel(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
mu[i][0] = buf[m++];
mu[i][1] = buf[m++];
mu[i][2] = buf[m++];
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
omega[i][0] = buf[m++];
omega[i][1] = buf[m++];
omega[i][2] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecDipole::unpack_comm_one(int i, double *buf)
{
mu[i][0] = buf[0];
mu[i][1] = buf[1];
mu[i][2] = buf[2];
return 3;
}
/* ---------------------------------------------------------------------- */
int AtomVecDipole::pack_reverse(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
buf[m++] = f[i][0];
buf[m++] = f[i][1];
buf[m++] = f[i][2];
buf[m++] = torque[i][0];
buf[m++] = torque[i][1];
buf[m++] = torque[i][2];
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecDipole::pack_reverse_one(int i, double *buf)
{
buf[0] = torque[i][0];
buf[1] = torque[i][1];
buf[2] = torque[i][2];
return 3;
}
/* ---------------------------------------------------------------------- */
void AtomVecDipole::unpack_reverse(int n, int *list, double *buf)
{
int i,j,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
f[j][0] += buf[m++];
f[j][1] += buf[m++];
f[j][2] += buf[m++];
torque[j][0] += buf[m++];
torque[j][1] += buf[m++];
torque[j][2] += buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecDipole::unpack_reverse_one(int i, double *buf)
{
torque[i][0] += buf[0];
torque[i][1] += buf[1];
torque[i][2] += buf[2];
return 3;
}
/* ---------------------------------------------------------------------- */
int AtomVecDipole::pack_border(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = q[j];
buf[m++] = mu[j][0];
buf[m++] = mu[j][1];
buf[m++] = mu[j][2];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0];
dy = pbc[1];
dz = pbc[2];
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = q[j];
buf[m++] = mu[j][0];
buf[m++] = mu[j][1];
buf[m++] = mu[j][2];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecDipole::pack_border_vel(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = q[j];
buf[m++] = mu[j][0];
buf[m++] = mu[j][1];
buf[m++] = mu[j][2];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
buf[m++] = omega[j][0];
buf[m++] = omega[j][1];
buf[m++] = omega[j][2];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0];
dy = pbc[1];
dz = pbc[2];
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = q[j];
buf[m++] = mu[j][0];
buf[m++] = mu[j][1];
buf[m++] = mu[j][2];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
buf[m++] = omega[j][0];
buf[m++] = omega[j][1];
buf[m++] = omega[j][2];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecDipole::pack_border_one(int i, double *buf)
{
buf[0] = q[i];
buf[1] = mu[i][0];
buf[2] = mu[i][1];
buf[3] = mu[i][2];
return 4;
}
/* ---------------------------------------------------------------------- */
void AtomVecDipole::unpack_border(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
if (i == nmax) grow(0);
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
tag[i] = static_cast<int> (buf[m++]);
type[i] = static_cast<int> (buf[m++]);
mask[i] = static_cast<int> (buf[m++]);
q[i] = buf[m++];
mu[i][0] = buf[m++];
mu[i][1] = buf[m++];
mu[i][2] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
void AtomVecDipole::unpack_border_vel(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
if (i == nmax) grow(0);
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
tag[i] = static_cast<int> (buf[m++]);
type[i] = static_cast<int> (buf[m++]);
mask[i] = static_cast<int> (buf[m++]);
q[i] = buf[m++];
mu[i][0] = buf[m++];
mu[i][1] = buf[m++];
mu[i][2] = buf[m++];
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
omega[i][0] = buf[m++];
omega[i][1] = buf[m++];
omega[i][2] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecDipole::unpack_border_one(int i, double *buf)
{
q[i] = buf[0];
mu[i][0] = buf[1];
mu[i][1] = buf[2];
mu[i][2] = buf[3];
return 4;
}
/* ----------------------------------------------------------------------
pack all atom quantities for shipping to another proc
xyz must be 1st 3 values, so that comm::exchange can test on them
------------------------------------------------------------------------- */
int AtomVecDipole::pack_exchange(int i, double *buf)
{
int m = 1;
buf[m++] = x[i][0];
buf[m++] = x[i][1];
buf[m++] = x[i][2];
buf[m++] = v[i][0];
buf[m++] = v[i][1];
buf[m++] = v[i][2];
buf[m++] = tag[i];
buf[m++] = type[i];
buf[m++] = mask[i];
buf[m++] = image[i];
buf[m++] = q[i];
buf[m++] = mu[i][0];
buf[m++] = mu[i][1];
buf[m++] = mu[i][2];
buf[m++] = omega[i][0];
buf[m++] = omega[i][1];
buf[m++] = omega[i][2];
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]);
buf[0] = m;
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecDipole::unpack_exchange(double *buf)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
int m = 1;
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
x[nlocal][2] = buf[m++];
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
tag[nlocal] = static_cast<int> (buf[m++]);
type[nlocal] = static_cast<int> (buf[m++]);
mask[nlocal] = static_cast<int> (buf[m++]);
image[nlocal] = static_cast<int> (buf[m++]);
q[nlocal] = buf[m++];
mu[nlocal][0] = buf[m++];
mu[nlocal][1] = buf[m++];
mu[nlocal][2] = buf[m++];
omega[nlocal][0] = buf[m++];
omega[nlocal][1] = buf[m++];
omega[nlocal][2] = buf[m++];
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->
unpack_exchange(nlocal,&buf[m]);
atom->nlocal++;
return m;
}
/* ----------------------------------------------------------------------
size of restart data for all atoms owned by this proc
include extra data stored by fixes
------------------------------------------------------------------------- */
int AtomVecDipole::size_restart()
{
int i;
int nlocal = atom->nlocal;
int n = 18 * nlocal;
if (atom->nextra_restart)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
for (i = 0; i < nlocal; i++)
n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
return n;
}
/* ----------------------------------------------------------------------
pack atom I's data for restart file including extra quantities
xyz must be 1st 3 values, so that read_restart can test on them
molecular types may be negative, but write as positive
------------------------------------------------------------------------- */
int AtomVecDipole::pack_restart(int i, double *buf)
{
int m = 1;
buf[m++] = x[i][0];
buf[m++] = x[i][1];
buf[m++] = x[i][2];
buf[m++] = tag[i];
buf[m++] = type[i];
buf[m++] = mask[i];
buf[m++] = image[i];
buf[m++] = v[i][0];
buf[m++] = v[i][1];
buf[m++] = v[i][2];
buf[m++] = q[i];
buf[m++] = mu[i][0];
buf[m++] = mu[i][1];
buf[m++] = mu[i][2];
buf[m++] = omega[i][0];
buf[m++] = omega[i][1];
buf[m++] = omega[i][2];
if (atom->nextra_restart)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]);
buf[0] = m;
return m;
}
/* ----------------------------------------------------------------------
unpack data for one atom from restart file including extra quantities
------------------------------------------------------------------------- */
int AtomVecDipole::unpack_restart(double *buf)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) {
grow(0);
if (atom->nextra_store)
atom->extra = memory->grow_2d_double_array(atom->extra,nmax,
atom->nextra_store,
"atom:extra");
}
int m = 1;
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
x[nlocal][2] = buf[m++];
tag[nlocal] = static_cast<int> (buf[m++]);
type[nlocal] = static_cast<int> (buf[m++]);
mask[nlocal] = static_cast<int> (buf[m++]);
image[nlocal] = static_cast<int> (buf[m++]);
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
q[nlocal] = buf[m++];
mu[nlocal][0] = buf[m++];
mu[nlocal][1] = buf[m++];
mu[nlocal][2] = buf[m++];
omega[nlocal][0] = buf[m++];
omega[nlocal][1] = buf[m++];
omega[nlocal][2] = buf[m++];
double **extra = atom->extra;
if (atom->nextra_store) {
int size = static_cast<int> (buf[0]) - m;
for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++];
}
atom->nlocal++;
return m;
}
/* ----------------------------------------------------------------------
create one atom of itype at coord
set other values to defaults
------------------------------------------------------------------------- */
void AtomVecDipole::create_atom(int itype, double *coord)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
tag[nlocal] = 0;
type[nlocal] = itype;
x[nlocal][0] = coord[0];
x[nlocal][1] = coord[1];
x[nlocal][2] = coord[2];
mask[nlocal] = 1;
image[nlocal] = (512 << 20) | (512 << 10) | 512;
v[nlocal][0] = 0.0;
v[nlocal][1] = 0.0;
v[nlocal][2] = 0.0;
q[nlocal] = 0.0;
mu[nlocal][0] = 0.0;
mu[nlocal][1] = 0.0;
mu[nlocal][2] = 0.0;
omega[nlocal][0] = 0.0;
omega[nlocal][1] = 0.0;
omega[nlocal][2] = 0.0;
atom->nlocal++;
}
/* ----------------------------------------------------------------------
unpack one line from Atoms section of data file
initialize other atom quantities
------------------------------------------------------------------------- */
void AtomVecDipole::data_atom(double *coord, int imagetmp, char **values)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
tag[nlocal] = atoi(values[0]);
if (tag[nlocal] <= 0)
error->one("Invalid atom ID in Atoms section of data file");
type[nlocal] = atoi(values[1]);
if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
error->one("Invalid atom type in Atoms section of data file");
q[nlocal] = atof(values[2]);
x[nlocal][0] = coord[0];
x[nlocal][1] = coord[1];
x[nlocal][2] = coord[2];
mu[nlocal][0] = atof(values[6]);
mu[nlocal][1] = atof(values[7]);
mu[nlocal][2] = atof(values[8]);
image[nlocal] = imagetmp;
mask[nlocal] = 1;
v[nlocal][0] = 0.0;
v[nlocal][1] = 0.0;
v[nlocal][2] = 0.0;
omega[nlocal][0] = 0.0;
omega[nlocal][1] = 0.0;
omega[nlocal][2] = 0.0;
atom->nlocal++;
}
/* ----------------------------------------------------------------------
unpack hybrid quantities from one line in Atoms section of data file
initialize other atom quantities for this sub-style
------------------------------------------------------------------------- */
int AtomVecDipole::data_atom_hybrid(int nlocal, char **values)
{
q[nlocal] = atof(values[0]);
mu[nlocal][0] = atof(values[1]);
mu[nlocal][1] = atof(values[2]);
mu[nlocal][2] = atof(values[3]);
return 4;
}
/* ----------------------------------------------------------------------
unpack one line from Velocities section of data file
------------------------------------------------------------------------- */
void AtomVecDipole::data_vel(int m, char **values)
{
v[m][0] = atof(values[0]);
v[m][1] = atof(values[1]);
v[m][2] = atof(values[2]);
omega[m][0] = atof(values[3]);
omega[m][1] = atof(values[4]);
omega[m][2] = atof(values[5]);
}
/* ----------------------------------------------------------------------
unpack hybrid quantities from one line in Velocities section of data file
------------------------------------------------------------------------- */
int AtomVecDipole::data_vel_hybrid(int m, char **values)
{
omega[m][0] = atof(values[0]);
omega[m][1] = atof(values[1]);
omega[m][2] = atof(values[2]);
return 3;
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
------------------------------------------------------------------------- */
double AtomVecDipole::memory_usage()
{
double bytes = 0.0;
if (atom->memcheck("tag")) bytes += nmax * sizeof(int);
if (atom->memcheck("type")) bytes += nmax * sizeof(int);
if (atom->memcheck("mask")) bytes += nmax * sizeof(int);
if (atom->memcheck("image")) bytes += nmax * sizeof(int);
if (atom->memcheck("x")) bytes += nmax*3 * sizeof(double);
if (atom->memcheck("v")) bytes += nmax*3 * sizeof(double);
if (atom->memcheck("f")) bytes += nmax*3 * sizeof(double);
if (atom->memcheck("q")) bytes += nmax * sizeof(double);
if (atom->memcheck("mu")) bytes += nmax*3 * sizeof(double);
if (atom->memcheck("omega")) bytes += nmax*3 * sizeof(double);
if (atom->memcheck("torque")) bytes += nmax*3 * sizeof(double);
return bytes;
}
diff --git a/src/GPU/pair_cg_cmm_coul_long_gpu.cpp b/src/GPU/pair_cg_cmm_coul_long_gpu.cpp
index 3a5a58c5b..6d11692d5 100644
--- a/src/GPU/pair_cg_cmm_coul_long_gpu.cpp
+++ b/src/GPU/pair_cg_cmm_coul_long_gpu.cpp
@@ -1,502 +1,502 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "pair_cg_cmm_coul_long_gpu.h"
-#include "lmptype.h"
#include "atom.h"
#include "atom_vec.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "integrate.h"
#include "memory.h"
#include "error.h"
#include "neigh_request.h"
#include "universe.h"
#include "update.h"
#include "domain.h"
#include "string.h"
#include "kspace.h"
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
#define EWALD_F 1.12837917
#define EWALD_P 0.3275911
#define A1 0.254829592
#define A2 -0.284496736
#define A3 1.421413741
#define A4 -1.453152027
#define A5 1.061405429
// External functions from cuda library for atom decomposition
bool cmml_gpu_init(const int ntypes, double **cutsq, int **cg_type,
double **host_lj1, double **host_lj2, double **host_lj3,
double **host_lj4, double **offset, double *special_lj,
const int nlocal, const int nall, const int max_nbors,
const int maxspecial, const double cell_size, int &gpu_mode,
FILE *screen, double **host_cut_ljsq, double host_cut_coulsq,
double *host_special_coul, const double qqrd2e,
const double g_ewald);
void cmml_gpu_clear();
int * cmml_gpu_compute_n(const int timestep, const int ago, const int inum,
const int nall, double **host_x, int *host_type,
double *boxlo, double *boxhi, int *tag, int **nspecial,
int **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success, double *host_q);
void cmml_gpu_compute(const int timestep, const int ago, const int inum,
const int nall, double **host_x, int *host_type,
int *ilist, int *numj, int **firstneigh,
const bool eflag, const bool vflag, const bool eatom,
const bool vatom, int &host_start, const double cpu_time,
bool &success, double *host_q);
double cmml_gpu_bytes();
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairCGCMMCoulLongGPU::PairCGCMMCoulLongGPU(LAMMPS *lmp) : PairCGCMMCoulLong(lmp), gpu_mode(GPU_PAIR)
{
respa_enable = 0;
cpu_time = 0.0;
}
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
PairCGCMMCoulLongGPU::~PairCGCMMCoulLongGPU()
{
cmml_gpu_clear();
}
/* ---------------------------------------------------------------------- */
void PairCGCMMCoulLongGPU::compute(int eflag, int vflag)
{
int ntimestep = static_cast<int>(update->ntimestep % MAXSMALLINT);
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
bool success = true;
if (gpu_mode == GPU_NEIGH) {
inum = atom->nlocal;
gpulist = cmml_gpu_compute_n(ntimestep, neighbor->ago, inum, nall,
atom->x, atom->type, domain->sublo,
domain->subhi, atom->tag, atom->nspecial,
atom->special, eflag, vflag, eflag_atom,
vflag_atom, host_start, cpu_time, success,
atom->q);
} else {
inum = list->inum;
cmml_gpu_compute(ntimestep, neighbor->ago, inum, nall, atom->x,
atom->type, list->ilist, list->numneigh, list->firstneigh,
eflag, vflag, eflag_atom, vflag_atom, host_start, cpu_time,
success, atom->q);
}
if (!success)
error->one("Out of memory on GPGPU");
if (host_start<inum) {
cpu_time = MPI_Wtime();
if (gpu_mode == GPU_NEIGH)
cpu_compute(gpulist, host_start, eflag, vflag);
else
cpu_compute(host_start, eflag, vflag);
cpu_time = MPI_Wtime() - cpu_time;
}
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairCGCMMCoulLongGPU::init_style()
{
cut_respa = NULL;
if (!atom->q_flag)
error->all("Pair style cg/cmm/coul/long requires atom attribute q");
if (force->pair_match("gpu",0) == NULL)
error->all("Cannot use pair hybrid with multiple GPU pair styles");
// Repeat cutsq calculation because done after call to init_style
double maxcut = -1.0;
double cut;
for (int i = 1; i <= atom->ntypes; i++) {
for (int j = i; j <= atom->ntypes; j++) {
if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) {
cut = init_one(i,j);
cut *= cut;
if (cut > maxcut)
maxcut = cut;
cutsq[i][j] = cutsq[j][i] = cut;
} else
cutsq[i][j] = cutsq[j][i] = 0.0;
}
}
double cell_size = sqrt(maxcut) + neighbor->skin;
// insure use of KSpace long-range solver, set g_ewald
if (force->kspace == NULL)
error->all("Pair style is incompatible with KSpace style");
g_ewald = force->kspace->g_ewald;
// setup force tables
if (ncoultablebits) init_tables();
int maxspecial=0;
if (atom->molecular)
maxspecial=atom->maxspecial;
bool init_ok = cmml_gpu_init(atom->ntypes+1, cutsq, cg_type, lj1, lj2, lj3,
lj4, offset, force->special_lj, atom->nlocal,
atom->nlocal+atom->nghost, 300, maxspecial,
cell_size, gpu_mode, screen, cut_ljsq,
cut_coulsq_global, force->special_coul,
force->qqrd2e, g_ewald);
if (!init_ok)
error->one("Insufficient memory on accelerator (or no fix gpu).\n");
if (force->newton_pair)
error->all("Cannot use newton pair with GPU cg/cmm pair style");
if (gpu_mode != GPU_NEIGH) {
int irequest = neighbor->request(this);
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
}
}
/* ---------------------------------------------------------------------- */
double PairCGCMMCoulLongGPU::memory_usage()
{
double bytes = Pair::memory_usage();
return bytes + cmml_gpu_bytes();
}
/* ---------------------------------------------------------------------- */
void PairCGCMMCoulLongGPU::cpu_compute(int start, int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype,itable;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz;
double fraction,table;
double r,r2inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj;
double grij,expm2,prefactor,t,erfc;
int *ilist,*jlist,*numneigh,**firstneigh;
double rsq;
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
double qqrd2e = force->qqrd2e;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (ii = start; ii < inum; ii++) {
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_coul = factor_lj = 1.0;
else {
factor_coul = special_coul[j/nall];
factor_lj = special_lj[j/nall];
j %= nall;
}
const double delx = xtmp - x[j][0];
const double dely = ytmp - x[j][1];
const double delz = ztmp - x[j][2];
const double rsq = delx*delx + dely*dely + delz*delz;
const int jtype = type[j];
double evdwl = 0.0;
double ecoul = 0.0;
double fpair = 0.0;
if (rsq < cutsq[itype][jtype]) {
const double r2inv = 1.0/rsq;
const int cgt=cg_type[itype][jtype];
double forcelj = 0.0;
double forcecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
forcelj=factor_lj;
if (eflag) evdwl=factor_lj;
if (cgt == CG_LJ12_4) {
const double r4inv=r2inv*r2inv;
forcelj *= r4inv*(lj1[itype][jtype]*r4inv*r4inv
- lj2[itype][jtype]);
if (eflag) {
evdwl *= r4inv*(lj3[itype][jtype]*r4inv*r4inv
- lj4[itype][jtype]) - offset[itype][jtype];
}
} else if (cgt == CG_LJ9_6) {
const double r3inv = r2inv*sqrt(r2inv);
const double r6inv = r3inv*r3inv;
forcelj *= r6inv*(lj1[itype][jtype]*r3inv
- lj2[itype][jtype]);
if (eflag) {
evdwl *= r6inv*(lj3[itype][jtype]*r3inv
- lj4[itype][jtype]) - offset[itype][jtype];
}
} else {
const double r6inv = r2inv*r2inv*r2inv;
forcelj *= r6inv*(lj1[itype][jtype]*r6inv
- lj2[itype][jtype]);
if (eflag) {
evdwl *= r6inv*(lj3[itype][jtype]*r6inv
- lj4[itype][jtype]) - offset[itype][jtype];
}
}
}
if (rsq < cut_coulsq_global) {
if (!ncoultablebits || rsq <= tabinnersq) {
const double r = sqrt(rsq);
const double grij = g_ewald * r;
const double expm2 = exp(-grij*grij);
const double t = 1.0 / (1.0 + EWALD_P*grij);
const double erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
const double prefactor = qqrd2e * qtmp*q[j]/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
if (eflag) ecoul = prefactor*erfc;
if (factor_coul < 1.0) {
forcecoul -= (1.0-factor_coul)*prefactor;
if (eflag) ecoul -= (1.0-factor_coul)*prefactor;
}
} else {
union_int_float_t rsq_lookup;
rsq_lookup.f = rsq;
int itable = rsq_lookup.i & ncoulmask;
itable >>= ncoulshiftbits;
const double fraction = (rsq_lookup.f - rtable[itable]) *
drtable[itable];
const double table = ftable[itable] + fraction*dftable[itable];
forcecoul = qtmp*q[j] * table;
if (eflag) {
const double table2 = etable[itable] + fraction*detable[itable];
ecoul = qtmp*q[j] * table2;
}
if (factor_coul < 1.0) {
const double table2 = ctable[itable] + fraction*dctable[itable];
const double prefactor = qtmp*q[j] * table2;
forcecoul -= (1.0-factor_coul)*prefactor;
if (eflag) ecoul -= (1.0-factor_coul)*prefactor;
}
}
}
fpair = (forcecoul + forcelj) * r2inv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (evflag) ev_tally_full(i,evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
}
/* ---------------------------------------------------------------------- */
void PairCGCMMCoulLongGPU::cpu_compute(int *nbors, int start, int eflag,
int vflag)
{
int i,j,jnum,itype,jtype,itable;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz;
double fraction,table;
double r,r2inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj;
double grij,expm2,prefactor,t,erfc;
double rsq;
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int stride = nlocal-start;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
double qqrd2e = force->qqrd2e;
// loop over neighbors of my atoms
for (i = start; i < nlocal; i++) {
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
int *nbor = nbors + i - start;
jnum = *nbor;
nbor += stride;
int *nbor_end = nbor + stride * jnum;
for (; nbor<nbor_end; nbor+=stride) {
j = *nbor;
if (j < nall) factor_coul = factor_lj = 1.0;
else {
factor_coul = special_coul[j/nall];
factor_lj = special_lj[j/nall];
j %= nall;
}
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
double evdwl = 0.0;
double ecoul = 0.0;
double fpair = 0.0;
if (rsq < cutsq[itype][jtype]) {
const double r2inv = 1.0/rsq;
const int cgt=cg_type[itype][jtype];
double forcelj = 0.0;
double forcecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
forcelj=factor_lj;
if (eflag) evdwl=factor_lj;
if (cgt == CG_LJ12_4) {
const double r4inv=r2inv*r2inv;
forcelj *= r4inv*(lj1[itype][jtype]*r4inv*r4inv
- lj2[itype][jtype]);
if (eflag) {
evdwl *= r4inv*(lj3[itype][jtype]*r4inv*r4inv
- lj4[itype][jtype]) - offset[itype][jtype];
}
} else if (cgt == CG_LJ9_6) {
const double r3inv = r2inv*sqrt(r2inv);
const double r6inv = r3inv*r3inv;
forcelj *= r6inv*(lj1[itype][jtype]*r3inv
- lj2[itype][jtype]);
if (eflag) {
evdwl *= r6inv*(lj3[itype][jtype]*r3inv
- lj4[itype][jtype]) - offset[itype][jtype];
}
} else {
const double r6inv = r2inv*r2inv*r2inv;
forcelj *= r6inv*(lj1[itype][jtype]*r6inv
- lj2[itype][jtype]);
if (eflag) {
evdwl *= r6inv*(lj3[itype][jtype]*r6inv
- lj4[itype][jtype]) - offset[itype][jtype];
}
}
}
if (rsq < cut_coulsq_global) {
if (!ncoultablebits || rsq <= tabinnersq) {
const double r = sqrt(rsq);
const double grij = g_ewald * r;
const double expm2 = exp(-grij*grij);
const double t = 1.0 / (1.0 + EWALD_P*grij);
const double erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
const double prefactor = qqrd2e * qtmp*q[j]/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
if (eflag) ecoul = prefactor*erfc;
if (factor_coul < 1.0) {
forcecoul -= (1.0-factor_coul)*prefactor;
if (eflag) ecoul -= (1.0-factor_coul)*prefactor;
}
} else {
union_int_float_t rsq_lookup;
rsq_lookup.f = rsq;
int itable = rsq_lookup.i & ncoulmask;
itable >>= ncoulshiftbits;
const double fraction = (rsq_lookup.f - rtable[itable]) *
drtable[itable];
const double table = ftable[itable] + fraction*dftable[itable];
forcecoul = qtmp*q[j] * table;
if (eflag) {
const double table2 = etable[itable] + fraction*detable[itable];
ecoul = qtmp*q[j] * table2;
}
if (factor_coul < 1.0) {
const double table2 = ctable[itable] + fraction*dctable[itable];
const double prefactor = qtmp*q[j] * table2;
forcecoul -= (1.0-factor_coul)*prefactor;
if (eflag) ecoul -= (1.0-factor_coul)*prefactor;
}
}
}
fpair = (forcecoul + forcelj) * r2inv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (j<start) {
if (evflag) ev_tally_full(i,evdwl,ecoul,fpair,delx,dely,delz);
} else {
if (j<nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
if (evflag) ev_tally(i,j,nlocal,0,
evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
}
}
diff --git a/src/GPU/pair_cg_cmm_gpu.cpp b/src/GPU/pair_cg_cmm_gpu.cpp
index a49464fd5..638815f36 100644
--- a/src/GPU/pair_cg_cmm_gpu.cpp
+++ b/src/GPU/pair_cg_cmm_gpu.cpp
@@ -1,365 +1,365 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "pair_cg_cmm_gpu.h"
-#include "lmptype.h"
#include "atom.h"
#include "atom_vec.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "integrate.h"
#include "memory.h"
#include "error.h"
#include "neigh_request.h"
#include "universe.h"
#include "update.h"
#include "domain.h"
#include "string.h"
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
// External functions from cuda library for atom decomposition
bool cmm_gpu_init(const int ntypes, double **cutsq, int **cg_types,
double **host_lj1, double **host_lj2, double **host_lj3,
double **host_lj4, double **offset, double *special_lj,
const int nlocal, const int nall, const int max_nbors,
const int maxspecial, const double cell_size, int &gpu_mode,
FILE *screen);
void cmm_gpu_clear();
int * cmm_gpu_compute_n(const int timestep, const int ago, const int inum,
const int nall, double **host_x, int *host_type,
double *boxlo, double *boxhi, int *tag, int **nspecial,
int **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success);
void cmm_gpu_compute(const int timestep, const int ago, const int inum,
const int nall, double **host_x, int *host_type,
int *ilist, int *numj, int **firstneigh,
const bool eflag, const bool vflag, const bool eatom,
const bool vatom, int &host_start, const double cpu_time,
bool &success);
double cmm_gpu_bytes();
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairCGCMMGPU::PairCGCMMGPU(LAMMPS *lmp) : PairCGCMM(lmp), gpu_mode(GPU_PAIR)
{
respa_enable = 0;
cpu_time = 0.0;
}
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
PairCGCMMGPU::~PairCGCMMGPU()
{
cmm_gpu_clear();
}
/* ---------------------------------------------------------------------- */
void PairCGCMMGPU::compute(int eflag, int vflag)
{
int ntimestep = static_cast<int>(update->ntimestep % MAXSMALLINT);
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
bool success = true;
if (gpu_mode == GPU_NEIGH) {
inum = atom->nlocal;
gpulist = cmm_gpu_compute_n(ntimestep, neighbor->ago, inum, nall,
atom->x, atom->type, domain->sublo,
domain->subhi, atom->tag, atom->nspecial,
atom->special, eflag, vflag, eflag_atom,
vflag_atom, host_start, cpu_time, success);
} else {
inum = list->inum;
cmm_gpu_compute(ntimestep, neighbor->ago, inum, nall, atom->x,
atom->type, list->ilist, list->numneigh, list->firstneigh,
eflag, vflag, eflag_atom, vflag_atom, host_start, cpu_time,
success);
}
if (!success)
error->one("Out of memory on GPGPU");
if (host_start<inum) {
cpu_time = MPI_Wtime();
if (gpu_mode == GPU_NEIGH)
cpu_compute(gpulist, host_start, eflag, vflag);
else
cpu_compute(host_start, eflag, vflag);
cpu_time = MPI_Wtime() - cpu_time;
}
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairCGCMMGPU::init_style()
{
cut_respa = NULL;
if (force->pair_match("gpu",0) == NULL)
error->all("Cannot use pair hybrid with multiple GPU pair styles");
// Repeat cutsq calculation because done after call to init_style
double maxcut = -1.0;
double cut;
for (int i = 1; i <= atom->ntypes; i++) {
for (int j = i; j <= atom->ntypes; j++) {
if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) {
cut = init_one(i,j);
cut *= cut;
if (cut > maxcut)
maxcut = cut;
cutsq[i][j] = cutsq[j][i] = cut;
} else
cutsq[i][j] = cutsq[j][i] = 0.0;
}
}
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial=0;
if (atom->molecular)
maxspecial=atom->maxspecial;
bool init_ok = cmm_gpu_init(atom->ntypes+1,cutsq,cg_type,lj1,lj2,lj3,lj4,
offset, force->special_lj, atom->nlocal,
atom->nlocal+atom->nghost, 300, maxspecial,
cell_size, gpu_mode, screen);
if (!init_ok)
error->one("Insufficient memory on accelerator (or no fix gpu).\n");
if (force->newton_pair)
error->all("Cannot use newton pair with GPU CGCMM pair style");
if (gpu_mode != GPU_NEIGH) {
int irequest = neighbor->request(this);
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
}
}
/* ---------------------------------------------------------------------- */
double PairCGCMMGPU::memory_usage()
{
double bytes = Pair::memory_usage();
return bytes + cmm_gpu_bytes();
}
/* ---------------------------------------------------------------------- */
void PairCGCMMGPU::cpu_compute(int start, int eflag, int vflag) {
int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,r2inv,r6inv,forcelj,factor_lj;
int *ilist,*jlist,*numneigh,**firstneigh;
double **x = atom->x;
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_lj = force->special_lj;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (ii = start; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_lj = 1.0;
else {
factor_lj = special_lj[j/nall];
j %= nall;
}
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
const int cgt=cg_type[itype][jtype];
r2inv = 1.0/rsq;
fpair = factor_lj;
if (eflag) evdwl = factor_lj;
if (cgt == CG_LJ12_4) {
const double r4inv = r2inv*r2inv;
fpair *= r4inv*(lj1[itype][jtype]*r4inv*r4inv
- lj2[itype][jtype]);
if (eflag) {
evdwl *= r4inv*(lj3[itype][jtype]*r4inv*r4inv
- lj4[itype][jtype]) - offset[itype][jtype];
}
} else if (cgt == CG_LJ9_6) {
const double r3inv = r2inv*sqrt(r2inv);
const double r6inv = r3inv*r3inv;
fpair *= r6inv*(lj1[itype][jtype]*r3inv
- lj2[itype][jtype]);
if (eflag) {
evdwl *= r6inv*(lj3[itype][jtype]*r3inv
- lj4[itype][jtype]) - offset[itype][jtype];
}
} else {
const double r6inv = r2inv*r2inv*r2inv;
fpair *= r6inv*(lj1[itype][jtype]*r6inv
- lj2[itype][jtype]);
if (eflag) {
evdwl *= r6inv*(lj3[itype][jtype]*r6inv
- lj4[itype][jtype]) - offset[itype][jtype];
}
}
fpair *= r2inv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (evflag) ev_tally_full(i,evdwl,0.0,fpair,delx,dely,delz);
}
}
}
}
/* ---------------------------------------------------------------------- */
void PairCGCMMGPU::cpu_compute(int *nbors, int start, int eflag, int vflag) {
int i,j,itype,jtype;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int stride = nlocal-start;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,r2inv,r6inv,forcelj,factor_lj;
double *special_lj = force->special_lj;
double **x = atom->x;
double **f = atom->f;
int *type = atom->type;
// loop over neighbors of my atoms
for (i = start; i < nlocal; i++) {
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
int *nbor = nbors + i - start;
int jnum = *nbor;
nbor += stride;
int *nbor_end = nbor + stride * jnum;
for (; nbor<nbor_end; nbor+=stride) {
j = *nbor;
if (j < nall) factor_lj = 1.0;
else {
factor_lj = special_lj[j/nall];
j %= nall;
}
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
const int cgt=cg_type[itype][jtype];
r2inv = 1.0/rsq;
fpair = factor_lj;
if (eflag) evdwl = factor_lj;
if (cgt == CG_LJ12_4) {
const double r4inv = r2inv*r2inv;
fpair *= r4inv*(lj1[itype][jtype]*r4inv*r4inv
- lj2[itype][jtype]);
if (eflag) {
evdwl *= r4inv*(lj3[itype][jtype]*r4inv*r4inv
- lj4[itype][jtype]) - offset[itype][jtype];
}
} else if (cgt == CG_LJ9_6) {
const double r3inv = r2inv*sqrt(r2inv);
const double r6inv = r3inv*r3inv;
fpair *= r6inv*(lj1[itype][jtype]*r3inv
- lj2[itype][jtype]);
if (eflag) {
evdwl *= r6inv*(lj3[itype][jtype]*r3inv
- lj4[itype][jtype]) - offset[itype][jtype];
}
} else {
const double r6inv = r2inv*r2inv*r2inv;
fpair *= r6inv*(lj1[itype][jtype]*r6inv
- lj2[itype][jtype]);
if (eflag) {
evdwl *= r6inv*(lj3[itype][jtype]*r6inv
- lj4[itype][jtype]) - offset[itype][jtype];
}
}
fpair *= r2inv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (j<start) {
if (evflag) ev_tally_full(i,evdwl,0.0,fpair,delx,dely,delz);
} else {
if (j<nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
if (evflag) ev_tally(i,j,nlocal,0,
evdwl,0.0,fpair,delx,dely,delz);
}
}
}
}
}
diff --git a/src/GPU/pair_gayberne_gpu.cpp b/src/GPU/pair_gayberne_gpu.cpp
index b0e8af1df..eea45ad97 100644
--- a/src/GPU/pair_gayberne_gpu.cpp
+++ b/src/GPU/pair_gayberne_gpu.cpp
@@ -1,464 +1,464 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "pair_gayberne_gpu.h"
-#include "lmptype.h"
#include "math_extra.h"
#include "atom.h"
#include "atom_vec.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "integrate.h"
#include "memory.h"
#include "error.h"
#include "neigh_request.h"
#include "universe.h"
#include "domain.h"
#include "update.h"
#include "string.h"
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
// External functions from cuda library for atom decomposition
bool gb_gpu_init(const int ntypes, const double gamma, const double upsilon,
const double mu, double **shape, double **well, double **cutsq,
double **sigma, double **epsilon, double *host_lshape,
int **form, double **host_lj1, double **host_lj2,
double **host_lj3, double **host_lj4, double **offset,
double *special_lj, const int nlocal, const int nall,
const int max_nbors, const double cell_size,
int &gpu_mode, FILE *screen);
void gb_gpu_clear();
int * gb_gpu_compute_n(const int timestep, const int ago, const int inum,
const int nall, double **host_x, int *host_type,
double *boxlo, double *boxhi, const bool eflag,
const bool vflag, const bool eatom, const bool vatom,
int &host_start, const double cpu_time, bool &success,
double **host_quat);
int * gb_gpu_compute(const int timestep, const int ago, const int inum,
const int nall, double **host_x, int *host_type,
int *ilist, int *numj, int **firstneigh,
const bool eflag, const bool vflag, const bool eatom,
const bool vatom, int &host_start, const double cpu_time,
bool &success, double **host_quat);
double gb_gpu_bytes();
using namespace LAMMPS_NS;
enum{SPHERE_SPHERE,SPHERE_ELLIPSE,ELLIPSE_SPHERE,ELLIPSE_ELLIPSE};
/* ---------------------------------------------------------------------- */
PairGayBerneGPU::PairGayBerneGPU(LAMMPS *lmp) : PairGayBerne(lmp),
gpu_mode(GPU_PAIR)
{
}
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
PairGayBerneGPU::~PairGayBerneGPU()
{
gb_gpu_clear();
cpu_time = 0.0;
}
/* ---------------------------------------------------------------------- */
void PairGayBerneGPU::compute(int eflag, int vflag)
{
int ntimestep = static_cast<int>(update->ntimestep % MAXSMALLINT);
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
bool success = true;
if (gpu_mode == GPU_NEIGH) {
inum = atom->nlocal;
gpulist = gb_gpu_compute_n(ntimestep, neighbor->ago, inum, nall,
atom->x, atom->type, domain->sublo, domain->subhi,
eflag, vflag, eflag_atom, vflag_atom, host_start,
cpu_time, success, atom->quat);
} else {
inum = list->inum;
olist = gb_gpu_compute(ntimestep, neighbor->ago, inum, nall, atom->x,
atom->type, list->ilist, list->numneigh,
list->firstneigh, eflag, vflag, eflag_atom,
vflag_atom, host_start, cpu_time, success,
atom->quat);
}
if (!success)
error->one("Out of memory on GPGPU");
if (host_start < inum) {
cpu_time = MPI_Wtime();
if (gpu_mode == GPU_NEIGH)
cpu_compute(gpulist,host_start,eflag,vflag);
else
cpu_compute(host_start,eflag,vflag);
cpu_time = MPI_Wtime() - cpu_time;
}
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairGayBerneGPU::init_style()
{
if (force->pair_match("gpu",0) == NULL)
error->all("Cannot use pair hybrid with multiple GPU pair styles");
if (!atom->quat_flag || !atom->torque_flag || !atom->avec->shape_type)
error->all("Pair gayberne requires atom attributes quat, torque, shape");
if (atom->radius_flag)
error->all("Pair gayberne cannot be used with atom attribute diameter");
// per-type shape precalculations
for (int i = 1; i <= atom->ntypes; i++) {
if (setwell[i]) {
double *one = atom->shape[i];
shape[i][0] = one[0]*one[0];
shape[i][1] = one[1]*one[1];
shape[i][2] = one[2]*one[2];
lshape[i] = (one[0]*one[1]+one[2]*one[2])*sqrt(one[0]*one[1]);
}
}
// Repeat cutsq calculation because done after call to init_style
double maxcut = -1.0;
double cut;
for (int i = 1; i <= atom->ntypes; i++) {
for (int j = i; j <= atom->ntypes; j++) {
if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) {
cut = init_one(i,j);
cut *= cut;
if (cut > maxcut)
maxcut = cut;
cutsq[i][j] = cutsq[j][i] = cut;
} else
cutsq[i][j] = cutsq[j][i] = 0.0;
}
}
double cell_size = sqrt(maxcut) + neighbor->skin;
bool init_ok = gb_gpu_init(atom->ntypes+1, gamma, upsilon, mu,
shape, well, cutsq, sigma, epsilon, lshape, form,
lj1, lj2, lj3, lj4, offset, force->special_lj,
atom->nlocal, atom->nlocal+atom->nghost, 300,
cell_size, gpu_mode, screen);
if (!init_ok)
error->one("Insufficient memory on accelerator (or no fix gpu).");
if (force->newton_pair)
error->all("Cannot use newton pair with GPU Gay-Berne pair style");
if (gpu_mode != GPU_NEIGH) {
int irequest = neighbor->request(this);
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
}
}
/* ---------------------------------------------------------------------- */
double PairGayBerneGPU::memory_usage()
{
double bytes = Pair::memory_usage();
return bytes + gb_gpu_bytes();
}
/* ---------------------------------------------------------------------- */
void PairGayBerneGPU::cpu_compute(int start, int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double evdwl,one_eng,rsq,r2inv,r6inv,forcelj,factor_lj;
double fforce[3],ttor[3],rtor[3],r12[3];
double a1[3][3],b1[3][3],g1[3][3],a2[3][3],b2[3][3],g2[3][3],temp[3][3];
int *ilist,*jlist,*numneigh,**firstneigh;
double **x = atom->x;
double **f = atom->f;
double **quat = atom->quat;
double **tor = atom->torque;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_lj = force->special_lj;
inum = list->inum;
ilist = olist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (ii = start; ii < inum; ii++) {
i = ilist[ii];
itype = type[i];
if (form[itype][itype] == ELLIPSE_ELLIPSE) {
MathExtra::quat_to_mat_trans(quat[i],a1);
MathExtra::diag_times3(well[itype],a1,temp);
MathExtra::transpose_times3(a1,temp,b1);
MathExtra::diag_times3(shape[itype],a1,temp);
MathExtra::transpose_times3(a1,temp,g1);
}
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_lj = 1.0;
else {
factor_lj = special_lj[j/nall];
j %= nall;
}
// r12 = center to center vector
r12[0] = x[j][0]-x[i][0];
r12[1] = x[j][1]-x[i][1];
r12[2] = x[j][2]-x[i][2];
rsq = MathExtra::dot3(r12,r12);
jtype = type[j];
// compute if less than cutoff
if (rsq < cutsq[itype][jtype]) {
switch (form[itype][jtype]) {
case SPHERE_SPHERE:
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
forcelj *= -r2inv;
if (eflag) one_eng =
r6inv*(r6inv*lj3[itype][jtype]-lj4[itype][jtype]) -
offset[itype][jtype];
fforce[0] = r12[0]*forcelj;
fforce[1] = r12[1]*forcelj;
fforce[2] = r12[2]*forcelj;
ttor[0] = ttor[1] = ttor[2] = 0.0;
rtor[0] = rtor[1] = rtor[2] = 0.0;
break;
case SPHERE_ELLIPSE:
MathExtra::quat_to_mat_trans(quat[j],a2);
MathExtra::diag_times3(well[jtype],a2,temp);
MathExtra::transpose_times3(a2,temp,b2);
MathExtra::diag_times3(shape[jtype],a2,temp);
MathExtra::transpose_times3(a2,temp,g2);
one_eng = gayberne_lj(j,i,a2,b2,g2,r12,rsq,fforce,rtor);
ttor[0] = ttor[1] = ttor[2] = 0.0;
break;
case ELLIPSE_SPHERE:
one_eng = gayberne_lj(i,j,a1,b1,g1,r12,rsq,fforce,ttor);
rtor[0] = rtor[1] = rtor[2] = 0.0;
break;
default:
MathExtra::quat_to_mat_trans(quat[j],a2);
MathExtra::diag_times3(well[jtype],a2,temp);
MathExtra::transpose_times3(a2,temp,b2);
MathExtra::diag_times3(shape[jtype],a2,temp);
MathExtra::transpose_times3(a2,temp,g2);
one_eng = gayberne_analytic(i,j,a1,a2,b1,b2,g1,g2,r12,rsq,
fforce,ttor,rtor);
break;
}
fforce[0] *= factor_lj;
fforce[1] *= factor_lj;
fforce[2] *= factor_lj;
ttor[0] *= factor_lj;
ttor[1] *= factor_lj;
ttor[2] *= factor_lj;
f[i][0] += fforce[0];
f[i][1] += fforce[1];
f[i][2] += fforce[2];
tor[i][0] += ttor[0];
tor[i][1] += ttor[1];
tor[i][2] += ttor[2];
if (eflag) evdwl = factor_lj*one_eng;
if (evflag) ev_tally_xyz_full(i,evdwl,0.0,fforce[0],fforce[1],fforce[2],
-r12[0],-r12[1],-r12[2]);
}
}
}
}
/* ---------------------------------------------------------------------- */
void PairGayBerneGPU::cpu_compute(int *nbors, int start, int eflag, int vflag)
{
int i,j,itype,jtype;
double evdwl,one_eng,rsq,r2inv,r6inv,forcelj,factor_lj;
double fforce[3],ttor[3],rtor[3],r12[3];
double a1[3][3],b1[3][3],g1[3][3],a2[3][3],b2[3][3],g2[3][3],temp[3][3];
double **x = atom->x;
double **f = atom->f;
double **quat = atom->quat;
double **tor = atom->torque;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int stride = nlocal-start;
double *special_lj = force->special_lj;
// loop over neighbors of my atoms
for (i = start; i < nlocal; i++) {
itype = type[i];
if (form[itype][itype] == ELLIPSE_ELLIPSE) {
MathExtra::quat_to_mat_trans(quat[i],a1);
MathExtra::diag_times3(well[itype],a1,temp);
MathExtra::transpose_times3(a1,temp,b1);
MathExtra::diag_times3(shape[itype],a1,temp);
MathExtra::transpose_times3(a1,temp,g1);
}
int *nbor = nbors+i-start;
int jnum =* nbor;
nbor += stride;
int *nbor_end = nbor + stride * jnum;
for ( ; nbor < nbor_end; nbor += stride) {
j = *nbor;
if (j < nall) factor_lj = 1.0;
else {
factor_lj = special_lj[j/nall];
j %= nall;
}
// r12 = center to center vector
r12[0] = x[j][0]-x[i][0];
r12[1] = x[j][1]-x[i][1];
r12[2] = x[j][2]-x[i][2];
rsq = MathExtra::dot3(r12,r12);
jtype = type[j];
// compute if less than cutoff
if (rsq < cutsq[itype][jtype]) {
switch (form[itype][jtype]) {
case SPHERE_SPHERE:
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
forcelj *= -r2inv;
if (eflag) one_eng =
r6inv*(r6inv*lj3[itype][jtype]-lj4[itype][jtype]) -
offset[itype][jtype];
fforce[0] = r12[0]*forcelj;
fforce[1] = r12[1]*forcelj;
fforce[2] = r12[2]*forcelj;
ttor[0] = ttor[1] = ttor[2] = 0.0;
rtor[0] = rtor[1] = rtor[2] = 0.0;
break;
case SPHERE_ELLIPSE:
MathExtra::quat_to_mat_trans(quat[j],a2);
MathExtra::diag_times3(well[jtype],a2,temp);
MathExtra::transpose_times3(a2,temp,b2);
MathExtra::diag_times3(shape[jtype],a2,temp);
MathExtra::transpose_times3(a2,temp,g2);
one_eng = gayberne_lj(j,i,a2,b2,g2,r12,rsq,fforce,rtor);
ttor[0] = ttor[1] = ttor[2] = 0.0;
break;
case ELLIPSE_SPHERE:
one_eng = gayberne_lj(i,j,a1,b1,g1,r12,rsq,fforce,ttor);
rtor[0] = rtor[1] = rtor[2] = 0.0;
break;
default:
MathExtra::quat_to_mat_trans(quat[j],a2);
MathExtra::diag_times3(well[jtype],a2,temp);
MathExtra::transpose_times3(a2,temp,b2);
MathExtra::diag_times3(shape[jtype],a2,temp);
MathExtra::transpose_times3(a2,temp,g2);
one_eng = gayberne_analytic(i,j,a1,a2,b1,b2,g1,g2,r12,rsq,
fforce,ttor,rtor);
break;
}
fforce[0] *= factor_lj;
fforce[1] *= factor_lj;
fforce[2] *= factor_lj;
ttor[0] *= factor_lj;
ttor[1] *= factor_lj;
ttor[2] *= factor_lj;
f[i][0] += fforce[0];
f[i][1] += fforce[1];
f[i][2] += fforce[2];
tor[i][0] += ttor[0];
tor[i][1] += ttor[1];
tor[i][2] += ttor[2];
if (eflag) evdwl = factor_lj*one_eng;
if (j<start) {
if (evflag) ev_tally_xyz_full(i,evdwl,0.0,fforce[0],fforce[1],
fforce[2],-r12[0],-r12[1],-r12[2]);
} else {
if (j < nlocal) {
rtor[0] *= factor_lj;
rtor[1] *= factor_lj;
rtor[2] *= factor_lj;
f[j][0] -= fforce[0];
f[j][1] -= fforce[1];
f[j][2] -= fforce[2];
tor[j][0] += rtor[0];
tor[j][1] += rtor[1];
tor[j][2] += rtor[2];
}
if (evflag) ev_tally_xyz(i,j,nlocal,0,
evdwl,0.0,fforce[0],fforce[1],fforce[2],
-r12[0],-r12[1],-r12[2]);
}
}
}
}
}
diff --git a/src/GPU/pair_lj96_cut_gpu.cpp b/src/GPU/pair_lj96_cut_gpu.cpp
index e36ea857f..8da239106 100644
--- a/src/GPU/pair_lj96_cut_gpu.cpp
+++ b/src/GPU/pair_lj96_cut_gpu.cpp
@@ -1,321 +1,321 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "pair_lj96_cut_gpu.h"
-#include "lmptype.h"
#include "atom.h"
#include "atom_vec.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "integrate.h"
#include "memory.h"
#include "error.h"
#include "neigh_request.h"
#include "universe.h"
#include "update.h"
#include "domain.h"
#include "string.h"
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
// External functions from cuda library for atom decomposition
bool lj96_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
double **host_lj2, double **host_lj3, double **host_lj4,
double **offset, double *special_lj, const int nlocal,
const int nall, const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen);
void lj96_gpu_clear();
int * lj96_gpu_compute_n(const int timestep, const int ago, const int inum,
const int nall, double **host_x, int *host_type,
double *boxlo, double *boxhi, int *tag, int **nspecial,
int **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success);
void lj96_gpu_compute(const int timestep, const int ago, const int inum,
const int nall, double **host_x, int *host_type,
int *ilist, int *numj, int **firstneigh,
const bool eflag, const bool vflag, const bool eatom,
const bool vatom, int &host_start, const double cpu_time,
bool &success);
double lj96_gpu_bytes();
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairLJ96CutGPU::PairLJ96CutGPU(LAMMPS *lmp) : PairLJ96Cut(lmp), gpu_mode(GPU_PAIR)
{
respa_enable = 0;
cpu_time = 0.0;
}
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
PairLJ96CutGPU::~PairLJ96CutGPU()
{
lj96_gpu_clear();
}
/* ---------------------------------------------------------------------- */
void PairLJ96CutGPU::compute(int eflag, int vflag)
{
int ntimestep = static_cast<int>(update->ntimestep % MAXSMALLINT);
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
bool success = true;
if (gpu_mode == GPU_NEIGH) {
inum = atom->nlocal;
gpulist = lj96_gpu_compute_n(ntimestep, neighbor->ago, inum, nall,
atom->x, atom->type, domain->sublo,
domain->subhi, atom->tag, atom->nspecial,
atom->special, eflag, vflag, eflag_atom,
vflag_atom, host_start, cpu_time, success);
} else {
inum = list->inum;
lj96_gpu_compute(ntimestep, neighbor->ago, inum, nall, atom->x,
atom->type, list->ilist, list->numneigh, list->firstneigh,
eflag, vflag, eflag_atom, vflag_atom, host_start, cpu_time,
success);
}
if (!success)
error->one("Out of memory on GPGPU");
if (host_start<inum) {
cpu_time = MPI_Wtime();
if (gpu_mode == GPU_NEIGH)
cpu_compute(gpulist, host_start, eflag, vflag);
else
cpu_compute(host_start, eflag, vflag);
cpu_time = MPI_Wtime() - cpu_time;
}
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairLJ96CutGPU::init_style()
{
cut_respa = NULL;
if (force->pair_match("gpu",0) == NULL)
error->all("Cannot use pair hybrid with multiple GPU pair styles");
// Repeat cutsq calculation because done after call to init_style
double maxcut = -1.0;
double cut;
for (int i = 1; i <= atom->ntypes; i++) {
for (int j = i; j <= atom->ntypes; j++) {
if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) {
cut = init_one(i,j);
cut *= cut;
if (cut > maxcut)
maxcut = cut;
cutsq[i][j] = cutsq[j][i] = cut;
} else
cutsq[i][j] = cutsq[j][i] = 0.0;
}
}
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial=0;
if (atom->molecular)
maxspecial=atom->maxspecial;
bool init_ok = lj96_gpu_init(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4,
offset, force->special_lj, atom->nlocal,
atom->nlocal+atom->nghost, 300, maxspecial,
cell_size, gpu_mode, screen);
if (!init_ok)
error->one("Insufficient memory on accelerator (or no fix gpu).\n");
if (force->newton_pair)
error->all("Cannot use newton pair with GPU LJ96 pair style");
if (gpu_mode != GPU_NEIGH) {
int irequest = neighbor->request(this);
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
}
}
/* ---------------------------------------------------------------------- */
double PairLJ96CutGPU::memory_usage()
{
double bytes = Pair::memory_usage();
return bytes + lj96_gpu_bytes();
}
/* ---------------------------------------------------------------------- */
void PairLJ96CutGPU::cpu_compute(int start, int eflag, int vflag) {
int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,r2inv,r3inv,r6inv,forcelj,factor_lj;
int *ilist,*jlist,*numneigh,**firstneigh;
double **x = atom->x;
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_lj = force->special_lj;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (ii = start; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_lj = 1.0;
else {
factor_lj = special_lj[j/nall];
j %= nall;
}
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
r3inv = sqrt(r6inv);
forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
fpair = factor_lj*forcelj*r2inv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (eflag) {
evdwl = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) -
offset[itype][jtype];
evdwl *= factor_lj;
}
if (evflag) ev_tally_full(i,evdwl,0.0,fpair,delx,dely,delz);
}
}
}
}
/* ---------------------------------------------------------------------- */
void PairLJ96CutGPU::cpu_compute(int *nbors, int start, int eflag, int vflag) {
int i,j,itype,jtype;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int stride = nlocal-start;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,r2inv,r3inv,r6inv,forcelj,factor_lj;
double *special_lj = force->special_lj;
double **x = atom->x;
double **f = atom->f;
int *type = atom->type;
// loop over neighbors of my atoms
for (i = start; i < nlocal; i++) {
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
int *nbor = nbors + i - start;
int jnum = *nbor;
nbor += stride;
int *nbor_end = nbor + stride * jnum;
for (; nbor<nbor_end; nbor+=stride) {
j = *nbor;
if (j < nall) factor_lj = 1.0;
else {
factor_lj = special_lj[j/nall];
j %= nall;
}
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
r3inv = sqrt(r6inv);
forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
fpair = factor_lj*forcelj*r2inv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (eflag) {
evdwl = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) -
offset[itype][jtype];
evdwl *= factor_lj;
}
if (j<start) {
if (evflag) ev_tally_full(i,evdwl,0.0,fpair,delx,dely,delz);
} else {
if (j<nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
if (evflag) ev_tally(i,j,nlocal,0,
evdwl,0.0,fpair,delx,dely,delz);
}
}
}
}
}
diff --git a/src/GPU/pair_lj_charmm_coul_long_gpu.cpp b/src/GPU/pair_lj_charmm_coul_long_gpu.cpp
index a02d7018c..7be632c00 100644
--- a/src/GPU/pair_lj_charmm_coul_long_gpu.cpp
+++ b/src/GPU/pair_lj_charmm_coul_long_gpu.cpp
@@ -1,488 +1,488 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "pair_lj_charmm_coul_long_gpu.h"
-#include "lmptype.h"
#include "atom.h"
#include "atom_vec.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "integrate.h"
#include "memory.h"
#include "error.h"
#include "neigh_request.h"
#include "universe.h"
#include "update.h"
#include "domain.h"
#include "string.h"
#include "kspace.h"
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
#define EWALD_F 1.12837917
#define EWALD_P 0.3275911
#define A1 0.254829592
#define A2 -0.284496736
#define A3 1.421413741
#define A4 -1.453152027
#define A5 1.061405429
// External functions from cuda library for atom decomposition
bool crml_gpu_init(const int ntypes, double cut_bothsq, double **host_lj1,
double **host_lj2, double **host_lj3, double **host_lj4,
double **offset, double *special_lj, const int nlocal,
const int nall, const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen,
double host_cut_ljsq, double host_cut_coulsq,
double *host_special_coul, const double qqrd2e,
const double g_ewald, const double cut_lj_innersq,
const double denom_lj, double **epsilon, double **sigma,
const bool mix_arithmetic);
void crml_gpu_clear();
int * crml_gpu_compute_n(const int timestep, const int ago, const int inum,
const int nall, double **host_x, int *host_type,
double *boxlo, double *boxhi, int *tag, int **nspecial,
int **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success, double *host_q);
void crml_gpu_compute(const int timestep, const int ago, const int inum,
const int nall, double **host_x, int *host_type,
int *ilist, int *numj, int **firstneigh,
const bool eflag, const bool vflag, const bool eatom,
const bool vatom, int &host_start, const double cpu_time,
bool &success, double *host_q);
double crml_gpu_bytes();
using namespace LAMMPS_NS;
enum{GEOMETRIC,ARITHMETIC,SIXTHPOWER};
/* ---------------------------------------------------------------------- */
PairLJCharmmCoulLongGPU::PairLJCharmmCoulLongGPU(LAMMPS *lmp) :
PairLJCharmmCoulLong(lmp), gpu_mode(GPU_PAIR)
{
respa_enable = 0;
cpu_time = 0.0;
}
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
PairLJCharmmCoulLongGPU::~PairLJCharmmCoulLongGPU()
{
crml_gpu_clear();
}
/* ---------------------------------------------------------------------- */
void PairLJCharmmCoulLongGPU::compute(int eflag, int vflag)
{
int ntimestep = static_cast<int>(update->ntimestep % MAXSMALLINT);
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
bool success = true;
if (gpu_mode == GPU_NEIGH) {
inum = atom->nlocal;
gpulist = crml_gpu_compute_n(ntimestep, neighbor->ago, inum, nall,
atom->x, atom->type, domain->sublo,
domain->subhi, atom->tag, atom->nspecial,
atom->special, eflag, vflag, eflag_atom,
vflag_atom, host_start, cpu_time, success,
atom->q);
} else {
inum = list->inum;
crml_gpu_compute(ntimestep, neighbor->ago, inum, nall, atom->x,
atom->type, list->ilist, list->numneigh, list->firstneigh,
eflag, vflag, eflag_atom, vflag_atom, host_start, cpu_time,
success, atom->q);
}
if (!success)
error->one("Out of memory on GPGPU");
if (host_start<inum) {
cpu_time = MPI_Wtime();
if (gpu_mode == GPU_NEIGH)
cpu_compute(gpulist, host_start, eflag, vflag);
else
cpu_compute(host_start, eflag, vflag);
cpu_time = MPI_Wtime() - cpu_time;
}
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairLJCharmmCoulLongGPU::init_style()
{
cut_respa = NULL;
if (!atom->q_flag)
error->all("Pair style lj/charmm/coul/long requires atom attribute q");
if (force->pair_match("gpu",0) == NULL)
error->all("Cannot use pair hybrid with multiple GPU pair styles");
// Repeat cutsq calculation because done after call to init_style
double cut;
for (int i = 1; i <= atom->ntypes; i++) {
for (int j = i; j <= atom->ntypes; j++) {
if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0))
cut = init_one(i,j);
}
}
cut_lj_innersq = cut_lj_inner * cut_lj_inner;
cut_ljsq = cut_lj * cut_lj;
cut_coulsq = cut_coul * cut_coul;
cut_bothsq = MAX(cut_ljsq,cut_coulsq);
denom_lj = (cut_ljsq-cut_lj_innersq) * (cut_ljsq-cut_lj_innersq) *
(cut_ljsq-cut_lj_innersq);
double cell_size = sqrt(cut_bothsq) + neighbor->skin;
// insure use of KSpace long-range solver, set g_ewald
if (force->kspace == NULL)
error->all("Pair style is incompatible with KSpace style");
g_ewald = force->kspace->g_ewald;
// setup force tables
if (ncoultablebits) init_tables();
int maxspecial=0;
if (atom->molecular)
maxspecial=atom->maxspecial;
bool init_ok = crml_gpu_init(atom->ntypes+1, cut_bothsq, lj1, lj2, lj3, lj4,
offset, force->special_lj, atom->nlocal,
atom->nlocal+atom->nghost, 300, maxspecial,
cell_size, gpu_mode, screen, cut_ljsq,
cut_coulsq, force->special_coul, force->qqrd2e,
g_ewald, cut_lj_innersq,denom_lj,epsilon,sigma,
mix_flag == ARITHMETIC);
if (!init_ok)
error->one("Insufficient memory on accelerator (or no fix gpu).\n");
if (force->newton_pair)
error->all("Cannot use newton pair with GPU CHARMM pair style");
if (gpu_mode != GPU_NEIGH) {
int irequest = neighbor->request(this);
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
}
}
/* ---------------------------------------------------------------------- */
double PairLJCharmmCoulLongGPU::memory_usage()
{
double bytes = Pair::memory_usage();
return bytes + crml_gpu_bytes();
}
/* ---------------------------------------------------------------------- */
void PairLJCharmmCoulLongGPU::cpu_compute(int start, int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype,itable;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
double fraction,table;
double r,r2inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj;
double grij,expm2,prefactor,t,erfc;
double philj,switch1,switch2;
int *ilist,*jlist,*numneigh,**firstneigh;
double rsq;
evdwl = ecoul = 0.0;
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
double qqrd2e = force->qqrd2e;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (ii = start; ii < inum; ii++) {
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_coul = factor_lj = 1.0;
else {
factor_coul = special_coul[j/nall];
factor_lj = special_lj[j/nall];
j %= nall;
}
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cut_bothsq) {
r2inv = 1.0/rsq;
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq) {
r = sqrt(rsq);
grij = g_ewald * r;
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
prefactor = qqrd2e * qtmp*q[j]/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
} else {
union_int_float_t rsq_lookup;
rsq_lookup.f = rsq;
itable = rsq_lookup.i & ncoulmask;
itable >>= ncoulshiftbits;
fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
table = ftable[itable] + fraction*dftable[itable];
forcecoul = qtmp*q[j] * table;
if (factor_coul < 1.0) {
table = ctable[itable] + fraction*dctable[itable];
prefactor = qtmp*q[j] * table;
forcecoul -= (1.0-factor_coul)*prefactor;
}
}
} else forcecoul = 0.0;
if (rsq < cut_ljsq) {
r6inv = r2inv*r2inv*r2inv;
jtype = type[j];
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
switch2 = 12.0*rsq * (cut_ljsq-rsq) *
(rsq-cut_lj_innersq) / denom_lj;
philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
forcelj = forcelj*switch1 + philj*switch2;
}
} else forcelj = 0.0;
fpair = (forcecoul + factor_lj*forcelj) * r2inv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (eflag) {
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq)
ecoul = prefactor*erfc;
else {
table = etable[itable] + fraction*detable[itable];
ecoul = qtmp*q[j] * table;
}
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
} else ecoul = 0.0;
if (rsq < cut_ljsq) {
evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
evdwl *= switch1;
}
evdwl *= factor_lj;
} else evdwl = 0.0;
}
if (evflag) ev_tally_full(i,evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
}
/* ---------------------------------------------------------------------- */
void PairLJCharmmCoulLongGPU::cpu_compute(int *nbors, int start, int eflag,
int vflag)
{
int i,j,jnum,itype,jtype,itable;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
double fraction,table;
double r,r2inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj;
double grij,expm2,prefactor,t,erfc;
double philj,switch1,switch2;
double rsq;
evdwl = ecoul = 0.0;
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int stride = nlocal - start;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
double qqrd2e = force->qqrd2e;
// loop over neighbors of my atoms
for (i = start; i < nlocal; i++) {
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
int *nbor = nbors + i - start;
jnum = *nbor;
nbor += stride;
int *nbor_end = nbor + stride * jnum;
for (; nbor<nbor_end; nbor+=stride) {
j = *nbor;
if (j < nall) factor_coul = factor_lj = 1.0;
else {
factor_coul = special_coul[j/nall];
factor_lj = special_lj[j/nall];
j %= nall;
}
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cut_bothsq) {
r2inv = 1.0/rsq;
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq) {
r = sqrt(rsq);
grij = g_ewald * r;
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
prefactor = qqrd2e * qtmp*q[j]/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
} else {
union_int_float_t rsq_lookup;
rsq_lookup.f = rsq;
itable = rsq_lookup.i & ncoulmask;
itable >>= ncoulshiftbits;
fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
table = ftable[itable] + fraction*dftable[itable];
forcecoul = qtmp*q[j] * table;
if (factor_coul < 1.0) {
table = ctable[itable] + fraction*dctable[itable];
prefactor = qtmp*q[j] * table;
forcecoul -= (1.0-factor_coul)*prefactor;
}
}
} else forcecoul = 0.0;
if (rsq < cut_ljsq) {
r6inv = r2inv*r2inv*r2inv;
jtype = type[j];
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
switch2 = 12.0*rsq * (cut_ljsq-rsq) *
(rsq-cut_lj_innersq) / denom_lj;
philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
forcelj = forcelj*switch1 + philj*switch2;
}
} else forcelj = 0.0;
fpair = (forcecoul + factor_lj*forcelj) * r2inv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (eflag) {
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq)
ecoul = prefactor*erfc;
else {
table = etable[itable] + fraction*detable[itable];
ecoul = qtmp*q[j] * table;
}
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
} else ecoul = 0.0;
if (rsq < cut_ljsq) {
evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
evdwl *= switch1;
}
evdwl *= factor_lj;
} else evdwl = 0.0;
}
if (j<start) {
if (evflag) ev_tally_full(i,evdwl,ecoul,fpair,delx,dely,delz);
} else {
if (j<nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
if (evflag) ev_tally(i,j,nlocal,0,
evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
}
}
diff --git a/src/GPU/pair_lj_cut_coul_cut_gpu.cpp b/src/GPU/pair_lj_cut_coul_cut_gpu.cpp
index 3c8b1271f..2cb4027bc 100644
--- a/src/GPU/pair_lj_cut_coul_cut_gpu.cpp
+++ b/src/GPU/pair_lj_cut_coul_cut_gpu.cpp
@@ -1,367 +1,367 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "pair_lj_cut_coul_cut_gpu.h"
-#include "lmptype.h"
#include "atom.h"
#include "atom_vec.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "integrate.h"
#include "memory.h"
#include "error.h"
#include "neigh_request.h"
#include "universe.h"
#include "update.h"
#include "domain.h"
#include "string.h"
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
// External functions from cuda library for atom decomposition
bool ljc_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
double **host_lj2, double **host_lj3, double **host_lj4,
double **offset, double *special_lj, const int nlocal,
const int nall, const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen,
double **host_cut_ljsq, double **host_cut_coulsq,
double *host_special_coul, const double qqrd2e);
void ljc_gpu_clear();
int * ljc_gpu_compute_n(const int timestep, const int ago, const int inum,
const int nall, double **host_x, int *host_type,
double *boxlo, double *boxhi, int *tag, int **nspecial,
int **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success, double *host_q);
void ljc_gpu_compute(const int timestep, const int ago, const int inum,
const int nall, double **host_x, int *host_type,
int *ilist, int *numj, int **firstneigh,
const bool eflag, const bool vflag, const bool eatom,
const bool vatom, int &host_start, const double cpu_time,
bool &success, double *host_q);
double ljc_gpu_bytes();
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairLJCutCoulCutGPU::PairLJCutCoulCutGPU(LAMMPS *lmp) : PairLJCutCoulCut(lmp), gpu_mode(GPU_PAIR)
{
respa_enable = 0;
cpu_time = 0.0;
}
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
PairLJCutCoulCutGPU::~PairLJCutCoulCutGPU()
{
ljc_gpu_clear();
}
/* ---------------------------------------------------------------------- */
void PairLJCutCoulCutGPU::compute(int eflag, int vflag)
{
int ntimestep = static_cast<int>(update->ntimestep % MAXSMALLINT);
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
bool success = true;
if (gpu_mode == GPU_NEIGH) {
inum = atom->nlocal;
gpulist = ljc_gpu_compute_n(ntimestep, neighbor->ago, inum, nall,
atom->x, atom->type, domain->sublo,
domain->subhi, atom->tag, atom->nspecial,
atom->special, eflag, vflag, eflag_atom,
vflag_atom, host_start, cpu_time, success,
atom->q);
} else {
inum = list->inum;
ljc_gpu_compute(ntimestep, neighbor->ago, inum, nall, atom->x,
atom->type, list->ilist, list->numneigh, list->firstneigh,
eflag, vflag, eflag_atom, vflag_atom, host_start, cpu_time,
success, atom->q);
}
if (!success)
error->one("Out of memory on GPGPU");
if (host_start<inum) {
cpu_time = MPI_Wtime();
if (gpu_mode == GPU_NEIGH)
cpu_compute(gpulist, host_start, eflag, vflag);
else
cpu_compute(host_start, eflag, vflag);
cpu_time = MPI_Wtime() - cpu_time;
}
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairLJCutCoulCutGPU::init_style()
{
if (!atom->q_flag)
error->all("Pair style lj/cut/coul/cut requires atom attribute q");
if (force->pair_match("gpu",0) == NULL)
error->all("Cannot use pair hybrid with multiple GPU pair styles");
// Repeat cutsq calculation because done after call to init_style
double maxcut = -1.0;
double cut;
for (int i = 1; i <= atom->ntypes; i++) {
for (int j = i; j <= atom->ntypes; j++) {
if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) {
cut = init_one(i,j);
cut *= cut;
if (cut > maxcut)
maxcut = cut;
cutsq[i][j] = cutsq[j][i] = cut;
} else
cutsq[i][j] = cutsq[j][i] = 0.0;
}
}
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial=0;
if (atom->molecular)
maxspecial=atom->maxspecial;
bool init_ok = ljc_gpu_init(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4,
offset, force->special_lj, atom->nlocal,
atom->nlocal+atom->nghost, 300, maxspecial,
cell_size, gpu_mode, screen, cut_ljsq, cut_coulsq,
force->special_coul, force->qqrd2e);
if (!init_ok)
error->one("Insufficient memory on accelerator (or no fix gpu).\n");
if (force->newton_pair)
error->all("Cannot use newton pair with GPU LJ pair style");
if (gpu_mode != GPU_NEIGH) {
int irequest = neighbor->request(this);
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
}
}
/* ---------------------------------------------------------------------- */
double PairLJCutCoulCutGPU::memory_usage()
{
double bytes = Pair::memory_usage();
return bytes + ljc_gpu_bytes();
}
/* ---------------------------------------------------------------------- */
void PairLJCutCoulCutGPU::cpu_compute(int start, int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
double rsq,r2inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj;
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = ecoul = 0.0;
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
double qqrd2e = force->qqrd2e;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (ii = start; ii < inum; ii++) {
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_coul = factor_lj = 1.0;
else {
factor_coul = special_coul[j/nall];
factor_lj = special_lj[j/nall];
j %= nall;
}
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
r2inv = 1.0/rsq;
if (rsq < cut_coulsq[itype][jtype])
forcecoul = qqrd2e * qtmp*q[j]*sqrt(r2inv);
else forcecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
} else forcelj = 0.0;
fpair = (factor_coul*forcecoul + factor_lj*forcelj) * r2inv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (eflag) {
if (rsq < cut_coulsq[itype][jtype])
ecoul = factor_coul * qqrd2e * qtmp*q[j]*sqrt(r2inv);
else ecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
offset[itype][jtype];
evdwl *= factor_lj;
} else evdwl = 0.0;
}
if (evflag) ev_tally_full(i,evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
}
/* ---------------------------------------------------------------------- */
void PairLJCutCoulCutGPU::cpu_compute(int *nbors, int start, int eflag,
int vflag)
{
int i,j,jnum,itype,jtype;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
double rsq,r2inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj;
evdwl = ecoul = 0.0;
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int stride = nlocal-start;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
double qqrd2e = force->qqrd2e;
// loop over neighbors of my atoms
for (i = start; i < nlocal; i++) {
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
int *nbor = nbors + i - start;
jnum = *nbor;
nbor += stride;
int *nbor_end = nbor + stride * jnum;
for (; nbor<nbor_end; nbor+=stride) {
j = *nbor;
if (j < nall) factor_coul = factor_lj = 1.0;
else {
factor_coul = special_coul[j/nall];
factor_lj = special_lj[j/nall];
j %= nall;
}
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
r2inv = 1.0/rsq;
if (rsq < cut_coulsq[itype][jtype])
forcecoul = qqrd2e * qtmp*q[j]*sqrt(r2inv);
else forcecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
} else forcelj = 0.0;
fpair = (factor_coul*forcecoul + factor_lj*forcelj) * r2inv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (eflag) {
if (rsq < cut_coulsq[itype][jtype])
ecoul = factor_coul * qqrd2e * qtmp*q[j]*sqrt(r2inv);
else ecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
offset[itype][jtype];
evdwl *= factor_lj;
} else evdwl = 0.0;
}
if (j<start) {
if (evflag) ev_tally_full(i,evdwl,ecoul,fpair,delx,dely,delz);
} else {
if (j<nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
if (evflag) ev_tally(i,j,nlocal,0,
evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
}
}
diff --git a/src/GPU/pair_lj_cut_coul_long_gpu.cpp b/src/GPU/pair_lj_cut_coul_long_gpu.cpp
index 9782317d7..86cba8070 100644
--- a/src/GPU/pair_lj_cut_coul_long_gpu.cpp
+++ b/src/GPU/pair_lj_cut_coul_long_gpu.cpp
@@ -1,456 +1,456 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "pair_lj_cut_coul_long_gpu.h"
-#include "lmptype.h"
#include "atom.h"
#include "atom_vec.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "integrate.h"
#include "memory.h"
#include "error.h"
#include "neigh_request.h"
#include "universe.h"
#include "update.h"
#include "domain.h"
#include "string.h"
#include "kspace.h"
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
#define EWALD_F 1.12837917
#define EWALD_P 0.3275911
#define A1 0.254829592
#define A2 -0.284496736
#define A3 1.421413741
#define A4 -1.453152027
#define A5 1.061405429
// External functions from cuda library for atom decomposition
bool ljcl_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
double **host_lj2, double **host_lj3, double **host_lj4,
double **offset, double *special_lj, const int nlocal,
const int nall, const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen,
double **host_cut_ljsq, double host_cut_coulsq,
double *host_special_coul, const double qqrd2e,
const double g_ewald);
void ljcl_gpu_clear();
int * ljcl_gpu_compute_n(const int timestep, const int ago, const int inum,
const int nall, double **host_x, int *host_type,
double *boxlo, double *boxhi, int *tag, int **nspecial,
int **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success, double *host_q);
void ljcl_gpu_compute(const int timestep, const int ago, const int inum,
const int nall, double **host_x, int *host_type,
int *ilist, int *numj, int **firstneigh,
const bool eflag, const bool vflag, const bool eatom,
const bool vatom, int &host_start, const double cpu_time,
bool &success, double *host_q);
double ljcl_gpu_bytes();
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairLJCutCoulLongGPU::PairLJCutCoulLongGPU(LAMMPS *lmp) :
PairLJCutCoulLong(lmp), gpu_mode(GPU_PAIR)
{
respa_enable = 0;
cpu_time = 0.0;
}
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
PairLJCutCoulLongGPU::~PairLJCutCoulLongGPU()
{
ljcl_gpu_clear();
}
/* ---------------------------------------------------------------------- */
void PairLJCutCoulLongGPU::compute(int eflag, int vflag)
{
int ntimestep = static_cast<int>(update->ntimestep % MAXSMALLINT);
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
bool success = true;
if (gpu_mode == GPU_NEIGH) {
inum = atom->nlocal;
gpulist = ljcl_gpu_compute_n(ntimestep, neighbor->ago, inum, nall,
atom->x, atom->type, domain->sublo,
domain->subhi, atom->tag, atom->nspecial,
atom->special, eflag, vflag, eflag_atom,
vflag_atom, host_start, cpu_time, success,
atom->q);
} else {
inum = list->inum;
ljcl_gpu_compute(ntimestep, neighbor->ago, inum, nall, atom->x,
atom->type, list->ilist, list->numneigh, list->firstneigh,
eflag, vflag, eflag_atom, vflag_atom, host_start, cpu_time,
success, atom->q);
}
if (!success)
error->one("Out of memory on GPGPU");
if (host_start<inum) {
cpu_time = MPI_Wtime();
if (gpu_mode == GPU_NEIGH)
cpu_compute(gpulist, host_start, eflag, vflag);
else
cpu_compute(host_start, eflag, vflag);
cpu_time = MPI_Wtime() - cpu_time;
}
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairLJCutCoulLongGPU::init_style()
{
cut_respa = NULL;
if (!atom->q_flag)
error->all("Pair style lj/cut/coul/cut requires atom attribute q");
if (force->pair_match("gpu",0) == NULL)
error->all("Cannot use pair hybrid with multiple GPU pair styles");
// Repeat cutsq calculation because done after call to init_style
double maxcut = -1.0;
double cut;
for (int i = 1; i <= atom->ntypes; i++) {
for (int j = i; j <= atom->ntypes; j++) {
if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) {
cut = init_one(i,j);
cut *= cut;
if (cut > maxcut)
maxcut = cut;
cutsq[i][j] = cutsq[j][i] = cut;
} else
cutsq[i][j] = cutsq[j][i] = 0.0;
}
}
double cell_size = sqrt(maxcut) + neighbor->skin;
cut_coulsq = cut_coul * cut_coul;
// insure use of KSpace long-range solver, set g_ewald
if (force->kspace == NULL)
error->all("Pair style is incompatible with KSpace style");
g_ewald = force->kspace->g_ewald;
// setup force tables
if (ncoultablebits) init_tables();
int maxspecial=0;
if (atom->molecular)
maxspecial=atom->maxspecial;
bool init_ok = ljcl_gpu_init(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4,
offset, force->special_lj, atom->nlocal,
atom->nlocal+atom->nghost, 300, maxspecial,
cell_size, gpu_mode, screen, cut_ljsq, cut_coulsq,
force->special_coul, force->qqrd2e, g_ewald);
if (!init_ok)
error->one("Insufficient memory on accelerator (or no fix gpu).\n");
if (force->newton_pair)
error->all("Cannot use newton pair with GPU LJ pair style");
if (gpu_mode != GPU_NEIGH) {
int irequest = neighbor->request(this);
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
}
}
/* ---------------------------------------------------------------------- */
double PairLJCutCoulLongGPU::memory_usage()
{
double bytes = Pair::memory_usage();
return bytes + ljcl_gpu_bytes();
}
/* ---------------------------------------------------------------------- */
void PairLJCutCoulLongGPU::cpu_compute(int start, int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype,itable;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
double fraction,table;
double r,r2inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj;
double grij,expm2,prefactor,t,erfc;
int *ilist,*jlist,*numneigh,**firstneigh;
double rsq;
evdwl = ecoul = 0.0;
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
double qqrd2e = force->qqrd2e;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (ii = start; ii < inum; ii++) {
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_coul = factor_lj = 1.0;
else {
factor_coul = special_coul[j/nall];
factor_lj = special_lj[j/nall];
j %= nall;
}
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
r2inv = 1.0/rsq;
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq) {
r = sqrt(rsq);
grij = g_ewald * r;
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
prefactor = qqrd2e * qtmp*q[j]/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
} else {
union_int_float_t rsq_lookup;
rsq_lookup.f = rsq;
itable = rsq_lookup.i & ncoulmask;
itable >>= ncoulshiftbits;
fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
table = ftable[itable] + fraction*dftable[itable];
forcecoul = qtmp*q[j] * table;
if (factor_coul < 1.0) {
table = ctable[itable] + fraction*dctable[itable];
prefactor = qtmp*q[j] * table;
forcecoul -= (1.0-factor_coul)*prefactor;
}
}
} else forcecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
} else forcelj = 0.0;
fpair = (forcecoul + factor_lj*forcelj) * r2inv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (eflag) {
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq)
ecoul = prefactor*erfc;
else {
table = etable[itable] + fraction*detable[itable];
ecoul = qtmp*q[j] * table;
}
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
} else ecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
offset[itype][jtype];
evdwl *= factor_lj;
} else evdwl = 0.0;
}
if (evflag) ev_tally_full(i,evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
}
/* ---------------------------------------------------------------------- */
void PairLJCutCoulLongGPU::cpu_compute(int *nbors, int start, int eflag,
int vflag)
{
int i,j,jnum,itype,jtype,itable;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
double fraction,table;
double r,r2inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj;
double grij,expm2,prefactor,t,erfc;
double rsq;
evdwl = ecoul = 0.0;
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int stride = nlocal-start;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
double qqrd2e = force->qqrd2e;
// loop over neighbors of my atoms
for (i = start; i < nlocal; i++) {
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
int *nbor = nbors + i - start;
jnum = *nbor;
nbor += stride;
int *nbor_end = nbor + stride * jnum;
for (; nbor<nbor_end; nbor+=stride) {
j = *nbor;
if (j < nall) factor_coul = factor_lj = 1.0;
else {
factor_coul = special_coul[j/nall];
factor_lj = special_lj[j/nall];
j %= nall;
}
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
r2inv = 1.0/rsq;
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq) {
r = sqrt(rsq);
grij = g_ewald * r;
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
prefactor = qqrd2e * qtmp*q[j]/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
} else {
union_int_float_t rsq_lookup;
rsq_lookup.f = rsq;
itable = rsq_lookup.i & ncoulmask;
itable >>= ncoulshiftbits;
fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
table = ftable[itable] + fraction*dftable[itable];
forcecoul = qtmp*q[j] * table;
if (factor_coul < 1.0) {
table = ctable[itable] + fraction*dctable[itable];
prefactor = qtmp*q[j] * table;
forcecoul -= (1.0-factor_coul)*prefactor;
}
}
} else forcecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
} else forcelj = 0.0;
fpair = (forcecoul + factor_lj*forcelj) * r2inv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (eflag) {
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq)
ecoul = prefactor*erfc;
else {
table = etable[itable] + fraction*detable[itable];
ecoul = qtmp*q[j] * table;
}
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
} else ecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
offset[itype][jtype];
evdwl *= factor_lj;
} else evdwl = 0.0;
}
if (j<start) {
if (evflag) ev_tally_full(i,evdwl,ecoul,fpair,delx,dely,delz);
} else {
if (j<nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
if (evflag) ev_tally(i,j,nlocal,0,
evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
}
}
diff --git a/src/GPU/pair_lj_cut_gpu.cpp b/src/GPU/pair_lj_cut_gpu.cpp
index 4c12e7d9f..612a8e918 100644
--- a/src/GPU/pair_lj_cut_gpu.cpp
+++ b/src/GPU/pair_lj_cut_gpu.cpp
@@ -1,320 +1,320 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "pair_lj_cut_gpu.h"
-#include "lmptype.h"
#include "atom.h"
#include "atom_vec.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "integrate.h"
#include "memory.h"
#include "error.h"
#include "neigh_request.h"
#include "universe.h"
#include "update.h"
#include "domain.h"
#include "string.h"
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
// External functions from cuda library for atom decomposition
bool ljl_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
double **host_lj2, double **host_lj3, double **host_lj4,
double **offset, double *special_lj, const int nlocal,
const int nall, const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen);
void ljl_gpu_clear();
int * ljl_gpu_compute_n(const int timestep, const int ago, const int inum,
const int nall, double **host_x, int *host_type,
double *boxlo, double *boxhi, int *tag, int **nspecial,
int **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success);
void ljl_gpu_compute(const int timestep, const int ago, const int inum,
const int nall, double **host_x, int *host_type,
int *ilist, int *numj, int **firstneigh,
const bool eflag, const bool vflag, const bool eatom,
const bool vatom, int &host_start, const double cpu_time,
bool &success);
double ljl_gpu_bytes();
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairLJCutGPU::PairLJCutGPU(LAMMPS *lmp) : PairLJCut(lmp), gpu_mode(GPU_PAIR)
{
respa_enable = 0;
cpu_time = 0.0;
}
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
PairLJCutGPU::~PairLJCutGPU()
{
ljl_gpu_clear();
}
/* ---------------------------------------------------------------------- */
void PairLJCutGPU::compute(int eflag, int vflag)
{
int ntimestep = static_cast<int>(update->ntimestep % MAXSMALLINT);
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
bool success = true;
if (gpu_mode == GPU_NEIGH) {
inum = atom->nlocal;
gpulist = ljl_gpu_compute_n(ntimestep, neighbor->ago, inum, nall,
atom->x, atom->type, domain->sublo,
domain->subhi, atom->tag, atom->nspecial,
atom->special, eflag, vflag, eflag_atom,
vflag_atom, host_start, cpu_time, success);
} else {
inum = list->inum;
ljl_gpu_compute(ntimestep, neighbor->ago, inum, nall, atom->x,
atom->type, list->ilist, list->numneigh, list->firstneigh,
eflag, vflag, eflag_atom, vflag_atom, host_start, cpu_time,
success);
}
if (!success)
error->one("Out of memory on GPGPU");
if (host_start<inum) {
cpu_time = MPI_Wtime();
if (gpu_mode == GPU_NEIGH)
cpu_compute(gpulist, host_start, eflag, vflag);
else
cpu_compute(host_start, eflag, vflag);
cpu_time = MPI_Wtime() - cpu_time;
}
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairLJCutGPU::init_style()
{
cut_respa = NULL;
if (force->pair_match("gpu",0) == NULL)
error->all("Cannot use pair hybrid with multiple GPU pair styles");
// Repeat cutsq calculation because done after call to init_style
double maxcut = -1.0;
double cut;
for (int i = 1; i <= atom->ntypes; i++) {
for (int j = i; j <= atom->ntypes; j++) {
if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) {
cut = init_one(i,j);
cut *= cut;
if (cut > maxcut)
maxcut = cut;
cutsq[i][j] = cutsq[j][i] = cut;
} else
cutsq[i][j] = cutsq[j][i] = 0.0;
}
}
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial=0;
if (atom->molecular)
maxspecial=atom->maxspecial;
bool init_ok = ljl_gpu_init(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4,
offset, force->special_lj, atom->nlocal,
atom->nlocal+atom->nghost, 300, maxspecial,
cell_size, gpu_mode, screen);
if (!init_ok)
error->one("Insufficient memory on accelerator (or no fix gpu).\n");
if (force->newton_pair)
error->all("Cannot use newton pair with GPU LJ pair style");
if (gpu_mode != GPU_NEIGH) {
int irequest = neighbor->request(this);
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
}
}
/* ---------------------------------------------------------------------- */
double PairLJCutGPU::memory_usage()
{
double bytes = Pair::memory_usage();
return bytes + ljl_gpu_bytes();
}
/* ---------------------------------------------------------------------- */
void PairLJCutGPU::cpu_compute(int start, int eflag, int vflag) {
int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,r2inv,r6inv,forcelj,factor_lj;
int *ilist,*jlist,*numneigh,**firstneigh;
double **x = atom->x;
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_lj = force->special_lj;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (ii = start; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_lj = 1.0;
else {
factor_lj = special_lj[j/nall];
j %= nall;
}
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
fpair = factor_lj*forcelj*r2inv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (eflag) {
evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
offset[itype][jtype];
evdwl *= factor_lj;
}
if (evflag) ev_tally_full(i,evdwl,0.0,fpair,delx,dely,delz);
}
}
}
}
/* ---------------------------------------------------------------------- */
void PairLJCutGPU::cpu_compute(int *nbors, int start, int eflag, int vflag) {
int i,j,itype,jtype;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int stride = nlocal-start;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,r2inv,r6inv,forcelj,factor_lj;
double *special_lj = force->special_lj;
double **x = atom->x;
double **f = atom->f;
int *type = atom->type;
// loop over neighbors of my atoms
for (i = start; i < nlocal; i++) {
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
int *nbor = nbors + i - start;
int jnum = *nbor;
nbor += stride;
int *nbor_end = nbor + stride * jnum;
for (; nbor<nbor_end; nbor+=stride) {
j = *nbor;
if (j < nall) factor_lj = 1.0;
else {
factor_lj = special_lj[j/nall];
j %= nall;
}
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
fpair = factor_lj*forcelj*r2inv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (eflag) {
evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
offset[itype][jtype];
evdwl *= factor_lj;
}
if (j<start) {
if (evflag) ev_tally_full(i,evdwl,0.0,fpair,delx,dely,delz);
} else {
if (j<nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
if (evflag) ev_tally(i,j,nlocal,0,
evdwl,0.0,fpair,delx,dely,delz);
}
}
}
}
}
diff --git a/src/GRANULAR/atom_vec_granular.cpp b/src/GRANULAR/atom_vec_granular.cpp
index 0ebb38d8f..d70b4051d 100644
--- a/src/GRANULAR/atom_vec_granular.cpp
+++ b/src/GRANULAR/atom_vec_granular.cpp
@@ -1,960 +1,960 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "math.h"
#include "stdlib.h"
#include "string.h"
#include "atom_vec_granular.h"
-#include "lmptype.h"
#include "atom.h"
#include "domain.h"
#include "modify.h"
#include "force.h"
#include "fix.h"
#include "fix_adapt.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define DELTA 10000
/* ---------------------------------------------------------------------- */
AtomVecGranular::AtomVecGranular(LAMMPS *lmp, int narg, char **arg) :
AtomVec(lmp, narg, arg)
{
molecular = 0;
comm_x_only = 1;
comm_f_only = 0;
size_forward = 3;
size_reverse = 6;
size_border = 8;
size_velocity = 6;
size_data_atom = 7;
size_data_vel = 7;
xcol_data = 5;
atom->radius_flag = atom->density_flag = atom->rmass_flag = 1;
atom->omega_flag = atom->torque_flag = 1;
radvary = 0;
PI = 4.0*atan(1.0);
}
/* ---------------------------------------------------------------------- */
void AtomVecGranular::init()
{
// set radvary if particle diameters are time-varying due to fix adapt
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"adapt") == 0) {
FixAdapt *fix = (FixAdapt *) modify->fix[i];
if (fix->diamflag) {
radvary = 1;
size_forward = 5;
}
}
}
/* ----------------------------------------------------------------------
grow atom arrays
n = 0 grows arrays by DELTA
n > 0 allocates arrays to size n
------------------------------------------------------------------------- */
void AtomVecGranular::grow(int n)
{
if (n == 0) nmax += DELTA;
else nmax = n;
atom->nmax = nmax;
if (nmax < 0 || nmax > MAXSMALLINT)
error->one("Per-processor system is too big");
tag = atom->tag = (int *)
memory->srealloc(atom->tag,nmax*sizeof(int),"atom:tag");
type = atom->type = (int *)
memory->srealloc(atom->type,nmax*sizeof(int),"atom:type");
mask = atom->mask = (int *)
memory->srealloc(atom->mask,nmax*sizeof(int),"atom:mask");
image = atom->image = (int *)
memory->srealloc(atom->image,nmax*sizeof(int),"atom:image");
x = atom->x = memory->grow_2d_double_array(atom->x,nmax,3,"atom:x");
v = atom->v = memory->grow_2d_double_array(atom->v,nmax,3,"atom:v");
f = atom->f = memory->grow_2d_double_array(atom->f,nmax,3,"atom:f");
radius = atom->radius = (double *)
memory->srealloc(atom->radius,nmax*sizeof(double),"atom:radius");
density = atom->density = (double *)
memory->srealloc(atom->density,nmax*sizeof(double),"atom:density");
rmass = atom->rmass = (double *)
memory->srealloc(atom->rmass,nmax*sizeof(double),"atom:rmass");
omega = atom->omega =
memory->grow_2d_double_array(atom->omega,nmax,3,"atom:omega");
torque = atom->torque =
memory->grow_2d_double_array(atom->torque,nmax,3,"atom:torque");
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
}
/* ----------------------------------------------------------------------
reset local array ptrs
------------------------------------------------------------------------- */
void AtomVecGranular::grow_reset()
{
tag = atom->tag; type = atom->type;
mask = atom->mask; image = atom->image;
x = atom->x; v = atom->v; f = atom->f;
radius = atom->radius; density = atom->density; rmass = atom->rmass;
omega = atom->omega; torque = atom->torque;
}
/* ---------------------------------------------------------------------- */
void AtomVecGranular::copy(int i, int j)
{
tag[j] = tag[i];
type[j] = type[i];
mask[j] = mask[i];
image[j] = image[i];
x[j][0] = x[i][0];
x[j][1] = x[i][1];
x[j][2] = x[i][2];
v[j][0] = v[i][0];
v[j][1] = v[i][1];
v[j][2] = v[i][2];
radius[j] = radius[i];
density[j] = density[i];
rmass[j] = rmass[i];
omega[j][0] = omega[i][0];
omega[j][1] = omega[i][1];
omega[j][2] = omega[i][2];
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j);
}
/* ---------------------------------------------------------------------- */
int AtomVecGranular::pack_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
if (radvary == 0) {
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
dz = pbc[2]*domain->zprd;
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
}
}
} else {
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = radius[j];
buf[m++] = rmass[j];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
dz = pbc[2]*domain->zprd;
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = radius[j];
buf[m++] = rmass[j];
}
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecGranular::pack_comm_vel(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
if (radvary == 0) {
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
buf[m++] = omega[j][0];
buf[m++] = omega[j][1];
buf[m++] = omega[j][2];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
dz = pbc[2]*domain->zprd;
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
buf[m++] = omega[j][0];
buf[m++] = omega[j][1];
buf[m++] = omega[j][2];
}
}
} else {
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = radius[j];
buf[m++] = rmass[j];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
buf[m++] = omega[j][0];
buf[m++] = omega[j][1];
buf[m++] = omega[j][2];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
dz = pbc[2]*domain->zprd;
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = radius[j];
buf[m++] = rmass[j];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
buf[m++] = omega[j][0];
buf[m++] = omega[j][1];
buf[m++] = omega[j][2];
}
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecGranular::pack_comm_one(int i, double *buf)
{
if (radvary == 0) return 0;
buf[0] = radius[i];
buf[1] = rmass[i];
return 2;
}
/* ---------------------------------------------------------------------- */
void AtomVecGranular::unpack_comm(int n, int first, double *buf)
{
int i,m,last;
if (radvary == 0) {
m = 0;
last = first + n;
for (i = first; i < last; i++) {
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
}
} else {
m = 0;
last = first + n;
for (i = first; i < last; i++) {
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
radius[i] = buf[m++];
rmass[i] = buf[m++];
}
}
}
/* ---------------------------------------------------------------------- */
void AtomVecGranular::unpack_comm_vel(int n, int first, double *buf)
{
int i,m,last;
if (radvary == 0) {
m = 0;
last = first + n;
for (i = first; i < last; i++) {
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
omega[i][0] = buf[m++];
omega[i][1] = buf[m++];
omega[i][2] = buf[m++];
}
} else {
m = 0;
last = first + n;
for (i = first; i < last; i++) {
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
radius[i] = buf[m++];
rmass[i] = buf[m++];
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
omega[i][0] = buf[m++];
omega[i][1] = buf[m++];
omega[i][2] = buf[m++];
}
}
}
/* ---------------------------------------------------------------------- */
int AtomVecGranular::unpack_comm_one(int i, double *buf)
{
if (radvary == 0) return 0;
radius[i] = buf[0];
rmass[i] = buf[1];
return 2;
}
/* ---------------------------------------------------------------------- */
int AtomVecGranular::pack_reverse(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
buf[m++] = f[i][0];
buf[m++] = f[i][1];
buf[m++] = f[i][2];
buf[m++] = torque[i][0];
buf[m++] = torque[i][1];
buf[m++] = torque[i][2];
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecGranular::pack_reverse_one(int i, double *buf)
{
buf[0] = torque[i][0];
buf[1] = torque[i][1];
buf[2] = torque[i][2];
return 3;
}
/* ---------------------------------------------------------------------- */
void AtomVecGranular::unpack_reverse(int n, int *list, double *buf)
{
int i,j,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
f[j][0] += buf[m++];
f[j][1] += buf[m++];
f[j][2] += buf[m++];
torque[j][0] += buf[m++];
torque[j][1] += buf[m++];
torque[j][2] += buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecGranular::unpack_reverse_one(int i, double *buf)
{
torque[i][0] += buf[0];
torque[i][1] += buf[1];
torque[i][2] += buf[2];
return 3;
}
/* ---------------------------------------------------------------------- */
int AtomVecGranular::pack_border(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = radius[j];
buf[m++] = rmass[j];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0];
dy = pbc[1];
dz = pbc[2];
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = radius[j];
buf[m++] = rmass[j];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecGranular::pack_border_vel(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = radius[j];
buf[m++] = rmass[j];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
buf[m++] = omega[j][0];
buf[m++] = omega[j][1];
buf[m++] = omega[j][2];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0];
dy = pbc[1];
dz = pbc[2];
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = radius[j];
buf[m++] = rmass[j];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
buf[m++] = omega[j][0];
buf[m++] = omega[j][1];
buf[m++] = omega[j][2];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecGranular::pack_border_one(int i, double *buf)
{
buf[0] = radius[i];
buf[1] = rmass[i];
return 2;
}
/* ---------------------------------------------------------------------- */
void AtomVecGranular::unpack_border(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
if (i == nmax) grow(0);
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
tag[i] = static_cast<int> (buf[m++]);
type[i] = static_cast<int> (buf[m++]);
mask[i] = static_cast<int> (buf[m++]);
radius[i] = buf[m++];
rmass[i] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
void AtomVecGranular::unpack_border_vel(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
if (i == nmax) grow(0);
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
tag[i] = static_cast<int> (buf[m++]);
type[i] = static_cast<int> (buf[m++]);
mask[i] = static_cast<int> (buf[m++]);
radius[i] = buf[m++];
rmass[i] = buf[m++];
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
omega[i][0] = buf[m++];
omega[i][1] = buf[m++];
omega[i][2] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecGranular::unpack_border_one(int i, double *buf)
{
radius[i] = buf[0];
rmass[i] = buf[1];
return 2;
}
/* ----------------------------------------------------------------------
pack data for atom I for sending to another proc
xyz must be 1st 3 values, so comm::exchange() can test on them
------------------------------------------------------------------------- */
int AtomVecGranular::pack_exchange(int i, double *buf)
{
int m = 1;
buf[m++] = x[i][0];
buf[m++] = x[i][1];
buf[m++] = x[i][2];
buf[m++] = v[i][0];
buf[m++] = v[i][1];
buf[m++] = v[i][2];
buf[m++] = tag[i];
buf[m++] = type[i];
buf[m++] = mask[i];
buf[m++] = image[i];
buf[m++] = radius[i];
buf[m++] = density[i];
buf[m++] = rmass[i];
buf[m++] = omega[i][0];
buf[m++] = omega[i][1];
buf[m++] = omega[i][2];
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]);
buf[0] = m;
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecGranular::unpack_exchange(double *buf)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
int m = 1;
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
x[nlocal][2] = buf[m++];
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
tag[nlocal] = static_cast<int> (buf[m++]);
type[nlocal] = static_cast<int> (buf[m++]);
mask[nlocal] = static_cast<int> (buf[m++]);
image[nlocal] = static_cast<int> (buf[m++]);
radius[nlocal] = buf[m++];
density[nlocal] = buf[m++];
rmass[nlocal] = buf[m++];
omega[nlocal][0] = buf[m++];
omega[nlocal][1] = buf[m++];
omega[nlocal][2] = buf[m++];
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->
unpack_exchange(nlocal,&buf[m]);
atom->nlocal++;
return m;
}
/* ----------------------------------------------------------------------
size of restart data for all atoms owned by this proc
include extra data stored by fixes
------------------------------------------------------------------------- */
int AtomVecGranular::size_restart()
{
int i;
int nlocal = atom->nlocal;
int n = 16 * nlocal;
if (atom->nextra_restart)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
for (i = 0; i < nlocal; i++)
n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
return n;
}
/* ----------------------------------------------------------------------
pack atom I's data for restart file including extra quantities
xyz must be 1st 3 values, so that read_restart can test on them
molecular types may be negative, but write as positive
------------------------------------------------------------------------- */
int AtomVecGranular::pack_restart(int i, double *buf)
{
int m = 1;
buf[m++] = x[i][0];
buf[m++] = x[i][1];
buf[m++] = x[i][2];
buf[m++] = tag[i];
buf[m++] = type[i];
buf[m++] = mask[i];
buf[m++] = image[i];
buf[m++] = v[i][0];
buf[m++] = v[i][1];
buf[m++] = v[i][2];
buf[m++] = radius[i];
buf[m++] = density[i];
buf[m++] = omega[i][0];
buf[m++] = omega[i][1];
buf[m++] = omega[i][2];
if (atom->nextra_restart)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]);
buf[0] = m;
return m;
}
/* ----------------------------------------------------------------------
unpack data for one atom from restart file including extra quantities
------------------------------------------------------------------------- */
int AtomVecGranular::unpack_restart(double *buf)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) {
grow(0);
if (atom->nextra_store)
atom->extra = memory->grow_2d_double_array(atom->extra,nmax,
atom->nextra_store,
"atom:extra");
}
int m = 1;
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
x[nlocal][2] = buf[m++];
tag[nlocal] = static_cast<int> (buf[m++]);
type[nlocal] = static_cast<int> (buf[m++]);
mask[nlocal] = static_cast<int> (buf[m++]);
image[nlocal] = static_cast<int> (buf[m++]);
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
radius[nlocal] = buf[m++];
density[nlocal] = buf[m++];
if (radius[nlocal] == 0.0) rmass[nlocal] = density[nlocal];
else
rmass[nlocal] = 4.0*PI/3.0 *
radius[nlocal]*radius[nlocal]*radius[nlocal] * density[nlocal];
omega[nlocal][0] = buf[m++];
omega[nlocal][1] = buf[m++];
omega[nlocal][2] = buf[m++];
double **extra = atom->extra;
if (atom->nextra_store) {
int size = static_cast<int> (buf[0]) - m;
for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++];
}
atom->nlocal++;
return m;
}
/* ----------------------------------------------------------------------
create one atom of itype at coord
set other values to defaults
------------------------------------------------------------------------- */
void AtomVecGranular::create_atom(int itype, double *coord)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
tag[nlocal] = 0;
type[nlocal] = itype;
x[nlocal][0] = coord[0];
x[nlocal][1] = coord[1];
x[nlocal][2] = coord[2];
mask[nlocal] = 1;
image[nlocal] = (512 << 20) | (512 << 10) | 512;
v[nlocal][0] = 0.0;
v[nlocal][1] = 0.0;
v[nlocal][2] = 0.0;
radius[nlocal] = 0.5;
density[nlocal] = 1.0;
rmass[nlocal] = 4.0*PI/3.0 *
radius[nlocal]*radius[nlocal]*radius[nlocal] * density[nlocal];
omega[nlocal][0] = 0.0;
omega[nlocal][1] = 0.0;
omega[nlocal][2] = 0.0;
atom->nlocal++;
}
/* ----------------------------------------------------------------------
unpack one line from Atoms section of data file
initialize other atom quantities
------------------------------------------------------------------------- */
void AtomVecGranular::data_atom(double *coord, int imagetmp, char **values)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
tag[nlocal] = atoi(values[0]);
if (tag[nlocal] <= 0)
error->one("Invalid atom ID in Atoms section of data file");
type[nlocal] = atoi(values[1]);
if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
error->one("Invalid atom type in Atoms section of data file");
radius[nlocal] = 0.5 * atof(values[2]);
if (radius[nlocal] < 0.0)
error->one("Invalid radius in Atoms section of data file");
density[nlocal] = atof(values[3]);
if (density[nlocal] <= 0.0)
error->one("Invalid density in Atoms section of data file");
if (radius[nlocal] == 0.0) rmass[nlocal] = density[nlocal];
else
rmass[nlocal] = 4.0*PI/3.0 *
radius[nlocal]*radius[nlocal]*radius[nlocal] * density[nlocal];
x[nlocal][0] = coord[0];
x[nlocal][1] = coord[1];
x[nlocal][2] = coord[2];
image[nlocal] = imagetmp;
mask[nlocal] = 1;
v[nlocal][0] = 0.0;
v[nlocal][1] = 0.0;
v[nlocal][2] = 0.0;
omega[nlocal][0] = 0.0;
omega[nlocal][1] = 0.0;
omega[nlocal][2] = 0.0;
atom->nlocal++;
}
/* ----------------------------------------------------------------------
unpack hybrid quantities from one line in Atoms section of data file
initialize other atom quantities for this sub-style
------------------------------------------------------------------------- */
int AtomVecGranular::data_atom_hybrid(int nlocal, char **values)
{
radius[nlocal] = 0.5 * atof(values[0]);
if (radius[nlocal] < 0.0)
error->one("Invalid radius in Atoms section of data file");
density[nlocal] = atof(values[1]);
if (density[nlocal] <= 0.0)
error->one("Invalid density in Atoms section of data file");
if (radius[nlocal] == 0.0) rmass[nlocal] = density[nlocal];
else
rmass[nlocal] = 4.0*PI/3.0 *
radius[nlocal]*radius[nlocal]*radius[nlocal] * density[nlocal];
return 2;
}
/* ----------------------------------------------------------------------
unpack one line from Velocities section of data file
------------------------------------------------------------------------- */
void AtomVecGranular::data_vel(int m, char **values)
{
v[m][0] = atof(values[0]);
v[m][1] = atof(values[1]);
v[m][2] = atof(values[2]);
omega[m][0] = atof(values[3]);
omega[m][1] = atof(values[4]);
omega[m][2] = atof(values[5]);
}
/* ----------------------------------------------------------------------
unpack hybrid quantities from one line in Velocities section of data file
------------------------------------------------------------------------- */
int AtomVecGranular::data_vel_hybrid(int m, char **values)
{
omega[m][0] = atof(values[0]);
omega[m][1] = atof(values[1]);
omega[m][2] = atof(values[2]);
return 3;
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
------------------------------------------------------------------------- */
double AtomVecGranular::memory_usage()
{
double bytes = 0.0;
if (atom->memcheck("tag")) bytes += nmax * sizeof(int);
if (atom->memcheck("type")) bytes += nmax * sizeof(int);
if (atom->memcheck("mask")) bytes += nmax * sizeof(int);
if (atom->memcheck("image")) bytes += nmax * sizeof(int);
if (atom->memcheck("x")) bytes += nmax*3 * sizeof(double);
if (atom->memcheck("v")) bytes += nmax*3 * sizeof(double);
if (atom->memcheck("f")) bytes += nmax*3 * sizeof(double);
if (atom->memcheck("radius")) bytes += nmax * sizeof(double);
if (atom->memcheck("density")) bytes += nmax * sizeof(double);
if (atom->memcheck("rmass")) bytes += nmax * sizeof(double);
if (atom->memcheck("omega")) bytes += nmax*3 * sizeof(double);
if (atom->memcheck("torque")) bytes += nmax*3 * sizeof(double);
return bytes;
}
diff --git a/src/KSPACE/pppm.cpp b/src/KSPACE/pppm.cpp
index 306efb8ea..ad43ff312 100644
--- a/src/KSPACE/pppm.cpp
+++ b/src/KSPACE/pppm.cpp
@@ -1,1929 +1,1929 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Roy Pollock (LLNL), Paul Crozier (SNL)
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "mpi.h"
#include "string.h"
#include "stdio.h"
#include "stdlib.h"
#include "math.h"
#include "pppm.h"
-#include "lmptype.h"
#include "atom.h"
#include "comm.h"
#include "neighbor.h"
#include "force.h"
#include "pair.h"
#include "bond.h"
#include "angle.h"
#include "domain.h"
#include "fft3d_wrap.h"
#include "remap_wrap.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MAXORDER 7
#define OFFSET 16384
#define SMALL 0.00001
#define LARGE 10000.0
#define EPS_HOC 1.0e-7
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
/* ---------------------------------------------------------------------- */
PPPM::PPPM(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg)
{
if (narg != 1) error->all("Illegal kspace_style pppm command");
precision = atof(arg[0]);
PI = 4.0*atan(1.0);
nfactors = 3;
factors = new int[nfactors];
factors[0] = 2;
factors[1] = 3;
factors[2] = 5;
MPI_Comm_rank(world,&me);
MPI_Comm_size(world,&nprocs);
density_brick = vdx_brick = vdy_brick = vdz_brick = NULL;
density_fft = NULL;
greensfn = NULL;
work1 = work2 = NULL;
vg = NULL;
fkx = fky = fkz = NULL;
buf1 = buf2 = NULL;
gf_b = NULL;
rho1d = rho_coeff = NULL;
fft1 = fft2 = NULL;
remap = NULL;
nmax = 0;
part2grid = NULL;
}
/* ----------------------------------------------------------------------
free all memory
------------------------------------------------------------------------- */
PPPM::~PPPM()
{
delete [] factors;
deallocate();
memory->destroy_2d_int_array(part2grid);
}
/* ----------------------------------------------------------------------
called once before run
------------------------------------------------------------------------- */
void PPPM::init()
{
if (me == 0) {
if (screen) fprintf(screen,"PPPM initialization ...\n");
if (logfile) fprintf(logfile,"PPPM initialization ...\n");
}
// error check
if (domain->triclinic)
error->all("Cannot (yet) use PPPM with triclinic box");
if (domain->dimension == 2) error->all("Cannot use PPPM with 2d simulation");
if (!atom->q_flag) error->all("Kspace style requires atom attribute q");
if (slabflag == 0 && domain->nonperiodic > 0)
error->all("Cannot use nonperiodic boundaries with PPPM");
if (slabflag == 1) {
if (domain->xperiodic != 1 || domain->yperiodic != 1 ||
domain->boundary[2][0] != 1 || domain->boundary[2][1] != 1)
error->all("Incorrect boundaries with slab PPPM");
}
if (order > MAXORDER) {
char str[128];
sprintf(str,"PPPM order cannot be greater than %d",MAXORDER);
error->all(str);
}
// free all arrays previously allocated
deallocate();
// extract short-range Coulombic cutoff from pair style
qqrd2e = force->qqrd2e;
scale = 1.0;
if (force->pair == NULL)
error->all("KSpace style is incompatible with Pair style");
int itmp;
double *p_cutoff = (double *) force->pair->extract("cut_coul",itmp);
if (p_cutoff == NULL)
error->all("KSpace style is incompatible with Pair style");
cutoff = *p_cutoff;
// if kspace is TIP4P, extract TIP4P params from pair style
// bond/angle are not yet init(), so insure equilibrium request is valid
qdist = 0.0;
if (strcmp(force->kspace_style,"pppm/tip4p") == 0) {
if (force->pair == NULL)
error->all("KSpace style is incompatible with Pair style");
double *p_qdist = (double *) force->pair->extract("qdist",itmp);
int *p_typeO = (int *) force->pair->extract("typeO",itmp);
int *p_typeH = (int *) force->pair->extract("typeH",itmp);
int *p_typeA = (int *) force->pair->extract("typeA",itmp);
int *p_typeB = (int *) force->pair->extract("typeB",itmp);
if (!p_qdist || !p_typeO || !p_typeH || !p_typeA || !p_typeB)
error->all("KSpace style is incompatible with Pair style");
qdist = *p_qdist;
typeO = *p_typeO;
typeH = *p_typeH;
int typeA = *p_typeA;
int typeB = *p_typeB;
if (force->angle == NULL || force->bond == NULL)
error->all("Bond and angle potentials must be defined for TIP4P");
if (typeA < 1 || typeA > atom->nangletypes ||
force->angle->setflag[typeA] == 0)
error->all("Bad TIP4P angle type for PPPM/TIP4P");
if (typeB < 1 || typeA > atom->nbondtypes ||
force->bond->setflag[typeB] == 0)
error->all("Bad TIP4P bond type for PPPM/TIP4P");
double theta = force->angle->equilibrium_angle(typeA);
double blen = force->bond->equilibrium_distance(typeB);
alpha = qdist / (2.0 * cos(0.5*theta) * blen);
}
// compute qsum & qsqsum and warn if not charge-neutral
qsum = qsqsum = 0.0;
for (int i = 0; i < atom->nlocal; i++) {
qsum += atom->q[i];
qsqsum += atom->q[i]*atom->q[i];
}
double tmp;
MPI_Allreduce(&qsum,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
qsum = tmp;
MPI_Allreduce(&qsqsum,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
qsqsum = tmp;
if (qsqsum == 0.0)
error->all("Cannot use kspace solver on system with no charge");
if (fabs(qsum) > SMALL && me == 0) {
char str[128];
sprintf(str,"System is not charge neutral, net charge = %g",qsum);
error->warning(str);
}
// setup FFT grid resolution and g_ewald
// normally one iteration thru while loop is all that is required
// if grid stencil extends beyond neighbor proc, reduce order and try again
int iteration = 0;
while (order > 0) {
if (iteration && me == 0)
error->warning("Reducing PPPM order b/c stencil extends "
"beyond neighbor processor");
iteration++;
set_grid();
if (nx_pppm >= OFFSET || ny_pppm >= OFFSET || nz_pppm >= OFFSET)
error->all("PPPM grid is too large");
// global indices of PPPM grid range from 0 to N-1
// nlo_in,nhi_in = lower/upper limits of the 3d sub-brick of
// global PPPM grid that I own without ghost cells
// for slab PPPM, assign z grid as if it were not extended
nxlo_in = comm->myloc[0]*nx_pppm / comm->procgrid[0];
nxhi_in = (comm->myloc[0]+1)*nx_pppm / comm->procgrid[0] - 1;
nylo_in = comm->myloc[1]*ny_pppm / comm->procgrid[1];
nyhi_in = (comm->myloc[1]+1)*ny_pppm / comm->procgrid[1] - 1;
nzlo_in = comm->myloc[2] *
(static_cast<int> (nz_pppm/slab_volfactor)) / comm->procgrid[2];
nzhi_in = (comm->myloc[2]+1) *
(static_cast<int> (nz_pppm/slab_volfactor)) / comm->procgrid[2] - 1;
// nlower,nupper = stencil size for mapping particles to PPPM grid
nlower = -(order-1)/2;
nupper = order/2;
// shift values for particle <-> grid mapping
// add/subtract OFFSET to avoid int(-0.75) = 0 when want it to be -1
if (order % 2) shift = OFFSET + 0.5;
else shift = OFFSET;
if (order % 2) shiftone = 0.0;
else shiftone = 0.5;
// nlo_out,nhi_out = lower/upper limits of the 3d sub-brick of
// global PPPM grid that my particles can contribute charge to
// effectively nlo_in,nhi_in + ghost cells
// nlo,nhi = global coords of grid pt to "lower left" of smallest/largest
// position a particle in my box can be at
// dist[3] = particle position bound = subbox + skin/2.0 + qdist
// qdist = offset due to TIP4P fictitious charge
// convert to triclinic if necessary
// nlo_out,nhi_out = nlo,nhi + stencil size for particle mapping
// for slab PPPM, assign z grid as if it were not extended
triclinic = domain->triclinic;
double *prd,*sublo,*subhi;
if (triclinic == 0) {
prd = domain->prd;
boxlo = domain->boxlo;
sublo = domain->sublo;
subhi = domain->subhi;
} else {
prd = domain->prd_lamda;
boxlo = domain->boxlo_lamda;
sublo = domain->sublo_lamda;
subhi = domain->subhi_lamda;
}
double xprd = prd[0];
double yprd = prd[1];
double zprd = prd[2];
double zprd_slab = zprd*slab_volfactor;
double dist[3];
double cuthalf = 0.5*neighbor->skin + qdist;
if (triclinic == 0) dist[0] = dist[1] = dist[2] = cuthalf;
else {
dist[0] = cuthalf/domain->prd[0];
dist[1] = cuthalf/domain->prd[1];
dist[2] = cuthalf/domain->prd[2];
}
int nlo,nhi;
nlo = static_cast<int> ((sublo[0]-dist[0]-boxlo[0]) *
nx_pppm/xprd + shift) - OFFSET;
nhi = static_cast<int> ((subhi[0]+dist[0]-boxlo[0]) *
nx_pppm/xprd + shift) - OFFSET;
nxlo_out = nlo + nlower;
nxhi_out = nhi + nupper;
nlo = static_cast<int> ((sublo[1]-dist[1]-boxlo[1]) *
ny_pppm/yprd + shift) - OFFSET;
nhi = static_cast<int> ((subhi[1]+dist[1]-boxlo[1]) *
ny_pppm/yprd + shift) - OFFSET;
nylo_out = nlo + nlower;
nyhi_out = nhi + nupper;
nlo = static_cast<int> ((sublo[2]-dist[2]-boxlo[2]) *
nz_pppm/zprd_slab + shift) - OFFSET;
nhi = static_cast<int> ((subhi[2]+dist[2]-boxlo[2]) *
nz_pppm/zprd_slab + shift) - OFFSET;
nzlo_out = nlo + nlower;
nzhi_out = nhi + nupper;
// for slab PPPM, change the grid boundary for processors at +z end
// to include the empty volume between periodically repeating slabs
// for slab PPPM, want charge data communicated from -z proc to +z proc,
// but not vice versa, also want field data communicated from +z proc to
// -z proc, but not vice versa
// this is accomplished by nzhi_in = nzhi_out on +z end (no ghost cells)
if (slabflag && ((comm->myloc[2]+1) == (comm->procgrid[2]))) {
nzhi_in = nz_pppm - 1;
nzhi_out = nz_pppm - 1;
}
// nlo_ghost,nhi_ghost = # of planes I will recv from 6 directions
// that overlay domain I own
// proc in that direction tells me via sendrecv()
// if no neighbor proc, value is from self since I have ghosts regardless
int nplanes;
MPI_Status status;
nplanes = nxlo_in - nxlo_out;
if (comm->procneigh[0][0] != me)
MPI_Sendrecv(&nplanes,1,MPI_INT,comm->procneigh[0][0],0,
&nxhi_ghost,1,MPI_INT,comm->procneigh[0][1],0,
world,&status);
else nxhi_ghost = nplanes;
nplanes = nxhi_out - nxhi_in;
if (comm->procneigh[0][1] != me)
MPI_Sendrecv(&nplanes,1,MPI_INT,comm->procneigh[0][1],0,
&nxlo_ghost,1,MPI_INT,comm->procneigh[0][0],
0,world,&status);
else nxlo_ghost = nplanes;
nplanes = nylo_in - nylo_out;
if (comm->procneigh[1][0] != me)
MPI_Sendrecv(&nplanes,1,MPI_INT,comm->procneigh[1][0],0,
&nyhi_ghost,1,MPI_INT,comm->procneigh[1][1],0,
world,&status);
else nyhi_ghost = nplanes;
nplanes = nyhi_out - nyhi_in;
if (comm->procneigh[1][1] != me)
MPI_Sendrecv(&nplanes,1,MPI_INT,comm->procneigh[1][1],0,
&nylo_ghost,1,MPI_INT,comm->procneigh[1][0],0,
world,&status);
else nylo_ghost = nplanes;
nplanes = nzlo_in - nzlo_out;
if (comm->procneigh[2][0] != me)
MPI_Sendrecv(&nplanes,1,MPI_INT,comm->procneigh[2][0],0,
&nzhi_ghost,1,MPI_INT,comm->procneigh[2][1],0,
world,&status);
else nzhi_ghost = nplanes;
nplanes = nzhi_out - nzhi_in;
if (comm->procneigh[2][1] != me)
MPI_Sendrecv(&nplanes,1,MPI_INT,comm->procneigh[2][1],0,
&nzlo_ghost,1,MPI_INT,comm->procneigh[2][0],0,
world,&status);
else nzlo_ghost = nplanes;
// test that ghost overlap is not bigger than my sub-domain
int flag = 0;
if (nxlo_ghost > nxhi_in-nxlo_in+1) flag = 1;
if (nxhi_ghost > nxhi_in-nxlo_in+1) flag = 1;
if (nylo_ghost > nyhi_in-nylo_in+1) flag = 1;
if (nyhi_ghost > nyhi_in-nylo_in+1) flag = 1;
if (nzlo_ghost > nzhi_in-nzlo_in+1) flag = 1;
if (nzhi_ghost > nzhi_in-nzlo_in+1) flag = 1;
int flag_all;
MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world);
if (flag_all == 0) break;
order--;
}
if (order == 0) error->all("PPPM order has been reduced to 0");
// decomposition of FFT mesh
// global indices range from 0 to N-1
// proc owns entire x-dimension, clump of columns in y,z dimensions
// npey_fft,npez_fft = # of procs in y,z dims
// if nprocs is small enough, proc can own 1 or more entire xy planes,
// else proc owns 2d sub-blocks of yz plane
// me_y,me_z = which proc (0-npe_fft-1) I am in y,z dimensions
// nlo_fft,nhi_fft = lower/upper limit of the section
// of the global FFT mesh that I own
int npey_fft,npez_fft;
if (nz_pppm >= nprocs) {
npey_fft = 1;
npez_fft = nprocs;
} else procs2grid2d(nprocs,ny_pppm,nz_pppm,&npey_fft,&npez_fft);
int me_y = me % npey_fft;
int me_z = me / npey_fft;
nxlo_fft = 0;
nxhi_fft = nx_pppm - 1;
nylo_fft = me_y*ny_pppm/npey_fft;
nyhi_fft = (me_y+1)*ny_pppm/npey_fft - 1;
nzlo_fft = me_z*nz_pppm/npez_fft;
nzhi_fft = (me_z+1)*nz_pppm/npez_fft - 1;
// PPPM grid for this proc, including ghosts
ngrid = (nxhi_out-nxlo_out+1) * (nyhi_out-nylo_out+1) *
(nzhi_out-nzlo_out+1);
// FFT arrays on this proc, without ghosts
// nfft = FFT points in FFT decomposition on this proc
// nfft_brick = FFT points in 3d brick-decomposition on this proc
// nfft_both = greater of 2 values
nfft = (nxhi_fft-nxlo_fft+1) * (nyhi_fft-nylo_fft+1) *
(nzhi_fft-nzlo_fft+1);
int nfft_brick = (nxhi_in-nxlo_in+1) * (nyhi_in-nylo_in+1) *
(nzhi_in-nzlo_in+1);
nfft_both = MAX(nfft,nfft_brick);
// buffer space for use in brick2fft and fillbrick
// idel = max # of ghost planes to send or recv in +/- dir of each dim
// nx,ny,nz = owned planes (including ghosts) in each dim
// nxx,nyy,nzz = max # of grid cells to send in each dim
// nbuf = max in any dim, augment by 3x for components of vd_xyz in fillbrick
int idelx,idely,idelz,nx,ny,nz,nxx,nyy,nzz;
idelx = MAX(nxlo_ghost,nxhi_ghost);
idelx = MAX(idelx,nxhi_out-nxhi_in);
idelx = MAX(idelx,nxlo_in-nxlo_out);
idely = MAX(nylo_ghost,nyhi_ghost);
idely = MAX(idely,nyhi_out-nyhi_in);
idely = MAX(idely,nylo_in-nylo_out);
idelz = MAX(nzlo_ghost,nzhi_ghost);
idelz = MAX(idelz,nzhi_out-nzhi_in);
idelz = MAX(idelz,nzlo_in-nzlo_out);
nx = nxhi_out - nxlo_out + 1;
ny = nyhi_out - nylo_out + 1;
nz = nzhi_out - nzlo_out + 1;
nxx = idelx * ny * nz;
nyy = idely * nx * nz;
nzz = idelz * nx * ny;
nbuf = MAX(nxx,nyy);
nbuf = MAX(nbuf,nzz);
nbuf *= 3;
// print stats
int ngrid_max,nfft_both_max,nbuf_max;
MPI_Allreduce(&ngrid,&ngrid_max,1,MPI_INT,MPI_MAX,world);
MPI_Allreduce(&nfft_both,&nfft_both_max,1,MPI_INT,MPI_MAX,world);
MPI_Allreduce(&nbuf,&nbuf_max,1,MPI_INT,MPI_MAX,world);
if (me == 0) {
if (screen) fprintf(screen," brick FFT buffer size/proc = %d %d %d\n",
ngrid_max,nfft_both_max,nbuf_max);
if (logfile) fprintf(logfile," brick FFT buffer size/proc = %d %d %d\n",
ngrid_max,nfft_both_max,nbuf_max);
}
// allocate K-space dependent memory
allocate();
// pre-compute Green's function denomiator expansion
// pre-compute 1d charge distribution coefficients
compute_gf_denom();
compute_rho_coeff();
}
/* ----------------------------------------------------------------------
adjust PPPM coeffs, called initially and whenever volume has changed
------------------------------------------------------------------------- */
void PPPM::setup()
{
int i,j,k,l,m,n;
double *prd;
// volume-dependent factors
// adjust z dimension for 2d slab PPPM
// z dimension for 3d PPPM is zprd since slab_volfactor = 1.0
if (triclinic == 0) prd = domain->prd;
else prd = domain->prd_lamda;
double xprd = prd[0];
double yprd = prd[1];
double zprd = prd[2];
double zprd_slab = zprd*slab_volfactor;
volume = xprd * yprd * zprd_slab;
delxinv = nx_pppm/xprd;
delyinv = ny_pppm/yprd;
delzinv = nz_pppm/zprd_slab;
delvolinv = delxinv*delyinv*delzinv;
double unitkx = (2.0*PI/xprd);
double unitky = (2.0*PI/yprd);
double unitkz = (2.0*PI/zprd_slab);
// fkx,fky,fkz for my FFT grid pts
double per;
for (i = nxlo_fft; i <= nxhi_fft; i++) {
per = i - nx_pppm*(2*i/nx_pppm);
fkx[i] = unitkx*per;
}
for (i = nylo_fft; i <= nyhi_fft; i++) {
per = i - ny_pppm*(2*i/ny_pppm);
fky[i] = unitky*per;
}
for (i = nzlo_fft; i <= nzhi_fft; i++) {
per = i - nz_pppm*(2*i/nz_pppm);
fkz[i] = unitkz*per;
}
// virial coefficients
double sqk,vterm;
n = 0;
for (k = nzlo_fft; k <= nzhi_fft; k++) {
for (j = nylo_fft; j <= nyhi_fft; j++) {
for (i = nxlo_fft; i <= nxhi_fft; i++) {
sqk = fkx[i]*fkx[i] + fky[j]*fky[j] + fkz[k]*fkz[k];
if (sqk == 0.0) {
vg[n][0] = 0.0;
vg[n][1] = 0.0;
vg[n][2] = 0.0;
vg[n][3] = 0.0;
vg[n][4] = 0.0;
vg[n][5] = 0.0;
} else {
vterm = -2.0 * (1.0/sqk + 0.25/(g_ewald*g_ewald));
vg[n][0] = 1.0 + vterm*fkx[i]*fkx[i];
vg[n][1] = 1.0 + vterm*fky[j]*fky[j];
vg[n][2] = 1.0 + vterm*fkz[k]*fkz[k];
vg[n][3] = vterm*fkx[i]*fky[j];
vg[n][4] = vterm*fkx[i]*fkz[k];
vg[n][5] = vterm*fky[j]*fkz[k];
}
n++;
}
}
}
// modified (Hockney-Eastwood) Coulomb Green's function
int nx,ny,nz,kper,lper,mper;
double snx,sny,snz,snx2,sny2,snz2;
double argx,argy,argz,wx,wy,wz,sx,sy,sz,qx,qy,qz;
double sum1,dot1,dot2;
double numerator,denominator;
int nbx = static_cast<int> ((g_ewald*xprd/(PI*nx_pppm)) *
pow(-log(EPS_HOC),0.25));
int nby = static_cast<int> ((g_ewald*yprd/(PI*ny_pppm)) *
pow(-log(EPS_HOC),0.25));
int nbz = static_cast<int> ((g_ewald*zprd_slab/(PI*nz_pppm)) *
pow(-log(EPS_HOC),0.25));
double form = 1.0;
n = 0;
for (m = nzlo_fft; m <= nzhi_fft; m++) {
mper = m - nz_pppm*(2*m/nz_pppm);
snz = sin(0.5*unitkz*mper*zprd_slab/nz_pppm);
snz2 = snz*snz;
for (l = nylo_fft; l <= nyhi_fft; l++) {
lper = l - ny_pppm*(2*l/ny_pppm);
sny = sin(0.5*unitky*lper*yprd/ny_pppm);
sny2 = sny*sny;
for (k = nxlo_fft; k <= nxhi_fft; k++) {
kper = k - nx_pppm*(2*k/nx_pppm);
snx = sin(0.5*unitkx*kper*xprd/nx_pppm);
snx2 = snx*snx;
sqk = pow(unitkx*kper,2.0) + pow(unitky*lper,2.0) +
pow(unitkz*mper,2.0);
if (sqk != 0.0) {
numerator = form*12.5663706/sqk;
denominator = gf_denom(snx2,sny2,snz2);
sum1 = 0.0;
for (nx = -nbx; nx <= nbx; nx++) {
qx = unitkx*(kper+nx_pppm*nx);
sx = exp(-.25*pow(qx/g_ewald,2.0));
wx = 1.0;
argx = 0.5*qx*xprd/nx_pppm;
if (argx != 0.0) wx = pow(sin(argx)/argx,order);
for (ny = -nby; ny <= nby; ny++) {
qy = unitky*(lper+ny_pppm*ny);
sy = exp(-.25*pow(qy/g_ewald,2.0));
wy = 1.0;
argy = 0.5*qy*yprd/ny_pppm;
if (argy != 0.0) wy = pow(sin(argy)/argy,order);
for (nz = -nbz; nz <= nbz; nz++) {
qz = unitkz*(mper+nz_pppm*nz);
sz = exp(-.25*pow(qz/g_ewald,2.0));
wz = 1.0;
argz = 0.5*qz*zprd_slab/nz_pppm;
if (argz != 0.0) wz = pow(sin(argz)/argz,order);
dot1 = unitkx*kper*qx + unitky*lper*qy + unitkz*mper*qz;
dot2 = qx*qx+qy*qy+qz*qz;
sum1 += (dot1/dot2) * sx*sy*sz * pow(wx*wy*wz,2.0);
}
}
}
greensfn[n++] = numerator*sum1/denominator;
} else greensfn[n++] = 0.0;
}
}
}
}
/* ----------------------------------------------------------------------
compute the PPPM long-range force, energy, virial
------------------------------------------------------------------------- */
void PPPM::compute(int eflag, int vflag)
{
int i;
// convert atoms from box to lamda coords
if (triclinic == 0) boxlo = domain->boxlo;
else {
boxlo = domain->boxlo_lamda;
domain->x2lamda(atom->nlocal);
}
// extend size of per-atom arrays if necessary
if (atom->nlocal > nmax) {
memory->destroy_2d_int_array(part2grid);
nmax = atom->nmax;
part2grid = memory->create_2d_int_array(nmax,3,"pppm:part2grid");
}
energy = 0.0;
if (vflag) for (i = 0; i < 6; i++) virial[i] = 0.0;
// find grid points for all my particles
// map my particle charge onto my local 3d density grid
particle_map();
make_rho();
// all procs communicate density values from their ghost cells
// to fully sum contribution in their 3d bricks
// remap from 3d decomposition to FFT decomposition
brick2fft();
// compute potential gradient on my FFT grid and
// portion of e_long on this proc's FFT grid
// return gradients (electric fields) in 3d brick decomposition
poisson(eflag,vflag);
// all procs communicate E-field values to fill ghost cells
// surrounding their 3d bricks
fillbrick();
// calculate the force on my particles
fieldforce();
// sum energy across procs and add in volume-dependent term
if (eflag) {
double energy_all;
MPI_Allreduce(&energy,&energy_all,1,MPI_DOUBLE,MPI_SUM,world);
energy = energy_all;
energy *= 0.5*volume;
energy -= g_ewald*qsqsum/1.772453851 +
0.5*PI*qsum*qsum / (g_ewald*g_ewald*volume);
energy *= qqrd2e*scale;
}
// sum virial across procs
if (vflag) {
double virial_all[6];
MPI_Allreduce(virial,virial_all,6,MPI_DOUBLE,MPI_SUM,world);
for (i = 0; i < 6; i++) virial[i] = 0.5*qqrd2e*scale*volume*virial_all[i];
}
// 2d slab correction
if (slabflag) slabcorr(eflag);
// convert atoms back from lamda to box coords
if (triclinic) domain->lamda2x(atom->nlocal);
}
/* ----------------------------------------------------------------------
allocate memory that depends on # of K-vectors and order
------------------------------------------------------------------------- */
void PPPM::allocate()
{
density_brick =
memory->create_3d_double_array(nzlo_out,nzhi_out,nylo_out,nyhi_out,
nxlo_out,nxhi_out,"pppm:density_brick");
vdx_brick =
memory->create_3d_double_array(nzlo_out,nzhi_out,nylo_out,nyhi_out,
nxlo_out,nxhi_out,"pppm:vdx_brick");
vdy_brick =
memory->create_3d_double_array(nzlo_out,nzhi_out,nylo_out,nyhi_out,
nxlo_out,nxhi_out,"pppm:vdy_brick");
vdz_brick =
memory->create_3d_double_array(nzlo_out,nzhi_out,nylo_out,nyhi_out,
nxlo_out,nxhi_out,"pppm:vdz_brick");
density_fft =
(double *) memory->smalloc(nfft_both*sizeof(double),"pppm:density_fft");
greensfn =
(double *) memory->smalloc(nfft_both*sizeof(double),"pppm:greensfn");
work1 = (double *) memory->smalloc(2*nfft_both*sizeof(double),"pppm:work1");
work2 = (double *) memory->smalloc(2*nfft_both*sizeof(double),"pppm:work2");
vg = memory->create_2d_double_array(nfft_both,6,"pppm:vg");
fkx = memory->create_1d_double_array(nxlo_fft,nxhi_fft,"pppm:fkx");
fky = memory->create_1d_double_array(nylo_fft,nyhi_fft,"pppm:fky");
fkz = memory->create_1d_double_array(nzlo_fft,nzhi_fft,"pppm:fkz");
buf1 = (double *) memory->smalloc(nbuf*sizeof(double),"pppm:buf1");
buf2 = (double *) memory->smalloc(nbuf*sizeof(double),"pppm:buf2");
// summation coeffs
gf_b = new double[order];
rho1d = memory->create_2d_double_array(3,-order/2,order/2,"pppm:rho1d");
rho_coeff = memory->create_2d_double_array(order,(1-order)/2,order/2,
"pppm:rho_coeff");
// create 2 FFTs and a Remap
// 1st FFT keeps data in FFT decompostion
// 2nd FFT returns data in 3d brick decomposition
// remap takes data from 3d brick to FFT decomposition
int tmp;
fft1 = new FFT3d(lmp,world,nx_pppm,ny_pppm,nz_pppm,
nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
0,0,&tmp);
fft2 = new FFT3d(lmp,world,nx_pppm,ny_pppm,nz_pppm,
nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in,
0,0,&tmp);
remap = new Remap(lmp,world,
nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in,
nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
1,0,0,2);
}
/* ----------------------------------------------------------------------
deallocate memory that depends on # of K-vectors and order
------------------------------------------------------------------------- */
void PPPM::deallocate()
{
memory->destroy_3d_double_array(density_brick,nzlo_out,nylo_out,nxlo_out);
memory->destroy_3d_double_array(vdx_brick,nzlo_out,nylo_out,nxlo_out);
memory->destroy_3d_double_array(vdy_brick,nzlo_out,nylo_out,nxlo_out);
memory->destroy_3d_double_array(vdz_brick,nzlo_out,nylo_out,nxlo_out);
memory->sfree(density_fft);
memory->sfree(greensfn);
memory->sfree(work1);
memory->sfree(work2);
memory->destroy_2d_double_array(vg);
memory->destroy_1d_double_array(fkx,nxlo_fft);
memory->destroy_1d_double_array(fky,nylo_fft);
memory->destroy_1d_double_array(fkz,nzlo_fft);
memory->sfree(buf1);
memory->sfree(buf2);
delete [] gf_b;
memory->destroy_2d_double_array(rho1d,-order/2);
memory->destroy_2d_double_array(rho_coeff,(1-order)/2);
delete fft1;
delete fft2;
delete remap;
}
/* ----------------------------------------------------------------------
set size of FFT grid (nx,ny,nz_pppm) and g_ewald
------------------------------------------------------------------------- */
void PPPM::set_grid()
{
// see JCP 109, pg 7698 for derivation of coefficients
// higher order coefficients may be computed if needed
double **acons = memory->create_2d_double_array(8,7,"pppm:acons");
acons[1][0] = 2.0 / 3.0;
acons[2][0] = 1.0 / 50.0;
acons[2][1] = 5.0 / 294.0;
acons[3][0] = 1.0 / 588.0;
acons[3][1] = 7.0 / 1440.0;
acons[3][2] = 21.0 / 3872.0;
acons[4][0] = 1.0 / 4320.0;
acons[4][1] = 3.0 / 1936.0;
acons[4][2] = 7601.0 / 2271360.0;
acons[4][3] = 143.0 / 28800.0;
acons[5][0] = 1.0 / 23232.0;
acons[5][1] = 7601.0 / 13628160.0;
acons[5][2] = 143.0 / 69120.0;
acons[5][3] = 517231.0 / 106536960.0;
acons[5][4] = 106640677.0 / 11737571328.0;
acons[6][0] = 691.0 / 68140800.0;
acons[6][1] = 13.0 / 57600.0;
acons[6][2] = 47021.0 / 35512320.0;
acons[6][3] = 9694607.0 / 2095994880.0;
acons[6][4] = 733191589.0 / 59609088000.0;
acons[6][5] = 326190917.0 / 11700633600.0;
acons[7][0] = 1.0 / 345600.0;
acons[7][1] = 3617.0 / 35512320.0;
acons[7][2] = 745739.0 / 838397952.0;
acons[7][3] = 56399353.0 / 12773376000.0;
acons[7][4] = 25091609.0 / 1560084480.0;
acons[7][5] = 1755948832039.0 / 36229939200000.0;
acons[7][6] = 4887769399.0 / 37838389248.0;
double q2 = qsqsum / force->dielectric;
bigint natoms = atom->natoms;
// use xprd,yprd,zprd even if triclinic so grid size is the same
// adjust z dimension for 2d slab PPPM
// 3d PPPM just uses zprd since slab_volfactor = 1.0
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
double zprd_slab = zprd*slab_volfactor;
// make initial g_ewald estimate
// based on desired error and real space cutoff
// fluid-occupied volume used to estimate real-space error
// zprd used rather than zprd_slab
double hx,hy,hz;
if (!gewaldflag)
g_ewald = sqrt(-log(precision*sqrt(natoms*cutoff*xprd*yprd*zprd) /
(2.0*q2))) / cutoff;
// set optimal nx_pppm,ny_pppm,nz_pppm based on order and precision
// nz_pppm uses extended zprd_slab instead of zprd
// h = 1/g_ewald is upper bound on h such that h*g_ewald <= 1
// reduce it until precision target is met
if (!gridflag) {
double err;
hx = hy = hz = 1/g_ewald;
nx_pppm = static_cast<int> (xprd/hx + 1);
ny_pppm = static_cast<int> (yprd/hy + 1);
nz_pppm = static_cast<int> (zprd_slab/hz + 1);
err = rms(hx,xprd,natoms,q2,acons);
while (err > precision) {
err = rms(hx,xprd,natoms,q2,acons);
nx_pppm++;
hx = xprd/nx_pppm;
}
err = rms(hy,yprd,natoms,q2,acons);
while (err > precision) {
err = rms(hy,yprd,natoms,q2,acons);
ny_pppm++;
hy = yprd/ny_pppm;
}
err = rms(hz,zprd_slab,natoms,q2,acons);
while (err > precision) {
err = rms(hz,zprd_slab,natoms,q2,acons);
nz_pppm++;
hz = zprd_slab/nz_pppm;
}
}
// boost grid size until it is factorable
while (!factorable(nx_pppm)) nx_pppm++;
while (!factorable(ny_pppm)) ny_pppm++;
while (!factorable(nz_pppm)) nz_pppm++;
// adjust g_ewald for new grid size
hx = xprd/nx_pppm;
hy = yprd/ny_pppm;
hz = zprd_slab/nz_pppm;
if (!gewaldflag) {
double gew1,gew2,dgew,f,fmid,hmin,rtb;
int ncount;
gew1 = 0.0;
g_ewald = gew1;
f = diffpr(hx,hy,hz,q2,acons);
hmin = MIN(hx,MIN(hy,hz));
gew2 = 10/hmin;
g_ewald = gew2;
fmid = diffpr(hx,hy,hz,q2,acons);
if (f*fmid >= 0.0) error->all("Cannot compute PPPM G");
rtb = f < 0.0 ? (dgew=gew2-gew1,gew1) : (dgew=gew1-gew2,gew2);
ncount = 0;
while (fabs(dgew) > SMALL && fmid != 0.0) {
dgew *= 0.5;
g_ewald = rtb + dgew;
fmid = diffpr(hx,hy,hz,q2,acons);
if (fmid <= 0.0) rtb = g_ewald;
ncount++;
if (ncount > LARGE) error->all("Cannot compute PPPM G");
}
}
// final RMS precision
double lprx = rms(hx,xprd,natoms,q2,acons);
double lpry = rms(hy,yprd,natoms,q2,acons);
double lprz = rms(hz,zprd_slab,natoms,q2,acons);
double lpr = sqrt(lprx*lprx + lpry*lpry + lprz*lprz) / sqrt(3.0);
double spr = 2.0*q2 * exp(-g_ewald*g_ewald*cutoff*cutoff) /
sqrt(natoms*cutoff*xprd*yprd*zprd_slab);
// free local memory
memory->destroy_2d_double_array(acons);
// print info
if (me == 0) {
if (screen) {
fprintf(screen," G vector = %g\n",g_ewald);
fprintf(screen," grid = %d %d %d\n",nx_pppm,ny_pppm,nz_pppm);
fprintf(screen," stencil order = %d\n",order);
fprintf(screen," RMS precision = %g\n",MAX(lpr,spr));
}
if (logfile) {
fprintf(logfile," G vector = %g\n",g_ewald);
fprintf(logfile," grid = %d %d %d\n",nx_pppm,ny_pppm,nz_pppm);
fprintf(logfile," stencil order = %d\n",order);
fprintf(logfile," RMS precision = %g\n",MAX(lpr,spr));
}
}
}
/* ----------------------------------------------------------------------
check if all factors of n are in list of factors
return 1 if yes, 0 if no
------------------------------------------------------------------------- */
int PPPM::factorable(int n)
{
int i;
while (n > 1) {
for (i = 0; i < nfactors; i++) {
if (n % factors[i] == 0) {
n /= factors[i];
break;
}
}
if (i == nfactors) return 0;
}
return 1;
}
/* ----------------------------------------------------------------------
compute RMS precision for a dimension
------------------------------------------------------------------------- */
double PPPM::rms(double h, double prd, bigint natoms,
double q2, double **acons)
{
double sum = 0.0;
for (int m = 0; m < order; m++)
sum += acons[order][m] * pow(h*g_ewald,2.0*m);
double value = q2 * pow(h*g_ewald,order) *
sqrt(g_ewald*prd*sqrt(2.0*PI)*sum/natoms) / (prd*prd);
return value;
}
/* ----------------------------------------------------------------------
compute difference in real-space and kspace RMS precision
------------------------------------------------------------------------- */
double PPPM::diffpr(double hx, double hy, double hz, double q2, double **acons)
{
double lprx,lpry,lprz,kspace_prec,real_prec;
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
bigint natoms = atom->natoms;
lprx = rms(hx,xprd,natoms,q2,acons);
lpry = rms(hy,yprd,natoms,q2,acons);
lprz = rms(hz,zprd*slab_volfactor,natoms,q2,acons);
kspace_prec = sqrt(lprx*lprx + lpry*lpry + lprz*lprz) / sqrt(3.0);
real_prec = 2.0*q2 * exp(-g_ewald*g_ewald*cutoff*cutoff) /
sqrt(natoms*cutoff*xprd*yprd*zprd);
double value = kspace_prec - real_prec;
return value;
}
/* ----------------------------------------------------------------------
denominator for Hockney-Eastwood Green's function
of x,y,z = sin(kx*deltax/2), etc
inf n-1
S(n,k) = Sum W(k+pi*j)**2 = Sum b(l)*(z*z)**l
j=-inf l=0
= -(z*z)**n /(2n-1)! * (d/dx)**(2n-1) cot(x) at z = sin(x)
gf_b = denominator expansion coeffs
------------------------------------------------------------------------- */
double PPPM::gf_denom(double x, double y, double z)
{
double sx,sy,sz;
sz = sy = sx = 0.0;
for (int l = order-1; l >= 0; l--) {
sx = gf_b[l] + sx*x;
sy = gf_b[l] + sy*y;
sz = gf_b[l] + sz*z;
}
double s = sx*sy*sz;
return s*s;
}
/* ----------------------------------------------------------------------
pre-compute Green's function denominator expansion coeffs, Gamma(2n)
------------------------------------------------------------------------- */
void PPPM::compute_gf_denom()
{
int k,l,m;
for (l = 1; l < order; l++) gf_b[l] = 0.0;
gf_b[0] = 1.0;
for (m = 1; m < order; m++) {
for (l = m; l > 0; l--)
gf_b[l] = 4.0 * (gf_b[l]*(l-m)*(l-m-0.5)-gf_b[l-1]*(l-m-1)*(l-m-1));
gf_b[0] = 4.0 * (gf_b[0]*(l-m)*(l-m-0.5));
}
int ifact = 1;
for (k = 1; k < 2*order; k++) ifact *= k;
double gaminv = 1.0/ifact;
for (l = 0; l < order; l++) gf_b[l] *= gaminv;
}
/* ----------------------------------------------------------------------
ghost-swap to accumulate full density in brick decomposition
remap density from 3d brick decomposition to FFT decomposition
------------------------------------------------------------------------- */
void PPPM::brick2fft()
{
int i,n,ix,iy,iz;
MPI_Request request;
MPI_Status status;
// pack my ghosts for +x processor
// pass data to self or +x processor
// unpack and sum recv data into my real cells
n = 0;
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_out; iy <= nyhi_out; iy++)
for (ix = nxhi_in+1; ix <= nxhi_out; ix++)
buf1[n++] = density_brick[iz][iy][ix];
if (comm->procneigh[0][1] == me)
for (i = 0; i < n; i++) buf2[i] = buf1[i];
else {
MPI_Irecv(buf2,nbuf,MPI_DOUBLE,comm->procneigh[0][0],0,world,&request);
MPI_Send(buf1,n,MPI_DOUBLE,comm->procneigh[0][1],0,world);
MPI_Wait(&request,&status);
}
n = 0;
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_out; iy <= nyhi_out; iy++)
for (ix = nxlo_in; ix < nxlo_in+nxlo_ghost; ix++)
density_brick[iz][iy][ix] += buf2[n++];
// pack my ghosts for -x processor
// pass data to self or -x processor
// unpack and sum recv data into my real cells
n = 0;
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_out; iy <= nyhi_out; iy++)
for (ix = nxlo_out; ix < nxlo_in; ix++)
buf1[n++] = density_brick[iz][iy][ix];
if (comm->procneigh[0][0] == me)
for (i = 0; i < n; i++) buf2[i] = buf1[i];
else {
MPI_Irecv(buf2,nbuf,MPI_DOUBLE,comm->procneigh[0][1],0,world,&request);
MPI_Send(buf1,n,MPI_DOUBLE,comm->procneigh[0][0],0,world);
MPI_Wait(&request,&status);
}
n = 0;
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_out; iy <= nyhi_out; iy++)
for (ix = nxhi_in-nxhi_ghost+1; ix <= nxhi_in; ix++)
density_brick[iz][iy][ix] += buf2[n++];
// pack my ghosts for +y processor
// pass data to self or +y processor
// unpack and sum recv data into my real cells
n = 0;
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nyhi_in+1; iy <= nyhi_out; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++)
buf1[n++] = density_brick[iz][iy][ix];
if (comm->procneigh[1][1] == me)
for (i = 0; i < n; i++) buf2[i] = buf1[i];
else {
MPI_Irecv(buf2,nbuf,MPI_DOUBLE,comm->procneigh[1][0],0,world,&request);
MPI_Send(buf1,n,MPI_DOUBLE,comm->procneigh[1][1],0,world);
MPI_Wait(&request,&status);
}
n = 0;
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_in; iy < nylo_in+nylo_ghost; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++)
density_brick[iz][iy][ix] += buf2[n++];
// pack my ghosts for -y processor
// pass data to self or -y processor
// unpack and sum recv data into my real cells
n = 0;
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_out; iy < nylo_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++)
buf1[n++] = density_brick[iz][iy][ix];
if (comm->procneigh[1][0] == me)
for (i = 0; i < n; i++) buf2[i] = buf1[i];
else {
MPI_Irecv(buf2,nbuf,MPI_DOUBLE,comm->procneigh[1][1],0,world,&request);
MPI_Send(buf1,n,MPI_DOUBLE,comm->procneigh[1][0],0,world);
MPI_Wait(&request,&status);
}
n = 0;
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nyhi_in-nyhi_ghost+1; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++)
density_brick[iz][iy][ix] += buf2[n++];
// pack my ghosts for +z processor
// pass data to self or +z processor
// unpack and sum recv data into my real cells
n = 0;
for (iz = nzhi_in+1; iz <= nzhi_out; iz++)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++)
buf1[n++] = density_brick[iz][iy][ix];
if (comm->procneigh[2][1] == me)
for (i = 0; i < n; i++) buf2[i] = buf1[i];
else {
MPI_Irecv(buf2,nbuf,MPI_DOUBLE,comm->procneigh[2][0],0,world,&request);
MPI_Send(buf1,n,MPI_DOUBLE,comm->procneigh[2][1],0,world);
MPI_Wait(&request,&status);
}
n = 0;
for (iz = nzlo_in; iz < nzlo_in+nzlo_ghost; iz++)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++)
density_brick[iz][iy][ix] += buf2[n++];
// pack my ghosts for -z processor
// pass data to self or -z processor
// unpack and sum recv data into my real cells
n = 0;
for (iz = nzlo_out; iz < nzlo_in; iz++)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++)
buf1[n++] = density_brick[iz][iy][ix];
if (comm->procneigh[2][0] == me)
for (i = 0; i < n; i++) buf2[i] = buf1[i];
else {
MPI_Irecv(buf2,nbuf,MPI_DOUBLE,comm->procneigh[2][1],0,world,&request);
MPI_Send(buf1,n,MPI_DOUBLE,comm->procneigh[2][0],0,world);
MPI_Wait(&request,&status);
}
n = 0;
for (iz = nzhi_in-nzhi_ghost+1; iz <= nzhi_in; iz++)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++)
density_brick[iz][iy][ix] += buf2[n++];
// remap from 3d brick decomposition to FFT decomposition
// copy grabs inner portion of density from 3d brick
// remap could be done as pre-stage of FFT,
// but this works optimally on only double values, not complex values
n = 0;
for (iz = nzlo_in; iz <= nzhi_in; iz++)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++)
density_fft[n++] = density_brick[iz][iy][ix];
remap->perform(density_fft,density_fft,work1);
}
/* ----------------------------------------------------------------------
ghost-swap to fill ghost cells of my brick with field values
------------------------------------------------------------------------- */
void PPPM::fillbrick()
{
int i,n,ix,iy,iz;
MPI_Request request;
MPI_Status status;
// pack my real cells for +z processor
// pass data to self or +z processor
// unpack and sum recv data into my ghost cells
n = 0;
for (iz = nzhi_in-nzhi_ghost+1; iz <= nzhi_in; iz++)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++) {
buf1[n++] = vdx_brick[iz][iy][ix];
buf1[n++] = vdy_brick[iz][iy][ix];
buf1[n++] = vdz_brick[iz][iy][ix];
}
if (comm->procneigh[2][1] == me)
for (i = 0; i < n; i++) buf2[i] = buf1[i];
else {
MPI_Irecv(buf2,nbuf,MPI_DOUBLE,comm->procneigh[2][0],0,world,&request);
MPI_Send(buf1,n,MPI_DOUBLE,comm->procneigh[2][1],0,world);
MPI_Wait(&request,&status);
}
n = 0;
for (iz = nzlo_out; iz < nzlo_in; iz++)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++) {
vdx_brick[iz][iy][ix] = buf2[n++];
vdy_brick[iz][iy][ix] = buf2[n++];
vdz_brick[iz][iy][ix] = buf2[n++];
}
// pack my real cells for -z processor
// pass data to self or -z processor
// unpack and sum recv data into my ghost cells
n = 0;
for (iz = nzlo_in; iz < nzlo_in+nzlo_ghost; iz++)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++) {
buf1[n++] = vdx_brick[iz][iy][ix];
buf1[n++] = vdy_brick[iz][iy][ix];
buf1[n++] = vdz_brick[iz][iy][ix];
}
if (comm->procneigh[2][0] == me)
for (i = 0; i < n; i++) buf2[i] = buf1[i];
else {
MPI_Irecv(buf2,nbuf,MPI_DOUBLE,comm->procneigh[2][1],0,world,&request);
MPI_Send(buf1,n,MPI_DOUBLE,comm->procneigh[2][0],0,world);
MPI_Wait(&request,&status);
}
n = 0;
for (iz = nzhi_in+1; iz <= nzhi_out; iz++)
for (iy = nylo_in; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++) {
vdx_brick[iz][iy][ix] = buf2[n++];
vdy_brick[iz][iy][ix] = buf2[n++];
vdz_brick[iz][iy][ix] = buf2[n++];
}
// pack my real cells for +y processor
// pass data to self or +y processor
// unpack and sum recv data into my ghost cells
n = 0;
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nyhi_in-nyhi_ghost+1; iy <= nyhi_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++) {
buf1[n++] = vdx_brick[iz][iy][ix];
buf1[n++] = vdy_brick[iz][iy][ix];
buf1[n++] = vdz_brick[iz][iy][ix];
}
if (comm->procneigh[1][1] == me)
for (i = 0; i < n; i++) buf2[i] = buf1[i];
else {
MPI_Irecv(buf2,nbuf,MPI_DOUBLE,comm->procneigh[1][0],0,world,&request);
MPI_Send(buf1,n,MPI_DOUBLE,comm->procneigh[1][1],0,world);
MPI_Wait(&request,&status);
}
n = 0;
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_out; iy < nylo_in; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++) {
vdx_brick[iz][iy][ix] = buf2[n++];
vdy_brick[iz][iy][ix] = buf2[n++];
vdz_brick[iz][iy][ix] = buf2[n++];
}
// pack my real cells for -y processor
// pass data to self or -y processor
// unpack and sum recv data into my ghost cells
n = 0;
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_in; iy < nylo_in+nylo_ghost; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++) {
buf1[n++] = vdx_brick[iz][iy][ix];
buf1[n++] = vdy_brick[iz][iy][ix];
buf1[n++] = vdz_brick[iz][iy][ix];
}
if (comm->procneigh[1][0] == me)
for (i = 0; i < n; i++) buf2[i] = buf1[i];
else {
MPI_Irecv(buf2,nbuf,MPI_DOUBLE,comm->procneigh[1][1],0,world,&request);
MPI_Send(buf1,n,MPI_DOUBLE,comm->procneigh[1][0],0,world);
MPI_Wait(&request,&status);
}
n = 0;
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nyhi_in+1; iy <= nyhi_out; iy++)
for (ix = nxlo_in; ix <= nxhi_in; ix++) {
vdx_brick[iz][iy][ix] = buf2[n++];
vdy_brick[iz][iy][ix] = buf2[n++];
vdz_brick[iz][iy][ix] = buf2[n++];
}
// pack my real cells for +x processor
// pass data to self or +x processor
// unpack and sum recv data into my ghost cells
n = 0;
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_out; iy <= nyhi_out; iy++)
for (ix = nxhi_in-nxhi_ghost+1; ix <= nxhi_in; ix++) {
buf1[n++] = vdx_brick[iz][iy][ix];
buf1[n++] = vdy_brick[iz][iy][ix];
buf1[n++] = vdz_brick[iz][iy][ix];
}
if (comm->procneigh[0][1] == me)
for (i = 0; i < n; i++) buf2[i] = buf1[i];
else {
MPI_Irecv(buf2,nbuf,MPI_DOUBLE,comm->procneigh[0][0],0,world,&request);
MPI_Send(buf1,n,MPI_DOUBLE,comm->procneigh[0][1],0,world);
MPI_Wait(&request,&status);
}
n = 0;
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_out; iy <= nyhi_out; iy++)
for (ix = nxlo_out; ix < nxlo_in; ix++) {
vdx_brick[iz][iy][ix] = buf2[n++];
vdy_brick[iz][iy][ix] = buf2[n++];
vdz_brick[iz][iy][ix] = buf2[n++];
}
// pack my real cells for -x processor
// pass data to self or -x processor
// unpack and sum recv data into my ghost cells
n = 0;
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_out; iy <= nyhi_out; iy++)
for (ix = nxlo_in; ix < nxlo_in+nxlo_ghost; ix++) {
buf1[n++] = vdx_brick[iz][iy][ix];
buf1[n++] = vdy_brick[iz][iy][ix];
buf1[n++] = vdz_brick[iz][iy][ix];
}
if (comm->procneigh[0][0] == me)
for (i = 0; i < n; i++) buf2[i] = buf1[i];
else {
MPI_Irecv(buf2,nbuf,MPI_DOUBLE,comm->procneigh[0][1],0,world,&request);
MPI_Send(buf1,n,MPI_DOUBLE,comm->procneigh[0][0],0,world);
MPI_Wait(&request,&status);
}
n = 0;
for (iz = nzlo_out; iz <= nzhi_out; iz++)
for (iy = nylo_out; iy <= nyhi_out; iy++)
for (ix = nxhi_in+1; ix <= nxhi_out; ix++) {
vdx_brick[iz][iy][ix] = buf2[n++];
vdy_brick[iz][iy][ix] = buf2[n++];
vdz_brick[iz][iy][ix] = buf2[n++];
}
}
/* ----------------------------------------------------------------------
find center grid pt for each of my particles
check that full stencil for the particle will fit in my 3d brick
store central grid pt indices in part2grid array
------------------------------------------------------------------------- */
void PPPM::particle_map()
{
int nx,ny,nz;
double **x = atom->x;
int nlocal = atom->nlocal;
int flag = 0;
for (int i = 0; i < nlocal; i++) {
// (nx,ny,nz) = global coords of grid pt to "lower left" of charge
// current particle coord can be outside global and local box
// add/subtract OFFSET to avoid int(-0.75) = 0 when want it to be -1
nx = static_cast<int> ((x[i][0]-boxlo[0])*delxinv+shift) - OFFSET;
ny = static_cast<int> ((x[i][1]-boxlo[1])*delyinv+shift) - OFFSET;
nz = static_cast<int> ((x[i][2]-boxlo[2])*delzinv+shift) - OFFSET;
part2grid[i][0] = nx;
part2grid[i][1] = ny;
part2grid[i][2] = nz;
// check that entire stencil around nx,ny,nz will fit in my 3d brick
if (nx+nlower < nxlo_out || nx+nupper > nxhi_out ||
ny+nlower < nylo_out || ny+nupper > nyhi_out ||
nz+nlower < nzlo_out || nz+nupper > nzhi_out) flag++;
}
int flag_all;
MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world);
if (flag_all) error->all("Out of range atoms - cannot compute PPPM");
}
/* ----------------------------------------------------------------------
create discretized "density" on section of global grid due to my particles
density(x,y,z) = charge "density" at grid points of my 3d brick
(nxlo:nxhi,nylo:nyhi,nzlo:nzhi) is extent of my brick (including ghosts)
in global grid
------------------------------------------------------------------------- */
void PPPM::make_rho()
{
int i,l,m,n,nx,ny,nz,mx,my,mz;
double dx,dy,dz,x0,y0,z0;
// clear 3d density array
double *vec = &density_brick[nzlo_out][nylo_out][nxlo_out];
for (i = 0; i < ngrid; i++) vec[i] = 0.0;
// loop over my charges, add their contribution to nearby grid points
// (nx,ny,nz) = global coords of grid pt to "lower left" of charge
// (dx,dy,dz) = distance to "lower left" grid pt
// (mx,my,mz) = global coords of moving stencil pt
double *q = atom->q;
double **x = atom->x;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
nx = part2grid[i][0];
ny = part2grid[i][1];
nz = part2grid[i][2];
dx = nx+shiftone - (x[i][0]-boxlo[0])*delxinv;
dy = ny+shiftone - (x[i][1]-boxlo[1])*delyinv;
dz = nz+shiftone - (x[i][2]-boxlo[2])*delzinv;
compute_rho1d(dx,dy,dz);
z0 = delvolinv * q[i];
for (n = nlower; n <= nupper; n++) {
mz = n+nz;
y0 = z0*rho1d[2][n];
for (m = nlower; m <= nupper; m++) {
my = m+ny;
x0 = y0*rho1d[1][m];
for (l = nlower; l <= nupper; l++) {
mx = l+nx;
density_brick[mz][my][mx] += x0*rho1d[0][l];
}
}
}
}
}
/* ----------------------------------------------------------------------
FFT-based Poisson solver
------------------------------------------------------------------------- */
void PPPM::poisson(int eflag, int vflag)
{
int i,j,k,n;
double eng;
// transform charge density (r -> k)
n = 0;
for (i = 0; i < nfft; i++) {
work1[n++] = density_fft[i];
work1[n++] = 0.0;
}
fft1->compute(work1,work1,1);
// if requested, compute energy and virial contribution
double scaleinv = 1.0/(nx_pppm*ny_pppm*nz_pppm);
double s2 = scaleinv*scaleinv;
if (eflag || vflag) {
if (vflag) {
n = 0;
for (i = 0; i < nfft; i++) {
eng = s2 * greensfn[i] * (work1[n]*work1[n] + work1[n+1]*work1[n+1]);
for (j = 0; j < 6; j++) virial[j] += eng*vg[i][j];
energy += eng;
n += 2;
}
} else {
n = 0;
for (i = 0; i < nfft; i++) {
energy +=
s2 * greensfn[i] * (work1[n]*work1[n] + work1[n+1]*work1[n+1]);
n += 2;
}
}
}
// scale by 1/total-grid-pts to get rho(k)
// multiply by Green's function to get V(k)
n = 0;
for (i = 0; i < nfft; i++) {
work1[n++] *= scaleinv * greensfn[i];
work1[n++] *= scaleinv * greensfn[i];
}
// compute gradients of V(r) in each of 3 dims by transformimg -ik*V(k)
// FFT leaves data in 3d brick decomposition
// copy it into inner portion of vdx,vdy,vdz arrays
// x direction gradient
n = 0;
for (k = nzlo_fft; k <= nzhi_fft; k++)
for (j = nylo_fft; j <= nyhi_fft; j++)
for (i = nxlo_fft; i <= nxhi_fft; i++) {
work2[n] = fkx[i]*work1[n+1];
work2[n+1] = -fkx[i]*work1[n];
n += 2;
}
fft2->compute(work2,work2,-1);
n = 0;
for (k = nzlo_in; k <= nzhi_in; k++)
for (j = nylo_in; j <= nyhi_in; j++)
for (i = nxlo_in; i <= nxhi_in; i++) {
vdx_brick[k][j][i] = work2[n];
n += 2;
}
// y direction gradient
n = 0;
for (k = nzlo_fft; k <= nzhi_fft; k++)
for (j = nylo_fft; j <= nyhi_fft; j++)
for (i = nxlo_fft; i <= nxhi_fft; i++) {
work2[n] = fky[j]*work1[n+1];
work2[n+1] = -fky[j]*work1[n];
n += 2;
}
fft2->compute(work2,work2,-1);
n = 0;
for (k = nzlo_in; k <= nzhi_in; k++)
for (j = nylo_in; j <= nyhi_in; j++)
for (i = nxlo_in; i <= nxhi_in; i++) {
vdy_brick[k][j][i] = work2[n];
n += 2;
}
// z direction gradient
n = 0;
for (k = nzlo_fft; k <= nzhi_fft; k++)
for (j = nylo_fft; j <= nyhi_fft; j++)
for (i = nxlo_fft; i <= nxhi_fft; i++) {
work2[n] = fkz[k]*work1[n+1];
work2[n+1] = -fkz[k]*work1[n];
n += 2;
}
fft2->compute(work2,work2,-1);
n = 0;
for (k = nzlo_in; k <= nzhi_in; k++)
for (j = nylo_in; j <= nyhi_in; j++)
for (i = nxlo_in; i <= nxhi_in; i++) {
vdz_brick[k][j][i] = work2[n];
n += 2;
}
}
/* ----------------------------------------------------------------------
interpolate from grid to get electric field & force on my particles
------------------------------------------------------------------------- */
void PPPM::fieldforce()
{
int i,l,m,n,nx,ny,nz,mx,my,mz;
double dx,dy,dz,x0,y0,z0;
double ek[3];
// loop over my charges, interpolate electric field from nearby grid points
// (nx,ny,nz) = global coords of grid pt to "lower left" of charge
// (dx,dy,dz) = distance to "lower left" grid pt
// (mx,my,mz) = global coords of moving stencil pt
// ek = 3 components of E-field on particle
double *q = atom->q;
double **x = atom->x;
double **f = atom->f;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
nx = part2grid[i][0];
ny = part2grid[i][1];
nz = part2grid[i][2];
dx = nx+shiftone - (x[i][0]-boxlo[0])*delxinv;
dy = ny+shiftone - (x[i][1]-boxlo[1])*delyinv;
dz = nz+shiftone - (x[i][2]-boxlo[2])*delzinv;
compute_rho1d(dx,dy,dz);
ek[0] = ek[1] = ek[2] = 0.0;
for (n = nlower; n <= nupper; n++) {
mz = n+nz;
z0 = rho1d[2][n];
for (m = nlower; m <= nupper; m++) {
my = m+ny;
y0 = z0*rho1d[1][m];
for (l = nlower; l <= nupper; l++) {
mx = l+nx;
x0 = y0*rho1d[0][l];
ek[0] -= x0*vdx_brick[mz][my][mx];;
ek[1] -= x0*vdy_brick[mz][my][mx];;
ek[2] -= x0*vdz_brick[mz][my][mx];;
}
}
}
// convert E-field to force
f[i][0] += qqrd2e*scale * q[i]*ek[0];
f[i][1] += qqrd2e*scale * q[i]*ek[1];
f[i][2] += qqrd2e*scale * q[i]*ek[2];
}
}
/* ----------------------------------------------------------------------
map nprocs to NX by NY grid as PX by PY procs - return optimal px,py
------------------------------------------------------------------------- */
void PPPM::procs2grid2d(int nprocs, int nx, int ny, int *px, int *py)
{
// loop thru all possible factorizations of nprocs
// surf = surface area of largest proc sub-domain
// innermost if test minimizes surface area and surface/volume ratio
int bestsurf = 2 * (nx + ny);
int bestboxx = 0;
int bestboxy = 0;
int boxx,boxy,surf,ipx,ipy;
ipx = 1;
while (ipx <= nprocs) {
if (nprocs % ipx == 0) {
ipy = nprocs/ipx;
boxx = nx/ipx;
if (nx % ipx) boxx++;
boxy = ny/ipy;
if (ny % ipy) boxy++;
surf = boxx + boxy;
if (surf < bestsurf ||
(surf == bestsurf && boxx*boxy > bestboxx*bestboxy)) {
bestsurf = surf;
bestboxx = boxx;
bestboxy = boxy;
*px = ipx;
*py = ipy;
}
}
ipx++;
}
}
/* ----------------------------------------------------------------------
charge assignment into rho1d
dx,dy,dz = distance of particle from "lower left" grid point
------------------------------------------------------------------------- */
void PPPM::compute_rho1d(double dx, double dy, double dz)
{
int k,l;
for (k = (1-order)/2; k <= order/2; k++) {
rho1d[0][k] = 0.0;
rho1d[1][k] = 0.0;
rho1d[2][k] = 0.0;
for (l = order-1; l >= 0; l--) {
rho1d[0][k] = rho_coeff[l][k] + rho1d[0][k]*dx;
rho1d[1][k] = rho_coeff[l][k] + rho1d[1][k]*dy;
rho1d[2][k] = rho_coeff[l][k] + rho1d[2][k]*dz;
}
}
}
/* ----------------------------------------------------------------------
generate coeffients for the weight function of order n
(n-1)
Wn(x) = Sum wn(k,x) , Sum is over every other integer
k=-(n-1)
For k=-(n-1),-(n-1)+2, ....., (n-1)-2,n-1
k is odd integers if n is even and even integers if n is odd
---
| n-1
| Sum a(l,j)*(x-k/2)**l if abs(x-k/2) < 1/2
wn(k,x) = < l=0
|
| 0 otherwise
---
a coeffients are packed into the array rho_coeff to eliminate zeros
rho_coeff(l,((k+mod(n+1,2))/2) = a(l,k)
------------------------------------------------------------------------- */
void PPPM::compute_rho_coeff()
{
int j,k,l,m;
double s;
double **a = memory->create_2d_double_array(order,-order,order,"pppm:a");
for (k = -order; k <= order; k++)
for (l = 0; l < order; l++)
a[l][k] = 0.0;
a[0][0] = 1.0;
for (j = 1; j < order; j++) {
for (k = -j; k <= j; k += 2) {
s = 0.0;
for (l = 0; l < j; l++) {
a[l+1][k] = (a[l][k+1]-a[l][k-1]) / (l+1);
s += pow(0.5,(double) l+1) *
(a[l][k-1] + pow(-1.0,(double) l) * a[l][k+1]) / (l+1);
}
a[0][k] = s;
}
}
m = (1-order)/2;
for (k = -(order-1); k < order; k += 2) {
for (l = 0; l < order; l++)
rho_coeff[l][m] = a[l][k];
m++;
}
memory->destroy_2d_double_array(a,-order);
}
/* ----------------------------------------------------------------------
Slab-geometry correction term to dampen inter-slab interactions between
periodically repeating slabs. Yields good approximation to 2D Ewald if
adequate empty space is left between repeating slabs (J. Chem. Phys.
111, 3155). Slabs defined here to be parallel to the xy plane.
------------------------------------------------------------------------- */
void PPPM::slabcorr(int eflag)
{
// compute local contribution to global dipole moment
double *q = atom->q;
double **x = atom->x;
int nlocal = atom->nlocal;
double dipole = 0.0;
for (int i = 0; i < nlocal; i++) dipole += q[i]*x[i][2];
// sum local contributions to get global dipole moment
double dipole_all;
MPI_Allreduce(&dipole,&dipole_all,1,MPI_DOUBLE,MPI_SUM,world);
// compute corrections
double e_slabcorr = 2.0*PI*dipole_all*dipole_all/volume;
if (eflag) energy += qqrd2e*scale * e_slabcorr;
// add on force corrections
double ffact = -4.0*PI*dipole_all/volume;
double **f = atom->f;
for (int i = 0; i < nlocal; i++) f[i][2] += qqrd2e*scale * q[i]*ffact;
}
/* ----------------------------------------------------------------------
perform and time the 4 FFTs required for N timesteps
------------------------------------------------------------------------- */
void PPPM::timing(int n, double &time3d, double &time1d)
{
double time1,time2;
for (int i = 0; i < 2*nfft_both; i++) work1[i] = 0.0;
MPI_Barrier(world);
time1 = MPI_Wtime();
for (int i = 0; i < n; i++) {
fft1->compute(work1,work1,1);
fft2->compute(work1,work1,-1);
fft2->compute(work1,work1,-1);
fft2->compute(work1,work1,-1);
}
MPI_Barrier(world);
time2 = MPI_Wtime();
time3d = time2 - time1;
MPI_Barrier(world);
time1 = MPI_Wtime();
for (int i = 0; i < n; i++) {
fft1->timing1d(work1,nfft_both,1);
fft2->timing1d(work1,nfft_both,-1);
fft2->timing1d(work1,nfft_both,-1);
fft2->timing1d(work1,nfft_both,-1);
}
MPI_Barrier(world);
time2 = MPI_Wtime();
time1d = time2 - time1;
}
/* ----------------------------------------------------------------------
memory usage of local arrays
------------------------------------------------------------------------- */
double PPPM::memory_usage()
{
double bytes = nmax*3 * sizeof(double);
int nbrick = (nxhi_out-nxlo_out+1) * (nyhi_out-nylo_out+1) *
(nzhi_out-nzlo_out+1);
bytes += 4 * nbrick * sizeof(double);
bytes += 6 * nfft_both * sizeof(double);
bytes += nfft_both*6 * sizeof(double);
bytes += 2 * nbuf * sizeof(double);
return bytes;
}
diff --git a/src/KSPACE/pppm.h b/src/KSPACE/pppm.h
index 9ca04a754..cb0285398 100644
--- a/src/KSPACE/pppm.h
+++ b/src/KSPACE/pppm.h
@@ -1,106 +1,106 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef KSPACE_CLASS
KSpaceStyle(pppm,PPPM)
#else
#ifndef LMP_PPPM_H
#define LMP_PPPM_H
-#include "kspace.h"
#include "lmptype.h"
+#include "kspace.h"
namespace LAMMPS_NS {
class PPPM : public KSpace {
public:
PPPM(class LAMMPS *, int, char **);
~PPPM();
void init();
void setup();
void compute(int, int);
void timing(int, double &, double &);
double memory_usage();
protected:
int me,nprocs;
double PI;
double precision;
int nfactors;
int *factors;
double qsum,qsqsum;
double qqrd2e;
double cutoff;
double volume;
double delxinv,delyinv,delzinv,delvolinv;
double shift,shiftone;
int nxlo_in,nylo_in,nzlo_in,nxhi_in,nyhi_in,nzhi_in;
int nxlo_out,nylo_out,nzlo_out,nxhi_out,nyhi_out,nzhi_out;
int nxlo_ghost,nxhi_ghost,nylo_ghost,nyhi_ghost,nzlo_ghost,nzhi_ghost;
int nxlo_fft,nylo_fft,nzlo_fft,nxhi_fft,nyhi_fft,nzhi_fft;
int nlower,nupper;
int ngrid,nfft,nbuf,nfft_both;
double ***density_brick;
double ***vdx_brick,***vdy_brick,***vdz_brick;
double *greensfn;
double **vg;
double *fkx,*fky,*fkz;
double *density_fft;
double *work1,*work2;
double *buf1,*buf2;
double *gf_b;
double **rho1d,**rho_coeff;
class FFT3d *fft1,*fft2;
class Remap *remap;
int **part2grid; // storage for particle -> grid mapping
int nmax;
int triclinic; // domain settings, orthog or triclinic
double *boxlo;
// TIP4P settings
int typeH,typeO; // atom types of TIP4P water H and O atoms
double qdist; // distance from O site to negative charge
double alpha; // geometric factor
void set_grid();
void allocate();
void deallocate();
int factorable(int);
double rms(double, double, bigint, double, double **);
double diffpr(double, double, double, double, double **);
void compute_gf_denom();
double gf_denom(double, double, double);
virtual void particle_map();
virtual void make_rho();
void brick2fft();
void fillbrick();
void poisson(int, int);
virtual void fieldforce();
void procs2grid2d(int,int,int,int *, int*);
void compute_rho1d(double, double, double);
void compute_rho_coeff();
void slabcorr(int);
};
}
#endif
#endif
diff --git a/src/MANYBODY/fix_qeq_comb.cpp b/src/MANYBODY/fix_qeq_comb.cpp
index b734c5a1c..3552519ff 100644
--- a/src/MANYBODY/fix_qeq_comb.cpp
+++ b/src/MANYBODY/fix_qeq_comb.cpp
@@ -1,255 +1,255 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Tzu-Ray Shan (U Florida, rayshan@ufl.edu)
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "mpi.h"
#include "math.h"
#include "stdlib.h"
#include "string.h"
#include "fix_qeq_comb.h"
-#include "lmptype.h"
#include "atom.h"
#include "force.h"
#include "group.h"
#include "respa.h"
#include "pair_comb.h"
#include "update.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MIN(A,B) ((A) < (B)) ? (A) : (B)
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
/* ---------------------------------------------------------------------- */
FixQEQComb::FixQEQComb(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
{
if (narg < 5) error->all("Illegal fix qeq/comb command");
peratom_flag = 1;
size_peratom_cols = 0;
peratom_freq = 1;
nevery = force->inumeric(arg[3]);
precision = force->numeric(arg[4]);
if (nevery <= 0 || precision <= 0.0)
error->all("Illegal fix qeq/comb command");
MPI_Comm_rank(world,&me);
// optional args
fp = NULL;
int iarg = 5;
while (iarg < narg) {
if (strcmp(arg[iarg],"file") == 0) {
if (iarg+2 > narg) error->all("Illegal fix qeq/comb command");
if (me == 0) {
fp = fopen(arg[iarg+1],"w");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open fix qeq/comb file %s",arg[iarg+1]);
error->one(str);
}
}
iarg += 2;
} else error->all("Illegal fix qeq/comb command");
}
nmax = atom->nmax;
qf = (double *) memory->smalloc(nmax*sizeof(double),"qeq:qf");
q1 = (double *) memory->smalloc(nmax*sizeof(double),"qeq:q1");
q2 = (double *) memory->smalloc(nmax*sizeof(double),"qeq:q2");
vector_atom = qf;
// zero the vector since dump may access it on timestep 0
// zero the vector since a variable may access it before first run
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) qf[i] = 0.0;
}
/* ---------------------------------------------------------------------- */
FixQEQComb::~FixQEQComb()
{
if (me == 0 && fp) fclose(fp);
memory->sfree(qf);
memory->sfree(q1);
memory->sfree(q2);
}
/* ---------------------------------------------------------------------- */
int FixQEQComb::setmask()
{
int mask = 0;
mask |= POST_FORCE;
mask |= POST_FORCE_RESPA;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixQEQComb::init()
{
if (!atom->q_flag)
error->all("Fix qeq/comb requires atom attribute q");
comb = (PairComb *) force->pair_match("comb",1);
if (comb == NULL) error->all("Must use pair_style comb with fix qeq/comb");
if (strcmp(update->integrate_style,"respa") == 0)
nlevels_respa = ((Respa *) update->integrate)->nlevels;
ngroup = group->count(igroup);
if (ngroup == 0) error->all("Fix qeq/comb group has no atoms");
}
/* ---------------------------------------------------------------------- */
void FixQEQComb::setup(int vflag)
{
firstflag = 1;
if (strcmp(update->integrate_style,"verlet") == 0)
post_force(vflag);
else {
((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
post_force_respa(vflag,nlevels_respa-1,0);
((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
}
firstflag = 0;
}
/* ---------------------------------------------------------------------- */
void FixQEQComb::post_force(int vflag)
{
int i,iloop,loopmax;
double heatpq,qmass,dtq,dtq2;
double enegchkall,enegmaxall;
if (update->ntimestep % nevery) return;
// reallocate work arrays if necessary
// qf = charge force
// q1 = charge displacement
// q2 = tmp storage of charge force for next iteration
if (atom->nmax > nmax) {
memory->sfree(qf);
memory->sfree(q1);
memory->sfree(q2);
nmax = atom->nmax;
qf = (double *) memory->smalloc(nmax*sizeof(double),"qeq:qf");
q1 = (double *) memory->smalloc(nmax*sizeof(double),"qeq:q1");
q2 = (double *) memory->smalloc(nmax*sizeof(double),"qeq:q2");
vector_atom = qf;
}
// more loops for first-time charge equilibrium
iloop = 0;
if (firstflag) loopmax = 5000;
else loopmax = 2000;
// charge-equilibration loop
if (me == 0 && fp)
fprintf(fp,"Charge equilibration on step " BIGINT_FORMAT "\n",
update->ntimestep);
heatpq = 0.05;
qmass = 0.000548580;
dtq = 0.0006;
dtq2 = 0.5*dtq*dtq/qmass;
double enegchk = 0.0;
double enegtot = 0.0;
double enegmax = 0.0;
double *q = atom->q;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++)
q1[i] = q2[i] = qf[i] = 0.0;
for (iloop = 0; iloop < loopmax; iloop ++ ) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
q1[i] += qf[i]*dtq2 - heatpq*q1[i];
q[i] += q1[i];
}
enegtot = comb->yasu_char(qf,igroup);
enegtot /= ngroup;
enegchk = enegmax = 0.0;
for (i = 0; i < nlocal ; i++)
if (mask[i] & groupbit) {
q2[i] = enegtot-qf[i];
enegmax = MAX(enegmax,fabs(q2[i]));
enegchk += fabs(q2[i]);
qf[i] = q2[i];
}
MPI_Allreduce(&enegchk,&enegchkall,1,MPI_DOUBLE,MPI_SUM,world);
enegchk = enegchkall/ngroup;
MPI_Allreduce(&enegmax,&enegmaxall,1,MPI_DOUBLE,MPI_MAX,world);
enegmax = enegmaxall;
if (enegchk <= precision && enegmax <= 100.0*precision) break;
if (me == 0 && fp)
fprintf(fp," iteration: %d, enegtot %.6g, "
"enegmax %.6g, fq deviation: %.6g\n",
iloop,enegtot,enegmax,enegchk);
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
q1[i] += qf[i]*dtq2 - heatpq*q1[i];
}
if (me == 0 && fp) {
if (iloop == loopmax)
fprintf(fp,"Charges did not converge in %d iterations\n",iloop);
else
fprintf(fp,"Charges converged in %d iterations to %.10f tolerance\n",
iloop,enegchk);
}
}
/* ---------------------------------------------------------------------- */
void FixQEQComb::post_force_respa(int vflag, int ilevel, int iloop)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double FixQEQComb::memory_usage()
{
double bytes = atom->nmax*3 * sizeof(double);
return bytes;
}
diff --git a/src/MANYBODY/fix_qeq_comb.h b/src/MANYBODY/fix_qeq_comb.h
index 235b4c9c3..be3d6b227 100644
--- a/src/MANYBODY/fix_qeq_comb.h
+++ b/src/MANYBODY/fix_qeq_comb.h
@@ -1,55 +1,55 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
FixStyle(qeq/comb,FixQEQComb)
#else
#ifndef LMP_FIX_QEQ_COMB_H
#define LMP_FIX_QEQ_COMB_H
+#include "lmptype.h"
#include "stdio.h"
#include "fix.h"
-#include "lmptype.h"
namespace LAMMPS_NS {
class FixQEQComb : public Fix {
public:
FixQEQComb(class LAMMPS *, int, char **);
~FixQEQComb();
int setmask();
void init();
void setup(int);
void post_force(int);
void post_force_respa(int,int,int);
double memory_usage();
private:
int me,firstflag;
double precision;
int nlevels_respa;
bigint ngroup;
FILE *fp;
class PairComb *comb;
int nmax;
double *qf,*q1,*q2;
};
}
#endif
#endif
diff --git a/src/MOLECULE/atom_vec_angle.cpp b/src/MOLECULE/atom_vec_angle.cpp
index 33390ee34..13688b002 100644
--- a/src/MOLECULE/atom_vec_angle.cpp
+++ b/src/MOLECULE/atom_vec_angle.cpp
@@ -1,814 +1,814 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "stdlib.h"
#include "atom_vec_angle.h"
-#include "lmptype.h"
#include "atom.h"
#include "domain.h"
#include "modify.h"
#include "fix.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MIN(A,B) ((A) < (B)) ? (A) : (B)
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
#define DELTA 10000
/* ---------------------------------------------------------------------- */
AtomVecAngle::AtomVecAngle(LAMMPS *lmp, int narg, char **arg) :
AtomVec(lmp, narg, arg)
{
molecular = 1;
bonds_allow = angles_allow = 1;
mass_type = 1;
comm_x_only = comm_f_only = 1;
size_forward = 3;
size_reverse = 3;
size_border = 7;
size_velocity = 3;
size_data_atom = 6;
size_data_vel = 4;
xcol_data = 4;
atom->molecule_flag = 1;
}
/* ----------------------------------------------------------------------
grow atom arrays
n = 0 grows arrays by DELTA
n > 0 allocates arrays to size n
------------------------------------------------------------------------- */
void AtomVecAngle::grow(int n)
{
if (n == 0) nmax += DELTA;
else nmax = n;
atom->nmax = nmax;
if (nmax < 0 || nmax > MAXSMALLINT)
error->one("Per-processor system is too big");
tag = atom->tag = (int *)
memory->srealloc(atom->tag,nmax*sizeof(int),"atom:tag");
type = atom->type = (int *)
memory->srealloc(atom->type,nmax*sizeof(int),"atom:type");
mask = atom->mask = (int *)
memory->srealloc(atom->mask,nmax*sizeof(int),"atom:mask");
image = atom->image = (int *)
memory->srealloc(atom->image,nmax*sizeof(int),"atom:image");
x = atom->x = memory->grow_2d_double_array(atom->x,nmax,3,"atom:x");
v = atom->v = memory->grow_2d_double_array(atom->v,nmax,3,"atom:v");
f = atom->f = memory->grow_2d_double_array(atom->f,nmax,3,"atom:f");
molecule = atom->molecule = (int *)
memory->srealloc(atom->molecule,nmax*sizeof(int),"atom:molecule");
nspecial = atom->nspecial =
memory->grow_2d_int_array(atom->nspecial,nmax,3,"atom:nspecial");
special = atom->special =
memory->grow_2d_int_array(atom->special,nmax,atom->maxspecial,
"atom:special");
num_bond = atom->num_bond = (int *)
memory->srealloc(atom->num_bond,nmax*sizeof(int),"atom:num_bond");
bond_type = atom->bond_type =
memory->grow_2d_int_array(atom->bond_type,nmax,atom->bond_per_atom,
"atom:bond_type");
bond_atom = atom->bond_atom =
memory->grow_2d_int_array(atom->bond_atom,nmax,atom->bond_per_atom,
"atom:bond_atom");
num_angle = atom->num_angle = (int *)
memory->srealloc(atom->num_angle,nmax*sizeof(int),"atom:num_angle");
angle_type = atom->angle_type =
memory->grow_2d_int_array(atom->angle_type,nmax,atom->angle_per_atom,
"atom:angle_type");
angle_atom1 = atom->angle_atom1 =
memory->grow_2d_int_array(atom->angle_atom1,nmax,atom->angle_per_atom,
"atom:angle_atom1");
angle_atom2 = atom->angle_atom2 =
memory->grow_2d_int_array(atom->angle_atom2,nmax,atom->angle_per_atom,
"atom:angle_atom2");
angle_atom3 = atom->angle_atom3 =
memory->grow_2d_int_array(atom->angle_atom3,nmax,atom->angle_per_atom,
"atom:angle_atom3");
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
}
/* ----------------------------------------------------------------------
reset local array ptrs
------------------------------------------------------------------------- */
void AtomVecAngle::grow_reset()
{
tag = atom->tag; type = atom->type;
mask = atom->mask; image = atom->image;
x = atom->x; v = atom->v; f = atom->f;
molecule = atom->molecule;
nspecial = atom->nspecial; special = atom->special;
num_bond = atom->num_bond; bond_type = atom->bond_type;
bond_atom = atom->bond_atom;
num_angle = atom->num_angle; angle_type = atom->angle_type;
angle_atom1 = atom->angle_atom1; angle_atom2 = atom->angle_atom2;
angle_atom3 = atom->angle_atom3;
}
/* ---------------------------------------------------------------------- */
void AtomVecAngle::copy(int i, int j)
{
int k;
tag[j] = tag[i];
type[j] = type[i];
mask[j] = mask[i];
image[j] = image[i];
x[j][0] = x[i][0];
x[j][1] = x[i][1];
x[j][2] = x[i][2];
v[j][0] = v[i][0];
v[j][1] = v[i][1];
v[j][2] = v[i][2];
molecule[j] = molecule[i];
num_bond[j] = num_bond[i];
for (k = 0; k < num_bond[j]; k++) {
bond_type[j][k] = bond_type[i][k];
bond_atom[j][k] = bond_atom[i][k];
}
num_angle[j] = num_angle[i];
for (k = 0; k < num_angle[j]; k++) {
angle_type[j][k] = angle_type[i][k];
angle_atom1[j][k] = angle_atom1[i][k];
angle_atom2[j][k] = angle_atom2[i][k];
angle_atom3[j][k] = angle_atom3[i][k];
}
nspecial[j][0] = nspecial[i][0];
nspecial[j][1] = nspecial[i][1];
nspecial[j][2] = nspecial[i][2];
for (k = 0; k < nspecial[j][2]; k++) special[j][k] = special[i][k];
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j);
}
/* ---------------------------------------------------------------------- */
int AtomVecAngle::pack_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
dz = pbc[2]*domain->zprd;
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecAngle::pack_comm_vel(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
dz = pbc[2]*domain->zprd;
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecAngle::unpack_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
void AtomVecAngle::unpack_comm_vel(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecAngle::pack_reverse(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
buf[m++] = f[i][0];
buf[m++] = f[i][1];
buf[m++] = f[i][2];
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecAngle::unpack_reverse(int n, int *list, double *buf)
{
int i,j,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
f[j][0] += buf[m++];
f[j][1] += buf[m++];
f[j][2] += buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecAngle::pack_border(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = molecule[j];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0];
dy = pbc[1];
dz = pbc[2];
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = molecule[j];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecAngle::pack_border_vel(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = molecule[j];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0];
dy = pbc[1];
dz = pbc[2];
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = molecule[j];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecAngle::pack_border_one(int i, double *buf)
{
buf[0] = molecule[i];
return 1;
}
/* ---------------------------------------------------------------------- */
void AtomVecAngle::unpack_border(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
if (i == nmax) grow(0);
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
tag[i] = static_cast<int> (buf[m++]);
type[i] = static_cast<int> (buf[m++]);
mask[i] = static_cast<int> (buf[m++]);
molecule[i] = static_cast<int> (buf[m++]);
}
}
/* ---------------------------------------------------------------------- */
void AtomVecAngle::unpack_border_vel(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
if (i == nmax) grow(0);
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
tag[i] = static_cast<int> (buf[m++]);
type[i] = static_cast<int> (buf[m++]);
mask[i] = static_cast<int> (buf[m++]);
molecule[i] = static_cast<int> (buf[m++]);
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecAngle::unpack_border_one(int i, double *buf)
{
molecule[i] = static_cast<int> (buf[0]);
return 1;
}
/* ----------------------------------------------------------------------
pack data for atom I for sending to another proc
xyz must be 1st 3 values, so comm::exchange() can test on them
------------------------------------------------------------------------- */
int AtomVecAngle::pack_exchange(int i, double *buf)
{
int k;
int m = 1;
buf[m++] = x[i][0];
buf[m++] = x[i][1];
buf[m++] = x[i][2];
buf[m++] = v[i][0];
buf[m++] = v[i][1];
buf[m++] = v[i][2];
buf[m++] = tag[i];
buf[m++] = type[i];
buf[m++] = mask[i];
buf[m++] = image[i];
buf[m++] = molecule[i];
buf[m++] = num_bond[i];
for (k = 0; k < num_bond[i]; k++) {
buf[m++] = bond_type[i][k];
buf[m++] = bond_atom[i][k];
}
buf[m++] = num_angle[i];
for (k = 0; k < num_angle[i]; k++) {
buf[m++] = angle_type[i][k];
buf[m++] = angle_atom1[i][k];
buf[m++] = angle_atom2[i][k];
buf[m++] = angle_atom3[i][k];
}
buf[m++] = nspecial[i][0];
buf[m++] = nspecial[i][1];
buf[m++] = nspecial[i][2];
for (k = 0; k < nspecial[i][2]; k++) buf[m++] = special[i][k];
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]);
buf[0] = m;
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecAngle::unpack_exchange(double *buf)
{
int k;
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
int m = 1;
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
x[nlocal][2] = buf[m++];
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
tag[nlocal] = static_cast<int> (buf[m++]);
type[nlocal] = static_cast<int> (buf[m++]);
mask[nlocal] = static_cast<int> (buf[m++]);
image[nlocal] = static_cast<int> (buf[m++]);
molecule[nlocal] = static_cast<int> (buf[m++]);
num_bond[nlocal] = static_cast<int> (buf[m++]);
for (k = 0; k < num_bond[nlocal]; k++) {
bond_type[nlocal][k] = static_cast<int> (buf[m++]);
bond_atom[nlocal][k] = static_cast<int> (buf[m++]);
}
num_angle[nlocal] = static_cast<int> (buf[m++]);
for (k = 0; k < num_angle[nlocal]; k++) {
angle_type[nlocal][k] = static_cast<int> (buf[m++]);
angle_atom1[nlocal][k] = static_cast<int> (buf[m++]);
angle_atom2[nlocal][k] = static_cast<int> (buf[m++]);
angle_atom3[nlocal][k] = static_cast<int> (buf[m++]);
}
nspecial[nlocal][0] = static_cast<int> (buf[m++]);
nspecial[nlocal][1] = static_cast<int> (buf[m++]);
nspecial[nlocal][2] = static_cast<int> (buf[m++]);
for (k = 0; k < nspecial[nlocal][2]; k++)
special[nlocal][k] = static_cast<int> (buf[m++]);
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->
unpack_exchange(nlocal,&buf[m]);
atom->nlocal++;
return m;
}
/* ----------------------------------------------------------------------
size of restart data for all atoms owned by this proc
include extra data stored by fixes
------------------------------------------------------------------------- */
int AtomVecAngle::size_restart()
{
int i;
int nlocal = atom->nlocal;
int n = 0;
for (i = 0; i < nlocal; i++)
n += 14 + 2*num_bond[i] + 4*num_angle[i];
if (atom->nextra_restart)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
for (i = 0; i < nlocal; i++)
n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
return n;
}
/* ----------------------------------------------------------------------
pack atom I's data for restart file including extra quantities
xyz must be 1st 3 values, so that read_restart can test on them
molecular types may be negative, but write as positive
------------------------------------------------------------------------- */
int AtomVecAngle::pack_restart(int i, double *buf)
{
int k;
int m = 1;
buf[m++] = x[i][0];
buf[m++] = x[i][1];
buf[m++] = x[i][2];
buf[m++] = tag[i];
buf[m++] = type[i];
buf[m++] = mask[i];
buf[m++] = image[i];
buf[m++] = v[i][0];
buf[m++] = v[i][1];
buf[m++] = v[i][2];
buf[m++] = molecule[i];
buf[m++] = num_bond[i];
for (k = 0; k < num_bond[i]; k++) {
buf[m++] = MAX(bond_type[i][k],-bond_type[i][k]);
buf[m++] = bond_atom[i][k];
}
buf[m++] = num_angle[i];
for (k = 0; k < num_angle[i]; k++) {
buf[m++] = MAX(angle_type[i][k],-angle_type[i][k]);
buf[m++] = angle_atom1[i][k];
buf[m++] = angle_atom2[i][k];
buf[m++] = angle_atom3[i][k];
}
if (atom->nextra_restart)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]);
buf[0] = m;
return m;
}
/* ----------------------------------------------------------------------
unpack data for one atom from restart file including extra quantities
------------------------------------------------------------------------- */
int AtomVecAngle::unpack_restart(double *buf)
{
int k;
int nlocal = atom->nlocal;
if (nlocal == nmax) {
grow(0);
if (atom->nextra_store)
atom->extra = memory->grow_2d_double_array(atom->extra,nmax,
atom->nextra_store,
"atom:extra");
}
int m = 1;
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
x[nlocal][2] = buf[m++];
tag[nlocal] = static_cast<int> (buf[m++]);
type[nlocal] = static_cast<int> (buf[m++]);
mask[nlocal] = static_cast<int> (buf[m++]);
image[nlocal] = static_cast<int> (buf[m++]);
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
molecule[nlocal] = static_cast<int> (buf[m++]);
num_bond[nlocal] = static_cast<int> (buf[m++]);
for (k = 0; k < num_bond[nlocal]; k++) {
bond_type[nlocal][k] = static_cast<int> (buf[m++]);
bond_atom[nlocal][k] = static_cast<int> (buf[m++]);
}
num_angle[nlocal] = static_cast<int> (buf[m++]);
for (k = 0; k < num_angle[nlocal]; k++) {
angle_type[nlocal][k] = static_cast<int> (buf[m++]);
angle_atom1[nlocal][k] = static_cast<int> (buf[m++]);
angle_atom2[nlocal][k] = static_cast<int> (buf[m++]);
angle_atom3[nlocal][k] = static_cast<int> (buf[m++]);
}
double **extra = atom->extra;
if (atom->nextra_store) {
int size = static_cast<int> (buf[0]) - m;
for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++];
}
atom->nlocal++;
return m;
}
/* ----------------------------------------------------------------------
create one atom of itype at coord
set other values to defaults
------------------------------------------------------------------------- */
void AtomVecAngle::create_atom(int itype, double *coord)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
tag[nlocal] = 0;
type[nlocal] = itype;
x[nlocal][0] = coord[0];
x[nlocal][1] = coord[1];
x[nlocal][2] = coord[2];
mask[nlocal] = 1;
image[nlocal] = (512 << 20) | (512 << 10) | 512;
v[nlocal][0] = 0.0;
v[nlocal][1] = 0.0;
v[nlocal][2] = 0.0;
molecule[nlocal] = 0;
num_bond[nlocal] = 0;
num_angle[nlocal] = 0;
nspecial[nlocal][0] = nspecial[nlocal][1] = nspecial[nlocal][2] = 0;
atom->nlocal++;
}
/* ----------------------------------------------------------------------
unpack one line from Atoms section of data file
initialize other atom quantities
------------------------------------------------------------------------- */
void AtomVecAngle::data_atom(double *coord, int imagetmp, char **values)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
tag[nlocal] = atoi(values[0]);
if (tag[nlocal] <= 0)
error->one("Invalid atom ID in Atoms section of data file");
molecule[nlocal] = atoi(values[1]);
type[nlocal] = atoi(values[2]);
if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
error->one("Invalid atom type in Atoms section of data file");
x[nlocal][0] = coord[0];
x[nlocal][1] = coord[1];
x[nlocal][2] = coord[2];
image[nlocal] = imagetmp;
mask[nlocal] = 1;
v[nlocal][0] = 0.0;
v[nlocal][1] = 0.0;
v[nlocal][2] = 0.0;
num_bond[nlocal] = 0;
num_angle[nlocal] = 0;
atom->nlocal++;
}
/* ----------------------------------------------------------------------
unpack hybrid quantities from one line in Atoms section of data file
initialize other atom quantities for this sub-style
------------------------------------------------------------------------- */
int AtomVecAngle::data_atom_hybrid(int nlocal, char **values)
{
molecule[nlocal] = atoi(values[0]);
num_bond[nlocal] = 0;
num_angle[nlocal] = 0;
return 1;
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
------------------------------------------------------------------------- */
double AtomVecAngle::memory_usage()
{
double bytes = 0.0;
if (atom->memcheck("tag")) bytes += nmax * sizeof(int);
if (atom->memcheck("type")) bytes += nmax * sizeof(int);
if (atom->memcheck("mask")) bytes += nmax * sizeof(int);
if (atom->memcheck("image")) bytes += nmax * sizeof(int);
if (atom->memcheck("x")) bytes += nmax*3 * sizeof(double);
if (atom->memcheck("v")) bytes += nmax*3 * sizeof(double);
if (atom->memcheck("f")) bytes += nmax*3 * sizeof(double);
if (atom->memcheck("molecule")) bytes += nmax * sizeof(int);
if (atom->memcheck("nspecial")) bytes += nmax*3 * sizeof(int);
if (atom->memcheck("special")) bytes += nmax*atom->maxspecial * sizeof(int);
if (atom->memcheck("num_bond")) bytes += nmax * sizeof(int);
if (atom->memcheck("bond_type"))
bytes += nmax*atom->bond_per_atom * sizeof(int);
if (atom->memcheck("bond_atom"))
bytes += nmax*atom->bond_per_atom * sizeof(int);
if (atom->memcheck("num_angle")) bytes += nmax * sizeof(int);
if (atom->memcheck("angle_type"))
bytes += nmax*atom->angle_per_atom * sizeof(int);
if (atom->memcheck("angle_atom1"))
bytes += nmax*atom->angle_per_atom * sizeof(int);
if (atom->memcheck("angle_atom2"))
bytes += nmax*atom->angle_per_atom * sizeof(int);
if (atom->memcheck("angle_atom3"))
bytes += nmax*atom->angle_per_atom * sizeof(int);
return bytes;
}
diff --git a/src/MOLECULE/atom_vec_bond.cpp b/src/MOLECULE/atom_vec_bond.cpp
index 13ea1e5e2..bda7cb97c 100644
--- a/src/MOLECULE/atom_vec_bond.cpp
+++ b/src/MOLECULE/atom_vec_bond.cpp
@@ -1,743 +1,743 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "stdlib.h"
#include "atom_vec_bond.h"
-#include "lmptype.h"
#include "atom.h"
#include "domain.h"
#include "modify.h"
#include "fix.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MIN(A,B) ((A) < (B)) ? (A) : (B)
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
#define DELTA 10000
/* ---------------------------------------------------------------------- */
AtomVecBond::AtomVecBond(LAMMPS *lmp, int narg, char **arg) :
AtomVec(lmp, narg, arg)
{
molecular = 1;
bonds_allow = 1;
mass_type = 1;
comm_x_only = comm_f_only = 1;
size_forward = 3;
size_reverse = 3;
size_border = 7;
size_velocity = 3;
size_data_atom = 6;
size_data_vel = 4;
xcol_data = 4;
atom->molecule_flag = 1;
}
/* ----------------------------------------------------------------------
grow atom arrays
n = 0 grows arrays by DELTA
n > 0 allocates arrays to size n
------------------------------------------------------------------------- */
void AtomVecBond::grow(int n)
{
if (n == 0) nmax += DELTA;
else nmax = n;
atom->nmax = nmax;
if (nmax < 0 || nmax > MAXSMALLINT)
error->one("Per-processor system is too big");
tag = atom->tag = (int *)
memory->srealloc(atom->tag,nmax*sizeof(int),"atom:tag");
type = atom->type = (int *)
memory->srealloc(atom->type,nmax*sizeof(int),"atom:type");
mask = atom->mask = (int *)
memory->srealloc(atom->mask,nmax*sizeof(int),"atom:mask");
image = atom->image = (int *)
memory->srealloc(atom->image,nmax*sizeof(int),"atom:image");
x = atom->x = memory->grow_2d_double_array(atom->x,nmax,3,"atom:x");
v = atom->v = memory->grow_2d_double_array(atom->v,nmax,3,"atom:v");
f = atom->f = memory->grow_2d_double_array(atom->f,nmax,3,"atom:f");
molecule = atom->molecule = (int *)
memory->srealloc(atom->molecule,nmax*sizeof(int),"atom:molecule");
nspecial = atom->nspecial =
memory->grow_2d_int_array(atom->nspecial,nmax,3,"atom:nspecial");
special = atom->special =
memory->grow_2d_int_array(atom->special,nmax,atom->maxspecial,
"atom:special");
num_bond = atom->num_bond = (int *)
memory->srealloc(atom->num_bond,nmax*sizeof(int),"atom:num_bond");
bond_type = atom->bond_type =
memory->grow_2d_int_array(atom->bond_type,nmax,atom->bond_per_atom,
"atom:bond_type");
bond_atom = atom->bond_atom =
memory->grow_2d_int_array(atom->bond_atom,nmax,atom->bond_per_atom,
"atom:bond_atom");
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
}
/* ----------------------------------------------------------------------
reset local array ptrs
------------------------------------------------------------------------- */
void AtomVecBond::grow_reset()
{
tag = atom->tag; type = atom->type;
mask = atom->mask; image = atom->image;
x = atom->x; v = atom->v; f = atom->f;
molecule = atom->molecule;
nspecial = atom->nspecial; special = atom->special;
num_bond = atom->num_bond; bond_type = atom->bond_type;
bond_atom = atom->bond_atom;
}
/* ---------------------------------------------------------------------- */
void AtomVecBond::copy(int i, int j)
{
int k;
tag[j] = tag[i];
type[j] = type[i];
mask[j] = mask[i];
image[j] = image[i];
x[j][0] = x[i][0];
x[j][1] = x[i][1];
x[j][2] = x[i][2];
v[j][0] = v[i][0];
v[j][1] = v[i][1];
v[j][2] = v[i][2];
molecule[j] = molecule[i];
num_bond[j] = num_bond[i];
for (k = 0; k < num_bond[j]; k++) {
bond_type[j][k] = bond_type[i][k];
bond_atom[j][k] = bond_atom[i][k];
}
nspecial[j][0] = nspecial[i][0];
nspecial[j][1] = nspecial[i][1];
nspecial[j][2] = nspecial[i][2];
for (k = 0; k < nspecial[j][2]; k++) special[j][k] = special[i][k];
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j);
}
/* ---------------------------------------------------------------------- */
int AtomVecBond::pack_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
dz = pbc[2]*domain->zprd;
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecBond::pack_comm_vel(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
dz = pbc[2]*domain->zprd;
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecBond::unpack_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
void AtomVecBond::unpack_comm_vel(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecBond::pack_reverse(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
buf[m++] = f[i][0];
buf[m++] = f[i][1];
buf[m++] = f[i][2];
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecBond::unpack_reverse(int n, int *list, double *buf)
{
int i,j,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
f[j][0] += buf[m++];
f[j][1] += buf[m++];
f[j][2] += buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecBond::pack_border(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = molecule[j];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0];
dy = pbc[1];
dz = pbc[2];
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = molecule[j];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecBond::pack_border_vel(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = molecule[j];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0];
dy = pbc[1];
dz = pbc[2];
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = molecule[j];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecBond::pack_border_one(int i, double *buf)
{
buf[0] = molecule[i];
return 1;
}
/* ---------------------------------------------------------------------- */
void AtomVecBond::unpack_border(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
if (i == nmax) grow(0);
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
tag[i] = static_cast<int> (buf[m++]);
type[i] = static_cast<int> (buf[m++]);
mask[i] = static_cast<int> (buf[m++]);
molecule[i] = static_cast<int> (buf[m++]);
}
}
/* ---------------------------------------------------------------------- */
void AtomVecBond::unpack_border_vel(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
if (i == nmax) grow(0);
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
tag[i] = static_cast<int> (buf[m++]);
type[i] = static_cast<int> (buf[m++]);
mask[i] = static_cast<int> (buf[m++]);
molecule[i] = static_cast<int> (buf[m++]);
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecBond::unpack_border_one(int i, double *buf)
{
molecule[i] = static_cast<int> (buf[0]);
return 1;
}
/* ----------------------------------------------------------------------
pack data for atom I for sending to another proc
xyz must be 1st 3 values, so comm::exchange() can test on them
------------------------------------------------------------------------- */
int AtomVecBond::pack_exchange(int i, double *buf)
{
int k;
int m = 1;
buf[m++] = x[i][0];
buf[m++] = x[i][1];
buf[m++] = x[i][2];
buf[m++] = v[i][0];
buf[m++] = v[i][1];
buf[m++] = v[i][2];
buf[m++] = tag[i];
buf[m++] = type[i];
buf[m++] = mask[i];
buf[m++] = image[i];
buf[m++] = molecule[i];
buf[m++] = num_bond[i];
for (k = 0; k < num_bond[i]; k++) {
buf[m++] = bond_type[i][k];
buf[m++] = bond_atom[i][k];
}
buf[m++] = nspecial[i][0];
buf[m++] = nspecial[i][1];
buf[m++] = nspecial[i][2];
for (k = 0; k < nspecial[i][2]; k++) buf[m++] = special[i][k];
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]);
buf[0] = m;
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecBond::unpack_exchange(double *buf)
{
int k;
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
int m = 1;
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
x[nlocal][2] = buf[m++];
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
tag[nlocal] = static_cast<int> (buf[m++]);
type[nlocal] = static_cast<int> (buf[m++]);
mask[nlocal] = static_cast<int> (buf[m++]);
image[nlocal] = static_cast<int> (buf[m++]);
molecule[nlocal] = static_cast<int> (buf[m++]);
num_bond[nlocal] = static_cast<int> (buf[m++]);
for (k = 0; k < num_bond[nlocal]; k++) {
bond_type[nlocal][k] = static_cast<int> (buf[m++]);
bond_atom[nlocal][k] = static_cast<int> (buf[m++]);
}
nspecial[nlocal][0] = static_cast<int> (buf[m++]);
nspecial[nlocal][1] = static_cast<int> (buf[m++]);
nspecial[nlocal][2] = static_cast<int> (buf[m++]);
for (k = 0; k < nspecial[nlocal][2]; k++)
special[nlocal][k] = static_cast<int> (buf[m++]);
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->
unpack_exchange(nlocal,&buf[m]);
atom->nlocal++;
return m;
}
/* ----------------------------------------------------------------------
size of restart data for all atoms owned by this proc
include extra data stored by fixes
------------------------------------------------------------------------- */
int AtomVecBond::size_restart()
{
int i;
int nlocal = atom->nlocal;
int n = 0;
for (i = 0; i < nlocal; i++)
n += 13 + 2*num_bond[i];
if (atom->nextra_restart)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
for (i = 0; i < nlocal; i++)
n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
return n;
}
/* ----------------------------------------------------------------------
pack atom I's data for restart file including extra quantities
xyz must be 1st 3 values, so that read_restart can test on them
molecular types may be negative, but write as positive
------------------------------------------------------------------------- */
int AtomVecBond::pack_restart(int i, double *buf)
{
int k;
int m = 1;
buf[m++] = x[i][0];
buf[m++] = x[i][1];
buf[m++] = x[i][2];
buf[m++] = tag[i];
buf[m++] = type[i];
buf[m++] = mask[i];
buf[m++] = image[i];
buf[m++] = v[i][0];
buf[m++] = v[i][1];
buf[m++] = v[i][2];
buf[m++] = molecule[i];
buf[m++] = num_bond[i];
for (k = 0; k < num_bond[i]; k++) {
buf[m++] = MAX(bond_type[i][k],-bond_type[i][k]);
buf[m++] = bond_atom[i][k];
}
if (atom->nextra_restart)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]);
buf[0] = m;
return m;
}
/* ----------------------------------------------------------------------
unpack data for one atom from restart file including extra quantities
------------------------------------------------------------------------- */
int AtomVecBond::unpack_restart(double *buf)
{
int k;
int nlocal = atom->nlocal;
if (nlocal == nmax) {
grow(0);
if (atom->nextra_store)
atom->extra = memory->grow_2d_double_array(atom->extra,nmax,
atom->nextra_store,
"atom:extra");
}
int m = 1;
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
x[nlocal][2] = buf[m++];
tag[nlocal] = static_cast<int> (buf[m++]);
type[nlocal] = static_cast<int> (buf[m++]);
mask[nlocal] = static_cast<int> (buf[m++]);
image[nlocal] = static_cast<int> (buf[m++]);
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
molecule[nlocal] = static_cast<int> (buf[m++]);
num_bond[nlocal] = static_cast<int> (buf[m++]);
for (k = 0; k < num_bond[nlocal]; k++) {
bond_type[nlocal][k] = static_cast<int> (buf[m++]);
bond_atom[nlocal][k] = static_cast<int> (buf[m++]);
}
double **extra = atom->extra;
if (atom->nextra_store) {
int size = static_cast<int> (buf[0]) - m;
for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++];
}
atom->nlocal++;
return m;
}
/* ----------------------------------------------------------------------
create one atom of itype at coord
set other values to defaults
------------------------------------------------------------------------- */
void AtomVecBond::create_atom(int itype, double *coord)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
tag[nlocal] = 0;
type[nlocal] = itype;
x[nlocal][0] = coord[0];
x[nlocal][1] = coord[1];
x[nlocal][2] = coord[2];
mask[nlocal] = 1;
image[nlocal] = (512 << 20) | (512 << 10) | 512;
v[nlocal][0] = 0.0;
v[nlocal][1] = 0.0;
v[nlocal][2] = 0.0;
molecule[nlocal] = 0;
num_bond[nlocal] = 0;
nspecial[nlocal][0] = nspecial[nlocal][1] = nspecial[nlocal][2] = 0;
atom->nlocal++;
}
/* ----------------------------------------------------------------------
unpack one line from Atoms section of data file
initialize other atom quantities
------------------------------------------------------------------------- */
void AtomVecBond::data_atom(double *coord, int imagetmp, char **values)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
tag[nlocal] = atoi(values[0]);
if (tag[nlocal] <= 0)
error->one("Invalid atom ID in Atoms section of data file");
molecule[nlocal] = atoi(values[1]);
type[nlocal] = atoi(values[2]);
if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
error->one("Invalid atom type in Atoms section of data file");
x[nlocal][0] = coord[0];
x[nlocal][1] = coord[1];
x[nlocal][2] = coord[2];
image[nlocal] = imagetmp;
mask[nlocal] = 1;
v[nlocal][0] = 0.0;
v[nlocal][1] = 0.0;
v[nlocal][2] = 0.0;
num_bond[nlocal] = 0;
atom->nlocal++;
}
/* ----------------------------------------------------------------------
unpack hybrid quantities from one line in Atoms section of data file
initialize other atom quantities for this sub-style
------------------------------------------------------------------------- */
int AtomVecBond::data_atom_hybrid(int nlocal, char **values)
{
molecule[nlocal] = atoi(values[0]);
num_bond[nlocal] = 0;
return 1;
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
------------------------------------------------------------------------- */
double AtomVecBond::memory_usage()
{
double bytes = 0.0;
if (atom->memcheck("tag")) bytes += nmax * sizeof(int);
if (atom->memcheck("type")) bytes += nmax * sizeof(int);
if (atom->memcheck("mask")) bytes += nmax * sizeof(int);
if (atom->memcheck("image")) bytes += nmax * sizeof(int);
if (atom->memcheck("x")) bytes += nmax*3 * sizeof(double);
if (atom->memcheck("v")) bytes += nmax*3 * sizeof(double);
if (atom->memcheck("f")) bytes += nmax*3 * sizeof(double);
if (atom->memcheck("molecule")) bytes += nmax * sizeof(int);
if (atom->memcheck("nspecial")) bytes += nmax*3 * sizeof(int);
if (atom->memcheck("special")) bytes += nmax*atom->maxspecial * sizeof(int);
if (atom->memcheck("num_bond")) bytes += nmax * sizeof(int);
if (atom->memcheck("bond_type"))
bytes += nmax*atom->bond_per_atom * sizeof(int);
if (atom->memcheck("bond_atom"))
bytes += nmax*atom->bond_per_atom * sizeof(int);
return bytes;
}
diff --git a/src/MOLECULE/atom_vec_full.cpp b/src/MOLECULE/atom_vec_full.cpp
index 2d733ebf4..1fe0d4fda 100644
--- a/src/MOLECULE/atom_vec_full.cpp
+++ b/src/MOLECULE/atom_vec_full.cpp
@@ -1,997 +1,997 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "stdlib.h"
#include "atom_vec_full.h"
-#include "lmptype.h"
#include "atom.h"
#include "domain.h"
#include "modify.h"
#include "fix.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MIN(A,B) ((A) < (B)) ? (A) : (B)
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
#define DELTA 10000
/* ---------------------------------------------------------------------- */
AtomVecFull::AtomVecFull(LAMMPS *lmp, int narg, char **arg) :
AtomVec(lmp, narg, arg)
{
molecular = 1;
bonds_allow = angles_allow = dihedrals_allow = impropers_allow = 1;
mass_type = 1;
comm_x_only = comm_f_only = 1;
size_forward = 3;
size_reverse = 3;
size_border = 8;
size_velocity = 3;
size_data_atom = 7;
size_data_vel = 4;
xcol_data = 5;
atom->molecule_flag = atom->q_flag = 1;
}
/* ----------------------------------------------------------------------
grow atom arrays
n = 0 grows arrays by DELTA
n > 0 allocates arrays to size n
------------------------------------------------------------------------- */
void AtomVecFull::grow(int n)
{
if (n == 0) nmax += DELTA;
else nmax = n;
atom->nmax = nmax;
if (nmax < 0 || nmax > MAXSMALLINT)
error->one("Per-processor system is too big");
tag = atom->tag = (int *)
memory->srealloc(atom->tag,nmax*sizeof(int),"atom:tag");
type = atom->type = (int *)
memory->srealloc(atom->type,nmax*sizeof(int),"atom:type");
mask = atom->mask = (int *)
memory->srealloc(atom->mask,nmax*sizeof(int),"atom:mask");
image = atom->image = (int *)
memory->srealloc(atom->image,nmax*sizeof(int),"atom:image");
x = atom->x = memory->grow_2d_double_array(atom->x,nmax,3,"atom:x");
v = atom->v = memory->grow_2d_double_array(atom->v,nmax,3,"atom:v");
f = atom->f = memory->grow_2d_double_array(atom->f,nmax,3,"atom:f");
q = atom->q = (double *)
memory->srealloc(atom->q,nmax*sizeof(double),"atom:q");
molecule = atom->molecule = (int *)
memory->srealloc(atom->molecule,nmax*sizeof(int),"atom:molecule");
nspecial = atom->nspecial =
memory->grow_2d_int_array(atom->nspecial,nmax,3,"atom:nspecial");
special = atom->special =
memory->grow_2d_int_array(atom->special,nmax,atom->maxspecial,
"atom:special");
num_bond = atom->num_bond = (int *)
memory->srealloc(atom->num_bond,nmax*sizeof(int),"atom:num_bond");
bond_type = atom->bond_type =
memory->grow_2d_int_array(atom->bond_type,nmax,atom->bond_per_atom,
"atom:bond_type");
bond_atom = atom->bond_atom =
memory->grow_2d_int_array(atom->bond_atom,nmax,atom->bond_per_atom,
"atom:bond_atom");
num_angle = atom->num_angle = (int *)
memory->srealloc(atom->num_angle,nmax*sizeof(int),"atom:num_angle");
angle_type = atom->angle_type =
memory->grow_2d_int_array(atom->angle_type,nmax,atom->angle_per_atom,
"atom:angle_type");
angle_atom1 = atom->angle_atom1 =
memory->grow_2d_int_array(atom->angle_atom1,nmax,atom->angle_per_atom,
"atom:angle_atom1");
angle_atom2 = atom->angle_atom2 =
memory->grow_2d_int_array(atom->angle_atom2,nmax,atom->angle_per_atom,
"atom:angle_atom2");
angle_atom3 = atom->angle_atom3 =
memory->grow_2d_int_array(atom->angle_atom3,nmax,atom->angle_per_atom,
"atom:angle_atom3");
num_dihedral = atom->num_dihedral = (int *)
memory->srealloc(atom->num_dihedral,nmax*sizeof(int),"atom:num_dihedral");
dihedral_type = atom->dihedral_type =
memory->grow_2d_int_array(atom->dihedral_type,nmax,atom->dihedral_per_atom,
"atom:dihedral_type");
dihedral_atom1 = atom->dihedral_atom1 =
memory->grow_2d_int_array(atom->dihedral_atom1,nmax,
atom->dihedral_per_atom,"atom:dihedral_atom1");
dihedral_atom2 = atom->dihedral_atom2 =
memory->grow_2d_int_array(atom->dihedral_atom2,nmax,
atom->dihedral_per_atom,"atom:dihedral_atom2");
dihedral_atom3 = atom->dihedral_atom3 =
memory->grow_2d_int_array(atom->dihedral_atom3,nmax,
atom->dihedral_per_atom,"atom:dihedral_atom3");
dihedral_atom4 = atom->dihedral_atom4 =
memory->grow_2d_int_array(atom->dihedral_atom4,nmax,
atom->dihedral_per_atom,"atom:dihedral_atom4");
num_improper = atom->num_improper = (int *)
memory->srealloc(atom->num_improper,nmax*sizeof(int),"atom:num_improper");
improper_type = atom->improper_type =
memory->grow_2d_int_array(atom->improper_type,nmax,atom->improper_per_atom,
"atom:improper_type");
improper_atom1 = atom->improper_atom1 =
memory->grow_2d_int_array(atom->improper_atom1,nmax,
atom->improper_per_atom,"atom:improper_atom1");
improper_atom2 = atom->improper_atom2 =
memory->grow_2d_int_array(atom->improper_atom2,nmax,
atom->improper_per_atom,"atom:improper_atom2");
improper_atom3 = atom->improper_atom3 =
memory->grow_2d_int_array(atom->improper_atom3,nmax,
atom->improper_per_atom,"atom:improper_atom3");
improper_atom4 = atom->improper_atom4 =
memory->grow_2d_int_array(atom->improper_atom4,nmax,
atom->improper_per_atom,"atom:improper_atom4");
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
}
/* ----------------------------------------------------------------------
reset local array ptrs
------------------------------------------------------------------------- */
void AtomVecFull::grow_reset()
{
tag = atom->tag; type = atom->type;
mask = atom->mask; image = atom->image;
x = atom->x; v = atom->v; f = atom->f;
q = atom->q; molecule = atom->molecule;
nspecial = atom->nspecial; special = atom->special;
num_bond = atom->num_bond; bond_type = atom->bond_type;
bond_atom = atom->bond_atom;
num_angle = atom->num_angle; angle_type = atom->angle_type;
angle_atom1 = atom->angle_atom1; angle_atom2 = atom->angle_atom2;
angle_atom3 = atom->angle_atom3;
num_dihedral = atom->num_dihedral; dihedral_type = atom->dihedral_type;
dihedral_atom1 = atom->dihedral_atom1; dihedral_atom2 = atom->dihedral_atom2;
dihedral_atom3 = atom->dihedral_atom3; dihedral_atom4 = atom->dihedral_atom4;
num_improper = atom->num_improper; improper_type = atom->improper_type;
improper_atom1 = atom->improper_atom1; improper_atom2 = atom->improper_atom2;
improper_atom3 = atom->improper_atom3; improper_atom4 = atom->improper_atom4;
}
/* ---------------------------------------------------------------------- */
void AtomVecFull::copy(int i, int j)
{
int k;
tag[j] = tag[i];
type[j] = type[i];
mask[j] = mask[i];
image[j] = image[i];
x[j][0] = x[i][0];
x[j][1] = x[i][1];
x[j][2] = x[i][2];
v[j][0] = v[i][0];
v[j][1] = v[i][1];
v[j][2] = v[i][2];
q[j] = q[i];
molecule[j] = molecule[i];
num_bond[j] = num_bond[i];
for (k = 0; k < num_bond[j]; k++) {
bond_type[j][k] = bond_type[i][k];
bond_atom[j][k] = bond_atom[i][k];
}
num_angle[j] = num_angle[i];
for (k = 0; k < num_angle[j]; k++) {
angle_type[j][k] = angle_type[i][k];
angle_atom1[j][k] = angle_atom1[i][k];
angle_atom2[j][k] = angle_atom2[i][k];
angle_atom3[j][k] = angle_atom3[i][k];
}
num_dihedral[j] = num_dihedral[i];
for (k = 0; k < num_dihedral[j]; k++) {
dihedral_type[j][k] = dihedral_type[i][k];
dihedral_atom1[j][k] = dihedral_atom1[i][k];
dihedral_atom2[j][k] = dihedral_atom2[i][k];
dihedral_atom3[j][k] = dihedral_atom3[i][k];
dihedral_atom4[j][k] = dihedral_atom4[i][k];
}
num_improper[j] = num_improper[i];
for (k = 0; k < num_improper[j]; k++) {
improper_type[j][k] = improper_type[i][k];
improper_atom1[j][k] = improper_atom1[i][k];
improper_atom2[j][k] = improper_atom2[i][k];
improper_atom3[j][k] = improper_atom3[i][k];
improper_atom4[j][k] = improper_atom4[i][k];
}
nspecial[j][0] = nspecial[i][0];
nspecial[j][1] = nspecial[i][1];
nspecial[j][2] = nspecial[i][2];
for (k = 0; k < nspecial[j][2]; k++) special[j][k] = special[i][k];
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j);
}
/* ---------------------------------------------------------------------- */
int AtomVecFull::pack_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
dz = pbc[2]*domain->zprd;
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecFull::pack_comm_vel(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
dz = pbc[2]*domain->zprd;
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecFull::unpack_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
void AtomVecFull::unpack_comm_vel(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecFull::pack_reverse(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
buf[m++] = f[i][0];
buf[m++] = f[i][1];
buf[m++] = f[i][2];
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecFull::unpack_reverse(int n, int *list, double *buf)
{
int i,j,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
f[j][0] += buf[m++];
f[j][1] += buf[m++];
f[j][2] += buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecFull::pack_border(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = q[j];
buf[m++] = molecule[j];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0];
dy = pbc[1];
dz = pbc[2];
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = q[j];
buf[m++] = molecule[j];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecFull::pack_border_vel(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = q[j];
buf[m++] = molecule[j];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0];
dy = pbc[1];
dz = pbc[2];
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = q[j];
buf[m++] = molecule[j];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecFull::pack_border_one(int i, double *buf)
{
buf[0] = q[i];
buf[1] = molecule[i];
return 2;
}
/* ---------------------------------------------------------------------- */
void AtomVecFull::unpack_border(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
if (i == nmax) grow(0);
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
tag[i] = static_cast<int> (buf[m++]);
type[i] = static_cast<int> (buf[m++]);
mask[i] = static_cast<int> (buf[m++]);
q[i] = buf[m++];
molecule[i] = static_cast<int> (buf[m++]);
}
}
/* ---------------------------------------------------------------------- */
void AtomVecFull::unpack_border_vel(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
if (i == nmax) grow(0);
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
tag[i] = static_cast<int> (buf[m++]);
type[i] = static_cast<int> (buf[m++]);
mask[i] = static_cast<int> (buf[m++]);
q[i] = buf[m++];
molecule[i] = static_cast<int> (buf[m++]);
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecFull::unpack_border_one(int i, double *buf)
{
q[i] = buf[0];
molecule[i] = static_cast<int> (buf[1]);
return 2;
}
/* ----------------------------------------------------------------------
pack data for atom I for sending to another proc
xyz must be 1st 3 values, so comm::exchange() can test on them
------------------------------------------------------------------------- */
int AtomVecFull::pack_exchange(int i, double *buf)
{
int k;
int m = 1;
buf[m++] = x[i][0];
buf[m++] = x[i][1];
buf[m++] = x[i][2];
buf[m++] = v[i][0];
buf[m++] = v[i][1];
buf[m++] = v[i][2];
buf[m++] = tag[i];
buf[m++] = type[i];
buf[m++] = mask[i];
buf[m++] = image[i];
buf[m++] = q[i];
buf[m++] = molecule[i];
buf[m++] = num_bond[i];
for (k = 0; k < num_bond[i]; k++) {
buf[m++] = bond_type[i][k];
buf[m++] = bond_atom[i][k];
}
buf[m++] = num_angle[i];
for (k = 0; k < num_angle[i]; k++) {
buf[m++] = angle_type[i][k];
buf[m++] = angle_atom1[i][k];
buf[m++] = angle_atom2[i][k];
buf[m++] = angle_atom3[i][k];
}
buf[m++] = num_dihedral[i];
for (k = 0; k < num_dihedral[i]; k++) {
buf[m++] = dihedral_type[i][k];
buf[m++] = dihedral_atom1[i][k];
buf[m++] = dihedral_atom2[i][k];
buf[m++] = dihedral_atom3[i][k];
buf[m++] = dihedral_atom4[i][k];
}
buf[m++] = num_improper[i];
for (k = 0; k < num_improper[i]; k++) {
buf[m++] = improper_type[i][k];
buf[m++] = improper_atom1[i][k];
buf[m++] = improper_atom2[i][k];
buf[m++] = improper_atom3[i][k];
buf[m++] = improper_atom4[i][k];
}
buf[m++] = nspecial[i][0];
buf[m++] = nspecial[i][1];
buf[m++] = nspecial[i][2];
for (k = 0; k < nspecial[i][2]; k++) buf[m++] = special[i][k];
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]);
buf[0] = m;
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecFull::unpack_exchange(double *buf)
{
int k;
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
int m = 1;
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
x[nlocal][2] = buf[m++];
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
tag[nlocal] = static_cast<int> (buf[m++]);
type[nlocal] = static_cast<int> (buf[m++]);
mask[nlocal] = static_cast<int> (buf[m++]);
image[nlocal] = static_cast<int> (buf[m++]);
q[nlocal] = buf[m++];
molecule[nlocal] = static_cast<int> (buf[m++]);
num_bond[nlocal] = static_cast<int> (buf[m++]);
for (k = 0; k < num_bond[nlocal]; k++) {
bond_type[nlocal][k] = static_cast<int> (buf[m++]);
bond_atom[nlocal][k] = static_cast<int> (buf[m++]);
}
num_angle[nlocal] = static_cast<int> (buf[m++]);
for (k = 0; k < num_angle[nlocal]; k++) {
angle_type[nlocal][k] = static_cast<int> (buf[m++]);
angle_atom1[nlocal][k] = static_cast<int> (buf[m++]);
angle_atom2[nlocal][k] = static_cast<int> (buf[m++]);
angle_atom3[nlocal][k] = static_cast<int> (buf[m++]);
}
num_dihedral[nlocal] = static_cast<int> (buf[m++]);
for (k = 0; k < num_dihedral[nlocal]; k++) {
dihedral_type[nlocal][k] = static_cast<int> (buf[m++]);
dihedral_atom1[nlocal][k] = static_cast<int> (buf[m++]);
dihedral_atom2[nlocal][k] = static_cast<int> (buf[m++]);
dihedral_atom3[nlocal][k] = static_cast<int> (buf[m++]);
dihedral_atom4[nlocal][k] = static_cast<int> (buf[m++]);
}
num_improper[nlocal] = static_cast<int> (buf[m++]);
for (k = 0; k < num_improper[nlocal]; k++) {
improper_type[nlocal][k] = static_cast<int> (buf[m++]);
improper_atom1[nlocal][k] = static_cast<int> (buf[m++]);
improper_atom2[nlocal][k] = static_cast<int> (buf[m++]);
improper_atom3[nlocal][k] = static_cast<int> (buf[m++]);
improper_atom4[nlocal][k] = static_cast<int> (buf[m++]);
}
nspecial[nlocal][0] = static_cast<int> (buf[m++]);
nspecial[nlocal][1] = static_cast<int> (buf[m++]);
nspecial[nlocal][2] = static_cast<int> (buf[m++]);
for (k = 0; k < nspecial[nlocal][2]; k++)
special[nlocal][k] = static_cast<int> (buf[m++]);
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->
unpack_exchange(nlocal,&buf[m]);
atom->nlocal++;
return m;
}
/* ----------------------------------------------------------------------
size of restart data for all atoms owned by this proc
include extra data stored by fixes
------------------------------------------------------------------------- */
int AtomVecFull::size_restart()
{
int i;
int nlocal = atom->nlocal;
int n = 0;
for (i = 0; i < nlocal; i++)
n += 17 + 2*num_bond[i] + 4*num_angle[i] +
5*num_dihedral[i] + 5*num_improper[i];
if (atom->nextra_restart)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
for (i = 0; i < nlocal; i++)
n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
return n;
}
/* ----------------------------------------------------------------------
pack atom I's data for restart file including extra quantities
xyz must be 1st 3 values, so that read_restart can test on them
molecular types may be negative, but write as positive
------------------------------------------------------------------------- */
int AtomVecFull::pack_restart(int i, double *buf)
{
int k;
int m = 1;
buf[m++] = x[i][0];
buf[m++] = x[i][1];
buf[m++] = x[i][2];
buf[m++] = tag[i];
buf[m++] = type[i];
buf[m++] = mask[i];
buf[m++] = image[i];
buf[m++] = v[i][0];
buf[m++] = v[i][1];
buf[m++] = v[i][2];
buf[m++] = q[i];
buf[m++] = molecule[i];
buf[m++] = num_bond[i];
for (k = 0; k < num_bond[i]; k++) {
buf[m++] = MAX(bond_type[i][k],-bond_type[i][k]);
buf[m++] = bond_atom[i][k];
}
buf[m++] = num_angle[i];
for (k = 0; k < num_angle[i]; k++) {
buf[m++] = MAX(angle_type[i][k],-angle_type[i][k]);
buf[m++] = angle_atom1[i][k];
buf[m++] = angle_atom2[i][k];
buf[m++] = angle_atom3[i][k];
}
buf[m++] = num_dihedral[i];
for (k = 0; k < num_dihedral[i]; k++) {
buf[m++] = MAX(dihedral_type[i][k],-dihedral_type[i][k]);
buf[m++] = dihedral_atom1[i][k];
buf[m++] = dihedral_atom2[i][k];
buf[m++] = dihedral_atom3[i][k];
buf[m++] = dihedral_atom4[i][k];
}
buf[m++] = num_improper[i];
for (k = 0; k < num_improper[i]; k++) {
buf[m++] = MAX(improper_type[i][k],-improper_type[i][k]);
buf[m++] = improper_atom1[i][k];
buf[m++] = improper_atom2[i][k];
buf[m++] = improper_atom3[i][k];
buf[m++] = improper_atom4[i][k];
}
if (atom->nextra_restart)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]);
buf[0] = m;
return m;
}
/* ----------------------------------------------------------------------
unpack data for one atom from restart file including extra quantities
------------------------------------------------------------------------- */
int AtomVecFull::unpack_restart(double *buf)
{
int k;
int nlocal = atom->nlocal;
if (nlocal == nmax) {
grow(0);
if (atom->nextra_store)
atom->extra = memory->grow_2d_double_array(atom->extra,nmax,
atom->nextra_store,
"atom:extra");
}
int m = 1;
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
x[nlocal][2] = buf[m++];
tag[nlocal] = static_cast<int> (buf[m++]);
type[nlocal] = static_cast<int> (buf[m++]);
mask[nlocal] = static_cast<int> (buf[m++]);
image[nlocal] = static_cast<int> (buf[m++]);
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
q[nlocal] = buf[m++];
molecule[nlocal] = static_cast<int> (buf[m++]);
num_bond[nlocal] = static_cast<int> (buf[m++]);
for (k = 0; k < num_bond[nlocal]; k++) {
bond_type[nlocal][k] = static_cast<int> (buf[m++]);
bond_atom[nlocal][k] = static_cast<int> (buf[m++]);
}
num_angle[nlocal] = static_cast<int> (buf[m++]);
for (k = 0; k < num_angle[nlocal]; k++) {
angle_type[nlocal][k] = static_cast<int> (buf[m++]);
angle_atom1[nlocal][k] = static_cast<int> (buf[m++]);
angle_atom2[nlocal][k] = static_cast<int> (buf[m++]);
angle_atom3[nlocal][k] = static_cast<int> (buf[m++]);
}
num_dihedral[nlocal] = static_cast<int> (buf[m++]);
for (k = 0; k < num_dihedral[nlocal]; k++) {
dihedral_type[nlocal][k] = static_cast<int> (buf[m++]);
dihedral_atom1[nlocal][k] = static_cast<int> (buf[m++]);
dihedral_atom2[nlocal][k] = static_cast<int> (buf[m++]);
dihedral_atom3[nlocal][k] = static_cast<int> (buf[m++]);
dihedral_atom4[nlocal][k] = static_cast<int> (buf[m++]);
}
num_improper[nlocal] = static_cast<int> (buf[m++]);
for (k = 0; k < num_improper[nlocal]; k++) {
improper_type[nlocal][k] = static_cast<int> (buf[m++]);
improper_atom1[nlocal][k] = static_cast<int> (buf[m++]);
improper_atom2[nlocal][k] = static_cast<int> (buf[m++]);
improper_atom3[nlocal][k] = static_cast<int> (buf[m++]);
improper_atom4[nlocal][k] = static_cast<int> (buf[m++]);
}
double **extra = atom->extra;
if (atom->nextra_store) {
int size = static_cast<int> (buf[0]) - m;
for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++];
}
atom->nlocal++;
return m;
}
/* ----------------------------------------------------------------------
create one atom of itype at coord
set other values to defaults
------------------------------------------------------------------------- */
void AtomVecFull::create_atom(int itype, double *coord)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
tag[nlocal] = 0;
type[nlocal] = itype;
x[nlocal][0] = coord[0];
x[nlocal][1] = coord[1];
x[nlocal][2] = coord[2];
mask[nlocal] = 1;
image[nlocal] = (512 << 20) | (512 << 10) | 512;
v[nlocal][0] = 0.0;
v[nlocal][1] = 0.0;
v[nlocal][2] = 0.0;
q[nlocal] = 0.0;
molecule[nlocal] = 0;
num_bond[nlocal] = 0;
num_angle[nlocal] = 0;
num_dihedral[nlocal] = 0;
num_improper[nlocal] = 0;
nspecial[nlocal][0] = nspecial[nlocal][1] = nspecial[nlocal][2] = 0;
atom->nlocal++;
}
/* ----------------------------------------------------------------------
unpack one line from Atoms section of data file
initialize other atom quantities
------------------------------------------------------------------------- */
void AtomVecFull::data_atom(double *coord, int imagetmp, char **values)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
tag[nlocal] = atoi(values[0]);
if (tag[nlocal] <= 0)
error->one("Invalid atom ID in Atoms section of data file");
molecule[nlocal] = atoi(values[1]);
type[nlocal] = atoi(values[2]);
if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
error->one("Invalid atom type in Atoms section of data file");
q[nlocal] = atof(values[3]);
x[nlocal][0] = coord[0];
x[nlocal][1] = coord[1];
x[nlocal][2] = coord[2];
image[nlocal] = imagetmp;
mask[nlocal] = 1;
v[nlocal][0] = 0.0;
v[nlocal][1] = 0.0;
v[nlocal][2] = 0.0;
num_bond[nlocal] = 0;
num_angle[nlocal] = 0;
num_dihedral[nlocal] = 0;
num_improper[nlocal] = 0;
atom->nlocal++;
}
/* ----------------------------------------------------------------------
unpack hybrid quantities from one line in Atoms section of data file
initialize other atom quantities for this sub-style
------------------------------------------------------------------------- */
int AtomVecFull::data_atom_hybrid(int nlocal, char **values)
{
molecule[nlocal] = atoi(values[1]);
q[nlocal] = atof(values[3]);
num_bond[nlocal] = 0;
num_angle[nlocal] = 0;
num_dihedral[nlocal] = 0;
num_improper[nlocal] = 0;
return 2;
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
------------------------------------------------------------------------- */
double AtomVecFull::memory_usage()
{
double bytes = 0.0;
if (atom->memcheck("tag")) bytes += nmax * sizeof(int);
if (atom->memcheck("type")) bytes += nmax * sizeof(int);
if (atom->memcheck("mask")) bytes += nmax * sizeof(int);
if (atom->memcheck("image")) bytes += nmax * sizeof(int);
if (atom->memcheck("x")) bytes += nmax*3 * sizeof(double);
if (atom->memcheck("v")) bytes += nmax*3 * sizeof(double);
if (atom->memcheck("f")) bytes += nmax*3 * sizeof(double);
if (atom->memcheck("q")) bytes += nmax * sizeof(double);
if (atom->memcheck("molecule")) bytes += nmax * sizeof(int);
if (atom->memcheck("nspecial")) bytes += nmax*3 * sizeof(int);
if (atom->memcheck("special")) bytes += nmax*atom->maxspecial * sizeof(int);
if (atom->memcheck("num_bond")) bytes += nmax * sizeof(int);
if (atom->memcheck("bond_type"))
bytes += nmax*atom->bond_per_atom * sizeof(int);
if (atom->memcheck("bond_atom"))
bytes += nmax*atom->bond_per_atom * sizeof(int);
if (atom->memcheck("num_angle")) bytes += nmax * sizeof(int);
if (atom->memcheck("angle_type"))
bytes += nmax*atom->angle_per_atom * sizeof(int);
if (atom->memcheck("angle_atom1"))
bytes += nmax*atom->angle_per_atom * sizeof(int);
if (atom->memcheck("angle_atom2"))
bytes += nmax*atom->angle_per_atom * sizeof(int);
if (atom->memcheck("angle_atom3"))
bytes += nmax*atom->angle_per_atom * sizeof(int);
if (atom->memcheck("num_dihedral")) bytes += nmax * sizeof(int);
if (atom->memcheck("dihedral_type"))
bytes += nmax*atom->dihedral_per_atom * sizeof(int);
if (atom->memcheck("dihedral_atom1"))
bytes += nmax*atom->dihedral_per_atom * sizeof(int);
if (atom->memcheck("dihedral_atom2"))
bytes += nmax*atom->dihedral_per_atom * sizeof(int);
if (atom->memcheck("dihedral_atom3"))
bytes += nmax*atom->dihedral_per_atom * sizeof(int);
if (atom->memcheck("dihedral_atom4"))
bytes += nmax*atom->dihedral_per_atom * sizeof(int);
if (atom->memcheck("num_improper")) bytes += nmax * sizeof(int);
if (atom->memcheck("improper_type"))
bytes += nmax*atom->improper_per_atom * sizeof(int);
if (atom->memcheck("improper_atom1"))
bytes += nmax*atom->improper_per_atom * sizeof(int);
if (atom->memcheck("improper_atom2"))
bytes += nmax*atom->improper_per_atom * sizeof(int);
if (atom->memcheck("improper_atom3"))
bytes += nmax*atom->improper_per_atom * sizeof(int);
if (atom->memcheck("improper_atom4"))
bytes += nmax*atom->improper_per_atom * sizeof(int);
return bytes;
}
diff --git a/src/MOLECULE/atom_vec_molecular.cpp b/src/MOLECULE/atom_vec_molecular.cpp
index 07c46724a..a2ff7c19c 100644
--- a/src/MOLECULE/atom_vec_molecular.cpp
+++ b/src/MOLECULE/atom_vec_molecular.cpp
@@ -1,977 +1,977 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "stdlib.h"
#include "atom_vec_molecular.h"
-#include "lmptype.h"
#include "atom.h"
#include "domain.h"
#include "modify.h"
#include "fix.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MIN(A,B) ((A) < (B)) ? (A) : (B)
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
#define DELTA 10000
/* ---------------------------------------------------------------------- */
AtomVecMolecular::AtomVecMolecular(LAMMPS *lmp, int narg, char **arg) :
AtomVec(lmp, narg, arg)
{
molecular = 1;
bonds_allow = angles_allow = dihedrals_allow = impropers_allow = 1;
mass_type = 1;
comm_x_only = comm_f_only = 1;
size_forward = 3;
size_reverse = 3;
size_border = 7;
size_velocity = 3;
size_data_atom = 6;
size_data_vel = 4;
xcol_data = 4;
atom->molecule_flag = 1;
}
/* ----------------------------------------------------------------------
grow atom arrays
n = 0 grows arrays by DELTA
n > 0 allocates arrays to size n
------------------------------------------------------------------------- */
void AtomVecMolecular::grow(int n)
{
if (n == 0) nmax += DELTA;
else nmax = n;
atom->nmax = nmax;
if (nmax < 0 || nmax > MAXSMALLINT)
error->one("Per-processor system is too big");
tag = atom->tag = (int *)
memory->srealloc(atom->tag,nmax*sizeof(int),"atom:tag");
type = atom->type = (int *)
memory->srealloc(atom->type,nmax*sizeof(int),"atom:type");
mask = atom->mask = (int *)
memory->srealloc(atom->mask,nmax*sizeof(int),"atom:mask");
image = atom->image = (int *)
memory->srealloc(atom->image,nmax*sizeof(int),"atom:image");
x = atom->x = memory->grow_2d_double_array(atom->x,nmax,3,"atom:x");
v = atom->v = memory->grow_2d_double_array(atom->v,nmax,3,"atom:v");
f = atom->f = memory->grow_2d_double_array(atom->f,nmax,3,"atom:f");
molecule = atom->molecule = (int *)
memory->srealloc(atom->molecule,nmax*sizeof(int),"atom:molecule");
nspecial = atom->nspecial =
memory->grow_2d_int_array(atom->nspecial,nmax,3,"atom:nspecial");
special = atom->special =
memory->grow_2d_int_array(atom->special,nmax,atom->maxspecial,
"atom:special");
num_bond = atom->num_bond = (int *)
memory->srealloc(atom->num_bond,nmax*sizeof(int),"atom:num_bond");
bond_type = atom->bond_type =
memory->grow_2d_int_array(atom->bond_type,nmax,atom->bond_per_atom,
"atom:bond_type");
bond_atom = atom->bond_atom =
memory->grow_2d_int_array(atom->bond_atom,nmax,atom->bond_per_atom,
"atom:bond_atom");
num_angle = atom->num_angle = (int *)
memory->srealloc(atom->num_angle,nmax*sizeof(int),"atom:num_angle");
angle_type = atom->angle_type =
memory->grow_2d_int_array(atom->angle_type,nmax,atom->angle_per_atom,
"atom:angle_type");
angle_atom1 = atom->angle_atom1 =
memory->grow_2d_int_array(atom->angle_atom1,nmax,atom->angle_per_atom,
"atom:angle_atom1");
angle_atom2 = atom->angle_atom2 =
memory->grow_2d_int_array(atom->angle_atom2,nmax,atom->angle_per_atom,
"atom:angle_atom2");
angle_atom3 = atom->angle_atom3 =
memory->grow_2d_int_array(atom->angle_atom3,nmax,atom->angle_per_atom,
"atom:angle_atom3");
num_dihedral = atom->num_dihedral = (int *)
memory->srealloc(atom->num_dihedral,nmax*sizeof(int),"atom:num_dihedral");
dihedral_type = atom->dihedral_type =
memory->grow_2d_int_array(atom->dihedral_type,nmax,atom->dihedral_per_atom,
"atom:dihedral_type");
dihedral_atom1 = atom->dihedral_atom1 =
memory->grow_2d_int_array(atom->dihedral_atom1,nmax,
atom->dihedral_per_atom,"atom:dihedral_atom1");
dihedral_atom2 = atom->dihedral_atom2 =
memory->grow_2d_int_array(atom->dihedral_atom2,nmax,
atom->dihedral_per_atom,"atom:dihedral_atom2");
dihedral_atom3 = atom->dihedral_atom3 =
memory->grow_2d_int_array(atom->dihedral_atom3,nmax,
atom->dihedral_per_atom,"atom:dihedral_atom3");
dihedral_atom4 = atom->dihedral_atom4 =
memory->grow_2d_int_array(atom->dihedral_atom4,nmax,
atom->dihedral_per_atom,"atom:dihedral_atom4");
num_improper = atom->num_improper = (int *)
memory->srealloc(atom->num_improper,nmax*sizeof(int),"atom:num_improper");
improper_type = atom->improper_type =
memory->grow_2d_int_array(atom->improper_type,nmax,atom->improper_per_atom,
"atom:improper_type");
improper_atom1 = atom->improper_atom1 =
memory->grow_2d_int_array(atom->improper_atom1,nmax,
atom->improper_per_atom,"atom:improper_atom1");
improper_atom2 = atom->improper_atom2 =
memory->grow_2d_int_array(atom->improper_atom2,nmax,
atom->improper_per_atom,"atom:improper_atom2");
improper_atom3 = atom->improper_atom3 =
memory->grow_2d_int_array(atom->improper_atom3,nmax,
atom->improper_per_atom,"atom:improper_atom3");
improper_atom4 = atom->improper_atom4 =
memory->grow_2d_int_array(atom->improper_atom4,nmax,
atom->improper_per_atom,"atom:improper_atom4");
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
}
/* ----------------------------------------------------------------------
reset local array ptrs
------------------------------------------------------------------------- */
void AtomVecMolecular::grow_reset()
{
tag = atom->tag; type = atom->type;
mask = atom->mask; image = atom->image;
x = atom->x; v = atom->v; f = atom->f;
molecule = atom->molecule;
nspecial = atom->nspecial; special = atom->special;
num_bond = atom->num_bond; bond_type = atom->bond_type;
bond_atom = atom->bond_atom;
num_angle = atom->num_angle; angle_type = atom->angle_type;
angle_atom1 = atom->angle_atom1; angle_atom2 = atom->angle_atom2;
angle_atom3 = atom->angle_atom3;
num_dihedral = atom->num_dihedral; dihedral_type = atom->dihedral_type;
dihedral_atom1 = atom->dihedral_atom1; dihedral_atom2 = atom->dihedral_atom2;
dihedral_atom3 = atom->dihedral_atom3; dihedral_atom4 = atom->dihedral_atom4;
num_improper = atom->num_improper; improper_type = atom->improper_type;
improper_atom1 = atom->improper_atom1; improper_atom2 = atom->improper_atom2;
improper_atom3 = atom->improper_atom3; improper_atom4 = atom->improper_atom4;
}
/* ---------------------------------------------------------------------- */
void AtomVecMolecular::copy(int i, int j)
{
int k;
tag[j] = tag[i];
type[j] = type[i];
mask[j] = mask[i];
image[j] = image[i];
x[j][0] = x[i][0];
x[j][1] = x[i][1];
x[j][2] = x[i][2];
v[j][0] = v[i][0];
v[j][1] = v[i][1];
v[j][2] = v[i][2];
molecule[j] = molecule[i];
num_bond[j] = num_bond[i];
for (k = 0; k < num_bond[j]; k++) {
bond_type[j][k] = bond_type[i][k];
bond_atom[j][k] = bond_atom[i][k];
}
num_angle[j] = num_angle[i];
for (k = 0; k < num_angle[j]; k++) {
angle_type[j][k] = angle_type[i][k];
angle_atom1[j][k] = angle_atom1[i][k];
angle_atom2[j][k] = angle_atom2[i][k];
angle_atom3[j][k] = angle_atom3[i][k];
}
num_dihedral[j] = num_dihedral[i];
for (k = 0; k < num_dihedral[j]; k++) {
dihedral_type[j][k] = dihedral_type[i][k];
dihedral_atom1[j][k] = dihedral_atom1[i][k];
dihedral_atom2[j][k] = dihedral_atom2[i][k];
dihedral_atom3[j][k] = dihedral_atom3[i][k];
dihedral_atom4[j][k] = dihedral_atom4[i][k];
}
num_improper[j] = num_improper[i];
for (k = 0; k < num_improper[j]; k++) {
improper_type[j][k] = improper_type[i][k];
improper_atom1[j][k] = improper_atom1[i][k];
improper_atom2[j][k] = improper_atom2[i][k];
improper_atom3[j][k] = improper_atom3[i][k];
improper_atom4[j][k] = improper_atom4[i][k];
}
nspecial[j][0] = nspecial[i][0];
nspecial[j][1] = nspecial[i][1];
nspecial[j][2] = nspecial[i][2];
for (k = 0; k < nspecial[j][2]; k++) special[j][k] = special[i][k];
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j);
}
/* ---------------------------------------------------------------------- */
int AtomVecMolecular::pack_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
dz = pbc[2]*domain->zprd;
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecMolecular::pack_comm_vel(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
dz = pbc[2]*domain->zprd;
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecMolecular::unpack_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
void AtomVecMolecular::unpack_comm_vel(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecMolecular::pack_reverse(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
buf[m++] = f[i][0];
buf[m++] = f[i][1];
buf[m++] = f[i][2];
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecMolecular::unpack_reverse(int n, int *list, double *buf)
{
int i,j,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
f[j][0] += buf[m++];
f[j][1] += buf[m++];
f[j][2] += buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecMolecular::pack_border(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = molecule[j];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0];
dy = pbc[1];
dz = pbc[2];
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = molecule[j];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecMolecular::pack_border_vel(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = molecule[j];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0];
dy = pbc[1];
dz = pbc[2];
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = molecule[j];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecMolecular::pack_border_one(int i, double *buf)
{
buf[0] = molecule[i];
return 1;
}
/* ---------------------------------------------------------------------- */
void AtomVecMolecular::unpack_border(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
if (i == nmax) grow(0);
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
tag[i] = static_cast<int> (buf[m++]);
type[i] = static_cast<int> (buf[m++]);
mask[i] = static_cast<int> (buf[m++]);
molecule[i] = static_cast<int> (buf[m++]);
}
}
/* ---------------------------------------------------------------------- */
void AtomVecMolecular::unpack_border_vel(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
if (i == nmax) grow(0);
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
tag[i] = static_cast<int> (buf[m++]);
type[i] = static_cast<int> (buf[m++]);
mask[i] = static_cast<int> (buf[m++]);
molecule[i] = static_cast<int> (buf[m++]);
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecMolecular::unpack_border_one(int i, double *buf)
{
molecule[i] = static_cast<int> (buf[0]);
return 1;
}
/* ----------------------------------------------------------------------
pack data for atom I for sending to another proc
xyz must be 1st 3 values, so comm::exchange() can test on them
------------------------------------------------------------------------- */
int AtomVecMolecular::pack_exchange(int i, double *buf)
{
int k;
int m = 1;
buf[m++] = x[i][0];
buf[m++] = x[i][1];
buf[m++] = x[i][2];
buf[m++] = v[i][0];
buf[m++] = v[i][1];
buf[m++] = v[i][2];
buf[m++] = tag[i];
buf[m++] = type[i];
buf[m++] = mask[i];
buf[m++] = image[i];
buf[m++] = molecule[i];
buf[m++] = num_bond[i];
for (k = 0; k < num_bond[i]; k++) {
buf[m++] = bond_type[i][k];
buf[m++] = bond_atom[i][k];
}
buf[m++] = num_angle[i];
for (k = 0; k < num_angle[i]; k++) {
buf[m++] = angle_type[i][k];
buf[m++] = angle_atom1[i][k];
buf[m++] = angle_atom2[i][k];
buf[m++] = angle_atom3[i][k];
}
buf[m++] = num_dihedral[i];
for (k = 0; k < num_dihedral[i]; k++) {
buf[m++] = dihedral_type[i][k];
buf[m++] = dihedral_atom1[i][k];
buf[m++] = dihedral_atom2[i][k];
buf[m++] = dihedral_atom3[i][k];
buf[m++] = dihedral_atom4[i][k];
}
buf[m++] = num_improper[i];
for (k = 0; k < num_improper[i]; k++) {
buf[m++] = improper_type[i][k];
buf[m++] = improper_atom1[i][k];
buf[m++] = improper_atom2[i][k];
buf[m++] = improper_atom3[i][k];
buf[m++] = improper_atom4[i][k];
}
buf[m++] = nspecial[i][0];
buf[m++] = nspecial[i][1];
buf[m++] = nspecial[i][2];
for (k = 0; k < nspecial[i][2]; k++) buf[m++] = special[i][k];
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]);
buf[0] = m;
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecMolecular::unpack_exchange(double *buf)
{
int k;
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
int m = 1;
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
x[nlocal][2] = buf[m++];
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
tag[nlocal] = static_cast<int> (buf[m++]);
type[nlocal] = static_cast<int> (buf[m++]);
mask[nlocal] = static_cast<int> (buf[m++]);
image[nlocal] = static_cast<int> (buf[m++]);
molecule[nlocal] = static_cast<int> (buf[m++]);
num_bond[nlocal] = static_cast<int> (buf[m++]);
for (k = 0; k < num_bond[nlocal]; k++) {
bond_type[nlocal][k] = static_cast<int> (buf[m++]);
bond_atom[nlocal][k] = static_cast<int> (buf[m++]);
}
num_angle[nlocal] = static_cast<int> (buf[m++]);
for (k = 0; k < num_angle[nlocal]; k++) {
angle_type[nlocal][k] = static_cast<int> (buf[m++]);
angle_atom1[nlocal][k] = static_cast<int> (buf[m++]);
angle_atom2[nlocal][k] = static_cast<int> (buf[m++]);
angle_atom3[nlocal][k] = static_cast<int> (buf[m++]);
}
num_dihedral[nlocal] = static_cast<int> (buf[m++]);
for (k = 0; k < num_dihedral[nlocal]; k++) {
dihedral_type[nlocal][k] = static_cast<int> (buf[m++]);
dihedral_atom1[nlocal][k] = static_cast<int> (buf[m++]);
dihedral_atom2[nlocal][k] = static_cast<int> (buf[m++]);
dihedral_atom3[nlocal][k] = static_cast<int> (buf[m++]);
dihedral_atom4[nlocal][k] = static_cast<int> (buf[m++]);
}
num_improper[nlocal] = static_cast<int> (buf[m++]);
for (k = 0; k < num_improper[nlocal]; k++) {
improper_type[nlocal][k] = static_cast<int> (buf[m++]);
improper_atom1[nlocal][k] = static_cast<int> (buf[m++]);
improper_atom2[nlocal][k] = static_cast<int> (buf[m++]);
improper_atom3[nlocal][k] = static_cast<int> (buf[m++]);
improper_atom4[nlocal][k] = static_cast<int> (buf[m++]);
}
nspecial[nlocal][0] = static_cast<int> (buf[m++]);
nspecial[nlocal][1] = static_cast<int> (buf[m++]);
nspecial[nlocal][2] = static_cast<int> (buf[m++]);
for (k = 0; k < nspecial[nlocal][2]; k++)
special[nlocal][k] = static_cast<int> (buf[m++]);
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->
unpack_exchange(nlocal,&buf[m]);
atom->nlocal++;
return m;
}
/* ----------------------------------------------------------------------
size of restart data for all atoms owned by this proc
include extra data stored by fixes
------------------------------------------------------------------------- */
int AtomVecMolecular::size_restart()
{
int i;
int nlocal = atom->nlocal;
int n = 0;
for (i = 0; i < nlocal; i++)
n += 16 + 2*num_bond[i] + 4*num_angle[i] +
5*num_dihedral[i] + 5*num_improper[i];
if (atom->nextra_restart)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
for (i = 0; i < nlocal; i++)
n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
return n;
}
/* ----------------------------------------------------------------------
pack atom I's data for restart file including extra quantities
xyz must be 1st 3 values, so that read_restart can test on them
molecular types may be negative, but write as positive
------------------------------------------------------------------------- */
int AtomVecMolecular::pack_restart(int i, double *buf)
{
int k;
int m = 1;
buf[m++] = x[i][0];
buf[m++] = x[i][1];
buf[m++] = x[i][2];
buf[m++] = tag[i];
buf[m++] = type[i];
buf[m++] = mask[i];
buf[m++] = image[i];
buf[m++] = v[i][0];
buf[m++] = v[i][1];
buf[m++] = v[i][2];
buf[m++] = molecule[i];
buf[m++] = num_bond[i];
for (k = 0; k < num_bond[i]; k++) {
buf[m++] = MAX(bond_type[i][k],-bond_type[i][k]);
buf[m++] = bond_atom[i][k];
}
buf[m++] = num_angle[i];
for (k = 0; k < num_angle[i]; k++) {
buf[m++] = MAX(angle_type[i][k],-angle_type[i][k]);
buf[m++] = angle_atom1[i][k];
buf[m++] = angle_atom2[i][k];
buf[m++] = angle_atom3[i][k];
}
buf[m++] = num_dihedral[i];
for (k = 0; k < num_dihedral[i]; k++) {
buf[m++] = MAX(dihedral_type[i][k],-dihedral_type[i][k]);
buf[m++] = dihedral_atom1[i][k];
buf[m++] = dihedral_atom2[i][k];
buf[m++] = dihedral_atom3[i][k];
buf[m++] = dihedral_atom4[i][k];
}
buf[m++] = num_improper[i];
for (k = 0; k < num_improper[i]; k++) {
buf[m++] = MAX(improper_type[i][k],-improper_type[i][k]);
buf[m++] = improper_atom1[i][k];
buf[m++] = improper_atom2[i][k];
buf[m++] = improper_atom3[i][k];
buf[m++] = improper_atom4[i][k];
}
if (atom->nextra_restart)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]);
buf[0] = m;
return m;
}
/* ----------------------------------------------------------------------
unpack data for one atom from restart file including extra quantities
------------------------------------------------------------------------- */
int AtomVecMolecular::unpack_restart(double *buf)
{
int k;
int nlocal = atom->nlocal;
if (nlocal == nmax) {
grow(0);
if (atom->nextra_store)
atom->extra = memory->grow_2d_double_array(atom->extra,nmax,
atom->nextra_store,
"atom:extra");
}
int m = 1;
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
x[nlocal][2] = buf[m++];
tag[nlocal] = static_cast<int> (buf[m++]);
type[nlocal] = static_cast<int> (buf[m++]);
mask[nlocal] = static_cast<int> (buf[m++]);
image[nlocal] = static_cast<int> (buf[m++]);
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
molecule[nlocal] = static_cast<int> (buf[m++]);
num_bond[nlocal] = static_cast<int> (buf[m++]);
for (k = 0; k < num_bond[nlocal]; k++) {
bond_type[nlocal][k] = static_cast<int> (buf[m++]);
bond_atom[nlocal][k] = static_cast<int> (buf[m++]);
}
num_angle[nlocal] = static_cast<int> (buf[m++]);
for (k = 0; k < num_angle[nlocal]; k++) {
angle_type[nlocal][k] = static_cast<int> (buf[m++]);
angle_atom1[nlocal][k] = static_cast<int> (buf[m++]);
angle_atom2[nlocal][k] = static_cast<int> (buf[m++]);
angle_atom3[nlocal][k] = static_cast<int> (buf[m++]);
}
num_dihedral[nlocal] = static_cast<int> (buf[m++]);
for (k = 0; k < num_dihedral[nlocal]; k++) {
dihedral_type[nlocal][k] = static_cast<int> (buf[m++]);
dihedral_atom1[nlocal][k] = static_cast<int> (buf[m++]);
dihedral_atom2[nlocal][k] = static_cast<int> (buf[m++]);
dihedral_atom3[nlocal][k] = static_cast<int> (buf[m++]);
dihedral_atom4[nlocal][k] = static_cast<int> (buf[m++]);
}
num_improper[nlocal] = static_cast<int> (buf[m++]);
for (k = 0; k < num_improper[nlocal]; k++) {
improper_type[nlocal][k] = static_cast<int> (buf[m++]);
improper_atom1[nlocal][k] = static_cast<int> (buf[m++]);
improper_atom2[nlocal][k] = static_cast<int> (buf[m++]);
improper_atom3[nlocal][k] = static_cast<int> (buf[m++]);
improper_atom4[nlocal][k] = static_cast<int> (buf[m++]);
}
double **extra = atom->extra;
if (atom->nextra_store) {
int size = static_cast<int> (buf[0]) - m;
for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++];
}
atom->nlocal++;
return m;
}
/* ----------------------------------------------------------------------
create one atom of itype at coord
set other values to defaults
------------------------------------------------------------------------- */
void AtomVecMolecular::create_atom(int itype, double *coord)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
tag[nlocal] = 0;
type[nlocal] = itype;
x[nlocal][0] = coord[0];
x[nlocal][1] = coord[1];
x[nlocal][2] = coord[2];
mask[nlocal] = 1;
image[nlocal] = (512 << 20) | (512 << 10) | 512;
v[nlocal][0] = 0.0;
v[nlocal][1] = 0.0;
v[nlocal][2] = 0.0;
molecule[nlocal] = 0;
num_bond[nlocal] = 0;
num_angle[nlocal] = 0;
num_dihedral[nlocal] = 0;
num_improper[nlocal] = 0;
nspecial[nlocal][0] = nspecial[nlocal][1] = nspecial[nlocal][2] = 0;
atom->nlocal++;
}
/* ----------------------------------------------------------------------
unpack one line from Atoms section of data file
initialize other atom quantities
------------------------------------------------------------------------- */
void AtomVecMolecular::data_atom(double *coord, int imagetmp, char **values)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
tag[nlocal] = atoi(values[0]);
if (tag[nlocal] <= 0)
error->one("Invalid atom ID in Atoms section of data file");
molecule[nlocal] = atoi(values[1]);
type[nlocal] = atoi(values[2]);
if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
error->one("Invalid atom type in Atoms section of data file");
x[nlocal][0] = coord[0];
x[nlocal][1] = coord[1];
x[nlocal][2] = coord[2];
image[nlocal] = imagetmp;
mask[nlocal] = 1;
v[nlocal][0] = 0.0;
v[nlocal][1] = 0.0;
v[nlocal][2] = 0.0;
num_bond[nlocal] = 0;
num_angle[nlocal] = 0;
num_dihedral[nlocal] = 0;
num_improper[nlocal] = 0;
atom->nlocal++;
}
/* ----------------------------------------------------------------------
unpack hybrid quantities from one line in Atoms section of data file
initialize other atom quantities for this sub-style
------------------------------------------------------------------------- */
int AtomVecMolecular::data_atom_hybrid(int nlocal, char **values)
{
molecule[nlocal] = atoi(values[0]);
num_bond[nlocal] = 0;
num_angle[nlocal] = 0;
num_dihedral[nlocal] = 0;
num_improper[nlocal] = 0;
return 1;
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
------------------------------------------------------------------------- */
double AtomVecMolecular::memory_usage()
{
double bytes = 0.0;
if (atom->memcheck("tag")) bytes += nmax * sizeof(int);
if (atom->memcheck("type")) bytes += nmax * sizeof(int);
if (atom->memcheck("mask")) bytes += nmax * sizeof(int);
if (atom->memcheck("image")) bytes += nmax * sizeof(int);
if (atom->memcheck("x")) bytes += nmax*3 * sizeof(double);
if (atom->memcheck("v")) bytes += nmax*3 * sizeof(double);
if (atom->memcheck("f")) bytes += nmax*3 * sizeof(double);
if (atom->memcheck("molecule")) bytes += nmax * sizeof(int);
if (atom->memcheck("nspecial")) bytes += nmax*3 * sizeof(int);
if (atom->memcheck("special")) bytes += nmax*atom->maxspecial * sizeof(int);
if (atom->memcheck("num_bond")) bytes += nmax * sizeof(int);
if (atom->memcheck("bond_type"))
bytes += nmax*atom->bond_per_atom * sizeof(int);
if (atom->memcheck("bond_atom"))
bytes += nmax*atom->bond_per_atom * sizeof(int);
if (atom->memcheck("num_angle")) bytes += nmax * sizeof(int);
if (atom->memcheck("angle_type"))
bytes += nmax*atom->angle_per_atom * sizeof(int);
if (atom->memcheck("angle_atom1"))
bytes += nmax*atom->angle_per_atom * sizeof(int);
if (atom->memcheck("angle_atom2"))
bytes += nmax*atom->angle_per_atom * sizeof(int);
if (atom->memcheck("angle_atom3"))
bytes += nmax*atom->angle_per_atom * sizeof(int);
if (atom->memcheck("num_dihedral")) bytes += nmax * sizeof(int);
if (atom->memcheck("dihedral_type"))
bytes += nmax*atom->dihedral_per_atom * sizeof(int);
if (atom->memcheck("dihedral_atom1"))
bytes += nmax*atom->dihedral_per_atom * sizeof(int);
if (atom->memcheck("dihedral_atom2"))
bytes += nmax*atom->dihedral_per_atom * sizeof(int);
if (atom->memcheck("dihedral_atom3"))
bytes += nmax*atom->dihedral_per_atom * sizeof(int);
if (atom->memcheck("dihedral_atom4"))
bytes += nmax*atom->dihedral_per_atom * sizeof(int);
if (atom->memcheck("num_improper")) bytes += nmax * sizeof(int);
if (atom->memcheck("improper_type"))
bytes += nmax*atom->improper_per_atom * sizeof(int);
if (atom->memcheck("improper_atom1"))
bytes += nmax*atom->improper_per_atom * sizeof(int);
if (atom->memcheck("improper_atom2"))
bytes += nmax*atom->improper_per_atom * sizeof(int);
if (atom->memcheck("improper_atom3"))
bytes += nmax*atom->improper_per_atom * sizeof(int);
if (atom->memcheck("improper_atom4"))
bytes += nmax*atom->improper_per_atom * sizeof(int);
return bytes;
}
diff --git a/src/MOLECULE/bond_fene.cpp b/src/MOLECULE/bond_fene.cpp
index a2ac3edcf..6c2f53cc8 100644
--- a/src/MOLECULE/bond_fene.cpp
+++ b/src/MOLECULE/bond_fene.cpp
@@ -1,263 +1,263 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "math.h"
#include "stdlib.h"
#include "bond_fene.h"
-#include "lmptype.h"
#include "atom.h"
#include "neighbor.h"
#include "domain.h"
#include "comm.h"
#include "update.h"
#include "force.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
BondFENE::BondFENE(LAMMPS *lmp) : Bond(lmp)
{
TWO_1_3 = pow(2.0,(1.0/3.0));
}
/* ---------------------------------------------------------------------- */
BondFENE::~BondFENE()
{
if (allocated) {
memory->sfree(setflag);
memory->sfree(k);
memory->sfree(r0);
memory->sfree(epsilon);
memory->sfree(sigma);
}
}
/* ---------------------------------------------------------------------- */
void BondFENE::compute(int eflag, int vflag)
{
int i1,i2,n,type;
double delx,dely,delz,ebond,fbond;
double rsq,r0sq,rlogarg,sr2,sr6;
ebond = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = 0;
double **x = atom->x;
double **f = atom->f;
int **bondlist = neighbor->bondlist;
int nbondlist = neighbor->nbondlist;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
for (n = 0; n < nbondlist; n++) {
i1 = bondlist[n][0];
i2 = bondlist[n][1];
type = bondlist[n][2];
delx = x[i1][0] - x[i2][0];
dely = x[i1][1] - x[i2][1];
delz = x[i1][2] - x[i2][2];
domain->minimum_image(delx,dely,delz);
// force from log term
rsq = delx*delx + dely*dely + delz*delz;
r0sq = r0[type] * r0[type];
rlogarg = 1.0 - rsq/r0sq;
// if r -> r0, then rlogarg < 0.0 which is an error
// issue a warning and reset rlogarg = epsilon
// if r > 2*r0 something serious is wrong, abort
if (rlogarg < 0.1) {
char str[128];
sprintf(str,"FENE bond too long: " BIGINT_FORMAT " %d %d %g",
update->ntimestep,atom->tag[i1],atom->tag[i2],sqrt(rsq));
error->warning(str,0);
if (rlogarg <= -3.0) error->one("Bad FENE bond");
rlogarg = 0.1;
}
fbond = -k[type]/rlogarg;
// force from LJ term
if (rsq < TWO_1_3*sigma[type]*sigma[type]) {
sr2 = sigma[type]*sigma[type]/rsq;
sr6 = sr2*sr2*sr2;
fbond += 48.0*epsilon[type]*sr6*(sr6-0.5)/rsq;
}
// energy
if (eflag) {
ebond = -0.5 * k[type]*r0sq*log(rlogarg);
if (rsq < TWO_1_3*sigma[type]*sigma[type])
ebond += 4.0*epsilon[type]*sr6*(sr6-1.0) + epsilon[type];
}
// apply force to each of 2 atoms
if (newton_bond || i1 < nlocal) {
f[i1][0] += delx*fbond;
f[i1][1] += dely*fbond;
f[i1][2] += delz*fbond;
}
if (newton_bond || i2 < nlocal) {
f[i2][0] -= delx*fbond;
f[i2][1] -= dely*fbond;
f[i2][2] -= delz*fbond;
}
if (evflag) ev_tally(i1,i2,nlocal,newton_bond,ebond,fbond,delx,dely,delz);
}
}
/* ---------------------------------------------------------------------- */
void BondFENE::allocate()
{
allocated = 1;
int n = atom->nbondtypes;
k = (double *) memory->smalloc((n+1)*sizeof(double),"bond:k");
r0 = (double *) memory->smalloc((n+1)*sizeof(double),"bond:r0");
epsilon = (double *) memory->smalloc((n+1)*sizeof(double),"bond:epsilon");
sigma = (double *) memory->smalloc((n+1)*sizeof(double),"bond:sigma");
setflag = (int *) memory->smalloc((n+1)*sizeof(int),"bond:setflag");
for (int i = 1; i <= n; i++) setflag[i] = 0;
}
/* ----------------------------------------------------------------------
set coeffs for one type
------------------------------------------------------------------------- */
void BondFENE::coeff(int narg, char **arg)
{
if (narg != 5) error->all("Incorrect args for bond coefficients");
if (!allocated) allocate();
int ilo,ihi;
force->bounds(arg[0],atom->nbondtypes,ilo,ihi);
double k_one = force->numeric(arg[1]);
double r0_one = force->numeric(arg[2]);
double epsilon_one = force->numeric(arg[3]);
double sigma_one = force->numeric(arg[4]);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
k[i] = k_one;
r0[i] = r0_one;
epsilon[i] = epsilon_one;
sigma[i] = sigma_one;
setflag[i] = 1;
count++;
}
if (count == 0) error->all("Incorrect args for bond coefficients");
}
/* ----------------------------------------------------------------------
check if special_bond settings are valid
------------------------------------------------------------------------- */
void BondFENE::init_style()
{
// special bonds should be 0 1 1
if (force->special_lj[1] != 0.0 || force->special_lj[2] != 1.0 ||
force->special_lj[3] != 1.0) {
if (comm->me == 0)
error->warning("Use special bonds = 0,1,1 with bond style fene");
}
}
/* ---------------------------------------------------------------------- */
double BondFENE::equilibrium_distance(int i)
{
return 0.97*sigma[i];
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void BondFENE::write_restart(FILE *fp)
{
fwrite(&k[1],sizeof(double),atom->nbondtypes,fp);
fwrite(&r0[1],sizeof(double),atom->nbondtypes,fp);
fwrite(&epsilon[1],sizeof(double),atom->nbondtypes,fp);
fwrite(&sigma[1],sizeof(double),atom->nbondtypes,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void BondFENE::read_restart(FILE *fp)
{
allocate();
if (comm->me == 0) {
fread(&k[1],sizeof(double),atom->nbondtypes,fp);
fread(&r0[1],sizeof(double),atom->nbondtypes,fp);
fread(&epsilon[1],sizeof(double),atom->nbondtypes,fp);
fread(&sigma[1],sizeof(double),atom->nbondtypes,fp);
}
MPI_Bcast(&k[1],atom->nbondtypes,MPI_DOUBLE,0,world);
MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world);
MPI_Bcast(&epsilon[1],atom->nbondtypes,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma[1],atom->nbondtypes,MPI_DOUBLE,0,world);
for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1;
}
/* ---------------------------------------------------------------------- */
double BondFENE::single(int type, double rsq, int i, int j)
{
double r0sq = r0[type] * r0[type];
double rlogarg = 1.0 - rsq/r0sq;
// if r -> r0, then rlogarg < 0.0 which is an error
// issue a warning and reset rlogarg = epsilon
// if r > 2*r0 something serious is wrong, abort
if (rlogarg < 0.1) {
char str[128];
sprintf(str,"FENE bond too long: " BIGINT_FORMAT " %g",
update->ntimestep,sqrt(rsq));
error->warning(str,0);
if (rlogarg <= -3.0) error->one("Bad FENE bond");
rlogarg = 0.1;
}
double eng = -0.5 * k[type]*r0sq*log(rlogarg);
if (rsq < TWO_1_3*sigma[type]*sigma[type]) {
double sr2,sr6;
sr2 = sigma[type]*sigma[type]/rsq;
sr6 = sr2*sr2*sr2;
eng += 4.0*epsilon[type]*sr6*(sr6-1.0) + epsilon[type];
}
return eng;
}
diff --git a/src/MOLECULE/bond_fene_expand.cpp b/src/MOLECULE/bond_fene_expand.cpp
index e62894102..cb2fc5d72 100644
--- a/src/MOLECULE/bond_fene_expand.cpp
+++ b/src/MOLECULE/bond_fene_expand.cpp
@@ -1,277 +1,277 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "math.h"
#include "stdlib.h"
#include "bond_fene_expand.h"
-#include "lmptype.h"
#include "atom.h"
#include "neighbor.h"
#include "domain.h"
#include "comm.h"
#include "update.h"
#include "force.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
BondFENEExpand::BondFENEExpand(LAMMPS *lmp) : Bond(lmp)
{
TWO_1_3 = pow(2.0,(1.0/3.0));
}
/* ---------------------------------------------------------------------- */
BondFENEExpand::~BondFENEExpand()
{
if (allocated) {
memory->sfree(setflag);
memory->sfree(k);
memory->sfree(r0);
memory->sfree(epsilon);
memory->sfree(sigma);
memory->sfree(shift);
}
}
/* ---------------------------------------------------------------------- */
void BondFENEExpand::compute(int eflag, int vflag)
{
int i1,i2,n,type;
double delx,dely,delz,ebond,fbond;
double rsq,r0sq,rlogarg,sr2,sr6;
double r,rshift,rshiftsq;
ebond = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = 0;
double **x = atom->x;
double **f = atom->f;
int **bondlist = neighbor->bondlist;
int nbondlist = neighbor->nbondlist;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
for (n = 0; n < nbondlist; n++) {
i1 = bondlist[n][0];
i2 = bondlist[n][1];
type = bondlist[n][2];
delx = x[i1][0] - x[i2][0];
dely = x[i1][1] - x[i2][1];
delz = x[i1][2] - x[i2][2];
domain->minimum_image(delx,dely,delz);
// force from log term
rsq = delx*delx + dely*dely + delz*delz;
r = sqrt(rsq);
rshift = r - shift[type];
rshiftsq = rshift*rshift;
r0sq = r0[type] * r0[type];
rlogarg = 1.0 - rshiftsq/r0sq;
// if r -> r0, then rlogarg < 0.0 which is an error
// issue a warning and reset rlogarg = epsilon
// if r > 2*r0 something serious is wrong, abort
if (rlogarg < 0.1) {
char str[128];
sprintf(str,"FENE bond too long: " BIGINT_FORMAT " %d %d %g",
update->ntimestep,atom->tag[i1],atom->tag[i2],sqrt(rsq));
error->warning(str,0);
if (rlogarg <= -3.0) error->one("Bad FENE bond");
rlogarg = 0.1;
}
fbond = -k[type]*rshift/rlogarg/r;
// force from LJ term
if (rshiftsq < TWO_1_3*sigma[type]*sigma[type]) {
sr2 = sigma[type]*sigma[type]/rshiftsq;
sr6 = sr2*sr2*sr2;
fbond += 48.0*epsilon[type]*sr6*(sr6-0.5)/rshift/r;
}
// energy
if (eflag) {
ebond = -0.5 * k[type]*r0sq*log(rlogarg);
if (rshiftsq < TWO_1_3*sigma[type]*sigma[type])
ebond += 4.0*epsilon[type]*sr6*(sr6-1.0) + epsilon[type];
}
// apply force to each of 2 atoms
if (newton_bond || i1 < nlocal) {
f[i1][0] += delx*fbond;
f[i1][1] += dely*fbond;
f[i1][2] += delz*fbond;
}
if (newton_bond || i2 < nlocal) {
f[i2][0] -= delx*fbond;
f[i2][1] -= dely*fbond;
f[i2][2] -= delz*fbond;
}
if (evflag) ev_tally(i1,i2,nlocal,newton_bond,ebond,fbond,delx,dely,delz);
}
}
/* ---------------------------------------------------------------------- */
void BondFENEExpand::allocate()
{
allocated = 1;
int n = atom->nbondtypes;
k = (double *) memory->smalloc((n+1)*sizeof(double),"bond:k");
r0 = (double *) memory->smalloc((n+1)*sizeof(double),"bond:r0");
epsilon = (double *) memory->smalloc((n+1)*sizeof(double),"bond:epsilon");
sigma = (double *) memory->smalloc((n+1)*sizeof(double),"bond:sigma");
shift = (double *) memory->smalloc((n+1)*sizeof(double),"bond:shift");
setflag = (int *) memory->smalloc((n+1)*sizeof(int),"bond:setflag");
for (int i = 1; i <= n; i++) setflag[i] = 0;
}
/* ----------------------------------------------------------------------
set coeffs for one type
------------------------------------------------------------------------- */
void BondFENEExpand::coeff(int narg, char **arg)
{
if (narg != 6) error->all("Incorrect args for bond coefficients");
if (!allocated) allocate();
int ilo,ihi;
force->bounds(arg[0],atom->nbondtypes,ilo,ihi);
double k_one = force->numeric(arg[1]);
double r0_one = force->numeric(arg[2]);
double epsilon_one = force->numeric(arg[3]);
double sigma_one = force->numeric(arg[4]);
double shift_one = force->numeric(arg[5]);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
k[i] = k_one;
r0[i] = r0_one;
epsilon[i] = epsilon_one;
sigma[i] = sigma_one;
shift[i] = shift_one;
setflag[i] = 1;
count++;
}
if (count == 0) error->all("Incorrect args for bond coefficients");
}
/* ----------------------------------------------------------------------
check if special_bond settings are valid
------------------------------------------------------------------------- */
void BondFENEExpand::init_style()
{
// special bonds should be 0 1 1
if (force->special_lj[1] != 0.0 || force->special_lj[2] != 1.0 ||
force->special_lj[3] != 1.0) {
if (comm->me == 0)
error->warning("Use special bonds = 0,1,1 with bond style fene/expand");
}
}
/* ---------------------------------------------------------------------- */
double BondFENEExpand::equilibrium_distance(int i)
{
return 0.97*sigma[i] + shift[i];
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void BondFENEExpand::write_restart(FILE *fp)
{
fwrite(&k[1],sizeof(double),atom->nbondtypes,fp);
fwrite(&r0[1],sizeof(double),atom->nbondtypes,fp);
fwrite(&epsilon[1],sizeof(double),atom->nbondtypes,fp);
fwrite(&sigma[1],sizeof(double),atom->nbondtypes,fp);
fwrite(&shift[1],sizeof(double),atom->nbondtypes,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void BondFENEExpand::read_restart(FILE *fp)
{
allocate();
if (comm->me == 0) {
fread(&k[1],sizeof(double),atom->nbondtypes,fp);
fread(&r0[1],sizeof(double),atom->nbondtypes,fp);
fread(&epsilon[1],sizeof(double),atom->nbondtypes,fp);
fread(&sigma[1],sizeof(double),atom->nbondtypes,fp);
fread(&shift[1],sizeof(double),atom->nbondtypes,fp);
}
MPI_Bcast(&k[1],atom->nbondtypes,MPI_DOUBLE,0,world);
MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world);
MPI_Bcast(&epsilon[1],atom->nbondtypes,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma[1],atom->nbondtypes,MPI_DOUBLE,0,world);
MPI_Bcast(&shift[1],atom->nbondtypes,MPI_DOUBLE,0,world);
for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1;
}
/* ---------------------------------------------------------------------- */
double BondFENEExpand::single(int type, double rsq, int i, int j)
{
double r = sqrt(rsq);
double rshift = r - shift[type];
double rshiftsq = rshift*rshift;
double r0sq = r0[type] * r0[type];
double rlogarg = 1.0 - rshiftsq/r0sq;
// if r -> r0, then rlogarg < 0.0 which is an error
// issue a warning and reset rlogarg = epsilon
// if r > 2*r0 something serious is wrong, abort
if (rlogarg < 0.1) {
char str[128];
sprintf(str,"FENE bond too long: " BIGINT_FORMAT " %g",
update->ntimestep,sqrt(rsq));
error->warning(str,0);
if (rlogarg <= -3.0) error->one("Bad FENE bond");
rlogarg = 0.1;
}
double eng = -0.5 * k[type]*r0sq*log(rlogarg);
if (rshiftsq < TWO_1_3*sigma[type]*sigma[type]) {
double sr2,sr6;
sr2 = sigma[type]*sigma[type]/rshiftsq;
sr6 = sr2*sr2*sr2;
eng += 4.0*epsilon[type]*sr6*(sr6-1.0) + epsilon[type];
}
return eng;
}
diff --git a/src/MOLECULE/dihedral_charmm.cpp b/src/MOLECULE/dihedral_charmm.cpp
index 5bfbd69aa..57248ff14 100644
--- a/src/MOLECULE/dihedral_charmm.cpp
+++ b/src/MOLECULE/dihedral_charmm.cpp
@@ -1,433 +1,433 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Paul Crozier (SNL)
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "mpi.h"
#include "math.h"
#include "stdlib.h"
#include "dihedral_charmm.h"
-#include "lmptype.h"
#include "atom.h"
#include "comm.h"
#include "neighbor.h"
#include "domain.h"
#include "force.h"
#include "pair.h"
#include "update.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define TOLERANCE 0.05
/* ---------------------------------------------------------------------- */
DihedralCharmm::DihedralCharmm(LAMMPS *lmp) : Dihedral(lmp) {}
/* ---------------------------------------------------------------------- */
DihedralCharmm::~DihedralCharmm()
{
if (allocated) {
memory->sfree(setflag);
memory->sfree(k);
memory->sfree(multiplicity);
memory->sfree(shift);
memory->sfree(cos_shift);
memory->sfree(sin_shift);
memory->sfree(weight);
}
}
/* ---------------------------------------------------------------------- */
void DihedralCharmm::compute(int eflag, int vflag)
{
int i1,i2,i3,i4,i,m,n,type;
double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm;
double edihedral,f1[3],f2[3],f3[3],f4[3];
double ax,ay,az,bx,by,bz,rasq,rbsq,rgsq,rg,rginv,ra2inv,rb2inv,rabinv;
double df,df1,ddf1,fg,hg,fga,hgb,gaa,gbb;
double dtfx,dtfy,dtfz,dtgx,dtgy,dtgz,dthx,dthy,dthz;
double c,s,p,sx2,sy2,sz2;
int itype,jtype;
double delx,dely,delz,rsq,r2inv,r6inv;
double forcecoul,forcelj,fpair,ecoul,evdwl;
edihedral = evdwl = ecoul = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = 0;
// insure pair->ev_tally() will use 1-4 virial contribution
if (weightflag && vflag_global == 2)
force->pair->vflag_either = force->pair->vflag_global = 1;
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
int *atomtype = atom->type;
int **dihedrallist = neighbor->dihedrallist;
int ndihedrallist = neighbor->ndihedrallist;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
double qqrd2e = force->qqrd2e;
for (n = 0; n < ndihedrallist; n++) {
i1 = dihedrallist[n][0];
i2 = dihedrallist[n][1];
i3 = dihedrallist[n][2];
i4 = dihedrallist[n][3];
type = dihedrallist[n][4];
// 1st bond
vb1x = x[i1][0] - x[i2][0];
vb1y = x[i1][1] - x[i2][1];
vb1z = x[i1][2] - x[i2][2];
domain->minimum_image(vb1x,vb1y,vb1z);
// 2nd bond
vb2x = x[i3][0] - x[i2][0];
vb2y = x[i3][1] - x[i2][1];
vb2z = x[i3][2] - x[i2][2];
domain->minimum_image(vb2x,vb2y,vb2z);
vb2xm = -vb2x;
vb2ym = -vb2y;
vb2zm = -vb2z;
domain->minimum_image(vb2xm,vb2ym,vb2zm);
// 3rd bond
vb3x = x[i4][0] - x[i3][0];
vb3y = x[i4][1] - x[i3][1];
vb3z = x[i4][2] - x[i3][2];
domain->minimum_image(vb3x,vb3y,vb3z);
ax = vb1y*vb2zm - vb1z*vb2ym;
ay = vb1z*vb2xm - vb1x*vb2zm;
az = vb1x*vb2ym - vb1y*vb2xm;
bx = vb3y*vb2zm - vb3z*vb2ym;
by = vb3z*vb2xm - vb3x*vb2zm;
bz = vb3x*vb2ym - vb3y*vb2xm;
rasq = ax*ax + ay*ay + az*az;
rbsq = bx*bx + by*by + bz*bz;
rgsq = vb2xm*vb2xm + vb2ym*vb2ym + vb2zm*vb2zm;
rg = sqrt(rgsq);
rginv = ra2inv = rb2inv = 0.0;
if (rg > 0) rginv = 1.0/rg;
if (rasq > 0) ra2inv = 1.0/rasq;
if (rbsq > 0) rb2inv = 1.0/rbsq;
rabinv = sqrt(ra2inv*rb2inv);
c = (ax*bx + ay*by + az*bz)*rabinv;
s = rg*rabinv*(ax*vb3x + ay*vb3y + az*vb3z);
// error check
if (c > 1.0 + TOLERANCE || c < (-1.0 - TOLERANCE)) {
int me;
MPI_Comm_rank(world,&me);
if (screen) {
char str[128];
sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " %d %d %d %d",
me,update->ntimestep,
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
error->warning(str,0);
fprintf(screen," 1st atom: %d %g %g %g\n",
me,x[i1][0],x[i1][1],x[i1][2]);
fprintf(screen," 2nd atom: %d %g %g %g\n",
me,x[i2][0],x[i2][1],x[i2][2]);
fprintf(screen," 3rd atom: %d %g %g %g\n",
me,x[i3][0],x[i3][1],x[i3][2]);
fprintf(screen," 4th atom: %d %g %g %g\n",
me,x[i4][0],x[i4][1],x[i4][2]);
}
}
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
m = multiplicity[type];
p = 1.0;
df1 = 0.0;
for (i = 0; i < m; i++) {
ddf1 = p*c - df1*s;
df1 = p*s + df1*c;
p = ddf1;
}
p = p*cos_shift[type] + df1*sin_shift[type];
df1 = df1*cos_shift[type] - ddf1*sin_shift[type];
df1 *= -m;
p += 1.0;
if (m == 0) {
p = 1.0 + cos_shift[type];
df1 = 0.0;
}
if (eflag) edihedral = k[type] * p;
fg = vb1x*vb2xm + vb1y*vb2ym + vb1z*vb2zm;
hg = vb3x*vb2xm + vb3y*vb2ym + vb3z*vb2zm;
fga = fg*ra2inv*rginv;
hgb = hg*rb2inv*rginv;
gaa = -ra2inv*rg;
gbb = rb2inv*rg;
dtfx = gaa*ax;
dtfy = gaa*ay;
dtfz = gaa*az;
dtgx = fga*ax - hgb*bx;
dtgy = fga*ay - hgb*by;
dtgz = fga*az - hgb*bz;
dthx = gbb*bx;
dthy = gbb*by;
dthz = gbb*bz;
df = -k[type] * df1;
sx2 = df*dtgx;
sy2 = df*dtgy;
sz2 = df*dtgz;
f1[0] = df*dtfx;
f1[1] = df*dtfy;
f1[2] = df*dtfz;
f2[0] = sx2 - f1[0];
f2[1] = sy2 - f1[1];
f2[2] = sz2 - f1[2];
f4[0] = df*dthx;
f4[1] = df*dthy;
f4[2] = df*dthz;
f3[0] = -sx2 - f4[0];
f3[1] = -sy2 - f4[1];
f3[2] = -sz2 - f4[2];
// apply force to each of 4 atoms
if (newton_bond || i1 < nlocal) {
f[i1][0] += f1[0];
f[i1][1] += f1[1];
f[i1][2] += f1[2];
}
if (newton_bond || i2 < nlocal) {
f[i2][0] += f2[0];
f[i2][1] += f2[1];
f[i2][2] += f2[2];
}
if (newton_bond || i3 < nlocal) {
f[i3][0] += f3[0];
f[i3][1] += f3[1];
f[i3][2] += f3[2];
}
if (newton_bond || i4 < nlocal) {
f[i4][0] += f4[0];
f[i4][1] += f4[1];
f[i4][2] += f4[2];
}
if (evflag)
ev_tally(i1,i2,i3,i4,nlocal,newton_bond,edihedral,f1,f3,f4,
vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
// 1-4 LJ and Coulomb interactions
// tally energy/virial in pair, using newton_bond as newton flag
if (weight[type] > 0.0) {
itype = atomtype[i1];
jtype = atomtype[i4];
delx = x[i1][0] - x[i4][0];
dely = x[i1][1] - x[i4][1];
delz = x[i1][2] - x[i4][2];
domain->minimum_image(delx,dely,delz);
rsq = delx*delx + dely*dely + delz*delz;
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
if (implicit) forcecoul = qqrd2e * q[i1]*q[i4]*r2inv;
else forcecoul = qqrd2e * q[i1]*q[i4]*sqrt(r2inv);
forcelj = r6inv * (lj14_1[itype][jtype]*r6inv - lj14_2[itype][jtype]);
fpair = weight[type] * (forcelj+forcecoul)*r2inv;
if (eflag) {
ecoul = weight[type] * forcecoul;
evdwl = r6inv * (lj14_3[itype][jtype]*r6inv - lj14_4[itype][jtype]);
evdwl *= weight[type];
}
if (newton_bond || i1 < nlocal) {
f[i1][0] += delx*fpair;
f[i1][1] += dely*fpair;
f[i1][2] += delz*fpair;
}
if (newton_bond || i4 < nlocal) {
f[i4][0] -= delx*fpair;
f[i4][1] -= dely*fpair;
f[i4][2] -= delz*fpair;
}
if (evflag) force->pair->ev_tally(i1,i4,nlocal,newton_bond,
evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
/* ---------------------------------------------------------------------- */
void DihedralCharmm::allocate()
{
allocated = 1;
int n = atom->ndihedraltypes;
k = (double *) memory->smalloc((n+1)*sizeof(double),"dihedral:k");
multiplicity = (int *)
memory->smalloc((n+1)*sizeof(double),"dihedral:multiplicity");
shift = (int *)
memory->smalloc((n+1)*sizeof(double),"dihedral:shift");
cos_shift = (double *)
memory->smalloc((n+1)*sizeof(double),"dihedral:cos_shift");
sin_shift = (double *)
memory->smalloc((n+1)*sizeof(double),"dihedral:sin_shift");
weight = (double *) memory->smalloc((n+1)*sizeof(double),"dihedral:weight");
setflag = (int *) memory->smalloc((n+1)*sizeof(int),"dihedral:setflag");
for (int i = 1; i <= n; i++) setflag[i] = 0;
}
/* ----------------------------------------------------------------------
set coeffs for one type
------------------------------------------------------------------------- */
void DihedralCharmm::coeff(int narg, char **arg)
{
if (narg != 5) error->all("Incorrect args for dihedral coefficients");
if (!allocated) allocate();
int ilo,ihi;
force->bounds(arg[0],atom->ndihedraltypes,ilo,ihi);
// require integer values of shift for backwards compatibility
// arbitrary phase angle shift could be allowed, but would break
// backwards compatibility and is probably not needed
double k_one = force->numeric(arg[1]);
int multiplicity_one = force->inumeric(arg[2]);
int shift_one = force->inumeric(arg[3]);
double weight_one = force->numeric(arg[4]);
if (multiplicity_one < 0)
error->all("Incorrect multiplicity arg for dihedral coefficients");
if (weight_one < 0.0 || weight_one > 1.0)
error->all("Incorrect weight arg for dihedral coefficients");
double PI = 4.0*atan(1.0);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
k[i] = k_one;
shift[i] = shift_one;
cos_shift[i] = cos(PI*shift_one/180.0);
sin_shift[i] = sin(PI*shift_one/180.0);
multiplicity[i] = multiplicity_one;
weight[i] = weight_one;
setflag[i] = 1;
count++;
}
if (count == 0) error->all("Incorrect args for dihedral coefficients");
}
/* ----------------------------------------------------------------------
error check and initialize all values needed for force computation
------------------------------------------------------------------------- */
void DihedralCharmm::init_style()
{
// insure use of CHARMM pair_style if any weight factors are non-zero
// set local ptrs to LJ 14 arrays setup by Pair
weightflag = 0;
for (int i = 1; i <= atom->ndihedraltypes; i++)
if (weight[i] > 0.0) weightflag = 1;
if (weightflag) {
int itmp;
if (force->pair == NULL)
error->all("Dihedral charmm is incompatible with Pair style");
lj14_1 = (double **) force->pair->extract("lj14_1",itmp);
lj14_2 = (double **) force->pair->extract("lj14_2",itmp);
lj14_3 = (double **) force->pair->extract("lj14_3",itmp);
lj14_4 = (double **) force->pair->extract("lj14_4",itmp);
int *ptr = (int *) force->pair->extract("implicit",itmp);
if (!lj14_1 || !lj14_2 || !lj14_3 || !lj14_4 || !ptr)
error->all("Dihedral charmm is incompatible with Pair style");
implicit = *ptr;
}
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void DihedralCharmm::write_restart(FILE *fp)
{
fwrite(&k[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&multiplicity[1],sizeof(int),atom->ndihedraltypes,fp);
fwrite(&shift[1],sizeof(int),atom->ndihedraltypes,fp);
fwrite(&weight[1],sizeof(double),atom->ndihedraltypes,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void DihedralCharmm::read_restart(FILE *fp)
{
allocate();
if (comm->me == 0) {
fread(&k[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&multiplicity[1],sizeof(int),atom->ndihedraltypes,fp);
fread(&shift[1],sizeof(int),atom->ndihedraltypes,fp);
fread(&weight[1],sizeof(double),atom->ndihedraltypes,fp);
}
MPI_Bcast(&k[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&multiplicity[1],atom->ndihedraltypes,MPI_INT,0,world);
MPI_Bcast(&shift[1],atom->ndihedraltypes,MPI_INT,0,world);
MPI_Bcast(&weight[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
double PI = 4.0*atan(1.0);
for (int i = 1; i <= atom->ndihedraltypes; i++) {
setflag[i] = 1;
cos_shift[i] = cos(PI*shift[i]/180.0);
sin_shift[i] = sin(PI*shift[i]/180.0);
}
}
diff --git a/src/MOLECULE/dihedral_harmonic.cpp b/src/MOLECULE/dihedral_harmonic.cpp
index f4dad7465..e4effc6f2 100644
--- a/src/MOLECULE/dihedral_harmonic.cpp
+++ b/src/MOLECULE/dihedral_harmonic.cpp
@@ -1,354 +1,354 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Paul Crozier (SNL)
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "mpi.h"
#include "math.h"
#include "stdlib.h"
#include "dihedral_harmonic.h"
-#include "lmptype.h"
#include "atom.h"
#include "comm.h"
#include "neighbor.h"
#include "domain.h"
#include "force.h"
#include "update.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define TOLERANCE 0.05
#define SMALL 0.001
/* ---------------------------------------------------------------------- */
DihedralHarmonic::DihedralHarmonic(LAMMPS *lmp) : Dihedral(lmp) {}
/* ---------------------------------------------------------------------- */
DihedralHarmonic::~DihedralHarmonic()
{
if (allocated) {
memory->sfree(setflag);
memory->sfree(k);
memory->sfree(sign);
memory->sfree(multiplicity);
memory->sfree(cos_shift);
memory->sfree(sin_shift);
}
}
/* ---------------------------------------------------------------------- */
void DihedralHarmonic::compute(int eflag, int vflag)
{
int i1,i2,i3,i4,i,m,n,type;
double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm;
double edihedral,f1[3],f2[3],f3[3],f4[3];
double ax,ay,az,bx,by,bz,rasq,rbsq,rgsq,rg,rginv,ra2inv,rb2inv,rabinv;
double df,df1,ddf1,fg,hg,fga,hgb,gaa,gbb;
double dtfx,dtfy,dtfz,dtgx,dtgy,dtgz,dthx,dthy,dthz;
double c,s,p,sx2,sy2,sz2;
edihedral = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = 0;
double **x = atom->x;
double **f = atom->f;
int **dihedrallist = neighbor->dihedrallist;
int ndihedrallist = neighbor->ndihedrallist;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
for (n = 0; n < ndihedrallist; n++) {
i1 = dihedrallist[n][0];
i2 = dihedrallist[n][1];
i3 = dihedrallist[n][2];
i4 = dihedrallist[n][3];
type = dihedrallist[n][4];
// 1st bond
vb1x = x[i1][0] - x[i2][0];
vb1y = x[i1][1] - x[i2][1];
vb1z = x[i1][2] - x[i2][2];
domain->minimum_image(vb1x,vb1y,vb1z);
// 2nd bond
vb2x = x[i3][0] - x[i2][0];
vb2y = x[i3][1] - x[i2][1];
vb2z = x[i3][2] - x[i2][2];
domain->minimum_image(vb2x,vb2y,vb2z);
vb2xm = -vb2x;
vb2ym = -vb2y;
vb2zm = -vb2z;
domain->minimum_image(vb2xm,vb2ym,vb2zm);
// 3rd bond
vb3x = x[i4][0] - x[i3][0];
vb3y = x[i4][1] - x[i3][1];
vb3z = x[i4][2] - x[i3][2];
domain->minimum_image(vb3x,vb3y,vb3z);
// c,s calculation
ax = vb1y*vb2zm - vb1z*vb2ym;
ay = vb1z*vb2xm - vb1x*vb2zm;
az = vb1x*vb2ym - vb1y*vb2xm;
bx = vb3y*vb2zm - vb3z*vb2ym;
by = vb3z*vb2xm - vb3x*vb2zm;
bz = vb3x*vb2ym - vb3y*vb2xm;
rasq = ax*ax + ay*ay + az*az;
rbsq = bx*bx + by*by + bz*bz;
rgsq = vb2xm*vb2xm + vb2ym*vb2ym + vb2zm*vb2zm;
rg = sqrt(rgsq);
rginv = ra2inv = rb2inv = 0.0;
if (rg > 0) rginv = 1.0/rg;
if (rasq > 0) ra2inv = 1.0/rasq;
if (rbsq > 0) rb2inv = 1.0/rbsq;
rabinv = sqrt(ra2inv*rb2inv);
c = (ax*bx + ay*by + az*bz)*rabinv;
s = rg*rabinv*(ax*vb3x + ay*vb3y + az*vb3z);
// error check
if (c > 1.0 + TOLERANCE || c < (-1.0 - TOLERANCE)) {
int me;
MPI_Comm_rank(world,&me);
if (screen) {
char str[128];
sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " %d %d %d %d",
me,update->ntimestep,
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
error->warning(str,0);
fprintf(screen," 1st atom: %d %g %g %g\n",
me,x[i1][0],x[i1][1],x[i1][2]);
fprintf(screen," 2nd atom: %d %g %g %g\n",
me,x[i2][0],x[i2][1],x[i2][2]);
fprintf(screen," 3rd atom: %d %g %g %g\n",
me,x[i3][0],x[i3][1],x[i3][2]);
fprintf(screen," 4th atom: %d %g %g %g\n",
me,x[i4][0],x[i4][1],x[i4][2]);
}
}
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
m = multiplicity[type];
p = 1.0;
df1 = 0.0;
for (i = 0; i < m; i++) {
ddf1 = p*c - df1*s;
df1 = p*s + df1*c;
p = ddf1;
}
p = p*cos_shift[type] + df1*sin_shift[type];
df1 = df1*cos_shift[type] - ddf1*sin_shift[type];
df1 *= -m;
p += 1.0;
if (m == 0) {
p = 1.0 + cos_shift[type];
df1 = 0.0;
}
if (eflag) edihedral = k[type] * p;
fg = vb1x*vb2xm + vb1y*vb2ym + vb1z*vb2zm;
hg = vb3x*vb2xm + vb3y*vb2ym + vb3z*vb2zm;
fga = fg*ra2inv*rginv;
hgb = hg*rb2inv*rginv;
gaa = -ra2inv*rg;
gbb = rb2inv*rg;
dtfx = gaa*ax;
dtfy = gaa*ay;
dtfz = gaa*az;
dtgx = fga*ax - hgb*bx;
dtgy = fga*ay - hgb*by;
dtgz = fga*az - hgb*bz;
dthx = gbb*bx;
dthy = gbb*by;
dthz = gbb*bz;
df = -k[type] * df1;
sx2 = df*dtgx;
sy2 = df*dtgy;
sz2 = df*dtgz;
f1[0] = df*dtfx;
f1[1] = df*dtfy;
f1[2] = df*dtfz;
f2[0] = sx2 - f1[0];
f2[1] = sy2 - f1[1];
f2[2] = sz2 - f1[2];
f4[0] = df*dthx;
f4[1] = df*dthy;
f4[2] = df*dthz;
f3[0] = -sx2 - f4[0];
f3[1] = -sy2 - f4[1];
f3[2] = -sz2 - f4[2];
// apply force to each of 4 atoms
if (newton_bond || i1 < nlocal) {
f[i1][0] += f1[0];
f[i1][1] += f1[1];
f[i1][2] += f1[2];
}
if (newton_bond || i2 < nlocal) {
f[i2][0] += f2[0];
f[i2][1] += f2[1];
f[i2][2] += f2[2];
}
if (newton_bond || i3 < nlocal) {
f[i3][0] += f3[0];
f[i3][1] += f3[1];
f[i3][2] += f3[2];
}
if (newton_bond || i4 < nlocal) {
f[i4][0] += f4[0];
f[i4][1] += f4[1];
f[i4][2] += f4[2];
}
if (evflag)
ev_tally(i1,i2,i3,i4,nlocal,newton_bond,edihedral,f1,f3,f4,
vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
}
}
/* ---------------------------------------------------------------------- */
void DihedralHarmonic::allocate()
{
allocated = 1;
int n = atom->ndihedraltypes;
k = (double *) memory->smalloc((n+1)*sizeof(double),"dihedral:k");
sign = (int *) memory->smalloc((n+1)*sizeof(double),"dihedral:sign");
multiplicity = (int *)
memory->smalloc((n+1)*sizeof(double),"dihedral:multiplicity");
cos_shift = (double *)
memory->smalloc((n+1)*sizeof(double),"dihedral:cos_shift");
sin_shift = (double *)
memory->smalloc((n+1)*sizeof(double),"dihedral:sin_shift");
setflag = (int *) memory->smalloc((n+1)*sizeof(int),"dihedral:setflag");
for (int i = 1; i <= n; i++) setflag[i] = 0;
}
/* ----------------------------------------------------------------------
set coeffs for one type
------------------------------------------------------------------------- */
void DihedralHarmonic::coeff(int narg, char **arg)
{
if (narg != 4) error->all("Incorrect args for dihedral coefficients");
if (!allocated) allocate();
int ilo,ihi;
force->bounds(arg[0],atom->ndihedraltypes,ilo,ihi);
double k_one = force->numeric(arg[1]);
int sign_one = force->inumeric(arg[2]);
int multiplicity_one = force->inumeric(arg[3]);
// require sign = +/- 1 for backwards compatibility
// arbitrary phase angle shift could be allowed, but would break
// backwards compatibility and is probably not needed
if (sign_one != -1 && sign_one != 1)
error->all("Incorrect sign arg for dihedral coefficients");
if (multiplicity_one < 0)
error->all("Incorrect multiplicity arg for dihedral coefficients");
int count = 0;
for (int i = ilo; i <= ihi; i++) {
k[i] = k_one;
sign[i] = sign_one;
if (sign[i] == 1) {
cos_shift[i] = 1;
sin_shift[i] = 0;
} else {
cos_shift[i] = -1;
sin_shift[i] = 0;
}
multiplicity[i] = multiplicity_one;
setflag[i] = 1;
count++;
}
if (count == 0) error->all("Incorrect args for dihedral coefficients");
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void DihedralHarmonic::write_restart(FILE *fp)
{
fwrite(&k[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&sign[1],sizeof(int),atom->ndihedraltypes,fp);
fwrite(&multiplicity[1],sizeof(int),atom->ndihedraltypes,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void DihedralHarmonic::read_restart(FILE *fp)
{
allocate();
if (comm->me == 0) {
fread(&k[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&sign[1],sizeof(int),atom->ndihedraltypes,fp);
fread(&multiplicity[1],sizeof(int),atom->ndihedraltypes,fp);
}
MPI_Bcast(&k[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&sign[1],atom->ndihedraltypes,MPI_INT,0,world);
MPI_Bcast(&multiplicity[1],atom->ndihedraltypes,MPI_INT,0,world);
for (int i = 1; i <= atom->ndihedraltypes; i++) {
setflag[i] = 1;
if (sign[i] == 1) {
cos_shift[i] = 1;
sin_shift[i] = 0;
} else {
cos_shift[i] = -1;
sin_shift[i] = 0;
}
}
}
diff --git a/src/MOLECULE/dihedral_helix.cpp b/src/MOLECULE/dihedral_helix.cpp
index d9c4b78f7..42c4d5eb4 100644
--- a/src/MOLECULE/dihedral_helix.cpp
+++ b/src/MOLECULE/dihedral_helix.cpp
@@ -1,338 +1,338 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Naveen Michaud-Agrawal (Johns Hopkins U) and
Mark Stevens (Sandia)
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "math.h"
#include "stdlib.h"
#include "mpi.h"
#include "dihedral_helix.h"
-#include "lmptype.h"
#include "atom.h"
#include "neighbor.h"
#include "domain.h"
#include "comm.h"
#include "force.h"
#include "update.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MIN(A,B) ((A) < (B)) ? (A) : (B)
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
#define TOLERANCE 0.05
#define SMALL 0.001
#define SMALLER 0.00001
/* ---------------------------------------------------------------------- */
DihedralHelix::DihedralHelix(LAMMPS *lmp) : Dihedral(lmp) {}
/* ---------------------------------------------------------------------- */
DihedralHelix::~DihedralHelix()
{
if (allocated) {
memory->sfree(setflag);
memory->sfree(aphi);
memory->sfree(bphi);
memory->sfree(cphi);
}
}
/* ---------------------------------------------------------------------- */
void DihedralHelix::compute(int eflag, int vflag)
{
int i1,i2,i3,i4,n,type;
double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm;
double edihedral,f1[3],f2[3],f3[3],f4[3];
double sb1,sb2,sb3,rb1,rb3,c0,b1mag2,b1mag,b2mag2;
double b2mag,b3mag2,b3mag,ctmp,r12c1,c1mag,r12c2;
double c2mag,sc1,sc2,s1,s12,c,p,pd,a,a11,a22;
double a33,a12,a13,a23,sx2,sy2,sz2;
double s2,cx,cy,cz,cmag,dx,phi,si,siinv,sin2;
edihedral = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = 0;
double **x = atom->x;
double **f = atom->f;
int **dihedrallist = neighbor->dihedrallist;
int ndihedrallist = neighbor->ndihedrallist;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
for (n = 0; n < ndihedrallist; n++) {
i1 = dihedrallist[n][0];
i2 = dihedrallist[n][1];
i3 = dihedrallist[n][2];
i4 = dihedrallist[n][3];
type = dihedrallist[n][4];
// 1st bond
vb1x = x[i1][0] - x[i2][0];
vb1y = x[i1][1] - x[i2][1];
vb1z = x[i1][2] - x[i2][2];
domain->minimum_image(vb1x,vb1y,vb1z);
// 2nd bond
vb2x = x[i3][0] - x[i2][0];
vb2y = x[i3][1] - x[i2][1];
vb2z = x[i3][2] - x[i2][2];
domain->minimum_image(vb2x,vb2y,vb2z);
vb2xm = -vb2x;
vb2ym = -vb2y;
vb2zm = -vb2z;
domain->minimum_image(vb2xm,vb2ym,vb2zm);
// 3rd bond
vb3x = x[i4][0] - x[i3][0];
vb3y = x[i4][1] - x[i3][1];
vb3z = x[i4][2] - x[i3][2];
domain->minimum_image(vb3x,vb3y,vb3z);
// c0 calculation
sb1 = 1.0 / (vb1x*vb1x + vb1y*vb1y + vb1z*vb1z);
sb2 = 1.0 / (vb2x*vb2x + vb2y*vb2y + vb2z*vb2z);
sb3 = 1.0 / (vb3x*vb3x + vb3y*vb3y + vb3z*vb3z);
rb1 = sqrt(sb1);
rb3 = sqrt(sb3);
c0 = (vb1x*vb3x + vb1y*vb3y + vb1z*vb3z) * rb1*rb3;
// 1st and 2nd angle
b1mag2 = vb1x*vb1x + vb1y*vb1y + vb1z*vb1z;
b1mag = sqrt(b1mag2);
b2mag2 = vb2x*vb2x + vb2y*vb2y + vb2z*vb2z;
b2mag = sqrt(b2mag2);
b3mag2 = vb3x*vb3x + vb3y*vb3y + vb3z*vb3z;
b3mag = sqrt(b3mag2);
ctmp = vb1x*vb2x + vb1y*vb2y + vb1z*vb2z;
r12c1 = 1.0 / (b1mag*b2mag);
c1mag = ctmp * r12c1;
ctmp = vb2xm*vb3x + vb2ym*vb3y + vb2zm*vb3z;
r12c2 = 1.0 / (b2mag*b3mag);
c2mag = ctmp * r12c2;
// cos and sin of 2 angles and final c
sin2 = MAX(1.0 - c1mag*c1mag,0.0);
sc1 = sqrt(sin2);
if (sc1 < SMALL) sc1 = SMALL;
sc1 = 1.0/sc1;
sin2 = MAX(1.0 - c2mag*c2mag,0.0);
sc2 = sqrt(sin2);
if (sc2 < SMALL) sc2 = SMALL;
sc2 = 1.0/sc2;
s1 = sc1 * sc1;
s2 = sc2 * sc2;
s12 = sc1 * sc2;
c = (c0 + c1mag*c2mag) * s12;
cx = vb1y*vb2z - vb1z*vb2y;
cy = vb1z*vb2x - vb1x*vb2z;
cz = vb1x*vb2y - vb1y*vb2x;
cmag = sqrt(cx*cx + cy*cy + cz*cz);
dx = (cx*vb3x + cy*vb3y + cz*vb3z)/cmag/b3mag;
// error check
if (c > 1.0 + TOLERANCE || c < (-1.0 - TOLERANCE)) {
int me;
MPI_Comm_rank(world,&me);
if (screen) {
char str[128];
sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " %d %d %d %d",
me,update->ntimestep,
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
error->warning(str,0);
fprintf(screen," 1st atom: %d %g %g %g\n",
me,x[i1][0],x[i1][1],x[i1][2]);
fprintf(screen," 2nd atom: %d %g %g %g\n",
me,x[i2][0],x[i2][1],x[i2][2]);
fprintf(screen," 3rd atom: %d %g %g %g\n",
me,x[i3][0],x[i3][1],x[i3][2]);
fprintf(screen," 4th atom: %d %g %g %g\n",
me,x[i4][0],x[i4][1],x[i4][2]);
}
}
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
phi = acos(c);
if (dx < 0.0) phi *= -1.0;
si = sin(phi);
if (fabs(si) < SMALLER) si = SMALLER;
siinv = 1.0/si;
p = aphi[type]*(1.0 - c) + bphi[type]*(1.0 + cos(3.0*phi)) +
cphi[type]*(1.0 + cos(phi + 0.25*PI));
pd = -aphi[type] + 3.0*bphi[type]*sin(3.0*phi)*siinv +
cphi[type]*sin(phi + 0.25*PI)*siinv;
if (eflag) edihedral = p;
a = pd;
c = c * a;
s12 = s12 * a;
a11 = c*sb1*s1;
a22 = -sb2 * (2.0*c0*s12 - c*(s1+s2));
a33 = c*sb3*s2;
a12 = -r12c1 * (c1mag*c*s1 + c2mag*s12);
a13 = -rb1*rb3*s12;
a23 = r12c2 * (c2mag*c*s2 + c1mag*s12);
sx2 = a12*vb1x + a22*vb2x + a23*vb3x;
sy2 = a12*vb1y + a22*vb2y + a23*vb3y;
sz2 = a12*vb1z + a22*vb2z + a23*vb3z;
f1[0] = a11*vb1x + a12*vb2x + a13*vb3x;
f1[1] = a11*vb1y + a12*vb2y + a13*vb3y;
f1[2] = a11*vb1z + a12*vb2z + a13*vb3z;
f2[0] = -sx2 - f1[0];
f2[1] = -sy2 - f1[1];
f2[2] = -sz2 - f1[2];
f4[0] = a13*vb1x + a23*vb2x + a33*vb3x;
f4[1] = a13*vb1y + a23*vb2y + a33*vb3y;
f4[2] = a13*vb1z + a23*vb2z + a33*vb3z;
f3[0] = sx2 - f4[0];
f3[1] = sy2 - f4[1];
f3[2] = sz2 - f4[2];
// apply force to each of 4 atoms
if (newton_bond || i1 < nlocal) {
f[i1][0] += f1[0];
f[i1][1] += f1[1];
f[i1][2] += f1[2];
}
if (newton_bond || i2 < nlocal) {
f[i2][0] += f2[0];
f[i2][1] += f2[1];
f[i2][2] += f2[2];
}
if (newton_bond || i3 < nlocal) {
f[i3][0] += f3[0];
f[i3][1] += f3[1];
f[i3][2] += f3[2];
}
if (newton_bond || i4 < nlocal) {
f[i4][0] += f4[0];
f[i4][1] += f4[1];
f[i4][2] += f4[2];
}
if (evflag)
ev_tally(i1,i2,i3,i4,nlocal,newton_bond,edihedral,f1,f3,f4,
vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
}
}
/* ---------------------------------------------------------------------- */
void DihedralHelix::allocate()
{
allocated = 1;
int n = atom->ndihedraltypes;
aphi = (double *) memory->smalloc((n+1)*sizeof(double),"dihedral:aphi");
bphi = (double *) memory->smalloc((n+1)*sizeof(double),"dihedral:bphi");
cphi = (double *) memory->smalloc((n+1)*sizeof(double),"dihedral:cphi");
setflag = (int *) memory->smalloc((n+1)*sizeof(int),"dihedral:setflag");
for (int i = 1; i <= n; i++) setflag[i] = 0;
}
/* ----------------------------------------------------------------------
set coeffs from one line in input script
------------------------------------------------------------------------- */
void DihedralHelix::coeff(int narg, char **arg)
{
if (narg != 4) error->all("Incorrect args for dihedral coefficients");
if (!allocated) allocate();
int ilo,ihi;
force->bounds(arg[0],atom->ndihedraltypes,ilo,ihi);
double aphi_one = force->numeric(arg[1]);
double bphi_one = force->numeric(arg[2]);
double cphi_one = force->numeric(arg[3]);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
aphi[i] = aphi_one;
bphi[i] = bphi_one;
cphi[i] = cphi_one;
setflag[i] = 1;
count++;
}
if (count == 0) error->all("Incorrect args for dihedral coefficients");
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void DihedralHelix::write_restart(FILE *fp)
{
fwrite(&aphi[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&bphi[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&cphi[1],sizeof(double),atom->ndihedraltypes,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void DihedralHelix::read_restart(FILE *fp)
{
allocate();
if (comm->me == 0) {
fread(&aphi[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&bphi[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&cphi[1],sizeof(double),atom->ndihedraltypes,fp);
}
MPI_Bcast(&aphi[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&bphi[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&cphi[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
for (int i = 1; i <= atom->ndihedraltypes; i++) setflag[i] = 1;
}
diff --git a/src/MOLECULE/dihedral_multi_harmonic.cpp b/src/MOLECULE/dihedral_multi_harmonic.cpp
index 4636089e4..4d4dd429d 100644
--- a/src/MOLECULE/dihedral_multi_harmonic.cpp
+++ b/src/MOLECULE/dihedral_multi_harmonic.cpp
@@ -1,339 +1,339 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Mathias Puetz (SNL) and friends
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "math.h"
#include "stdlib.h"
#include "dihedral_multi_harmonic.h"
-#include "lmptype.h"
#include "atom.h"
#include "neighbor.h"
#include "domain.h"
#include "comm.h"
#include "force.h"
#include "update.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MIN(A,B) ((A) < (B)) ? (A) : (B)
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
#define TOLERANCE 0.05
#define SMALL 0.001
/* ---------------------------------------------------------------------- */
DihedralMultiHarmonic::DihedralMultiHarmonic(LAMMPS *lmp) : Dihedral(lmp) {}
/* ---------------------------------------------------------------------- */
DihedralMultiHarmonic::~DihedralMultiHarmonic()
{
if (allocated) {
memory->sfree(setflag);
memory->sfree(a1);
memory->sfree(a2);
memory->sfree(a3);
memory->sfree(a4);
memory->sfree(a5);
}
}
/* ---------------------------------------------------------------------- */
void DihedralMultiHarmonic::compute(int eflag, int vflag)
{
int i1,i2,i3,i4,n,type;
double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm;
double edihedral,f1[3],f2[3],f3[3],f4[3];
double sb1,sb2,sb3,rb1,rb3,c0,b1mag2,b1mag,b2mag2;
double b2mag,b3mag2,b3mag,ctmp,r12c1,c1mag,r12c2;
double c2mag,sc1,sc2,s1,s12,c,p,pd,a,a11,a22;
double a33,a12,a13,a23,sx2,sy2,sz2;
double s2,sin2;
edihedral = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = 0;
double **x = atom->x;
double **f = atom->f;
int **dihedrallist = neighbor->dihedrallist;
int ndihedrallist = neighbor->ndihedrallist;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
for (n = 0; n < ndihedrallist; n++) {
i1 = dihedrallist[n][0];
i2 = dihedrallist[n][1];
i3 = dihedrallist[n][2];
i4 = dihedrallist[n][3];
type = dihedrallist[n][4];
// 1st bond
vb1x = x[i1][0] - x[i2][0];
vb1y = x[i1][1] - x[i2][1];
vb1z = x[i1][2] - x[i2][2];
domain->minimum_image(vb1x,vb1y,vb1z);
// 2nd bond
vb2x = x[i3][0] - x[i2][0];
vb2y = x[i3][1] - x[i2][1];
vb2z = x[i3][2] - x[i2][2];
domain->minimum_image(vb2x,vb2y,vb2z);
vb2xm = -vb2x;
vb2ym = -vb2y;
vb2zm = -vb2z;
domain->minimum_image(vb2xm,vb2ym,vb2zm);
// 3rd bond
vb3x = x[i4][0] - x[i3][0];
vb3y = x[i4][1] - x[i3][1];
vb3z = x[i4][2] - x[i3][2];
domain->minimum_image(vb3x,vb3y,vb3z);
// c0 calculation
sb1 = 1.0 / (vb1x*vb1x + vb1y*vb1y + vb1z*vb1z);
sb2 = 1.0 / (vb2x*vb2x + vb2y*vb2y + vb2z*vb2z);
sb3 = 1.0 / (vb3x*vb3x + vb3y*vb3y + vb3z*vb3z);
rb1 = sqrt(sb1);
rb3 = sqrt(sb3);
c0 = (vb1x*vb3x + vb1y*vb3y + vb1z*vb3z) * rb1*rb3;
// 1st and 2nd angle
b1mag2 = vb1x*vb1x + vb1y*vb1y + vb1z*vb1z;
b1mag = sqrt(b1mag2);
b2mag2 = vb2x*vb2x + vb2y*vb2y + vb2z*vb2z;
b2mag = sqrt(b2mag2);
b3mag2 = vb3x*vb3x + vb3y*vb3y + vb3z*vb3z;
b3mag = sqrt(b3mag2);
ctmp = vb1x*vb2x + vb1y*vb2y + vb1z*vb2z;
r12c1 = 1.0 / (b1mag*b2mag);
c1mag = ctmp * r12c1;
ctmp = vb2xm*vb3x + vb2ym*vb3y + vb2zm*vb3z;
r12c2 = 1.0 / (b2mag*b3mag);
c2mag = ctmp * r12c2;
// cos and sin of 2 angles and final c
sin2 = MAX(1.0 - c1mag*c1mag,0.0);
sc1 = sqrt(sin2);
if (sc1 < SMALL) sc1 = SMALL;
sc1 = 1.0/sc1;
sin2 = MAX(1.0 - c2mag*c2mag,0.0);
sc2 = sqrt(sin2);
if (sc2 < SMALL) sc2 = SMALL;
sc2 = 1.0/sc2;
s1 = sc1 * sc1;
s2 = sc2 * sc2;
s12 = sc1 * sc2;
c = (c0 + c1mag*c2mag) * s12;
// error check
if (c > 1.0 + TOLERANCE || c < (-1.0 - TOLERANCE)) {
int me;
MPI_Comm_rank(world,&me);
if (screen) {
char str[128];
sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " %d %d %d %d",
me,update->ntimestep,
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
error->warning(str,0);
fprintf(screen," 1st atom: %d %g %g %g\n",
me,x[i1][0],x[i1][1],x[i1][2]);
fprintf(screen," 2nd atom: %d %g %g %g\n",
me,x[i2][0],x[i2][1],x[i2][2]);
fprintf(screen," 3rd atom: %d %g %g %g\n",
me,x[i3][0],x[i3][1],x[i3][2]);
fprintf(screen," 4th atom: %d %g %g %g\n",
me,x[i4][0],x[i4][1],x[i4][2]);
}
}
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
// force & energy
// p = sum (i=1,5) a_i * c**(i-1)
// pd = dp/dc
p = a1[type] + c*(a2[type] + c*(a3[type] + c*(a4[type] + c*a5[type])));
pd = a2[type] + c*(2.0*a3[type] + c*(3.0*a4[type] + c*4.0*a5[type]));
if (eflag) edihedral = p;
a = pd;
c = c * a;
s12 = s12 * a;
a11 = c*sb1*s1;
a22 = -sb2 * (2.0*c0*s12 - c*(s1+s2));
a33 = c*sb3*s2;
a12 = -r12c1*(c1mag*c*s1 + c2mag*s12);
a13 = -rb1*rb3*s12;
a23 = r12c2*(c2mag*c*s2 + c1mag*s12);
sx2 = a12*vb1x + a22*vb2x + a23*vb3x;
sy2 = a12*vb1y + a22*vb2y + a23*vb3y;
sz2 = a12*vb1z + a22*vb2z + a23*vb3z;
f1[0] = a11*vb1x + a12*vb2x + a13*vb3x;
f1[1] = a11*vb1y + a12*vb2y + a13*vb3y;
f1[2] = a11*vb1z + a12*vb2z + a13*vb3z;
f2[0] = -sx2 - f1[0];
f2[1] = -sy2 - f1[1];
f2[2] = -sz2 - f1[2];
f4[0] = a13*vb1x + a23*vb2x + a33*vb3x;
f4[1] = a13*vb1y + a23*vb2y + a33*vb3y;
f4[2] = a13*vb1z + a23*vb2z + a33*vb3z;
f3[0] = sx2 - f4[0];
f3[1] = sy2 - f4[1];
f3[2] = sz2 - f4[2];
// apply force to each of 4 atoms
if (newton_bond || i1 < nlocal) {
f[i1][0] += f1[0];
f[i1][1] += f1[1];
f[i1][2] += f1[2];
}
if (newton_bond || i2 < nlocal) {
f[i2][0] += f2[0];
f[i2][1] += f2[1];
f[i2][2] += f2[2];
}
if (newton_bond || i3 < nlocal) {
f[i3][0] += f3[0];
f[i3][1] += f3[1];
f[i3][2] += f3[2];
}
if (newton_bond || i4 < nlocal) {
f[i4][0] += f4[0];
f[i4][1] += f4[1];
f[i4][2] += f4[2];
}
if (evflag)
ev_tally(i1,i2,i3,i4,nlocal,newton_bond,edihedral,f1,f3,f4,
vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
}
}
/* ---------------------------------------------------------------------- */
void DihedralMultiHarmonic::allocate()
{
allocated = 1;
int n = atom->ndihedraltypes;
a1 = (double *) memory->smalloc((n+1)*sizeof(double),"dihedral:a1");
a2 = (double *) memory->smalloc((n+1)*sizeof(double),"dihedral:a2");
a3 = (double *) memory->smalloc((n+1)*sizeof(double),"dihedral:a3");
a4 = (double *) memory->smalloc((n+1)*sizeof(double),"dihedral:a4");
a5 = (double *) memory->smalloc((n+1)*sizeof(double),"dihedral:a5");
setflag = (int *) memory->smalloc((n+1)*sizeof(int),"dihedral:setflag");
for (int i = 1; i <= n; i++) setflag[i] = 0;
}
/* ----------------------------------------------------------------------
set coeffs for one type
------------------------------------------------------------------------- */
void DihedralMultiHarmonic::coeff(int narg, char **arg)
{
if (narg != 6) error->all("Incorrect args for dihedral coefficients");
if (!allocated) allocate();
int ilo,ihi;
force->bounds(arg[0],atom->ndihedraltypes,ilo,ihi);
double a1_one = force->numeric(arg[1]);
double a2_one = force->numeric(arg[2]);
double a3_one = force->numeric(arg[3]);
double a4_one = force->numeric(arg[4]);
double a5_one = force->numeric(arg[5]);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
a1[i] = a1_one;
a2[i] = a2_one;
a3[i] = a3_one;
a4[i] = a4_one;
a5[i] = a5_one;
setflag[i] = 1;
count++;
}
if (count == 0) error->all("Incorrect args for dihedral coefficients");
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void DihedralMultiHarmonic::write_restart(FILE *fp)
{
fwrite(&a1[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&a2[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&a3[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&a4[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&a5[1],sizeof(double),atom->ndihedraltypes,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void DihedralMultiHarmonic::read_restart(FILE *fp)
{
allocate();
if (comm->me == 0) {
fread(&a1[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&a2[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&a3[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&a4[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&a5[1],sizeof(double),atom->ndihedraltypes,fp);
}
MPI_Bcast(&a1[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&a2[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&a3[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&a4[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&a5[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
for (int i = 1; i <= atom->ndihedraltypes; i++) setflag[i] = 1;
}
diff --git a/src/MOLECULE/dihedral_opls.cpp b/src/MOLECULE/dihedral_opls.cpp
index 5ef2d0b7c..6750d3b15 100644
--- a/src/MOLECULE/dihedral_opls.cpp
+++ b/src/MOLECULE/dihedral_opls.cpp
@@ -1,349 +1,349 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Mark Stevens (SNL)
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "math.h"
#include "stdlib.h"
#include "dihedral_opls.h"
-#include "lmptype.h"
#include "atom.h"
#include "comm.h"
#include "neighbor.h"
#include "domain.h"
#include "force.h"
#include "update.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MIN(A,B) ((A) < (B)) ? (A) : (B)
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
#define TOLERANCE 0.05
#define SMALL 0.001
#define SMALLER 0.00001
/* ---------------------------------------------------------------------- */
DihedralOPLS::DihedralOPLS(LAMMPS *lmp) : Dihedral(lmp) {}
/* ---------------------------------------------------------------------- */
DihedralOPLS::~DihedralOPLS()
{
if (allocated) {
memory->sfree(setflag);
memory->sfree(k1);
memory->sfree(k2);
memory->sfree(k3);
memory->sfree(k4);
}
}
/* ---------------------------------------------------------------------- */
void DihedralOPLS::compute(int eflag, int vflag)
{
int i1,i2,i3,i4,n,type;
double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm;
double edihedral,f1[3],f2[3],f3[3],f4[3];
double sb1,sb2,sb3,rb1,rb3,c0,b1mag2,b1mag,b2mag2;
double b2mag,b3mag2,b3mag,ctmp,r12c1,c1mag,r12c2;
double c2mag,sc1,sc2,s1,s12,c,p,pd,a,a11,a22;
double a33,a12,a13,a23,sx2,sy2,sz2;
double s2,cx,cy,cz,cmag,dx,phi,si,siinv,sin2;
edihedral = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = 0;
double **x = atom->x;
double **f = atom->f;
int **dihedrallist = neighbor->dihedrallist;
int ndihedrallist = neighbor->ndihedrallist;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
for (n = 0; n < ndihedrallist; n++) {
i1 = dihedrallist[n][0];
i2 = dihedrallist[n][1];
i3 = dihedrallist[n][2];
i4 = dihedrallist[n][3];
type = dihedrallist[n][4];
// 1st bond
vb1x = x[i1][0] - x[i2][0];
vb1y = x[i1][1] - x[i2][1];
vb1z = x[i1][2] - x[i2][2];
domain->minimum_image(vb1x,vb1y,vb1z);
// 2nd bond
vb2x = x[i3][0] - x[i2][0];
vb2y = x[i3][1] - x[i2][1];
vb2z = x[i3][2] - x[i2][2];
domain->minimum_image(vb2x,vb2y,vb2z);
vb2xm = -vb2x;
vb2ym = -vb2y;
vb2zm = -vb2z;
domain->minimum_image(vb2xm,vb2ym,vb2zm);
// 3rd bond
vb3x = x[i4][0] - x[i3][0];
vb3y = x[i4][1] - x[i3][1];
vb3z = x[i4][2] - x[i3][2];
domain->minimum_image(vb3x,vb3y,vb3z);
// c0 calculation
sb1 = 1.0 / (vb1x*vb1x + vb1y*vb1y + vb1z*vb1z);
sb2 = 1.0 / (vb2x*vb2x + vb2y*vb2y + vb2z*vb2z);
sb3 = 1.0 / (vb3x*vb3x + vb3y*vb3y + vb3z*vb3z);
rb1 = sqrt(sb1);
rb3 = sqrt(sb3);
c0 = (vb1x*vb3x + vb1y*vb3y + vb1z*vb3z) * rb1*rb3;
// 1st and 2nd angle
b1mag2 = vb1x*vb1x + vb1y*vb1y + vb1z*vb1z;
b1mag = sqrt(b1mag2);
b2mag2 = vb2x*vb2x + vb2y*vb2y + vb2z*vb2z;
b2mag = sqrt(b2mag2);
b3mag2 = vb3x*vb3x + vb3y*vb3y + vb3z*vb3z;
b3mag = sqrt(b3mag2);
ctmp = vb1x*vb2x + vb1y*vb2y + vb1z*vb2z;
r12c1 = 1.0 / (b1mag*b2mag);
c1mag = ctmp * r12c1;
ctmp = vb2xm*vb3x + vb2ym*vb3y + vb2zm*vb3z;
r12c2 = 1.0 / (b2mag*b3mag);
c2mag = ctmp * r12c2;
// cos and sin of 2 angles and final c
sin2 = MAX(1.0 - c1mag*c1mag,0.0);
sc1 = sqrt(sin2);
if (sc1 < SMALL) sc1 = SMALL;
sc1 = 1.0/sc1;
sin2 = MAX(1.0 - c2mag*c2mag,0.0);
sc2 = sqrt(sin2);
if (sc2 < SMALL) sc2 = SMALL;
sc2 = 1.0/sc2;
s1 = sc1 * sc1;
s2 = sc2 * sc2;
s12 = sc1 * sc2;
c = (c0 + c1mag*c2mag) * s12;
cx = vb1y*vb2z - vb1z*vb2y;
cy = vb1z*vb2x - vb1x*vb2z;
cz = vb1x*vb2y - vb1y*vb2x;
cmag = sqrt(cx*cx + cy*cy + cz*cz);
dx = (cx*vb3x + cy*vb3y + cz*vb3z)/cmag/b3mag;
// error check
if (c > 1.0 + TOLERANCE || c < (-1.0 - TOLERANCE)) {
int me;
MPI_Comm_rank(world,&me);
if (screen) {
char str[128];
sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " %d %d %d %d",
me,update->ntimestep,
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
error->warning(str,0);
fprintf(screen," 1st atom: %d %g %g %g\n",
me,x[i1][0],x[i1][1],x[i1][2]);
fprintf(screen," 2nd atom: %d %g %g %g\n",
me,x[i2][0],x[i2][1],x[i2][2]);
fprintf(screen," 3rd atom: %d %g %g %g\n",
me,x[i3][0],x[i3][1],x[i3][2]);
fprintf(screen," 4th atom: %d %g %g %g\n",
me,x[i4][0],x[i4][1],x[i4][2]);
}
}
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
// force & energy
// p = sum (i=1,4) k_i * (1 + (-1)**(i+1)*cos(i*phi) )
// pd = dp/dc
phi = acos(c);
if (dx < 0.0) phi *= -1.0;
si = sin(phi);
if (fabs(si) < SMALLER) si = SMALLER;
siinv = 1.0/si;
p = k1[type]*(1.0 + c) + k2[type]*(1.0 - cos(2.0*phi)) +
k3[type]*(1.0 + cos(3.0*phi)) + k4[type]*(1.0 - cos(4.0*phi)) ;
pd = k1[type] - 2.0*k2[type]*sin(2.0*phi)*siinv +
3.0*k3[type]*sin(3.0*phi)*siinv - 4.0*k4[type]*sin(4.0*phi)*siinv;
if (eflag) edihedral = p;
a = pd;
c = c * a;
s12 = s12 * a;
a11 = c*sb1*s1;
a22 = -sb2 * (2.0*c0*s12 - c*(s1+s2));
a33 = c*sb3*s2;
a12 = -r12c1 * (c1mag*c*s1 + c2mag*s12);
a13 = -rb1*rb3*s12;
a23 = r12c2 * (c2mag*c*s2 + c1mag*s12);
sx2 = a12*vb1x + a22*vb2x + a23*vb3x;
sy2 = a12*vb1y + a22*vb2y + a23*vb3y;
sz2 = a12*vb1z + a22*vb2z + a23*vb3z;
f1[0] = a11*vb1x + a12*vb2x + a13*vb3x;
f1[1] = a11*vb1y + a12*vb2y + a13*vb3y;
f1[2] = a11*vb1z + a12*vb2z + a13*vb3z;
f2[0] = -sx2 - f1[0];
f2[1] = -sy2 - f1[1];
f2[2] = -sz2 - f1[2];
f4[0] = a13*vb1x + a23*vb2x + a33*vb3x;
f4[1] = a13*vb1y + a23*vb2y + a33*vb3y;
f4[2] = a13*vb1z + a23*vb2z + a33*vb3z;
f3[0] = sx2 - f4[0];
f3[1] = sy2 - f4[1];
f3[2] = sz2 - f4[2];
// apply force to each of 4 atoms
if (newton_bond || i1 < nlocal) {
f[i1][0] += f1[0];
f[i1][1] += f1[1];
f[i1][2] += f1[2];
}
if (newton_bond || i2 < nlocal) {
f[i2][0] += f2[0];
f[i2][1] += f2[1];
f[i2][2] += f2[2];
}
if (newton_bond || i3 < nlocal) {
f[i3][0] += f3[0];
f[i3][1] += f3[1];
f[i3][2] += f3[2];
}
if (newton_bond || i4 < nlocal) {
f[i4][0] += f4[0];
f[i4][1] += f4[1];
f[i4][2] += f4[2];
}
if (evflag)
ev_tally(i1,i2,i3,i4,nlocal,newton_bond,edihedral,f1,f3,f4,
vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
}
}
/* ---------------------------------------------------------------------- */
void DihedralOPLS::allocate()
{
allocated = 1;
int n = atom->ndihedraltypes;
k1 = (double *) memory->smalloc((n+1)*sizeof(double),"dihedral:k1");
k2 = (double *) memory->smalloc((n+1)*sizeof(double),"dihedral:k2");
k3 = (double *) memory->smalloc((n+1)*sizeof(double),"dihedral:k3");
k4 = (double *) memory->smalloc((n+1)*sizeof(double),"dihedral:k4");
setflag = (int *) memory->smalloc((n+1)*sizeof(int),"dihedral:setflag");
for (int i = 1; i <= n; i++) setflag[i] = 0;
}
/* ----------------------------------------------------------------------
set coeffs for one type
------------------------------------------------------------------------- */
void DihedralOPLS::coeff(int narg, char **arg)
{
if (narg != 5) error->all("Incorrect args for dihedral coefficients");
if (!allocated) allocate();
int ilo,ihi;
force->bounds(arg[0],atom->ndihedraltypes,ilo,ihi);
double k1_one = force->numeric(arg[1]);
double k2_one = force->numeric(arg[2]);
double k3_one = force->numeric(arg[3]);
double k4_one = force->numeric(arg[4]);
// store 1/2 factor with prefactor
int count = 0;
for (int i = ilo; i <= ihi; i++) {
k1[i] = 0.5*k1_one;
k2[i] = 0.5*k2_one;
k3[i] = 0.5*k3_one;
k4[i] = 0.5*k4_one;
setflag[i] = 1;
count++;
}
if (count == 0) error->all("Incorrect args for dihedral coefficients");
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void DihedralOPLS::write_restart(FILE *fp)
{
fwrite(&k1[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&k2[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&k3[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&k4[1],sizeof(double),atom->ndihedraltypes,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void DihedralOPLS::read_restart(FILE *fp)
{
allocate();
if (comm->me == 0) {
fread(&k1[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&k2[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&k3[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&k4[1],sizeof(double),atom->ndihedraltypes,fp);
}
MPI_Bcast(&k1[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&k2[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&k3[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&k4[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
for (int i = 1; i <= atom->ndihedraltypes; i++) setflag[i] = 1;
}
diff --git a/src/MOLECULE/improper_cvff.cpp b/src/MOLECULE/improper_cvff.cpp
index b688a5998..4fdb71094 100644
--- a/src/MOLECULE/improper_cvff.cpp
+++ b/src/MOLECULE/improper_cvff.cpp
@@ -1,350 +1,350 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "mpi.h"
#include "math.h"
#include "stdlib.h"
#include "improper_cvff.h"
-#include "lmptype.h"
#include "atom.h"
#include "comm.h"
#include "neighbor.h"
#include "domain.h"
#include "force.h"
#include "update.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define TOLERANCE 0.05
#define SMALL 0.001
/* ---------------------------------------------------------------------- */
ImproperCvff::ImproperCvff(LAMMPS *lmp) : Improper(lmp) {}
/* ---------------------------------------------------------------------- */
ImproperCvff::~ImproperCvff()
{
if (allocated) {
memory->sfree(setflag);
memory->sfree(k);
memory->sfree(sign);
memory->sfree(multiplicity);
}
}
/* ---------------------------------------------------------------------- */
void ImproperCvff::compute(int eflag, int vflag)
{
int i1,i2,i3,i4,m,n,type;
double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm;
double eimproper,f1[3],f2[3],f3[3],f4[3];
double sb1,sb2,sb3,rb1,rb3,c0,b1mag2,b1mag,b2mag2;
double b2mag,b3mag2,b3mag,ctmp,r12c1,c1mag,r12c2;
double c2mag,sc1,sc2,s1,s2,s12,c,p,pd,rc2,a,a11,a22;
double a33,a12,a13,a23,sx2,sy2,sz2;
eimproper = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = 0;
double **x = atom->x;
double **f = atom->f;
int **improperlist = neighbor->improperlist;
int nimproperlist = neighbor->nimproperlist;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
for (n = 0; n < nimproperlist; n++) {
i1 = improperlist[n][0];
i2 = improperlist[n][1];
i3 = improperlist[n][2];
i4 = improperlist[n][3];
type = improperlist[n][4];
// 1st bond
vb1x = x[i1][0] - x[i2][0];
vb1y = x[i1][1] - x[i2][1];
vb1z = x[i1][2] - x[i2][2];
domain->minimum_image(vb1x,vb1y,vb1z);
// 2nd bond
vb2x = x[i3][0] - x[i2][0];
vb2y = x[i3][1] - x[i2][1];
vb2z = x[i3][2] - x[i2][2];
domain->minimum_image(vb2x,vb2y,vb2z);
vb2xm = -vb2x;
vb2ym = -vb2y;
vb2zm = -vb2z;
domain->minimum_image(vb2xm,vb2ym,vb2zm);
// 3rd bond
vb3x = x[i4][0] - x[i3][0];
vb3y = x[i4][1] - x[i3][1];
vb3z = x[i4][2] - x[i3][2];
domain->minimum_image(vb3x,vb3y,vb3z);
// c0 calculation
sb1 = 1.0 / (vb1x*vb1x + vb1y*vb1y + vb1z*vb1z);
sb2 = 1.0 / (vb2x*vb2x + vb2y*vb2y + vb2z*vb2z);
sb3 = 1.0 / (vb3x*vb3x + vb3y*vb3y + vb3z*vb3z);
rb1 = sqrt(sb1);
rb3 = sqrt(sb3);
c0 = (vb1x*vb3x + vb1y*vb3y + vb1z*vb3z) * rb1*rb3;
// 1st and 2nd angle
b1mag2 = vb1x*vb1x + vb1y*vb1y + vb1z*vb1z;
b1mag = sqrt(b1mag2);
b2mag2 = vb2x*vb2x + vb2y*vb2y + vb2z*vb2z;
b2mag = sqrt(b2mag2);
b3mag2 = vb3x*vb3x + vb3y*vb3y + vb3z*vb3z;
b3mag = sqrt(b3mag2);
ctmp = vb1x*vb2x + vb1y*vb2y + vb1z*vb2z;
r12c1 = 1.0 / (b1mag*b2mag);
c1mag = ctmp * r12c1;
ctmp = vb2xm*vb3x + vb2ym*vb3y + vb2zm*vb3z;
r12c2 = 1.0 / (b2mag*b3mag);
c2mag = ctmp * r12c2;
// cos and sin of 2 angles and final c
sc1 = sqrt(1.0 - c1mag*c1mag);
if (sc1 < SMALL) sc1 = SMALL;
sc1 = 1.0/sc1;
sc2 = sqrt(1.0 - c2mag*c2mag);
if (sc2 < SMALL) sc2 = SMALL;
sc2 = 1.0/sc2;
s1 = sc1 * sc1;
s2 = sc2 * sc2;
s12 = sc1 * sc2;
c = (c0 + c1mag*c2mag) * s12;
// error check
if (c > 1.0 + TOLERANCE || c < (-1.0 - TOLERANCE)) {
int me;
MPI_Comm_rank(world,&me);
if (screen) {
char str[128];
sprintf(str,
"Improper problem: %d " BIGINT_FORMAT " %d %d %d %d",
me,update->ntimestep,
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
error->warning(str,0);
fprintf(screen," 1st atom: %d %g %g %g\n",
me,x[i1][0],x[i1][1],x[i1][2]);
fprintf(screen," 2nd atom: %d %g %g %g\n",
me,x[i2][0],x[i2][1],x[i2][2]);
fprintf(screen," 3rd atom: %d %g %g %g\n",
me,x[i3][0],x[i3][1],x[i3][2]);
fprintf(screen," 4th atom: %d %g %g %g\n",
me,x[i4][0],x[i4][1],x[i4][2]);
}
}
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
// force & energy
// p = 1 + cos(n*phi) for d = 1
// p = 1 - cos(n*phi) for d = -1
// pd = dp/dc / 2
m = multiplicity[type];
if (m == 2) {
p = 2.0*c*c;
pd = 2.0*c;
} else if (m == 3) {
rc2 = c*c;
p = (4.0*rc2-3.0)*c + 1.0;
pd = 6.0*rc2 - 1.5;
} else if (m == 4) {
rc2 = c*c;
p = 8.0*(rc2-1)*rc2 + 2.0;
pd = (16.0*rc2-8.0)*c;
} else if (m == 6) {
rc2 = c*c;
p = ((32.0*rc2-48.0)*rc2 + 18.0)*rc2;
pd = (96.0*(rc2-1.0)*rc2 + 18.0)*c;
} else if (m == 1) {
p = c + 1.0;
pd = 0.5;
} else if (m == 5) {
rc2 = c*c;
p = ((16.0*rc2-20.0)*rc2 + 5.0)*c + 1.0;
pd = (40.0*rc2-30.0)*rc2 + 2.5;
} else if (m == 0) {
p = 2.0;
pd = 0.0;
}
if (sign[type] == -1) {
p = 2.0 - p;
pd = -pd;
}
if (eflag) eimproper = k[type]*p;
a = 2.0 * k[type] * pd;
c = c * a;
s12 = s12 * a;
a11 = c*sb1*s1;
a22 = -sb2*(2.0*c0*s12 - c*(s1+s2));
a33 = c*sb3*s2;
a12 = -r12c1*(c1mag*c*s1 + c2mag*s12);
a13 = -rb1*rb3*s12;
a23 = r12c2*(c2mag*c*s2 + c1mag*s12);
sx2 = a12*vb1x + a22*vb2x + a23*vb3x;
sy2 = a12*vb1y + a22*vb2y + a23*vb3y;
sz2 = a12*vb1z + a22*vb2z + a23*vb3z;
f1[0] = a11*vb1x + a12*vb2x + a13*vb3x;
f1[1] = a11*vb1y + a12*vb2y + a13*vb3y;
f1[2] = a11*vb1z + a12*vb2z + a13*vb3z;
f2[0] = -sx2 - f1[0];
f2[1] = -sy2 - f1[1];
f2[2] = -sz2 - f1[2];
f4[0] = a13*vb1x + a23*vb2x + a33*vb3x;
f4[1] = a13*vb1y + a23*vb2y + a33*vb3y;
f4[2] = a13*vb1z + a23*vb2z + a33*vb3z;
f3[0] = sx2 - f4[0];
f3[1] = sy2 - f4[1];
f3[2] = sz2 - f4[2];
// apply force to each of 4 atoms
if (newton_bond || i1 < nlocal) {
f[i1][0] += f1[0];
f[i1][1] += f1[1];
f[i1][2] += f1[2];
}
if (newton_bond || i2 < nlocal) {
f[i2][0] += f2[0];
f[i2][1] += f2[1];
f[i2][2] += f2[2];
}
if (newton_bond || i3 < nlocal) {
f[i3][0] += f3[0];
f[i3][1] += f3[1];
f[i3][2] += f3[2];
}
if (newton_bond || i4 < nlocal) {
f[i4][0] += f4[0];
f[i4][1] += f4[1];
f[i4][2] += f4[2];
}
if (evflag)
ev_tally(i1,i2,i3,i4,nlocal,newton_bond,eimproper,f1,f3,f4,
vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
}
}
/* ---------------------------------------------------------------------- */
void ImproperCvff::allocate()
{
allocated = 1;
int n = atom->nimpropertypes;
k = (double *) memory->smalloc((n+1)*sizeof(double),"improper:k");
sign = (int *) memory->smalloc((n+1)*sizeof(int),"improper:sign");
multiplicity = (int *)
memory->smalloc((n+1)*sizeof(int),"improper:multiplicity");
setflag = (int *) memory->smalloc((n+1)*sizeof(int),"improper:setflag");
for (int i = 1; i <= n; i++) setflag[i] = 0;
}
/* ----------------------------------------------------------------------
set coeffs for one type
------------------------------------------------------------------------- */
void ImproperCvff::coeff(int narg, char **arg)
{
if (narg != 4) error->all("Incorrect args for improper coefficients");
if (!allocated) allocate();
int ilo,ihi;
force->bounds(arg[0],atom->nimpropertypes,ilo,ihi);
double k_one = force->numeric(arg[1]);
int sign_one = force->inumeric(arg[2]);
int multiplicity_one = force->inumeric(arg[3]);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
k[i] = k_one;
sign[i] = sign_one;
multiplicity[i] = multiplicity_one;
setflag[i] = 1;
count++;
}
if (count == 0) error->all("Incorrect args for improper coefficients");
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void ImproperCvff::write_restart(FILE *fp)
{
fwrite(&k[1],sizeof(double),atom->nimpropertypes,fp);
fwrite(&sign[1],sizeof(int),atom->nimpropertypes,fp);
fwrite(&multiplicity[1],sizeof(int),atom->nimpropertypes,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void ImproperCvff::read_restart(FILE *fp)
{
allocate();
if (comm->me == 0) {
fread(&k[1],sizeof(double),atom->nimpropertypes,fp);
fread(&sign[1],sizeof(int),atom->nimpropertypes,fp);
fread(&multiplicity[1],sizeof(int),atom->nimpropertypes,fp);
}
MPI_Bcast(&k[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
MPI_Bcast(&sign[1],atom->nimpropertypes,MPI_INT,0,world);
MPI_Bcast(&multiplicity[1],atom->nimpropertypes,MPI_INT,0,world);
for (int i = 1; i <= atom->nimpropertypes; i++) setflag[i] = 1;
}
diff --git a/src/MOLECULE/improper_harmonic.cpp b/src/MOLECULE/improper_harmonic.cpp
index 527fbf19b..feae8a386 100644
--- a/src/MOLECULE/improper_harmonic.cpp
+++ b/src/MOLECULE/improper_harmonic.cpp
@@ -1,285 +1,285 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "mpi.h"
#include "math.h"
#include "stdlib.h"
#include "improper_harmonic.h"
-#include "lmptype.h"
#include "atom.h"
#include "comm.h"
#include "neighbor.h"
#include "domain.h"
#include "force.h"
#include "update.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define TOLERANCE 0.05
#define SMALL 0.001
/* ---------------------------------------------------------------------- */
ImproperHarmonic::ImproperHarmonic(LAMMPS *lmp) : Improper(lmp) {}
/* ---------------------------------------------------------------------- */
ImproperHarmonic::~ImproperHarmonic()
{
if (allocated) {
memory->sfree(setflag);
memory->sfree(k);
memory->sfree(chi);
}
}
/* ---------------------------------------------------------------------- */
void ImproperHarmonic::compute(int eflag, int vflag)
{
int i1,i2,i3,i4,n,type;
double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z;
double eimproper,f1[3],f2[3],f3[3],f4[3];
double ss1,ss2,ss3,r1,r2,r3,c0,c1,c2,s1,s2;
double s12,c,s,domega,a,a11,a22,a33,a12,a13,a23;
double sx2,sy2,sz2;
eimproper = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = 0;
double **x = atom->x;
double **f = atom->f;
int **improperlist = neighbor->improperlist;
int nimproperlist = neighbor->nimproperlist;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
for (n = 0; n < nimproperlist; n++) {
i1 = improperlist[n][0];
i2 = improperlist[n][1];
i3 = improperlist[n][2];
i4 = improperlist[n][3];
type = improperlist[n][4];
// geometry of 4-body
vb1x = x[i1][0] - x[i2][0];
vb1y = x[i1][1] - x[i2][1];
vb1z = x[i1][2] - x[i2][2];
domain->minimum_image(vb1x,vb1y,vb1z);
vb2x = x[i3][0] - x[i2][0];
vb2y = x[i3][1] - x[i2][1];
vb2z = x[i3][2] - x[i2][2];
domain->minimum_image(vb2x,vb2y,vb2z);
vb3x = x[i4][0] - x[i3][0];
vb3y = x[i4][1] - x[i3][1];
vb3z = x[i4][2] - x[i3][2];
domain->minimum_image(vb3x,vb3y,vb3z);
ss1 = 1.0 / (vb1x*vb1x + vb1y*vb1y + vb1z*vb1z);
ss2 = 1.0 / (vb2x*vb2x + vb2y*vb2y + vb2z*vb2z);
ss3 = 1.0 / (vb3x*vb3x + vb3y*vb3y + vb3z*vb3z);
r1 = sqrt(ss1);
r2 = sqrt(ss2);
r3 = sqrt(ss3);
// sin and cos of angle
c0 = (vb1x * vb3x + vb1y * vb3y + vb1z * vb3z) * r1 * r3;
c1 = (vb1x * vb2x + vb1y * vb2y + vb1z * vb2z) * r1 * r2;
c2 = -(vb3x * vb2x + vb3y * vb2y + vb3z * vb2z) * r3 * r2;
s1 = 1.0 - c1*c1;
if (s1 < SMALL) s1 = SMALL;
s1 = 1.0 / s1;
s2 = 1.0 - c2*c2;
if (s2 < SMALL) s2 = SMALL;
s2 = 1.0 / s2;
s12 = sqrt(s1*s2);
c = (c1*c2 + c0) * s12;
// error check
if (c > 1.0 + TOLERANCE || c < (-1.0 - TOLERANCE)) {
int me;
MPI_Comm_rank(world,&me);
if (screen) {
char str[128];
sprintf(str,
"Improper problem: %d " BIGINT_FORMAT " %d %d %d %d",
me,update->ntimestep,
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
error->warning(str,0);
fprintf(screen," 1st atom: %d %g %g %g\n",
me,x[i1][0],x[i1][1],x[i1][2]);
fprintf(screen," 2nd atom: %d %g %g %g\n",
me,x[i2][0],x[i2][1],x[i2][2]);
fprintf(screen," 3rd atom: %d %g %g %g\n",
me,x[i3][0],x[i3][1],x[i3][2]);
fprintf(screen," 4th atom: %d %g %g %g\n",
me,x[i4][0],x[i4][1],x[i4][2]);
}
}
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
s = sqrt(1.0 - c*c);
if (s < SMALL) s = SMALL;
// force & energy
domega = acos(c) - chi[type];
a = k[type] * domega;
if (eflag) eimproper = a*domega;
a = -a * 2.0/s;
c = c * a;
s12 = s12 * a;
a11 = c*ss1*s1;
a22 = -ss2 * (2.0*c0*s12 - c*(s1+s2));
a33 = c*ss3*s2;
a12 = -r1*r2*(c1*c*s1 + c2*s12);
a13 = -r1*r3*s12;
a23 = r2*r3*(c2*c*s2 + c1*s12);
sx2 = a22*vb2x + a23*vb3x + a12*vb1x;
sy2 = a22*vb2y + a23*vb3y + a12*vb1y;
sz2 = a22*vb2z + a23*vb3z + a12*vb1z;
f1[0] = a12*vb2x + a13*vb3x + a11*vb1x;
f1[1] = a12*vb2y + a13*vb3y + a11*vb1y;
f1[2] = a12*vb2z + a13*vb3z + a11*vb1z;
f2[0] = -sx2 - f1[0];
f2[1] = -sy2 - f1[1];
f2[2] = -sz2 - f1[2];
f4[0] = a23*vb2x + a33*vb3x + a13*vb1x;
f4[1] = a23*vb2y + a33*vb3y + a13*vb1y;
f4[2] = a23*vb2z + a33*vb3z + a13*vb1z;
f3[0] = sx2 - f4[0];
f3[1] = sy2 - f4[1];
f3[2] = sz2 - f4[2];
// apply force to each of 4 atoms
if (newton_bond || i1 < nlocal) {
f[i1][0] += f1[0];
f[i1][1] += f1[1];
f[i1][2] += f1[2];
}
if (newton_bond || i2 < nlocal) {
f[i2][0] += f2[0];
f[i2][1] += f2[1];
f[i2][2] += f2[2];
}
if (newton_bond || i3 < nlocal) {
f[i3][0] += f3[0];
f[i3][1] += f3[1];
f[i3][2] += f3[2];
}
if (newton_bond || i4 < nlocal) {
f[i4][0] += f4[0];
f[i4][1] += f4[1];
f[i4][2] += f4[2];
}
if (evflag)
ev_tally(i1,i2,i3,i4,nlocal,newton_bond,eimproper,f1,f3,f4,
vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
}
}
/* ---------------------------------------------------------------------- */
void ImproperHarmonic::allocate()
{
allocated = 1;
int n = atom->nimpropertypes;
k = (double *) memory->smalloc((n+1)*sizeof(double),"improper:k");
chi = (double *) memory->smalloc((n+1)*sizeof(double),"improper:chi");
setflag = (int *) memory->smalloc((n+1)*sizeof(int),"improper:setflag");
for (int i = 1; i <= n; i++) setflag[i] = 0;
}
/* ----------------------------------------------------------------------
set coeffs for one type
------------------------------------------------------------------------- */
void ImproperHarmonic::coeff(int narg, char **arg)
{
if (narg != 3) error->all("Incorrect args for improper coefficients");
if (!allocated) allocate();
int ilo,ihi;
force->bounds(arg[0],atom->nimpropertypes,ilo,ihi);
double k_one = force->numeric(arg[1]);
double chi_one = force->numeric(arg[2]);
// convert chi from degrees to radians
int count = 0;
for (int i = ilo; i <= ihi; i++) {
k[i] = k_one;
chi[i] = chi_one/180.0 * PI;
setflag[i] = 1;
count++;
}
if (count == 0) error->all("Incorrect args for improper coefficients");
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void ImproperHarmonic::write_restart(FILE *fp)
{
fwrite(&k[1],sizeof(double),atom->nimpropertypes,fp);
fwrite(&chi[1],sizeof(double),atom->nimpropertypes,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void ImproperHarmonic::read_restart(FILE *fp)
{
allocate();
if (comm->me == 0) {
fread(&k[1],sizeof(double),atom->nimpropertypes,fp);
fread(&chi[1],sizeof(double),atom->nimpropertypes,fp);
}
MPI_Bcast(&k[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
MPI_Bcast(&chi[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
for (int i = 1; i <= atom->nimpropertypes; i++) setflag[i] = 1;
}
diff --git a/src/PERI/atom_vec_peri.cpp b/src/PERI/atom_vec_peri.cpp
index d20809e6b..a674ab3bc 100644
--- a/src/PERI/atom_vec_peri.cpp
+++ b/src/PERI/atom_vec_peri.cpp
@@ -1,777 +1,777 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Mike Parks (SNL)
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "float.h"
#include "stdlib.h"
#include "atom_vec_peri.h"
-#include "lmptype.h"
#include "atom.h"
#include "domain.h"
#include "modify.h"
#include "fix.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define DELTA 10000
/* ---------------------------------------------------------------------- */
AtomVecPeri::AtomVecPeri(LAMMPS *lmp, int narg, char **arg) :
AtomVec(lmp, narg, arg)
{
molecular = 0;
comm_x_only = 0;
comm_f_only = 1;
size_forward = 4;
size_reverse = 3;
size_border = 11;
size_velocity = 3;
size_data_atom = 7;
size_data_vel = 4;
xcol_data = 5;
atom->vfrac_flag = atom->density_flag = atom->rmass_flag = 1;
}
/* ----------------------------------------------------------------------
grow atom arrays
n = 0 grows arrays by DELTA
n > 0 allocates arrays to size n
------------------------------------------------------------------------- */
void AtomVecPeri::grow(int n)
{
if (n == 0) nmax += DELTA;
else nmax = n;
atom->nmax = nmax;
if (nmax < 0 || nmax > MAXSMALLINT)
error->one("Per-processor system is too big");
tag = atom->tag = (int *)
memory->srealloc(atom->tag,nmax*sizeof(int),"atom:tag");
type = atom->type = (int *)
memory->srealloc(atom->type,nmax*sizeof(int),"atom:type");
mask = atom->mask = (int *)
memory->srealloc(atom->mask,nmax*sizeof(int),"atom:mask");
image = atom->image = (int *)
memory->srealloc(atom->image,nmax*sizeof(int),"atom:image");
x = atom->x = memory->grow_2d_double_array(atom->x,nmax,3,"atom:x");
v = atom->v = memory->grow_2d_double_array(atom->v,nmax,3,"atom:v");
f = atom->f = memory->grow_2d_double_array(atom->f,nmax,3,"atom:f");
vfrac = atom->vfrac = (double *)
memory->srealloc(atom->vfrac,nmax*sizeof(double),"atom:vfrac");
density = atom->density = (double *)
memory->srealloc(atom->density,nmax*sizeof(double),"atom:density");
rmass = atom->rmass = (double *)
memory->srealloc(atom->rmass,nmax*sizeof(double),"atom:rmass");
s0 = atom->s0 = (double *)
memory->srealloc(atom->s0,nmax*sizeof(double),"atom:s0");
x0 = atom->x0 = memory->grow_2d_double_array(atom->x0,nmax,3,"atom:x0");
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
}
/* ----------------------------------------------------------------------
reset local array ptrs
------------------------------------------------------------------------- */
void AtomVecPeri::grow_reset()
{
tag = atom->tag; type = atom->type;
mask = atom->mask; image = atom->image;
x = atom->x; v = atom->v; f = atom->f;
vfrac = atom->vfrac; density = atom->density; rmass = atom->rmass;
s0 = atom->s0; x0 = atom->x0;
}
/* ---------------------------------------------------------------------- */
void AtomVecPeri::copy(int i, int j)
{
tag[j] = tag[i];
type[j] = type[i];
mask[j] = mask[i];
image[j] = image[i];
x[j][0] = x[i][0];
x[j][1] = x[i][1];
x[j][2] = x[i][2];
v[j][0] = v[i][0];
v[j][1] = v[i][1];
v[j][2] = v[i][2];
vfrac[j] = vfrac[i];
density[j] = density[i];
rmass[j] = rmass[i];
s0[j] = s0[i];
x0[j][0] = x0[i][0];
x0[j][1] = x0[i][1];
x0[j][2] = x0[i][2];
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j);
}
/* ---------------------------------------------------------------------- */
int AtomVecPeri::pack_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = s0[j];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
dz = pbc[2]*domain->zprd;
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = s0[j];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecPeri::pack_comm_vel(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = s0[j];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
dz = pbc[2]*domain->zprd;
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = s0[j];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecPeri::pack_comm_one(int i, double *buf)
{
buf[0] = s0[i];
return 1;
}
/* ---------------------------------------------------------------------- */
void AtomVecPeri::unpack_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
s0[i] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
void AtomVecPeri::unpack_comm_vel(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
s0[i] = buf[m++];
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecPeri::unpack_comm_one(int i, double *buf)
{
s0[i] = buf[0];
return 1;
}
/* ---------------------------------------------------------------------- */
int AtomVecPeri::pack_reverse(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
buf[m++] = f[i][0];
buf[m++] = f[i][1];
buf[m++] = f[i][2];
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecPeri::unpack_reverse(int n, int *list, double *buf)
{
int i,j,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
f[j][0] += buf[m++];
f[j][1] += buf[m++];
f[j][2] += buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecPeri::pack_border(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = vfrac[j];
buf[m++] = s0[j];
buf[m++] = x0[j][0];
buf[m++] = x0[j][1];
buf[m++] = x0[j][2];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0];
dy = pbc[1];
dz = pbc[2];
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = vfrac[j];
buf[m++] = s0[j];
buf[m++] = x0[j][0];
buf[m++] = x0[j][1];
buf[m++] = x0[j][2];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecPeri::pack_border_vel(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = vfrac[j];
buf[m++] = s0[j];
buf[m++] = x0[j][0];
buf[m++] = x0[j][1];
buf[m++] = x0[j][2];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0];
dy = pbc[1];
dz = pbc[2];
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = vfrac[j];
buf[m++] = s0[j];
buf[m++] = x0[j][0];
buf[m++] = x0[j][1];
buf[m++] = x0[j][2];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecPeri::pack_border_one(int i, double *buf)
{
buf[0] = vfrac[i];
buf[1] = s0[i];
buf[2] = x0[i][0];
buf[3] = x0[i][1];
buf[4] = x0[i][2];
return 5;
}
/* ---------------------------------------------------------------------- */
void AtomVecPeri::unpack_border(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
if (i == nmax) grow(0);
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
tag[i] = static_cast<int> (buf[m++]);
type[i] = static_cast<int> (buf[m++]);
mask[i] = static_cast<int> (buf[m++]);
vfrac[i] = buf[m++];
s0[i] = buf[m++];
x0[i][0] = buf[m++];
x0[i][1] = buf[m++];
x0[i][2] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
void AtomVecPeri::unpack_border_vel(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
if (i == nmax) grow(0);
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
tag[i] = static_cast<int> (buf[m++]);
type[i] = static_cast<int> (buf[m++]);
mask[i] = static_cast<int> (buf[m++]);
vfrac[i] = buf[m++];
s0[i] = buf[m++];
x0[i][0] = buf[m++];
x0[i][1] = buf[m++];
x0[i][2] = buf[m++];
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecPeri::unpack_border_one(int i, double *buf)
{
vfrac[i] = buf[0];
s0[i] = buf[1];
x0[i][0] = buf[2];
x0[i][1] = buf[3];
x0[i][2] = buf[4];
return 5;
}
/* ----------------------------------------------------------------------
pack data for atom I for sending to another proc
xyz must be 1st 3 values, so comm::exchange() can test on them
------------------------------------------------------------------------- */
int AtomVecPeri::pack_exchange(int i, double *buf)
{
int m = 1;
buf[m++] = x[i][0];
buf[m++] = x[i][1];
buf[m++] = x[i][2];
buf[m++] = v[i][0];
buf[m++] = v[i][1];
buf[m++] = v[i][2];
buf[m++] = tag[i];
buf[m++] = type[i];
buf[m++] = mask[i];
buf[m++] = image[i];
buf[m++] = vfrac[i];
buf[m++] = density[i];
buf[m++] = rmass[i];
buf[m++] = s0[i];
buf[m++] = x0[i][0];
buf[m++] = x0[i][1];
buf[m++] = x0[i][2];
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]);
buf[0] = m;
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecPeri::unpack_exchange(double *buf)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
int m = 1;
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
x[nlocal][2] = buf[m++];
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
tag[nlocal] = static_cast<int> (buf[m++]);
type[nlocal] = static_cast<int> (buf[m++]);
mask[nlocal] = static_cast<int> (buf[m++]);
image[nlocal] = static_cast<int> (buf[m++]);
vfrac[nlocal] = buf[m++];
density[nlocal] = buf[m++];
rmass[nlocal] = buf[m++];
s0[nlocal] = buf[m++];
x0[nlocal][0] = buf[m++];
x0[nlocal][1] = buf[m++];
x0[nlocal][2] = buf[m++];
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->
unpack_exchange(nlocal,&buf[m]);
atom->nlocal++;
return m;
}
/* ----------------------------------------------------------------------
size of restart data for all atoms owned by this proc
include extra data stored by fixes
------------------------------------------------------------------------- */
int AtomVecPeri::size_restart()
{
int i;
int nlocal = atom->nlocal;
int n = 18 * nlocal;
if (atom->nextra_restart)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
for (i = 0; i < nlocal; i++)
n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
return n;
}
/* ----------------------------------------------------------------------
pack atom I's data for restart file including extra quantities
xyz must be 1st 3 values, so that read_restart can test on them
molecular types may be negative, but write as positive
------------------------------------------------------------------------- */
int AtomVecPeri::pack_restart(int i, double *buf)
{
int m = 1;
buf[m++] = x[i][0];
buf[m++] = x[i][1];
buf[m++] = x[i][2];
buf[m++] = tag[i];
buf[m++] = type[i];
buf[m++] = mask[i];
buf[m++] = image[i];
buf[m++] = v[i][0];
buf[m++] = v[i][1];
buf[m++] = v[i][2];
buf[m++] = vfrac[i];
buf[m++] = density[i];
buf[m++] = rmass[i];
buf[m++] = s0[i];
buf[m++] = x0[i][0];
buf[m++] = x0[i][1];
buf[m++] = x0[i][2];
if (atom->nextra_restart)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]);
buf[0] = m;
return m;
}
/* ----------------------------------------------------------------------
unpack data for one atom from restart file including extra quantities
------------------------------------------------------------------------- */
int AtomVecPeri::unpack_restart(double *buf)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) {
grow(0);
if (atom->nextra_store)
atom->extra = memory->grow_2d_double_array(atom->extra,nmax,
atom->nextra_store,
"atom:extra");
}
int m = 1;
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
x[nlocal][2] = buf[m++];
tag[nlocal] = static_cast<int> (buf[m++]);
type[nlocal] = static_cast<int> (buf[m++]);
mask[nlocal] = static_cast<int> (buf[m++]);
image[nlocal] = static_cast<int> (buf[m++]);
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
vfrac[nlocal] = buf[m++];
density[nlocal] = buf[m++];
rmass[nlocal] = buf[m++];
s0[nlocal] = buf[m++];
x0[nlocal][0] = buf[m++];
x0[nlocal][1] = buf[m++];
x0[nlocal][2] = buf[m++];
double **extra = atom->extra;
if (atom->nextra_store) {
int size = static_cast<int> (buf[0]) - m;
for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++];
}
atom->nlocal++;
return m;
}
/* ----------------------------------------------------------------------
create one atom of itype at coord
set other values to defaults
------------------------------------------------------------------------- */
void AtomVecPeri::create_atom(int itype, double *coord)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
tag[nlocal] = 0;
type[nlocal] = itype;
x[nlocal][0] = coord[0];
x[nlocal][1] = coord[1];
x[nlocal][2] = coord[2];
mask[nlocal] = 1;
image[nlocal] = (512 << 20) | (512 << 10) | 512;
v[nlocal][0] = 0.0;
v[nlocal][1] = 0.0;
v[nlocal][2] = 0.0;
vfrac[nlocal] = 1.0;
density[nlocal] = 1.0;
rmass[nlocal] = density[nlocal];
s0[nlocal] = DBL_MAX;
x0[nlocal][0] = coord[0];
x0[nlocal][1] = coord[1];
x0[nlocal][2] = coord[2];
atom->nlocal++;
}
/* ----------------------------------------------------------------------
unpack one line from Atoms section of data file
initialize other atom quantities
------------------------------------------------------------------------- */
void AtomVecPeri::data_atom(double *coord, int imagetmp, char **values)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
tag[nlocal] = atoi(values[0]);
if (tag[nlocal] <= 0)
error->one("Invalid atom ID in Atoms section of data file");
type[nlocal] = atoi(values[1]);
if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
error->one("Invalid atom type in Atoms section of data file");
vfrac[nlocal] = atof(values[2]);
density[nlocal] = atof(values[3]);
rmass[nlocal] = density[nlocal];
if (rmass[nlocal] <= 0.0) error->one("Invalid mass value");
x[nlocal][0] = coord[0];
x[nlocal][1] = coord[1];
x[nlocal][2] = coord[2];
image[nlocal] = imagetmp;
mask[nlocal] = 1;
v[nlocal][0] = 0.0;
v[nlocal][1] = 0.0;
v[nlocal][2] = 0.0;
s0[nlocal] = DBL_MAX;
x0[nlocal][0] = coord[0];
x0[nlocal][1] = coord[1];
x0[nlocal][2] = coord[2];
atom->nlocal++;
}
/* ----------------------------------------------------------------------
unpack hybrid quantities from one line in Atoms section of data file
initialize other atom quantities for this sub-style
------------------------------------------------------------------------- */
int AtomVecPeri::data_atom_hybrid(int nlocal, char **values)
{
vfrac[nlocal] = atof(values[0]);
density[nlocal] = atof(values[1]);
rmass[nlocal] = density[nlocal];
if (rmass[nlocal] <= 0.0) error->one("Invalid mass value");
s0[nlocal] = DBL_MAX;
x0[nlocal][0] = x[nlocal][0];
x0[nlocal][1] = x[nlocal][1];
x0[nlocal][2] = x[nlocal][2];
return 2;
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
------------------------------------------------------------------------- */
double AtomVecPeri::memory_usage()
{
double bytes = 0.0;
if (atom->memcheck("tag")) bytes += nmax * sizeof(int);
if (atom->memcheck("type")) bytes += nmax * sizeof(int);
if (atom->memcheck("mask")) bytes += nmax * sizeof(int);
if (atom->memcheck("image")) bytes += nmax * sizeof(int);
if (atom->memcheck("x")) bytes += nmax*3 * sizeof(double);
if (atom->memcheck("v")) bytes += nmax*3 * sizeof(double);
if (atom->memcheck("f")) bytes += nmax*3 * sizeof(double);
if (atom->memcheck("vfrac")) bytes += nmax * sizeof(double);
if (atom->memcheck("density")) bytes += nmax * sizeof(double);
if (atom->memcheck("rmass")) bytes += nmax * sizeof(double);
if (atom->memcheck("s0")) bytes += nmax * sizeof(double);
if (atom->memcheck("x0")) bytes += nmax*3 * sizeof(double);
return bytes;
}
diff --git a/src/REAX/fix_reax_bonds.cpp b/src/REAX/fix_reax_bonds.cpp
index 0607acc5b..3d3698b77 100644
--- a/src/REAX/fix_reax_bonds.cpp
+++ b/src/REAX/fix_reax_bonds.cpp
@@ -1,238 +1,238 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Aidan Thompson (Sandia)
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "stdlib.h"
#include "string.h"
#include "fix_reax_bonds.h"
-#include "lmptype.h"
#include "pair_reax_fortran.h"
#include "atom.h"
#include "update.h"
#include "force.h"
#include "modify.h"
#include "compute.h"
#include "input.h"
#include "variable.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
FixReaxBonds::FixReaxBonds(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 5) error->all("Illegal fix reax/bonds command");
MPI_Comm_rank(world,&me);
nevery = atoi(arg[3]);
if (nevery < 1) error->all("Illegal fix reax/bonds command");
if (me == 0) {
fp = fopen(arg[4],"w");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open fix reax/bonds file %s",arg[4]);
error->one(str);
}
}
}
/* ---------------------------------------------------------------------- */
FixReaxBonds::~FixReaxBonds()
{
if (me == 0) fclose(fp);
}
/* ---------------------------------------------------------------------- */
int FixReaxBonds::setmask()
{
int mask = 0;
mask |= END_OF_STEP;
return mask;
}
/* ----------------------------------------------------------------------
perform initial write
------------------------------------------------------------------------- */
void FixReaxBonds::setup(int vflag)
{
end_of_step();
}
/* ---------------------------------------------------------------------- */
void FixReaxBonds::init()
{
// insure ReaxFF is defined
if (force->pair_match("reax",1) == NULL)
error->all("Cannot use fix reax/bonds without pair_style reax");
}
/* ---------------------------------------------------------------------- */
void FixReaxBonds::end_of_step()
{
OutputReaxBonds(update->ntimestep,fp);
if (me == 0) fflush(fp);
}
/* ---------------------------------------------------------------------- */
void FixReaxBonds::OutputReaxBonds(bigint ntimestep, FILE *fp)
{
int nparticles,nparticles_tot,nbuf,nbuf_local,most,j;
int ii,jn,mbond,numbonds,nsbmax,nsbmax_most;
int nprocs,nlocal_tmp,itmp;
double cutof3;
double *buf;
MPI_Request irequest;
MPI_Status istatus;
MPI_Comm_size(world,&nprocs);
nparticles = atom->nlocal;
nparticles_tot = static_cast<int> (atom->natoms);
mbond = ReaxParams::mbond;
FORTRAN(getnsbmax,GETNSBMAX)(&nsbmax);
FORTRAN(getcutof3,GETCUTOF3)(&cutof3);
MPI_Allreduce(&nparticles,&most,1,MPI_INT,MPI_MAX,world);
MPI_Allreduce(&nsbmax,&nsbmax_most,1,MPI_INT,MPI_MAX,world);
if (me == 0) {
fprintf(fp,"# Timestep " BIGINT_FORMAT " \n",ntimestep);
fprintf(fp,"# \n");
fprintf(fp,"# Number of particles %d \n",nparticles_tot);
fprintf(fp,"# \n");
fprintf(fp,"# Max number of bonds per atom %d with "
"coarse bond order cutoff %5.3f \n",
nsbmax_most,cutof3);
fprintf(fp,"# Particle connection table and bond orders \n");
fprintf(fp,"# id type nb id_1...id_nb mol bo_1...bo_nb abo nlp q \n");
}
// allocate a temporary buffer for the snapshot info
// big enough for largest number of atoms on any one proc
// nbuf_local = size of local buffer for table of atom bonds
nbuf = 1+(2*nsbmax_most+7)*most;
buf = (double *) memory->smalloc(nbuf*sizeof(double),"reax/bonds:buf");
j = 2;
jn = ReaxParams::nat;
buf[0] = nparticles;
for (int iparticle=0;iparticle<nparticles;iparticle++) {
buf[j-1] = atom->tag[iparticle]; //atom tag
buf[j+0] = FORTRAN(cbkia,CBKIA).iag[iparticle]; //atom type
buf[j+1] = FORTRAN(cbkia,CBKIA).iag[iparticle+jn]; //no.bonds
int k;
numbonds = nint(buf[j+1]);
// connection table based on coarse bond order cutoff (> cutof3)
for (k=2;k<2+numbonds;k++) {
ii = FORTRAN(cbkia,CBKIA).iag[iparticle+jn*k];
buf[j+k] = FORTRAN(cbkc,CBKC).itag[ii-1];
}
buf[j+k]=FORTRAN(cbkia,CBKIA).iag[iparticle+jn*(mbond+2)]; //molec.id
j+=(3+numbonds);
// bond orders (> cutof3)
for (k=0;k<numbonds;k++) {
ii = FORTRAN(cbknubon2,CBKNUBON2).nubon1[iparticle+jn*k];
buf[j+k] = FORTRAN(cbkbo,CBKBO).bo[ii-1];
}
// sum of bond orders (abo), no. of lone pairs (vlp), charge (ch)
buf[j+k] = FORTRAN(cbkabo,CBKABO).abo[iparticle];
buf[j+k+1] = FORTRAN(cbklonpar,CBKLONPAR).vlp[iparticle];
// buf[j+k+2] = FORTRAN(cbkch,CBKCH).ch[iparticle];
buf[j+k+2] = atom->q[iparticle];
j+=(4+numbonds);
}
nbuf_local = j-1;
// node 0 pings each node, receives their buffer, writes to file
// all other nodes wait for ping, send buffer to node 0
if (me == 0) {
for (int inode = 0; inode<nprocs; inode++) {
if (inode == 0) {
nlocal_tmp = nparticles;
} else {
MPI_Irecv(&buf[0],nbuf,MPI_DOUBLE,inode,0,world,&irequest);
MPI_Send(&itmp,0,MPI_INT,inode,0,world);
MPI_Wait(&irequest,&istatus);
nlocal_tmp = nint(buf[0]);
}
j = 2;
for (int iparticle=0;iparticle<nlocal_tmp;iparticle++) {
// print atom tag, atom type, no.bonds
fprintf(fp," %d %d %d",nint(buf[j-1]),nint(buf[j+0]),nint(buf[j+1]));
int k;
numbonds = nint(buf[j+1]);
if (numbonds > nsbmax_most) {
char str[128];
sprintf(str,"Fix reax/bonds numbonds > nsbmax_most");
error->one(str);
}
// print connection table
for (k=2;k<2+numbonds;k++)
fprintf(fp," %d",nint(buf[j+k]));
fprintf(fp," %d",nint(buf[j+k]));
j+=(3+numbonds);
// print bond orders
for (k=0;k<numbonds;k++)
fprintf(fp,"%14.3f",buf[j+k]);
// print sum of bond orders, no. of lone pairs, charge
fprintf(fp,"%14.3f%14.3f%14.3f\n",buf[j+k],buf[j+k+1],buf[j+k+2]);
j+=(4+numbonds);
}
}
} else {
MPI_Recv(&itmp,0,MPI_INT,0,0,world,&istatus);
MPI_Rsend(&buf[0],nbuf_local,MPI_DOUBLE,0,0,world);
}
if (me == 0) fprintf(fp,"# \n");
memory->sfree(buf);
}
/* ---------------------------------------------------------------------- */
int FixReaxBonds::nint(const double &r)
{
int i = 0;
if (r>0.0) i = static_cast<int>(r+0.5);
else if (r<0.0) i = static_cast<int>(r-0.5);
return i;
}
diff --git a/src/REAX/fix_reax_bonds.h b/src/REAX/fix_reax_bonds.h
index 42bc6ea06..678984f02 100644
--- a/src/REAX/fix_reax_bonds.h
+++ b/src/REAX/fix_reax_bonds.h
@@ -1,50 +1,50 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
FixStyle(reax/bonds,FixReaxBonds)
#else
#ifndef LMP_FIX_REAX_BONDS_H
#define LMP_FIX_REAX_BONDS_H
+#include "lmptype.h"
#include "stdio.h"
#include "fix.h"
-#include "lmptype.h"
namespace LAMMPS_NS {
class FixReaxBonds : public Fix {
public:
FixReaxBonds(class LAMMPS *, int, char **);
~FixReaxBonds();
int setmask();
void init();
void setup(int);
void end_of_step();
private:
int me;
int nfreq;
FILE *fp;
void OutputReaxBonds(bigint, FILE*);
int nint(const double&);
};
}
#endif
#endif
diff --git a/src/REPLICA/fix_event_prd.cpp b/src/REPLICA/fix_event_prd.cpp
index 3fba4da90..ac428f371 100644
--- a/src/REPLICA/fix_event_prd.cpp
+++ b/src/REPLICA/fix_event_prd.cpp
@@ -1,101 +1,101 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "stdlib.h"
#include "string.h"
#include "fix_event_prd.h"
-#include "lmptype.h"
#include "atom.h"
#include "update.h"
#include "domain.h"
#include "neighbor.h"
#include "comm.h"
#include "universe.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
FixEventPRD::FixEventPRD(LAMMPS *lmp, int narg, char **arg) :
FixEvent(lmp, narg, arg)
{
if (narg != 3) error->all("Illegal fix event command");
restart_global = 1;
event_number = 0;
event_timestep = update->ntimestep;
clock = 0;
}
/* ----------------------------------------------------------------------
save current atom coords as an event (via call to base class)
called when an event occurs in some replica
set event_timestep = when event occurred in a particular replica
update clock = elapsed time since last event, across all replicas
------------------------------------------------------------------------- */
void FixEventPRD::store_event_prd(bigint ntimestep, int delta_clock)
{
store_event();
event_timestep = ntimestep;
clock += delta_clock;
event_number++;
}
/* ----------------------------------------------------------------------
pack entire state of Fix into one write
------------------------------------------------------------------------- */
void FixEventPRD::write_restart(FILE *fp)
{
int n = 0;
double list[6];
list[n++] = event_number;
list[n++] = event_timestep;
list[n++] = clock;
list[n++] = replica_number;
list[n++] = correlated_event;
list[n++] = ncoincident;
if (comm->me == 0) {
int size = n * sizeof(double);
fwrite(&size,sizeof(int),1,fp);
fwrite(list,sizeof(double),n,fp);
}
}
/* ----------------------------------------------------------------------
use state info from restart file to restart the Fix
------------------------------------------------------------------------- */
void FixEventPRD::restart(char *buf)
{
int n = 0;
double *list = (double *) buf;
event_number = static_cast<int> (list[n++]);
event_timestep = static_cast<int> (list[n++]);
clock = static_cast<int> (list[n++]);
replica_number = static_cast<int> (list[n++]);
correlated_event = static_cast<int> (list[n++]);
ncoincident = static_cast<int> (list[n++]);
}
diff --git a/src/REPLICA/fix_event_prd.h b/src/REPLICA/fix_event_prd.h
index 18f77b324..e5aaa8ccd 100644
--- a/src/REPLICA/fix_event_prd.h
+++ b/src/REPLICA/fix_event_prd.h
@@ -1,54 +1,54 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
FixStyle(EVENT/PRD,FixEventPRD)
#else
#ifndef LMP_FIX_EVENT_PRD_H
#define LMP_FIX_EVENT_PRD_H
-#include "fix_event.h"
#include "lmptype.h"
+#include "fix_event.h"
namespace LAMMPS_NS {
class FixEventPRD : public FixEvent {
public:
int event_number; // event counter
bigint event_timestep; // timestep of last event on any replica
int clock; // total elapsed timesteps across all replicas
int replica_number; // replica where last event occured
int correlated_event; // 1 if last event was correlated, 0 otherwise
int ncoincident; // # of simultaneous events on different replicas
FixEventPRD(class LAMMPS *, int, char **);
~FixEventPRD() {}
void write_restart(FILE *);
void restart(char *);
// methods specific to FixEventPRD, invoked by PRD
void store_event_prd(bigint, int);
private:
};
}
#endif
#endif
diff --git a/src/REPLICA/fix_event_tad.cpp b/src/REPLICA/fix_event_tad.cpp
index 8968ec8b7..950fcd6b8 100644
--- a/src/REPLICA/fix_event_tad.cpp
+++ b/src/REPLICA/fix_event_tad.cpp
@@ -1,95 +1,95 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "stdlib.h"
#include "string.h"
#include "fix_event_tad.h"
-#include "lmptype.h"
#include "atom.h"
#include "update.h"
#include "domain.h"
#include "neighbor.h"
#include "comm.h"
#include "universe.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
FixEventTAD::FixEventTAD(LAMMPS *lmp, int narg, char **arg) :
FixEvent(lmp, narg, arg)
{
if (narg != 3) error->all("Illegal fix event command");
restart_global = 1;
event_number = 0;
event_timestep = update->ntimestep;
tlo = 0.0;
ebarrier = 0.0;
}
/* ----------------------------------------------------------------------
save current atom coords as an event (via call to base class)
called when an event occurs in some replica
set event_timestep = when event occurred
------------------------------------------------------------------------- */
void FixEventTAD::store_event_tad(bigint ntimestep)
{
store_event();
event_timestep = ntimestep;
}
/* ----------------------------------------------------------------------
pack entire state of Fix into one write
------------------------------------------------------------------------- */
void FixEventTAD::write_restart(FILE *fp)
{
int n = 0;
double list[4];
list[n++] = event_number;
list[n++] = event_timestep;
list[n++] = tlo;
list[n++] = ebarrier;
if (comm->me == 0) {
int size = n * sizeof(double);
fwrite(&size,sizeof(int),1,fp);
fwrite(list,sizeof(double),n,fp);
}
}
/* ----------------------------------------------------------------------
use state info from restart file to restart the Fix
------------------------------------------------------------------------- */
void FixEventTAD::restart(char *buf)
{
int n = 0;
double *list = (double *) buf;
event_number = static_cast<int> (list[n++]);
event_timestep = static_cast<int> (list[n++]);
tlo = list[n++];
ebarrier = list[n++];
}
diff --git a/src/REPLICA/fix_event_tad.h b/src/REPLICA/fix_event_tad.h
index 2b6067e9e..ccd3c1cd4 100644
--- a/src/REPLICA/fix_event_tad.h
+++ b/src/REPLICA/fix_event_tad.h
@@ -1,52 +1,52 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
FixStyle(EVENT/TAD,FixEventTAD)
#else
#ifndef LMP_FIX_EVENT_TAD_H
#define LMP_FIX_EVENT_TAD_H
-#include "fix_event.h"
#include "lmptype.h"
+#include "fix_event.h"
namespace LAMMPS_NS {
class FixEventTAD : public FixEvent {
public:
int event_number; // event counter
bigint event_timestep; // timestep of last event
double tlo; // event time at low temperature
double ebarrier; // energy barrier for this event
FixEventTAD(class LAMMPS *, int, char **);
~FixEventTAD() {}
void write_restart(FILE *);
void restart(char *);
// methods specific to FixEventTAD, invoked by TAD
void store_event_tad(bigint);
private:
};
}
#endif
#endif
diff --git a/src/REPLICA/neb.cpp b/src/REPLICA/neb.cpp
index fe5e74a1d..ebe45eeee 100644
--- a/src/REPLICA/neb.cpp
+++ b/src/REPLICA/neb.cpp
@@ -1,512 +1,512 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "mpi.h"
#include "math.h"
#include "stdlib.h"
#include "string.h"
#include "neb.h"
-#include "lmptype.h"
#include "universe.h"
#include "atom.h"
#include "update.h"
#include "domain.h"
#include "min.h"
#include "modify.h"
#include "fix.h"
#include "fix_neb.h"
#include "output.h"
#include "thermo.h"
#include "finish.h"
#include "timer.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define CHUNK 1000
#define MAXLINE 256
/* ---------------------------------------------------------------------- */
NEB::NEB(LAMMPS *lmp) : Pointers(lmp) {}
/* ----------------------------------------------------------------------
internal NEB constructor
------------------------------------------------------------------------- */
NEB::NEB(LAMMPS *lmp, double etol_in, double ftol_in, int n1steps_in,
int n2steps_in, int nevery_in, double *buf_init, double *buf_final)
: Pointers(lmp)
{
double delx,dely,delz;
etol = etol_in;
ftol = ftol_in;
n1steps = n1steps_in;
n2steps = n2steps_in;
nevery = nevery_in;
// replica info
nreplica = universe->nworlds;
ireplica = universe->iworld;
me_universe = universe->me;
uworld = universe->uworld;
MPI_Comm_rank(world,&me);
// generate linear interpolate replica
double fraction = ireplica/(nreplica-1.0);
double **x = atom->x;
int nlocal = atom->nlocal;
int ii = 0;
for (int i = 0; i < nlocal; i++) {
delx = buf_final[ii] - buf_init[ii];
dely = buf_final[ii+1] - buf_init[ii+1];
delz = buf_final[ii+2] - buf_init[ii+2];
domain->minimum_image(delx,dely,delz);
x[i][0] = buf_init[ii] + fraction*delx;
x[i][1] = buf_init[ii+1] + fraction*dely;
x[i][2] = buf_init[ii+2] + fraction*delz;
ii += 3;
}
}
/* ---------------------------------------------------------------------- */
NEB::~NEB()
{
MPI_Comm_free(&roots);
memory->destroy_2d_double_array(all);
delete [] rdist;
}
/* ----------------------------------------------------------------------
perform NEB on multiple replicas
------------------------------------------------------------------------- */
void NEB::command(int narg, char **arg)
{
if (domain->box_exist == 0)
error->all("NEB command before simulation box is defined");
if (narg != 6) error->universe_all("Illegal NEB command");
etol = atof(arg[0]);
ftol = atof(arg[1]);
n1steps = atoi(arg[2]);
n2steps = atoi(arg[3]);
nevery = atoi(arg[4]);
infile = arg[5];
// error checks
if (etol < 0.0) error->all("Illegal NEB command");
if (ftol < 0.0) error->all("Illegal NEB command");
if (nevery == 0) error->universe_all("Illegal NEB command");
if (n1steps % nevery || n2steps % nevery)
error->universe_all("Illegal NEB command");
// replica info
nreplica = universe->nworlds;
ireplica = universe->iworld;
me_universe = universe->me;
uworld = universe->uworld;
MPI_Comm_rank(world,&me);
// read in file of final state atom coords and reset my coords
readfile(infile);
// run the NEB calculation
run();
}
/* ----------------------------------------------------------------------
run NEB on multiple replicas
------------------------------------------------------------------------- */
void NEB::run()
{
// create MPI communicator for root proc from each world
int color;
if (me == 0) color = 0;
else color = 1;
MPI_Comm_split(uworld,color,0,&roots);
// error checks
if (nreplica == 1) error->all("Cannot use NEB with a single replica");
if (nreplica != universe->nprocs)
error->all("Can only use NEB with 1-processor replicas");
if (atom->sortfreq > 0)
error->all("Cannot use NEB with atom_modify sort enabled");
if (atom->map_style == 0)
error->all("Cannot use NEB unless atom map exists");
int ineb,idamp;
for (ineb = 0; ineb < modify->nfix; ineb++)
if (strcmp(modify->fix[ineb]->style,"neb") == 0) break;
if (ineb == modify->nfix) error->all("NEB requires use of fix neb");
fneb = (FixNEB *) modify->fix[ineb];
nall = 4;
all = memory->create_2d_double_array(nreplica,nall,"neb:all");
rdist = new double[nreplica];
// initialize LAMMPS
update->whichflag = 2;
update->etol = etol;
update->ftol = ftol;
update->multireplica = 1;
lmp->init();
if (update->minimize->searchflag)
error->all("NEB requires damped dynamics minimizer");
// setup regular NEB minimization
if (me_universe == 0 && universe->uscreen)
fprintf(universe->uscreen,"Setting up regular NEB ...\n");
update->beginstep = update->firststep = update->ntimestep;
update->endstep = update->laststep = update->firststep + n1steps;
update->nsteps = n1steps;
update->max_eval = n1steps;
if (update->laststep < 0 || update->laststep > MAXBIGINT)
error->all("Too many timesteps");
update->minimize->setup();
if (me_universe == 0) {
if (universe->uscreen)
fprintf(universe->uscreen,"Step MaxReplicaForce MaxAtomForce "
"GradV0 GradV1 GradVc "
"EBF EBR RDT "
"RD1 PE1 RD2 PE2 ... RDN PEN\n");
if (universe->ulogfile)
fprintf(universe->ulogfile,"Step MaxReplicaForce MaxAtomForce "
"GradV0 GradV1 GradVc "
"EBF EBR RDT "
"RD1 PE1 RD2 PE2 ... RDN PEN\n");
}
print_status();
// perform regular NEB for n1steps or until replicas converge
// retrieve PE values from fix NEB and print every nevery iterations
// break induced if converged
// damped dynamic min styles insure all replicas converge together
int flag,flagall;
timer->barrier_start(TIME_LOOP);
while (update->minimize->niter < n1steps) {
update->minimize->run(nevery);
print_status();
if (update->minimize->stop_condition) break;
}
timer->barrier_stop(TIME_LOOP);
update->minimize->cleanup();
Finish finish(lmp);
finish.end(1);
// switch fix NEB to climbing mode
// top = replica that becomes hill climber
double vmax = all[0][0];
int top = 0;
for (int m = 1; m < nreplica; m++)
if (vmax < all[m][0]) {
vmax = all[m][0];
top = m;
}
// setup climbing NEB minimization
// must reinitialize minimizer so it re-creates its fix MINIMIZE
if (me_universe == 0 && universe->uscreen)
fprintf(universe->uscreen,"Setting up climbing ...\n");
if (me_universe == 0) {
if (universe->uscreen)
fprintf(universe->uscreen,"Climbing replica = %d\n",top+1);
if (universe->ulogfile)
fprintf(universe->ulogfile,"Climbing replica = %d\n",top+1);
}
update->beginstep = update->firststep = update->ntimestep;
update->endstep = update->laststep = update->firststep + n2steps;
update->nsteps = n2steps;
update->max_eval = n2steps;
if (update->laststep < 0 || update->laststep > MAXBIGINT)
error->all("Too many timesteps");
update->minimize->init();
fneb->rclimber = top;
update->minimize->setup();
if (me_universe == 0) {
if (universe->uscreen)
fprintf(universe->uscreen,"Step MaxReplicaForce MaxAtomForce "
"GradV0 GradV1 GradVc "
"EBF EBR RDT "
"RD1 PE1 RD2 PE2 ... RDN PEN\n");
if (universe->ulogfile)
fprintf(universe->ulogfile,"Step MaxReplicaForce MaxAtomForce "
"GradV0 GradV1 GradVc "
"EBF EBR RDT "
"RD1 PE1 RD2 PE2 ... RDN PEN\n");
}
print_status();
// perform climbing NEB for n2steps or until replicas converge
// retrieve PE values from fix NEB and print every nevery iterations
// break induced if converged
// damped dynamic min styles insure all replicas converge together
timer->barrier_start(TIME_LOOP);
while (update->minimize->niter < n2steps) {
update->minimize->run(nevery);
print_status();
if (update->minimize->stop_condition) break;
}
timer->barrier_stop(TIME_LOOP);
update->minimize->cleanup();
finish.end(1);
update->whichflag = 0;
update->multireplica = 0;
update->firststep = update->laststep = 0;
update->beginstep = update->endstep = 0;
}
/* ----------------------------------------------------------------------
read target coordinates from file, store with appropriate atom
adjust coords of each atom based on ireplica
new coord = replica fraction between current and final state
------------------------------------------------------------------------- */
void NEB::readfile(char *file)
{
if (me_universe == 0) {
if (screen) fprintf(screen,"Reading NEB coordinate file %s ...\n",file);
open(file);
}
double fraction = ireplica/(nreplica-1.0);
double **x = atom->x;
int *image = atom->image;
int nlocal = atom->nlocal;
char *buffer = new char[CHUNK*MAXLINE];
char *ptr,*next,*bufptr;
int i,m,nlines,tag;
double xx,yy,zz,delx,dely,delz;
int firstline = 1;
int ncount = 0;
int eof = 0;
while (!eof) {
if (me_universe == 0) {
m = 0;
for (nlines = 0; nlines < CHUNK; nlines++) {
ptr = fgets(&buffer[m],MAXLINE,fp);
if (ptr == NULL) break;
m += strlen(&buffer[m]);
}
if (ptr == NULL) eof = 1;
buffer[m++] = '\n';
}
MPI_Bcast(&eof,1,MPI_INT,0,uworld);
MPI_Bcast(&nlines,1,MPI_INT,0,uworld);
MPI_Bcast(&m,1,MPI_INT,0,uworld);
MPI_Bcast(buffer,m,MPI_CHAR,0,uworld);
bufptr = buffer;
for (i = 0; i < nlines; i++) {
next = strchr(bufptr,'\n');
*next = '\0';
if (firstline) {
if (atom->count_words(bufptr) == 4) firstline = 0;
else error->all("Incorrect format in NEB coordinate file");
}
sscanf(bufptr,"%d %lg %lg %lg",&tag,&xx,&yy,&zz);
// adjust atom coord based on replica fraction
// ignore image flags of final x
// new x is displacement from old x
// if final x is across periodic boundary:
// new x may be outside box
// will be remapped back into box when simulation starts
// its image flags will be adjusted appropriately
m = atom->map(tag);
if (m >= 0 && m < nlocal) {
delx = xx - x[m][0];
dely = yy - x[m][1];
delz = zz - x[m][2];
domain->minimum_image(delx,dely,delz);
x[m][0] += fraction*delx;
x[m][1] += fraction*dely;
x[m][2] += fraction*delz;
ncount++;
}
bufptr = next + 1;
}
}
// clean up
delete [] buffer;
if (me_universe == 0) {
if (compressed) pclose(fp);
else fclose(fp);
}
}
/* ----------------------------------------------------------------------
universe proc 0 opens NEB data file
test if gzipped
------------------------------------------------------------------------- */
void NEB::open(char *file)
{
compressed = 0;
char *suffix = file + strlen(file) - 3;
if (suffix > file && strcmp(suffix,".gz") == 0) compressed = 1;
if (!compressed) fp = fopen(file,"r");
else {
#ifdef LAMMPS_GZIP
char gunzip[128];
sprintf(gunzip,"gunzip -c %s",file);
fp = popen(gunzip,"r");
#else
error->one("Cannot open gzipped file");
#endif
}
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open file %s",file);
error->one(str);
}
}
/* ----------------------------------------------------------------------
query fix NEB for PE of each replica
proc 0 prints current NEB status
------------------------------------------------------------------------- */
void NEB::print_status()
{
double fnorm2 = sqrt(update->minimize->fnorm_sqr());
double fmaxreplica;
MPI_Allreduce(&fnorm2,&fmaxreplica,1,MPI_DOUBLE,MPI_MAX,roots);
double fnorminf = update->minimize->fnorm_inf();
double fmaxatom;
MPI_Allreduce(&fnorminf,&fmaxatom,1,MPI_DOUBLE,MPI_MAX,roots);
double one[4];
one[0] = fneb->veng;
one[1] = fneb->plen;
one[2] = fneb->nlen;
one[nall-1] = fneb->gradvnorm;
if (output->thermo->normflag) one[0] /= atom->natoms;
if (me == 0)
MPI_Allgather(one,nall,MPI_DOUBLE,&all[0][0],nall,MPI_DOUBLE,roots);
rdist[0] = 0.0;
for (int i = 1; i < nreplica; i++)
rdist[i] = rdist[i-1] + all[i][1];
double endpt = rdist[nreplica-1] = rdist[nreplica-2] + all[nreplica-2][2];
for (int i = 1; i < nreplica; i++)
rdist[i] /= endpt;
// look up GradV for the initial, final, and climbing replicas
// these are identical to fnorm2, but to be safe we
// take them straight from fix_neb
double gradvnorm0, gradvnorm1, gradvnormc;
int irep;
irep = 0;
gradvnorm0 = all[irep][3];
irep = nreplica-1;
gradvnorm1 = all[irep][3];
irep = fneb->rclimber;
if (irep > -1) {
gradvnormc = all[irep][3];
ebf = all[irep][0]-all[0][0];
ebr = all[irep][0]-all[nreplica-1][0];
} else {
double vmax = all[0][0];
int top = 0;
for (int m = 1; m < nreplica; m++)
if (vmax < all[m][0]) {
vmax = all[m][0];
top = m;
}
irep = top;
gradvnormc = all[irep][3];
ebf = all[irep][0]-all[0][0];
ebr = all[irep][0]-all[nreplica-1][0];
}
if (me_universe == 0) {
if (universe->uscreen) {
fprintf(universe->uscreen,BIGINT_FORMAT " %g %g ",update->ntimestep,
fmaxreplica,fmaxatom);
fprintf(universe->uscreen,"%g %g %g ",
gradvnorm0,gradvnorm1,gradvnormc);
fprintf(universe->uscreen,"%g %g %g ",ebf,ebr,endpt);
for (int i = 0; i < nreplica; i++)
fprintf(universe->uscreen,"%g %g ",rdist[i],all[i][0]);
fprintf(universe->uscreen,"\n");
}
if (universe->ulogfile) {
fprintf(universe->ulogfile,BIGINT_FORMAT " %g %g ",update->ntimestep,
fmaxreplica,fmaxatom);
fprintf(universe->ulogfile,"%g %g %g ",
gradvnorm0,gradvnorm1,gradvnormc);
fprintf(universe->ulogfile,"%g %g %g ",ebf,ebr,endpt);
for (int i = 0; i < nreplica; i++)
fprintf(universe->ulogfile,"%g %g ",rdist[i],all[i][0]);
fprintf(universe->ulogfile,"\n");
fflush(universe->ulogfile);
}
}
}
diff --git a/src/REPLICA/prd.cpp b/src/REPLICA/prd.cpp
index 28ec841d4..84d711270 100644
--- a/src/REPLICA/prd.cpp
+++ b/src/REPLICA/prd.cpp
@@ -1,817 +1,817 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "mpi.h"
#include "math.h"
#include "stdlib.h"
#include "string.h"
#include "prd.h"
-#include "lmptype.h"
#include "universe.h"
#include "update.h"
#include "atom.h"
#include "domain.h"
#include "region.h"
#include "comm.h"
#include "velocity.h"
#include "integrate.h"
#include "min.h"
#include "neighbor.h"
#include "modify.h"
#include "compute.h"
#include "fix.h"
#include "fix_event_prd.h"
#include "force.h"
#include "pair.h"
#include "random_park.h"
#include "random_mars.h"
#include "output.h"
#include "dump.h"
#include "finish.h"
#include "timer.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PRD::PRD(LAMMPS *lmp) : Pointers(lmp) {}
/* ----------------------------------------------------------------------
perform PRD simulation on one or more replicas
------------------------------------------------------------------------- */
void PRD::command(int narg, char **arg)
{
int flag,ireplica;
// error checks
if (domain->box_exist == 0)
error->all("PRD command before simulation box is defined");
if (universe->nworlds != universe->nprocs &&
atom->map_style == 0)
error->all("Cannot use PRD with multi-processor replicas "
"unless atom map exists");
if (universe->nworlds == 1 && comm->me == 0)
error->warning("Running PRD with only one replica");
if (narg < 7) error->universe_all("Illegal prd command");
nsteps = atoi(arg[0]);
t_event = atoi(arg[1]);
n_dephase = atoi(arg[2]);
t_dephase = atoi(arg[3]);
t_corr = atoi(arg[4]);
char id_compute[strlen(arg[5])+1];
strcpy(id_compute,arg[5]);
int seed = atoi(arg[6]);
options(narg-7,&arg[7]);
// total # of timesteps must be multiple of t_event
if (t_event <= 0) error->universe_all("Invalid t_event in prd command");
if (nsteps % t_event)
error->universe_all("PRD nsteps must be multiple of t_event");
if (t_corr % t_event)
error->universe_all("PRD t_corr must be multiple of t_event");
// local storage
int me_universe = universe->me;
int nprocs_universe = universe->nprocs;
int nreplica = universe->nworlds;
int iworld = universe->iworld;
MPI_Comm_rank(world,&me);
MPI_Comm_size(world,&nprocs);
// comm_replica = communicator between same proc across replicas
// not used if replicas have unequal number of procs
// equal_size_replicas = 1 if all replicas have same # of procs
int color = me;
MPI_Comm_split(universe->uworld,color,0,&comm_replica);
flag = 0;
if (nreplica*nprocs == nprocs_universe) flag = 1;
MPI_Allreduce(&flag,&equal_size_replicas,1,MPI_INT,MPI_MIN,universe->uworld);
// workspace for inter-replica communication via gathers
natoms = atom->natoms;
displacements = NULL;
tagall = NULL;
xall = NULL;
imageall = NULL;
if (nreplica != nprocs_universe) {
displacements = new int[nprocs];
tagall = (int *) memory->smalloc(natoms*sizeof(int),"prd:tagall");
xall = memory->create_2d_double_array(natoms,3,"prd:xall");
imageall = (int *) memory->smalloc(natoms*sizeof(int),"prd:imageall");
}
// random_select = same RNG for each replica for multiple event selection
// random_dephase = unique RNG for each replica for dephasing
random_select = new RanPark(lmp,seed);
random_dephase = new RanMars(lmp,seed+iworld);
// create ComputeTemp class to monitor temperature
char **args = new char*[3];
args[0] = (char *) "prd_temp";
args[1] = (char *) "all";
args[2] = (char *) "temp";
modify->add_compute(3,args);
temperature = modify->compute[modify->ncompute-1];
// create Velocity class for velocity creation in dephasing
// pass it temperature compute, loop_setting, dist_setting settings
atom->check_mass();
velocity = new Velocity(lmp);
velocity->init_external("all");
args[0] = (char *) "temp";
args[1] = (char *) "prd_temp";
velocity->options(2,args);
args[0] = (char *) "loop";
args[1] = (char *) loop_setting;
if (loop_setting) velocity->options(2,args);
args[0] = (char *) "dist";
args[1] = (char *) dist_setting;
if (dist_setting) velocity->options(2,args);
// create FixEventPRD class to store event and pre-quench states
args[0] = (char *) "prd_event";
args[1] = (char *) "all";
args[2] = (char *) "EVENT/PRD";
modify->add_fix(3,args);
fix_event = (FixEventPRD *) modify->fix[modify->nfix-1];
// create Finish for timing output
finish = new Finish(lmp);
// string clean-up
delete [] args;
delete [] loop_setting;
delete [] dist_setting;
// assign FixEventPRD to event-detection compute
// necessary so it will know atom coords at last event
int icompute = modify->find_compute(id_compute);
if (icompute < 0) error->all("Could not find compute ID for PRD");
compute_event = modify->compute[icompute];
compute_event->reset_extra_compute_fix("prd_event");
// reset reneighboring criteria since will perform minimizations
neigh_every = neighbor->every;
neigh_delay = neighbor->delay;
neigh_dist_check = neighbor->dist_check;
if (neigh_every != 1 || neigh_delay != 0 || neigh_dist_check != 1) {
if (me == 0)
error->warning("Resetting reneighboring criteria during PRD");
}
neighbor->every = 1;
neighbor->delay = 0;
neighbor->dist_check = 1;
// initialize PRD as if one long dynamics run
update->whichflag = 1;
update->nsteps = nsteps;
update->beginstep = update->firststep = update->ntimestep;
update->endstep = update->laststep = update->firststep + nsteps;
update->restrict_output = 1;
if (update->laststep < 0 || update->laststep > MAXBIGINT)
error->all("Too many timesteps");
lmp->init();
// init minimizer settings and minimizer itself
update->etol = etol;
update->ftol = ftol;
update->max_eval = maxeval;
update->minimize->init();
// cannot use PRD with time-dependent fixes or regions or atom sorting
for (int i = 0; i < modify->nfix; i++)
if (modify->fix[i]->time_depend)
error->all("Cannot use PRD with a time-dependent fix defined");
for (int i = 0; i < domain->nregion; i++)
if (domain->regions[i]->dynamic_check())
error->all("Cannot use PRD with a time-dependent region defined");
if (atom->sortfreq > 0)
error->all("Cannot use PRD with atom_modify sort enabled");
// perform PRD simulation
if (me_universe == 0 && universe->uscreen)
fprintf(universe->uscreen,"Setting up PRD ...\n");
if (me_universe == 0) {
if (universe->uscreen)
fprintf(universe->uscreen,"Step CPU Clock Event "
"Correlated Coincident Replica\n");
if (universe->ulogfile)
fprintf(universe->ulogfile,"Step CPU Clock Event "
"Correlated Coincident Replica\n");
}
// store hot state and quenched event for replica 0
// use share_event() to copy that info to all replicas
// this insures all start from same place
// need this line if quench() does only setup_minimal()
// update->minimize->setup();
fix_event->store_state();
quench();
ncoincident = 0;
share_event(0,0);
timer->barrier_start(TIME_LOOP);
time_start = timer->array[TIME_LOOP];
log_event();
// do full init/setup since are starting all replicas after event
// replica 0 bcasts temp to all replicas if temp_dephase is not set
update->whichflag = 1;
lmp->init();
update->integrate->setup();
if (temp_flag == 0) {
if (universe->iworld == 0) temp_dephase = temperature->compute_scalar();
MPI_Bcast(&temp_dephase,1,MPI_DOUBLE,universe->root_proc[0],
universe->uworld);
}
// main loop: look for events until out of time
// (1) dephase independently on each proc after event
// (2) loop: dynamics, store state, quench, check event, restore state
// (3) share and record event
nbuild = ndanger = 0;
time_dephase = time_dynamics = time_quench = time_comm = time_output = 0.0;
timer->barrier_start(TIME_LOOP);
time_start = timer->array[TIME_LOOP];
while (update->ntimestep < update->endstep) {
dephase();
ireplica = -1;
while (update->ntimestep < update->endstep) {
dynamics();
fix_event->store_state();
quench();
ireplica = check_event();
if (ireplica >= 0) break;
fix_event->restore_state();
}
if (ireplica < 0) break;
// potentially more efficient for correlated events if don't
// share until correlated check has completed
// this will complicate the dump (always on replica 0)
share_event(ireplica,1);
log_event();
int restart_flag = 0;
if (output->restart_every && universe->iworld == 0)
if (fix_event->event_number % output->restart_every == 0)
restart_flag = 1;
// correlated event loop
// other procs could be dephasing during this time
int corr_endstep = update->ntimestep + t_corr;
while (update->ntimestep < corr_endstep) {
if (update->ntimestep == update->endstep) {
restart_flag = 0;
break;
}
dynamics();
fix_event->store_state();
quench();
int corr_event_check = check_event(ireplica);
if (corr_event_check >= 0) {
share_event(ireplica,2);
log_event();
corr_endstep = update->ntimestep + t_corr;
} else fix_event->restore_state();
}
// full init/setup since are starting all replicas after event
// event replica bcasts temp to all replicas if temp_dephase is not set
update->whichflag = 1;
lmp->init();
update->integrate->setup();
timer->barrier_start(TIME_LOOP);
if (t_corr > 0) replicate(ireplica);
if (temp_flag == 0) {
if (ireplica == universe->iworld)
temp_dephase = temperature->compute_scalar();
MPI_Bcast(&temp_dephase,1,MPI_DOUBLE,universe->root_proc[ireplica],
universe->uworld);
}
timer->barrier_stop(TIME_LOOP);
time_comm += timer->array[TIME_LOOP];
// write restart file of hot coords
if (restart_flag) {
timer->barrier_start(TIME_LOOP);
output->write_restart(update->ntimestep);
timer->barrier_stop(TIME_LOOP);
time_output += timer->array[TIME_LOOP];
}
}
// set total timers and counters so Finish() will process them
timer->array[TIME_LOOP] = time_start;
timer->barrier_stop(TIME_LOOP);
timer->array[TIME_PAIR] = time_dephase;
timer->array[TIME_BOND] = time_dynamics;
timer->array[TIME_KSPACE] = time_quench;
timer->array[TIME_COMM] = time_comm;
timer->array[TIME_OUTPUT] = time_output;
neighbor->ncalls = nbuild;
neighbor->ndanger = ndanger;
if (me_universe == 0) {
if (universe->uscreen)
fprintf(universe->uscreen,
"Loop time of %g on %d procs for %d steps with " BIGINT_FORMAT
" atoms\n",
timer->array[TIME_LOOP],nprocs_universe,nsteps,atom->natoms);
if (universe->ulogfile)
fprintf(universe->ulogfile,
"Loop time of %g on %d procs for %d steps with " BIGINT_FORMAT
" atoms\n",
timer->array[TIME_LOOP],nprocs_universe,nsteps,atom->natoms);
}
finish->end(2);
update->whichflag = 0;
update->firststep = update->laststep = 0;
update->beginstep = update->endstep = 0;
update->restrict_output = 0;
// reset reneighboring criteria
neighbor->every = neigh_every;
neighbor->delay = neigh_delay;
neighbor->dist_check = neigh_dist_check;
// clean up
delete [] displacements;
memory->sfree(tagall);
memory->destroy_2d_double_array(xall);
memory->sfree(imageall);
MPI_Comm_free(&comm_replica);
delete random_select;
delete random_dephase;
delete velocity;
delete finish;
modify->delete_compute("prd_temp");
modify->delete_fix("prd_event");
compute_event->reset_extra_compute_fix(NULL);
}
/* ----------------------------------------------------------------------
dephasing = one or more short runs with new random velocities
------------------------------------------------------------------------- */
void PRD::dephase()
{
bigint ntimestep_hold = update->ntimestep;
update->whichflag = 1;
update->nsteps = n_dephase*t_dephase;
timer->barrier_start(TIME_LOOP);
for (int i = 0; i < n_dephase; i++) {
int seed = static_cast<int> (random_dephase->uniform() * MAXSMALLINT);
if (seed == 0) seed = 1;
velocity->create(temp_dephase,seed);
update->integrate->run(t_dephase);
if (temp_flag == 0) temp_dephase = temperature->compute_scalar();
}
timer->barrier_stop(TIME_LOOP);
time_dephase += timer->array[TIME_LOOP];
update->integrate->cleanup();
finish->end(0);
// reset timestep as if dephase did not occur
// clear timestep storage from computes, since now invalid
update->ntimestep = ntimestep_hold;
for (int i = 0; i < modify->ncompute; i++)
if (modify->compute[i]->timeflag) modify->compute[i]->clearstep();
}
/* ----------------------------------------------------------------------
single short dynamics run
------------------------------------------------------------------------- */
void PRD::dynamics()
{
update->whichflag = 1;
update->nsteps = t_event;
lmp->init();
update->integrate->setup();
// this may be needed if don't do full init
//modify->addstep_compute_all(update->ntimestep);
int ncalls = neighbor->ncalls;
timer->barrier_start(TIME_LOOP);
update->integrate->run(t_event);
timer->barrier_stop(TIME_LOOP);
time_dynamics += timer->array[TIME_LOOP];
nbuild += neighbor->ncalls - ncalls;
ndanger += neighbor->ndanger;
update->integrate->cleanup();
finish->end(0);
}
/* ----------------------------------------------------------------------
quench minimization
------------------------------------------------------------------------- */
void PRD::quench()
{
bigint ntimestep_hold = update->ntimestep;
bigint endstep_hold = update->endstep;
// need to change whichflag so that minimize->setup() calling
// modify->setup() will call fix->min_setup()
update->whichflag = 2;
update->nsteps = maxiter;
update->endstep = update->laststep = update->firststep + maxiter;
if (update->laststep < 0 || update->laststep > MAXBIGINT)
error->all("Too many iterations");
// full init works
lmp->init();
update->minimize->setup();
// partial init does not work
//modify->addstep_compute_all(update->ntimestep);
//update->minimize->setup_minimal(1);
int ncalls = neighbor->ncalls;
timer->barrier_start(TIME_LOOP);
update->minimize->run(maxiter);
timer->barrier_stop(TIME_LOOP);
time_quench += timer->array[TIME_LOOP];
if (neighbor->ncalls == ncalls) quench_reneighbor = 0;
else quench_reneighbor = 1;
update->minimize->cleanup();
finish->end(0);
// reset timestep as if dephase did not occur
// clear timestep storage from computes, since now invalid
update->ntimestep = ntimestep_hold;
update->endstep = update->laststep = endstep_hold;
for (int i = 0; i < modify->ncompute; i++)
if (modify->compute[i]->timeflag) modify->compute[i]->clearstep();
}
/* ----------------------------------------------------------------------
check for an event in any replica
if replica_num is non-negative only check for event on replica_num
if multiple events, choose one at random
return -1 if no event
else return ireplica = world in which event occured
------------------------------------------------------------------------- */
int PRD::check_event(int replica_num)
{
int worldflag,universeflag,scanflag,replicaflag,ireplica;
worldflag = 0;
if (compute_event->compute_scalar() > 0.0) worldflag = 1;
if (replica_num >= 0 && replica_num != universe->iworld) worldflag = 0;
timer->barrier_start(TIME_LOOP);
if (me == 0) MPI_Allreduce(&worldflag,&universeflag,1,
MPI_INT,MPI_SUM,comm_replica);
MPI_Bcast(&universeflag,1,MPI_INT,0,world);
ncoincident = universeflag;
if (!universeflag) ireplica = -1;
else {
if (universeflag > 1) {
int iwhich = static_cast<int>
(universeflag*random_select->uniform()) + 1;
if (me == 0) MPI_Scan(&worldflag,&scanflag,1,
MPI_INT,MPI_SUM,comm_replica);
MPI_Bcast(&scanflag,1,MPI_INT,0,world);
if (scanflag != iwhich) worldflag = 0;
}
if (worldflag) replicaflag = universe->iworld;
else replicaflag = 0;
if (me == 0) MPI_Allreduce(&replicaflag,&ireplica,1,
MPI_INT,MPI_SUM,comm_replica);
MPI_Bcast(&ireplica,1,MPI_INT,0,world);
}
timer->barrier_stop(TIME_LOOP);
time_comm += timer->array[TIME_LOOP];
return ireplica;
}
/* ----------------------------------------------------------------------
share quenched and hot coords owned by ireplica with all replicas
all replicas store event in fix_event
replica 0 dumps event snapshot
flag = 0 = called before PRD run
flag = 1 = called during PRD run = not correlated event
flag = 2 = called during PRD run = correlated event
------------------------------------------------------------------------- */
void PRD::share_event(int ireplica, int flag)
{
timer->barrier_start(TIME_LOOP);
// communicate quenched coords to all replicas and store as event
// decrement event counter if flag = 0 since not really an event
replicate(ireplica);
timer->barrier_stop(TIME_LOOP);
time_comm += timer->array[TIME_LOOP];
// adjust time for last correlated event check (not on first event)
int corr_adjust = t_corr;
if (fix_event->event_number < 1 || flag == 2) corr_adjust = 0;
// delta = time since last correlated event check
int delta = update->ntimestep - fix_event->event_timestep - corr_adjust;
// if this is a correlated event, time elapsed only on one partition
if (flag != 2) delta *= universe->nworlds;
delta += corr_adjust;
// don't change the clock or timestep if this is a restart
if (flag == 0 && fix_event->event_number != 0)
fix_event->store_event_prd(fix_event->event_timestep,0);
else {
fix_event->store_event_prd(update->ntimestep,delta);
fix_event->replica_number = ireplica;
fix_event->correlated_event = 0;
if (flag == 2) fix_event->correlated_event = 1;
fix_event->ncoincident = ncoincident;
}
if (flag == 0) fix_event->event_number--;
// dump snapshot of quenched coords
// must reneighbor and compute forces before dumping
// since replica 0 possibly has new state from another replica
// addstep_compute_all insures eng/virial are calculated if needed
if (output->ndump && universe->iworld == 0) {
timer->barrier_start(TIME_LOOP);
modify->addstep_compute_all(update->ntimestep);
update->integrate->setup_minimal(1);
output->write_dump(update->ntimestep);
timer->barrier_stop(TIME_LOOP);
time_output += timer->array[TIME_LOOP];
}
// restore and communicate hot coords to all replicas
fix_event->restore_state();
timer->barrier_start(TIME_LOOP);
replicate(ireplica);
timer->barrier_stop(TIME_LOOP);
time_comm += timer->array[TIME_LOOP];
}
/* ----------------------------------------------------------------------
universe proc 0 prints event info
------------------------------------------------------------------------- */
void PRD::log_event()
{
timer->array[TIME_LOOP] = time_start;
if (universe->me == 0) {
if (universe->uscreen)
fprintf(universe->uscreen,
BIGINT_FORMAT " %.3f %d %d %d %d %d\n",
fix_event->event_timestep,
timer->elapsed(TIME_LOOP),
fix_event->clock,
fix_event->event_number,fix_event->correlated_event,
fix_event->ncoincident,
fix_event->replica_number);
if (universe->ulogfile)
fprintf(universe->ulogfile,
BIGINT_FORMAT " %.3f %d %d %d %d %d\n",
fix_event->event_timestep,
timer->elapsed(TIME_LOOP),
fix_event->clock,
fix_event->event_number,fix_event->correlated_event,
fix_event->ncoincident,
fix_event->replica_number);
}
}
/* ----------------------------------------------------------------------
communicate atom coords and image flags in ireplica to all other replicas
one proc per replica:
direct overwrite via bcast
equal procs per replica and no replica reneighbored:
direct overwrite via bcast
unequal procs per replica or reneighboring occurred:
collect to root proc of event replica
bcast to roots of other replicas
bcast within each replica
each proc extracts info for atoms it owns using atom IDs
------------------------------------------------------------------------- */
void PRD::replicate(int ireplica)
{
int nreplica = universe->nworlds;
int nprocs_universe = universe->nprocs;
int i,m,flag,commflag;
int counts[nprocs];
if (nreplica == nprocs_universe) commflag = 0;
else if (equal_size_replicas) {
flag = 0;
if (quench_reneighbor) flag = 1;
MPI_Allreduce(&flag,&commflag,1,MPI_INT,MPI_MAX,universe->uworld);
} else commflag = 1;
if (commflag == 0) {
MPI_Bcast(atom->image,atom->nlocal,MPI_INT,ireplica,comm_replica);
MPI_Bcast(atom->x[0],3*atom->nlocal,MPI_DOUBLE,ireplica,comm_replica);
} else {
if (universe->iworld == ireplica) {
MPI_Gather(&atom->nlocal,1,MPI_INT,counts,1,MPI_INT,0,world);
displacements[0] = 0;
for (i = 0; i < nprocs-1; i++)
displacements[i+1] = displacements[i] + counts[i];
MPI_Gatherv(atom->tag,atom->nlocal,MPI_INT,
tagall,counts,displacements,MPI_INT,0,world);
MPI_Gatherv(atom->image,atom->nlocal,MPI_INT,
imageall,counts,displacements,MPI_INT,0,world);
for (i = 0; i < nprocs; i++) counts[i] *= 3;
for (i = 0; i < nprocs-1; i++)
displacements[i+1] = displacements[i] + counts[i];
MPI_Gatherv(atom->x[0],3*atom->nlocal,MPI_DOUBLE,
xall[0],counts,displacements,MPI_DOUBLE,0,world);
}
if (me == 0) {
MPI_Bcast(tagall,natoms,MPI_INT,ireplica,comm_replica);
MPI_Bcast(imageall,natoms,MPI_INT,ireplica,comm_replica);
MPI_Bcast(xall[0],3*natoms,MPI_DOUBLE,ireplica,comm_replica);
}
MPI_Bcast(tagall,natoms,MPI_INT,0,world);
MPI_Bcast(imageall,natoms,MPI_INT,0,world);
MPI_Bcast(xall[0],3*natoms,MPI_DOUBLE,0,world);
double **x = atom->x;
int nlocal = atom->nlocal;
for (i = 0; i < natoms; i++) {
m = atom->map(tagall[i]);
if (m >= 0 && m < nlocal) {
x[m][0] = xall[i][0];
x[m][1] = xall[i][1];
x[m][2] = xall[i][2];
atom->image[m] = imageall[i];
}
}
}
}
/* ----------------------------------------------------------------------
parse optional parameters at end of PRD input line
------------------------------------------------------------------------- */
void PRD::options(int narg, char **arg)
{
if (narg < 0) error->all("Illegal prd command");
// set defaults
etol = 0.1;
ftol = 0.1;
maxiter = 40;
maxeval = 50;
temp_flag = 0;
char *str = "geom";
int n = strlen(str) + 1;
loop_setting = new char[n];
strcpy(loop_setting,str);
str = "gaussian";
n = strlen(str) + 1;
dist_setting = new char[n];
strcpy(dist_setting,str);
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"min") == 0) {
if (iarg+5 > narg) error->all("Illegal prd command");
etol = atof(arg[iarg+1]);
ftol = atof(arg[iarg+2]);
maxiter = atoi(arg[iarg+3]);
maxeval = atoi(arg[iarg+4]);
if (maxiter < 0) error->all("Illegal prd command");
iarg += 5;
} else if (strcmp(arg[iarg],"temp") == 0) {
if (iarg+2 > narg) error->all("Illegal prd command");
temp_flag = 1;
temp_dephase = atof(arg[iarg+1]);
if (temp_dephase <= 0.0) error->all("Illegal prd command");
iarg += 2;
} else if (strcmp(arg[iarg],"vel") == 0) {
if (iarg+3 > narg) error->all("Illegal prd command");
delete [] loop_setting;
delete [] dist_setting;
if (strcmp(arg[iarg+1],"all") == 0) loop_setting = NULL;
else if (strcmp(arg[iarg+1],"local") == 0) loop_setting = NULL;
else if (strcmp(arg[iarg+1],"geom") == 0) loop_setting = NULL;
else error->all("Illegal prd command");
int n = strlen(arg[iarg+1]) + 1;
loop_setting = new char[n];
strcpy(loop_setting,arg[iarg+1]);
if (strcmp(arg[iarg+2],"uniform") == 0) dist_setting = NULL;
else if (strcmp(arg[iarg+2],"gaussian") == 0) dist_setting = NULL;
else error->all("Illegal prd command");
n = strlen(arg[iarg+2]) + 1;
dist_setting = new char[n];
strcpy(dist_setting,arg[iarg+2]);
iarg += 3;
} else error->all("Illegal prd command");
}
}
diff --git a/src/REPLICA/temper.cpp b/src/REPLICA/temper.cpp
index 4befb443b..ea8fcfaab 100644
--- a/src/REPLICA/temper.cpp
+++ b/src/REPLICA/temper.cpp
@@ -1,360 +1,360 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Mark Sears (SNL)
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "math.h"
#include "stdlib.h"
#include "string.h"
#include "temper.h"
-#include "lmptype.h"
#include "universe.h"
#include "domain.h"
#include "atom.h"
#include "update.h"
#include "integrate.h"
#include "modify.h"
#include "compute.h"
#include "force.h"
#include "output.h"
#include "thermo.h"
#include "fix.h"
#include "random_park.h"
#include "finish.h"
#include "timer.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
// #define TEMPER_DEBUG 1
/* ---------------------------------------------------------------------- */
Temper::Temper(LAMMPS *lmp) : Pointers(lmp) {}
/* ---------------------------------------------------------------------- */
Temper::~Temper()
{
MPI_Comm_free(&roots);
if (ranswap) delete ranswap;
delete ranboltz;
delete [] set_temp;
delete [] temp2world;
delete [] world2temp;
delete [] world2root;
}
/* ----------------------------------------------------------------------
perform tempering with inter-world swaps
------------------------------------------------------------------------- */
void Temper::command(int narg, char **arg)
{
if (universe->nworlds == 1)
error->all("Must have more than one processor partition to temper");
if (domain->box_exist == 0)
error->all("Temper command before simulation box is defined");
if (narg != 6 && narg != 7) error->universe_all("Illegal temper command");
int nsteps = atoi(arg[0]);
nevery = atoi(arg[1]);
double temp = atof(arg[2]);
for (whichfix = 0; whichfix < modify->nfix; whichfix++)
if (strcmp(arg[3],modify->fix[whichfix]->id) == 0) break;
if (whichfix == modify->nfix)
error->universe_all("Tempering fix ID is not defined");
seed_swap = atoi(arg[4]);
seed_boltz = atoi(arg[5]);
my_set_temp = universe->iworld;
if (narg == 7) my_set_temp = atoi(arg[6]);
// swap frequency must evenly divide total # of timesteps
if (nevery == 0) error->universe_all("Invalid frequency in temper command");
nswaps = nsteps/nevery;
if (nswaps*nevery != nsteps)
error->universe_all("Non integer # of swaps in temper command");
// fix style must be appropriate for temperature control
if ((strcmp(modify->fix[whichfix]->style,"nvt") != 0) &&
(strcmp(modify->fix[whichfix]->style,"langevin") != 0) &&
(strcmp(modify->fix[whichfix]->style,"temp/berendsen") != 0) &&
(strcmp(modify->fix[whichfix]->style,"temp/rescale") != 0))
error->universe_all("Tempering temperature fix is not valid");
// setup for long tempering run
update->whichflag = 1;
update->nsteps = nsteps;
update->beginstep = update->firststep = update->ntimestep;
update->endstep = update->laststep = update->firststep + nsteps;
if (update->laststep < 0 || update->laststep > MAXBIGINT)
error->all("Too many timesteps");
lmp->init();
// local storage
me_universe = universe->me;
MPI_Comm_rank(world,&me);
nworlds = universe->nworlds;
iworld = universe->iworld;
boltz = force->boltz;
// pe_compute = ptr to thermo_pe compute
// notify compute it will be called at first swap
int id = modify->find_compute("thermo_pe");
if (id < 0) error->all("Tempering could not find thermo_pe compute");
Compute *pe_compute = modify->compute[id];
pe_compute->addstep(update->ntimestep + nevery);
// create MPI communicator for root proc from each world
int color;
if (me == 0) color = 0;
else color = 1;
MPI_Comm_split(universe->uworld,color,0,&roots);
// RNGs for swaps and Boltzmann test
// warm up Boltzmann RNG
if (seed_swap) ranswap = new RanPark(lmp,seed_swap);
else ranswap = NULL;
ranboltz = new RanPark(lmp,seed_boltz + me_universe);
for (int i = 0; i < 100; i++) ranboltz->uniform();
// world2root[i] = global proc that is root proc of world i
world2root = new int[nworlds];
if (me == 0)
MPI_Allgather(&me_universe,1,MPI_INT,world2root,1,MPI_INT,roots);
MPI_Bcast(world2root,nworlds,MPI_INT,0,world);
// create static list of set temperatures
// allgather tempering arg "temp" across root procs
// bcast from each root to other procs in world
set_temp = new double[nworlds];
if (me == 0) MPI_Allgather(&temp,1,MPI_DOUBLE,set_temp,1,MPI_DOUBLE,roots);
MPI_Bcast(set_temp,nworlds,MPI_DOUBLE,0,world);
// create world2temp only on root procs from my_set_temp
// create temp2world on root procs from world2temp,
// then bcast to all procs within world
world2temp = new int[nworlds];
temp2world = new int[nworlds];
if (me == 0) {
MPI_Allgather(&my_set_temp,1,MPI_INT,world2temp,1,MPI_INT,roots);
for (int i = 0; i < nworlds; i++) temp2world[world2temp[i]] = i;
}
MPI_Bcast(temp2world,nworlds,MPI_INT,0,world);
// if restarting tempering, reset temp target of Fix to current my_set_temp
if (narg == 7) {
double new_temp = set_temp[my_set_temp];
modify->fix[whichfix]->reset_target(new_temp);
}
// setup tempering runs
int i,which,partner,swap,partner_set_temp,partner_world;
double pe,pe_partner,boltz_factor,new_temp;
MPI_Status status;
if (me_universe == 0 && universe->uscreen)
fprintf(universe->uscreen,"Setting up tempering ...\n");
update->integrate->setup();
if (me_universe == 0) {
if (universe->uscreen) {
fprintf(universe->uscreen,"Step");
for (int i = 0; i < nworlds; i++)
fprintf(universe->uscreen," T%d",i);
fprintf(universe->uscreen,"\n");
}
if (universe->ulogfile) {
fprintf(universe->ulogfile,"Step");
for (int i = 0; i < nworlds; i++)
fprintf(universe->ulogfile," T%d",i);
fprintf(universe->ulogfile,"\n");
}
print_status();
}
timer->barrier_start(TIME_LOOP);
for (int iswap = 0; iswap < nswaps; iswap++) {
// run for nevery timesteps
update->integrate->run(nevery);
// compute PE
// notify compute it will be called at next swap
pe = pe_compute->compute_scalar();
pe_compute->addstep(update->ntimestep + nevery);
// which = which of 2 kinds of swaps to do (0,1)
if (!ranswap) which = iswap % 2;
else if (ranswap->uniform() < 0.5) which = 0;
else which = 1;
// partner_set_temp = which set temp I am partnering with for this swap
if (which == 0) {
if (my_set_temp % 2 == 0) partner_set_temp = my_set_temp + 1;
else partner_set_temp = my_set_temp - 1;
} else {
if (my_set_temp % 2 == 1) partner_set_temp = my_set_temp + 1;
else partner_set_temp = my_set_temp - 1;
}
// partner = proc ID to swap with
// if partner = -1, then I am not a proc that swaps
partner = -1;
if (me == 0 && partner_set_temp >= 0 && partner_set_temp < nworlds) {
partner_world = temp2world[partner_set_temp];
partner = world2root[partner_world];
}
// swap with a partner, only root procs in each world participate
// hi proc sends PE to low proc
// lo proc make Boltzmann decision on whether to swap
// lo proc communicates decision back to hi proc
swap = 0;
if (partner != -1) {
if (me_universe > partner)
MPI_Send(&pe,1,MPI_DOUBLE,partner,0,universe->uworld);
else
MPI_Recv(&pe_partner,1,MPI_DOUBLE,partner,0,universe->uworld,&status);
if (me_universe < partner) {
boltz_factor = (pe - pe_partner) *
(1.0/(boltz*set_temp[my_set_temp]) -
1.0/(boltz*set_temp[partner_set_temp]));
if (boltz_factor >= 0.0) swap = 1;
else if (ranboltz->uniform() < exp(boltz_factor)) swap = 1;
}
if (me_universe < partner)
MPI_Send(&swap,1,MPI_INT,partner,0,universe->uworld);
else
MPI_Recv(&swap,1,MPI_INT,partner,0,universe->uworld,&status);
#ifdef TEMPER_DEBUG
if (me_universe < partner)
printf("SWAP %d & %d: yes = %d,Ts = %d %d, PEs = %g %g, Bz = %g %g\n",
me_universe,partner,swap,my_set_temp,partner_set_temp,
pe,pe_partner,boltz_factor,exp(boltz_factor));
#endif
}
// bcast swap result to other procs in my world
MPI_Bcast(&swap,1,MPI_INT,0,world);
// rescale kinetic energy via velocities if move is accepted
if (swap) scale_velocities(partner_set_temp,my_set_temp);
// if my world swapped, all procs in world reset temp target of Fix
if (swap) {
new_temp = set_temp[partner_set_temp];
modify->fix[whichfix]->reset_target(new_temp);
}
// update my_set_temp and temp2world on every proc
// root procs update their value if swap took place
// allgather across root procs
// bcast within my world
if (swap) my_set_temp = partner_set_temp;
if (me == 0) {
MPI_Allgather(&my_set_temp,1,MPI_INT,world2temp,1,MPI_INT,roots);
for (i = 0; i < nworlds; i++) temp2world[world2temp[i]] = i;
}
MPI_Bcast(temp2world,nworlds,MPI_INT,0,world);
// print out current swap status
if (me_universe == 0) print_status();
}
timer->barrier_stop(TIME_LOOP);
update->integrate->cleanup();
Finish finish(lmp);
finish.end(1);
update->whichflag = 0;
update->firststep = update->laststep = 0;
update->beginstep = update->endstep = 0;
}
/* ----------------------------------------------------------------------
scale kinetic energy via velocities a la Sugita
------------------------------------------------------------------------- */
void Temper::scale_velocities(int t_partner, int t_me)
{
double sfactor = sqrt(set_temp[t_partner]/set_temp[t_me]);
double **v = atom->v;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
v[i][0] = v[i][0]*sfactor;
v[i][1] = v[i][1]*sfactor;
v[i][2] = v[i][2]*sfactor;
}
}
/* ----------------------------------------------------------------------
proc 0 prints current tempering status
------------------------------------------------------------------------- */
void Temper::print_status()
{
if (universe->uscreen) {
fprintf(universe->uscreen,BIGINT_FORMAT,update->ntimestep);
for (int i = 0; i < nworlds; i++)
fprintf(universe->uscreen," %d",world2temp[i]);
fprintf(universe->uscreen,"\n");
}
if (universe->ulogfile) {
fprintf(universe->ulogfile,BIGINT_FORMAT,update->ntimestep);
for (int i = 0; i < nworlds; i++)
fprintf(universe->ulogfile," %d",world2temp[i]);
fprintf(universe->ulogfile,"\n");
fflush(universe->ulogfile);
}
}
diff --git a/src/SRD/fix_wall_srd.h b/src/SRD/fix_wall_srd.h
index ed5afcde3..2ad5fdcdf 100644
--- a/src/SRD/fix_wall_srd.h
+++ b/src/SRD/fix_wall_srd.h
@@ -1,60 +1,60 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
FixStyle(wall/srd,FixWallSRD)
#else
#ifndef LMP_FIX_WALL_SRD_H
#define LMP_FIX_WALL_SRD_H
-#include "fix.h"
#include "lmptype.h"
+#include "fix.h"
namespace LAMMPS_NS {
class FixWallSRD : public Fix {
public:
int nwall,varflag,overlap;
int wallwhich[6];
double xwall[6],xwallhold[6],vwall[6];
double **fwall;
FixWallSRD(class LAMMPS *, int, char **);
~FixWallSRD();
int setmask();
void init();
double compute_array(int, int);
void wall_params(int);
private:
int wallstyle[6];
double coord0[6];
char *varstr[6];
int varindex[6];
double dt;
double xwalllast[6];
bigint laststep;
double **fwall_all;
int force_flag;
};
}
#endif
#endif
diff --git a/src/USER-EFF/atom_vec_electron.cpp b/src/USER-EFF/atom_vec_electron.cpp
index ceba59846..20e33a091 100644
--- a/src/USER-EFF/atom_vec_electron.cpp
+++ b/src/USER-EFF/atom_vec_electron.cpp
@@ -1,801 +1,801 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Andres Jaramillo-Botero (Caltech)
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "stdlib.h"
#include "atom_vec_electron.h"
-#include "lmptype.h"
#include "atom.h"
#include "domain.h"
#include "modify.h"
#include "force.h"
#include "fix.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define DELTA 10000
/* ---------------------------------------------------------------------- */
AtomVecElectron::AtomVecElectron(LAMMPS *lmp, int narg, char **arg) :
AtomVec(lmp, narg, arg)
{
comm_x_only = comm_f_only = 0;
mass_type = 1;
molecular = 0;
size_forward = 5;
size_reverse = 4;
size_border = 10;
size_velocity = 4;
size_data_atom = 8;
size_data_vel = 5;
xcol_data = 6;
atom->q_flag = atom->spin_flag = atom->eradius_flag =
atom->ervel_flag = atom->erforce_flag = 1;
}
/* ----------------------------------------------------------------------
grow atom-electron arrays
n = 0 grows arrays by DELTA
n > 0 allocates arrays to size n
------------------------------------------------------------------------- */
void AtomVecElectron::grow(int n)
{
if (n == 0) nmax += DELTA;
else nmax = n;
atom->nmax = nmax;
if (nmax < 0 || nmax > MAXSMALLINT)
error->one("Per-processor system is too big");
tag = atom->tag = (int *)
memory->srealloc(atom->tag,nmax*sizeof(int),"atom:tag");
type = atom->type = (int *)
memory->srealloc(atom->type,nmax*sizeof(int),"atom:type");
mask = atom->mask = (int *)
memory->srealloc(atom->mask,nmax*sizeof(int),"atom:mask");
image = atom->image = (int *)
memory->srealloc(atom->image,nmax*sizeof(int),"atom:image");
x = atom->x = memory->grow_2d_double_array(atom->x,nmax,3,"atom:x");
v = atom->v = memory->grow_2d_double_array(atom->v,nmax,3,"atom:v");
f = atom->f = memory->grow_2d_double_array(atom->f,nmax,3,"atom:f");
q = atom->q = (double *)
memory->srealloc(atom->q,nmax*sizeof(double),"atom:q");
spin = atom->spin = (int *)
memory->srealloc(atom->spin,nmax*sizeof(int),"atom:spin");
eradius = atom->eradius = (double *)
memory->srealloc(atom->eradius,nmax*sizeof(double),"atom:eradius");
ervel = atom->ervel = (double *)
memory->srealloc(atom->ervel,nmax*sizeof(double),"atom:ervel");
erforce = atom->erforce = (double *)
memory->srealloc(atom->erforce,nmax*sizeof(double),"atom:erforce");
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
}
/* ----------------------------------------------------------------------
reset local array ptrs
------------------------------------------------------------------------- */
void AtomVecElectron::grow_reset()
{
tag = atom->tag; type = atom->type;
mask = atom->mask; image = atom->image;
x = atom->x; v = atom->v; f = atom->f;
q = atom->q;
eradius = atom->eradius; ervel = atom->ervel; erforce = atom->erforce;
}
/* ---------------------------------------------------------------------- */
void AtomVecElectron::copy(int i, int j)
{
tag[j] = tag[i];
type[j] = type[i];
mask[j] = mask[i];
image[j] = image[i];
x[j][0] = x[i][0];
x[j][1] = x[i][1];
x[j][2] = x[i][2];
v[j][0] = v[i][0];
v[j][1] = v[i][1];
v[j][2] = v[i][2];
q[j] = q[i];
spin[j] = spin[i];
eradius[j] = eradius[i];
ervel[j] = ervel[i];
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j);
}
/* ---------------------------------------------------------------------- */
int AtomVecElectron::pack_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = eradius[j];
buf[m++] = ervel[j];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
dz = pbc[2]*domain->zprd;
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = eradius[j];
buf[m++] = ervel[j];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecElectron::pack_comm_vel(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
buf[m++] = eradius[j];
buf[m++] = ervel[j];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
dz = pbc[2]*domain->zprd;
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
buf[m++] = eradius[j];
buf[m++] = ervel[j];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecElectron::unpack_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
eradius[i] = buf[m++];
ervel[i] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
void AtomVecElectron::unpack_comm_vel(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
eradius[i] = buf[m++];
ervel[i] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecElectron::pack_comm_one(int i, double *buf)
{
buf[0] = eradius[i];
buf[1] = ervel[i];
return 2;
}
/* ---------------------------------------------------------------------- */
int AtomVecElectron::unpack_comm_one(int i, double *buf)
{
eradius[i] = buf[0];
ervel[i] = buf[1];
return 2;
}
/* ---------------------------------------------------------------------- */
int AtomVecElectron::pack_reverse(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
buf[m++] = f[i][0];
buf[m++] = f[i][1];
buf[m++] = f[i][2];
buf[m++] = erforce[i];
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecElectron::pack_reverse_one(int i, double *buf)
{
buf[0] = erforce[i];
return 1;
}
/* ---------------------------------------------------------------------- */
void AtomVecElectron::unpack_reverse(int n, int *list, double *buf)
{
int i,j,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
f[j][0] += buf[m++];
f[j][1] += buf[m++];
f[j][2] += buf[m++];
erforce[j] += buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecElectron::unpack_reverse_one(int i, double *buf)
{
erforce[i] += buf[0];
return 1;
}
/* ---------------------------------------------------------------------- */
int AtomVecElectron::pack_border_vel(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
buf[m++] = q[j];
buf[m++] = spin[j];
buf[m++] = eradius[j];
buf[m++] = ervel[j];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0];
dy = pbc[1];
dz = pbc[2];
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
buf[m++] = q[j];
buf[m++] = spin[j];
buf[m++] = eradius[j];
buf[m++] = ervel[j];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecElectron::unpack_border_vel(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
if (i == nmax) grow(0);
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
tag[i] = static_cast<int> (buf[m++]);
type[i] = static_cast<int> (buf[m++]);
mask[i] = static_cast<int> (buf[m++]);
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
q[i] = buf[m++];
spin[i] = static_cast<int> (buf[m++]);
eradius[i] = buf[m++];
ervel[i] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecElectron::pack_border(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = q[j];
buf[m++] = spin[j];
buf[m++] = eradius[j];
buf[m++] = ervel[j];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0];
dy = pbc[1];
dz = pbc[2];
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = q[j];
buf[m++] = spin[j];
buf[m++] = eradius[j];
buf[m++] = ervel[j];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecElectron::pack_border_one(int i, double *buf)
{
buf[0] = q[i];
buf[1] = spin[i];
buf[2] = eradius[i];
buf[3] = ervel[i];
return 4;
}
/* ---------------------------------------------------------------------- */
void AtomVecElectron::unpack_border(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
if (i == nmax) grow(0);
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
tag[i] = static_cast<int> (buf[m++]);
type[i] = static_cast<int> (buf[m++]);
mask[i] = static_cast<int> (buf[m++]);
q[i] = buf[m++];
spin[i] = static_cast<int> (buf[m++]);
eradius[i] = buf[m++];
ervel[i] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecElectron::unpack_border_one(int i, double *buf)
{
q[i] = buf[0];
spin[i] = static_cast<int> (buf[1]);
eradius[i] = buf[2];
ervel[i] = buf[3];
return 4;
}
/* ----------------------------------------------------------------------
pack data for atom I for sending to another proc
xyz must be 1st 3 values, so comm::exchange() can test on them
------------------------------------------------------------------------- */
int AtomVecElectron::pack_exchange(int i, double *buf)
{
int m = 1;
buf[m++] = x[i][0];
buf[m++] = x[i][1];
buf[m++] = x[i][2];
buf[m++] = v[i][0];
buf[m++] = v[i][1];
buf[m++] = v[i][2];
buf[m++] = tag[i];
buf[m++] = type[i];
buf[m++] = mask[i];
buf[m++] = image[i];
buf[m++] = q[i];
buf[m++] = spin[i];
buf[m++] = eradius[i];
buf[m++] = ervel[i];
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]);
buf[0] = m;
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecElectron::unpack_exchange(double *buf)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
int m = 1;
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
x[nlocal][2] = buf[m++];
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
tag[nlocal] = static_cast<int> (buf[m++]);
type[nlocal] = static_cast<int> (buf[m++]);
mask[nlocal] = static_cast<int> (buf[m++]);
image[nlocal] = static_cast<int> (buf[m++]);
q[nlocal] = buf[m++];
spin[nlocal] = static_cast<int> (buf[m++]);
eradius[nlocal] = buf[m++];
ervel[nlocal] = buf[m++];
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->
unpack_exchange(nlocal,&buf[m]);
atom->nlocal++;
return m;
}
/* ----------------------------------------------------------------------
size of restart data for all atoms owned by this proc
include extra data stored by fixes
------------------------------------------------------------------------- */
int AtomVecElectron::size_restart()
{
int i;
int nlocal = atom->nlocal;
int n = 15 * nlocal; // Associated with pack_restart
if (atom->nextra_restart)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
for (i = 0; i < nlocal; i++)
n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
return n;
}
/* ----------------------------------------------------------------------
pack atom I's data for restart file including extra quantities
xyz must be 1st 3 values, so that read_restart can test on them
molecular types may be negative, but write as positive
------------------------------------------------------------------------- */
int AtomVecElectron::pack_restart(int i, double *buf)
{
int m = 1;
buf[m++] = x[i][0];
buf[m++] = x[i][1];
buf[m++] = x[i][2];
buf[m++] = tag[i];
buf[m++] = type[i];
buf[m++] = mask[i];
buf[m++] = image[i];
buf[m++] = v[i][0];
buf[m++] = v[i][1];
buf[m++] = v[i][2];
buf[m++] = q[i];
buf[m++] = spin[i];
buf[m++] = eradius[i];
buf[m++] = ervel[i];
if (atom->nextra_restart)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]);
buf[0] = m;
return m;
}
/* ----------------------------------------------------------------------
unpack data for one atom from restart file including extra quantities
------------------------------------------------------------------------- */
int AtomVecElectron::unpack_restart(double *buf)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) {
grow(0);
if (atom->nextra_store)
atom->extra = memory->grow_2d_double_array(atom->extra,nmax,
atom->nextra_store,
"atom:extra");
}
int m = 1;
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
x[nlocal][2] = buf[m++];
tag[nlocal] = static_cast<int> (buf[m++]);
type[nlocal] = static_cast<int> (buf[m++]);
mask[nlocal] = static_cast<int> (buf[m++]);
image[nlocal] = static_cast<int> (buf[m++]);
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
q[nlocal] = buf[m++];
spin[nlocal] = static_cast<int> (buf[m++]);
eradius[nlocal] = buf[m++];
ervel[nlocal] = buf[m++];
double **extra = atom->extra;
if (atom->nextra_store) {
int size = static_cast<int> (buf[0]) - m;
for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++];
}
atom->nlocal++;
return m;
}
/* ----------------------------------------------------------------------
create one atom of itype at coord
set other values to defaults
------------------------------------------------------------------------- */
void AtomVecElectron::create_atom(int itype, double *coord)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
tag[nlocal] = 0;
type[nlocal] = itype;
x[nlocal][0] = coord[0];
x[nlocal][1] = coord[1];
x[nlocal][2] = coord[2];
mask[nlocal] = 1;
image[nlocal] = (512 << 20) | (512 << 10) | 512;
v[nlocal][0] = 0.0;
v[nlocal][1] = 0.0;
v[nlocal][2] = 0.0;
q[nlocal] = 0.0;
spin[nlocal] = 1;
eradius[nlocal] = 1.0;
ervel[nlocal] = 0.0;
atom->nlocal++;
}
/* ----------------------------------------------------------------------
unpack one line from Atoms section of data file
initialize other atom quantities
------------------------------------------------------------------------- */
void AtomVecElectron::data_atom(double *coord, int imagetmp, char **values)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
tag[nlocal] = atoi(values[0]);
if (tag[nlocal] <= 0)
error->one("Invalid atom ID in Atoms section of data file");
type[nlocal] = atoi(values[1]);
if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
error->one("Invalid atom type in Atoms section of data file");
q[nlocal] = atof(values[2]);
spin[nlocal] = atoi(values[3]);
eradius[nlocal] = atof(values[4]);
x[nlocal][0] = coord[0];
x[nlocal][1] = coord[1];
x[nlocal][2] = coord[2];
image[nlocal] = imagetmp;
mask[nlocal] = 1;
v[nlocal][0] = 0.0;
v[nlocal][1] = 0.0;
v[nlocal][2] = 0.0;
ervel[nlocal] = 0.0;
atom->nlocal++;
}
/* ----------------------------------------------------------------------
unpack hybrid quantities from one line in Atoms section of data file
initialize other atom quantities for this sub-style
------------------------------------------------------------------------- */
int AtomVecElectron::data_atom_hybrid(int nlocal, char **values)
{
q[nlocal] = atof(values[0]);
spin[nlocal] = atoi(values[1]);
eradius[nlocal] = atof(values[2]);
if (eradius[nlocal] < 0.0)
error->one("Invalid eradius in Atoms section of data file");
v[nlocal][0] = 0.0;
v[nlocal][1] = 0.0;
v[nlocal][2] = 0.0;
ervel[nlocal] = 0.0;
return 2;
}
/* ----------------------------------------------------------------------
unpack one line from Velocities section of data file
------------------------------------------------------------------------- */
void AtomVecElectron::data_vel(int m, char **values)
{
v[m][0] = atof(values[0]);
v[m][1] = atof(values[1]);
v[m][2] = atof(values[2]);
ervel[m] = atof(values[3]);
}
/* ----------------------------------------------------------------------
unpack hybrid quantities from one line in Velocities section of data file
------------------------------------------------------------------------- */
int AtomVecElectron::data_vel_hybrid(int m, char **values)
{
ervel[m] = atof(values[0]);
return 1;
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
------------------------------------------------------------------------- */
double AtomVecElectron::memory_usage()
{
double bytes = 0.0;
if (atom->memcheck("tag")) bytes += nmax * sizeof(int);
if (atom->memcheck("type")) bytes += nmax * sizeof(int);
if (atom->memcheck("mask")) bytes += nmax * sizeof(int);
if (atom->memcheck("image")) bytes += nmax * sizeof(int);
if (atom->memcheck("x")) bytes += nmax*3 * sizeof(double);
if (atom->memcheck("v")) bytes += nmax*3 * sizeof(double);
if (atom->memcheck("f")) bytes += nmax*3 * sizeof(double);
if (atom->memcheck("q")) bytes += nmax * sizeof(double);
if (atom->memcheck("spin")) bytes += nmax * sizeof(int);
if (atom->memcheck("eradius")) bytes += nmax * sizeof(double);
if (atom->memcheck("ervel")) bytes += nmax * sizeof(double);
if (atom->memcheck("erforce")) bytes += nmax * sizeof(double);
return bytes;
}
diff --git a/src/atom.h b/src/atom.h
index 563bc9b1c..8821e7c48 100644
--- a/src/atom.h
+++ b/src/atom.h
@@ -1,223 +1,223 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifndef LMP_ATOM_H
#define LMP_ATOM_H
-#include "pointers.h"
#include "lmptype.h"
+#include "pointers.h"
namespace LAMMPS_NS {
class Atom : protected Pointers {
public:
char *atom_style;
class AtomVec *avec;
// atom counts
bigint natoms; // total # of atoms in system, could be 0
int nlocal,nghost; // # of owned and ghost atoms on this proc
int nmax; // max # of owned+ghost in arrays on this proc
int tag_enable; // 0/1 if atom ID tags are defined
int molecular; // 0 = atomic, 1 = molecular system
bigint nbonds,nangles,ndihedrals,nimpropers;
int ntypes,nbondtypes,nangletypes,ndihedraltypes,nimpropertypes;
int bond_per_atom,angle_per_atom,dihedral_per_atom,improper_per_atom;
int extra_bond_per_atom;
int firstgroup; // store atoms in this group first, -1 if unset
int nfirst; // # of atoms in first group on this proc
char *firstgroupname; // group-ID to store first, NULL if unset
// per-atom arrays
// customize by adding new array
int *tag,*type,*mask,*image;
double **x,**v,**f;
int *molecule;
double *q,**mu;
double **quat,**omega,**angmom,**torque;
double *radius,*density,*rmass,*vfrac,*s0;
double **x0;
int *spin;
double *eradius,*ervel,*erforce;
int **nspecial; // 0,1,2 = cummulative # of 1-2,1-3,1-4 neighs
int **special; // IDs of 1-2,1-3,1-4 neighs of each atom
int maxspecial; // special[nlocal][maxspecial]
int *num_bond;
int **bond_type;
int **bond_atom;
int *num_angle;
int **angle_type;
int **angle_atom1,**angle_atom2,**angle_atom3;
int *num_dihedral;
int **dihedral_type;
int **dihedral_atom1,**dihedral_atom2,**dihedral_atom3,**dihedral_atom4;
int *num_improper;
int **improper_type;
int **improper_atom1,**improper_atom2,**improper_atom3,**improper_atom4;
// per-atom array existence flags
// these can be checked before array is allocated
// customize by adding new flag
int molecule_flag;
int q_flag,mu_flag;
int quat_flag,omega_flag,angmom_flag,torque_flag;
int radius_flag,density_flag,rmass_flag,vfrac_flag;
int spin_flag,eradius_flag,ervel_flag,erforce_flag;
// extra peratom info in restart file destined for fix & diag
double **extra;
// per-type arrays
double *mass,**shape,*dipole;
int *mass_setflag,*shape_setflag,*dipole_setflag;
// callback ptrs for atom arrays managed by fix classes
int nextra_grow,nextra_restart; // # of callbacks of each type
int *extra_grow,*extra_restart; // index of fix to callback to
int nextra_grow_max,nextra_restart_max; // size of callback lists
int nextra_store;
int map_style; // default or user-specified style of map
// 0 = none, 1 = array, 2 = hash
// spatial sorting of atoms
int sortfreq; // sort atoms every this many steps, 0 = off
bigint nextsort; // next timestep to sort on
// functions
Atom(class LAMMPS *);
~Atom();
void settings(class Atom *);
void create_avec(const char *, int, char **);
class AtomVec *new_avec(const char *, int, char **);
void init();
void setup();
int style_match(const char *);
void modify_params(int, char **);
void tag_extend();
int tag_consecutive();
int parse_data(const char *);
int count_words(const char *);
void data_atoms(int, char *);
void data_vels(int, char *);
void data_bonds(int, char *);
void data_angles(int, char *);
void data_dihedrals(int, char *);
void data_impropers(int, char *);
void allocate_type_arrays();
void set_mass(const char *);
void set_mass(int, double);
void set_mass(int, char **);
void set_mass(double *);
void check_mass();
void set_shape(const char *);
void set_shape(int, char **);
void set_shape(double **);
void check_shape();
void set_dipole(const char *);
void set_dipole(int, char **);
void set_dipole(double *);
void check_dipole();
void first_reorder();
void sort();
void add_callback(int);
void delete_callback(const char *, int);
void update_callback(int);
void *extract(char *);
double memory_usage();
int memcheck(const char *);
// functions for global to local ID mapping
// map lookup function inlined for efficiency
inline int map(int global) {
if (map_style == 1) return map_array[global];
else return map_find_hash(global);
};
void map_init();
void map_clear();
void map_set();
void map_one(int, int);
void map_delete();
int map_find_hash(int);
private:
// global to local ID mapping
int map_tag_max;
int *map_array;
struct HashElem {
int global; // key to search on = global ID
int local; // value associated with key = local index
int next; // next entry in this bucket, -1 if last
};
int map_nhash; // # of entries hash table can hold
int map_nused; // # of actual entries in hash table
int map_free; // ptr to 1st unused entry in hash table
int map_nbucket; // # of hash buckets
int *map_bucket; // ptr to 1st entry in each bucket
HashElem *map_hash; // hash table
int *primes; // table of prime #s for hashing
int nprimes; // # of primes
// spatial sorting of atoms
int nbins; // # of sorting bins
int nbinx,nbiny,nbinz; // bins in each dimension
int maxbin; // max # of bins
int maxnext; // max size of next,permute
int *binhead; // 1st atom in each bin
int *next; // next atom in bin
int *permute; // permutation vector
double userbinsize; // requested sort bin size
double bininvx,bininvy,bininvz; // inverse actual bin sizes
double bboxlo[3],bboxhi[3]; // bounding box of my sub-domain
int memlength; // allocated size of memstr
char *memstr; // string of array names already counted
void setup_sort_bins();
};
}
#endif
diff --git a/src/atom_vec_atomic.cpp b/src/atom_vec_atomic.cpp
index 13dd6b4a9..e574c387a 100644
--- a/src/atom_vec_atomic.cpp
+++ b/src/atom_vec_atomic.cpp
@@ -1,594 +1,594 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "stdlib.h"
#include "atom_vec_atomic.h"
-#include "lmptype.h"
#include "atom.h"
#include "domain.h"
#include "modify.h"
#include "fix.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define DELTA 10000
/* ---------------------------------------------------------------------- */
AtomVecAtomic::AtomVecAtomic(LAMMPS *lmp, int narg, char **arg) :
AtomVec(lmp, narg, arg)
{
molecular = 0;
mass_type = 1;
comm_x_only = comm_f_only = 1;
size_forward = 3;
size_reverse = 3;
size_border = 6;
size_velocity = 3;
size_data_atom = 5;
size_data_vel = 4;
xcol_data = 3;
}
/* ----------------------------------------------------------------------
grow atom arrays
n = 0 grows arrays by DELTA
n > 0 allocates arrays to size n
------------------------------------------------------------------------- */
void AtomVecAtomic::grow(int n)
{
if (n == 0) nmax += DELTA;
else nmax = n;
atom->nmax = nmax;
if (nmax < 0 || nmax > MAXSMALLINT)
error->one("Per-processor system is too big");
tag = atom->tag = (int *)
memory->srealloc(atom->tag,nmax*sizeof(int),"atom:tag");
type = atom->type = (int *)
memory->srealloc(atom->type,nmax*sizeof(int),"atom:type");
mask = atom->mask = (int *)
memory->srealloc(atom->mask,nmax*sizeof(int),"atom:mask");
image = atom->image = (int *)
memory->srealloc(atom->image,nmax*sizeof(int),"atom:image");
x = atom->x = memory->grow_2d_double_array(atom->x,nmax,3,"atom:x");
v = atom->v = memory->grow_2d_double_array(atom->v,nmax,3,"atom:v");
f = atom->f = memory->grow_2d_double_array(atom->f,nmax,3,"atom:f");
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
}
/* ----------------------------------------------------------------------
reset local array ptrs
------------------------------------------------------------------------- */
void AtomVecAtomic::grow_reset()
{
tag = atom->tag; type = atom->type;
mask = atom->mask; image = atom->image;
x = atom->x; v = atom->v; f = atom->f;
}
/* ---------------------------------------------------------------------- */
void AtomVecAtomic::copy(int i, int j)
{
tag[j] = tag[i];
type[j] = type[i];
mask[j] = mask[i];
image[j] = image[i];
x[j][0] = x[i][0];
x[j][1] = x[i][1];
x[j][2] = x[i][2];
v[j][0] = v[i][0];
v[j][1] = v[i][1];
v[j][2] = v[i][2];
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j);
}
/* ---------------------------------------------------------------------- */
int AtomVecAtomic::pack_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
dz = pbc[2]*domain->zprd;
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecAtomic::pack_comm_vel(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
dz = pbc[2]*domain->zprd;
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecAtomic::unpack_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
void AtomVecAtomic::unpack_comm_vel(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecAtomic::pack_reverse(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
buf[m++] = f[i][0];
buf[m++] = f[i][1];
buf[m++] = f[i][2];
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecAtomic::unpack_reverse(int n, int *list, double *buf)
{
int i,j,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
f[j][0] += buf[m++];
f[j][1] += buf[m++];
f[j][2] += buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecAtomic::pack_border(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0];
dy = pbc[1];
dz = pbc[2];
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecAtomic::pack_border_vel(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0];
dy = pbc[1];
dz = pbc[2];
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecAtomic::unpack_border(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
if (i == nmax) grow(0);
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
tag[i] = static_cast<int> (buf[m++]);
type[i] = static_cast<int> (buf[m++]);
mask[i] = static_cast<int> (buf[m++]);
}
}
/* ---------------------------------------------------------------------- */
void AtomVecAtomic::unpack_border_vel(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
if (i == nmax) grow(0);
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
tag[i] = static_cast<int> (buf[m++]);
type[i] = static_cast<int> (buf[m++]);
mask[i] = static_cast<int> (buf[m++]);
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
}
}
/* ----------------------------------------------------------------------
pack data for atom I for sending to another proc
xyz must be 1st 3 values, so comm::exchange() can test on them
------------------------------------------------------------------------- */
int AtomVecAtomic::pack_exchange(int i, double *buf)
{
int m = 1;
buf[m++] = x[i][0];
buf[m++] = x[i][1];
buf[m++] = x[i][2];
buf[m++] = v[i][0];
buf[m++] = v[i][1];
buf[m++] = v[i][2];
buf[m++] = tag[i];
buf[m++] = type[i];
buf[m++] = mask[i];
buf[m++] = image[i];
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]);
buf[0] = m;
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecAtomic::unpack_exchange(double *buf)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
int m = 1;
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
x[nlocal][2] = buf[m++];
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
tag[nlocal] = static_cast<int> (buf[m++]);
type[nlocal] = static_cast<int> (buf[m++]);
mask[nlocal] = static_cast<int> (buf[m++]);
image[nlocal] = static_cast<int> (buf[m++]);
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->
unpack_exchange(nlocal,&buf[m]);
atom->nlocal++;
return m;
}
/* ----------------------------------------------------------------------
size of restart data for all atoms owned by this proc
include extra data stored by fixes
------------------------------------------------------------------------- */
int AtomVecAtomic::size_restart()
{
int i;
int nlocal = atom->nlocal;
int n = 11 * nlocal;
if (atom->nextra_restart)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
for (i = 0; i < nlocal; i++)
n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
return n;
}
/* ----------------------------------------------------------------------
pack atom I's data for restart file including extra quantities
xyz must be 1st 3 values, so that read_restart can test on them
molecular types may be negative, but write as positive
------------------------------------------------------------------------- */
int AtomVecAtomic::pack_restart(int i, double *buf)
{
int m = 1;
buf[m++] = x[i][0];
buf[m++] = x[i][1];
buf[m++] = x[i][2];
buf[m++] = tag[i];
buf[m++] = type[i];
buf[m++] = mask[i];
buf[m++] = image[i];
buf[m++] = v[i][0];
buf[m++] = v[i][1];
buf[m++] = v[i][2];
if (atom->nextra_restart)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]);
buf[0] = m;
return m;
}
/* ----------------------------------------------------------------------
unpack data for one atom from restart file including extra quantities
------------------------------------------------------------------------- */
int AtomVecAtomic::unpack_restart(double *buf)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) {
grow(0);
if (atom->nextra_store)
atom->extra = memory->grow_2d_double_array(atom->extra,nmax,
atom->nextra_store,
"atom:extra");
}
int m = 1;
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
x[nlocal][2] = buf[m++];
tag[nlocal] = static_cast<int> (buf[m++]);
type[nlocal] = static_cast<int> (buf[m++]);
mask[nlocal] = static_cast<int> (buf[m++]);
image[nlocal] = static_cast<int> (buf[m++]);
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
double **extra = atom->extra;
if (atom->nextra_store) {
int size = static_cast<int> (buf[0]) - m;
for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++];
}
atom->nlocal++;
return m;
}
/* ----------------------------------------------------------------------
create one atom of itype at coord
set other values to defaults
------------------------------------------------------------------------- */
void AtomVecAtomic::create_atom(int itype, double *coord)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
tag[nlocal] = 0;
type[nlocal] = itype;
x[nlocal][0] = coord[0];
x[nlocal][1] = coord[1];
x[nlocal][2] = coord[2];
mask[nlocal] = 1;
image[nlocal] = (512 << 20) | (512 << 10) | 512;
v[nlocal][0] = 0.0;
v[nlocal][1] = 0.0;
v[nlocal][2] = 0.0;
atom->nlocal++;
}
/* ----------------------------------------------------------------------
unpack one line from Atoms section of data file
initialize other atom quantities
------------------------------------------------------------------------- */
void AtomVecAtomic::data_atom(double *coord, int imagetmp, char **values)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
tag[nlocal] = atoi(values[0]);
if (tag[nlocal] <= 0)
error->one("Invalid atom ID in Atoms section of data file");
type[nlocal] = atoi(values[1]);
if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
error->one("Invalid atom type in Atoms section of data file");
x[nlocal][0] = coord[0];
x[nlocal][1] = coord[1];
x[nlocal][2] = coord[2];
image[nlocal] = imagetmp;
mask[nlocal] = 1;
v[nlocal][0] = 0.0;
v[nlocal][1] = 0.0;
v[nlocal][2] = 0.0;
atom->nlocal++;
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
------------------------------------------------------------------------- */
double AtomVecAtomic::memory_usage()
{
double bytes = 0.0;
if (atom->memcheck("tag")) bytes += nmax * sizeof(int);
if (atom->memcheck("type")) bytes += nmax * sizeof(int);
if (atom->memcheck("mask")) bytes += nmax * sizeof(int);
if (atom->memcheck("image")) bytes += nmax * sizeof(int);
if (atom->memcheck("x")) bytes += nmax*3 * sizeof(double);
if (atom->memcheck("v")) bytes += nmax*3 * sizeof(double);
if (atom->memcheck("f")) bytes += nmax*3 * sizeof(double);
return bytes;
}
diff --git a/src/atom_vec_charge.cpp b/src/atom_vec_charge.cpp
index 69a918562..ed2053a52 100644
--- a/src/atom_vec_charge.cpp
+++ b/src/atom_vec_charge.cpp
@@ -1,650 +1,650 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "stdlib.h"
#include "atom_vec_charge.h"
-#include "lmptype.h"
#include "atom.h"
#include "domain.h"
#include "modify.h"
#include "fix.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define DELTA 10000
/* ---------------------------------------------------------------------- */
AtomVecCharge::AtomVecCharge(LAMMPS *lmp, int narg, char **arg) :
AtomVec(lmp, narg, arg)
{
molecular = 0;
mass_type = 1;
comm_x_only = comm_f_only = 1;
size_forward = 3;
size_reverse = 3;
size_border = 7;
size_velocity = 3;
size_data_atom = 6;
size_data_vel = 4;
xcol_data = 4;
atom->q_flag = 1;
}
/* ----------------------------------------------------------------------
grow atom arrays
n = 0 grows arrays by DELTA
n > 0 allocates arrays to size n
------------------------------------------------------------------------- */
void AtomVecCharge::grow(int n)
{
if (n == 0) nmax += DELTA;
else nmax = n;
atom->nmax = nmax;
if (nmax < 0 || nmax > MAXSMALLINT)
error->one("Per-processor system is too big");
tag = atom->tag = (int *)
memory->srealloc(atom->tag,nmax*sizeof(int),"atom:tag");
type = atom->type = (int *)
memory->srealloc(atom->type,nmax*sizeof(int),"atom:type");
mask = atom->mask = (int *)
memory->srealloc(atom->mask,nmax*sizeof(int),"atom:mask");
image = atom->image = (int *)
memory->srealloc(atom->image,nmax*sizeof(int),"atom:image");
x = atom->x = memory->grow_2d_double_array(atom->x,nmax,3,"atom:x");
v = atom->v = memory->grow_2d_double_array(atom->v,nmax,3,"atom:v");
f = atom->f = memory->grow_2d_double_array(atom->f,nmax,3,"atom:f");
q = atom->q = (double *)
memory->srealloc(atom->q,nmax*sizeof(double),"atom:q");
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
}
/* ----------------------------------------------------------------------
reset local array ptrs
------------------------------------------------------------------------- */
void AtomVecCharge::grow_reset()
{
tag = atom->tag; type = atom->type;
mask = atom->mask; image = atom->image;
x = atom->x; v = atom->v; f = atom->f;
q = atom->q;
}
/* ---------------------------------------------------------------------- */
void AtomVecCharge::copy(int i, int j)
{
tag[j] = tag[i];
type[j] = type[i];
mask[j] = mask[i];
image[j] = image[i];
x[j][0] = x[i][0];
x[j][1] = x[i][1];
x[j][2] = x[i][2];
v[j][0] = v[i][0];
v[j][1] = v[i][1];
v[j][2] = v[i][2];
q[j] = q[i];
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j);
}
/* ---------------------------------------------------------------------- */
int AtomVecCharge::pack_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
dz = pbc[2]*domain->zprd;
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecCharge::pack_comm_vel(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
dz = pbc[2]*domain->zprd;
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecCharge::unpack_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
void AtomVecCharge::unpack_comm_vel(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecCharge::pack_reverse(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
buf[m++] = f[i][0];
buf[m++] = f[i][1];
buf[m++] = f[i][2];
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecCharge::unpack_reverse(int n, int *list, double *buf)
{
int i,j,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
f[j][0] += buf[m++];
f[j][1] += buf[m++];
f[j][2] += buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecCharge::pack_border(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = q[j];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0];
dy = pbc[1];
dz = pbc[2];
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = q[j];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecCharge::pack_border_vel(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = q[j];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0];
dy = pbc[1];
dz = pbc[2];
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = q[j];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecCharge::pack_border_one(int i, double *buf)
{
buf[0] = q[i];
return 1;
}
/* ---------------------------------------------------------------------- */
void AtomVecCharge::unpack_border(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
if (i == nmax) grow(0);
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
tag[i] = static_cast<int> (buf[m++]);
type[i] = static_cast<int> (buf[m++]);
mask[i] = static_cast<int> (buf[m++]);
q[i] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
void AtomVecCharge::unpack_border_vel(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
if (i == nmax) grow(0);
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
tag[i] = static_cast<int> (buf[m++]);
type[i] = static_cast<int> (buf[m++]);
mask[i] = static_cast<int> (buf[m++]);
q[i] = buf[m++];
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecCharge::unpack_border_one(int i, double *buf)
{
q[i] = buf[0];
return 1;
}
/* ----------------------------------------------------------------------
pack data for atom I for sending to another proc
xyz must be 1st 3 values, so comm::exchange() can test on them
------------------------------------------------------------------------- */
int AtomVecCharge::pack_exchange(int i, double *buf)
{
int m = 1;
buf[m++] = x[i][0];
buf[m++] = x[i][1];
buf[m++] = x[i][2];
buf[m++] = v[i][0];
buf[m++] = v[i][1];
buf[m++] = v[i][2];
buf[m++] = tag[i];
buf[m++] = type[i];
buf[m++] = mask[i];
buf[m++] = image[i];
buf[m++] = q[i];
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]);
buf[0] = m;
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecCharge::unpack_exchange(double *buf)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
int m = 1;
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
x[nlocal][2] = buf[m++];
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
tag[nlocal] = static_cast<int> (buf[m++]);
type[nlocal] = static_cast<int> (buf[m++]);
mask[nlocal] = static_cast<int> (buf[m++]);
image[nlocal] = static_cast<int> (buf[m++]);
q[nlocal] = buf[m++];
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->
unpack_exchange(nlocal,&buf[m]);
atom->nlocal++;
return m;
}
/* ----------------------------------------------------------------------
size of restart data for all atoms owned by this proc
include extra data stored by fixes
------------------------------------------------------------------------- */
int AtomVecCharge::size_restart()
{
int i;
int nlocal = atom->nlocal;
int n = 12 * nlocal;
if (atom->nextra_restart)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
for (i = 0; i < nlocal; i++)
n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
return n;
}
/* ----------------------------------------------------------------------
pack atom I's data for restart file including extra quantities
xyz must be 1st 3 values, so that read_restart can test on them
molecular types may be negative, but write as positive
------------------------------------------------------------------------- */
int AtomVecCharge::pack_restart(int i, double *buf)
{
int m = 1;
buf[m++] = x[i][0];
buf[m++] = x[i][1];
buf[m++] = x[i][2];
buf[m++] = tag[i];
buf[m++] = type[i];
buf[m++] = mask[i];
buf[m++] = image[i];
buf[m++] = v[i][0];
buf[m++] = v[i][1];
buf[m++] = v[i][2];
buf[m++] = q[i];
if (atom->nextra_restart)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]);
buf[0] = m;
return m;
}
/* ----------------------------------------------------------------------
unpack data for one atom from restart file including extra quantities
------------------------------------------------------------------------- */
int AtomVecCharge::unpack_restart(double *buf)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) {
grow(0);
if (atom->nextra_store)
atom->extra = memory->grow_2d_double_array(atom->extra,nmax,
atom->nextra_store,
"atom:extra");
}
int m = 1;
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
x[nlocal][2] = buf[m++];
tag[nlocal] = static_cast<int> (buf[m++]);
type[nlocal] = static_cast<int> (buf[m++]);
mask[nlocal] = static_cast<int> (buf[m++]);
image[nlocal] = static_cast<int> (buf[m++]);
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
q[nlocal] = buf[m++];
double **extra = atom->extra;
if (atom->nextra_store) {
int size = static_cast<int> (buf[0]) - m;
for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++];
}
atom->nlocal++;
return m;
}
/* ----------------------------------------------------------------------
create one atom of itype at coord
set other values to defaults
------------------------------------------------------------------------- */
void AtomVecCharge::create_atom(int itype, double *coord)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
tag[nlocal] = 0;
type[nlocal] = itype;
x[nlocal][0] = coord[0];
x[nlocal][1] = coord[1];
x[nlocal][2] = coord[2];
mask[nlocal] = 1;
image[nlocal] = (512 << 20) | (512 << 10) | 512;
v[nlocal][0] = 0.0;
v[nlocal][1] = 0.0;
v[nlocal][2] = 0.0;
q[nlocal] = 0.0;
atom->nlocal++;
}
/* ----------------------------------------------------------------------
unpack one line from Atoms section of data file
initialize other atom quantities
------------------------------------------------------------------------- */
void AtomVecCharge::data_atom(double *coord, int imagetmp, char **values)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
tag[nlocal] = atoi(values[0]);
if (tag[nlocal] <= 0)
error->one("Invalid atom ID in Atoms section of data file");
type[nlocal] = atoi(values[1]);
if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
error->one("Invalid atom type in Atoms section of data file");
q[nlocal] = atof(values[2]);
x[nlocal][0] = coord[0];
x[nlocal][1] = coord[1];
x[nlocal][2] = coord[2];
image[nlocal] = imagetmp;
mask[nlocal] = 1;
v[nlocal][0] = 0.0;
v[nlocal][1] = 0.0;
v[nlocal][2] = 0.0;
atom->nlocal++;
}
/* ----------------------------------------------------------------------
unpack hybrid quantities from one line in Atoms section of data file
initialize other atom quantities for this sub-style
------------------------------------------------------------------------- */
int AtomVecCharge::data_atom_hybrid(int nlocal, char **values)
{
q[nlocal] = atof(values[0]);
return 1;
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
------------------------------------------------------------------------- */
double AtomVecCharge::memory_usage()
{
double bytes = 0.0;
if (atom->memcheck("tag")) bytes += nmax * sizeof(int);
if (atom->memcheck("type")) bytes += nmax * sizeof(int);
if (atom->memcheck("mask")) bytes += nmax * sizeof(int);
if (atom->memcheck("image")) bytes += nmax * sizeof(int);
if (atom->memcheck("x")) bytes += nmax*3 * sizeof(double);
if (atom->memcheck("v")) bytes += nmax*3 * sizeof(double);
if (atom->memcheck("f")) bytes += nmax*3 * sizeof(double);
if (atom->memcheck("q")) bytes += nmax * sizeof(double);
return bytes;
}
diff --git a/src/atom_vec_hybrid.cpp b/src/atom_vec_hybrid.cpp
index 8be54a102..12b159158 100644
--- a/src/atom_vec_hybrid.cpp
+++ b/src/atom_vec_hybrid.cpp
@@ -1,773 +1,773 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "stdlib.h"
#include "string.h"
#include "atom_vec_hybrid.h"
-#include "lmptype.h"
#include "atom.h"
#include "domain.h"
#include "modify.h"
#include "fix.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MIN(A,B) ((A) < (B)) ? (A) : (B)
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
#define DELTA 10000
/* ---------------------------------------------------------------------- */
AtomVecHybrid::AtomVecHybrid(LAMMPS *lmp, int narg, char **arg) :
AtomVec(lmp, narg, arg)
{
int i,k;
if (narg < 1) error->all("Illegal atom_style command");
// create sub-styles
nstyles = narg;
styles = new AtomVec*[nstyles];
keywords = new char*[nstyles];
for (i = 0; i < narg; i++) {
for (k = 0; k < i; k++)
if (strcmp(arg[i],keywords[k]) == 0)
error->all("Atom style hybrid cannot use same atom style twice");
if (strcmp(arg[i],"hybrid") == 0)
error->all("Atom style hybrid cannot have hybrid as an argument");
styles[i] = atom->new_avec(arg[i],0,NULL);
keywords[i] = new char[strlen(arg[i])+1];
strcpy(keywords[i],arg[i]);
}
// hybrid settings are MAX or MIN of sub-style settings
// hybrid sizes are minimial values plus extra values for each sub-style
molecular = 0;
comm_x_only = comm_f_only = 1;
size_forward = 3;
size_reverse = 3;
size_border = 6;
size_data_atom = 5;
size_data_vel = 4;
xcol_data = 3;
for (k = 0; k < nstyles; k++) {
molecular = MAX(molecular,styles[k]->molecular);
bonds_allow = MAX(bonds_allow,styles[k]->bonds_allow);
angles_allow = MAX(angles_allow,styles[k]->angles_allow);
dihedrals_allow = MAX(dihedrals_allow,styles[k]->dihedrals_allow);
impropers_allow = MAX(impropers_allow,styles[k]->impropers_allow);
mass_type = MAX(mass_type,styles[k]->mass_type);
shape_type = MAX(shape_type,styles[k]->shape_type);
dipole_type = MAX(dipole_type,styles[k]->dipole_type);
comm_x_only = MIN(comm_x_only,styles[k]->comm_x_only);
comm_f_only = MIN(comm_f_only,styles[k]->comm_f_only);
size_forward += styles[k]->size_forward - 3;
size_reverse += styles[k]->size_reverse - 3;
size_border += styles[k]->size_border - 6;
size_data_atom += styles[k]->size_data_atom - 5;
size_data_vel += styles[k]->size_data_vel - 4;
}
size_velocity = 3;
if (atom->omega_flag) size_velocity += 3;
if (atom->angmom_flag) size_velocity += 3;
}
/* ---------------------------------------------------------------------- */
AtomVecHybrid::~AtomVecHybrid()
{
for (int k = 0; k < nstyles; k++) delete styles[k];
delete [] styles;
for (int k = 0; k < nstyles; k++) delete [] keywords[k];
delete [] keywords;
}
/* ----------------------------------------------------------------------
grow atom arrays
n = 0 grows arrays by DELTA
n > 0 allocates arrays to size n
------------------------------------------------------------------------- */
void AtomVecHybrid::grow(int n)
{
if (n == 0) nmax += DELTA;
else nmax = n;
atom->nmax = nmax;
if (nmax < 0 || nmax > MAXSMALLINT)
error->one("Per-processor system is too big");
// sub-styles perform all reallocation
// turn off nextra_grow so hybrid can do that once below
int tmp = atom->nextra_grow;
atom->nextra_grow = 0;
for (int k = 0; k < nstyles; k++) styles[k]->grow(nmax);
atom->nextra_grow = tmp;
// insure hybrid local ptrs and sub-style ptrs are up to date
// for sub-styles, do this in case
// multiple sub-style reallocs of same array occurred
grow_reset();
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
}
/* ----------------------------------------------------------------------
reset local array ptrs
------------------------------------------------------------------------- */
void AtomVecHybrid::grow_reset()
{
tag = atom->tag; type = atom->type;
mask = atom->mask; image = atom->image;
x = atom->x; v = atom->v; f = atom->f;
omega = atom->omega; angmom = atom->angmom;
for (int k = 0; k < nstyles; k++) styles[k]->grow_reset();
}
/* ----------------------------------------------------------------------
copy array values for all sub-styles
------------------------------------------------------------------------- */
void AtomVecHybrid::copy(int i, int j)
{
int tmp = atom->nextra_grow;
atom->nextra_grow = 0;
for (int k = 0; k < nstyles; k++) styles[k]->copy(i,j);
atom->nextra_grow = tmp;
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j);
}
/* ---------------------------------------------------------------------- */
int AtomVecHybrid::pack_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,k,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
for (k = 0; k < nstyles; k++)
m += styles[k]->pack_comm_one(j,&buf[m]);
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
dz = pbc[2]*domain->zprd;
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
for (k = 0; k < nstyles; k++)
m += styles[k]->pack_comm_one(j,&buf[m]);
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecHybrid::pack_comm_vel(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,k,m;
double dx,dy,dz;
int omega_flag = atom->omega_flag;
int angmom_flag = atom->angmom_flag;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
if (omega_flag) {
buf[m++] = omega[j][0];
buf[m++] = omega[j][1];
buf[m++] = omega[j][2];
}
if (angmom_flag) {
buf[m++] = angmom[j][0];
buf[m++] = angmom[j][1];
buf[m++] = angmom[j][2];
}
for (k = 0; k < nstyles; k++)
m += styles[k]->pack_comm_one(j,&buf[m]);
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
dz = pbc[2]*domain->zprd;
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
if (omega_flag) {
buf[m++] = omega[j][0];
buf[m++] = omega[j][1];
buf[m++] = omega[j][2];
}
if (angmom_flag) {
buf[m++] = angmom[j][0];
buf[m++] = angmom[j][1];
buf[m++] = angmom[j][2];
}
for (k = 0; k < nstyles; k++)
m += styles[k]->pack_comm_one(j,&buf[m]);
}
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecHybrid::unpack_comm(int n, int first, double *buf)
{
int i,k,last;
int m = 0;
last = first + n;
for (i = first; i < last; i++) {
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
for (k = 0; k < nstyles; k++)
m += styles[k]->unpack_comm_one(i,&buf[m]);
}
}
/* ---------------------------------------------------------------------- */
void AtomVecHybrid::unpack_comm_vel(int n, int first, double *buf)
{
int i,k,last;
int omega_flag = atom->omega_flag;
int angmom_flag = atom->angmom_flag;
int m = 0;
last = first + n;
for (i = first; i < last; i++) {
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
if (omega_flag) {
omega[i][0] = buf[m++];
omega[i][1] = buf[m++];
omega[i][2] = buf[m++];
}
if (angmom_flag) {
angmom[i][0] = buf[m++];
angmom[i][1] = buf[m++];
angmom[i][2] = buf[m++];
}
for (k = 0; k < nstyles; k++)
m += styles[k]->unpack_comm_one(i,&buf[m]);
}
}
/* ---------------------------------------------------------------------- */
int AtomVecHybrid::pack_reverse(int n, int first, double *buf)
{
int i,k,last;
int m = 0;
last = first + n;
for (i = first; i < last; i++) {
buf[m++] = f[i][0];
buf[m++] = f[i][1];
buf[m++] = f[i][2];
for (k = 0; k < nstyles; k++)
m += styles[k]->pack_reverse_one(i,&buf[m]);
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecHybrid::unpack_reverse(int n, int *list, double *buf)
{
int i,j,k,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
f[j][0] += buf[m++];
f[j][1] += buf[m++];
f[j][2] += buf[m++];
for (k = 0; k < nstyles; k++)
m += styles[k]->unpack_reverse_one(j,&buf[m]);
}
}
/* ---------------------------------------------------------------------- */
int AtomVecHybrid::pack_border(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,k,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
for (k = 0; k < nstyles; k++)
m += styles[k]->pack_border_one(j,&buf[m]);
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0];
dy = pbc[1];
dz = pbc[2];
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
for (k = 0; k < nstyles; k++)
m += styles[k]->pack_border_one(j,&buf[m]);
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecHybrid::pack_border_vel(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,k,m;
double dx,dy,dz;
int omega_flag = atom->omega_flag;
int angmom_flag = atom->angmom_flag;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
if (omega_flag) {
buf[m++] = omega[j][0];
buf[m++] = omega[j][1];
buf[m++] = omega[j][2];
}
if (angmom_flag) {
buf[m++] = angmom[j][0];
buf[m++] = angmom[j][1];
buf[m++] = angmom[j][2];
}
for (k = 0; k < nstyles; k++)
m += styles[k]->pack_border_one(j,&buf[m]);
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0];
dy = pbc[1];
dz = pbc[2];
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
if (omega_flag) {
buf[m++] = omega[j][0];
buf[m++] = omega[j][1];
buf[m++] = omega[j][2];
}
if (angmom_flag) {
buf[m++] = angmom[j][0];
buf[m++] = angmom[j][1];
buf[m++] = angmom[j][2];
}
for (k = 0; k < nstyles; k++)
m += styles[k]->pack_border_one(j,&buf[m]);
}
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecHybrid::unpack_border(int n, int first, double *buf)
{
int i,k,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
if (i == nmax) grow(0);
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
tag[i] = static_cast<int> (buf[m++]);
type[i] = static_cast<int> (buf[m++]);
mask[i] = static_cast<int> (buf[m++]);
for (k = 0; k < nstyles; k++)
m += styles[k]->unpack_border_one(i,&buf[m]);
}
}
/* ---------------------------------------------------------------------- */
void AtomVecHybrid::unpack_border_vel(int n, int first, double *buf)
{
int i,k,m,last;
int omega_flag = atom->omega_flag;
int angmom_flag = atom->angmom_flag;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
if (i == nmax) grow(0);
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
tag[i] = static_cast<int> (buf[m++]);
type[i] = static_cast<int> (buf[m++]);
mask[i] = static_cast<int> (buf[m++]);
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
if (omega_flag) {
omega[i][0] = buf[m++];
omega[i][1] = buf[m++];
omega[i][2] = buf[m++];
}
if (angmom_flag) {
angmom[i][0] = buf[m++];
angmom[i][1] = buf[m++];
angmom[i][2] = buf[m++];
}
for (k = 0; k < nstyles; k++)
m += styles[k]->unpack_border_one(i,&buf[m]);
}
}
/* ----------------------------------------------------------------------
pack data for atom I for sending to another proc
pack each sub-style one after the other
------------------------------------------------------------------------- */
int AtomVecHybrid::pack_exchange(int i, double *buf)
{
int k;
int tmp = atom->nextra_grow;
atom->nextra_grow = 0;
int m = 0;
for (k = 0; k < nstyles; k++)
m += styles[k]->pack_exchange(i,&buf[m]);
atom->nextra_grow = tmp;
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]);
buf[0] = m;
return m;
}
/* ----------------------------------------------------------------------
unpack data for single atom received from another proc
unpack each sub-style one after the other
grow() occurs here so arrays for all sub-styles are grown
------------------------------------------------------------------------- */
int AtomVecHybrid::unpack_exchange(double *buf)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
int tmp = atom->nextra_grow;
atom->nextra_grow = 0;
int m = 0;
for (int k = 0; k < nstyles; k++) {
m += styles[k]->unpack_exchange(&buf[m]);
atom->nlocal--;
}
atom->nextra_grow = tmp;
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->
unpack_exchange(nlocal,&buf[m]);
atom->nlocal++;
return m;
}
/* ----------------------------------------------------------------------
size of restart data for all atoms owned by this proc
include extra data stored by fixes
------------------------------------------------------------------------- */
int AtomVecHybrid::size_restart()
{
int tmp = atom->nextra_restart;
atom->nextra_restart = 0;
int n = 0;
for (int k = 0; k < nstyles; k++)
n += styles[k]->size_restart();
atom->nextra_restart = tmp;
int nlocal = atom->nlocal;
if (atom->nextra_restart)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
for (int i = 0; i < nlocal; i++)
n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
return n;
}
/* ----------------------------------------------------------------------
pack atom I's data for restart file including extra quantities
xyz must be 1st 3 values, so that read_restart can test on them
pack each sub-style one after the other
------------------------------------------------------------------------- */
int AtomVecHybrid::pack_restart(int i, double *buf)
{
int tmp = atom->nextra_restart;
atom->nextra_restart = 0;
int m = 0;
for (int k = 0; k < nstyles; k++)
m += styles[k]->pack_restart(i,&buf[m]);
atom->nextra_restart = tmp;
if (atom->nextra_restart)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]);
buf[0] = m;
return m;
}
/* ----------------------------------------------------------------------
unpack data for one atom from restart file including extra quantities
unpack each sub-style one after the other
grow() occurs here so arrays for all sub-styles are grown
------------------------------------------------------------------------- */
int AtomVecHybrid::unpack_restart(double *buf)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) {
grow(0);
if (atom->nextra_store)
atom->extra = memory->grow_2d_double_array(atom->extra,nmax,
atom->nextra_store,
"atom:extra");
}
int tmp = atom->nextra_store;
atom->nextra_store = 0;
int m = 0;
for (int k = 0; k < nstyles; k++) {
m += styles[k]->unpack_restart(&buf[m]);
atom->nlocal--;
}
atom->nextra_store = tmp;
double **extra = atom->extra;
if (atom->nextra_store) {
int size = static_cast<int> (buf[0]) - m;
for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++];
}
atom->nlocal++;
return m;
}
/* ----------------------------------------------------------------------
create one atom of itype at coord
create each sub-style one after the other
grow() occurs here so arrays for all sub-styles are grown
------------------------------------------------------------------------- */
void AtomVecHybrid::create_atom(int itype, double *coord)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
for (int k = 0; k < nstyles; k++) {
styles[k]->create_atom(itype,coord);
atom->nlocal--;
}
atom->nlocal++;
}
/* ----------------------------------------------------------------------
unpack one line from Atoms section of data file
grow() occurs here so arrays for all sub-styles are grown
------------------------------------------------------------------------- */
void AtomVecHybrid::data_atom(double *coord, int imagetmp, char **values)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
tag[nlocal] = atoi(values[0]);
if (tag[nlocal] <= 0)
error->one("Invalid atom ID in Atoms section of data file");
type[nlocal] = atoi(values[1]);
if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
error->one("Invalid atom type in Atoms section of data file");
x[nlocal][0] = coord[0];
x[nlocal][1] = coord[1];
x[nlocal][2] = coord[2];
image[nlocal] = imagetmp;
mask[nlocal] = 1;
v[nlocal][0] = 0.0;
v[nlocal][1] = 0.0;
v[nlocal][2] = 0.0;
if (atom->omega_flag) {
omega[nlocal][0] = 0.0;
omega[nlocal][1] = 0.0;
omega[nlocal][2] = 0.0;
}
if (atom->angmom_flag) {
angmom[nlocal][0] = 0.0;
angmom[nlocal][1] = 0.0;
angmom[nlocal][2] = 0.0;
}
// each sub-style parses sub-style specific values
int m = 5;
for (int k = 0; k < nstyles; k++)
m += styles[k]->data_atom_hybrid(nlocal,&values[m]);
atom->nlocal++;
}
/* ----------------------------------------------------------------------
unpack one line from Velocities section of data file
------------------------------------------------------------------------- */
void AtomVecHybrid::data_vel(int m, char **values)
{
v[m][0] = atof(values[0]);
v[m][1] = atof(values[1]);
v[m][2] = atof(values[2]);
// each sub-style parses sub-style specific values
int n = 3;
for (int k = 0; k < nstyles; k++)
n += styles[k]->data_vel_hybrid(m,&values[n]);
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
------------------------------------------------------------------------- */
double AtomVecHybrid::memory_usage()
{
double bytes = 0.0;
for (int k = 0; k < nstyles; k++) bytes += styles[k]->memory_usage();
return bytes;
}
diff --git a/src/compute.cpp b/src/compute.cpp
index 27e7ff564..44c628e27 100644
--- a/src/compute.cpp
+++ b/src/compute.cpp
@@ -1,296 +1,296 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "mpi.h"
#include "stdlib.h"
#include "string.h"
#include "ctype.h"
#include "compute.h"
-#include "lmptype.h"
#include "atom.h"
#include "domain.h"
#include "comm.h"
#include "group.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define DELTA 4
#define BIG 2000000000
#define MIN(A,B) ((A) < (B)) ? (A) : (B)
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
/* ---------------------------------------------------------------------- */
Compute::Compute(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
{
if (narg < 3) error->all("Illegal compute command");
// compute ID, group, and style
// ID must be all alphanumeric chars or underscores
int n = strlen(arg[0]) + 1;
id = new char[n];
strcpy(id,arg[0]);
for (int i = 0; i < n-1; i++)
if (!isalnum(id[i]) && id[i] != '_')
error->all("Compute ID must be alphanumeric or underscore characters");
igroup = group->find(arg[1]);
if (igroup == -1) error->all("Could not find compute group ID");
groupbit = group->bitmask[igroup];
n = strlen(arg[2]) + 1;
style = new char[n];
strcpy(style,arg[2]);
// set child class defaults
scalar_flag = vector_flag = array_flag = 0;
peratom_flag = local_flag = 0;
tempflag = pressflag = peflag = 0;
pressatomflag = peatomflag = 0;
tempbias = 0;
timeflag = 0;
comm_forward = comm_reverse = 0;
invoked_scalar = invoked_vector = invoked_array = -1;
invoked_peratom = invoked_local = -1;
// set modify defaults
extra_dof = domain->dimension;
dynamic = 0;
// setup list of timesteps
ntime = maxtime = 0;
tlist = NULL;
// setup map for molecule IDs
molmap = NULL;
}
/* ---------------------------------------------------------------------- */
Compute::~Compute()
{
delete [] id;
delete [] style;
memory->sfree(tlist);
memory->sfree(molmap);
}
/* ---------------------------------------------------------------------- */
void Compute::modify_params(int narg, char **arg)
{
if (narg == 0) error->all("Illegal compute_modify command");
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"extra") == 0) {
if (iarg+2 > narg) error->all("Illegal compute_modify command");
extra_dof = atoi(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"dynamic") == 0) {
if (iarg+2 > narg) error->all("Illegal compute_modify command");
if (strcmp(arg[iarg+1],"no") == 0) dynamic = 0;
else if (strcmp(arg[iarg+1],"yes") == 0) dynamic = 1;
else error->all("Illegal compute_modify command");
iarg += 2;
} else if (strcmp(arg[iarg],"thermo") == 0) {
if (iarg+2 > narg) error->all("Illegal compute_modify command");
if (strcmp(arg[iarg+1],"no") == 0) thermoflag = 0;
else if (strcmp(arg[iarg+1],"yes") == 0) thermoflag = 1;
else error->all("Illegal compute_modify command");
iarg += 2;
} else error->all("Illegal compute_modify command");
}
}
/* ----------------------------------------------------------------------
reset extra_dof to its default value
------------------------------------------------------------------------- */
void Compute::reset_extra_dof()
{
extra_dof = domain->dimension;
}
/* ---------------------------------------------------------------------- */
void Compute::reset_extra_compute_fix(char *)
{
error->all("Compute does not allow an extra compute or fix to be reset");
}
/* ----------------------------------------------------------------------
add ntimestep to list of timesteps the compute will be called on
do not add if already in list
search from top downward, since list of times is in decreasing order
------------------------------------------------------------------------- */
void Compute::addstep(bigint ntimestep)
{
// i = location in list to insert ntimestep
int i;
for (i = ntime-1; i >= 0; i--) {
if (ntimestep == tlist[i]) return;
if (ntimestep < tlist[i]) break;
}
i++;
// extend list as needed
if (ntime == maxtime) {
maxtime += DELTA;
tlist = (bigint *)
memory->srealloc(tlist,maxtime*sizeof(bigint),"compute:tlist");
}
// move remainder of list upward and insert ntimestep
for (int j = ntime-1; j >= i; j--) tlist[j+1] = tlist[j];
tlist[i] = ntimestep;
ntime++;
}
/* ----------------------------------------------------------------------
return 1/0 if ntimestep is or is not in list of calling timesteps
if value(s) on top of list are less than ntimestep, delete them
search from top downward, since list of times is in decreasing order
------------------------------------------------------------------------- */
int Compute::matchstep(bigint ntimestep)
{
for (int i = ntime-1; i >= 0; i--) {
if (ntimestep < tlist[i]) return 0;
if (ntimestep == tlist[i]) return 1;
if (ntimestep > tlist[i]) ntime--;
}
return 0;
}
/* ----------------------------------------------------------------------
clean out list of timesteps to call the compute on
------------------------------------------------------------------------- */
void Compute::clearstep()
{
ntime = 0;
}
/* ----------------------------------------------------------------------
identify molecule IDs with atoms in group
warn if any atom in group has molecule ID = 0
warn if any molecule has only some atoms in group
return Ncount = # of molecules with atoms in group
set molmap to NULL if molecule IDs include all in range from 1 to Ncount
else: molecule IDs range from idlo to idhi
set molmap to vector of length idhi-idlo+1
molmap[id-idlo] = index from 0 to Ncount-1
return idlo and idhi
------------------------------------------------------------------------- */
int Compute::molecules_in_group(int &idlo, int &idhi)
{
int i;
memory->sfree(molmap);
molmap = NULL;
// find lo/hi molecule ID for any atom in group
// warn if atom in group has ID = 0
int *molecule = atom->molecule;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int lo = BIG;
int hi = -BIG;
int flag = 0;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (molecule[i] == 0) {
flag = 1;
continue;
}
lo = MIN(lo,molecule[i]);
hi = MAX(hi,molecule[i]);
}
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall && comm->me == 0)
error->warning("Atom with molecule ID = 0 included in "
"compute molecule group");
MPI_Allreduce(&lo,&idlo,1,MPI_INT,MPI_MIN,world);
MPI_Allreduce(&hi,&idhi,1,MPI_INT,MPI_MAX,world);
if (idlo == BIG) return 0;
// molmap = vector of length nlen
// set to 1 for IDs that appear in group across all procs, else 0
int nlen = idhi-idlo+1;
molmap = (int *) memory->smalloc(nlen*sizeof(int),"compute:molmap");
for (i = 0; i < nlen; i++) molmap[i] = 0;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
molmap[molecule[i]-idlo] = 1;
int *molmapall =
(int *) memory->smalloc(nlen*sizeof(int),"compute:molmapall");
MPI_Allreduce(molmap,molmapall,nlen,MPI_INT,MPI_MAX,world);
// nmolecules = # of non-zero IDs in molmap
// molmap[i] = index of molecule, skipping molecules not in group with -1
int nmolecules = 0;
for (i = 0; i < nlen; i++)
if (molmapall[i]) molmap[i] = nmolecules++;
else molmap[i] = -1;
memory->sfree(molmapall);
// warn if any molecule has some atoms in group and some not in group
flag = 0;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) continue;
if (molecule[i] == 0) continue;
if (molecule[i] < idlo || molecule[i] > idhi) continue;
if (molmap[molecule[i]-idlo] >= 0) flag = 1;
}
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall && comm->me == 0)
error->warning("One or more compute molecules has atoms not in group");
// if molmap simply stores 1 to Nmolecules, then free it
if (nmolecules < nlen) return nmolecules;
if (idlo > 1) return nmolecules;
memory->sfree(molmap);
molmap = NULL;
return nmolecules;
}
diff --git a/src/compute.h b/src/compute.h
index cb7c3152f..f7ece5d38 100644
--- a/src/compute.h
+++ b/src/compute.h
@@ -1,129 +1,129 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifndef LMP_COMPUTE_H
#define LMP_COMPUTE_H
-#include "pointers.h"
#include "lmptype.h"
+#include "pointers.h"
namespace LAMMPS_NS {
class Compute : protected Pointers {
public:
char *id,*style;
int igroup,groupbit;
double scalar; // computed global scalar
double *vector; // computed global vector
double **array; // computed global array
double *vector_atom; // computed per-atom vector
double **array_atom; // computed per-atom array
double *vector_local; // computed local vector
double **array_local; // computed local array
int scalar_flag; // 0/1 if compute_scalar() function exists
int vector_flag; // 0/1 if compute_vector() function exists
int array_flag; // 0/1 if compute_array() function exists
int size_vector; // length of global vector
int size_array_rows; // rows in global array
int size_array_cols; // columns in global array
int peratom_flag; // 0/1 if compute_peratom() function exists
int size_peratom_cols; // 0 = vector, N = columns in peratom array
int local_flag; // 0/1 if compute_local() function exists
int size_local_rows; // rows in local vector or array
int size_local_cols; // 0 = vector, N = columns in local array
int extscalar; // 0/1 if global scalar is intensive/extensive
int extvector; // 0/1/-1 if global vector is all int/ext/extlist
int *extlist; // list of 0/1 int/ext for each vec component
int extarray; // 0/1 if global array is all intensive/extensive
int tempflag; // 1 if Compute can be used as temperature
// must have both compute_scalar, compute_vector
int pressflag; // 1 if Compute can be used as pressure (uses virial)
// must have both compute_scalar, compute_vector
int pressatomflag; // 1 if Compute calculates per-atom virial
int peflag; // 1 if Compute calculates PE (uses Force energies)
int peatomflag; // 1 if Compute calculates per-atom PE
int tempbias; // 0/1 if Compute temp includes self/extra bias
int timeflag; // 1 if Compute stores list of timesteps it's called on
int ntime; // # of entries in time list
int maxtime; // max # of entries time list can hold
bigint *tlist; // list of timesteps the Compute is called on
int invoked_flag; // non-zero if invoked or accessed this step, 0 if not
bigint invoked_scalar; // last timestep on which compute_scalar() was invoked
bigint invoked_vector; // ditto for compute_vector()
bigint invoked_array; // ditto for compute_array()
bigint invoked_peratom; // ditto for compute_peratom()
bigint invoked_local; // ditto for compute_local()
double dof; // degrees-of-freedom for temperature
int comm_forward; // size of forward communication (0 if none)
int comm_reverse; // size of reverse communication (0 if none)
Compute(class LAMMPS *, int, char **);
virtual ~Compute();
void modify_params(int, char **);
void reset_extra_dof();
virtual void init() = 0;
virtual void init_list(int, class NeighList *) {}
virtual double compute_scalar() {return 0.0;}
virtual void compute_vector() {}
virtual void compute_array() {}
virtual void compute_peratom() {}
virtual void compute_local() {}
virtual int pack_comm(int, int *, double *, int, int *) {return 0;}
virtual void unpack_comm(int, int, double *) {}
virtual int pack_reverse_comm(int, int, double *) {return 0;}
virtual void unpack_reverse_comm(int, int *, double *) {}
virtual int dof_remove(int) {return 0;}
virtual void remove_bias(int, double *) {}
virtual void remove_bias_all() {}
virtual void restore_bias(int, double *) {}
virtual void restore_bias_all() {}
virtual void reset_extra_compute_fix(char *);
void addstep(bigint);
int matchstep(bigint);
void clearstep();
virtual double memory_usage() {return 0.0;}
protected:
int extra_dof; // extra DOF for temperature computes
int dynamic; // recount atoms for temperature computes
int thermoflag; // 1 if include fix PE for PE computes
double vbias[3]; // stored velocity bias for one atom
double **vbiasall; // stored velocity bias for all atoms
int maxbias; // size of vbiasall array
int *molmap; // convert molecule ID to local index
int molecules_in_group(int &, int &);
};
}
#endif
diff --git a/src/compute_reduce.cpp b/src/compute_reduce.cpp
index da1ff6bcb..149517ae3 100644
--- a/src/compute_reduce.cpp
+++ b/src/compute_reduce.cpp
@@ -1,656 +1,656 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "string.h"
#include "stdlib.h"
#include "compute_reduce.h"
-#include "lmptype.h"
#include "atom.h"
#include "update.h"
#include "domain.h"
#include "modify.h"
#include "fix.h"
#include "force.h"
#include "comm.h"
#include "group.h"
#include "input.h"
#include "variable.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
enum{SUM,MINN,MAXX,AVE};
enum{X,V,F,COMPUTE,FIX,VARIABLE};
enum{PERATOM,LOCAL};
#define INVOKED_VECTOR 2
#define INVOKED_ARRAY 4
#define INVOKED_PERATOM 8
#define INVOKED_LOCAL 16
#define MIN(A,B) ((A) < (B)) ? (A) : (B)
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
#define BIG 1.0e20
/* ---------------------------------------------------------------------- */
ComputeReduce::ComputeReduce(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
int iarg;
if (strcmp(style,"reduce") == 0) {
if (narg < 5) error->all("Illegal compute reduce command");
idregion = NULL;
iarg = 3;
} else if (strcmp(style,"reduce/region") == 0) {
if (narg < 6) error->all("Illegal compute reduce/region command");
iregion = domain->find_region(arg[3]);
if (iregion == -1)
error->all("Region ID for compute reduce/region does not exist");
int n = strlen(arg[3]) + 1;
idregion = new char[n];
strcpy(idregion,arg[3]);
iarg = 4;
}
if (strcmp(arg[iarg],"sum") == 0) mode = SUM;
else if (strcmp(arg[iarg],"min") == 0) mode = MINN;
else if (strcmp(arg[iarg],"max") == 0) mode = MAXX;
else if (strcmp(arg[iarg],"ave") == 0) mode = AVE;
else error->all("Illegal compute reduce command");
iarg++;
MPI_Comm_rank(world,&me);
// parse remaining values until one isn't recognized
which = new int[narg-4];
argindex = new int[narg-4];
flavor = new int[narg-4];
ids = new char*[narg-4];
value2index = new int[narg-4];
nvalues = 0;
while (iarg < narg) {
ids[nvalues] = NULL;
if (strcmp(arg[iarg],"x") == 0) {
which[nvalues] = X;
argindex[nvalues++] = 0;
} else if (strcmp(arg[iarg],"y") == 0) {
which[nvalues] = X;
argindex[nvalues++] = 1;
} else if (strcmp(arg[iarg],"z") == 0) {
which[nvalues] = X;
argindex[nvalues++] = 2;
} else if (strcmp(arg[iarg],"vx") == 0) {
which[nvalues] = V;
argindex[nvalues++] = 0;
} else if (strcmp(arg[iarg],"vy") == 0) {
which[nvalues] = V;
argindex[nvalues++] = 1;
} else if (strcmp(arg[iarg],"vz") == 0) {
which[nvalues] = V;
argindex[nvalues++] = 2;
} else if (strcmp(arg[iarg],"fx") == 0) {
which[nvalues] = F;
argindex[nvalues++] = 0;
} else if (strcmp(arg[iarg],"fy") == 0) {
which[nvalues] = F;
argindex[nvalues++] = 1;
} else if (strcmp(arg[iarg],"fz") == 0) {
which[nvalues] = F;
argindex[nvalues++] = 2;
} else if (strncmp(arg[iarg],"c_",2) == 0 ||
strncmp(arg[iarg],"f_",2) == 0 ||
strncmp(arg[iarg],"v_",2) == 0) {
if (arg[iarg][0] == 'c') which[nvalues] = COMPUTE;
else if (arg[iarg][0] == 'f') which[nvalues] = FIX;
else if (arg[iarg][0] == 'v') which[nvalues] = VARIABLE;
int n = strlen(arg[iarg]);
char *suffix = new char[n];
strcpy(suffix,&arg[iarg][2]);
char *ptr = strchr(suffix,'[');
if (ptr) {
if (suffix[strlen(suffix)-1] != ']')
error->all("Illegal compute reduce command");
argindex[nvalues] = atoi(ptr+1);
*ptr = '\0';
} else argindex[nvalues] = 0;
n = strlen(suffix) + 1;
ids[nvalues] = new char[n];
strcpy(ids[nvalues],suffix);
nvalues++;
delete [] suffix;
} else break;
iarg++;
}
// optional args
replace = new int[nvalues];
for (int i = 0; i < nvalues; i++) replace[i] = -1;
while (iarg < narg) {
if (strcmp(arg[iarg],"replace") == 0) {
if (iarg+3 > narg) error->all("Illegal compute reduce command");
if (mode != MINN && mode != MAXX)
error->all("Compute reduce replace requires min or max mode");
int col1 = atoi(arg[iarg+1]) - 1;
int col2 = atoi(arg[iarg+2]) - 1;
if (col1 < 0 || col1 >= nvalues || col2 < 0 || col2 >= nvalues)
error->all("Illegal compute reduce command");
if (col1 == col2) error->all("Illegal compute reduce command");
if (replace[col1] >= 0 || replace[col2] >= 0)
error->all("Invalid replace values in compute reduce");
replace[col1] = col2;
iarg += 3;
} else error->all("Illegal compute reduce command");
}
// delete replace if not set
int flag = 0;
for (int i = 0; i < nvalues; i++)
if (replace[i] >= 0) flag = 1;
if (!flag) {
delete [] replace;
replace = NULL;
}
// setup and error check
for (int i = 0; i < nvalues; i++) {
if (which[i] == X || which[i] == V || which[i] == F)
flavor[i] = PERATOM;
else if (which[i] == COMPUTE) {
int icompute = modify->find_compute(ids[i]);
if (icompute < 0)
error->all("Compute ID for compute reduce does not exist");
if (modify->compute[icompute]->peratom_flag) {
flavor[i] = PERATOM;
if (argindex[i] == 0 &&
modify->compute[icompute]->size_peratom_cols != 0)
error->all("Compute reduce compute does not "
"calculate a per-atom vector");
if (argindex[i] && modify->compute[icompute]->size_peratom_cols == 0)
error->all("Compute reduce compute does not "
"calculate a per-atom array");
if (argindex[i] &&
argindex[i] > modify->compute[icompute]->size_peratom_cols)
error->all("Compute reduce compute array is accessed out-of-range");
} else if (modify->compute[icompute]->local_flag) {
flavor[i] = LOCAL;
if (argindex[i] == 0 &&
modify->compute[icompute]->size_local_cols != 0)
error->all("Compute reduce compute does not "
"calculate a local vector");
if (argindex[i] && modify->compute[icompute]->size_local_cols == 0)
error->all("Compute reduce compute does not "
"calculate a local array");
if (argindex[i] &&
argindex[i] > modify->compute[icompute]->size_local_cols)
error->all("Compute reduce compute array is accessed out-of-range");
} else error->all("Compute reduce compute calculates global values");
} else if (which[i] == FIX) {
int ifix = modify->find_fix(ids[i]);
if (ifix < 0)
error->all("Fix ID for compute reduce does not exist");
if (modify->fix[ifix]->peratom_flag) {
flavor[i] = PERATOM;
if (argindex[i] == 0 &&
modify->fix[ifix]->size_peratom_cols != 0)
error->all("Compute reduce fix does not "
"calculate a per-atom vector");
if (argindex[i] && modify->fix[ifix]->size_peratom_cols == 0)
error->all("Compute reduce fix does not "
"calculate a per-atom array");
if (argindex[i] &&
argindex[i] > modify->fix[ifix]->size_peratom_cols)
error->all("Compute reduce fix array is accessed out-of-range");
} else if (modify->fix[ifix]->local_flag) {
flavor[i] = LOCAL;
if (argindex[i] == 0 &&
modify->fix[ifix]->size_local_cols != 0)
error->all("Compute reduce fix does not "
"calculate a local vector");
if (argindex[i] && modify->fix[ifix]->size_local_cols == 0)
error->all("Compute reduce fix does not "
"calculate a local array");
if (argindex[i] &&
argindex[i] > modify->fix[ifix]->size_local_cols)
error->all("Compute reduce fix array is accessed out-of-range");
} else error->all("Compute reduce fix calculates global values");
} else if (which[i] == VARIABLE) {
int ivariable = input->variable->find(ids[i]);
if (ivariable < 0)
error->all("Variable name for compute reduce does not exist");
if (input->variable->atomstyle(ivariable) == 0)
error->all("Compute reduce variable is not atom-style variable");
flavor[i] = PERATOM;
}
}
// this compute produces either a scalar or vector
if (nvalues == 1) {
scalar_flag = 1;
if (mode == SUM) extscalar = 1;
else extscalar = 0;
vector = onevec = NULL;
indices = owner = NULL;
} else {
vector_flag = 1;
size_vector = nvalues;
if (mode == SUM) extvector = 1;
else extvector = 0;
vector = new double[size_vector];
onevec = new double[size_vector];
indices = new int[size_vector];
owner = new int[size_vector];
}
maxatom = 0;
varatom = NULL;
}
/* ---------------------------------------------------------------------- */
ComputeReduce::~ComputeReduce()
{
delete [] which;
delete [] argindex;
delete [] flavor;
for (int m = 0; m < nvalues; m++) delete [] ids[m];
delete [] ids;
delete [] value2index;
delete [] replace;
delete [] idregion;
delete [] vector;
delete [] onevec;
delete [] indices;
delete [] owner;
memory->sfree(varatom);
}
/* ---------------------------------------------------------------------- */
void ComputeReduce::init()
{
// set indices and check validity of all computes,fixes,variables
for (int m = 0; m < nvalues; m++) {
if (which[m] == COMPUTE) {
int icompute = modify->find_compute(ids[m]);
if (icompute < 0)
error->all("Compute ID for compute reduce does not exist");
value2index[m] = icompute;
} else if (which[m] == FIX) {
int ifix = modify->find_fix(ids[m]);
if (ifix < 0)
error->all("Fix ID for compute reduce does not exist");
value2index[m] = ifix;
} else if (which[m] == VARIABLE) {
int ivariable = input->variable->find(ids[m]);
if (ivariable < 0)
error->all("Variable name for compute reduce does not exist");
value2index[m] = ivariable;
} else value2index[m] = -1;
}
// set index and check validity of region
if (idregion) {
iregion = domain->find_region(idregion);
if (iregion == -1)
error->all("Region ID for compute reduce/region does not exist");
}
}
/* ---------------------------------------------------------------------- */
double ComputeReduce::compute_scalar()
{
invoked_scalar = update->ntimestep;
double one = compute_one(0,-1);
if (mode == SUM) {
MPI_Allreduce(&one,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
} else if (mode == MINN) {
MPI_Allreduce(&one,&scalar,1,MPI_DOUBLE,MPI_MIN,world);
} else if (mode == MAXX) {
MPI_Allreduce(&one,&scalar,1,MPI_DOUBLE,MPI_MAX,world);
} else if (mode == AVE) {
MPI_Allreduce(&one,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
scalar /= count(0);
}
return scalar;
}
/* ---------------------------------------------------------------------- */
void ComputeReduce::compute_vector()
{
invoked_vector = update->ntimestep;
for (int m = 0; m < nvalues; m++)
if (!replace || replace[m] < 0) {
onevec[m] = compute_one(m,-1);
indices[m] = index;
}
if (mode == SUM) {
for (int m = 0; m < nvalues; m++)
MPI_Allreduce(&onevec[m],&vector[m],1,MPI_DOUBLE,MPI_SUM,world);
} else if (mode == MINN) {
if (!replace) {
for (int m = 0; m < nvalues; m++)
MPI_Allreduce(&onevec[m],&vector[m],1,MPI_DOUBLE,MPI_MIN,world);
} else {
for (int m = 0; m < nvalues; m++)
if (replace[m] < 0) {
pairme.value = onevec[m];
pairme.proc = me;
MPI_Allreduce(&pairme,&pairall,1,MPI_DOUBLE_INT,MPI_MINLOC,world);
vector[m] = pairall.value;
owner[m] = pairall.proc;
}
for (int m = 0; m < nvalues; m++)
if (replace[m] >= 0) {
if (me == owner[replace[m]])
vector[m] = compute_one(m,indices[replace[m]]);
MPI_Bcast(&vector[m],1,MPI_DOUBLE,owner[replace[m]],world);
}
}
} else if (mode == MAXX) {
if (!replace) {
for (int m = 0; m < nvalues; m++)
MPI_Allreduce(&onevec[m],&vector[m],1,MPI_DOUBLE,MPI_MAX,world);
} else {
for (int m = 0; m < nvalues; m++)
if (replace[m] < 0) {
pairme.value = onevec[m];
pairme.proc = me;
MPI_Allreduce(&pairme,&pairall,1,MPI_DOUBLE_INT,MPI_MAXLOC,world);
vector[m] = pairall.value;
owner[m] = pairall.proc;
}
for (int m = 0; m < nvalues; m++)
if (replace[m] >= 0) {
if (me == owner[replace[m]])
vector[m] = compute_one(m,indices[replace[m]]);
MPI_Bcast(&vector[m],1,MPI_DOUBLE,owner[replace[m]],world);
}
}
} else if (mode == AVE) {
for (int m = 0; m < nvalues; m++) {
MPI_Allreduce(&onevec[m],&vector[m],1,MPI_DOUBLE,MPI_SUM,world);
vector[m] /= count(m);
}
}
}
/* ----------------------------------------------------------------------
calculate reduced value for one input M and return it
if flag = -1:
sum/min/max/ave all values in vector
for per-atom quantities, limit to atoms in group
if mode = MIN or MAX, also set index to which vector value wins
if flag >= 0: simply return vector[flag]
------------------------------------------------------------------------- */
double ComputeReduce::compute_one(int m, int flag)
{
int i;
// invoke the appropriate attribute,compute,fix,variable
// for flag = -1, compute scalar quantity by scanning over atom properties
// only include atoms in group for atom properties and per-atom quantities
index = -1;
int vidx = value2index[m];
int aidx = argindex[m];
int *mask = atom->mask;
int nlocal = atom->nlocal;
double one;
if (mode == SUM) one = 0.0;
else if (mode == MINN) one = BIG;
else if (mode == MAXX) one = -BIG;
else if (mode == AVE) one = 0.0;
if (which[m] == X) {
double **x = atom->x;
if (flag < 0) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) combine(one,x[i][aidx],i);
} else one = x[flag][aidx];
} else if (which[m] == V) {
double **v = atom->v;
if (flag < 0) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) combine(one,v[i][aidx],i);
} else one = v[flag][aidx];
} else if (which[m] == F) {
double **f = atom->f;
if (flag < 0) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) combine(one,f[i][aidx],i);
} else one = f[flag][aidx];
// invoke compute if not previously invoked
} else if (which[m] == COMPUTE) {
Compute *compute = modify->compute[vidx];
if (flavor[m] == PERATOM) {
if (!(compute->invoked_flag & INVOKED_PERATOM)) {
compute->compute_peratom();
compute->invoked_flag |= INVOKED_PERATOM;
}
if (aidx == 0) {
double *comp_vec = compute->vector_atom;
int n = nlocal;
if (flag < 0) {
for (i = 0; i < n; i++)
if (mask[i] & groupbit) combine(one,comp_vec[i],i);
} else one = comp_vec[flag];
} else {
double **carray_atom = compute->array_atom;
int n = nlocal;
int aidxm1 = aidx - 1;
if (flag < 0) {
for (i = 0; i < n; i++)
if (mask[i] & groupbit) combine(one,carray_atom[i][aidxm1],i);
} else one = carray_atom[flag][aidxm1];
}
} else if (flavor[m] == LOCAL) {
if (!(compute->invoked_flag & INVOKED_LOCAL)) {
compute->compute_local();
compute->invoked_flag |= INVOKED_LOCAL;
}
if (aidx == 0) {
double *comp_vec = compute->vector_local;
int n = compute->size_local_rows;
if (flag < 0)
for (i = 0; i < n; i++)
combine(one,comp_vec[i],i);
else one = comp_vec[flag];
} else {
double **carray_local = compute->array_local;
int n = compute->size_local_rows;
int aidxm1 = aidx - 1;
if (flag < 0)
for (i = 0; i < n; i++)
combine(one,carray_local[i][aidxm1],i);
else one = carray_local[flag][aidxm1];
}
}
// access fix fields, check if fix frequency is a match
} else if (which[m] == FIX) {
if (update->ntimestep % modify->fix[vidx]->peratom_freq)
error->all("Fix used in compute reduce not computed at compatible time");
Fix *fix = modify->fix[vidx];
if (flavor[m] == PERATOM) {
if (aidx == 0) {
double *fix_vector = fix->vector_atom;
int n = nlocal;
if (flag < 0) {
for (i = 0; i < n; i++)
if (mask[i] & groupbit) combine(one,fix_vector[i],i);
} else one = fix_vector[flag];
} else {
double **fix_array = fix->array_atom;
int aidxm1 = aidx - 1;
if (flag < 0) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) combine(one,fix_array[i][aidxm1],i);
} else one = fix_array[flag][aidxm1];
}
} else if (flavor[m] == LOCAL) {
if (aidx == 0) {
double *fix_vector = fix->vector_local;
int n = fix->size_local_rows;
if (flag < 0)
for (i = 0; i < n; i++)
combine(one,fix_vector[i],i);
else one = fix_vector[flag];
} else {
double **fix_array = fix->array_local;
int n = fix->size_local_rows;
int aidxm1 = aidx - 1;
if (flag < 0)
for (i = 0; i < n; i++)
combine(one,fix_array[i][aidxm1],i);
else one = fix_array[flag][aidxm1];
}
}
// evaluate atom-style variable
} else if (which[m] == VARIABLE) {
if (nlocal > maxatom) {
maxatom = atom->nmax;
memory->sfree(varatom);
varatom = (double *)
memory->smalloc(maxatom*sizeof(double),"reduce:varatom");
}
input->variable->compute_atom(vidx,igroup,varatom,1,0);
if (flag < 0) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) combine(one,varatom[i],i);
} else one = varatom[flag];
}
return one;
}
/* ---------------------------------------------------------------------- */
bigint ComputeReduce::count(int m)
{
int vidx = value2index[m];
int aidx = argindex[m];
if (which[m] == X || which[m] == V || which[m] == F)
return group->count(igroup);
else if (which[m] == COMPUTE) {
Compute *compute = modify->compute[vidx];
if (flavor[m] == PERATOM) {
return group->count(igroup);
} else if (flavor[m] == LOCAL) {
bigint ncount = compute->size_local_rows;
bigint ncountall;
MPI_Allreduce(&ncount,&ncountall,1,MPI_LMP_BIGINT,MPI_SUM,world);
return ncountall;
}
} else if (which[m] == FIX) {
Fix *fix = modify->fix[vidx];
if (flavor[m] == PERATOM) {
return group->count(igroup);
} else if (flavor[m] == LOCAL) {
bigint ncount = fix->size_local_rows;
bigint ncountall;
MPI_Allreduce(&ncount,&ncountall,1,MPI_LMP_BIGINT,MPI_SUM,world);
return ncountall;
}
} else if (which[m] == VARIABLE)
return group->count(igroup);
bigint dummy = 0;
return dummy;
}
/* ----------------------------------------------------------------------
combine two values according to reduction mode
for MIN/MAX, also update index with winner
------------------------------------------------------------------------- */
void ComputeReduce::combine(double &one, double two, int i)
{
if (mode == SUM || mode == AVE) one += two;
else if (mode == MINN) {
if (two < one) {
one = two;
index = i;
}
} else if (mode == MAXX) {
if (two > one) {
one = two;
index = i;
}
}
}
/* ----------------------------------------------------------------------
memory usage of varatom
------------------------------------------------------------------------- */
double ComputeReduce::memory_usage()
{
double bytes = maxatom * sizeof(double);
return bytes;
}
diff --git a/src/compute_reduce.h b/src/compute_reduce.h
index c0d6a5976..04ffd40c6 100644
--- a/src/compute_reduce.h
+++ b/src/compute_reduce.h
@@ -1,64 +1,64 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef COMPUTE_CLASS
ComputeStyle(reduce,ComputeReduce)
#else
#ifndef LMP_COMPUTE_REDUCE_H
#define LMP_COMPUTE_REDUCE_H
-#include "compute.h"
#include "lmptype.h"
+#include "compute.h"
namespace LAMMPS_NS {
class ComputeReduce : public Compute {
public:
ComputeReduce(class LAMMPS *, int, char **);
virtual ~ComputeReduce();
void init();
double compute_scalar();
void compute_vector();
double memory_usage();
protected:
int me;
int mode,nvalues,iregion;
int *which,*argindex,*flavor,*value2index;
char **ids;
double *onevec;
int *replace,*indices,*owner;
int index;
char *idregion;
int maxatom;
double *varatom;
struct Pair {
double value;
int proc;
};
Pair pairme,pairall;
virtual double compute_one(int, int);
virtual bigint count(int);
void combine(double &, double, int);
};
}
#endif
#endif
diff --git a/src/compute_reduce_region.h b/src/compute_reduce_region.h
index 55249b0ef..a1b9ee169 100644
--- a/src/compute_reduce_region.h
+++ b/src/compute_reduce_region.h
@@ -1,41 +1,41 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef COMPUTE_CLASS
ComputeStyle(reduce/region,ComputeReduceRegion)
#else
#ifndef LMP_COMPUTE_REDUCE_REGION_H
#define LMP_COMPUTE_REDUCE_REGION_H
-#include "compute_reduce.h"
#include "lmptype.h"
+#include "compute_reduce.h"
namespace LAMMPS_NS {
class ComputeReduceRegion : public ComputeReduce {
public:
ComputeReduceRegion(class LAMMPS *, int, char **);
~ComputeReduceRegion() {}
private:
double compute_one(int, int);
bigint count(int);
};
}
#endif
#endif
diff --git a/src/create_atoms.cpp b/src/create_atoms.cpp
index 11eda7d7e..1f7d3ef65 100644
--- a/src/create_atoms.cpp
+++ b/src/create_atoms.cpp
@@ -1,487 +1,487 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "math.h"
#include "stdlib.h"
#include "string.h"
#include "create_atoms.h"
-#include "lmptype.h"
#include "atom.h"
#include "atom_vec.h"
#include "comm.h"
#include "modify.h"
#include "fix.h"
#include "domain.h"
#include "lattice.h"
#include "region.h"
#include "random_park.h"
#include "error.h"
using namespace LAMMPS_NS;
#define BIG 1.0e30
#define EPSILON 1.0e-6
enum{BOX,REGION,SINGLE,RANDOM};
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
/* ---------------------------------------------------------------------- */
CreateAtoms::CreateAtoms(LAMMPS *lmp) : Pointers(lmp) {}
/* ---------------------------------------------------------------------- */
void CreateAtoms::command(int narg, char **arg)
{
if (domain->box_exist == 0)
error->all("Create_atoms command before simulation box is defined");
if (modify->nfix_restart_peratom)
error->all("Cannot create_atoms after "
"reading restart file with per-atom info");
// parse arguments
if (narg < 2) error->all("Illegal create_atoms command");
itype = atoi(arg[0]);
if (itype <= 0 || itype > atom->ntypes)
error->all("Invalid atom type in create_atoms command");
int iarg;
if (strcmp(arg[1],"box") == 0) {
style = BOX;
iarg = 2;
} else if (strcmp(arg[1],"region") == 0) {
style = REGION;
if (narg < 3) error->all("Illegal create_atoms command");
nregion = domain->find_region(arg[2]);
if (nregion == -1) error->all("Create_atoms region ID does not exist");
iarg = 3;;
} else if (strcmp(arg[1],"single") == 0) {
style = SINGLE;
if (narg < 5) error->all("Illegal create_atoms command");
xone[0] = atof(arg[2]);
xone[1] = atof(arg[3]);
xone[2] = atof(arg[4]);
iarg = 5;
} else if (strcmp(arg[1],"random") == 0) {
style = RANDOM;
if (narg < 5) error->all("Illegal create_atoms command");
nrandom = atoi(arg[2]);
seed = atoi(arg[3]);
if (strcmp(arg[4],"NULL") == 0) nregion = -1;
else {
nregion = domain->find_region(arg[4]);
if (nregion == -1) error->all("Create_atoms region ID does not exist");
}
iarg = 5;
} else error->all("Illegal create_atoms command");
// process optional keywords
int scaleflag = 1;
if (domain->lattice) {
nbasis = domain->lattice->nbasis;
basistype = new int[nbasis];
for (int i = 0; i < nbasis; i++) basistype[i] = itype;
}
while (iarg < narg) {
if (strcmp(arg[iarg],"basis") == 0) {
if (iarg+3 > narg) error->all("Illegal create_atoms command");
if (domain->lattice == NULL)
error->all("Cannot create atoms with undefined lattice");
int ibasis = atoi(arg[iarg+1]);
itype = atoi(arg[iarg+2]);
if (ibasis <= 0 || ibasis > nbasis ||
itype <= 0 || itype > atom->ntypes)
error->all("Illegal create_atoms command");
basistype[ibasis-1] = itype;
iarg += 3;
} else if (strcmp(arg[iarg],"units") == 0) {
if (iarg+2 > narg) error->all("Illegal create_atoms command");
if (strcmp(arg[iarg+1],"box") == 0) scaleflag = 0;
else if (strcmp(arg[iarg+1],"lattice") == 0) scaleflag = 1;
else error->all("Illegal create_atoms command");
iarg += 2;
} else error->all("Illegal create_atoms command");
}
// error checks
if (style == RANDOM) {
if (nrandom < 0) error->all("Illegal create_atoms command");
if (seed <= 0) error->all("Illegal create_atoms command");
}
// demand lattice be defined
// else setup scaling for single atom
// could use domain->lattice->lattice2box() to do conversion of
// lattice to box, but not consistent with other uses of units=lattice
// triclinic remapping occurs in add_single()
if (style == BOX || style == REGION) {
if (domain->lattice == NULL)
error->all("Cannot create atoms with undefined lattice");
} else if (scaleflag == 1) {
if (domain->lattice == NULL)
error->all("Cannot create atoms with undefined lattice");
xone[0] *= domain->lattice->xlattice;
xone[1] *= domain->lattice->ylattice;
xone[2] *= domain->lattice->zlattice;
}
// add atoms
bigint natoms_previous = atom->natoms;
int nlocal_previous = atom->nlocal;
if (style == SINGLE) add_single();
else if (style == RANDOM) add_random();
else add_lattice();
// invoke set_arrays() for fixes that need initialization of new atoms
int nlocal = atom->nlocal;
for (int m = 0; m < modify->nfix; m++) {
Fix *fix = modify->fix[m];
if (fix->create_attribute)
for (int i = nlocal_previous; i < nlocal; i++)
fix->set_arrays(i);
}
// clean up
if (domain->lattice) delete [] basistype;
// new total # of atoms
bigint nblocal = atom->nlocal;
MPI_Allreduce(&nblocal,&atom->natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);
if (atom->natoms < 0 || atom->natoms > MAXBIGINT)
error->all("Too many total atoms");
// print status
if (comm->me == 0) {
if (screen)
fprintf(screen,"Created " BIGINT_FORMAT " atoms\n",
atom->natoms-natoms_previous);
if (logfile)
fprintf(logfile,"Created " BIGINT_FORMAT " atoms\n",
atom->natoms-natoms_previous);
}
// reset simulation now that more atoms are defined
// add tags for newly created atoms if possible
// if global map exists, reset it
// if a molecular system, set nspecial to 0 for new atoms
if (atom->natoms > MAXTAGINT) atom->tag_enable = 0;
if (atom->natoms <= MAXTAGINT) atom->tag_extend();
if (atom->map_style) {
atom->nghost = 0;
atom->map_init();
atom->map_set();
}
if (atom->molecular) {
int **nspecial = atom->nspecial;
for (int i = nlocal_previous; i < atom->nlocal; i++) {
nspecial[i][0] = 0;
nspecial[i][1] = 0;
nspecial[i][2] = 0;
}
}
}
/* ----------------------------------------------------------------------
add single atom with coords at xone if it's in my sub-box
if triclinic, xone is in lamda coords
------------------------------------------------------------------------- */
void CreateAtoms::add_single()
{
double *sublo,*subhi;
// sub-domain bounding box, in lamda units if triclinic
if (domain->triclinic == 0) {
sublo = domain->sublo;
subhi = domain->subhi;
} else {
sublo = domain->sublo_lamda;
subhi = domain->subhi_lamda;
}
// if triclinic, convert to lamda coords (0-1)
double lamda[3],*coord;
if (domain->triclinic) {
domain->x2lamda(xone,lamda);
coord = lamda;
} else coord = xone;
// if atom is in my subbox, create it
if (coord[0] >= sublo[0] && coord[0] < subhi[0] &&
coord[1] >= sublo[1] && coord[1] < subhi[1] &&
coord[2] >= sublo[2] && coord[2] < subhi[2])
atom->avec->create_atom(itype,xone);
}
/* ----------------------------------------------------------------------
add Nrandom atoms at random locations
------------------------------------------------------------------------- */
void CreateAtoms::add_random()
{
double xlo,ylo,zlo,xhi,yhi,zhi,zmid;
double lamda[3],*coord;
double *sublo,*subhi,*boxlo,*boxhi;
// random number generator, same for all procs
RanPark *random = new RanPark(lmp,seed);
// bounding box for atom creation
// in real units, even if triclinic
// only limit bbox by region if its bboxflag is set (interior region)
if (domain->triclinic == 0) {
xlo = domain->boxlo[0]; xhi = domain->boxhi[0];
ylo = domain->boxlo[1]; yhi = domain->boxhi[1];
zlo = domain->boxlo[2]; zhi = domain->boxhi[2];
zmid = zlo + 0.5*(zhi-zlo);
} else {
xlo = domain->boxlo_bound[0]; xhi = domain->boxhi_bound[0];
ylo = domain->boxlo_bound[1]; yhi = domain->boxhi_bound[1];
zlo = domain->boxlo_bound[2]; zhi = domain->boxhi_bound[2];
zmid = zlo + 0.5*(zhi-zlo);
}
if (nregion >= 0 && domain->regions[nregion]->bboxflag) {
xlo = MAX(xlo,domain->regions[nregion]->extent_xlo);
xhi = MIN(xhi,domain->regions[nregion]->extent_xhi);
ylo = MAX(ylo,domain->regions[nregion]->extent_ylo);
yhi = MIN(yhi,domain->regions[nregion]->extent_yhi);
zlo = MAX(zlo,domain->regions[nregion]->extent_zlo);
zhi = MIN(zhi,domain->regions[nregion]->extent_zhi);
}
// sub-domain bounding box, in lamda units if triclinic
if (domain->triclinic == 0) {
sublo = domain->sublo;
subhi = domain->subhi;
} else {
sublo = domain->sublo_lamda;
subhi = domain->subhi_lamda;
boxlo = domain->boxlo_lamda;
boxhi = domain->boxhi_lamda;
}
// generate random positions for each new atom within bounding box
// iterate until atom is within region and triclinic simulation box
// if final atom position is in my subbox, create it
int valid;
for (int i = 0; i < nrandom; i++) {
while (1) {
xone[0] = xlo + random->uniform() * (xhi-xlo);
xone[1] = ylo + random->uniform() * (yhi-ylo);
xone[2] = zlo + random->uniform() * (zhi-zlo);
if (domain->dimension == 2) xone[2] = zmid;
valid = 1;
if (nregion >= 0 &&
domain->regions[nregion]->match(xone[0],xone[1],xone[2]) == 0)
valid = 0;
if (domain->triclinic) {
domain->x2lamda(xone,lamda);
coord = lamda;
if (coord[0] < boxlo[0] || coord[0] >= boxhi[0] ||
coord[1] < boxlo[1] || coord[1] >= boxhi[1] ||
coord[2] < boxlo[2] || coord[2] >= boxhi[2]) valid = 0;
} else coord = xone;
if (valid) break;
}
// if triclinic, coord is now in lamda units
if (coord[0] >= sublo[0] && coord[0] < subhi[0] &&
coord[1] >= sublo[1] && coord[1] < subhi[1] &&
coord[2] >= sublo[2] && coord[2] < subhi[2])
atom->avec->create_atom(itype,xone);
}
// clean-up
delete random;
}
/* ----------------------------------------------------------------------
add many atoms by looping over lattice
------------------------------------------------------------------------- */
void CreateAtoms::add_lattice()
{
// convert 8 corners of my subdomain from box coords to lattice coords
// for orthogonal, use corner pts of my subbox
// for triclinic, use bounding box of my subbox
// xyz min to max = bounding box around the domain corners in lattice space
int triclinic = domain->triclinic;
double bboxlo[3],bboxhi[3];
if (triclinic == 0) {
bboxlo[0] = domain->sublo[0]; bboxhi[0] = domain->subhi[0];
bboxlo[1] = domain->sublo[1]; bboxhi[1] = domain->subhi[1];
bboxlo[2] = domain->sublo[2]; bboxhi[2] = domain->subhi[2];
} else domain->bbox(domain->sublo_lamda,domain->subhi_lamda,bboxlo,bboxhi);
double xmin,ymin,zmin,xmax,ymax,zmax;
xmin = ymin = zmin = BIG;
xmax = ymax = zmax = -BIG;
domain->lattice->bbox(1,bboxlo[0],bboxlo[1],bboxlo[2],
xmin,ymin,zmin,xmax,ymax,zmax);
domain->lattice->bbox(1,bboxhi[0],bboxlo[1],bboxlo[2],
xmin,ymin,zmin,xmax,ymax,zmax);
domain->lattice->bbox(1,bboxlo[0],bboxhi[1],bboxlo[2],
xmin,ymin,zmin,xmax,ymax,zmax);
domain->lattice->bbox(1,bboxhi[0],bboxhi[1],bboxlo[2],
xmin,ymin,zmin,xmax,ymax,zmax);
domain->lattice->bbox(1,bboxlo[0],bboxlo[1],bboxhi[2],
xmin,ymin,zmin,xmax,ymax,zmax);
domain->lattice->bbox(1,bboxhi[0],bboxlo[1],bboxhi[2],
xmin,ymin,zmin,xmax,ymax,zmax);
domain->lattice->bbox(1,bboxlo[0],bboxhi[1],bboxhi[2],
xmin,ymin,zmin,xmax,ymax,zmax);
domain->lattice->bbox(1,bboxhi[0],bboxhi[1],bboxhi[2],
xmin,ymin,zmin,xmax,ymax,zmax);
// ilo:ihi,jlo:jhi,klo:khi = loop bounds for lattice overlap of my subbox
// overlap = any part of a unit cell (face,edge,pt) in common with my subbox
// in lattice space, subbox is a tilted box
// but bbox of subbox is aligned with lattice axes
// so ilo:khi unit cells should completely tile bounding box
// decrement lo, increment hi to avoid round-off issues in lattice->bbox(),
// which can lead to missing atoms in rare cases
// extra decrement of lo if min < 0, since static_cast(-1.5) = -1
int ilo,ihi,jlo,jhi,klo,khi;
ilo = static_cast<int> (xmin) - 1;
jlo = static_cast<int> (ymin) - 1;
klo = static_cast<int> (zmin) - 1;
ihi = static_cast<int> (xmax) + 1;
jhi = static_cast<int> (ymax) + 1;
khi = static_cast<int> (zmax) + 1;
if (xmin < 0.0) ilo--;
if (ymin < 0.0) jlo--;
if (zmin < 0.0) klo--;
// set bounds for my proc
// if periodic:
// should create exactly 1 atom when 2 images are both "on" the boundary
// either image may be slightly inside/outside true box due to round-off
// if I am lo proc, decrement lower bound by EPSILON
// this will insure lo image is created
// if I am hi proc, decrement upper bound by 2.0*EPSILON
// this will insure hi image is not created
// thus insertion box is EPSILON smaller than true box
// and is shifted away from true boundary
// which is where atoms are likely to be generated
double epsilon[3];
if (triclinic) epsilon[0] = epsilon[1] = epsilon[2] = EPSILON;
else {
epsilon[0] = domain->prd[0] * EPSILON;
epsilon[1] = domain->prd[1] * EPSILON;
epsilon[2] = domain->prd[2] * EPSILON;
}
double sublo[3],subhi[3];
if (triclinic == 0) {
sublo[0] = domain->sublo[0]; subhi[0] = domain->subhi[0];
sublo[1] = domain->sublo[1]; subhi[1] = domain->subhi[1];
sublo[2] = domain->sublo[2]; subhi[2] = domain->subhi[2];
} else {
sublo[0] = domain->sublo_lamda[0]; subhi[0] = domain->subhi_lamda[0];
sublo[1] = domain->sublo_lamda[1]; subhi[1] = domain->subhi_lamda[1];
sublo[2] = domain->sublo_lamda[2]; subhi[2] = domain->subhi_lamda[2];
}
if (domain->xperiodic) {
if (comm->myloc[0] == 0) sublo[0] -= epsilon[0];
if (comm->myloc[0] == comm->procgrid[0]-1) subhi[0] -= 2.0*epsilon[0];
}
if (domain->yperiodic) {
if (comm->myloc[1] == 0) sublo[1] -= epsilon[1];
if (comm->myloc[1] == comm->procgrid[1]-1) subhi[1] -= 2.0*epsilon[1];
}
if (domain->zperiodic) {
if (comm->myloc[2] == 0) sublo[2] -= epsilon[2];
if (comm->myloc[2] == comm->procgrid[2]-1) subhi[2] -= 2.0*epsilon[2];
}
// iterate on 3d periodic lattice of unit cells using loop bounds
// iterate on nbasis atoms in each unit cell
// convert lattice coords to box coords
// add atom if it meets all criteria
double **basis = domain->lattice->basis;
double x[3],lamda[3];
double *coord;
int i,j,k,m;
for (k = klo; k <= khi; k++)
for (j = jlo; j <= jhi; j++)
for (i = ilo; i <= ihi; i++)
for (m = 0; m < nbasis; m++) {
x[0] = i + basis[m][0];
x[1] = j + basis[m][1];
x[2] = k + basis[m][2];
// convert from lattice coords to box coords
domain->lattice->lattice2box(x[0],x[1],x[2]);
// if a region was specified, test if atom is in it
if (style == REGION)
if (!domain->regions[nregion]->match(x[0],x[1],x[2])) continue;
// test if atom is in my subbox
if (triclinic) {
domain->x2lamda(x,lamda);
coord = lamda;
} else coord = x;
if (coord[0] < sublo[0] || coord[0] >= subhi[0] ||
coord[1] < sublo[1] || coord[1] >= subhi[1] ||
coord[2] < sublo[2] || coord[2] >= subhi[2]) continue;
// add the atom to my list of atoms
atom->avec->create_atom(basistype[m],x);
}
}
diff --git a/src/delete_atoms.cpp b/src/delete_atoms.cpp
index d92085ffe..ecddab700 100644
--- a/src/delete_atoms.cpp
+++ b/src/delete_atoms.cpp
@@ -1,364 +1,364 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "stdlib.h"
#include "string.h"
#include "delete_atoms.h"
-#include "lmptype.h"
#include "atom.h"
#include "atom_vec.h"
#include "comm.h"
#include "domain.h"
#include "force.h"
#include "group.h"
#include "region.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "random_mars.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
/* ---------------------------------------------------------------------- */
DeleteAtoms::DeleteAtoms(LAMMPS *lmp) : Pointers(lmp) {}
/* ---------------------------------------------------------------------- */
void DeleteAtoms::command(int narg, char **arg)
{
if (domain->box_exist == 0)
error->all("Delete_atoms command before simulation box is defined");
if (narg < 1) error->all("Illegal delete_atoms command");
if (atom->tag_enable == 0)
error->all("Cannot use delete_atoms unless atoms have IDs");
// store state before delete
bigint natoms_previous = atom->natoms;
// delete the atoms
if (strcmp(arg[0],"group") == 0) delete_group(narg,arg);
else if (strcmp(arg[0],"region") == 0) delete_region(narg,arg);
else if (strcmp(arg[0],"overlap") == 0) delete_overlap(narg,arg);
else if (strcmp(arg[0],"porosity") == 0) delete_porosity(narg,arg);
else error->all("Illegal delete_atoms command");
// delete local atoms flagged in dlist
// reset nlocal
AtomVec *avec = atom->avec;
int nlocal = atom->nlocal;
int i = 0;
while (i < nlocal) {
if (dlist[i]) {
avec->copy(nlocal-1,i);
dlist[i] = dlist[nlocal-1];
nlocal--;
} else i++;
}
atom->nlocal = nlocal;
memory->sfree(dlist);
// if non-molecular system and compress flag set,
// reset atom tags to be contiguous
// set all atom IDs to 0, call tag_extend()
if (atom->molecular == 0 && compress_flag) {
int *tag = atom->tag;
for (i = 0; i < nlocal; i++) tag[i] = 0;
atom->tag_extend();
}
// reset atom->natoms
// reset atom->map if it exists
// set nghost to 0 so old ghosts of deleted atoms won't be mapped
bigint nblocal = atom->nlocal;
MPI_Allreduce(&nblocal,&atom->natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);
if (atom->map_style) {
atom->nghost = 0;
atom->map_init();
atom->map_set();
}
// print before and after atom count
bigint ndelete = natoms_previous - atom->natoms;
if (comm->me == 0) {
if (screen) fprintf(screen,"Deleted " BIGINT_FORMAT
" atoms, new total = " BIGINT_FORMAT "\n",
ndelete,atom->natoms);
if (logfile) fprintf(logfile,"Deleted " BIGINT_FORMAT
" atoms, new total = " BIGINT_FORMAT "\n",
ndelete,atom->natoms);
}
}
/* ----------------------------------------------------------------------
delete all atoms in group
group will still exist
------------------------------------------------------------------------- */
void DeleteAtoms::delete_group(int narg, char **arg)
{
if (narg < 2) error->all("Illegal delete_atoms command");
int igroup = group->find(arg[1]);
if (igroup == -1) error->all("Could not find delete_atoms group ID");
options(narg-2,&arg[2]);
// allocate and initialize deletion list
int nlocal = atom->nlocal;
dlist = (int *) memory->smalloc(nlocal*sizeof(int),"delete_atoms:dlist");
for (int i = 0; i < nlocal; i++) dlist[i] = 0;
int *mask = atom->mask;
int groupbit = group->bitmask[igroup];
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) dlist[i] = 1;
}
/* ----------------------------------------------------------------------
delete all atoms in region
------------------------------------------------------------------------- */
void DeleteAtoms::delete_region(int narg, char **arg)
{
if (narg < 2) error->all("Illegal delete_atoms command");
int iregion = domain->find_region(arg[1]);
if (iregion == -1) error->all("Could not find delete_atoms region ID");
options(narg-2,&arg[2]);
// allocate and initialize deletion list
int nlocal = atom->nlocal;
dlist = (int *) memory->smalloc(nlocal*sizeof(int),"delete_atoms:dlist");
for (int i = 0; i < nlocal; i++) dlist[i] = 0;
double **x = atom->x;
for (int i = 0; i < nlocal; i++)
if (domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2])) dlist[i] = 1;
}
/* ----------------------------------------------------------------------
delete atoms so there are no pairs within cutoff
which atoms are deleted depends on ordering of atoms within proc
deletions can vary with processor count
no guarantee that minimium number of atoms will be deleted
------------------------------------------------------------------------- */
void DeleteAtoms::delete_overlap(int narg, char **arg)
{
if (narg < 4) error->all("Illegal delete_atoms command");
// read args
double cut = atof(arg[1]);
double cutsq = cut*cut;
int igroup1 = group->find(arg[2]);
int igroup2 = group->find(arg[3]);
if (igroup1 < 0 || igroup2 < 0)
error->all("Could not find delete_atoms group ID");
options(narg-4,&arg[4]);
int group1bit = group->bitmask[igroup1];
int group2bit = group->bitmask[igroup2];
if (comm->me == 0 && screen)
fprintf(screen,"System init for delete_atoms ...\n");
// request a full neighbor list for use by this command
int irequest = neighbor->request((void *) this);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->command = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->occasional = 1;
// init entire system since comm->borders and neighbor->build is done
// comm::init needs neighbor::init needs pair::init needs kspace::init, etc
lmp->init();
// error check on cutoff
// if no pair style, neighbor list will be empty
if (force->pair == NULL)
error->all("Delete_atoms requires a pair style be defined");
if (cut > neighbor->cutneighmax)
error->all("Delete_atoms cutoff > neighbor cutoff");
// setup domain, communication and neighboring
// acquire ghosts
// build neighbor list based on earlier request
if (domain->triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
domain->reset_box();
comm->setup();
if (neighbor->style) neighbor->setup_bins();
comm->exchange();
comm->borders();
if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
NeighList *list = neighbor->lists[irequest];
neighbor->build_one(irequest);
// allocate and initialize deletion list
// must be after exchange potentially changes nlocal
int nlocal = atom->nlocal;
dlist = (int *) memory->smalloc(nlocal*sizeof(int),"delete_atoms:dlist");
for (int i = 0; i < nlocal; i++) dlist[i] = 0;
// double loop over owned atoms and their full neighbor list
// at end of loop, there are no more overlaps
// only ever delete owned atom I, never J even if owned
int *tag = atom->tag;
int *mask = atom->mask;
double **x = atom->x;
int nall = atom->nlocal + atom->nghost;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int i,j,ii,jj,inum,jnum;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *ilist,*jlist,*numneigh,**firstneigh;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
// if weighting factors are 0, skip this pair
// could be 0 and still be in neigh list for long-range Coulombics
// want consistency with non-charged pairs which wouldn't be in list
if (j >= nall) {
if (special_coul[j/nall] == 0.0 && special_lj[j/nall] == 0.0) continue;
j %= nall;
}
// only consider deletion if I,J distance < cutoff
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq >= cutsq) continue;
// only consider deletion if I,J are in groups 1,2 respectively
// true whether J is owned or ghost atom
if (!(mask[i] & group1bit)) continue;
if (!(mask[j] & group2bit)) continue;
// J is owned atom:
// delete atom I if atom J has not already been deleted
// J is ghost atom:
// delete atom I if J,I is not a candidate deletion pair
// due to being in groups 1,2 respectively
// if they are candidate pair, then either:
// another proc owns J and could delete J
// J is a ghost of another of my owned atoms, and I could delete J
// test on tags of I,J insures that only I or J is deleted
if (j < nlocal) {
if (dlist[j]) continue;
} else if ((mask[i] & group2bit) && (mask[j] & group1bit)) {
if (tag[i] > tag[j]) continue;
}
dlist[i] = 1;
break;
}
}
}
/* ----------------------------------------------------------------------
create porosity by deleting atoms in a specified region
------------------------------------------------------------------------- */
void DeleteAtoms::delete_porosity(int narg, char **arg)
{
if (narg < 4) error->all("Illegal delete_atoms command");
int iregion = domain->find_region(arg[1]);
if (iregion == -1) error->all("Could not find delete_atoms region ID");
double porosity_fraction = atof(arg[2]);
int seed = atoi(arg[3]);
options(narg-4,&arg[4]);
RanMars *random = new RanMars(lmp,seed + comm->me);
// allocate and initialize deletion list
int nlocal = atom->nlocal;
dlist = (int *) memory->smalloc(nlocal*sizeof(int),"delete_atoms:dlist");
for (int i = 0; i < nlocal; i++) dlist[i] = 0;
double **x = atom->x;
for (int i = 0; i < nlocal; i++)
if (domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2]))
if (random->uniform() <= porosity_fraction) dlist[i] = 1;
}
/* ----------------------------------------------------------------------
process command options
------------------------------------------------------------------------- */
void DeleteAtoms::options(int narg, char **arg)
{
compress_flag = 1;
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"compress") == 0) {
if (iarg+2 > narg) error->all("Illegal delete_bonds command");
if (strcmp(arg[iarg+1],"yes") == 0) compress_flag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) compress_flag = 0;
else error->all("Illegal delete_bonds command");
iarg += 2;
} else error->all("Illegal delete_bonds command");
}
}
diff --git a/src/displace_atoms.cpp b/src/displace_atoms.cpp
index 64cb195df..f433541d9 100644
--- a/src/displace_atoms.cpp
+++ b/src/displace_atoms.cpp
@@ -1,243 +1,243 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "mpi.h"
#include "stdlib.h"
#include "string.h"
#include "displace_atoms.h"
-#include "lmptype.h"
#include "atom.h"
#include "modify.h"
#include "domain.h"
#include "lattice.h"
#include "comm.h"
#include "irregular.h"
#include "group.h"
#include "random_park.h"
#include "error.h"
using namespace LAMMPS_NS;
enum{MOVE,RAMP,RANDOM};
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
/* ---------------------------------------------------------------------- */
DisplaceAtoms::DisplaceAtoms(LAMMPS *lmp) : Pointers(lmp) {}
/* ---------------------------------------------------------------------- */
void DisplaceAtoms::command(int narg, char **arg)
{
int i;
if (domain->box_exist == 0)
error->all("Displace_atoms command before simulation box is defined");
if (narg < 2) error->all("Illegal displace_atoms command");
if (modify->nfix_restart_peratom)
error->all("Cannot displace_atoms after "
"reading restart file with per-atom info");
if (comm->me == 0 && screen) fprintf(screen,"Displacing atoms ...\n");
// group and style
int igroup = group->find(arg[0]);
if (igroup == -1) error->all("Could not find displace_atoms group ID");
int groupbit = group->bitmask[igroup];
int style;
if (strcmp(arg[1],"move") == 0) style = MOVE;
else if (strcmp(arg[1],"ramp") == 0) style = RAMP;
else if (strcmp(arg[1],"random") == 0) style = RANDOM;
else error->all("Illegal displace_atoms command");
// set option defaults
scaleflag = 1;
// read options from end of input line
if (style == MOVE) options(narg-5,&arg[5]);
else if (style == RAMP) options(narg-8,&arg[8]);
else if (style == RANDOM) options(narg-6,&arg[6]);
// setup scaling
if (scaleflag && domain->lattice == NULL)
error->all("Use of displace_atoms with undefined lattice");
double xscale,yscale,zscale;
if (scaleflag) {
xscale = domain->lattice->xlattice;
yscale = domain->lattice->ylattice;
zscale = domain->lattice->zlattice;
}
else xscale = yscale = zscale = 1.0;
// move atoms by 3-vector
if (style == MOVE) {
double delx = xscale*atof(arg[2]);
double dely = yscale*atof(arg[3]);
double delz = zscale*atof(arg[4]);
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
x[i][0] += delx;
x[i][1] += dely;
x[i][2] += delz;
}
}
}
// move atoms in ramped fashion
if (style == RAMP) {
int d_dim;
if (strcmp(arg[2],"x") == 0) d_dim = 0;
else if (strcmp(arg[2],"y") == 0) d_dim = 1;
else if (strcmp(arg[2],"z") == 0) d_dim = 2;
else error->all("Illegal displace_atoms ramp command");
double d_lo,d_hi;
if (d_dim == 0) {
d_lo = xscale*atof(arg[3]);
d_hi = xscale*atof(arg[4]);
} else if (d_dim == 1) {
d_lo = yscale*atof(arg[3]);
d_hi = yscale*atof(arg[4]);
} else if (d_dim == 2) {
d_lo = zscale*atof(arg[3]);
d_hi = zscale*atof(arg[4]);
}
int coord_dim;
if (strcmp(arg[5],"x") == 0) coord_dim = 0;
else if (strcmp(arg[5],"y") == 0) coord_dim = 1;
else if (strcmp(arg[5],"z") == 0) coord_dim = 2;
else error->all("Illegal displace_atoms ramp command");
double coord_lo,coord_hi;
if (coord_dim == 0) {
coord_lo = xscale*atof(arg[6]);
coord_hi = xscale*atof(arg[7]);
} else if (coord_dim == 1) {
coord_lo = yscale*atof(arg[6]);
coord_hi = yscale*atof(arg[7]);
} else if (coord_dim == 2) {
coord_lo = zscale*atof(arg[6]);
coord_hi = zscale*atof(arg[7]);
}
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double fraction,dramp;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
fraction = (x[i][coord_dim] - coord_lo) / (coord_hi - coord_lo);
fraction = MAX(fraction,0.0);
fraction = MIN(fraction,1.0);
dramp = d_lo + fraction*(d_hi - d_lo);
x[i][d_dim] += dramp;
}
}
}
// move atoms randomly
// makes atom result independent of what proc owns it via random->reset()
if (style == RANDOM) {
RanPark *random = new RanPark(lmp,1);
double dx = xscale*atof(arg[2]);
double dy = yscale*atof(arg[3]);
double dz = zscale*atof(arg[4]);
int seed = atoi(arg[5]);
if (seed <= 0) error->all("Illegal displace_atoms random command");
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
random->reset(seed,x[i]);
x[i][0] += dx * 2.0*(random->uniform()-0.5);
x[i][1] += dy * 2.0*(random->uniform()-0.5);
x[i][2] += dz * 2.0*(random->uniform()-0.5);
}
}
delete random;
}
// move atoms back inside simulation box and to new processors
// use remap() instead of pbc() in case atoms moved a long distance
// use irregular() in case atoms moved a long distance
double **x = atom->x;
int *image = atom->image;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) domain->remap(x[i],image[i]);
if (domain->triclinic) domain->x2lamda(atom->nlocal);
domain->reset_box();
Irregular *irregular = new Irregular(lmp);
irregular->migrate_atoms();
delete irregular;
if (domain->triclinic) domain->lamda2x(atom->nlocal);
// check if any atoms were lost
bigint natoms;
bigint nblocal = atom->nlocal;
MPI_Allreduce(&nblocal,&natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);
if (natoms != atom->natoms) {
char str[128];
sprintf(str,"Lost atoms via displace_atoms: original " BIGINT_FORMAT
" current " BIGINT_FORMAT,atom->natoms,natoms);
error->all(str);
}
}
/* ----------------------------------------------------------------------
parse optional parameters at end of displace_atoms input line
------------------------------------------------------------------------- */
void DisplaceAtoms::options(int narg, char **arg)
{
if (narg < 0) error->all("Illegal displace_atoms command");
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"units") == 0) {
if (iarg+2 > narg) error->all("Illegal displace_atoms command");
if (strcmp(arg[iarg+1],"box") == 0) scaleflag = 0;
else if (strcmp(arg[iarg+1],"lattice") == 0) scaleflag = 1;
else error->all("Illegal displace_atoms command");
iarg += 2;
} else error->all("Illegal displace_atoms command");
}
}
diff --git a/src/displace_box.cpp b/src/displace_box.cpp
index e8b88fb31..f2e3363a6 100644
--- a/src/displace_box.cpp
+++ b/src/displace_box.cpp
@@ -1,418 +1,418 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "mpi.h"
#include "math.h"
#include "stdlib.h"
#include "string.h"
#include "displace_box.h"
-#include "lmptype.h"
#include "atom.h"
#include "modify.h"
#include "domain.h"
#include "lattice.h"
#include "comm.h"
#include "irregular.h"
#include "group.h"
#include "error.h"
using namespace LAMMPS_NS;
enum{NONE,FINAL,DELTA,SCALE,VOLUME};
enum{ONE_FROM_ONE,ONE_FROM_TWO,TWO_FROM_ONE};
enum{NO_REMAP,X_REMAP};
/* ---------------------------------------------------------------------- */
DisplaceBox::DisplaceBox(LAMMPS *lmp) : Pointers(lmp) {}
/* ---------------------------------------------------------------------- */
void DisplaceBox::command(int narg, char **arg)
{
int i;
if (domain->box_exist == 0)
error->all("Displace_box command before simulation box is defined");
if (narg < 2) error->all("Illegal displace_box command");
if (modify->nfix_restart_peratom)
error->all("Cannot displace_box after "
"reading restart file with per-atom info");
if (comm->me == 0 && screen) fprintf(screen,"Displacing box ...\n");
// group
int igroup = group->find(arg[0]);
if (igroup == -1) error->all("Could not find displace_box group ID");
int groupbit = group->bitmask[igroup];
// set defaults
set = new Set[6];
set[0].style = set[1].style = set[2].style =
set[3].style = set[4].style = set[5].style = NONE;
// parse arguments
int triclinic = domain->triclinic;
int index;
int iarg = 1;
while (iarg < narg) {
if (strcmp(arg[iarg],"x") == 0 || strcmp(arg[iarg],"y") == 0 ||
strcmp(arg[iarg],"z") == 0) {
if (strcmp(arg[iarg],"x") == 0) index = 0;
else if (strcmp(arg[iarg],"y") == 0) index = 1;
else if (strcmp(arg[iarg],"z") == 0) index = 2;
if (iarg+2 > narg) error->all("Illegal displace_box command");
if (strcmp(arg[iarg+1],"final") == 0) {
if (iarg+4 > narg) error->all("Illegal displace_box command");
set[index].style = FINAL;
set[index].flo = atof(arg[iarg+2]);
set[index].fhi = atof(arg[iarg+3]);
iarg += 4;
} else if (strcmp(arg[iarg+1],"delta") == 0) {
if (iarg+4 > narg) error->all("Illegal displace_box command");
set[index].style = DELTA;
set[index].dlo = atof(arg[iarg+2]);
set[index].dhi = atof(arg[iarg+3]);
iarg += 4;
} else if (strcmp(arg[iarg+1],"scale") == 0) {
if (iarg+3 > narg) error->all("Illegal displace_box command");
set[index].style = SCALE;
set[index].scale = atof(arg[iarg+2]);
iarg += 3;
} else if (strcmp(arg[iarg+1],"volume") == 0) {
set[index].style = VOLUME;
iarg += 2;
} else error->all("Illegal displace_box command");
} else if (strcmp(arg[iarg],"xy") == 0 || strcmp(arg[iarg],"xz") == 0 ||
strcmp(arg[iarg],"yz") == 0) {
if (triclinic == 0)
error->all("Displace_box tilt factors require triclinic box");
if (strcmp(arg[iarg],"xy") == 0) index = 5;
else if (strcmp(arg[iarg],"xz") == 0) index = 4;
else if (strcmp(arg[iarg],"yz") == 0) index = 3;
if (iarg+2 > narg) error->all("Illegal displace_box command");
if (strcmp(arg[iarg+1],"final") == 0) {
if (iarg+3 > narg) error->all("Illegal displace_box command");
set[index].style = FINAL;
set[index].ftilt = atof(arg[iarg+2]);
iarg += 3;
} else if (strcmp(arg[iarg+1],"delta") == 0) {
if (iarg+3 > narg) error->all("Illegal displace_box command");
set[index].style = DELTA;
set[index].dtilt = atof(arg[iarg+2]);
iarg += 3;
} else error->all("Illegal displace_box command");
} else break;
}
// read options from end of input line
options(narg-iarg,&arg[iarg]);
// check periodicity
if ((set[0].style && domain->xperiodic == 0) ||
(set[1].style && domain->yperiodic == 0) ||
(set[2].style && domain->zperiodic == 0))
error->all("Cannot displace_box on a non-periodic boundary");
if (set[3].style && (domain->yperiodic == 0 || domain->zperiodic == 0))
error->all("Cannot displace_box on a non-periodic boundary");
if (set[4].style && (domain->xperiodic == 0 || domain->zperiodic == 0))
error->all("Cannot displace_box on a non-periodic boundary");
if (set[5].style && (domain->xperiodic == 0 || domain->yperiodic == 0))
error->all("Cannot displace_box on a non-periodic boundary");
// apply scaling to FINAL,DELTA since they have distance units
int flag = 0;
for (int i = 0; i < 6; i++)
if (set[i].style == FINAL || set[i].style == DELTA) flag = 1;
if (flag && scaleflag && domain->lattice == NULL)
error->all("Use of displace_box with undefined lattice");
double xscale,yscale,zscale;
if (flag && scaleflag) {
xscale = domain->lattice->xlattice;
yscale = domain->lattice->ylattice;
zscale = domain->lattice->zlattice;
}
else xscale = yscale = zscale = 1.0;
// for 3,4,5 scaling is in 1st dimension, e.g. x for xz
double map[6];
map[0] = xscale; map[1] = yscale; map[2] = zscale;
map[3] = yscale; map[4] = xscale; map[5] = xscale;
for (int i = 0; i < 3; i++) {
if (set[i].style == FINAL) {
set[i].flo *= map[i];
set[i].fhi *= map[i];
} else if (set[i].style == DELTA) {
set[i].dlo *= map[i];
set[i].dhi *= map[i];
}
}
for (int i = 3; i < 6; i++) {
if (set[i].style == FINAL) set[i].ftilt *= map[i];
else if (set[i].style == DELTA) set[i].dtilt *= map[i];
}
// set initial/final values for box size and shape
// final = initial if no setting
for (int i = 0; i < 3; i++) {
set[i].lo_stop = set[i].lo_start = domain->boxlo[i];
set[i].hi_stop = set[i].hi_start = domain->boxhi[i];
if (set[i].style == FINAL) {
set[i].lo_stop = set[i].flo;
set[i].hi_stop = set[i].fhi;
} else if (set[i].style == DELTA) {
set[i].lo_stop = set[i].lo_start + set[i].dlo;
set[i].hi_stop = set[i].hi_start + set[i].dhi;
} else if (set[i].style == SCALE) {
set[i].lo_stop = 0.5*(set[i].lo_start+set[i].hi_start) -
0.5*set[i].scale*(set[i].hi_start-set[i].lo_start);
set[i].hi_stop = 0.5*(set[i].lo_start+set[i].hi_start) +
0.5*set[i].scale*(set[i].hi_start-set[i].lo_start);
}
}
for (int i = 3; i < 6; i++) {
if (i == 5) set[i].tilt_start = domain->xy;
else if (i == 4) set[i].tilt_start = domain->xz;
else if (i == 3) set[i].tilt_start = domain->yz;
set[i].tilt_stop = set[i].tilt_start;
if (set[i].style == FINAL) {
set[i].tilt_stop = set[i].ftilt;
} else if (set[i].style == DELTA) {
set[i].tilt_stop = set[i].tilt_start + set[i].dtilt;
}
}
// for VOLUME, setup links to other dims
// fixed, dynamic1,2, vol_start
for (int i = 0; i < 3; i++) {
set[i].vol_start = domain->xprd * domain->yprd * domain->zprd;
if (set[i].style != VOLUME) continue;
int other1 = (i+1) % 3;
int other2 = (i+2) % 3;
if (set[other1].style == NONE) {
if (set[other2].style == NONE || set[other2].style == VOLUME)
error->all("Fix deform volume setting is invalid");
set[i].substyle = ONE_FROM_ONE;
set[i].fixed = other1;
set[i].dynamic1 = other2;
} else if (set[other2].style == NONE) {
if (set[other1].style == NONE || set[other1].style == VOLUME)
error->all("Fix deform volume setting is invalid");
set[i].substyle = ONE_FROM_ONE;
set[i].fixed = other2;
set[i].dynamic1 = other1;
} else if (set[other1].style == VOLUME) {
if (set[other2].style == NONE || set[other2].style == VOLUME)
error->all("Fix deform volume setting is invalid");
set[i].substyle = TWO_FROM_ONE;
set[i].fixed = other1;
set[i].dynamic1 = other2;
} else if (set[other2].style == VOLUME) {
if (set[other1].style == NONE || set[other1].style == VOLUME)
error->all("Fix deform volume setting is invalid");
set[i].substyle = TWO_FROM_ONE;
set[i].fixed = other2;
set[i].dynamic1 = other1;
} else {
set[i].substyle = ONE_FROM_TWO;
set[i].dynamic2 = other1;
set[i].dynamic2 = other2;
}
}
// set new box size for VOLUME dims that are linked to other dims
for (int i = 0; i < 3; i++) {
if (set[i].style != VOLUME) continue;
if (set[i].substyle == ONE_FROM_ONE) {
set[i].lo_stop = 0.5*(set[i].lo_start+set[i].hi_start) -
0.5*(set[i].vol_start /
(set[set[i].dynamic1].hi_stop -
set[set[i].dynamic1].lo_stop) /
(set[set[i].fixed].hi_start-set[set[i].fixed].lo_start));
set[i].hi_stop = 0.5*(set[i].lo_start+set[i].hi_start) +
0.5*(set[i].vol_start /
(set[set[i].dynamic1].hi_stop -
set[set[i].dynamic1].lo_stop) /
(set[set[i].fixed].hi_start-set[set[i].fixed].lo_start));
} else if (set[i].substyle == ONE_FROM_TWO) {
set[i].lo_stop = 0.5*(set[i].lo_start+set[i].hi_start) -
0.5*(set[i].vol_start /
(set[set[i].dynamic1].hi_stop -
set[set[i].dynamic1].lo_stop) /
(set[set[i].dynamic2].hi_stop -
set[set[i].dynamic2].lo_stop));
set[i].hi_stop = 0.5*(set[i].lo_start+set[i].hi_start) +
0.5*(set[i].vol_start /
(set[set[i].dynamic1].hi_stop -
set[set[i].dynamic1].lo_stop) /
(set[set[i].dynamic2].hi_stop -
set[set[i].dynamic2].lo_stop));
} else if (set[i].substyle == TWO_FROM_ONE) {
set[i].lo_stop = 0.5*(set[i].lo_start+set[i].hi_start) -
0.5*sqrt(set[i].vol_start /
(set[set[i].dynamic1].hi_stop -
set[set[i].dynamic1].lo_stop) /
(set[set[i].fixed].hi_start -
set[set[i].fixed].lo_start) *
(set[i].hi_start - set[i].lo_start));
set[i].hi_stop = 0.5*(set[i].lo_start+set[i].hi_start) +
0.5*sqrt(set[i].vol_start /
(set[set[i].dynamic1].hi_stop -
set[set[i].dynamic1].lo_stop) /
(set[set[i].fixed].hi_start -
set[set[i].fixed].lo_start) *
(set[i].hi_start - set[i].lo_start));
}
}
// check that final tilt is not illegal value
double xprd_stop = set[0].hi_stop - set[0].lo_stop;
double yprd_stop = set[0].hi_stop - set[0].lo_stop;
if (set[3].tilt_stop < -0.5*yprd_stop || set[3].tilt_stop > 0.5*yprd_stop ||
set[4].tilt_stop < -0.5*xprd_stop || set[4].tilt_stop > 0.5*xprd_stop ||
set[5].tilt_stop < -0.5*xprd_stop || set[5].tilt_stop > 0.5*xprd_stop)
error->all("Induced tilt by displace_box is too large");
// convert atoms to lamda coords
if (remapflag == X_REMAP) {
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
domain->x2lamda(x[i],x[i]);
}
// reset global and local box to new size/shape
domain->boxlo[0] = set[0].lo_stop;
domain->boxlo[1] = set[1].lo_stop;
domain->boxlo[2] = set[2].lo_stop;
domain->boxhi[0] = set[0].hi_stop;
domain->boxhi[1] = set[1].hi_stop;
domain->boxhi[2] = set[2].hi_stop;
if (triclinic) {
domain->yz = set[3].tilt_stop;
domain->xz = set[4].tilt_stop;
domain->xy = set[5].tilt_stop;
}
domain->set_global_box();
domain->set_local_box();
// convert atoms back to box coords
if (remapflag == X_REMAP) {
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
domain->lamda2x(x[i],x[i]);
}
// move atoms back inside simulation box and to new processors
// use remap() instead of pbc()
// in case box moved a long distance relative to atoms
// use irregular() in case box moved a long distance relative to atoms
double **x = atom->x;
int *image = atom->image;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) domain->remap(x[i],image[i]);
if (domain->triclinic) domain->x2lamda(atom->nlocal);
domain->reset_box();
Irregular *irregular = new Irregular(lmp);
irregular->migrate_atoms();
delete irregular;
if (domain->triclinic) domain->lamda2x(atom->nlocal);
// clean up
delete [] set;
// check if any atoms were lost
bigint natoms;
bigint nblocal = atom->nlocal;
MPI_Allreduce(&nblocal,&natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);
if (natoms != atom->natoms) {
char str[128];
sprintf(str,"Lost atoms via displace_box: original " BIGINT_FORMAT
" current " BIGINT_FORMAT,atom->natoms,natoms);
error->all(str);
}
}
/* ----------------------------------------------------------------------
parse optional parameters at end of displace_box input line
------------------------------------------------------------------------- */
void DisplaceBox::options(int narg, char **arg)
{
if (narg < 0) error->all("Illegal displace_box command");
remapflag = X_REMAP;
scaleflag = 1;
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"remap") == 0) {
if (iarg+2 > narg) error->all("Illegal displace_box command");
if (strcmp(arg[iarg+1],"x") == 0) remapflag = X_REMAP;
else if (strcmp(arg[iarg+1],"none") == 0) remapflag = NO_REMAP;
else error->all("Illegal displace_box command");
iarg += 2;
} else if (strcmp(arg[iarg],"units") == 0) {
if (iarg+2 > narg) error->all("Illegal displace_box command");
if (strcmp(arg[iarg+1],"box") == 0) scaleflag = 0;
else if (strcmp(arg[iarg+1],"lattice") == 0) scaleflag = 1;
else error->all("Illegal displace_box command");
iarg += 2;
} else error->all("Illegal displace_box command");
}
}
diff --git a/src/dump.cpp b/src/dump.cpp
index 6bd3018a0..d082ac29d 100644
--- a/src/dump.cpp
+++ b/src/dump.cpp
@@ -1,712 +1,712 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "mpi.h"
#include "stdlib.h"
#include "string.h"
#include "stdio.h"
#include "dump.h"
-#include "lmptype.h"
#include "atom.h"
#include "irregular.h"
#include "update.h"
#include "domain.h"
#include "group.h"
#include "output.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
// allocate space for static class variable
Dump *Dump::dumpptr;
#define BIG 1.0e20
#define IBIG 2147483647
#define EPSILON 1.0e-6
#define MIN(A,B) ((A) < (B)) ? (A) : (B)
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
enum{ASCEND,DESCEND};
/* ---------------------------------------------------------------------- */
Dump::Dump(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
{
MPI_Comm_rank(world,&me);
MPI_Comm_size(world,&nprocs);
int n = strlen(arg[0]) + 1;
id = new char[n];
strcpy(id,arg[0]);
igroup = group->find(arg[1]);
groupbit = group->bitmask[igroup];
n = strlen(arg[2]) + 1;
style = new char[n];
strcpy(style,arg[2]);
n = strlen(arg[4]) + 1;
filename = new char[n];
strcpy(filename,arg[4]);
first_flag = 0;
flush_flag = 1;
format = NULL;
format_user = NULL;
clearstep = 0;
sort_flag = 0;
append_flag = 0;
maxbuf = maxids = maxsort = maxproc = 0;
buf = bufsort = NULL;
ids = idsort = index = proclist = NULL;
irregular = NULL;
// parse filename for special syntax
// if contains '%', write one file per proc and replace % with proc-ID
// if contains '*', write one file per timestep and replace * with timestep
// check file suffixes
// if ends in .bin = binary file
// else if ends in .gz = gzipped text file
// else ASCII text file
fp = NULL;
singlefile_opened = 0;
compressed = 0;
binary = 0;
multifile = 0;
multiproc = 0;
char *ptr;
if (ptr = strchr(filename,'%')) {
multiproc = 1;
char *extend = new char[strlen(filename) + 16];
*ptr = '\0';
sprintf(extend,"%s%d%s",filename,me,ptr+1);
delete [] filename;
n = strlen(extend) + 1;
filename = new char[n];
strcpy(filename,extend);
delete [] extend;
}
if (strchr(filename,'*')) multifile = 1;
char *suffix = filename + strlen(filename) - strlen(".bin");
if (suffix > filename && strcmp(suffix,".bin") == 0) binary = 1;
suffix = filename + strlen(filename) - strlen(".gz");
if (suffix > filename && strcmp(suffix,".gz") == 0) compressed = 1;
}
/* ---------------------------------------------------------------------- */
Dump::~Dump()
{
delete [] id;
delete [] style;
delete [] filename;
delete [] format;
delete [] format_default;
delete [] format_user;
memory->sfree(buf);
memory->sfree(bufsort);
memory->sfree(ids);
memory->sfree(idsort);
memory->sfree(index);
memory->sfree(proclist);
delete irregular;
// XTC style sets fp to NULL since it closes file in its destructor
if (multifile == 0 && fp != NULL) {
if (compressed) {
if (multiproc) pclose(fp);
else if (me == 0) pclose(fp);
} else {
if (multiproc) fclose(fp);
else if (me == 0) fclose(fp);
}
}
}
/* ---------------------------------------------------------------------- */
void Dump::init()
{
init_style();
if (!sort_flag) {
memory->sfree(bufsort);
memory->sfree(ids);
memory->sfree(idsort);
memory->sfree(index);
memory->sfree(proclist);
delete irregular;
maxids = maxsort = maxproc = 0;
bufsort = NULL;
ids = idsort = index = proclist = NULL;
irregular = NULL;
}
if (sort_flag) {
if (sortcol == 0 && atom->tag_enable == 0)
error->all("Cannot dump sort on atom IDs with no atom IDs defined");
if (sortcol && sortcol > size_one)
error->all("Dump sort column is invalid");
if (nprocs > 1 && irregular == NULL)
irregular = new Irregular(lmp);
bigint size = group->count(igroup);
if (size > MAXSMALLINT) error->all("Too many atoms to dump sort");
// set reorderflag = 1 if can simply reorder local atoms rather than sort
// criteria: sorting by ID, atom IDs are consecutive from 1 to Natoms
// min/max IDs of group match size of group
// compute ntotal_reorder, nme_reorder, idlo/idhi to test against later
reorderflag = 0;
if (sortcol == 0 && atom->tag_consecutive()) {
int *tag = atom->tag;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int min = IBIG;
int max = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
min = MIN(min,tag[i]);
max = MAX(max,tag[i]);
}
int minall,maxall;
MPI_Allreduce(&min,&minall,1,MPI_INT,MPI_MIN,world);
MPI_Allreduce(&max,&maxall,1,MPI_INT,MPI_MAX,world);
int isize = static_cast<int> (size);
if (maxall-minall+1 == isize) {
reorderflag = 1;
double range = maxall-minall + EPSILON;
idlo = static_cast<int> (range*me/nprocs + minall);
int idhi = static_cast<int> (range*(me+1)/nprocs + minall);
int lom1 = static_cast<int> ((idlo-1-minall)/range * nprocs);
int lo = static_cast<int> ((idlo-minall)/range * nprocs);
int him1 = static_cast<int> ((idhi-1-minall)/range * nprocs);
int hi = static_cast<int> ((idhi-minall)/range * nprocs);
if (me && me == lom1) idlo--;
else if (me && me != lo) idlo++;
if (me+1 == him1) idhi--;
else if (me+1 != hi) idhi++;
nme_reorder = idhi-idlo;
ntotal_reorder = isize;
}
}
}
}
/* ---------------------------------------------------------------------- */
void Dump::write()
{
// if file per timestep, open new file
if (multifile) openfile();
// simulation box bounds
if (domain->triclinic == 0) {
boxxlo = domain->boxlo[0];
boxxhi = domain->boxhi[0];
boxylo = domain->boxlo[1];
boxyhi = domain->boxhi[1];
boxzlo = domain->boxlo[2];
boxzhi = domain->boxhi[2];
} else {
boxxlo = domain->boxlo_bound[0];
boxxhi = domain->boxhi_bound[0];
boxylo = domain->boxlo_bound[1];
boxyhi = domain->boxhi_bound[1];
boxzlo = domain->boxlo_bound[2];
boxzhi = domain->boxhi_bound[2];
boxxy = domain->xy;
boxxz = domain->xz;
boxyz = domain->yz;
}
// nme = # of dump lines this proc will contribute to dump
nme = count();
bigint bnme = nme;
// ntotal = total # of dump lines
// nmax = max # of dump lines on any proc
int nmax;
if (multiproc) nmax = nme;
else {
MPI_Allreduce(&bnme,&ntotal,1,MPI_LMP_BIGINT,MPI_SUM,world);
MPI_Allreduce(&nme,&nmax,1,MPI_INT,MPI_MAX,world);
}
// write timestep header
if (multiproc) write_header(bnme);
else write_header(ntotal);
// insure proc 0 can receive everyone's info
// limit nmax*size_one to int since used as arg in MPI_Rsend() below
// pack my data into buf
// if sorting on IDs also request ID list from pack()
// sort buf as needed
if (nmax > maxbuf) {
if ((bigint) nmax * size_one > MAXSMALLINT)
error->all("Too much per-proc info for dump");
maxbuf = nmax;
memory->sfree(buf);
buf = (double *)
memory->smalloc(maxbuf*size_one*sizeof(double),"dump:buf");
}
if (sort_flag && sortcol == 0 && nmax > maxids) {
maxids = nmax;
memory->sfree(ids);
ids = (int *) memory->smalloc(maxids*sizeof(int),"dump:ids");
}
if (sort_flag && sortcol == 0) pack(ids);
else pack(NULL);
if (sort_flag) sort();
// multiproc = 1 = each proc writes own data to own file
// multiproc = 0 = all procs write to one file thru proc 0
// proc 0 pings each proc, receives it's data, writes to file
// all other procs wait for ping, send their data to proc 0
if (multiproc) write_data(nme,buf);
else {
int tmp,nlines;
MPI_Status status;
MPI_Request request;
if (me == 0) {
for (int iproc = 0; iproc < nprocs; iproc++) {
if (iproc) {
MPI_Irecv(buf,maxbuf*size_one,MPI_DOUBLE,iproc,0,world,&request);
MPI_Send(&tmp,0,MPI_INT,iproc,0,world);
MPI_Wait(&request,&status);
MPI_Get_count(&status,MPI_DOUBLE,&nlines);
nlines /= size_one;
} else nlines = nme;
write_data(nlines,buf);
}
if (flush_flag) fflush(fp);
} else {
MPI_Recv(&tmp,0,MPI_INT,0,0,world,&status);
MPI_Rsend(buf,nme*size_one,MPI_DOUBLE,0,0,world);
}
}
// if file per timestep, close file
if (multifile) {
if (compressed) {
if (multiproc) pclose(fp);
else if (me == 0) pclose(fp);
} else {
if (multiproc) fclose(fp);
else if (me == 0) fclose(fp);
}
}
}
/* ----------------------------------------------------------------------
generic opening of a dump file
ASCII or binary or gzipped
some derived classes override this function
------------------------------------------------------------------------- */
void Dump::openfile()
{
// single file, already opened, so just return
if (singlefile_opened) return;
if (multifile == 0) singlefile_opened = 1;
// if one file per timestep, replace '*' with current timestep
char *filecurrent;
if (multifile == 0) filecurrent = filename;
else {
filecurrent = new char[strlen(filename) + 16];
char *ptr = strchr(filename,'*');
*ptr = '\0';
sprintf(filecurrent,"%s" BIGINT_FORMAT "%s",
filename,update->ntimestep,ptr+1);
*ptr = '*';
}
// open one file on proc 0 or file on every proc
if (me == 0 || multiproc) {
if (compressed) {
#ifdef LAMMPS_GZIP
char gzip[128];
sprintf(gzip,"gzip -6 > %s",filecurrent);
fp = popen(gzip,"w");
#else
error->one("Cannot open gzipped file");
#endif
} else if (binary) {
fp = fopen(filecurrent,"wb");
} else if (append_flag) {
fp = fopen(filecurrent,"a");
} else {
fp = fopen(filecurrent,"w");
}
if (fp == NULL) error->one("Cannot open dump file");
} else fp = NULL;
// delete string with timestep replaced
if (multifile) delete [] filecurrent;
}
/* ----------------------------------------------------------------------
parallel sort of buf across all procs
changes nme, reorders datums in buf, grows buf if necessary
------------------------------------------------------------------------- */
void Dump::sort()
{
int i,iproc;
double value;
// if single proc, swap ptrs to buf,ids <-> bufsort,idsort
if (nprocs == 1) {
if (nme > maxsort) {
maxsort = nme;
memory->sfree(bufsort);
bufsort = (double *)
memory->smalloc(maxsort*size_one*sizeof(double),"dump:bufsort");
memory->sfree(index);
index = (int *) memory->smalloc(maxsort*sizeof(int),"dump:index");
if (sortcol == 0) {
memory->sfree(idsort);
idsort = (int *) memory->smalloc(maxsort*sizeof(int),"dump:idsort");
}
}
double *dptr = buf;
buf = bufsort;
bufsort = dptr;
if (sortcol == 0) {
int *iptr = ids;
ids = idsort;
idsort = iptr;
}
// if multiple procs, exchange datums between procs via irregular
} else {
// grow proclist if necessary
if (nme > maxproc) {
maxproc = nme;
memory->sfree(proclist);
proclist = (int *) memory->smalloc(maxproc*sizeof(int),"dump:proclist");
}
// proclist[i] = which proc Ith datum will be sent to
if (sortcol == 0) {
int min = IBIG;
int max = 0;
for (i = 0; i < nme; i++) {
min = MIN(min,ids[i]);
max = MAX(max,ids[i]);
}
int minall,maxall;
MPI_Allreduce(&min,&minall,1,MPI_INT,MPI_MIN,world);
MPI_Allreduce(&max,&maxall,1,MPI_INT,MPI_MAX,world);
double range = maxall-minall + EPSILON;
for (i = 0; i < nme; i++) {
iproc = static_cast<int> ((ids[i]-minall)/range * nprocs);
proclist[i] = iproc;
}
} else {
double min = BIG;
double max = -BIG;
for (i = 0; i < nme; i++) {
value = buf[i*size_one + sortcolm1];
min = MIN(min,value);
max = MAX(max,value);
}
double minall,maxall;
MPI_Allreduce(&min,&minall,1,MPI_DOUBLE,MPI_MIN,world);
MPI_Allreduce(&max,&maxall,1,MPI_DOUBLE,MPI_MAX,world);
double range = maxall-minall + EPSILON*(maxall-minall);
if (range == 0.0) range = EPSILON;
for (i = 0; i < nme; i++) {
value = buf[i*size_one + sortcolm1];
iproc = static_cast<int> ((value-minall)/range * nprocs);
proclist[i] = iproc;
}
}
// create comm plan, grow recv bufs if necessary,
// exchange datums, destroy plan
// if sorting on atom IDs, exchange IDs also
nme = irregular->create_data(nme,proclist);
if (nme > maxsort) {
maxsort = nme;
memory->sfree(bufsort);
bufsort = (double *)
memory->smalloc(maxsort*size_one*sizeof(double),"dump:bufsort");
memory->sfree(index);
index = (int *) memory->smalloc(maxsort*sizeof(int),"dump:index");
if (sortcol == 0) {
memory->sfree(idsort);
idsort = (int *) memory->smalloc(maxsort*sizeof(int),"dump:idsort");
}
}
irregular->exchange_data((char *) buf,size_one*sizeof(double),
(char *) bufsort);
if (sortcol == 0)
irregular->exchange_data((char *) ids,sizeof(int),(char *) idsort);
irregular->destroy_data();
}
// if reorder flag is set & total/per-proc counts match pre-computed values,
// then create index directly from idsort
// else quicksort of index using IDs or buf column as comparator
if (reorderflag) {
if (ntotal != ntotal_reorder) reorderflag = 0;
int flag = 0;
if (nme != nme_reorder) flag = 1;
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall) reorderflag = 0;
if (reorderflag)
for (i = 0; i < nme; i++)
index[idsort[i]-idlo] = i;
}
if (!reorderflag) {
dumpptr = this;
for (i = 0; i < nme; i++) index[i] = i;
if (sortcol == 0) qsort(index,nme,sizeof(int),idcompare);
else if (sortorder == ASCEND) qsort(index,nme,sizeof(int),bufcompare);
else qsort(index,nme,sizeof(int),bufcompare_reverse);
}
// reset buf size and maxbuf to largest of any post-sort nme values
// this insures proc 0 can receive everyone's info
int nmax;
if (multiproc) nmax = nme;
else MPI_Allreduce(&nme,&nmax,1,MPI_INT,MPI_MAX,world);
if (nmax > maxbuf) {
maxbuf = nmax;
memory->sfree(buf);
buf = (double *)
memory->smalloc(maxbuf*size_one*sizeof(double),"dump:buf");
}
// copy data from bufsort to buf using index
int nbytes = size_one*sizeof(double);
for (i = 0; i < nme; i++)
memcpy(&buf[i*size_one],&bufsort[index[i]*size_one],nbytes);
}
/* ----------------------------------------------------------------------
compare two atom IDs
called via qsort() in sort() method
is a static method so access data via dumpptr
------------------------------------------------------------------------- */
int Dump::idcompare(const void *pi, const void *pj)
{
int *idsort = dumpptr->idsort;
int i = *((int *) pi);
int j = *((int *) pj);
if (idsort[i] < idsort[j]) return -1;
if (idsort[i] > idsort[j]) return 1;
return 0;
}
/* ----------------------------------------------------------------------
compare two buffer values with size_one stride
called via qsort() in sort() method
is a static method so access data via dumpptr
sort in ASCENDing order
------------------------------------------------------------------------- */
int Dump::bufcompare(const void *pi, const void *pj)
{
double *bufsort = dumpptr->bufsort;
int size_one = dumpptr->size_one;
int sortcolm1 = dumpptr->sortcolm1;
int i = *((int *) pi)*size_one + sortcolm1;
int j = *((int *) pj)*size_one + sortcolm1;
if (bufsort[i] < bufsort[j]) return -1;
if (bufsort[i] > bufsort[j]) return 1;
return 0;
}
/* ----------------------------------------------------------------------
compare two buffer values with size_one stride
called via qsort() in sort() method
is a static method so access data via dumpptr
sort in DESCENDing order
------------------------------------------------------------------------- */
int Dump::bufcompare_reverse(const void *pi, const void *pj)
{
double *bufsort = dumpptr->bufsort;
int size_one = dumpptr->size_one;
int sortcolm1 = dumpptr->sortcolm1;
int i = *((int *) pi)*size_one + sortcolm1;
int j = *((int *) pj)*size_one + sortcolm1;
if (bufsort[i] > bufsort[j]) return -1;
if (bufsort[i] < bufsort[j]) return 1;
return 0;
}
/* ----------------------------------------------------------------------
process params common to all dumps here
if unknown param, call modify_param specific to the dump
------------------------------------------------------------------------- */
void Dump::modify_params(int narg, char **arg)
{
if (narg == 0) error->all("Illegal dump_modify command");
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"append") == 0) {
if (iarg+2 > narg) error->all("Illegal dump_modify command");
if (strcmp(arg[iarg+1],"yes") == 0) append_flag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) append_flag = 0;
else error->all("Illegal dump_modify command");
iarg += 2;
} else if (strcmp(arg[iarg],"every") == 0) {
if (iarg+2 > narg) error->all("Illegal dump_modify command");
int idump;
for (idump = 0; idump < output->ndump; idump++)
if (strcmp(id,output->dump[idump]->id) == 0) break;
int n;
if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) {
delete [] output->var_dump[idump];
n = strlen(&arg[iarg+1][2]) + 1;
output->var_dump[idump] = new char[n];
strcpy(output->var_dump[idump],&arg[iarg+1][2]);
n = 0;
} else {
n = atoi(arg[iarg+1]);
if (n <= 0) error->all("Illegal dump_modify command");
}
output->every_dump[idump] = n;
iarg += 2;
} else if (strcmp(arg[iarg],"first") == 0) {
if (iarg+2 > narg) error->all("Illegal dump_modify command");
if (strcmp(arg[iarg+1],"yes") == 0) first_flag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) first_flag = 0;
else error->all("Illegal dump_modify command");
iarg += 2;
} else if (strcmp(arg[iarg],"flush") == 0) {
if (iarg+2 > narg) error->all("Illegal dump_modify command");
if (strcmp(arg[iarg+1],"yes") == 0) flush_flag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) flush_flag = 0;
else error->all("Illegal dump_modify command");
iarg += 2;
} else if (strcmp(arg[iarg],"format") == 0) {
if (iarg+2 > narg) error->all("Illegal dump_modify command");
delete [] format_user;
format_user = NULL;
if (strcmp(arg[iarg+1],"none")) {
int n = strlen(arg[iarg+1]) + 1;
format_user = new char[n];
strcpy(format_user,arg[iarg+1]);
}
iarg += 2;
} else if (strcmp(arg[iarg],"sort") == 0) {
if (iarg+2 > narg) error->all("Illegal dump_modify command");
if (strcmp(arg[iarg+1],"off") == 0) sort_flag = 0;
else if (strcmp(arg[iarg+1],"id") == 0) {
sort_flag = 1;
sortcol = 0;
sortorder = ASCEND;
} else {
sort_flag = 1;
sortcol = atoi(arg[iarg+1]);
sortorder = ASCEND;
if (sortcol == 0) error->all("Illegal dump_modify command");
if (sortcol < 0) {
sortorder = DESCEND;
sortcol = -sortcol;
}
sortcolm1 = sortcol - 1;
}
iarg += 2;
} else {
int n = modify_param(narg-iarg,&arg[iarg]);
if (n == 0) error->all("Illegal dump_modify command");
iarg += n;
}
}
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
------------------------------------------------------------------------- */
double Dump::memory_usage()
{
double bytes = maxbuf*size_one * sizeof(double); // buf
if (sort_flag) {
if (sortcol == 0) bytes += maxids * sizeof(int); // ids
bytes += maxsort*size_one * sizeof(double); // bufsort
if (sortcol == 0) bytes += maxsort * sizeof(int); // idsort
bytes += maxsort * sizeof(int); // index
bytes += maxproc * sizeof(int); // proclist
if (irregular) bytes += irregular->memory_usage();
}
return bytes;
}
diff --git a/src/dump.h b/src/dump.h
index 4b4aeb289..0f50c20bf 100644
--- a/src/dump.h
+++ b/src/dump.h
@@ -1,108 +1,108 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifndef LMP_DUMP_H
#define LMP_DUMP_H
+#include "lmptype.h"
#include "stdio.h"
#include "pointers.h"
-#include "lmptype.h"
namespace LAMMPS_NS {
class Dump : protected Pointers {
public:
char *id; // user-defined name of Dump
char *style; // style of Dump
int igroup,groupbit; // group that Dump is performed on
int first_flag; // 0 if no initial dump, 1 if yes initial dump
int clearstep; // 1 if dump invokes computes, 0 if not
// static variable across all Dump objects
static Dump *dumpptr; // holds a ptr to Dump currently being used
Dump(class LAMMPS *, int, char **);
virtual ~Dump();
void init();
void write();
void modify_params(int, char **);
virtual double memory_usage();
protected:
int me,nprocs; // proc info
char *filename; // user-specified file
int compressed; // 1 if dump file is written compressed, 0 no
int binary; // 1 if dump file is written binary, 0 no
int multifile; // 0 = one big file, 1 = one file per timestep
int multiproc; // 0 = proc 0 writes for all, 1 = one file/proc
int header_flag; // 0 = item, 2 = xyz
int flush_flag; // 0 if no flush, 1 if flush every dump
int sort_flag; // 1 if sorted output
int append_flag; // 1 if open file in append mode, 0 if not
int singlefile_opened; // 1 = one big file, already opened, else 0
int sortcol; // 0 to sort on ID, 1-N on columns
int sortcolm1; // sortcol - 1
int sortorder; // ASCEND or DESCEND
char *format_default; // default format string
char *format_user; // format string set by user
char *format; // format string for the file write
FILE *fp; // file to write dump to
int size_one; // # of quantities for one atom
int nme; // # of atoms in this dump from me
double boxxlo,boxxhi; // local copies of domain values
double boxylo,boxyhi; // lo/hi are bounding box for triclinic
double boxzlo,boxzhi;
double boxxy,boxxz,boxyz;
bigint ntotal; // # of per-atom lines in snapshot
int reorderflag; // 1 if OK to reorder instead of sort
int ntotal_reorder; // # of atoms that must be in snapshot
int nme_reorder; // # of atoms I must own in snapshot
int idlo; // lowest ID I own when reordering
int maxbuf; // size of buf
double *buf; // memory for atom quantities
int maxids; // size of ids
int maxsort; // size of bufsort, idsort, index
int maxproc; // size of proclist
int *ids; // list of atom IDs, if sorting on IDs
double *bufsort;
int *idsort,*index,*proclist;
class Irregular *irregular;
virtual void init_style() = 0;
virtual void openfile();
virtual int modify_param(int, char **) {return 0;}
virtual void write_header(bigint) = 0;
virtual int count() = 0;
virtual void pack(int *) = 0;
virtual void write_data(int, double *) = 0;
void sort();
static int idcompare(const void *, const void *);
static int bufcompare(const void *, const void *);
static int bufcompare_reverse(const void *, const void *);
};
}
#endif
diff --git a/src/dump_dcd.cpp b/src/dump_dcd.cpp
index 5235ccdf8..ebf9e72e9 100644
--- a/src/dump_dcd.cpp
+++ b/src/dump_dcd.cpp
@@ -1,371 +1,371 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Naveen Michaud-Agrawal (Johns Hopkins U)
Axel Kohlmeyer (Temple U), support for groups
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "math.h"
#include "inttypes.h"
#include "stdio.h"
#include "time.h"
#include "string.h"
#include "dump_dcd.h"
-#include "lmptype.h"
#include "domain.h"
#include "atom.h"
#include "update.h"
#include "output.h"
#include "group.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define NFILE_POS 8L
#define NSTEP_POS 20L
// necessary to set SEEK params b/c MPI-2 messes with these settings
#ifndef SEEK_SET
#define SEEK_SET 0
#define SEEK_CUR 1
#define SEEK_END 2
#endif
/* ---------------------------------------------------------------------- */
static inline void fwrite_int32(FILE* fd, uint32_t i)
{
fwrite(&i,sizeof(uint32_t),1,fd);
}
/* ---------------------------------------------------------------------- */
DumpDCD::DumpDCD(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg)
{
if (narg != 5) error->all("Illegal dump dcd command");
if (binary || compressed || multifile || multiproc)
error->all("Invalid dump dcd filename");
size_one = 3;
sort_flag = 1;
sortcol = 0;
unwrap_flag = 0;
format_default = NULL;
// allocate global array for atom coords
bigint n = group->count(igroup);
if (n > MAXSMALLINT/sizeof(float)) error->all("Too many atoms for dump dcd");
natoms = static_cast<int> (n);
coords = (float *) memory->smalloc(3*natoms*sizeof(float),"dump:coords");
xf = &coords[0*natoms];
yf = &coords[1*natoms];
zf = &coords[2*natoms];
openfile();
headerflag = 0;
nevery_save = 0;
ntotal = 0;
}
/* ---------------------------------------------------------------------- */
DumpDCD::~DumpDCD()
{
memory->sfree(coords);
}
/* ---------------------------------------------------------------------- */
void DumpDCD::init_style()
{
if (sort_flag == 0 || sortcol != 0)
error->all("Dump dcd requires sorting by atom ID");
// check that dump frequency has not changed and is not a variable
int idump;
for (idump = 0; idump < output->ndump; idump++)
if (strcmp(id,output->dump[idump]->id) == 0) break;
if (output->every_dump[idump] == 0)
error->all("Cannot use variable every setting for dump dcd");
if (nevery_save == 0) nevery_save = output->every_dump[idump];
else if (nevery_save != output->every_dump[idump])
error->all("Cannot change dump_modify every for dump dcd");
}
/* ---------------------------------------------------------------------- */
void DumpDCD::openfile()
{
if (me == 0) {
fp = fopen(filename,"wb");
if (fp == NULL) error->one("Cannot open dump file");
}
}
/* ---------------------------------------------------------------------- */
void DumpDCD::write_header(bigint n)
{
if (n != natoms) error->all("Dump dcd of non-matching # of atoms");
if (update->ntimestep > MAXSMALLINT)
error->all("Too big a timestep for dump dcd");
// first time, write header for entire file
if (headerflag == 0) {
if (me == 0) write_dcd_header("Written by LAMMPS");
headerflag = 1;
nframes = 0;
}
// dim[] = size and angle cosines of orthogonal or triclinic box
// dim[0] = a = length of unit cell vector along x-axis
// dim[1] = gamma = cosine of angle between a and b
// dim[2] = b = length of unit cell vector in xy-plane
// dim[3] = beta = cosine of angle between a and c
// dim[4] = alpha = cosine of angle between b and c
// dim[5] = c = length of final unit cell vector
// 48 = 6 doubles
double dim[6];
if (domain->triclinic) {
double *h = domain->h;
double alen = h[0];
double blen = sqrt(h[5]*h[5] + h[1]*h[1]);
double clen = sqrt(h[4]*h[4] + h[3]*h[3] + h[2]*h[2]);
dim[0] = alen;
dim[2] = blen;
dim[5] = clen;
dim[4] = (h[5]*h[4] + h[1]*h[3]) / blen/clen; // alpha
dim[3] = (h[0]*h[4]) / alen/clen; // beta
dim[1] = (h[0]*h[5]) / alen/blen; // gamma
} else {
dim[0] = domain->xprd;
dim[2] = domain->yprd;
dim[5] = domain->zprd;
dim[1] = dim[3] = dim[4] = 0.0;
}
if (me == 0) {
uint32_t out_integer = 48;
fwrite_int32(fp,out_integer);
fwrite(dim,out_integer,1,fp);
fwrite_int32(fp,out_integer);
if (flush_flag) fflush(fp);
}
}
/* ---------------------------------------------------------------------- */
int DumpDCD::count()
{
if (igroup == 0) return atom->nlocal;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int m = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) m++;
return m;
}
/* ---------------------------------------------------------------------- */
void DumpDCD::pack(int *ids)
{
int m,n;
int *tag = atom->tag;
double **x = atom->x;
int *image = atom->image;
int *mask = atom->mask;
int nlocal = atom->nlocal;
m = n = 0;
if (unwrap_flag) {
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
double xy = domain->xy;
double xz = domain->xz;
double yz = domain->yz;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
int ix = (image[i] & 1023) - 512;
int iy = (image[i] >> 10 & 1023) - 512;
int iz = (image[i] >> 20) - 512;
if (domain->triclinic) {
buf[m++] = x[i][0] + ix * xprd + iy * xy + iz * xz;
buf[m++] = x[i][1] + iy * yprd + iz * yz;
buf[m++] = x[i][2] + iz * zprd;
} else {
buf[m++] = x[i][0] + ix * xprd;
buf[m++] = x[i][1] + iy * yprd;
buf[m++] = x[i][2] + iz * zprd;
}
ids[n++] = tag[i];
}
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
buf[m++] = x[i][0];
buf[m++] = x[i][1];
buf[m++] = x[i][2];
ids[n++] = tag[i];
}
}
}
/* ---------------------------------------------------------------------- */
void DumpDCD::write_data(int n, double *mybuf)
{
// copy buf atom coords into 3 global arrays
int m = 0;
for (int i = 0; i < n; i++) {
xf[ntotal] = mybuf[m++];
yf[ntotal] = mybuf[m++];
zf[ntotal] = mybuf[m++];
ntotal++;
}
// if last chunk of atoms in this snapshot, write global arrays to file
if (ntotal == natoms) {
write_frame();
ntotal = 0;
}
}
/* ---------------------------------------------------------------------- */
int DumpDCD::modify_param(int narg, char **arg)
{
if (strcmp(arg[0],"unwrap") == 0) {
if (narg < 2) error->all("Illegal dump_modify command");
if (strcmp(arg[1],"yes") == 0) unwrap_flag = 1;
else if (strcmp(arg[1],"no") == 0) unwrap_flag = 0;
else error->all("Illegal dump_modify command");
return 2;
}
return 0;
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory in buf and global coords array
------------------------------------------------------------------------- */
double DumpDCD::memory_usage()
{
double bytes = Dump::memory_usage();
bytes += 3*natoms * sizeof(float);
return bytes;
}
/* ---------------------------------------------------------------------- */
void DumpDCD::write_frame()
{
// write coords
uint32_t out_integer = natoms*sizeof(float);
fwrite_int32(fp,out_integer);
fwrite(xf,out_integer,1,fp);
fwrite_int32(fp,out_integer);
fwrite_int32(fp,out_integer);
fwrite(yf,out_integer,1,fp);
fwrite_int32(fp,out_integer);
fwrite_int32(fp,out_integer);
fwrite(zf,out_integer,1,fp);
fwrite_int32(fp,out_integer);
// update NFILE and NSTEP fields in DCD header
nframes++;
out_integer = nframes;
fseek(fp,NFILE_POS,SEEK_SET);
fwrite_int32(fp,out_integer);
out_integer = update->ntimestep;
fseek(fp,NSTEP_POS,SEEK_SET);
fwrite_int32(fp,out_integer);
fseek(fp,0,SEEK_END);
}
/* ---------------------------------------------------------------------- */
void DumpDCD::write_dcd_header(const char *remarks)
{
uint32_t out_integer;
float out_float;
char title_string[200];
time_t cur_time;
struct tm *tmbuf;
int ntimestep = update->ntimestep;
out_integer = 84;
fwrite_int32(fp,out_integer);
strcpy(title_string,"CORD");
fwrite(title_string,4,1,fp);
fwrite_int32(fp,0); // NFILE = # of snapshots in file
fwrite_int32(fp,ntimestep); // START = timestep of first snapshot
fwrite_int32(fp,nevery_save); // SKIP = interval between snapshots
fwrite_int32(fp,ntimestep); // NSTEP = timestep of last snapshot
fwrite_int32(fp,0); // NAMD writes NSTEP or ISTART
fwrite_int32(fp,0);
fwrite_int32(fp,0);
fwrite_int32(fp,0);
fwrite_int32(fp,0);
out_float = update->dt;
fwrite(&out_float,sizeof(float),1,fp);
fwrite_int32(fp,1);
fwrite_int32(fp,0);
fwrite_int32(fp,0);
fwrite_int32(fp,0);
fwrite_int32(fp,0);
fwrite_int32(fp,0);
fwrite_int32(fp,0);
fwrite_int32(fp,0);
fwrite_int32(fp,0);
fwrite_int32(fp,24); // pretend to be Charmm version 24
fwrite_int32(fp,84);
fwrite_int32(fp,164);
fwrite_int32(fp,2);
strncpy(title_string,remarks,80);
title_string[79] = '\0';
fwrite(title_string,80,1,fp);
cur_time=time(NULL);
tmbuf=localtime(&cur_time);
memset(title_string,' ',81);
strftime(title_string,80,"REMARKS Created %d %B,%Y at %R",tmbuf);
fwrite(title_string,80,1,fp);
fwrite_int32(fp,164);
fwrite_int32(fp,4);
fwrite_int32(fp,natoms); // number of atoms in each snapshot
fwrite_int32(fp,4);
if (flush_flag) fflush(fp);
}
diff --git a/src/fix.h b/src/fix.h
index c44cccfa2..4cd938e05 100644
--- a/src/fix.h
+++ b/src/fix.h
@@ -1,171 +1,171 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifndef LMP_FIX_H
#define LMP_FIX_H
-#include "pointers.h"
#include "lmptype.h"
+#include "pointers.h"
namespace LAMMPS_NS {
class Fix : protected Pointers {
public:
char *id,*style;
int igroup,groupbit;
int restart_global; // 1 if Fix saves global state, 0 if not
int restart_peratom; // 1 if Fix saves peratom state, 0 if not
int force_reneighbor; // 1 if Fix forces reneighboring, 0 if not
int box_change; // 1 if Fix changes box, 0 if not
int box_change_size; // 1 if Fix changes box size, 0 if not
int box_change_shape; // 1 if Fix changes box shape, 0 if not
bigint next_reneighbor; // next timestep to force a reneighboring
int thermo_energy; // 1 if fix_modify enabled ThEng, 0 if not
int nevery; // how often to call an end_of_step fix
int rigid_flag; // 1 if Fix integrates rigid bodies, 0 if not
int virial_flag; // 1 if Fix contributes to virial, 0 if not
int no_change_box; // 1 if cannot swap ortho <-> triclinic
int time_integrate; // 1 if fix performs time integration, 0 if no
int time_depend; // 1 if fix is timestep dependent, 0 if not
int create_attribute; // 1 if fix stores attributes that need
// setting when a new atom is created
int restart_pbc; // 1 if fix moves atoms (except integrate)
// so write_restart must remap to PBC
int scalar_flag; // 0/1 if compute_scalar() function exists
int vector_flag; // 0/1 if compute_vector() function exists
int array_flag; // 0/1 if compute_array() function exists
int size_vector; // length of global vector
int size_array_rows; // rows in global array
int size_array_cols; // columns in global array
int global_freq; // frequency s/v data is available at
int peratom_flag; // 0/1 if per-atom data is stored
int size_peratom_cols; // 0 = vector, N = columns in peratom array
int peratom_freq; // frequency per-atom data is available at
int local_flag; // 0/1 if local data is stored
int size_local_rows; // rows in local vector or array
int size_local_cols; // 0 = vector, N = columns in local array
int local_freq; // frequency local data is available at
int extscalar; // 0/1 if global scalar is intensive/extensive
int extvector; // 0/1/-1 if global vector is all int/ext/extlist
int *extlist; // list of 0/1 int/ext for each vec component
int extarray; // 0/1 if global array is intensive/extensive
double *vector_atom; // computed per-atom vector
double **array_atom; // computed per-atom array
double *vector_local; // computed local vector
double **array_local; // computed local array
int comm_forward; // size of forward communication (0 if none)
int comm_reverse; // size of reverse communication (0 if none)
double virial[6]; // accumlated virial
double **vatom; // accumulated per-atom virial
int INITIAL_INTEGRATE,POST_INTEGRATE; // mask settings
int PRE_EXCHANGE,PRE_NEIGHBOR;
int PRE_FORCE,POST_FORCE,FINAL_INTEGRATE,END_OF_STEP,THERMO_ENERGY;
int INITIAL_INTEGRATE_RESPA,POST_INTEGRATE_RESPA;
int PRE_FORCE_RESPA,POST_FORCE_RESPA,FINAL_INTEGRATE_RESPA;
int MIN_PRE_EXCHANGE,MIN_PRE_FORCE,MIN_POST_FORCE,MIN_ENERGY;
int POST_RUN;
Fix(class LAMMPS *, int, char **);
virtual ~Fix();
void modify_params(int, char **);
virtual int setmask() = 0;
virtual void init() {}
virtual void init_list(int, class NeighList *) {}
virtual void setup(int) {}
virtual void setup_pre_force(int) {}
virtual void min_setup(int) {}
virtual void initial_integrate(int) {}
virtual void post_integrate() {}
virtual void pre_exchange() {}
virtual void pre_neighbor() {}
virtual void pre_force(int) {}
virtual void post_force(int) {}
virtual void final_integrate() {}
virtual void end_of_step() {}
virtual void post_run() {}
virtual void write_restart(FILE *) {}
virtual void restart(char *) {}
virtual void grow_arrays(int) {}
virtual void copy_arrays(int, int) {}
virtual void set_arrays(int) {}
virtual int pack_exchange(int, double *) {return 0;}
virtual int unpack_exchange(int, double *) {return 0;}
virtual int pack_restart(int, double *) {return 0;}
virtual void unpack_restart(int, int) {}
virtual int size_restart(int) {return 0;}
virtual int maxsize_restart() {return 0;}
virtual void setup_pre_force_respa(int, int) {}
virtual void initial_integrate_respa(int, int, int) {}
virtual void post_integrate_respa(int, int) {}
virtual void pre_force_respa(int, int, int) {}
virtual void post_force_respa(int, int, int) {}
virtual void final_integrate_respa(int, int) {}
virtual void min_setup_pre_force(int) {}
virtual void min_pre_exchange() {}
virtual void min_pre_force(int) {}
virtual void min_post_force(int) {}
virtual double min_energy(double *) {return 0.0;}
virtual void min_store() {}
virtual void min_clearstore() {}
virtual void min_pushstore() {}
virtual void min_popstore() {}
virtual int min_reset_ref() {return 0;}
virtual void min_step(double, double *) {}
virtual double max_alpha(double *) {return 0.0;}
virtual int min_dof() {return 0;}
virtual int pack_comm(int, int *, double *, int, int *) {return 0;}
virtual void unpack_comm(int, int, double *) {}
virtual int pack_reverse_comm(int, int, double *) {return 0;}
virtual void unpack_reverse_comm(int, int *, double *) {}
virtual double compute_scalar() {return 0.0;}
virtual double compute_vector(int) {return 0.0;}
virtual double compute_array(int,int) {return 0.0;}
virtual int dof(int) {return 0;}
virtual void deform(int) {}
virtual void reset_target(double) {}
virtual void reset_dt() {}
virtual int modify_param(int, char **) {return 0;}
virtual double memory_usage() {return 0.0;}
protected:
int evflag;
int vflag_global,vflag_atom;
int maxvatom;
void v_setup(int);
void v_tally(int, int *, double, double *);
};
}
#endif
diff --git a/src/fix_ave_atom.cpp b/src/fix_ave_atom.cpp
index ef7de11d3..ee2cf2b2d 100644
--- a/src/fix_ave_atom.cpp
+++ b/src/fix_ave_atom.cpp
@@ -1,448 +1,448 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "stdlib.h"
#include "string.h"
#include "fix_ave_atom.h"
-#include "lmptype.h"
#include "atom.h"
#include "domain.h"
#include "update.h"
#include "modify.h"
#include "compute.h"
#include "input.h"
#include "variable.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
enum{X,V,F,COMPUTE,FIX,VARIABLE};
#define INVOKED_PERATOM 8
/* ---------------------------------------------------------------------- */
FixAveAtom::FixAveAtom(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 7) error->all("Illegal fix ave/atom command");
time_depend = 1;
nevery = atoi(arg[3]);
nrepeat = atoi(arg[4]);
peratom_freq = atoi(arg[5]);
// parse remaining values
which = new int[narg-6];
argindex = new int[narg-6];
ids = new char*[narg-6];
value2index = new int[narg-6];
nvalues = 0;
int iarg = 6;
while (iarg < narg) {
ids[nvalues] = NULL;
if (strcmp(arg[iarg],"x") == 0) {
which[nvalues] = X;
argindex[nvalues++] = 0;
} else if (strcmp(arg[iarg],"y") == 0) {
which[nvalues] = X;
argindex[nvalues++] = 1;
} else if (strcmp(arg[iarg],"z") == 0) {
which[nvalues] = X;
argindex[nvalues++] = 2;
} else if (strcmp(arg[iarg],"vx") == 0) {
which[nvalues] = V;
argindex[nvalues++] = 0;
} else if (strcmp(arg[iarg],"vy") == 0) {
which[nvalues] = V;
argindex[nvalues++] = 1;
} else if (strcmp(arg[iarg],"vz") == 0) {
which[nvalues] = V;
argindex[nvalues++] = 2;
} else if (strcmp(arg[iarg],"fx") == 0) {
which[nvalues] = F;
argindex[nvalues++] = 0;
} else if (strcmp(arg[iarg],"fy") == 0) {
which[nvalues] = F;
argindex[nvalues++] = 1;
} else if (strcmp(arg[iarg],"fz") == 0) {
which[nvalues] = F;
argindex[nvalues++] = 2;
} else if (strncmp(arg[iarg],"c_",2) == 0 ||
strncmp(arg[iarg],"f_",2) == 0 ||
strncmp(arg[iarg],"v_",2) == 0) {
if (arg[iarg][0] == 'c') which[nvalues] = COMPUTE;
else if (arg[iarg][0] == 'f') which[nvalues] = FIX;
else if (arg[iarg][0] == 'v') which[nvalues] = VARIABLE;
int n = strlen(arg[iarg]);
char *suffix = new char[n];
strcpy(suffix,&arg[iarg][2]);
char *ptr = strchr(suffix,'[');
if (ptr) {
if (suffix[strlen(suffix)-1] != ']')
error->all("Illegal fix ave/atom command");
argindex[nvalues] = atoi(ptr+1);
*ptr = '\0';
} else argindex[nvalues] = 0;
n = strlen(suffix) + 1;
ids[nvalues] = new char[n];
strcpy(ids[nvalues],suffix);
nvalues++;
delete [] suffix;
} else error->all("Illegal fix ave/atom command");
iarg++;
}
// setup and error check
// for fix inputs, check that fix frequency is acceptable
if (nevery <= 0 || nrepeat <= 0 || peratom_freq <= 0)
error->all("Illegal fix ave/atom command");
if (peratom_freq % nevery || (nrepeat-1)*nevery >= peratom_freq)
error->all("Illegal fix ave/atom command");
for (int i = 0; i < nvalues; i++) {
if (which[i] == COMPUTE) {
int icompute = modify->find_compute(ids[i]);
if (icompute < 0)
error->all("Compute ID for fix ave/atom does not exist");
if (modify->compute[icompute]->peratom_flag == 0)
error->all("Fix ave/atom compute does not calculate per-atom values");
if (argindex[i] == 0 &&
modify->compute[icompute]->size_peratom_cols != 0)
error->all("Fix ave/atom compute does not "
"calculate a per-atom vector");
if (argindex[i] && modify->compute[icompute]->size_peratom_cols == 0)
error->all("Fix ave/atom compute does not "
"calculate a per-atom array");
if (argindex[i] &&
argindex[i] > modify->compute[icompute]->size_peratom_cols)
error->all("Fix ave/atom compute array is accessed out-of-range");
} else if (which[i] == FIX) {
int ifix = modify->find_fix(ids[i]);
if (ifix < 0)
error->all("Fix ID for fix ave/atom does not exist");
if (modify->fix[ifix]->peratom_flag == 0)
error->all("Fix ave/atom fix does not calculate per-atom values");
if (argindex[i] == 0 && modify->fix[ifix]->size_peratom_cols != 0)
error->all("Fix ave/atom fix does not calculate a per-atom vector");
if (argindex[i] && modify->fix[ifix]->size_peratom_cols == 0)
error->all("Fix ave/atom fix does not calculate a per-atom array");
if (argindex[i] && argindex[i] > modify->fix[ifix]->size_peratom_cols)
error->all("Fix ave/atom fix array is accessed out-of-range");
if (nevery % modify->fix[ifix]->peratom_freq)
error->all("Fix for fix ave/atom not computed at compatible time");
} else if (which[i] == VARIABLE) {
int ivariable = input->variable->find(ids[i]);
if (ivariable < 0)
error->all("Variable name for fix ave/atom does not exist");
if (input->variable->atomstyle(ivariable) == 0)
error->all("Fix ave/atom variable is not atom-style variable");
}
}
// this fix produces either a per-atom vector or array
peratom_flag = 1;
if (nvalues == 1) size_peratom_cols = 0;
else size_peratom_cols = nvalues;
// perform initial allocation of atom-based array
// register with Atom class
array = NULL;
grow_arrays(atom->nmax);
atom->add_callback(0);
// zero the array since dump may access it on timestep 0
// zero the array since a variable may access it before first run
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
for (int m = 0; m < nvalues; m++)
array[i][m] = 0.0;
// nvalid = next step on which end_of_step does something
// add nvalid to all computes that store invocation times
// since don't know a priori which are invoked by this fix
// once in end_of_step() can set timestep for ones actually invoked
irepeat = 0;
nvalid = nextvalid();
modify->addstep_compute_all(nvalid);
}
/* ---------------------------------------------------------------------- */
FixAveAtom::~FixAveAtom()
{
// unregister callback to this fix from Atom class
atom->delete_callback(id,0);
delete [] which;
delete [] argindex;
for (int m = 0; m < nvalues; m++) delete [] ids[m];
delete [] ids;
delete [] value2index;
memory->destroy_2d_double_array(array);
}
/* ---------------------------------------------------------------------- */
int FixAveAtom::setmask()
{
int mask = 0;
mask |= END_OF_STEP;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixAveAtom::init()
{
// set indices and check validity of all computes,fixes,variables
for (int m = 0; m < nvalues; m++) {
if (which[m] == COMPUTE) {
int icompute = modify->find_compute(ids[m]);
if (icompute < 0)
error->all("Compute ID for fix ave/atom does not exist");
value2index[m] = icompute;
} else if (which[m] == FIX) {
int ifix = modify->find_fix(ids[m]);
if (ifix < 0)
error->all("Fix ID for fix ave/atom does not exist");
value2index[m] = ifix;
} else if (which[m] == VARIABLE) {
int ivariable = input->variable->find(ids[m]);
if (ivariable < 0)
error->all("Variable name for fix ave/atom does not exist");
value2index[m] = ivariable;
} else value2index[m] = -1;
}
// need to reset nvalid if nvalid < ntimestep b/c minimize was performed
if (nvalid < update->ntimestep) {
irepeat = 0;
nvalid = nextvalid();
modify->addstep_compute_all(nvalid);
}
}
/* ----------------------------------------------------------------------
only does something if nvalid = current timestep
------------------------------------------------------------------------- */
void FixAveAtom::setup(int vflag)
{
end_of_step();
}
/* ---------------------------------------------------------------------- */
void FixAveAtom::end_of_step()
{
int i,j,m,n;
// skip if not step which requires doing something
bigint ntimestep = update->ntimestep;
if (ntimestep != nvalid) return;
// zero if first step
int nlocal = atom->nlocal;
if (irepeat == 0)
for (i = 0; i < nlocal; i++)
for (m = 0; m < nvalues; m++)
array[i][m] = 0.0;
// accumulate results of attributes,computes,fixes,variables to local copy
// compute/fix/variable may invoke computes so wrap with clear/add
modify->clearstep_compute();
int *mask = atom->mask;
for (m = 0; m < nvalues; m++) {
n = value2index[m];
j = argindex[m];
if (which[m] == X) {
double **x = atom->x;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) array[i][m] += x[i][j];
} else if (which[m] == V) {
double **v = atom->v;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) array[i][m] += v[i][j];
} else if (which[m] == F) {
double **f = atom->f;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) array[i][m] += f[i][j];
// invoke compute if not previously invoked
} else if (which[m] == COMPUTE) {
Compute *compute = modify->compute[n];
if (!(compute->invoked_flag & INVOKED_PERATOM)) {
compute->compute_peratom();
compute->invoked_flag |= INVOKED_PERATOM;
}
if (j == 0) {
double *compute_vector = compute->vector_atom;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) array[i][m] += compute_vector[i];
} else {
int jm1 = j - 1;
double **compute_array = compute->array_atom;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) array[i][m] += compute_array[i][jm1];
}
// access fix fields, guaranteed to be ready
} else if (which[m] == FIX) {
if (j == 0) {
double *fix_vector = modify->fix[n]->vector_atom;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) array[i][m] += fix_vector[i];
} else {
int jm1 = j - 1;
double **fix_array = modify->fix[n]->array_atom;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) array[i][m] += fix_array[i][jm1];
}
// evaluate atom-style variable
} else if (which[m] == VARIABLE)
input->variable->compute_atom(n,igroup,&array[0][m],nvalues,1);
}
// done if irepeat < nrepeat
// else reset irepeat and nvalid
irepeat++;
if (irepeat < nrepeat) {
nvalid += nevery;
modify->addstep_compute(nvalid);
return;
}
irepeat = 0;
nvalid = ntimestep+peratom_freq - (nrepeat-1)*nevery;
modify->addstep_compute(nvalid);
// average the final result for the Nfreq timestep
double repeat = nrepeat;
for (i = 0; i < nlocal; i++)
for (m = 0; m < nvalues; m++)
array[i][m] /= repeat;
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
double FixAveAtom::memory_usage()
{
double bytes;
bytes = atom->nmax*nvalues * sizeof(double);
return bytes;
}
/* ----------------------------------------------------------------------
allocate atom-based array
------------------------------------------------------------------------- */
void FixAveAtom::grow_arrays(int nmax)
{
array = memory->grow_2d_double_array(array,nmax,nvalues,
"fix_ave/atom:array");
array_atom = array;
vector_atom = array[0];
}
/* ----------------------------------------------------------------------
copy values within local atom-based array
------------------------------------------------------------------------- */
void FixAveAtom::copy_arrays(int i, int j)
{
for (int m = 0; m < nvalues; m++)
array[j][m] = array[i][m];
}
/* ----------------------------------------------------------------------
pack values in local atom-based array for exchange with another proc
------------------------------------------------------------------------- */
int FixAveAtom::pack_exchange(int i, double *buf)
{
for (int m = 0; m < nvalues; m++) buf[m] = array[i][m];
return nvalues;
}
/* ----------------------------------------------------------------------
unpack values in local atom-based array from exchange with another proc
------------------------------------------------------------------------- */
int FixAveAtom::unpack_exchange(int nlocal, double *buf)
{
for (int m = 0; m < nvalues; m++) array[nlocal][m] = buf[m];
return nvalues;
}
/* ----------------------------------------------------------------------
calculate nvalid = next step on which end_of_step does something
can be this timestep if multiple of nfreq and nrepeat = 1
else backup from next multiple of nfreq
------------------------------------------------------------------------- */
bigint FixAveAtom::nextvalid()
{
bigint nvalid = (update->ntimestep/peratom_freq)*peratom_freq + peratom_freq;
if (nvalid-peratom_freq == update->ntimestep && nrepeat == 1)
nvalid = update->ntimestep;
else
nvalid -= (nrepeat-1)*nevery;
if (nvalid < update->ntimestep) nvalid += peratom_freq;
return nvalid;
}
diff --git a/src/fix_ave_atom.h b/src/fix_ave_atom.h
index 409b78cc2..790b6252f 100644
--- a/src/fix_ave_atom.h
+++ b/src/fix_ave_atom.h
@@ -1,58 +1,58 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
FixStyle(ave/atom,FixAveAtom)
#else
#ifndef LMP_FIX_AVE_ATOM_H
#define LMP_FIX_AVE_ATOM_H
+#include "lmptype.h"
#include "stdio.h"
#include "fix.h"
-#include "lmptype.h"
namespace LAMMPS_NS {
class FixAveAtom : public Fix {
public:
FixAveAtom(class LAMMPS *, int, char **);
~FixAveAtom();
int setmask();
void init();
void setup(int);
void end_of_step();
double memory_usage();
void grow_arrays(int);
void copy_arrays(int, int);
int pack_exchange(int, double *);
int unpack_exchange(int, double *);
private:
int nvalues;
int nrepeat,irepeat;
bigint nvalid;
int *which,*argindex,*value2index;
char **ids;
double **array;
bigint nextvalid();
};
}
#endif
#endif
diff --git a/src/fix_ave_correlate.cpp b/src/fix_ave_correlate.cpp
index 4984c587c..4660662e0 100644
--- a/src/fix_ave_correlate.cpp
+++ b/src/fix_ave_correlate.cpp
@@ -1,595 +1,595 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors:
Benoit Leblanc, Dave Rigby, Paul Saxe (Materials Design)
Reese Jones (Sandia)
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "stdlib.h"
#include "string.h"
#include "fix_ave_correlate.h"
-#include "lmptype.h"
#include "update.h"
#include "modify.h"
#include "compute.h"
#include "input.h"
#include "variable.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
enum{COMPUTE,FIX,VARIABLE};
enum{ONE,RUNNING};
enum{AUTO,UPPER,LOWER,AUTOUPPER,AUTOLOWER,FULL};
#define INVOKED_SCALAR 1
#define INVOKED_VECTOR 2
#define INVOKED_ARRAY 4
/* ---------------------------------------------------------------------- */
FixAveCorrelate::FixAveCorrelate(LAMMPS * lmp, int narg, char **arg):
Fix (lmp, narg, arg)
{
if (narg < 7) error->all ("Illegal fix ave/correlate command");
MPI_Comm_rank(world,&me);
nevery = atoi(arg[3]);
nrepeat = atoi(arg[4]);
nfreq = atoi(arg[5]);
global_freq = nfreq;
time_depend = 1;
// parse values until one isn't recognized
which = new int[narg-6];
argindex = new int[narg-6];
ids = new char*[narg-6];
value2index = new int[narg-6];
nvalues = 0;
int iarg = 6;
while (iarg < narg) {
if (strncmp(arg[iarg],"c_",2) == 0 ||
strncmp(arg[iarg],"f_",2) == 0 ||
strncmp(arg[iarg],"v_",2) == 0) {
if (arg[iarg][0] == 'c') which[nvalues] = COMPUTE;
else if (arg[iarg][0] == 'f') which[nvalues] = FIX;
else if (arg[iarg][0] == 'v') which[nvalues] = VARIABLE;
int n = strlen(arg[iarg]);
char *suffix = new char[n];
strcpy(suffix,&arg[iarg][2]);
char *ptr = strchr(suffix,'[');
if (ptr) {
if (suffix[strlen(suffix)-1] != ']')
error->all("Illegal fix ave/correlate command");
argindex[nvalues] = atoi(ptr+1);
*ptr = '\0';
} else argindex[nvalues] = 0;
n = strlen(suffix) + 1;
ids[nvalues] = new char[n];
strcpy(ids[nvalues],suffix);
delete [] suffix;
nvalues++;
iarg++;
} else break;
}
// optional args
type = AUTO;
ave = ONE;
startstep = 0;
prefactor = 1.0;
fp = NULL;
char *title1 = NULL;
char *title2 = NULL;
char *title3 = NULL;
while (iarg < narg) {
if (strcmp(arg[iarg],"type") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/correlate command");
if (strcmp(arg[iarg+1],"auto") == 0) type = AUTO;
else if (strcmp(arg[iarg+1],"upper") == 0) type = UPPER;
else if (strcmp(arg[iarg+1],"lower") == 0) type = LOWER;
else if (strcmp(arg[iarg+1],"auto/upper") == 0) type = AUTOUPPER;
else if (strcmp(arg[iarg+1],"auto/lower") == 0) type = AUTOLOWER;
else if (strcmp(arg[iarg+1],"full") == 0) type = FULL;
else error->all("Illegal fix ave/correlate command");
iarg += 2;
} else if (strcmp(arg[iarg],"ave") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/correlate command");
if (strcmp(arg[iarg+1],"one") == 0) ave = ONE;
else if (strcmp(arg[iarg+1],"running") == 0) ave = RUNNING;
else error->all("Illegal fix ave/correlate command");
iarg += 2;
} else if (strcmp(arg[iarg],"start") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/correlate command");
startstep = atoi(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"prefactor") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/correlate command");
prefactor = atof(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"file") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/correlate command");
if (me == 0) {
fp = fopen(arg[iarg+1],"w");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open fix ave/correlate file %s",arg[iarg+1]);
error->one(str);
}
}
iarg += 2;
} else if (strcmp(arg[iarg],"title1") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/correlate command");
delete [] title1;
int n = strlen(arg[iarg+1]) + 1;
title1 = new char[n];
strcpy(title1,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"title2") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/correlate command");
delete [] title2;
int n = strlen(arg[iarg+1]) + 1;
title2 = new char[n];
strcpy(title2,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"title3") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/correlate command");
delete [] title3;
int n = strlen(arg[iarg+1]) + 1;
title3 = new char[n];
strcpy(title3,arg[iarg+1]);
iarg += 2;
} else error->all("Illegal fix ave/correlate command");
}
// setup and error check
// for fix inputs, check that fix frequency is acceptable
if (nevery <= 0 || nrepeat <= 0 || nfreq <= 0)
error->all("Illegal fix ave/correlate command");
if (nfreq % nevery)
error->all("Illegal fix ave/correlate command");
if (ave == ONE && nfreq < (nrepeat-1)*nevery)
error->all("Illegal fix ave/correlate command");
for (int i = 0; i < nvalues; i++) {
if (which[i] == COMPUTE) {
int icompute = modify->find_compute(ids[i]);
if (icompute < 0)
error->all ("Compute ID for fix ave/correlate does not exist");
if (argindex[i] == 0 && modify->compute[icompute]->scalar_flag == 0)
error->all ("Fix ave/correlate compute does not calculate a scalar");
if (argindex[i] && modify->compute[icompute]->vector_flag == 0)
error->all ("Fix ave/correlate compute does not calculate a vector");
if (argindex[i] && argindex[i] > modify->compute[icompute]->size_vector)
error->all ("Fix ave/correlate compute vector "
"is accessed out-of-range");
} else if (which[i] == FIX) {
int ifix = modify->find_fix(ids[i]);
if (ifix < 0)
error->all ("Fix ID for fix ave/correlate does not exist");
if (argindex[i] == 0 && modify->fix[ifix]->scalar_flag == 0)
error->all ("Fix ave/correlate fix does not calculate a scalar");
if (argindex[i] && modify->fix[ifix]->vector_flag == 0)
error->all ("Fix ave/correlate fix does not calculate a vector");
if (argindex[i] && argindex[i] > modify->fix[ifix]->size_vector)
error->all ("Fix ave/correlate fix vector is accessed out-of-range");
if (nevery % modify->fix[ifix]->global_freq)
error->all("Fix for fix ave/correlate "
"not computed at compatible time");
} else if (which[i] == VARIABLE) {
int ivariable = input->variable->find(ids[i]);
if (ivariable < 0)
error->all ("Variable name for fix ave/correlate does not exist");
if (input->variable->equalstyle(ivariable) == 0)
error->all ("Fix ave/correlate variable is not equal-style variable");
}
}
// npair = # of correlation pairs to calculate
if (type == AUTO) npair = nvalues;
if (type == UPPER || type == LOWER) npair = nvalues*(nvalues-1)/2;
if (type == AUTOUPPER || type == AUTOLOWER) npair = nvalues*(nvalues+1)/2;
if (type == FULL) npair = nvalues*nvalues;
// print file comment lines
if (fp && me == 0) {
if (title1) fprintf(fp,"%s\n",title1);
else fprintf(fp,"# Time-correlated data for fix %s\n",id);
if (title2) fprintf(fp,"%s\n",title2);
else fprintf(fp,"# Timestep Number-of-time-windows\n");
if (title3) fprintf(fp,"%s\n",title3);
else {
fprintf(fp,"# Index TimeDelta Ncount");
if (type == AUTO)
for (int i = 0; i < nvalues; i++)
fprintf(fp," %s*%s",arg[6+i],arg[6+i]);
else if (type == UPPER)
for (int i = 0; i < nvalues; i++)
for (int j = i+1; j < nvalues; j++)
fprintf(fp," %s*%s",arg[6+i],arg[6+j]);
else if (type == LOWER)
for (int i = 0; i < nvalues; i++)
for (int j = 0; j < i-1; j++)
fprintf(fp," %s*%s",arg[6+i],arg[6+j]);
else if (type == AUTOUPPER)
for (int i = 0; i < nvalues; i++)
for (int j = i; j < nvalues; j++)
fprintf(fp," %s*%s",arg[6+i],arg[6+j]);
else if (type == AUTOLOWER)
for (int i = 0; i < nvalues; i++)
for (int j = 0; j < i; j++)
fprintf(fp," %s*%s",arg[6+i],arg[6+j]);
else if (type == FULL)
for (int i = 0; i < nvalues; i++)
for (int j = 0; j < nvalues; j++)
fprintf(fp," %s*%s",arg[6+i],arg[6+j]);
fprintf(fp,"\n");
}
}
delete [] title1;
delete [] title2;
delete [] title3;
// allocate and initialize memory for averaging
// set count and corr to zero since they accumulate
// also set save versions to zero in case accessed via compute_array()
values = memory->create_2d_double_array(nrepeat,nvalues,
"ave/correlate:values");
count = (int *) memory->smalloc(nrepeat*sizeof(int),
"ave/correlate:count");
save_count = (int *) memory->smalloc(nrepeat*sizeof(int),
"ave/correlate:save_count");
corr = memory->create_2d_double_array(nrepeat,npair,
"ave/correlate:corr");
save_corr = memory->create_2d_double_array(nrepeat,npair,
"ave/correlate:save_corr");
int i,j;
for (i = 0; i < nrepeat; i++) {
save_count[i] = count[i] = 0;
for (j = 0; j < npair; j++)
save_corr[i][j] = corr[i][j] = 0.0;
}
// this fix produces a global array
array_flag = 1;
size_array_rows = nrepeat;
size_array_cols = npair+2;
extarray = 0;
// nvalid = next step on which end_of_step does something
// add nvalid to all computes that store invocation times
// since don't know a priori which are invoked by this fix
// once in end_of_step() can set timestep for ones actually invoked
lastindex = -1;
firstindex = 0;
nsample = 0;
nvalid = nextvalid();
modify->addstep_compute_all(nvalid);
}
/* ---------------------------------------------------------------------- */
FixAveCorrelate::~FixAveCorrelate()
{
delete [] which;
delete [] argindex;
delete [] value2index;
for (int i = 0; i < nvalues; i++) delete [] ids[i];
delete [] ids;
memory->destroy_2d_double_array(values);
memory->sfree(count);
memory->sfree(save_count);
memory->destroy_2d_double_array(corr);
memory->destroy_2d_double_array(save_corr);
if (fp && me == 0) fclose(fp);
}
/* ---------------------------------------------------------------------- */
int FixAveCorrelate::setmask()
{
int mask = 0;
mask |= END_OF_STEP;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixAveCorrelate::init()
{
// set current indices for all computes,fixes,variables
for (int i = 0; i < nvalues; i++) {
if (which[i] == COMPUTE) {
int icompute = modify->find_compute(ids[i]);
if (icompute < 0)
error->all("Compute ID for fix ave/correlate does not exist");
value2index[i] = icompute;
} else if (which[i] == FIX) {
int ifix = modify->find_fix(ids[i]);
if (ifix < 0)
error->all("Fix ID for fix ave/correlate does not exist");
value2index[i] = ifix;
} else if (which[i] == VARIABLE) {
int ivariable = input->variable->find(ids[i]);
if (ivariable < 0)
error->all("Variable name for fix ave/correlate does not exist");
value2index[i] = ivariable;
}
}
// need to reset nvalid if nvalid < ntimestep b/c minimize was performed
if (nvalid < update->ntimestep) {
lastindex = -1;
firstindex = 0;
nsample = 0;
nvalid = nextvalid();
modify->addstep_compute_all(nvalid);
}
}
/* ----------------------------------------------------------------------
only does something if nvalid = current timestep
------------------------------------------------------------------------- */
void FixAveCorrelate::setup(int vflag)
{
end_of_step();
}
/* ---------------------------------------------------------------------- */
void FixAveCorrelate::end_of_step()
{
int i,j,k,m;
double scalar;
// skip if not step which requires doing something
bigint ntimestep = update->ntimestep;
if (ntimestep != nvalid) return;
// accumulate results of computes,fixes,variables to origin
// compute/fix/variable may invoke computes so wrap with clear/add
modify->clearstep_compute();
// lastindex = index in values ring of latest time sample
lastindex++;
if (lastindex == nrepeat) lastindex = 0;
for (i = 0; i < nvalues; i++) {
m = value2index[i];
// invoke compute if not previously invoked
if (which[i] == COMPUTE) {
Compute *compute = modify->compute[m];
if (argindex[i] == 0) {
if (!(compute->invoked_flag & INVOKED_SCALAR)) {
compute->compute_scalar();
compute->invoked_flag |= INVOKED_SCALAR;
}
scalar = compute->scalar;
} else {
if (!(compute->invoked_flag & INVOKED_VECTOR)) {
compute->compute_vector();
compute->invoked_flag |= INVOKED_VECTOR;
}
scalar = compute->vector[argindex[i]-1];
}
// access fix fields, guaranteed to be ready
} else if (which[i] == FIX) {
if (argindex[i] == 0)
scalar = modify->fix[m]->compute_scalar();
else
scalar = modify->fix[m]->compute_vector(argindex[i]-1);
// evaluate equal-style variable
} else if (which[i] == VARIABLE)
scalar = input->variable->compute_equal(m);
values[lastindex][i] = scalar;
}
// fistindex = index in values ring of earliest time sample
// nsample = number of time samples in values ring
if (nsample < nrepeat) nsample++;
else {
firstindex++;
if (firstindex == nrepeat) firstindex = 0;
}
nvalid += nevery;
modify->addstep_compute(nvalid);
// calculate all Cij() enabled by latest values
accumulate();
if (ntimestep % nfreq) return;
// save results in save_count and save_corr
for (i = 0; i < nrepeat; i++) {
save_count[i] = count[i];
if (count[i])
for (j = 0; j < npair; j++)
save_corr[i][j] = prefactor*corr[i][j]/count[i];
else
for (j = 0; j < npair; j++)
save_corr[i][j] = 0.0;
}
// output to file
if (fp && me == 0) {
fprintf(fp,BIGINT_FORMAT " %d\n",ntimestep,nrepeat);
for (i = 0; i < nrepeat; i++) {
fprintf(fp,"%d %d %d",i+1,i*nevery,count[i]);
if (count[i])
for (j = 0; j < npair; j++)
fprintf(fp," %g",prefactor*corr[i][j]/count[i]);
else
for (j = 0; j < npair; j++)
fprintf(fp," 0.0");
fprintf(fp,"\n");
}
fflush(fp);
}
// zero accumulation if requested
// recalculate Cij(0)
if (ave == ONE) {
for (i = 0; i < nrepeat; i++) {
count[i] = 0;
for (j = 0; j < npair; j++)
corr[i][j] = 0.0;
}
nsample = 1;
accumulate();
}
}
/* ----------------------------------------------------------------------
accumulate correlation data using more recently added values
------------------------------------------------------------------------- */
void FixAveCorrelate::accumulate()
{
int i,j,k,m,n,ipair;
for (k = 0; k < nsample; k++) count[k]++;
if (type == AUTO) {
m = n = lastindex;
for (k = 0; k < nsample; k++) {
ipair = 0;
for (i = 0; i < nvalues; i++) {
corr[k][ipair++] += values[m][i]*values[n][i];
}
m--;
if (m < 0) m = nrepeat-1;
}
} else if (type == UPPER) {
m = n = lastindex;
for (k = 0; k < nsample; k++) {
ipair = 0;
for (i = 0; i < nvalues; i++)
for (j = i+1; j < nvalues; j++)
corr[k][ipair++] += values[m][i]*values[n][j];
m--;
if (m < 0) m = nrepeat-1;
}
} else if (type == LOWER) {
m = n = lastindex;
for (k = 0; k < nsample; k++) {
ipair = 0;
for (i = 0; i < nvalues; i++)
for (j = 0; j < i-1; j++)
corr[k][ipair++] += values[m][i]*values[n][j];
m--;
if (m < 0) m = nrepeat-1;
}
} else if (type == AUTOUPPER) {
m = n = lastindex;
for (k = 0; k < nsample; k++) {
ipair = 0;
for (i = 0; i < nvalues; i++)
for (j = i; j < nvalues; j++)
corr[k][ipair++] += values[m][i]*values[n][j];
m--;
if (m < 0) m = nrepeat-1;
}
} else if (type == AUTOLOWER) {
m = n = lastindex;
for (k = 0; k < nsample; k++) {
ipair = 0;
for (i = 0; i < nvalues; i++)
for (j = 0; j < i; j++)
corr[k][ipair++] += values[m][i]*values[n][j];
m--;
if (m < 0) m = nrepeat-1;
}
} else if (type == FULL) {
m = n = lastindex;
for (k = 0; k < nsample; k++) {
ipair = 0;
for (i = 0; i < nvalues; i++)
for (j = 0; j < nvalues; j++)
corr[k][ipair++] += values[m][i]*values[n][j];
m--;
if (m < 0) m = nrepeat-1;
}
}
}
/* ----------------------------------------------------------------------
return I,J array value
------------------------------------------------------------------------- */
double FixAveCorrelate::compute_array(int i, int j)
{
if (j == 0) return 1.0*i*nevery;
else if (j == 1) return 1.0*save_count[i];
else if (save_count[i]) return save_corr[i][j-2];
return 0.0;
}
/* ----------------------------------------------------------------------
nvalid = next step on which end_of_step does something
this step if multiple of nevery, else next multiple
startstep is lower bound
------------------------------------------------------------------------- */
bigint FixAveCorrelate::nextvalid()
{
bigint nvalid = update->ntimestep;
if (startstep > nvalid) nvalid = startstep;
if (nvalid % nevery) nvalid = (nvalid/nevery)*nevery + nevery;
return nvalid;
}
diff --git a/src/fix_ave_correlate.h b/src/fix_ave_correlate.h
index e5dc5046c..ea8a5cb4e 100644
--- a/src/fix_ave_correlate.h
+++ b/src/fix_ave_correlate.h
@@ -1,69 +1,69 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
FixStyle(ave/correlate,FixAveCorrelate)
#else
#ifndef LMP_FIX_AVE_CORRELATE_H
#define LMP_FIX_AVE_CORRELATE_H
+#include "lmptype.h"
#include "stdio.h"
#include "fix.h"
-#include "lmptype.h"
namespace LAMMPS_NS {
class FixAveCorrelate : public Fix {
public:
FixAveCorrelate(class LAMMPS *, int, char **);
~FixAveCorrelate();
int setmask();
void init();
void setup(int);
void end_of_step();
double compute_array(int,int);
private:
int me,nvalues;
int nrepeat,nfreq;
bigint nvalid;
int *which,*argindex,*value2index;
char **ids;
FILE *fp;
int type,ave,startstep;
double prefactor;
char *title1,*title2,*title3;
int firstindex; // index in values ring of earliest time sample
int lastindex; // index in values ring of latest time sample
int nsample; // number of time samples in values ring
int npair; // number of correlation pairs to calculate
int *count;
double **values,**corr;
int *save_count; // saved values at Nfreq for output via compute_array()
double **save_corr;
void accumulate();
bigint nextvalid();
};
}
#endif
#endif
diff --git a/src/fix_ave_histo.cpp b/src/fix_ave_histo.cpp
index c90c5a0fe..b5f94b3e7 100644
--- a/src/fix_ave_histo.cpp
+++ b/src/fix_ave_histo.cpp
@@ -1,1001 +1,1001 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "stdlib.h"
#include "string.h"
#include "fix_ave_histo.h"
-#include "lmptype.h"
#include "atom.h"
#include "update.h"
#include "modify.h"
#include "compute.h"
#include "group.h"
#include "input.h"
#include "variable.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
enum{X,V,F,COMPUTE,FIX,VARIABLE};
enum{ONE,RUNNING};
enum{SCALAR,VECTOR,WINDOW};
enum{GLOBAL,PERATOM,LOCAL};
enum{IGNORE,END,EXTRA};
#define INVOKED_SCALAR 1
#define INVOKED_VECTOR 2
#define INVOKED_ARRAY 4
#define INVOKED_PERATOM 8
#define INVOKED_LOCAL 16
#define BIG 1.0e20
#define MIN(A,B) ((A) < (B)) ? (A) : (B)
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
/* ---------------------------------------------------------------------- */
FixAveHisto::FixAveHisto(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 10) error->all("Illegal fix ave/histo command");
MPI_Comm_rank(world,&me);
nevery = atoi(arg[3]);
nrepeat = atoi(arg[4]);
nfreq = atoi(arg[5]);
global_freq = nfreq;
vector_flag = 1;
size_vector = 4;
extvector = 0;
array_flag = 1;
size_array_cols = 3;
extarray = 0;
time_depend = 1;
lo = atof(arg[6]);
hi = atof(arg[7]);
nbins = atoi(arg[8]);
// scan values to count them
// then read options so know mode = SCALAR/VECTOR before re-reading values
nvalues = 0;
int iarg = 9;
while (iarg < narg) {
if (strcmp(arg[iarg],"x") == 0 ||
strcmp(arg[iarg],"y") == 0 ||
strcmp(arg[iarg],"z") == 0 ||
strcmp(arg[iarg],"vx") == 0 ||
strcmp(arg[iarg],"vy") == 0 ||
strcmp(arg[iarg],"vz") == 0 ||
strcmp(arg[iarg],"fx") == 0 ||
strcmp(arg[iarg],"fy") == 0 ||
strcmp(arg[iarg],"fz") == 0 ||
strncmp(arg[iarg],"c_",2) == 0 ||
strncmp(arg[iarg],"f_",2) == 0 ||
strncmp(arg[iarg],"v_",2) == 0) {
nvalues++;
iarg++;
} else break;
}
options(narg,arg);
// parse values until one isn't recognized
// if mode = VECTOR and value is a global array:
// expand it as if columns listed one by one
// adjust nvalues accordingly via maxvalues
which = argindex = value2index = NULL;
ids = NULL;
int maxvalues = nvalues;
allocate_values(maxvalues);
nvalues = 0;
iarg = 9;
while (iarg < narg) {
if (strcmp(arg[iarg],"x") == 0) {
which[nvalues] = X;
argindex[nvalues] = 0;
ids[nvalues] = NULL;
nvalues++;
iarg++;
} else if (strcmp(arg[iarg],"y") == 0) {
which[nvalues] = X;
argindex[nvalues] = 1;
ids[nvalues] = NULL;
nvalues++;
iarg++;
} else if (strcmp(arg[iarg],"z") == 0) {
which[nvalues] = X;
argindex[nvalues] = 2;
ids[nvalues] = NULL;
nvalues++;
iarg++;
} else if (strcmp(arg[iarg],"vx") == 0) {
which[nvalues] = V;
argindex[nvalues] = 0;
ids[nvalues] = NULL;
nvalues++;
iarg++;
} else if (strcmp(arg[iarg],"vy") == 0) {
which[nvalues] = V;
argindex[nvalues] = 1;
ids[nvalues] = NULL;
nvalues++;
iarg++;
} else if (strcmp(arg[iarg],"vz") == 0) {
which[nvalues] = V;
argindex[nvalues] = 2;
ids[nvalues] = NULL;
nvalues++;
iarg++;
} else if (strcmp(arg[iarg],"fx") == 0) {
which[nvalues] = F;
argindex[nvalues] = 0;
ids[nvalues] = NULL;
nvalues++;
iarg++;
} else if (strcmp(arg[iarg],"fy") == 0) {
which[nvalues] = F;
argindex[nvalues] = 1;
ids[nvalues] = NULL;
nvalues++;
iarg++;
} else if (strcmp(arg[iarg],"fz") == 0) {
which[nvalues] = F;
argindex[nvalues] = 2;
ids[nvalues] = NULL;
nvalues++;
iarg++;
} else if ((strncmp(arg[iarg],"c_",2) == 0) ||
(strncmp(arg[iarg],"f_",2) == 0) ||
(strncmp(arg[iarg],"v_",2) == 0)) {
if (arg[iarg][0] == 'c') which[nvalues] = COMPUTE;
else if (arg[iarg][0] == 'f') which[nvalues] = FIX;
else if (arg[iarg][0] == 'v') which[nvalues] = VARIABLE;
int n = strlen(arg[iarg]);
char *suffix = new char[n];
strcpy(suffix,&arg[iarg][2]);
char *ptr = strchr(suffix,'[');
if (ptr) {
if (suffix[strlen(suffix)-1] != ']')
error->all("Illegal fix ave/histo command");
argindex[nvalues] = atoi(ptr+1);
*ptr = '\0';
} else argindex[nvalues] = 0;
n = strlen(suffix) + 1;
ids[nvalues] = new char[n];
strcpy(ids[nvalues],suffix);
delete [] suffix;
if (mode == VECTOR && which[nvalues] == COMPUTE &&
argindex[nvalues] == 0) {
int icompute = modify->find_compute(ids[nvalues]);
if (icompute < 0)
error->all("Compute ID for fix ave/histo does not exist");
if (modify->compute[icompute]->array_flag) {
int ncols = modify->compute[icompute]->size_array_cols;
maxvalues += ncols-1;
allocate_values(maxvalues);
argindex[nvalues] = 1;
for (int icol = 1; icol < ncols; icol++) {
which[nvalues+icol] = which[nvalues];
argindex[nvalues+icol] = icol+1;
n = strlen(ids[nvalues]) + 1;
ids[nvalues+icol] = new char[n];
strcpy(ids[nvalues+icol],ids[nvalues]);
}
nvalues += ncols-1;
}
} else if (mode == VECTOR && which[nvalues] == FIX &&
argindex[nvalues] == 0) {
int ifix = modify->find_fix(ids[nvalues]);
if (ifix < 0)
error->all("Fix ID for fix ave/histo does not exist");
if (modify->fix[ifix]->array_flag) {
int ncols = modify->fix[ifix]->size_array_cols;
maxvalues += ncols-1;
allocate_values(maxvalues);
argindex[nvalues] = 1;
for (int icol = 1; icol < ncols; icol++) {
which[nvalues+icol] = which[nvalues];
argindex[nvalues+icol] = icol+1;
n = strlen(ids[nvalues]) + 1;
ids[nvalues+icol] = new char[n];
strcpy(ids[nvalues+icol],ids[nvalues]);
}
nvalues += ncols-1;
}
}
nvalues++;
iarg++;
} else break;
}
// setup and error check
// kind = inputs are all global, or all per-atom, or all local
// for fix inputs, check that fix frequency is acceptable
if (nevery <= 0 || nrepeat <= 0 || nfreq <= 0)
error->all("Illegal fix ave/histo command");
if (nfreq % nevery || (nrepeat-1)*nevery >= nfreq)
error->all("Illegal fix ave/histo command");
if (lo >= hi) error->all("Illegal fix ave/histo command");
if (nbins <= 0) error->all("Illegal fix ave/histo command");
int kindflag;
for (int i = 0; i < nvalues; i++) {
if (which[i] == X || which[i] == V || which[i] == F) kindflag = PERATOM;
else if (which[i] == COMPUTE) {
Compute *compute = modify->compute[modify->find_compute(ids[0])];
if (compute->scalar_flag || compute->vector_flag || compute->array_flag)
kindflag = GLOBAL;
else if (compute->peratom_flag) kindflag = PERATOM;
else if (compute->local_flag) kindflag = LOCAL;
else error->all("Fix ave/histo input is invalid compute");
} else if (which[i] == FIX) {
Fix *fix = modify->fix[modify->find_fix(ids[0])];
if (fix->scalar_flag || fix->vector_flag || fix->array_flag)
kindflag = GLOBAL;
else if (fix->peratom_flag) kindflag = PERATOM;
else if (fix->local_flag) kindflag = LOCAL;
else error->all("Fix ave/histo input is invalid fix");
} else if (which[i] == VARIABLE) {
int ivariable = input->variable->find(ids[i]);
if (input->variable->equalstyle(ivariable)) kindflag = GLOBAL;
else if (input->variable->atomstyle(ivariable)) kindflag = PERATOM;
else error->all("Fix ave/histo input is invalid variable");
}
if (i == 0) kind = kindflag;
else if (kindflag != kind)
error->all("Fix ave/histo inputs are not all global, peratom, or local");
}
if (kind == PERATOM && mode == SCALAR)
error->all("Fix ave/histo cannot input per-atom values in scalar mode");
if (kind == LOCAL && mode == SCALAR)
error->all("Fix ave/histo cannot input local values in scalar mode");
for (int i = 0; i < nvalues; i++) {
if (which[i] == COMPUTE && kind == GLOBAL && mode == SCALAR) {
int icompute = modify->find_compute(ids[i]);
if (icompute < 0)
error->all("Compute ID for fix ave/histo does not exist");
if (argindex[i] == 0 && modify->compute[icompute]->scalar_flag == 0)
error->all("Fix ave/histo compute does not calculate a global scalar");
if (argindex[i] && modify->compute[icompute]->vector_flag == 0)
error->all("Fix ave/histo compute does not calculate a global vector");
if (argindex[i] && argindex[i] > modify->compute[icompute]->size_vector)
error->all("Fix ave/histo compute vector is accessed out-of-range");
} else if (which[i] == COMPUTE && kind == GLOBAL && mode == VECTOR) {
int icompute = modify->find_compute(ids[i]);
if (icompute < 0)
error->all("Compute ID for fix ave/histo does not exist");
if (argindex[i] == 0 && modify->compute[icompute]->vector_flag == 0)
error->all("Fix ave/histo compute does not calculate a global vector");
if (argindex[i] && modify->compute[icompute]->array_flag == 0)
error->all("Fix ave/histo compute does not calculate a global array");
if (argindex[i] &&
argindex[i] > modify->compute[icompute]->size_array_cols)
error->all("Fix ave/histo compute array is accessed out-of-range");
} else if (which[i] == COMPUTE && kind == PERATOM) {
int icompute = modify->find_compute(ids[i]);
if (icompute < 0)
error->all("Compute ID for fix ave/histo does not exist");
if (modify->compute[icompute]->peratom_flag == 0)
error->all("Fix ave/histo compute does not calculate per-atom values");
if (argindex[i] == 0 &&
modify->compute[icompute]->size_peratom_cols != 0)
error->all("Fix ave/histo compute does not "
"calculate a per-atom vector");
if (argindex[i] && modify->compute[icompute]->size_peratom_cols == 0)
error->all("Fix ave/histo compute does not "
"calculate a per-atom array");
if (argindex[i] &&
argindex[i] > modify->compute[icompute]->size_peratom_cols)
error->all("Fix ave/histo compute array is accessed out-of-range");
} else if (which[i] == COMPUTE && kind == LOCAL) {
int icompute = modify->find_compute(ids[i]);
if (icompute < 0)
error->all("Compute ID for fix ave/histo does not exist");
if (modify->compute[icompute]->local_flag == 0)
error->all("Fix ave/histo compute does not calculate local values");
if (argindex[i] == 0 &&
modify->compute[icompute]->size_local_cols != 0)
error->all("Fix ave/histo compute does not "
"calculate a local vector");
if (argindex[i] && modify->compute[icompute]->size_local_cols == 0)
error->all("Fix ave/histo compute does not "
"calculate a local array");
if (argindex[i] &&
argindex[i] > modify->compute[icompute]->size_local_cols)
error->all("Fix ave/histo compute array is accessed out-of-range");
} else if (which[i] == FIX && kind == GLOBAL && mode == SCALAR) {
int ifix = modify->find_fix(ids[i]);
if (ifix < 0)
error->all("Fix ID for fix ave/histo does not exist");
if (argindex[i] == 0 && modify->fix[ifix]->scalar_flag == 0)
error->all("Fix ave/histo fix does not calculate a global scalar");
if (argindex[i] && modify->fix[ifix]->vector_flag == 0)
error->all("Fix ave/histo fix does not calculate a global vector");
if (argindex[i] && argindex[i] > modify->fix[ifix]->size_vector)
error->all("Fix ave/histo fix vector is accessed out-of-range");
if (nevery % modify->fix[ifix]->global_freq)
error->all("Fix for fix ave/histo not computed at compatible time");
} else if (which[i] == FIX && kind == GLOBAL && mode == VECTOR) {
int ifix = modify->find_fix(ids[i]);
if (ifix < 0)
error->all("Fix ID for fix ave/histo does not exist");
if (argindex[i] == 0 && modify->fix[ifix]->vector_flag == 0)
error->all("Fix ave/histo fix does not calculate a global vector");
if (argindex[i] && modify->fix[ifix]->array_flag == 0)
error->all("Fix ave/histo fix does not calculate a global array");
if (argindex[i] && argindex[i] > modify->fix[ifix]->size_array_cols)
error->all("Fix ave/histo fix array is accessed out-of-range");
if (nevery % modify->fix[ifix]->global_freq)
error->all("Fix for fix ave/histo not computed at compatible time");
} else if (which[i] == FIX && kind == PERATOM) {
int ifix = modify->find_fix(ids[i]);
if (ifix < 0)
error->all("Fix ID for fix ave/histo does not exist");
if (modify->fix[ifix]->peratom_flag == 0)
error->all("Fix ave/histo fix does not calculate per-atom values");
if (argindex[i] == 0 &&
modify->fix[ifix]->size_peratom_cols != 0)
error->all("Fix ave/histo fix does not "
"calculate a per-atom vector");
if (argindex[i] && modify->fix[ifix]->size_peratom_cols == 0)
error->all("Fix ave/histo fix does not "
"calculate a per-atom array");
if (argindex[i] &&
argindex[i] > modify->fix[ifix]->size_peratom_cols)
error->all("Fix ave/histo fix array is accessed out-of-range");
if (nevery % modify->fix[ifix]->global_freq)
error->all("Fix for fix ave/histo not computed at compatible time");
} else if (which[i] == FIX && kind == LOCAL) {
int ifix = modify->find_fix(ids[i]);
if (ifix < 0)
error->all("Fix ID for fix ave/histo does not exist");
if (modify->fix[ifix]->local_flag == 0)
error->all("Fix ave/histo fix does not calculate local values");
if (argindex[i] == 0 &&
modify->fix[ifix]->size_local_cols != 0)
error->all("Fix ave/histo fix does not "
"calculate a local vector");
if (argindex[i] && modify->fix[ifix]->size_local_cols == 0)
error->all("Fix ave/histo fix does not "
"calculate a local array");
if (argindex[i] &&
argindex[i] > modify->fix[ifix]->size_local_cols)
error->all("Fix ave/histo fix array is accessed out-of-range");
if (nevery % modify->fix[ifix]->global_freq)
error->all("Fix for fix ave/histo not computed at compatible time");
} else if (which[i] == VARIABLE && kind == GLOBAL) {
int ivariable = input->variable->find(ids[i]);
if (ivariable < 0)
error->all("Variable name for fix ave/histo does not exist");
} else if (which[i] == VARIABLE && kind == PERATOM) {
int ivariable = input->variable->find(ids[i]);
if (ivariable < 0)
error->all("Variable name for fix ave/histo does not exist");
}
}
// print file comment lines
if (fp && me == 0) {
if (title1) fprintf(fp,"%s\n",title1);
else fprintf(fp,"# Histogrammed data for fix %s\n",id);
if (title2) fprintf(fp,"%s\n",title2);
else fprintf(fp,"# TimeStep Number-of-bins "
"Total-counts Missing-counts Min-value Max-value\n");
if (title3) fprintf(fp,"%s\n",title3);
else fprintf(fp,"# Bin Coord Count Count/Total\n");
}
delete [] title1;
delete [] title2;
delete [] title3;
// allocate and initialize memory for averaging
if (beyond == EXTRA) nbins += 2;
size_array_rows = nbins;
bin = new double[nbins];
bin_total = new double[nbins];
bin_all = new double[nbins];
coord = new double[nbins];
stats_list = NULL;
bin_list = NULL;
vector = NULL;
maxatom = 0;
if (ave == WINDOW) {
stats_list = memory->create_2d_double_array(nwindow,4,
"ave/histo:stats_list");
bin_list = memory->create_2d_double_array(nwindow,nbins,
"ave/histo:bin_list");
}
// initializations
// set coord to bin centers
if (beyond == EXTRA) {
binsize = (hi-lo)/(nbins-2);
bininv = 1.0/binsize;
} else {
binsize = (hi-lo)/nbins;
bininv = 1.0/binsize;
}
if (beyond == EXTRA) {
coord[0] = lo;
coord[nbins-1] = hi;
for (int i = 1; i < nbins-1; i++)
coord[i] = lo + (i-1+0.5)*binsize;
} else {
for (int i = 0; i < nbins; i++)
coord[i] = lo + (i+0.5)*binsize;
}
irepeat = 0;
iwindow = window_limit = 0;
stats_total[0] = stats_total[1] = stats_total[2] = stats_total[3] = 0.0;
for (int i = 0; i < nbins; i++) bin_total[i] = 0.0;
// nvalid = next step on which end_of_step does something
// add nvalid to all computes that store invocation times
// since don't know a priori which are invoked by this fix
// once in end_of_step() can set timestep for ones actually invoked
nvalid = nextvalid();
modify->addstep_compute_all(nvalid);
}
/* ---------------------------------------------------------------------- */
FixAveHisto::~FixAveHisto()
{
memory->sfree(which);
memory->sfree(argindex);
memory->sfree(value2index);
for (int i = 0; i < nvalues; i++) delete [] ids[i];
memory->sfree(ids);
if (fp && me == 0) fclose(fp);
delete [] bin;
delete [] bin_total;
delete [] bin_all;
delete [] coord;
memory->destroy_2d_double_array(stats_list);
memory->destroy_2d_double_array(bin_list);
memory->sfree(vector);
}
/* ---------------------------------------------------------------------- */
int FixAveHisto::setmask()
{
int mask = 0;
mask |= END_OF_STEP;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixAveHisto::init()
{
// set current indices for all computes,fixes,variables
for (int i = 0; i < nvalues; i++) {
if (which[i] == COMPUTE) {
int icompute = modify->find_compute(ids[i]);
if (icompute < 0)
error->all("Compute ID for fix ave/histo does not exist");
value2index[i] = icompute;
} else if (which[i] == FIX) {
int ifix = modify->find_fix(ids[i]);
if (ifix < 0)
error->all("Fix ID for fix ave/histo does not exist");
value2index[i] = ifix;
} else if (which[i] == VARIABLE) {
int ivariable = input->variable->find(ids[i]);
if (ivariable < 0)
error->all("Variable name for fix ave/histo does not exist");
value2index[i] = ivariable;
}
}
// need to reset nvalid if nvalid < ntimestep b/c minimize was performed
if (nvalid < update->ntimestep) {
irepeat = 0;
nvalid = nextvalid();
modify->addstep_compute_all(nvalid);
}
}
/* ----------------------------------------------------------------------
only does something if nvalid = current timestep
------------------------------------------------------------------------- */
void FixAveHisto::setup(int vflag)
{
end_of_step();
}
/* ---------------------------------------------------------------------- */
void FixAveHisto::end_of_step()
{
int i,j,m;
// skip if not step which requires doing something
bigint ntimestep = update->ntimestep;
if (ntimestep != nvalid) return;
// zero if first step
if (irepeat == 0) {
stats[0] = stats[1] = 0.0;
stats[2] = BIG;
stats[3] = -BIG;
for (i = 0; i < nbins; i++) bin[i] = 0.0;
}
// accumulate results of computes,fixes,variables to local copy
// compute/fix/variable may invoke computes so wrap with clear/add
modify->clearstep_compute();
for (i = 0; i < nvalues; i++) {
m = value2index[i];
j = argindex[i];
// atom attributes
if (which[i] == X)
bin_atoms(&atom->x[0][j],3);
else if (which[i] == V)
bin_atoms(&atom->v[0][j],3);
else if (which[i] == F)
bin_atoms(&atom->f[0][j],3);
// invoke compute if not previously invoked
if (which[i] == COMPUTE) {
Compute *compute = modify->compute[m];
if (kind == GLOBAL && mode == SCALAR) {
if (j == 0) {
if (!(compute->invoked_flag & INVOKED_SCALAR)) {
compute->compute_scalar();
compute->invoked_flag |= INVOKED_SCALAR;
}
bin_one(compute->scalar);
} else {
if (!(compute->invoked_flag & INVOKED_VECTOR)) {
compute->compute_vector();
compute->invoked_flag |= INVOKED_VECTOR;
}
bin_one(compute->vector[j-1]);
}
} else if (kind == GLOBAL && mode == VECTOR) {
if (j == 0) {
if (!(compute->invoked_flag & INVOKED_VECTOR)) {
compute->compute_vector();
compute->invoked_flag |= INVOKED_VECTOR;
}
bin_vector(compute->size_vector,compute->vector,1);
} else {
if (!(compute->invoked_flag & INVOKED_ARRAY)) {
compute->compute_array();
compute->invoked_flag |= INVOKED_ARRAY;
}
bin_vector(compute->size_array_rows,&compute->array[0][j-1],
compute->size_array_cols);
}
} else if (kind == PERATOM) {
if (!(compute->invoked_flag & INVOKED_PERATOM)) {
compute->compute_peratom();
compute->invoked_flag |= INVOKED_PERATOM;
}
if (j == 0)
bin_atoms(compute->vector_atom,1);
else
bin_atoms(compute->array_atom[j-1],
compute->size_peratom_cols);
} else if (kind == LOCAL) {
if (!(compute->invoked_flag & INVOKED_LOCAL)) {
compute->compute_local();
compute->invoked_flag |= INVOKED_LOCAL;
}
if (j == 0)
bin_vector(compute->size_local_rows,compute->vector_local,1);
else
bin_vector(compute->size_local_rows,&compute->array_local[0][j-1],
compute->size_local_cols);
}
// access fix fields, guaranteed to be ready
} else if (which[i] == FIX) {
Fix *fix = modify->fix[m];
if (kind == GLOBAL && mode == SCALAR) {
if (j == 0) bin_one(fix->compute_scalar());
else bin_one(fix->compute_vector(j-1));
} else if (kind == GLOBAL && mode == VECTOR) {
if (j == 0) {
int n = fix->size_vector;
for (i = 0; i < n; i++) bin_one(fix->compute_vector(i));
} else {
int n = fix->size_vector;
for (i = 0; i < n; i++) bin_one(fix->compute_array(i,j-1));
}
} else if (kind == PERATOM) {
if (j == 0) bin_atoms(fix->vector_atom,1);
else bin_atoms(fix->array_atom[j-1],fix->size_peratom_cols);
} else if (kind == LOCAL) {
if (j == 0) bin_vector(fix->size_local_rows,fix->vector_local,1);
else
bin_vector(fix->size_local_rows,&fix->array_local[0][j-1],
fix->size_local_cols);
}
// evaluate equal-style variable
} else if (which[i] == VARIABLE && kind == GLOBAL) {
bin_one(input->variable->compute_equal(m));
} else if (which[i] == VARIABLE && kind == PERATOM) {
if (atom->nlocal > maxatom) {
memory->sfree(vector);
maxatom = atom->nmax;
vector = (double *) memory->smalloc(maxatom*sizeof(double),
"ave/histo:vector");
}
input->variable->compute_atom(m,igroup,vector,1,0);
bin_atoms(vector,1);
}
}
// done if irepeat < nrepeat
// else reset irepeat and nvalid
irepeat++;
if (irepeat < nrepeat) {
nvalid += nevery;
modify->addstep_compute(nvalid);
return;
}
irepeat = 0;
nvalid = ntimestep + nfreq - (nrepeat-1)*nevery;
modify->addstep_compute(nvalid);
// merge histogram stats across procs if necessary
if (kind == PERATOM || kind == LOCAL) {
MPI_Allreduce(stats,stats_all,2,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(&stats[2],&stats_all[2],1,MPI_DOUBLE,MPI_MIN,world);
MPI_Allreduce(&stats[3],&stats_all[3],1,MPI_DOUBLE,MPI_MAX,world);
MPI_Allreduce(bin,bin_all,nbins,MPI_DOUBLE,MPI_SUM,world);
stats[0] = stats_all[0];
stats[1] = stats_all[1];
stats[2] = stats_all[2];
stats[3] = stats_all[3];
for (i = 0; i < nbins; i++) bin[i] = bin_all[i];
}
// if ave = ONE, only single Nfreq timestep value is needed
// if ave = RUNNING, combine with all previous Nfreq timestep values
// if ave = WINDOW, combine with nwindow most recent Nfreq timestep values
if (ntimestep >= startstep) {
if (ave == ONE) {
stats_total[0] = stats[0];
stats_total[1] = stats[1];
stats_total[2] = stats[2];
stats_total[3] = stats[3];
for (i = 0; i < nbins; i++) bin_total[i] = bin[i];
} else if (ave == RUNNING) {
stats_total[0] += stats[0];
stats_total[1] += stats[1];
stats_total[2] = MIN(stats_total[2],stats[2]);
stats_total[3] = MAX(stats_total[3],stats[3]);
for (i = 0; i < nbins; i++) bin_total[i] += bin[i];
} else if (ave == WINDOW) {
stats_total[0] += stats[0];
if (window_limit) stats_total[0] -= stats_list[iwindow][0];
stats_list[iwindow][0] = stats[0];
stats_total[1] += stats[1];
if (window_limit) stats_total[1] -= stats_list[iwindow][1];
stats_list[iwindow][1] = stats[1];
if (window_limit) m = nwindow;
else m = iwindow+1;
stats_list[iwindow][2] = stats[2];
stats_total[2] = stats_list[0][2];
for (i = 1; i < m; i++)
stats_total[2] = MIN(stats_total[2],stats_list[i][2]);
stats_list[iwindow][3] = stats[3];
stats_total[3] = stats_list[0][3];
for (i = 1; i < m; i++)
stats_total[3] = MAX(stats_total[3],stats_list[i][3]);
for (i = 0; i < nbins; i++) {
bin_total[i] += bin[i];
if (window_limit) bin_total[i] -= bin_list[iwindow][i];
bin_list[iwindow][i] = bin[i];
}
iwindow++;
if (iwindow == nwindow) {
iwindow = 0;
window_limit = 1;
}
}
}
// output result to file
if (fp && me == 0) {
fprintf(fp,BIGINT_FORMAT " %d %g %g %g %g\n",ntimestep,nbins,
stats_total[0],stats_total[1],stats_total[2],stats_total[3]);
if (stats_total[0] != 0.0)
for (i = 0; i < nbins; i++)
fprintf(fp,"%d %g %g %g\n",
i+1,coord[i],bin_total[i],bin_total[i]/stats_total[0]);
else
for (i = 0; i < nbins; i++)
fprintf(fp,"%d %g %g %g\n",i+1,coord[i],0.0,0.0);
fflush(fp);
}
}
/* ----------------------------------------------------------------------
return Ith vector value
------------------------------------------------------------------------- */
double FixAveHisto::compute_vector(int i)
{
return stats_total[i];
}
/* ----------------------------------------------------------------------
return I,J array value
------------------------------------------------------------------------- */
double FixAveHisto::compute_array(int i, int j)
{
if (j == 0) return coord[i];
else if (j == 1) return bin_total[i];
else if (stats_total[0] != 0.0) return bin_total[i]/stats_total[0];
return 0.0;
}
/* ----------------------------------------------------------------------
bin a single value
------------------------------------------------------------------------- */
void FixAveHisto::bin_one(double value)
{
stats[2] = MIN(stats[2],value);
stats[3] = MAX(stats[3],value);
if (value < lo) {
if (beyond == IGNORE) {
stats[1] += 1.0;
return;
} else bin[0] += 1.0;
} else if (value > hi) {
if (beyond == IGNORE) {
stats[1] += 1.0;
return;
} else bin[nbins-1] += 1.0;
} else {
int ibin = static_cast<int> ((value-lo)*bininv);
ibin = MIN(ibin,nbins-1);
if (beyond == EXTRA) ibin++;
bin[ibin] += 1.0;
}
stats[0] += 1.0;
}
/* ----------------------------------------------------------------------
bin a vector of values with stride
------------------------------------------------------------------------- */
void FixAveHisto::bin_vector(int n, double *values, int stride)
{
int m = 0;
for (int i = 0; i < n; i++) {
bin_one(values[m]);
m += stride;
}
}
/* ----------------------------------------------------------------------
bin a per-atom vector of values with stride
only bin if atom is in group
------------------------------------------------------------------------- */
void FixAveHisto::bin_atoms(double *values, int stride)
{
int *mask = atom->mask;
int nlocal = atom->nlocal;
int m = 0;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) bin_one(values[m]);
m += stride;
}
}
/* ----------------------------------------------------------------------
parse optional args
------------------------------------------------------------------------- */
void FixAveHisto::options(int narg, char **arg)
{
// option defaults
fp = NULL;
ave = ONE;
startstep = 0;
mode = SCALAR;
beyond = IGNORE;
title1 = NULL;
title2 = NULL;
title3 = NULL;
// optional args
int iarg = 9 + nvalues;
while (iarg < narg) {
if (strcmp(arg[iarg],"file") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/histo command");
if (me == 0) {
fp = fopen(arg[iarg+1],"w");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open fix ave/histo file %s",arg[iarg+1]);
error->one(str);
}
}
iarg += 2;
} else if (strcmp(arg[iarg],"ave") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/histo command");
if (strcmp(arg[iarg+1],"one") == 0) ave = ONE;
else if (strcmp(arg[iarg+1],"running") == 0) ave = RUNNING;
else if (strcmp(arg[iarg+1],"window") == 0) ave = WINDOW;
else error->all("Illegal fix ave/histo command");
if (ave == WINDOW) {
if (iarg+3 > narg) error->all("Illegal fix ave/histo command");
nwindow = atoi(arg[iarg+2]);
if (nwindow <= 0) error->all("Illegal fix ave/histo command");
}
iarg += 2;
if (ave == WINDOW) iarg++;
} else if (strcmp(arg[iarg],"start") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/histo command");
startstep = atoi(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"mode") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/histo command");
if (strcmp(arg[iarg+1],"scalar") == 0) mode = SCALAR;
else if (strcmp(arg[iarg+1],"vector") == 0) mode = VECTOR;
else error->all("Illegal fix ave/histo command");
iarg += 2;
} else if (strcmp(arg[iarg],"beyond") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/histo command");
if (strcmp(arg[iarg+1],"ignore") == 0) beyond = IGNORE;
else if (strcmp(arg[iarg+1],"end") == 0) beyond = END;
else if (strcmp(arg[iarg+1],"extra") == 0) beyond = EXTRA;
else error->all("Illegal fix ave/histo command");
iarg += 2;
} else if (strcmp(arg[iarg],"title1") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/spatial command");
delete [] title1;
int n = strlen(arg[iarg+1]) + 1;
title1 = new char[n];
strcpy(title1,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"title2") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/spatial command");
delete [] title2;
int n = strlen(arg[iarg+1]) + 1;
title2 = new char[n];
strcpy(title2,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"title3") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/spatial command");
delete [] title3;
int n = strlen(arg[iarg+1]) + 1;
title3 = new char[n];
strcpy(title3,arg[iarg+1]);
iarg += 2;
} else error->all("Illegal fix ave/histo command");
}
}
/* ----------------------------------------------------------------------
reallocate vectors for each input value, of length N
------------------------------------------------------------------------- */
void FixAveHisto::allocate_values(int n)
{
which = (int *) memory->srealloc(which,n*sizeof(int),"ave/time:which");
argindex = (int *) memory->srealloc(argindex,n*sizeof(int),
"ave/time:argindex");
value2index = (int *) memory->srealloc(value2index,n*sizeof(int),
"ave/time:value2index");
ids = (char **) memory->srealloc(ids,n*sizeof(char *),"ave/time:ids");
}
/* ----------------------------------------------------------------------
calculate nvalid = next step on which end_of_step does something
can be this timestep if multiple of nfreq and nrepeat = 1
else backup from next multiple of nfreq
------------------------------------------------------------------------- */
bigint FixAveHisto::nextvalid()
{
bigint nvalid = (update->ntimestep/nfreq)*nfreq + nfreq;
if (nvalid-nfreq == update->ntimestep && nrepeat == 1)
nvalid = update->ntimestep;
else
nvalid -= (nrepeat-1)*nevery;
if (nvalid < update->ntimestep) nvalid += nfreq;
return nvalid;
}
diff --git a/src/fix_ave_histo.h b/src/fix_ave_histo.h
index 7dc63220b..c2c870223 100644
--- a/src/fix_ave_histo.h
+++ b/src/fix_ave_histo.h
@@ -1,76 +1,76 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
FixStyle(ave/histo,FixAveHisto)
#else
#ifndef LMP_FIX_AVE_HISTO_H
#define LMP_FIX_AVE_HISTO_H
+#include "lmptype.h"
#include "stdio.h"
#include "fix.h"
-#include "lmptype.h"
namespace LAMMPS_NS {
class FixAveHisto : public Fix {
public:
FixAveHisto(class LAMMPS *, int, char **);
~FixAveHisto();
int setmask();
void init();
void setup(int);
void end_of_step();
double compute_vector(int);
double compute_array(int,int);
private:
int me,nvalues;
int nrepeat,nfreq,irepeat;
bigint nvalid;
int *which,*argindex,*value2index;
char **ids;
FILE *fp;
double lo,hi,binsize,bininv;
int kind,beyond;
double stats[4],stats_total[4],stats_all[4];
double **stats_list;
int nbins;
double *bin,*bin_total,*bin_all;
double **bin_list;
double *coord;
double *vector;
int maxatom;
int ave,nwindow,nsum,startstep,mode;
char *title1,*title2,*title3;
int iwindow,window_limit;
void bin_one(double);
void bin_vector(int, double *, int);
void bin_atoms(double *, int);
void options(int, char **);
void allocate_values(int);
bigint nextvalid();
};
}
#endif
#endif
diff --git a/src/fix_ave_spatial.cpp b/src/fix_ave_spatial.cpp
index 511e429fa..734425b3a 100644
--- a/src/fix_ave_spatial.cpp
+++ b/src/fix_ave_spatial.cpp
@@ -1,1297 +1,1297 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Pieter in 't Veld (SNL)
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "stdlib.h"
#include "string.h"
#include "fix_ave_spatial.h"
-#include "lmptype.h"
#include "atom.h"
#include "update.h"
#include "force.h"
#include "domain.h"
#include "region.h"
#include "lattice.h"
#include "modify.h"
#include "compute.h"
#include "input.h"
#include "variable.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
enum{LOWER,CENTER,UPPER,COORD};
enum{V,F,DENSITY_NUMBER,DENSITY_MASS,COMPUTE,FIX,VARIABLE};
enum{SAMPLE,ALL};
enum{BOX,LATTICE,REDUCED};
enum{ONE,RUNNING,WINDOW};
#define INVOKED_PERATOM 8
#define BIG 1000000000
#define MIN(A,B) ((A) < (B)) ? (A) : (B)
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
/* ---------------------------------------------------------------------- */
FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 6) error->all("Illegal fix ave/spatial command");
MPI_Comm_rank(world,&me);
nevery = atoi(arg[3]);
nrepeat = atoi(arg[4]);
nfreq = atoi(arg[5]);
global_freq = nfreq;
no_change_box = 1;
time_depend = 1;
ndim = 0;
int iarg = 6;
while (iarg < narg && ndim < 3) {
if (iarg+3 > narg) break;
if (strcmp(arg[iarg],"x") == 0) dim[ndim] = 0;
else if (strcmp(arg[iarg],"y") == 0) dim[ndim] = 1;
else if (strcmp(arg[iarg],"z") == 0) dim[ndim] = 2;
else break;
if (dim[ndim] == 2 && domain->dimension == 2)
error->all("Cannot use fix ave/spatial z for 2 dimensional model");
if (strcmp(arg[iarg+1],"lower") == 0) originflag[ndim] = LOWER;
if (strcmp(arg[iarg+1],"center") == 0) originflag[ndim] = CENTER;
if (strcmp(arg[iarg+1],"upper") == 0) originflag[ndim] = UPPER;
else originflag[ndim] = COORD;
if (originflag[ndim] == COORD) origin[ndim] = atof(arg[iarg+1]);
delta[ndim] = atof(arg[iarg+2]);
ndim++;
iarg += 3;
}
if (!ndim) error->all("Illegal fix ave/spatial command");
if (ndim == 2 && dim[0] == dim[1])
error->all("Same dimension twice in fix ave/spatial");
if (ndim == 3 && (dim[0] == dim[1] || dim[1] == dim[2] || dim[0] == dim[2]))
error->all("Same dimension twice in fix ave/spatial");
// parse values until one isn't recognized
which = new int[narg-9];
argindex = new int[narg-9];
ids = new char*[narg-9];
value2index = new int[narg-9];
nvalues = 0;
while (iarg < narg) {
ids[nvalues] = NULL;
if (strcmp(arg[iarg],"vx") == 0) {
which[nvalues] = V;
argindex[nvalues++] = 0;
} else if (strcmp(arg[iarg],"vy") == 0) {
which[nvalues] = V;
argindex[nvalues++] = 1;
} else if (strcmp(arg[iarg],"vz") == 0) {
which[nvalues] = V;
argindex[nvalues++] = 2;
} else if (strcmp(arg[iarg],"fx") == 0) {
which[nvalues] = F;
argindex[nvalues++] = 0;
} else if (strcmp(arg[iarg],"fy") == 0) {
which[nvalues] = F;
argindex[nvalues++] = 1;
} else if (strcmp(arg[iarg],"fz") == 0) {
which[nvalues] = F;
argindex[nvalues++] = 2;
} else if (strcmp(arg[iarg],"density/number") == 0) {
which[nvalues] = DENSITY_NUMBER;
argindex[nvalues++] = 0;
} else if (strcmp(arg[iarg],"density/mass") == 0) {
which[nvalues] = DENSITY_MASS;
argindex[nvalues++] = 0;
} else if (strncmp(arg[iarg],"c_",2) == 0 ||
strncmp(arg[iarg],"f_",2) == 0 ||
strncmp(arg[iarg],"v_",2) == 0) {
if (arg[iarg][0] == 'c') which[nvalues] = COMPUTE;
else if (arg[iarg][0] == 'f') which[nvalues] = FIX;
else if (arg[iarg][0] == 'v') which[nvalues] = VARIABLE;
int n = strlen(arg[iarg]);
char *suffix = new char[n];
strcpy(suffix,&arg[iarg][2]);
char *ptr = strchr(suffix,'[');
if (ptr) {
if (suffix[strlen(suffix)-1] != ']')
error->all("Illegal fix ave/spatial command");
argindex[nvalues] = atoi(ptr+1);
*ptr = '\0';
} else argindex[nvalues] = 0;
n = strlen(suffix) + 1;
ids[nvalues] = new char[n];
strcpy(ids[nvalues],suffix);
nvalues++;
delete [] suffix;
} else break;
iarg++;
}
// optional args
normflag = ALL;
scaleflag = LATTICE;
regionflag = 0;
idregion = NULL;
fp = NULL;
ave = ONE;
char *title1 = NULL;
char *title2 = NULL;
char *title3 = NULL;
while (iarg < narg) {
if (strcmp(arg[iarg],"norm") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/spatial command");
if (strcmp(arg[iarg+1],"all") == 0) normflag = ALL;
else if (strcmp(arg[iarg+1],"sample") == 0) normflag = SAMPLE;
else error->all("Illegal fix ave/spatial command");
iarg += 2;
} else if (strcmp(arg[iarg],"units") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/spatial command");
if (strcmp(arg[iarg+1],"box") == 0) scaleflag = BOX;
else if (strcmp(arg[iarg+1],"lattice") == 0) scaleflag = LATTICE;
else if (strcmp(arg[iarg+1],"reduced") == 0) scaleflag = REDUCED;
else error->all("Illegal fix ave/spatial command");
iarg += 2;
} else if (strcmp(arg[iarg],"region") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/spatial command");
iregion = domain->find_region(arg[iarg+1]);
if (iregion == -1)
error->all("Region ID for fix ave/spatial does not exist");
int n = strlen(arg[iarg+1]) + 1;
idregion = new char[n];
strcpy(idregion,arg[iarg+1]);
regionflag = 1;
iarg += 2;
} else if (strcmp(arg[iarg],"file") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/spatial command");
if (me == 0) {
fp = fopen(arg[iarg+1],"w");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open fix ave/spatial file %s",arg[iarg+1]);
error->one(str);
}
}
iarg += 2;
} else if (strcmp(arg[iarg],"ave") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/spatial command");
if (strcmp(arg[iarg+1],"one") == 0) ave = ONE;
else if (strcmp(arg[iarg+1],"running") == 0) ave = RUNNING;
else if (strcmp(arg[iarg+1],"window") == 0) ave = WINDOW;
else error->all("Illegal fix ave/spatial command");
if (ave == WINDOW) {
if (iarg+3 > narg) error->all("Illegal fix ave/spatial command");
nwindow = atoi(arg[iarg+2]);
if (nwindow <= 0) error->all("Illegal fix ave/spatial command");
}
iarg += 2;
if (ave == WINDOW) iarg++;
} else if (strcmp(arg[iarg],"title1") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/spatial command");
delete [] title1;
int n = strlen(arg[iarg+1]) + 1;
title1 = new char[n];
strcpy(title1,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"title2") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/spatial command");
delete [] title2;
int n = strlen(arg[iarg+1]) + 1;
title2 = new char[n];
strcpy(title2,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"title3") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/spatial command");
delete [] title3;
int n = strlen(arg[iarg+1]) + 1;
title3 = new char[n];
strcpy(title3,arg[iarg+1]);
iarg += 2;
} else error->all("Illegal fix ave/spatial command");
}
// setup and error check
if (nevery <= 0 || nrepeat <= 0 || nfreq <= 0)
error->all("Illegal fix ave/spatial command");
if (nfreq % nevery || (nrepeat-1)*nevery >= nfreq)
error->all("Illegal fix ave/spatial command");
if (delta[0] <= 0.0) error->all("Illegal fix ave/spatial command");
if (ndim >= 2 && delta[1] <= 0.0)
error->all("Illegal fix ave/spatial command");
if (ndim == 3 && delta[2] <= 0.0)
error->all("Illegal fix ave/spatial command");
for (int i = 0; i < nvalues; i++) {
if (which[i] == COMPUTE) {
int icompute = modify->find_compute(ids[i]);
if (icompute < 0)
error->all("Compute ID for fix ave/spatial does not exist");
if (modify->compute[icompute]->peratom_flag == 0)
error->all("Fix ave/spatial compute does not "
"calculate per-atom values");
if (argindex[i] == 0 &&
modify->compute[icompute]->size_peratom_cols != 0)
error->all("Fix ave/spatial compute does not "
"calculate a per-atom vector");
if (argindex[i] && modify->compute[icompute]->size_peratom_cols == 0)
error->all("Fix ave/spatial compute does not "
"calculate a per-atom array");
if (argindex[i] &&
argindex[i] > modify->compute[icompute]->size_peratom_cols)
error->all("Fix ave/spatial compute vector is accessed out-of-range");
} else if (which[i] == FIX) {
int ifix = modify->find_fix(ids[i]);
if (ifix < 0)
error->all("Fix ID for fix ave/spatial does not exist");
if (modify->fix[ifix]->peratom_flag == 0)
error->all("Fix ave/spatial fix does not calculate per-atom values");
if (argindex[i] && modify->fix[ifix]->size_peratom_cols != 0)
error->all("Fix ave/spatial fix does not calculate a per-atom vector");
if (argindex[i] && modify->fix[ifix]->size_peratom_cols == 0)
error->all("Fix ave/spatial fix does not calculate a per-atom array");
if (argindex[i] && argindex[i] > modify->fix[ifix]->size_peratom_cols)
error->all("Fix ave/spatial fix vector is accessed out-of-range");
} else if (which[i] == VARIABLE) {
int ivariable = input->variable->find(ids[i]);
if (ivariable < 0)
error->all("Variable name for fix ave/spatial does not exist");
if (input->variable->atomstyle(ivariable) == 0)
error->all("Fix ave/spatial variable is not atom-style variable");
}
}
// print file comment lines
if (fp && me == 0) {
if (title1) fprintf(fp,"%s\n",title1);
else fprintf(fp,"# Spatial-averaged data for fix %s and group %s\n",
id,arg[1]);
if (title2) fprintf(fp,"%s\n",title2);
else fprintf(fp,"# Timestep Number-of-bins\n");
if (title3) fprintf(fp,"%s\n",title3);
else {
if (ndim == 1) fprintf(fp,"# Bin Coord Ncount");
else if (ndim == 2) fprintf(fp,"# Bin Coord1 Coord2 Ncount");
else if (ndim == 3) fprintf(fp,"# Bin Coord1 Coord2 Coord3 Ncount");
for (int i = 0; i < nvalues; i++) fprintf(fp," %s",arg[9+i]);
fprintf(fp,"\n");
}
}
delete [] title1;
delete [] title2;
delete [] title3;
// this fix produces a global array
array_flag = 1;
size_local_rows = BIG;
size_local_cols = 1 + ndim + nvalues;
extarray = 0;
// setup scaling
int triclinic = domain->triclinic;
if (triclinic == 1 && scaleflag != REDUCED)
error->all("Fix ave/spatial for triclinic boxes requires units reduced");
if (scaleflag == LATTICE && domain->lattice == NULL)
error->all("Use of fix ave/spatial with undefined lattice");
if (scaleflag == LATTICE) {
xscale = domain->lattice->xlattice;
yscale = domain->lattice->ylattice;
zscale = domain->lattice->zlattice;
}
else xscale = yscale = zscale = 1.0;
// apply scaling factors
double scale;
for (int idim = 0; idim < ndim; idim++) {
if (dim[idim] == 0) scale = xscale;
else if (dim[idim] == 1) scale = yscale;
else if (dim[idim] == 2) scale = zscale;
delta[idim] *= scale;
if (originflag[idim] == COORD) origin[idim] *= scale;
invdelta[idim] = 1.0/delta[idim];
}
// initializations
irepeat = 0;
iwindow = window_limit = 0;
norm = 0;
maxvar = 0;
varatom = NULL;
maxatom = 0;
bin = NULL;
nbins = maxbin = 0;
count_one = count_many = count_sum = count_total = NULL;
coord = NULL;
count_list = NULL;
values_one = values_many = values_sum = values_total = NULL;
values_list = NULL;
// nvalid = next step on which end_of_step does something
// add nvalid to all computes that store invocation times
// since don't know a priori which are invoked by this fix
// once in end_of_step() can set timestep for ones actually invoked
nvalid = nextvalid();
modify->addstep_compute_all(nvalid);
}
/* ---------------------------------------------------------------------- */
FixAveSpatial::~FixAveSpatial()
{
delete [] which;
delete [] argindex;
for (int i = 0; i < nvalues; i++) delete [] ids[i];
delete [] ids;
delete [] value2index;
delete [] idregion;
if (fp && me == 0) fclose(fp);
memory->sfree(varatom);
memory->sfree(bin);
memory->sfree(count_one);
memory->sfree(count_many);
memory->sfree(count_sum);
memory->sfree(count_total);
memory->destroy_2d_double_array(coord);
memory->destroy_2d_double_array(count_list);
memory->destroy_2d_double_array(values_one);
memory->destroy_2d_double_array(values_many);
memory->destroy_2d_double_array(values_sum);
memory->destroy_2d_double_array(values_total);
memory->destroy_3d_double_array(values_list);
}
/* ---------------------------------------------------------------------- */
int FixAveSpatial::setmask()
{
int mask = 0;
mask |= END_OF_STEP;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixAveSpatial::init()
{
// set and check validity of region
if (regionflag) {
iregion = domain->find_region(idregion);
if (iregion == -1)
error->all("Region ID for fix ave/spatial does not exist");
region = domain->regions[iregion];
}
// # of bins cannot vary for ave = RUNNING or WINDOW
if (ave == RUNNING || ave == WINDOW) {
if (scaleflag != REDUCED && domain->box_change)
error->all("Fix ave/spatial settings invalid with changing box");
}
// set indices and check validity of all computes,fixes,variables
// check that fix frequency is acceptable
for (int m = 0; m < nvalues; m++) {
if (which[m] == COMPUTE) {
int icompute = modify->find_compute(ids[m]);
if (icompute < 0)
error->all("Compute ID for fix ave/spatial does not exist");
value2index[m] = icompute;
} else if (which[m] == FIX) {
int ifix = modify->find_fix(ids[m]);
if (ifix < 0)
error->all("Fix ID for fix ave/spatial does not exist");
value2index[m] = ifix;
if (nevery % modify->fix[ifix]->peratom_freq)
error->all("Fix for fix ave/spatial not computed at compatible time");
} else if (which[m] == VARIABLE) {
int ivariable = input->variable->find(ids[m]);
if (ivariable < 0)
error->all("Variable name for fix ave/spatial does not exist");
value2index[m] = ivariable;
} else value2index[m] = -1;
}
// need to reset nvalid if nvalid < ntimestep b/c minimize was performed
if (nvalid < update->ntimestep) {
irepeat = 0;
nvalid = nextvalid();
modify->addstep_compute_all(nvalid);
}
}
/* ----------------------------------------------------------------------
setup initial bins
only does averaging if nvalid = current timestep
------------------------------------------------------------------------- */
void FixAveSpatial::setup(int vflag)
{
setup_bins();
end_of_step();
}
/* ---------------------------------------------------------------------- */
void FixAveSpatial::end_of_step()
{
int i,j,m,n;
// skip if not step which requires doing something
bigint ntimestep = update->ntimestep;
if (ntimestep != nvalid) return;
// zero out arrays that accumulate over many samples
// if box changes, first re-setup bins
if (irepeat == 0) {
if (domain->box_change) setup_bins();
for (m = 0; m < nbins; m++) {
count_many[m] = count_sum[m] = 0.0;
for (i = 0; i < nvalues; i++) values_many[m][i] = 0.0;
}
}
// zero out arrays for one sample
for (m = 0; m < nbins; m++) {
count_one[m] = 0.0;
for (i = 0; i < nvalues; i++) values_one[m][i] = 0.0;
}
// assign each atom to a bin
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (nlocal > maxatom) {
maxatom = atom->nmax;
memory->sfree(bin);
bin = (int *)
memory->smalloc(maxatom*sizeof(int),"ave/spatial:bin");
}
if (ndim == 1) atom2bin1d();
else if (ndim == 2) atom2bin2d();
else atom2bin3d();
// perform the computation for one sample
// accumulate results of attributes,computes,fixes,variables to local copy
// sum within each bin, only include atoms in fix group
// compute/fix/variable may invoke computes so wrap with clear/add
modify->clearstep_compute();
for (m = 0; m < nvalues; m++) {
n = value2index[m];
j = argindex[m];
// V,F adds velocities,forces to values
if (which[m] == V || which[m] == F) {
double **attribute;
if (which[m] == V) attribute = atom->v;
else attribute = atom->f;
if (regionflag == 0) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
values_one[bin[i]][m] += attribute[i][j];
} else {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]))
values_one[bin[i]][m] += attribute[i][j];
}
// DENSITY_NUMBER adds 1 to values
} else if (which[m] == DENSITY_NUMBER) {
if (regionflag == 0) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
values_one[bin[i]][m] += 1.0;
} else {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]))
values_one[bin[i]][m] += 1.0;
}
// DENSITY_MASS adds mass to values
} else if (which[m] == DENSITY_MASS) {
int *type = atom->type;
double *mass = atom->mass;
double *rmass = atom->rmass;
if (regionflag == 0) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (rmass) values_one[bin[i]][m] += rmass[i];
else values_one[bin[i]][m] += mass[type[i]];
}
} else {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
if (rmass) values_one[bin[i]][m] += rmass[i];
else values_one[bin[i]][m] += mass[type[i]];
}
}
// COMPUTE adds its scalar or vector component to values
// invoke compute if not previously invoked
} else if (which[m] == COMPUTE) {
Compute *compute = modify->compute[n];
if (!(compute->invoked_flag & INVOKED_PERATOM)) {
compute->compute_peratom();
compute->invoked_flag |= INVOKED_PERATOM;
}
double *vector = compute->vector_atom;
double **array = compute->array_atom;
int jm1 = j - 1;
if (regionflag == 0) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (j == 0) values_one[bin[i]][m] += vector[i];
else values_one[bin[i]][m] += array[i][jm1];
}
} else {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
if (j == 0) values_one[bin[i]][m] += vector[i];
else values_one[bin[i]][m] += array[i][jm1];
}
}
// FIX adds its scalar or vector component to values
// access fix fields, guaranteed to be ready
} else if (which[m] == FIX) {
double *vector = modify->fix[n]->vector_atom;
double **array = modify->fix[n]->array_atom;
int jm1 = j - 1;
if (regionflag == 0) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (j == 0) values_one[bin[i]][m] += vector[i];
else values_one[bin[i]][m] += array[i][jm1];
}
} else {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
if (j == 0) values_one[bin[i]][m] += vector[i];
else values_one[bin[i]][m] += array[i][jm1];
}
}
// VARIABLE adds its per-atom quantities to values
// evaluate atom-style variable
} else if (which[m] == VARIABLE) {
if (nlocal > maxvar) {
maxvar = atom->nmax;
memory->sfree(varatom);
varatom = (double *)
memory->smalloc(maxvar*sizeof(double),"ave/spatial:varatom");
}
input->variable->compute_atom(n,igroup,varatom,1,0);
if (regionflag == 0) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
values_one[bin[i]][m] += varatom[i];
} else {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]))
values_one[bin[i]][m] += varatom[i];
}
}
}
// process a single sample
// if normflag = ALL, accumulate values,count separately to many
// if normflag = SAMPLE, one = value/count, accumulate one to many
// exception is SAMPLE density: no normalization by atom count
if (normflag == ALL) {
for (m = 0; m < nbins; m++) {
count_many[m] += count_one[m];
for (j = 0; j < nvalues; j++)
values_many[m][j] += values_one[m][j];
}
} else {
MPI_Allreduce(count_one,count_many,nbins,MPI_DOUBLE,MPI_SUM,world);
for (m = 0; m < nbins; m++) {
if (count_many[m] > 0.0)
for (j = 0; j < nvalues; j++) {
if (which[j] == DENSITY_NUMBER || which[j] == DENSITY_MASS)
values_many[m][j] += values_one[m][j];
else values_many[m][j] += values_one[m][j]/count_many[m];
}
count_sum[m] += count_many[m];
}
}
// done if irepeat < nrepeat
// else reset irepeat and nvalid
irepeat++;
if (irepeat < nrepeat) {
nvalid += nevery;
modify->addstep_compute(nvalid);
return;
}
irepeat = 0;
nvalid = ntimestep+nfreq - (nrepeat-1)*nevery;
modify->addstep_compute(nvalid);
// time average across samples
// if normflag = ALL, final is total value / total count
// if normflag = SAMPLE, final is sum of ave / repeat
// exception is densities: normalized by repeat, not total count
double repeat = nrepeat;
double mv2d = force->mv2d;
if (normflag == ALL) {
MPI_Allreduce(count_many,count_sum,nbins,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(&values_many[0][0],&values_sum[0][0],nbins*nvalues,
MPI_DOUBLE,MPI_SUM,world);
for (m = 0; m < nbins; m++) {
if (count_sum[m] > 0.0)
for (j = 0; j < nvalues; j++)
if (which[j] == DENSITY_NUMBER) values_sum[m][j] /= repeat;
else if (which[j] == DENSITY_MASS) values_sum[m][j] *= mv2d/repeat;
else values_sum[m][j] /= count_sum[m];
count_sum[m] /= repeat;
}
} else {
MPI_Allreduce(&values_many[0][0],&values_sum[0][0],nbins*nvalues,
MPI_DOUBLE,MPI_SUM,world);
for (m = 0; m < nbins; m++) {
for (j = 0; j < nvalues; j++)
values_sum[m][j] /= repeat;
count_sum[m] /= repeat;
}
}
// density is additionally normalized by bin volume
for (j = 0; j < nvalues; j++)
if (which[j] == DENSITY_NUMBER || which[j] == DENSITY_MASS)
for (m = 0; m < nbins; m++)
values_sum[m][j] /= bin_volume;
// if ave = ONE, only single Nfreq timestep value is needed
// if ave = RUNNING, combine with all previous Nfreq timestep values
// if ave = WINDOW, comine with nwindow most recent Nfreq timestep values
if (ave == ONE) {
for (m = 0; m < nbins; m++) {
for (i = 0; i < nvalues; i++)
values_total[m][i] = values_sum[m][i];
count_total[m] = count_sum[m];
}
norm = 1;
} else if (ave == RUNNING) {
for (m = 0; m < nbins; m++) {
for (i = 0; i < nvalues; i++)
values_total[m][i] += values_sum[m][i];
count_total[m] += count_sum[m];
}
norm++;
} else if (ave == WINDOW) {
for (m = 0; m < nbins; m++) {
for (i = 0; i < nvalues; i++) {
values_total[m][i] += values_sum[m][i];
if (window_limit) values_total[m][i] -= values_list[iwindow][m][i];
values_list[iwindow][m][i] = values_sum[m][i];
}
count_total[m] += count_sum[m];
if (window_limit) count_total[m] -= count_list[iwindow][m];
count_list[iwindow][m] = count_sum[m];
}
iwindow++;
if (iwindow == nwindow) {
iwindow = 0;
window_limit = 1;
}
if (window_limit) norm = nwindow;
else norm = iwindow;
}
// output result to file
if (fp && me == 0) {
fprintf(fp,BIGINT_FORMAT " %d\n",ntimestep,nbins);
if (ndim == 1)
for (m = 0; m < nbins; m++) {
fprintf(fp," %d %g %g",m+1,coord[m][0],
count_total[m]/norm);
for (i = 0; i < nvalues; i++)
fprintf(fp," %g",values_total[m][i]/norm);
fprintf(fp,"\n");
}
else if (ndim == 2)
for (m = 0; m < nbins; m++) {
fprintf(fp," %d %g %g %g",m+1,coord[m][0],coord[m][1],
count_total[m]/norm);
for (i = 0; i < nvalues; i++)
fprintf(fp," %g",values_total[m][i]/norm);
fprintf(fp,"\n");
}
else
for (m = 0; m < nbins; m++) {
fprintf(fp," %d %g %g %g %g",m+1,coord[m][0],coord[m][1],coord[m][2],
count_total[m]/norm);
for (i = 0; i < nvalues; i++)
fprintf(fp," %g",values_total[m][i]/norm);
fprintf(fp,"\n");
}
fflush(fp);
}
}
/* ----------------------------------------------------------------------
setup 1d, 2d, or 3d bins and their extent and coordinates
called at setup() and when averaging occurs if box size changes
------------------------------------------------------------------------- */
void FixAveSpatial::setup_bins()
{
int i,j,k,m,n;
double lo,hi,coord1,coord2;
// lo = bin boundary immediately below boxlo
// hi = bin boundary immediately above boxhi
// allocate and initialize arrays based on new bin count
double *boxlo,*boxhi,*prd;
if (scaleflag == REDUCED) {
boxlo = domain->boxlo_lamda;
boxhi = domain->boxhi_lamda;
prd = domain->prd_lamda;
} else {
boxlo = domain->boxlo;
boxhi = domain->boxhi;
prd = domain->prd;
}
if (domain->dimension == 3)
bin_volume = domain->xprd * domain->yprd * domain->zprd;
else bin_volume = domain->xprd * domain->yprd;
nbins = 1;
for (m = 0; m < ndim; m++) {
if (originflag[m] == LOWER) origin[m] = boxlo[dim[m]];
else if (originflag[m] == UPPER) origin[m] = boxhi[dim[m]];
else if (originflag[m] == CENTER)
origin[m] = 0.5 * (boxlo[dim[m]] + boxhi[dim[m]]);
if (origin[m] < boxlo[dim[m]]) {
n = static_cast<int> ((boxlo[dim[m]] - origin[m]) * invdelta[m]);
lo = origin[m] + n*delta[m];
} else {
n = static_cast<int> ((origin[m] - boxlo[dim[m]]) * invdelta[m]);
lo = origin[m] - n*delta[m];
if (lo > boxlo[dim[m]]) lo -= delta[m];
}
if (origin[m] < boxhi[dim[m]]) {
n = static_cast<int> ((boxhi[dim[m]] - origin[m]) * invdelta[m]);
hi = origin[m] + n*delta[m];
if (hi < boxhi[dim[m]]) hi += delta[m];
} else {
n = static_cast<int> ((origin[m] - boxhi[dim[m]]) * invdelta[m]);
hi = origin[m] - n*delta[m];
}
offset[m] = lo;
nlayers[m] = static_cast<int> ((hi-lo) * invdelta[m] + 0.5);
nbins *= nlayers[m];
bin_volume *= delta[m]/prd[dim[m]];
}
// reallocate bin arrays if needed
if (nbins > maxbin) {
maxbin = nbins;
count_one = (double *)
memory->srealloc(count_one,nbins*sizeof(double),
"ave/spatial:count_one");
count_many = (double *)
memory->srealloc(count_many,nbins*sizeof(double),
"ave/spatial:count_many");
count_sum = (double *)
memory->srealloc(count_sum,nbins*sizeof(double),
"ave/spatial:count_sum");
count_total = (double *)
memory->srealloc(count_total,nbins*sizeof(double),
"ave/spatial:count_total");
coord =
memory->grow_2d_double_array(coord,nbins,ndim,"ave/spatial:coord");
values_one = memory->grow_2d_double_array(values_one,nbins,nvalues,
"ave/spatial:values_one");
values_many = memory->grow_2d_double_array(values_many,nbins,nvalues,
"ave/spatial:values_many");
values_sum = memory->grow_2d_double_array(values_sum,nbins,nvalues,
"ave/spatial:values_sum");
values_total = memory->grow_2d_double_array(values_total,nbins,nvalues,
"ave/spatial:values_total");
// only allocate count and values list for ave = WINDOW
if (ave == WINDOW) {
count_list =
memory->create_2d_double_array(nwindow,nbins,
"ave/spatial:count_list");
values_list =
memory->create_3d_double_array(nwindow,nbins,nvalues,
"ave/spatial:values_list");
}
// reinitialize regrown count/values total since they accumulate
for (m = 0; m < nbins; m++) {
for (i = 0; i < nvalues; i++) values_total[m][i] = 0.0;
count_total[m] = 0.0;
}
}
// set bin coordinates
if (ndim == 1) {
for (i = 0; i < nlayers[0]; i++)
coord[i][0] = offset[0] + (i+0.5)*delta[0];
} else if (ndim == 2) {
m = 0;
for (i = 0; i < nlayers[0]; i++) {
coord1 = offset[0] + (i+0.5)*delta[0];
for (j = 0; j < nlayers[1]; j++) {
coord[m][0] = coord1;
coord[m][1] = offset[1] + (j+0.5)*delta[1];
m++;
}
}
} else if (ndim == 3) {
m = 0;
for (i = 0; i < nlayers[0]; i++) {
coord1 = offset[0] + (i+0.5)*delta[0];
for (j = 0; j < nlayers[1]; j++) {
coord2 = offset[1] + (j+0.5)*delta[1];
for (k = 0; k < nlayers[2]; k++) {
coord[m][0] = coord1;
coord[m][1] = coord2;
coord[m][2] = offset[2] + (k+0.5)*delta[2];
m++;
}
}
}
}
}
/* ----------------------------------------------------------------------
assign each atom to a 1d bin
------------------------------------------------------------------------- */
void FixAveSpatial::atom2bin1d()
{
int i,ibin;
double *boxlo,*boxhi,*prd;
double xremap;
double lamda[3];
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int idim = dim[0];
int nlayerm1 = nlayers[0] - 1;
int periodicity = domain->periodicity[idim];
if (periodicity) {
if (scaleflag == REDUCED) {
boxlo = domain->boxlo_lamda;
boxhi = domain->boxhi_lamda;
prd = domain->prd_lamda;
} else {
boxlo = domain->boxlo;
boxhi = domain->boxhi;
prd = domain->prd;
}
}
// remap each atom's relevant coord back into box via PBC if necessary
// if scaleflag = REDUCED, box coords -> lamda coords
if (regionflag == 0) {
if (scaleflag == REDUCED) domain->x2lamda(nlocal);
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
xremap = x[i][idim];
if (periodicity) {
if (xremap < boxlo[idim]) xremap += prd[idim];
if (xremap >= boxhi[idim]) xremap -= prd[idim];
}
ibin = static_cast<int> ((xremap - offset[0]) * invdelta[0]);
ibin = MAX(ibin,0);
ibin = MIN(ibin,nlayerm1);
bin[i] = ibin;
count_one[ibin] += 1.0;
}
if (scaleflag == REDUCED) domain->lamda2x(nlocal);
} else {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
if (scaleflag == REDUCED) {
domain->x2lamda(x[i],lamda);
xremap = lamda[idim];
} else xremap = x[i][idim];
if (periodicity) {
if (xremap < boxlo[idim]) xremap += prd[idim];
if (xremap >= boxhi[idim]) xremap -= prd[idim];
}
ibin = static_cast<int> ((xremap - offset[0]) * invdelta[0]);
ibin = MAX(ibin,0);
ibin = MIN(ibin,nlayerm1);
bin[i] = ibin;
count_one[ibin] += 1.0;
}
}
}
/* ----------------------------------------------------------------------
assign each atom to a 2d bin
------------------------------------------------------------------------- */
void FixAveSpatial::atom2bin2d()
{
int i,ibin,i1bin,i2bin;
double *boxlo,*boxhi,*prd;
double xremap,yremap;
double lamda[3];
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int idim = dim[0];
int jdim = dim[1];
int nlayer1m1 = nlayers[0] - 1;
int nlayer2m1 = nlayers[1] - 1;
int* periodicity = domain->periodicity;
if (periodicity[idim] || periodicity[jdim]) {
if (scaleflag == REDUCED) {
boxlo = domain->boxlo_lamda;
boxhi = domain->boxhi_lamda;
prd = domain->prd_lamda;
} else {
boxlo = domain->boxlo;
boxhi = domain->boxhi;
prd = domain->prd;
}
}
// remap each atom's relevant coord back into box via PBC if necessary
// if scaleflag = REDUCED, box coords -> lamda coords
if (regionflag == 0) {
if (scaleflag == REDUCED) domain->x2lamda(nlocal);
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
xremap = x[i][idim];
if (periodicity[idim]) {
if (xremap < boxlo[idim]) xremap += prd[idim];
if (xremap >= boxhi[idim]) xremap -= prd[idim];
}
i1bin = static_cast<int> ((xremap - offset[0]) * invdelta[0]);
i1bin = MAX(i1bin,0);
i1bin = MIN(i1bin,nlayer1m1);
yremap = x[i][jdim];
if (periodicity[jdim]) {
if (yremap < boxlo[jdim]) yremap += prd[jdim];
if (yremap >= boxhi[jdim]) yremap -= prd[jdim];
}
i2bin = static_cast<int> ((yremap - offset[1]) * invdelta[1]);
i2bin = MAX(i2bin,0);
i2bin = MIN(i2bin,nlayer2m1);
ibin = i1bin*nlayers[1] + i2bin;
bin[i] = ibin;
count_one[ibin] += 1.0;
}
if (scaleflag == REDUCED) domain->lamda2x(nlocal);
} else {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
if (scaleflag == REDUCED) {
domain->x2lamda(x[i],lamda);
xremap = lamda[idim];
yremap = lamda[jdim];
} else {
xremap = x[i][idim];
yremap = x[i][jdim];
}
if (periodicity[idim]) {
if (xremap < boxlo[idim]) xremap += prd[idim];
if (xremap >= boxhi[idim]) xremap -= prd[idim];
}
i1bin = static_cast<int> ((xremap - offset[0]) * invdelta[0]);
i1bin = MAX(i1bin,0);
i1bin = MIN(i1bin,nlayer1m1-1);
if (periodicity[jdim]) {
if (yremap < boxlo[jdim]) yremap += prd[jdim];
if (yremap >= boxhi[jdim]) yremap -= prd[jdim];
}
i2bin = static_cast<int> ((yremap - offset[1]) * invdelta[1]);
i2bin = MAX(i2bin,0);
i2bin = MIN(i2bin,nlayer2m1-1);
ibin = i1bin*nlayers[1] + i2bin;
bin[i] = ibin;
count_one[ibin] += 1.0;
}
}
}
/* ----------------------------------------------------------------------
assign each atom to a 3d bin
------------------------------------------------------------------------- */
void FixAveSpatial::atom2bin3d()
{
int i,ibin,i1bin,i2bin,i3bin;
double *boxlo,*boxhi,*prd;
double xremap,yremap,zremap;
double lamda[3];
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int idim = dim[0];
int jdim = dim[1];
int kdim = dim[2];
int nlayer1m1 = nlayers[0] - 1;
int nlayer2m1 = nlayers[1] - 1;
int nlayer3m1 = nlayers[2] - 1;
int* periodicity = domain->periodicity;
if (periodicity[idim] || periodicity[jdim] || periodicity[kdim]) {
if (scaleflag == REDUCED) {
boxlo = domain->boxlo_lamda;
boxhi = domain->boxhi_lamda;
prd = domain->prd_lamda;
} else {
boxlo = domain->boxlo;
boxhi = domain->boxhi;
prd = domain->prd;
}
}
// remap each atom's relevant coord back into box via PBC if necessary
// if scaleflag = REDUCED, box coords -> lamda coords
if (regionflag == 0) {
if (scaleflag == REDUCED) domain->x2lamda(nlocal);
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
xremap = x[i][idim];
if (periodicity[idim]) {
if (xremap < boxlo[idim]) xremap += prd[idim];
if (xremap >= boxhi[idim]) xremap -= prd[idim];
}
i1bin = static_cast<int> ((xremap - offset[0]) * invdelta[0]);
i1bin = MAX(i1bin,0);
i1bin = MIN(i1bin,nlayer1m1);
yremap = x[i][jdim];
if (periodicity[jdim]) {
if (yremap < boxlo[jdim]) yremap += prd[jdim];
if (yremap >= boxhi[jdim]) yremap -= prd[jdim];
}
i2bin = static_cast<int> ((yremap - offset[1]) * invdelta[1]);
i2bin = MAX(i2bin,0);
i2bin = MIN(i2bin,nlayer2m1);
zremap = x[i][kdim];
if (periodicity[kdim]) {
if (zremap < boxlo[kdim]) yremap += prd[kdim];
if (zremap >= boxhi[kdim]) yremap -= prd[kdim];
}
i3bin = static_cast<int> ((zremap - offset[2]) * invdelta[2]);
i3bin = MAX(i3bin,0);
i3bin = MIN(i3bin,nlayer3m1);
ibin = i1bin*nlayers[1]*nlayers[2] + i2bin*nlayers[2] + i3bin;
bin[i] = ibin;
count_one[ibin] += 1.0;
}
if (scaleflag == REDUCED) domain->lamda2x(nlocal);
} else {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
if (scaleflag == REDUCED) {
domain->x2lamda(x[i],lamda);
xremap = lamda[idim];
yremap = lamda[jdim];
zremap = lamda[kdim];
} else {
xremap = x[i][idim];
yremap = x[i][jdim];
zremap = x[i][kdim];
}
if (periodicity[idim]) {
if (xremap < boxlo[idim]) xremap += prd[idim];
if (xremap >= boxhi[idim]) xremap -= prd[idim];
}
i1bin = static_cast<int> ((xremap - offset[0]) * invdelta[0]);
i1bin = MAX(i1bin,0);
i1bin = MIN(i1bin,nlayer1m1);
if (periodicity[jdim]) {
if (yremap < boxlo[jdim]) yremap += prd[jdim];
if (yremap >= boxhi[jdim]) yremap -= prd[jdim];
}
i2bin = static_cast<int> ((yremap - offset[1]) * invdelta[1]);
i2bin = MAX(i2bin,0);
i2bin = MIN(i2bin,nlayer2m1);
if (periodicity[kdim]) {
if (zremap < boxlo[kdim]) yremap += prd[kdim];
if (zremap >= boxhi[kdim]) yremap -= prd[kdim];
}
i3bin = static_cast<int> ((zremap - offset[2]) * invdelta[2]);
i3bin = MAX(i3bin,0);
i3bin = MIN(i3bin,nlayer3m1);
ibin = i1bin*nlayers[1]*nlayers[2] + i2bin*nlayers[2] + i3bin;
bin[i] = ibin;
count_one[ibin] += 1.0;
}
}
}
/* ----------------------------------------------------------------------
return I,J array value
if I exceeds current bins, return 0.0 instead of generating an error
column 1,2,3 = bin coords, next column = count, remaining columns = Nvalues
------------------------------------------------------------------------- */
double FixAveSpatial::compute_array(int i, int j)
{
if (values_total == NULL) return 0.0;
if (i >= nbins) return 0.0;
if (j < ndim) return coord[i][j];
j -= ndim+1;
if (j < 0) return count_total[i]/norm;
return values_total[i][j]/norm;
}
/* ----------------------------------------------------------------------
calculate nvalid = next step on which end_of_step does something
can be this timestep if multiple of nfreq and nrepeat = 1
else backup from next multiple of nfreq
------------------------------------------------------------------------- */
bigint FixAveSpatial::nextvalid()
{
bigint nvalid = (update->ntimestep/nfreq)*nfreq + nfreq;
if (nvalid-nfreq == update->ntimestep && nrepeat == 1)
nvalid = update->ntimestep;
else
nvalid -= (nrepeat-1)*nevery;
if (nvalid < update->ntimestep) nvalid += nfreq;
return nvalid;
}
/* ----------------------------------------------------------------------
memory usage of varatom and bins
------------------------------------------------------------------------- */
double FixAveSpatial::memory_usage()
{
double bytes = maxvar * sizeof(double); // varatom
bytes += maxatom * sizeof(int); // bin
bytes += 4*nbins * sizeof(double); // count one,many,sum,total
bytes += ndim*nbins * sizeof(double); // coord
bytes += nvalues*nbins * sizeof(double); // values one,many,sum,total
bytes += nwindow*nbins * sizeof(double); // count_list
bytes += nwindow*nbins*nvalues * sizeof(double); // values_list
return bytes;
}
diff --git a/src/fix_ave_spatial.h b/src/fix_ave_spatial.h
index eefd20347..80dcee004 100644
--- a/src/fix_ave_spatial.h
+++ b/src/fix_ave_spatial.h
@@ -1,83 +1,83 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
FixStyle(ave/spatial,FixAveSpatial)
#else
#ifndef LMP_FIX_AVE_SPATIAL_H
#define LMP_FIX_AVE_SPATIAL_H
+#include "lmptype.h"
#include "stdio.h"
#include "fix.h"
-#include "lmptype.h"
namespace LAMMPS_NS {
class FixAveSpatial : public Fix {
public:
FixAveSpatial(class LAMMPS *, int, char **);
~FixAveSpatial();
int setmask();
void init();
void setup(int);
void end_of_step();
double compute_array(int,int);
double memory_usage();
private:
int me,nvalues;
int nrepeat,nfreq,irepeat;
bigint nvalid;
int ndim,normflag,regionflag,iregion;
char *tstring,*sstring,*idregion;
int *which,*argindex,*value2index;
char **ids;
FILE *fp;
class Region *region;
int ave,nwindow,scaleflag;
int norm,iwindow,window_limit;
double xscale,yscale,zscale;
double bin_volume;
int dim[3],originflag[3],nlayers[3];
double origin[3],delta[3];
double offset[3],invdelta[3];
int maxvar;
double *varatom;
int maxatom;
int *bin;
int nbins,maxbin;
double **coord;
double *count_one,*count_many,*count_sum;
double **values_one,**values_many,**values_sum;
double *count_total,**count_list;
double **values_total,***values_list;
void setup_bins();
void atom2bin1d();
void atom2bin2d();
void atom2bin3d();
bigint nextvalid();
};
}
#endif
#endif
diff --git a/src/fix_ave_time.cpp b/src/fix_ave_time.cpp
index d3c4f3207..8a72d054a 100644
--- a/src/fix_ave_time.cpp
+++ b/src/fix_ave_time.cpp
@@ -1,933 +1,933 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Pieter in 't Veld (SNL)
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "stdlib.h"
#include "string.h"
#include "fix_ave_time.h"
-#include "lmptype.h"
#include "update.h"
#include "modify.h"
#include "compute.h"
#include "group.h"
#include "input.h"
#include "variable.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
enum{COMPUTE,FIX,VARIABLE};
enum{ONE,RUNNING,WINDOW};
enum{SCALAR,VECTOR};
#define INVOKED_SCALAR 1
#define INVOKED_VECTOR 2
#define INVOKED_ARRAY 4
/* ---------------------------------------------------------------------- */
FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 7) error->all("Illegal fix ave/time command");
MPI_Comm_rank(world,&me);
nevery = atoi(arg[3]);
nrepeat = atoi(arg[4]);
nfreq = atoi(arg[5]);
global_freq = nfreq;
time_depend = 1;
// scan values to count them
// then read options so know mode = SCALAR/VECTOR before re-reading values
nvalues = 0;
int iarg = 6;
while (iarg < narg) {
if ((strncmp(arg[iarg],"c_",2) == 0) ||
(strncmp(arg[iarg],"f_",2) == 0) ||
(strncmp(arg[iarg],"v_",2) == 0)) {
nvalues++;
iarg++;
} else break;
}
options(narg,arg);
// parse values until one isn't recognized
// if mode = VECTOR and value is a global array:
// expand it as if columns listed one by one
// adjust nvalues accordingly via maxvalues
which = argindex = value2index = offcol = NULL;
ids = NULL;
int maxvalues = nvalues;
allocate_values(maxvalues);
nvalues = 0;
iarg = 6;
while (iarg < narg) {
if (strncmp(arg[iarg],"c_",2) == 0 ||
strncmp(arg[iarg],"f_",2) == 0 ||
strncmp(arg[iarg],"v_",2) == 0) {
if (arg[iarg][0] == 'c') which[nvalues] = COMPUTE;
else if (arg[iarg][0] == 'f') which[nvalues] = FIX;
else if (arg[iarg][0] == 'v') which[nvalues] = VARIABLE;
int n = strlen(arg[iarg]);
char *suffix = new char[n];
strcpy(suffix,&arg[iarg][2]);
char *ptr = strchr(suffix,'[');
if (ptr) {
if (suffix[strlen(suffix)-1] != ']')
error->all("Illegal fix ave/time command");
argindex[nvalues] = atoi(ptr+1);
*ptr = '\0';
} else argindex[nvalues] = 0;
n = strlen(suffix) + 1;
ids[nvalues] = new char[n];
strcpy(ids[nvalues],suffix);
delete [] suffix;
if (mode == VECTOR && which[nvalues] == COMPUTE &&
argindex[nvalues] == 0) {
int icompute = modify->find_compute(ids[nvalues]);
if (icompute < 0)
error->all("Compute ID for fix ave/time does not exist");
if (modify->compute[icompute]->array_flag) {
int ncols = modify->compute[icompute]->size_array_cols;
maxvalues += ncols-1;
allocate_values(maxvalues);
argindex[nvalues] = 1;
for (int icol = 1; icol < ncols; icol++) {
which[nvalues+icol] = which[nvalues];
argindex[nvalues+icol] = icol+1;
n = strlen(ids[nvalues]) + 1;
ids[nvalues+icol] = new char[n];
strcpy(ids[nvalues+icol],ids[nvalues]);
}
nvalues += ncols-1;
}
} else if (mode == VECTOR && which[nvalues] == FIX &&
argindex[nvalues] == 0) {
int ifix = modify->find_fix(ids[nvalues]);
if (ifix < 0)
error->all("Fix ID for fix ave/time does not exist");
if (modify->fix[ifix]->array_flag) {
int ncols = modify->fix[ifix]->size_array_cols;
maxvalues += ncols-1;
allocate_values(maxvalues);
argindex[nvalues] = 1;
for (int icol = 1; icol < ncols; icol++) {
which[nvalues+icol] = which[nvalues];
argindex[nvalues+icol] = icol+1;
n = strlen(ids[nvalues]) + 1;
ids[nvalues+icol] = new char[n];
strcpy(ids[nvalues+icol],ids[nvalues]);
}
nvalues += ncols-1;
}
}
nvalues++;
iarg++;
} else break;
}
// set off columns now that nvalues is finalized
for (int i = 0; i < nvalues; i++) offcol[i] = 0;
for (int i = 0; i < noff; i++) {
if (offlist[i] < 1 || offlist[i] > nvalues)
error->all("Invalid fix ave/time off column");
offcol[offlist[i]-1] = 1;
}
// setup and error check
// for fix inputs, check that fix frequency is acceptable
if (nevery <= 0 || nrepeat <= 0 || nfreq <= 0)
error->all("Illegal fix ave/time command");
if (nfreq % nevery || (nrepeat-1)*nevery >= nfreq)
error->all("Illegal fix ave/time command");
for (int i = 0; i < nvalues; i++) {
if (which[i] == COMPUTE && mode == SCALAR) {
int icompute = modify->find_compute(ids[i]);
if (icompute < 0)
error->all("Compute ID for fix ave/time does not exist");
if (argindex[i] == 0 && modify->compute[icompute]->scalar_flag == 0)
error->all("Fix ave/time compute does not calculate a scalar");
if (argindex[i] && modify->compute[icompute]->vector_flag == 0)
error->all("Fix ave/time compute does not calculate a vector");
if (argindex[i] && argindex[i] > modify->compute[icompute]->size_vector)
error->all("Fix ave/time compute vector is accessed out-of-range");
} else if (which[i] == COMPUTE && mode == VECTOR) {
int icompute = modify->find_compute(ids[i]);
if (icompute < 0)
error->all("Compute ID for fix ave/time does not exist");
if (argindex[i] == 0 && modify->compute[icompute]->vector_flag == 0)
error->all("Fix ave/time compute does not calculate a vector");
if (argindex[i] && modify->compute[icompute]->array_flag == 0)
error->all("Fix ave/time compute does not calculate an array");
if (argindex[i] &&
argindex[i] > modify->compute[icompute]->size_array_cols)
error->all("Fix ave/time compute array is accessed out-of-range");
} else if (which[i] == FIX && mode == SCALAR) {
int ifix = modify->find_fix(ids[i]);
if (ifix < 0)
error->all("Fix ID for fix ave/time does not exist");
if (argindex[i] == 0 && modify->fix[ifix]->scalar_flag == 0)
error->all("Fix ave/time fix does not calculate a scalar");
if (argindex[i] && modify->fix[ifix]->vector_flag == 0)
error->all("Fix ave/time fix does not calculate a vector");
if (argindex[i] && argindex[i] > modify->fix[ifix]->size_vector)
error->all("Fix ave/time fix vector is accessed out-of-range");
if (nevery % modify->fix[ifix]->global_freq)
error->all("Fix for fix ave/time not computed at compatible time");
} else if (which[i] == FIX && mode == VECTOR) {
int ifix = modify->find_fix(ids[i]);
if (ifix < 0)
error->all("Fix ID for fix ave/time does not exist");
if (argindex[i] == 0 && modify->fix[ifix]->vector_flag == 0)
error->all("Fix ave/time fix does not calculate a vector");
if (argindex[i] && modify->fix[ifix]->array_flag == 0)
error->all("Fix ave/time fix does not calculate an array");
if (argindex[i] && argindex[i] > modify->fix[ifix]->size_array_cols)
error->all("Fix ave/time fix array is accessed out-of-range");
if (nevery % modify->fix[ifix]->global_freq)
error->all("Fix for fix ave/time not computed at compatible time");
} else if (which[i] == VARIABLE) {
int ivariable = input->variable->find(ids[i]);
if (ivariable < 0)
error->all("Variable name for fix ave/time does not exist");
if (input->variable->equalstyle(ivariable) == 0)
error->all("Fix ave/time variable is not equal-style variable");
if (mode == VECTOR)
error->all("Fix ave/time cannot use variable with vector mode");
}
}
// if VECTOR mode, check that all columns are same length
// nrows = # of rows in output array
if (mode == VECTOR) {
int length;
for (int i = 0; i < nvalues; i++) {
if (which[i] == COMPUTE) {
int icompute = modify->find_compute(ids[i]);
if (argindex[i] == 0) length = modify->compute[icompute]->size_vector;
else length = modify->compute[icompute]->size_array_rows;
} else if (which[i] == FIX) {
int ifix = modify->find_fix(ids[i]);
if (argindex[i] == 0) length = modify->fix[ifix]->size_vector;
else length = modify->fix[ifix]->size_array_rows;
}
if (i == 0) nrows = length;
else if (length != nrows)
error->all("Fix ave/time columns are inconsistent lengths");
}
column = new double[nrows];
} else column = NULL;
// print file comment lines
// for mode = VECTOR, cannot use arg to print
// since array args may have been expanded to multiple vectors
if (fp && me == 0) {
if (title1) fprintf(fp,"%s\n",title1);
else fprintf(fp,"# Time-averaged data for fix %s\n",id);
if (title2) fprintf(fp,"%s\n",title2);
else if (mode == SCALAR) {
fprintf(fp,"# TimeStep");
for (int i = 0; i < nvalues; i++) fprintf(fp," %s",arg[6+i]);
fprintf(fp,"\n");
} else fprintf(fp,"# TimeStep Number-of-rows\n");
if (title3 && mode == VECTOR) fprintf(fp,"%s\n",title3);
else if (mode == VECTOR) {
fprintf(fp,"# Row");
for (int i = 0; i < nvalues; i++) {
if (which[i] == COMPUTE) fprintf(fp," c_%s",ids[i]);
else if (which[i] == FIX) fprintf(fp," f_%s",ids[i]);
else if (which[i] == VARIABLE) fprintf(fp," v_%s",ids[i]);
if (argindex[i]) fprintf(fp,"[%d]",argindex[i]);
}
fprintf(fp,"\n");
}
}
delete [] title1;
delete [] title2;
delete [] title3;
// allocate memory for averaging
vector = vector_total = NULL;
vector_list = NULL;
array = array_total = NULL;
array_list = NULL;
if (mode == SCALAR) {
vector = new double[nvalues];
vector_total = new double[nvalues];
if (ave == WINDOW)
vector_list = memory->create_2d_double_array(nwindow,nvalues,
"ave/time:vector_list");
} else {
array = memory->create_2d_double_array(nrows,nvalues,"ave/time:array");
array_total = memory->create_2d_double_array(nrows,nvalues,
"ave/time:array_total");
if (ave == WINDOW)
array_list = memory->create_3d_double_array(nwindow,nrows,nvalues,
"ave/time:array_list");
}
// this fix produces either a global scalar or vector or array
// SCALAR mode produces either a scalar or vector
// VECTOR mode produces either a vector or array
// intensive/extensive flags set by compute,fix,variable that produces value
extlist = NULL;
if (mode == SCALAR) {
if (nvalues == 1) {
scalar_flag = 1;
if (which[0] == COMPUTE) {
Compute *compute = modify->compute[modify->find_compute(ids[0])];
if (argindex[0] == 0) extscalar = compute->extscalar;
else if (compute->extvector >= 0) extscalar = compute->extvector;
else extscalar = compute->extlist[argindex[0]-1];
} else if (which[0] == FIX) {
Fix *fix = modify->fix[modify->find_fix(ids[0])];
if (argindex[0] == 0) extscalar = fix->extscalar;
else if (fix->extvector >= 0) extscalar = fix->extvector;
else extscalar = fix->extlist[argindex[0]-1];
} else if (which[0] == VARIABLE)
extscalar = 0;
} else {
vector_flag = 1;
size_vector = nvalues;
extvector = -1;
extlist = new int[nvalues];
for (int i = 0; i < nvalues; i++) {
if (which[i] == COMPUTE) {
Compute *compute = modify->compute[modify->find_compute(ids[i])];
if (argindex[i] == 0) extlist[i] = compute->extscalar;
else if (compute->extvector >= 0) extlist[i] = compute->extvector;
else extlist[i] = compute->extlist[argindex[i]-1];
} else if (which[i] == FIX) {
Fix *fix = modify->fix[modify->find_fix(ids[i])];
if (argindex[i] == 0) extlist[i] = fix->extscalar;
else if (fix->extvector >= 0) extlist[i] = fix->extvector;
else extlist[i] = fix->extlist[argindex[i]-1];
} else if (which[i] == VARIABLE)
extlist[i] = 0;
}
}
} else {
if (nvalues == 1) {
vector_flag = 1;
size_vector = nrows;
if (which[0] == COMPUTE) {
Compute *compute = modify->compute[modify->find_compute(ids[0])];
if (argindex[0] == 0) {
extvector = compute->extvector;
if (extvector == -1) {
extlist = new int[nrows];
for (int i = 0; i < nrows; i++) extlist[i] = compute->extlist[i];
}
} else extvector = compute->extarray;
} else if (which[0] == FIX) {
Fix *fix = modify->fix[modify->find_fix(ids[0])];
if (argindex[0] == 0) {
extvector = fix->extvector;
if (extvector == -1) {
extlist = new int[nrows];
for (int i = 0; i < nrows; i++) extlist[i] = fix->extlist[i];
}
} else extvector = fix->extarray;
}
} else {
array_flag = 1;
size_local_rows = nrows;
size_local_cols = nvalues;
int value;
for (int i = 0; i < nvalues; i++) {
if (which[i] == COMPUTE) {
Compute *compute = modify->compute[modify->find_compute(ids[i])];
if (argindex[i] == 0) value = compute->extvector;
else value = compute->extarray;
} else if (which[i] == FIX) {
Fix *fix = modify->fix[modify->find_fix(ids[i])];
if (argindex[i] == 0) value = fix->extvector;
else value = fix->extarray;
}
if (value == -1)
error->all("Fix ave/time cannot set output array "
"intensive/extensive from these inputs");
if (i == 0) extarray = value;
else if (value != extarray)
error->all("Fix ave/time cannot set output array "
"intensive/extensive from these inputs");
}
}
}
// initializations
// set vector_total/array_total to zero since it accumulates
irepeat = 0;
iwindow = window_limit = 0;
norm = 0;
if (mode == SCALAR)
for (int i = 0; i < nvalues; i++) vector_total[i] = 0.0;
else
for (int i = 0; i < nrows; i++)
for (int j = 0; j < nvalues; j++) array_total[i][j] = 0.0;
// nvalid = next step on which end_of_step does something
// add nvalid to all computes that store invocation times
// since don't know a priori which are invoked by this fix
// once in end_of_step() can set timestep for ones actually invoked
nvalid = nextvalid();
modify->addstep_compute_all(nvalid);
}
/* ---------------------------------------------------------------------- */
FixAveTime::~FixAveTime()
{
memory->sfree(which);
memory->sfree(argindex);
memory->sfree(value2index);
memory->sfree(offcol);
for (int i = 0; i < nvalues; i++) delete [] ids[i];
memory->sfree(ids);
delete [] extlist;
if (fp && me == 0) fclose(fp);
delete [] vector;
delete [] vector_total;
delete [] column;
memory->destroy_2d_double_array(array);
memory->destroy_2d_double_array(array_total);
memory->destroy_3d_double_array(array_list);
}
/* ---------------------------------------------------------------------- */
int FixAveTime::setmask()
{
int mask = 0;
mask |= END_OF_STEP;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixAveTime::init()
{
// set current indices for all computes,fixes,variables
for (int i = 0; i < nvalues; i++) {
if (which[i] == COMPUTE) {
int icompute = modify->find_compute(ids[i]);
if (icompute < 0)
error->all("Compute ID for fix ave/time does not exist");
value2index[i] = icompute;
} else if (which[i] == FIX) {
int ifix = modify->find_fix(ids[i]);
if (ifix < 0)
error->all("Fix ID for fix ave/time does not exist");
value2index[i] = ifix;
} else if (which[i] == VARIABLE) {
int ivariable = input->variable->find(ids[i]);
if (ivariable < 0)
error->all("Variable name for fix ave/time does not exist");
value2index[i] = ivariable;
}
}
// need to reset nvalid if nvalid < ntimestep b/c minimize was performed
if (nvalid < update->ntimestep) {
irepeat = 0;
nvalid = nextvalid();
modify->addstep_compute_all(nvalid);
}
}
/* ----------------------------------------------------------------------
only does something if nvalid = current timestep
------------------------------------------------------------------------- */
void FixAveTime::setup(int vflag)
{
end_of_step();
}
/* ---------------------------------------------------------------------- */
void FixAveTime::end_of_step()
{
// skip if not step which requires doing something
bigint ntimestep = update->ntimestep;
if (ntimestep != nvalid) return;
if (mode == SCALAR) invoke_scalar(ntimestep);
else invoke_vector(ntimestep);
}
/* ---------------------------------------------------------------------- */
void FixAveTime::invoke_scalar(bigint ntimestep)
{
int i,m;
double scalar;
// zero if first step
if (irepeat == 0)
for (i = 0; i < nvalues; i++) vector[i] = 0.0;
// accumulate results of computes,fixes,variables to local copy
// compute/fix/variable may invoke computes so wrap with clear/add
modify->clearstep_compute();
for (i = 0; i < nvalues; i++) {
m = value2index[i];
// invoke compute if not previously invoked
if (which[i] == COMPUTE) {
Compute *compute = modify->compute[m];
if (argindex[i] == 0) {
if (!(compute->invoked_flag & INVOKED_SCALAR)) {
compute->compute_scalar();
compute->invoked_flag |= INVOKED_SCALAR;
}
scalar = compute->scalar;
} else {
if (!(compute->invoked_flag & INVOKED_VECTOR)) {
compute->compute_vector();
compute->invoked_flag |= INVOKED_VECTOR;
}
scalar = compute->vector[argindex[i]-1];
}
// access fix fields, guaranteed to be ready
} else if (which[i] == FIX) {
if (argindex[i] == 0)
scalar = modify->fix[m]->compute_scalar();
else
scalar = modify->fix[m]->compute_vector(argindex[i]-1);
// evaluate equal-style variable
} else if (which[i] == VARIABLE)
scalar = input->variable->compute_equal(m);
// add value to vector or just set directly if offcol is set
if (offcol[i]) vector[i] = scalar;
else vector[i] += scalar;
}
// done if irepeat < nrepeat
// else reset irepeat and nvalid
irepeat++;
if (irepeat < nrepeat) {
nvalid += nevery;
modify->addstep_compute(nvalid);
return;
}
irepeat = 0;
nvalid = ntimestep + nfreq - (nrepeat-1)*nevery;
modify->addstep_compute(nvalid);
// average the final result for the Nfreq timestep
double repeat = nrepeat;
for (i = 0; i < nvalues; i++)
if (offcol[i] == 0) vector[i] /= repeat;
// if ave = ONE, only single Nfreq timestep value is needed
// if ave = RUNNING, combine with all previous Nfreq timestep values
// if ave = WINDOW, combine with nwindow most recent Nfreq timestep values
if (ntimestep >= startstep) {
if (ave == ONE) {
for (i = 0; i < nvalues; i++) vector_total[i] = vector[i];
norm = 1;
} else if (ave == RUNNING) {
for (i = 0; i < nvalues; i++) vector_total[i] += vector[i];
norm++;
} else if (ave == WINDOW) {
for (i = 0; i < nvalues; i++) {
vector_total[i] += vector[i];
if (window_limit) vector_total[i] -= vector_list[iwindow][i];
vector_list[iwindow][i] = vector[i];
}
iwindow++;
if (iwindow == nwindow) {
iwindow = 0;
window_limit = 1;
}
if (window_limit) norm = nwindow;
else norm = iwindow;
}
}
// insure any columns with offcol set are effectively set to last value
for (i = 0; i < nvalues; i++)
if (offcol[i]) vector_total[i] = norm*vector[i];
// output result to file
if (fp && me == 0) {
fprintf(fp,BIGINT_FORMAT,ntimestep);
for (i = 0; i < nvalues; i++) fprintf(fp," %g",vector_total[i]/norm);
fprintf(fp,"\n");
fflush(fp);
}
}
/* ---------------------------------------------------------------------- */
void FixAveTime::invoke_vector(bigint ntimestep)
{
int i,j,m;
// zero if first step
if (irepeat == 0)
for (i = 0; i < nrows; i++)
for (j = 0; j < nvalues; j++) array[i][j] = 0.0;
// accumulate results of computes,fixes,variables to local copy
// compute/fix/variable may invoke computes so wrap with clear/add
modify->clearstep_compute();
for (j = 0; j < nvalues; j++) {
m = value2index[j];
// invoke compute if not previously invoked
if (which[j] == COMPUTE) {
Compute *compute = modify->compute[m];
if (argindex[j] == 0) {
if (!(compute->invoked_flag & INVOKED_VECTOR)) {
compute->compute_vector();
compute->invoked_flag |= INVOKED_VECTOR;
}
double *cvector = compute->vector;
for (i = 0; i < nrows; i++)
column[i] = cvector[i];
} else {
if (!(compute->invoked_flag & INVOKED_ARRAY)) {
compute->compute_array();
compute->invoked_flag |= INVOKED_ARRAY;
}
double **carray = compute->array;
int icol = argindex[j]-1;
for (i = 0; i < nrows; i++)
column[i] = carray[i][icol];
}
// access fix fields, guaranteed to be ready
} else if (which[j] == FIX) {
Fix *fix = modify->fix[m];
if (argindex[j] == 0)
for (i = 0; i < nrows; i++)
column[i] = fix->compute_vector(i);
else {
int icol = argindex[j]-1;
for (i = 0; i < nrows; i++)
column[i] = fix->compute_array(i,icol);
}
}
// add columns of values to array or just set directly if offcol is set
if (offcol[j]) {
for (i = 0; i < nrows; i++)
array[i][j] = column[i];
} else {
for (i = 0; i < nrows; i++)
array[i][j] += column[i];
}
}
// done if irepeat < nrepeat
// else reset irepeat and nvalid
irepeat++;
if (irepeat < nrepeat) {
nvalid += nevery;
modify->addstep_compute(nvalid);
return;
}
irepeat = 0;
nvalid = ntimestep+nfreq - (nrepeat-1)*nevery;
modify->addstep_compute(nvalid);
// average the final result for the Nfreq timestep
double repeat = nrepeat;
for (i = 0; i < nrows; i++)
for (j = 0; j < nvalues; j++)
if (offcol[j] == 0) array[i][j] /= repeat;
// if ave = ONE, only single Nfreq timestep value is needed
// if ave = RUNNING, combine with all previous Nfreq timestep values
// if ave = WINDOW, combine with nwindow most recent Nfreq timestep values
if (ntimestep >= startstep) {
if (ave == ONE) {
for (i = 0; i < nrows; i++)
for (j = 0; j < nvalues; j++) array_total[i][j] = array[i][j];
norm = 1;
} else if (ave == RUNNING) {
for (i = 0; i < nrows; i++)
for (j = 0; j < nvalues; j++) array_total[i][j] += array[i][j];
norm++;
} else if (ave == WINDOW) {
for (i = 0; i < nrows; i++)
for (j = 0; j < nvalues; j++) {
array_total[i][j] += array[i][j];
if (window_limit) array_total[i][j] -= array_list[iwindow][i][j];
array_list[iwindow][i][j] = array[i][j];
}
iwindow++;
if (iwindow == nwindow) {
iwindow = 0;
window_limit = 1;
}
if (window_limit) norm = nwindow;
else norm = iwindow;
}
}
// insure any columns with offcol set are effectively set to last value
for (i = 0; i < nrows; i++)
for (j = 0; j < nvalues; j++)
if (offcol[j]) array_total[i][j] = norm*array[i][j];
// output result to file
if (fp && me == 0) {
fprintf(fp,BIGINT_FORMAT " %d\n",ntimestep,nrows);
for (i = 0; i < nrows; i++) {
fprintf(fp,"%d",i+1);
for (j = 0; j < nvalues; j++) fprintf(fp," %g",array_total[i][j]/norm);
fprintf(fp,"\n");
}
fflush(fp);
}
}
/* ----------------------------------------------------------------------
return scalar value
------------------------------------------------------------------------- */
double FixAveTime::compute_scalar()
{
if (norm) return vector_total[0]/norm;
return 0.0;
}
/* ----------------------------------------------------------------------
return Ith vector value
------------------------------------------------------------------------- */
double FixAveTime::compute_vector(int i)
{
if (norm) {
if (mode == SCALAR) return vector_total[i]/norm;
if (mode == VECTOR) return array_total[i][0];
}
return 0.0;
}
/* ----------------------------------------------------------------------
return I,J array value
------------------------------------------------------------------------- */
double FixAveTime::compute_array(int i, int j)
{
if (norm) return array_total[i][j]/norm;
return 0.0;
}
/* ----------------------------------------------------------------------
parse optional args
------------------------------------------------------------------------- */
void FixAveTime::options(int narg, char **arg)
{
// option defaults
fp = NULL;
ave = ONE;
startstep = 0;
mode = SCALAR;
noff = 0;
offlist = NULL;
title1 = NULL;
title2 = NULL;
title3 = NULL;
// optional args
int iarg = 6 + nvalues;
while (iarg < narg) {
if (strcmp(arg[iarg],"file") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/time command");
if (me == 0) {
fp = fopen(arg[iarg+1],"w");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open fix ave/time file %s",arg[iarg+1]);
error->one(str);
}
}
iarg += 2;
} else if (strcmp(arg[iarg],"ave") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/time command");
if (strcmp(arg[iarg+1],"one") == 0) ave = ONE;
else if (strcmp(arg[iarg+1],"running") == 0) ave = RUNNING;
else if (strcmp(arg[iarg+1],"window") == 0) ave = WINDOW;
else error->all("Illegal fix ave/time command");
if (ave == WINDOW) {
if (iarg+3 > narg) error->all("Illegal fix ave/time command");
nwindow = atoi(arg[iarg+2]);
if (nwindow <= 0) error->all("Illegal fix ave/time command");
}
iarg += 2;
if (ave == WINDOW) iarg++;
} else if (strcmp(arg[iarg],"start") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/time command");
startstep = atoi(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"mode") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/time command");
if (strcmp(arg[iarg+1],"scalar") == 0) mode = SCALAR;
else if (strcmp(arg[iarg+1],"vector") == 0) mode = VECTOR;
else error->all("Illegal fix ave/time command");
iarg += 2;
} else if (strcmp(arg[iarg],"off") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/time command");
offlist = (int *)
memory->srealloc(offlist,(noff+1)*sizeof(int),"ave/time:offlist");
offlist[noff++] = atoi(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"title1") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/spatial command");
delete [] title1;
int n = strlen(arg[iarg+1]) + 1;
title1 = new char[n];
strcpy(title1,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"title2") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/spatial command");
delete [] title2;
int n = strlen(arg[iarg+1]) + 1;
title2 = new char[n];
strcpy(title2,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"title3") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/spatial command");
delete [] title3;
int n = strlen(arg[iarg+1]) + 1;
title3 = new char[n];
strcpy(title3,arg[iarg+1]);
iarg += 2;
} else error->all("Illegal fix ave/time command");
}
}
/* ----------------------------------------------------------------------
reallocate vectors for each input value, of length N
------------------------------------------------------------------------- */
void FixAveTime::allocate_values(int n)
{
which = (int *) memory->srealloc(which,n*sizeof(int),"ave/time:which");
argindex = (int *) memory->srealloc(argindex,n*sizeof(int),
"ave/time:argindex");
value2index = (int *) memory->srealloc(value2index,n*sizeof(int),
"ave/time:value2index");
offcol = (int *) memory->srealloc(offcol,n*sizeof(int),"ave/time:offcol");
ids = (char **) memory->srealloc(ids,n*sizeof(char *),"ave/time:ids");
}
/* ----------------------------------------------------------------------
calculate nvalid = next step on which end_of_step does something
can be this timestep if multiple of nfreq and nrepeat = 1
else backup from next multiple of nfreq
------------------------------------------------------------------------- */
bigint FixAveTime::nextvalid()
{
bigint nvalid = (update->ntimestep/nfreq)*nfreq + nfreq;
if (nvalid-nfreq == update->ntimestep && nrepeat == 1)
nvalid = update->ntimestep;
else
nvalid -= (nrepeat-1)*nevery;
if (nvalid < update->ntimestep) nvalid += nfreq;
return nvalid;
}
diff --git a/src/fix_ave_time.h b/src/fix_ave_time.h
index a8c118d39..fafd21e50 100644
--- a/src/fix_ave_time.h
+++ b/src/fix_ave_time.h
@@ -1,74 +1,74 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
FixStyle(ave/time,FixAveTime)
#else
#ifndef LMP_FIX_AVE_TIME_H
#define LMP_FIX_AVE_TIME_H
+#include "lmptype.h"
#include "stdio.h"
#include "fix.h"
-#include "lmptype.h"
namespace LAMMPS_NS {
class FixAveTime : public Fix {
public:
FixAveTime(class LAMMPS *, int, char **);
~FixAveTime();
int setmask();
void init();
void setup(int);
void end_of_step();
double compute_scalar();
double compute_vector(int);
double compute_array(int,int);
private:
int me,nvalues;
int nrepeat,nfreq,irepeat;
bigint nvalid;
int *which,*argindex,*value2index,*offcol;
char **ids;
FILE *fp;
int nrows;
int ave,nwindow,nsum,startstep,mode;
int noff;
int *offlist;
char *title1,*title2,*title3;
int norm,iwindow,window_limit;
double *vector;
double *vector_total;
double **vector_list;
double *column;
double **array;
double **array_total;
double ***array_list;
void invoke_scalar(bigint);
void invoke_vector(bigint);
void options(int, char **);
void allocate_values(int);
bigint nextvalid();
};
}
#endif
#endif
diff --git a/src/fix_dt_reset.h b/src/fix_dt_reset.h
index ddba09c73..095f8c9ca 100644
--- a/src/fix_dt_reset.h
+++ b/src/fix_dt_reset.h
@@ -1,51 +1,51 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
FixStyle(dt/reset,FixDtReset)
#else
#ifndef LMP_FIX_DT_RESET_H
#define LMP_FIX_DT_RESET_H
-#include "fix.h"
#include "lmptype.h"
+#include "fix.h"
namespace LAMMPS_NS {
class FixDtReset : public Fix {
public:
FixDtReset(class LAMMPS *, int, char **);
~FixDtReset() {}
int setmask();
void init();
void setup(int);
void end_of_step();
double compute_scalar();
double compute_vector(int);
private:
bigint laststep;
int minbound,maxbound;
double tmin,tmax,xmax;
double ftm2v;
double t_elapsed;
int respaflag;
};
}
#endif
#endif
diff --git a/src/fix_shake.cpp b/src/fix_shake.cpp
index 70e1fbb4e..83ff40911 100644
--- a/src/fix_shake.cpp
+++ b/src/fix_shake.cpp
@@ -1,2436 +1,2436 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "mpi.h"
#include "math.h"
#include "stdlib.h"
#include "string.h"
#include "stdio.h"
#include "fix_shake.h"
-#include "lmptype.h"
#include "atom.h"
#include "atom_vec.h"
#include "update.h"
#include "respa.h"
#include "modify.h"
#include "domain.h"
#include "force.h"
#include "bond.h"
#include "angle.h"
#include "comm.h"
#include "group.h"
#include "fix_respa.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define BIG 1.0e20
#define MASSDELTA 0.1
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
/* ---------------------------------------------------------------------- */
FixShake::FixShake(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
MPI_Comm_rank(world,&me);
MPI_Comm_size(world,&nprocs);
PI = 4.0*atan(1.0);
virial_flag = 1;
create_attribute = 1;
// error check
if (atom->molecular == 0)
error->all("Cannot use fix shake with non-molecular system");
// perform initial allocation of atom-based arrays
// register with Atom class
shake_flag = NULL;
shake_atom = shake_type = NULL;
xshake = NULL;
grow_arrays(atom->nmax);
atom->add_callback(0);
// set comm size needed by this fix
comm_forward = 3;
// parse SHAKE args
if (narg < 8) error->all("Illegal fix shake command");
tolerance = atof(arg[3]);
max_iter = atoi(arg[4]);
output_every = atoi(arg[5]);
// parse SHAKE args for bond and angle types
// will be used by find_clusters
// store args for "b" "a" "t" as flags in (1:n) list for fast access
// store args for "m" in list of length nmass for looping over
// for "m" verify that atom masses have been set
bond_flag = new int[atom->nbondtypes+1];
for (int i = 1; i <= atom->nbondtypes; i++) bond_flag[i] = 0;
angle_flag = new int[atom->nangletypes+1];
for (int i = 1; i <= atom->nangletypes; i++) angle_flag[i] = 0;
type_flag = new int[atom->ntypes+1];
for (int i = 1; i <= atom->ntypes; i++) type_flag[i] = 0;
mass_list = new double[atom->ntypes];
nmass = 0;
char mode = '\0';
int next = 6;
while (next < narg) {
if (strcmp(arg[next],"b") == 0) mode = 'b';
else if (strcmp(arg[next],"a") == 0) mode = 'a';
else if (strcmp(arg[next],"t") == 0) mode = 't';
else if (strcmp(arg[next],"m") == 0) {
mode = 'm';
atom->check_mass();
} else if (mode == 'b') {
int i = atoi(arg[next]);
if (i < 1 || i > atom->nbondtypes)
error->all("Invalid bond type index for fix shake");
bond_flag[i] = 1;
} else if (mode == 'a') {
int i = atoi(arg[next]);
if (i < 1 || i > atom->nangletypes)
error->all("Invalid angle type index for fix shake");
angle_flag[i] = 1;
} else if (mode == 't') {
int i = atoi(arg[next]);
if (i < 1 || i > atom->ntypes)
error->all("Invalid atom type index for fix shake");
type_flag[i] = 1;
} else if (mode == 'm') {
double massone = atof(arg[next]);
if (massone == 0.0) error->all("Invalid atom mass for fix shake");
if (nmass == atom->ntypes) error->all("Too many masses for fix shake");
mass_list[nmass++] = massone;
} else error->all("Illegal fix shake command");
next++;
}
// allocate bond and angle distance arrays, indexed from 1 to n
bond_distance = new double[atom->nbondtypes+1];
angle_distance = new double[atom->nangletypes+1];
// allocate statistics arrays
if (output_every) {
int nb = atom->nbondtypes + 1;
b_count = new int[nb];
b_count_all = new int[nb];
b_ave = new double[nb];
b_ave_all = new double[nb];
b_max = new double[nb];
b_max_all = new double[nb];
b_min = new double[nb];
b_min_all = new double[nb];
int na = atom->nangletypes + 1;
a_count = new int[na];
a_count_all = new int[na];
a_ave = new double[na];
a_ave_all = new double[na];
a_max = new double[na];
a_max_all = new double[na];
a_min = new double[na];
a_min_all = new double[na];
}
// identify all SHAKE clusters
find_clusters();
// initialize list of SHAKE clusters to constrain
maxlist = 0;
list = NULL;
}
/* ---------------------------------------------------------------------- */
FixShake::~FixShake()
{
// unregister callbacks to this fix from Atom class
atom->delete_callback(id,0);
// set bond_type and angle_type back to positive for SHAKE clusters
// must set for all SHAKE bonds and angles stored by each atom
int **bond_type = atom->bond_type;
int **angle_type = atom->angle_type;
int nlocal = atom->nlocal;
int n;
for (int i = 0; i < nlocal; i++) {
if (shake_flag[i] == 0) continue;
else if (shake_flag[i] == 1) {
n = bondfind(i,shake_atom[i][0],shake_atom[i][1]);
if (n >= 0) bond_type[i][n] = -bond_type[i][n];
n = bondfind(i,shake_atom[i][0],shake_atom[i][2]);
if (n >= 0) bond_type[i][n] = -bond_type[i][n];
n = anglefind(i,shake_atom[i][1],shake_atom[i][2]);
if (n >= 0) angle_type[i][n] = -angle_type[i][n];
} else if (shake_flag[i] == 2) {
n = bondfind(i,shake_atom[i][0],shake_atom[i][1]);
if (n >= 0) bond_type[i][n] = -bond_type[i][n];
} else if (shake_flag[i] == 3) {
n = bondfind(i,shake_atom[i][0],shake_atom[i][1]);
if (n >= 0) bond_type[i][n] = -bond_type[i][n];
n = bondfind(i,shake_atom[i][0],shake_atom[i][2]);
if (n >= 0) bond_type[i][n] = -bond_type[i][n];
} else if (shake_flag[i] == 4) {
n = bondfind(i,shake_atom[i][0],shake_atom[i][1]);
if (n >= 0) bond_type[i][n] = -bond_type[i][n];
n = bondfind(i,shake_atom[i][0],shake_atom[i][2]);
if (n >= 0) bond_type[i][n] = -bond_type[i][n];
n = bondfind(i,shake_atom[i][0],shake_atom[i][3]);
if (n >= 0) bond_type[i][n] = -bond_type[i][n];
}
}
// delete locally stored arrays
memory->sfree(shake_flag);
memory->destroy_2d_int_array(shake_atom);
memory->destroy_2d_int_array(shake_type);
memory->destroy_2d_double_array(xshake);
delete [] bond_flag;
delete [] angle_flag;
delete [] type_flag;
delete [] mass_list;
delete [] bond_distance;
delete [] angle_distance;
if (output_every) {
delete [] b_count;
delete [] b_count_all;
delete [] b_ave;
delete [] b_ave_all;
delete [] b_max;
delete [] b_max_all;
delete [] b_min;
delete [] b_min_all;
delete [] a_count;
delete [] a_count_all;
delete [] a_ave;
delete [] a_ave_all;
delete [] a_max;
delete [] a_max_all;
delete [] a_min;
delete [] a_min_all;
}
memory->sfree(list);
}
/* ---------------------------------------------------------------------- */
int FixShake::setmask()
{
int mask = 0;
mask |= PRE_NEIGHBOR;
mask |= POST_FORCE;
mask |= POST_FORCE_RESPA;
return mask;
}
/* ----------------------------------------------------------------------
set bond and angle distances
this init must happen after force->bond and force->angle inits
------------------------------------------------------------------------- */
void FixShake::init()
{
int i,m,flag,flag_all,type1,type2,bond1_type,bond2_type;
double rsq,angle;
// error if more than one shake fix
int count = 0;
for (i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"shake") == 0) count++;
if (count > 1) error->all("More than one fix shake");
// cannot use with minimization since SHAKE turns off bonds
// that should contribute to potential energy
if (update->whichflag == 2)
error->all("Fix shake cannot be used with minimization");
// error if npt,nph fix comes before shake fix
for (i = 0; i < modify->nfix; i++) {
if (strcmp(modify->fix[i]->style,"npt") == 0) break;
if (strcmp(modify->fix[i]->style,"nph") == 0) break;
}
if (i < modify->nfix) {
for (int j = i; j < modify->nfix; j++)
if (strcmp(modify->fix[j]->style,"shake") == 0)
error->all("Shake fix must come before NPT/NPH fix");
}
// if rRESPA, find associated fix that must exist
// could have changed locations in fix list since created
// set ptrs to rRESPA variables
if (strcmp(update->integrate_style,"respa") == 0) {
for (i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"RESPA") == 0) ifix_respa = i;
nlevels_respa = ((Respa *) update->integrate)->nlevels;
loop_respa = ((Respa *) update->integrate)->loop;
step_respa = ((Respa *) update->integrate)->step;
}
// set equilibrium bond distances
if (force->bond == NULL)
error->all("Bond potential must be defined for SHAKE");
for (i = 1; i <= atom->nbondtypes; i++)
bond_distance[i] = force->bond->equilibrium_distance(i);
// set equilibrium angle distances
int nlocal = atom->nlocal;
for (i = 1; i <= atom->nangletypes; i++) {
if (angle_flag[i] == 0) continue;
if (force->angle == NULL)
error->all("Angle potential must be defined for SHAKE");
// scan all atoms for a SHAKE angle cluster
// extract bond types for the 2 bonds in the cluster
// bond types must be same in all clusters of this angle type,
// else set error flag
flag = 0;
bond1_type = bond2_type = 0;
for (m = 0; m < nlocal; m++) {
if (shake_flag[m] != 1) continue;
if (shake_type[m][2] != i) continue;
type1 = MIN(shake_type[m][0],shake_type[m][1]);
type2 = MAX(shake_type[m][0],shake_type[m][1]);
if (bond1_type > 0) {
if (type1 != bond1_type || type2 != bond2_type) {
flag = 1;
break;
}
}
bond1_type = type1;
bond2_type = type2;
}
// error check for any bond types that are not the same
MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_MAX,world);
if (flag_all) error->all("Shake angles have different bond types");
// insure all procs have bond types
MPI_Allreduce(&bond1_type,&flag_all,1,MPI_INT,MPI_MAX,world);
bond1_type = flag_all;
MPI_Allreduce(&bond2_type,&flag_all,1,MPI_INT,MPI_MAX,world);
bond2_type = flag_all;
// if bond types are 0, no SHAKE angles of this type exist
// just skip this angle
if (bond1_type == 0) {
angle_distance[i] = 0.0;
continue;
}
// compute the angle distance as a function of 2 bond distances
angle = force->angle->equilibrium_angle(i);
rsq = 2.0*bond_distance[bond1_type]*bond_distance[bond2_type] *
(1.0-cos(angle));
angle_distance[i] = sqrt(rsq);
}
}
/* ----------------------------------------------------------------------
SHAKE as pre-integrator constraint
------------------------------------------------------------------------- */
void FixShake::setup(int vflag)
{
pre_neighbor();
if (output_every) stats();
// setup SHAKE output
bigint ntimestep = update->ntimestep;
next_output = ntimestep + output_every;
if (output_every == 0) next_output = update->laststep + 1;
if (output_every && ntimestep % output_every != 0)
next_output = (ntimestep/output_every)*output_every + output_every;
// half timestep constraint on pre-step, full timestep thereafter
if (strcmp(update->integrate_style,"verlet") == 0) {
dtv = update->dt;
dtfsq = 0.5 * update->dt * update->dt * force->ftm2v;
post_force(vflag);
dtfsq = update->dt * update->dt * force->ftm2v;
} else {
dtv = step_respa[0];
dtf_innerhalf = 0.5 * step_respa[0] * force->ftm2v;
dtf_inner = dtf_innerhalf;
((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
post_force_respa(vflag,nlevels_respa-1,0);
((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
dtf_inner = step_respa[0] * force->ftm2v;
}
}
/* ----------------------------------------------------------------------
build list of SHAKE clusters to constrain
if one or more atoms in cluster are on this proc,
this proc lists the cluster exactly once
------------------------------------------------------------------------- */
void FixShake::pre_neighbor()
{
int atom1,atom2,atom3,atom4;
// local copies of atom quantities
// used by SHAKE until next re-neighboring
x = atom->x;
v = atom->v;
f = atom->f;
mass = atom->mass;
rmass = atom->rmass;
type = atom->type;
nlocal = atom->nlocal;
// extend size of SHAKE list if necessary
if (nlocal > maxlist) {
maxlist = nlocal;
memory->sfree(list);
list = (int *) memory->smalloc(maxlist*sizeof(int),"shake:list");
}
// build list of SHAKE clusters I compute
nlist = 0;
for (int i = 0; i < nlocal; i++)
if (shake_flag[i]) {
if (shake_flag[i] == 2) {
atom1 = atom->map(shake_atom[i][0]);
atom2 = atom->map(shake_atom[i][1]);
if (atom1 == -1 || atom2 == -1) {
char str[128];
sprintf(str,
"Shake atoms %d %d missing on proc %d at step " BIGINT_FORMAT,
shake_atom[i][0],shake_atom[i][1],me,update->ntimestep);
error->one(str);
}
if (i <= atom1 && i <= atom2) list[nlist++] = i;
} else if (shake_flag[i] % 2 == 1) {
atom1 = atom->map(shake_atom[i][0]);
atom2 = atom->map(shake_atom[i][1]);
atom3 = atom->map(shake_atom[i][2]);
if (atom1 == -1 || atom2 == -1 || atom3 == -1) {
char str[128];
sprintf(str,
"Shake atoms %d %d %d missing on proc %d at step "
BIGINT_FORMAT,
shake_atom[i][0],shake_atom[i][1],shake_atom[i][2],
me,update->ntimestep);
error->one(str);
}
if (i <= atom1 && i <= atom2 && i <= atom3) list[nlist++] = i;
} else {
atom1 = atom->map(shake_atom[i][0]);
atom2 = atom->map(shake_atom[i][1]);
atom3 = atom->map(shake_atom[i][2]);
atom4 = atom->map(shake_atom[i][3]);
if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
char str[128];
sprintf(str,
"Shake atoms %d %d %d %d missing on proc %d at step "
BIGINT_FORMAT,
shake_atom[i][0],shake_atom[i][1],
shake_atom[i][2],shake_atom[i][3],
me,update->ntimestep);
error->one(str);
}
if (i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)
list[nlist++] = i;
}
}
}
/* ----------------------------------------------------------------------
compute the force adjustment for SHAKE constraint
------------------------------------------------------------------------- */
void FixShake::post_force(int vflag)
{
if (update->ntimestep == next_output) stats();
// xshake = unconstrained move with current v,f
// communicate results if necessary
unconstrained_update();
if (nprocs > 1) comm->forward_comm_fix(this);
// virial setup
if (vflag) v_setup(vflag);
else evflag = 0;
// loop over clusters to add constraint forces
int m;
for (int i = 0; i < nlist; i++) {
m = list[i];
if (shake_flag[m] == 2) shake2(m);
else if (shake_flag[m] == 3) shake3(m);
else if (shake_flag[m] == 4) shake4(m);
else shake3angle(m);
}
}
/* ----------------------------------------------------------------------
enforce SHAKE constraints from rRESPA
xshake prediction portion is different than Verlet
------------------------------------------------------------------------- */
void FixShake::post_force_respa(int vflag, int ilevel, int iloop)
{
// call stats only on outermost level
if (ilevel == nlevels_respa-1 && update->ntimestep == next_output) stats();
// enforce SHAKE constraints on every loop iteration of every rRESPA level
// except last loop iteration of inner levels
if (ilevel < nlevels_respa-1 && iloop == loop_respa[ilevel]-1) return;
// xshake = unconstrained move with current v,f as function of level
// communicate results if necessary
unconstrained_update_respa(ilevel);
if (nprocs > 1) comm->forward_comm_fix(this);
// virial setup, only need to compute on outermost level
if (ilevel == nlevels_respa-1 && vflag) v_setup(vflag);
else evflag = 0;
// loop over clusters to add constraint forces
int m;
for (int i = 0; i < nlist; i++) {
m = list[i];
if (shake_flag[m] == 2) shake2(m);
else if (shake_flag[m] == 3) shake3(m);
else if (shake_flag[m] == 4) shake4(m);
else shake3angle(m);
}
}
/* ----------------------------------------------------------------------
count # of degrees-of-freedom removed by SHAKE for atoms in igroup
------------------------------------------------------------------------- */
int FixShake::dof(int igroup)
{
int groupbit = group->bitmask[igroup];
int *mask = atom->mask;
int *tag = atom->tag;
int nlocal = atom->nlocal;
// count dof in a cluster if and only if
// the central atom is in group and atom i is the central atom
int n = 0;
for (int i = 0; i < nlocal; i++) {
if (!(mask[i] & groupbit)) continue;
if (shake_flag[i] == 0) continue;
if (shake_atom[i][0] != tag[i]) continue;
if (shake_flag[i] == 1) n += 3;
else if (shake_flag[i] == 2) n += 1;
else if (shake_flag[i] == 3) n += 2;
else if (shake_flag[i] == 4) n += 3;
}
int nall;
MPI_Allreduce(&n,&nall,1,MPI_INT,MPI_SUM,world);
return nall;
}
/* ----------------------------------------------------------------------
identify whether each atom is in a SHAKE cluster
only include atoms in fix group and those bonds/angles specified in input
test whether all clusters are valid
set shake_flag, shake_atom, shake_type values
set bond,angle types negative so will be ignored in neighbor lists
------------------------------------------------------------------------- */
void FixShake::find_clusters()
{
int i,j,m,n;
int flag,flag_all,messtag,loop,nbuf,nbufmax,size;
double massone;
int *buf,*bufcopy;
MPI_Request request;
MPI_Status status;
if (me == 0 && screen) fprintf(screen,"Finding SHAKE clusters ...\n");
// local copies of atom ptrs
int *tag = atom->tag;
int *type = atom->type;
int *mask = atom->mask;
double *mass = atom->mass;
double *rmass = atom->rmass;
int **bond_type = atom->bond_type;
int **angle_type = atom->angle_type;
int **nspecial = atom->nspecial;
int **special = atom->special;
int nlocal = atom->nlocal;
int angles_allow = atom->avec->angles_allow;
// setup ring of procs
int next = me + 1;
int prev = me -1;
if (next == nprocs) next = 0;
if (prev < 0) prev = nprocs - 1;
// -----------------------------------------------------
// allocate arrays for self (1d) and bond partners (2d)
// max = max # of bond partners for owned atoms = 2nd dim of partner arrays
// npartner[i] = # of bonds attached to atom i
// nshake[i] = # of SHAKE bonds attached to atom i
// partner_tag[i][] = global IDs of each partner
// partner_mask[i][] = mask of each partner
// partner_type[i][] = type of each partner
// partner_massflag[i][] = 1 if partner meets mass criterion, 0 if not
// partner_bondtype[i][] = type of bond attached to each partner
// partner_shake[i][] = 1 if SHAKE bonded to partner, 0 if not
// partner_nshake[i][] = nshake value for each partner
// -----------------------------------------------------
int max = 0;
for (i = 0; i < nlocal; i++) max = MAX(max,nspecial[i][0]);
int *npartner = (int *)
memory->smalloc(nlocal*sizeof(double),"shake:npartner");
int *nshake = (int *)
memory->smalloc(nlocal*sizeof(double),"shake:nshake");
int **partner_tag =
memory->create_2d_int_array(nlocal,max,"shake:partner_tag");
int **partner_mask =
memory->create_2d_int_array(nlocal,max,"shake:partner_mask");
int **partner_type =
memory->create_2d_int_array(nlocal,max,"shake:partner_type");
int **partner_massflag =
memory->create_2d_int_array(nlocal,max,"shake:partner_massflag");
int **partner_bondtype =
memory->create_2d_int_array(nlocal,max,"shake:partner_bondtype");
int **partner_shake =
memory->create_2d_int_array(nlocal,max,"shake:partner_shake");
int **partner_nshake =
memory->create_2d_int_array(nlocal,max,"shake:partner_nshake");
// -----------------------------------------------------
// set npartner and partner_tag from special arrays
// -----------------------------------------------------
for (i = 0; i < nlocal; i++) {
npartner[i] = nspecial[i][0];
for (j = 0; j < npartner[i]; j++) partner_tag[i][j] = special[i][j];
}
// -----------------------------------------------------
// set partner_mask, partner_type, partner_massflag, partner_bondtype
// for bonded partners
// requires communication for off-proc partners
// -----------------------------------------------------
// fill in mask, type, massflag, bondtype if own bond partner
// info to store in buf for each off-proc bond = nper = 6
// 2 atoms IDs in bond, space for mask, type, massflag, bondtype
// nbufmax = largest buffer needed to hold info from any proc
int nper = 6;
nbuf = 0;
for (i = 0; i < nlocal; i++) {
for (j = 0; j < npartner[i]; j++) {
partner_mask[i][j] = 0;
partner_type[i][j] = 0;
partner_massflag[i][j] = 0;
partner_bondtype[i][j] = 0;
m = atom->map(partner_tag[i][j]);
if (m >= 0 && m < nlocal) {
partner_mask[i][j] = mask[m];
partner_type[i][j] = type[m];
if (nmass) {
if (rmass) massone = rmass[m];
else massone = mass[type[m]];
partner_massflag[i][j] = masscheck(massone);
}
n = bondfind(i,tag[i],partner_tag[i][j]);
if (n >= 0) partner_bondtype[i][j] = bond_type[i][n];
else {
n = bondfind(m,tag[i],partner_tag[i][j]);
if (n >= 0) partner_bondtype[i][j] = bond_type[m][n];
}
} else nbuf += nper;
}
}
MPI_Allreduce(&nbuf,&nbufmax,1,MPI_INT,MPI_MAX,world);
buf = new int[nbufmax];
bufcopy = new int[nbufmax];
// fill buffer with info
size = 0;
for (i = 0; i < nlocal; i++) {
for (j = 0; j < npartner[i]; j++) {
m = atom->map(partner_tag[i][j]);
if (m < 0 || m >= nlocal) {
buf[size] = tag[i];
buf[size+1] = partner_tag[i][j];
buf[size+2] = 0;
buf[size+3] = 0;
buf[size+4] = 0;
n = bondfind(i,tag[i],partner_tag[i][j]);
if (n >= 0) buf[size+5] = bond_type[i][n];
else buf[size+5] = 0;
size += nper;
}
}
}
// cycle buffer around ring of procs back to self
// when receive buffer, scan bond partner IDs for atoms I own
// if I own partner:
// fill in mask and type and massflag
// search for bond with 1st atom and fill in bondtype
messtag = 1;
for (loop = 0; loop < nprocs; loop++) {
i = 0;
while (i < size) {
m = atom->map(buf[i+1]);
if (m >= 0 && m < nlocal) {
buf[i+2] = mask[m];
buf[i+3] = type[m];
if (nmass) {
if (rmass) massone = rmass[m];
else massone = mass[type[m]];
buf[i+4] = masscheck(massone);
}
if (buf[i+5] == 0) {
n = bondfind(m,buf[i],buf[i+1]);
if (n >= 0) buf[i+5] = bond_type[m][n];
}
}
i += nper;
}
if (me != next) {
MPI_Irecv(bufcopy,nbufmax,MPI_INT,prev,messtag,world,&request);
MPI_Send(buf,size,MPI_INT,next,messtag,world);
MPI_Wait(&request,&status);
MPI_Get_count(&status,MPI_INT,&size);
for (j = 0; j < size; j++) buf[j] = bufcopy[j];
}
}
// store partner info returned to me
m = 0;
while (m < size) {
i = atom->map(buf[m]);
for (j = 0; j < npartner[i]; j++)
if (buf[m+1] == partner_tag[i][j]) break;
partner_mask[i][j] = buf[m+2];
partner_type[i][j] = buf[m+3];
partner_massflag[i][j] = buf[m+4];
partner_bondtype[i][j] = buf[m+5];
m += nper;
}
delete [] buf;
delete [] bufcopy;
// error check for unfilled partner info
// if partner_type not set, is an error
// partner_bondtype may not be set if special list is not consistent
// with bondatom (e.g. due to delete_bonds command)
// this is OK if one or both atoms are not in fix group, since
// bond won't be SHAKEn anyway
// else it's an error
flag = 0;
for (i = 0; i < nlocal; i++)
for (j = 0; j < npartner[i]; j++) {
if (partner_type[i][j] == 0) flag = 1;
if (!(mask[i] & groupbit)) continue;
if (!(partner_mask[i][j] & groupbit)) continue;
if (partner_bondtype[i][j] == 0) flag = 1;
}
MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world);
if (flag_all) error->all("Did not find fix shake partner info");
// -----------------------------------------------------
// identify SHAKEable bonds
// set nshake[i] = # of SHAKE bonds attached to atom i
// set partner_shake[i][] = 1 if SHAKE bonded to partner, 0 if not
// both atoms must be in group, bondtype must be > 0
// check if bondtype is in input bond_flag
// check if type of either atom is in input type_flag
// check if mass of either atom is in input mass_list
// -----------------------------------------------------
int np;
for (i = 0; i < nlocal; i++) {
nshake[i] = 0;
np = npartner[i];
for (j = 0; j < np; j++) {
partner_shake[i][j] = 0;
if (!(mask[i] & groupbit)) continue;
if (!(partner_mask[i][j] & groupbit)) continue;
if (partner_bondtype[i][j] <= 0) continue;
if (bond_flag[partner_bondtype[i][j]]) {
partner_shake[i][j] = 1;
nshake[i]++;
continue;
}
if (type_flag[type[i]] || type_flag[partner_type[i][j]]) {
partner_shake[i][j] = 1;
nshake[i]++;
continue;
}
if (nmass) {
if (partner_massflag[i][j]) {
partner_shake[i][j] = 1;
nshake[i]++;
continue;
} else {
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
if (masscheck(massone)) {
partner_shake[i][j] = 1;
nshake[i]++;
continue;
}
}
}
}
}
// -----------------------------------------------------
// set partner_nshake for bonded partners
// requires communication for off-proc partners
// -----------------------------------------------------
// fill in partner_nshake if own bond partner
// info to store in buf for each off-proc bond =
// 2 atoms IDs in bond, space for nshake value
// nbufmax = largest buffer needed to hold info from any proc
nbuf = 0;
for (i = 0; i < nlocal; i++) {
for (j = 0; j < npartner[i]; j++) {
m = atom->map(partner_tag[i][j]);
if (m >= 0 && m < nlocal) partner_nshake[i][j] = nshake[m];
else nbuf += 3;
}
}
MPI_Allreduce(&nbuf,&nbufmax,1,MPI_INT,MPI_MAX,world);
buf = new int[nbufmax];
bufcopy = new int[nbufmax];
// fill buffer with info
size = 0;
for (i = 0; i < nlocal; i++) {
for (j = 0; j < npartner[i]; j++) {
m = atom->map(partner_tag[i][j]);
if (m < 0 || m >= nlocal) {
buf[size] = tag[i];
buf[size+1] = partner_tag[i][j];
size += 3;
}
}
}
// cycle buffer around ring of procs back to self
// when receive buffer, scan bond partner IDs for atoms I own
// if I own partner, fill in nshake value
messtag = 2;
for (loop = 0; loop < nprocs; loop++) {
i = 0;
while (i < size) {
m = atom->map(buf[i+1]);
if (m >= 0 && m < nlocal) buf[i+2] = nshake[m];
i += 3;
}
if (me != next) {
MPI_Irecv(bufcopy,nbufmax,MPI_INT,prev,messtag,world,&request);
MPI_Send(buf,size,MPI_INT,next,messtag,world);
MPI_Wait(&request,&status);
MPI_Get_count(&status,MPI_INT,&size);
for (j = 0; j < size; j++) buf[j] = bufcopy[j];
}
}
// store partner info returned to me
m = 0;
while (m < size) {
i = atom->map(buf[m]);
for (j = 0; j < npartner[i]; j++)
if (buf[m+1] == partner_tag[i][j]) break;
partner_nshake[i][j] = buf[m+2];
m += 3;
}
delete [] buf;
delete [] bufcopy;
// -----------------------------------------------------
// error checks
// no atom with nshake > 3
// no connected atoms which both have nshake > 1
// -----------------------------------------------------
flag = 0;
for (i = 0; i < nlocal; i++) if (nshake[i] > 3) flag = 1;
MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world);
if (flag_all) error->all("Shake cluster of more than 4 atoms");
flag = 0;
for (i = 0; i < nlocal; i++) {
if (nshake[i] <= 1) continue;
for (j = 0; j < npartner[i]; j++)
if (partner_shake[i][j] && partner_nshake[i][j] > 1) flag = 1;
}
MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world);
if (flag_all) error->all("Shake clusters are connected");
// -----------------------------------------------------
// set SHAKE arrays that are stored with atoms & add angle constraints
// zero shake arrays for all owned atoms
// if I am central atom set shake_flag & shake_atom & shake_type
// for 2-atom clusters, I am central atom if my atom ID < partner ID
// for 3-atom clusters, test for angle constraint
// angle will be stored by this atom if it exists
// if angle type matches angle_flag, then it is angle-constrained
// shake_flag[] = 0 if atom not in SHAKE cluster
// 2,3,4 = size of bond-only cluster
// 1 = 3-atom angle cluster
// shake_atom[][] = global IDs of 2,3,4 atoms in cluster
// central atom is 1st
// for 2-atom cluster, lowest ID is 1st
// shake_type[][] = bondtype of each bond in cluster
// for 3-atom angle cluster, 3rd value is angletype
// -----------------------------------------------------
for (i = 0; i < nlocal; i++) {
shake_flag[i] = 0;
shake_atom[i][0] = 0;
shake_atom[i][1] = 0;
shake_atom[i][2] = 0;
shake_atom[i][3] = 0;
shake_type[i][0] = 0;
shake_type[i][1] = 0;
shake_type[i][2] = 0;
if (nshake[i] == 1) {
for (j = 0; j < npartner[i]; j++)
if (partner_shake[i][j]) break;
if (partner_nshake[i][j] == 1 && tag[i] < partner_tag[i][j]) {
shake_flag[i] = 2;
shake_atom[i][0] = tag[i];
shake_atom[i][1] = partner_tag[i][j];
shake_type[i][0] = partner_bondtype[i][j];
}
}
if (nshake[i] > 1) {
shake_flag[i] = 1;
shake_atom[i][0] = tag[i];
for (j = 0; j < npartner[i]; j++)
if (partner_shake[i][j]) {
m = shake_flag[i];
shake_atom[i][m] = partner_tag[i][j];
shake_type[i][m-1] = partner_bondtype[i][j];
shake_flag[i]++;
}
}
if (nshake[i] == 2 && angles_allow) {
n = anglefind(i,shake_atom[i][1],shake_atom[i][2]);
if (n < 0) continue;
if (angle_type[i][n] < 0) continue;
if (angle_flag[angle_type[i][n]]) {
shake_flag[i] = 1;
shake_type[i][2] = angle_type[i][n];
}
}
}
// -----------------------------------------------------
// set shake_flag,shake_atom,shake_type for non-central atoms
// requires communication for off-proc atoms
// -----------------------------------------------------
// fill in shake arrays for each bond partner I own
// info to store in buf for each off-proc bond =
// all values from shake_flag, shake_atom, shake_type
// nbufmax = largest buffer needed to hold info from any proc
nbuf = 0;
for (i = 0; i < nlocal; i++) {
if (shake_flag[i] == 0) continue;
for (j = 0; j < npartner[i]; j++) {
if (partner_shake[i][j] == 0) continue;
m = atom->map(partner_tag[i][j]);
if (m >= 0 && m < nlocal) {
shake_flag[m] = shake_flag[i];
shake_atom[m][0] = shake_atom[i][0];
shake_atom[m][1] = shake_atom[i][1];
shake_atom[m][2] = shake_atom[i][2];
shake_atom[m][3] = shake_atom[i][3];
shake_type[m][0] = shake_type[i][0];
shake_type[m][1] = shake_type[i][1];
shake_type[m][2] = shake_type[i][2];
} else nbuf += 9;
}
}
MPI_Allreduce(&nbuf,&nbufmax,1,MPI_INT,MPI_MAX,world);
buf = new int[nbufmax];
bufcopy = new int[nbufmax];
// fill buffer with info
size = 0;
for (i = 0; i < nlocal; i++) {
if (shake_flag[i] == 0) continue;
for (j = 0; j < npartner[i]; j++) {
if (partner_shake[i][j] == 0) continue;
m = atom->map(partner_tag[i][j]);
if (m < 0 || m >= nlocal) {
buf[size] = partner_tag[i][j];
buf[size+1] = shake_flag[i];
buf[size+2] = shake_atom[i][0];
buf[size+3] = shake_atom[i][1];
buf[size+4] = shake_atom[i][2];
buf[size+5] = shake_atom[i][3];
buf[size+6] = shake_type[i][0];
buf[size+7] = shake_type[i][1];
buf[size+8] = shake_type[i][2];
size += 9;
}
}
}
// cycle buffer around ring of procs back to self
// when receive buffer, scan for ID that I own
// if I own ID, fill in shake array values
messtag = 3;
for (loop = 0; loop < nprocs; loop++) {
i = 0;
while (i < size) {
m = atom->map(buf[i]);
if (m >= 0 && m < nlocal) {
shake_flag[m] = buf[i+1];
shake_atom[m][0] = buf[i+2];
shake_atom[m][1] = buf[i+3];
shake_atom[m][2] = buf[i+4];
shake_atom[m][3] = buf[i+5];
shake_type[m][0] = buf[i+6];
shake_type[m][1] = buf[i+7];
shake_type[m][2] = buf[i+8];
}
i += 9;
}
if (me != next) {
MPI_Irecv(bufcopy,nbufmax,MPI_INT,prev,messtag,world,&request);
MPI_Send(buf,size,MPI_INT,next,messtag,world);
MPI_Wait(&request,&status);
MPI_Get_count(&status,MPI_INT,&size);
for (j = 0; j < size; j++) buf[j] = bufcopy[j];
}
}
delete [] buf;
delete [] bufcopy;
// -----------------------------------------------------
// free local memory
// -----------------------------------------------------
memory->sfree(npartner);
memory->sfree(nshake);
memory->destroy_2d_int_array(partner_tag);
memory->destroy_2d_int_array(partner_mask);
memory->destroy_2d_int_array(partner_type);
memory->destroy_2d_int_array(partner_massflag);
memory->destroy_2d_int_array(partner_bondtype);
memory->destroy_2d_int_array(partner_shake);
memory->destroy_2d_int_array(partner_nshake);
// -----------------------------------------------------
// set bond_type and angle_type negative for SHAKE clusters
// must set for all SHAKE bonds and angles stored by each atom
// -----------------------------------------------------
for (i = 0; i < nlocal; i++) {
if (shake_flag[i] == 0) continue;
else if (shake_flag[i] == 1) {
n = bondfind(i,shake_atom[i][0],shake_atom[i][1]);
if (n >= 0) bond_type[i][n] = -bond_type[i][n];
n = bondfind(i,shake_atom[i][0],shake_atom[i][2]);
if (n >= 0) bond_type[i][n] = -bond_type[i][n];
n = anglefind(i,shake_atom[i][1],shake_atom[i][2]);
if (n >= 0) angle_type[i][n] = -angle_type[i][n];
} else if (shake_flag[i] == 2) {
n = bondfind(i,shake_atom[i][0],shake_atom[i][1]);
if (n >= 0) bond_type[i][n] = -bond_type[i][n];
} else if (shake_flag[i] == 3) {
n = bondfind(i,shake_atom[i][0],shake_atom[i][1]);
if (n >= 0) bond_type[i][n] = -bond_type[i][n];
n = bondfind(i,shake_atom[i][0],shake_atom[i][2]);
if (n >= 0) bond_type[i][n] = -bond_type[i][n];
} else if (shake_flag[i] == 4) {
n = bondfind(i,shake_atom[i][0],shake_atom[i][1]);
if (n >= 0) bond_type[i][n] = -bond_type[i][n];
n = bondfind(i,shake_atom[i][0],shake_atom[i][2]);
if (n >= 0) bond_type[i][n] = -bond_type[i][n];
n = bondfind(i,shake_atom[i][0],shake_atom[i][3]);
if (n >= 0) bond_type[i][n] = -bond_type[i][n];
}
}
// -----------------------------------------------------
// print info on SHAKE clusters
// -----------------------------------------------------
int count1,count2,count3,count4;
count1 = count2 = count3 = count4 = 0;
for (i = 0; i < nlocal; i++) {
if (shake_flag[i] == 1) count1++;
else if (shake_flag[i] == 2) count2++;
else if (shake_flag[i] == 3) count3++;
else if (shake_flag[i] == 4) count4++;
}
int tmp;
tmp = count1;
MPI_Allreduce(&tmp,&count1,1,MPI_INT,MPI_SUM,world);
tmp = count2;
MPI_Allreduce(&tmp,&count2,1,MPI_INT,MPI_SUM,world);
tmp = count3;
MPI_Allreduce(&tmp,&count3,1,MPI_INT,MPI_SUM,world);
tmp = count4;
MPI_Allreduce(&tmp,&count4,1,MPI_INT,MPI_SUM,world);
if (me == 0) {
if (screen) {
fprintf(screen," %d = # of size 2 clusters\n",count2/2);
fprintf(screen," %d = # of size 3 clusters\n",count3/3);
fprintf(screen," %d = # of size 4 clusters\n",count4/4);
fprintf(screen," %d = # of frozen angles\n",count1/3);
}
if (logfile) {
fprintf(logfile," %d = # of size 2 clusters\n",count2/2);
fprintf(logfile," %d = # of size 3 clusters\n",count3/3);
fprintf(logfile," %d = # of size 4 clusters\n",count4/4);
fprintf(logfile," %d = # of frozen angles\n",count1/3);
}
}
}
/* ----------------------------------------------------------------------
check if massone is within MASSDELTA of any mass in mass_list
return 1 if yes, 0 if not
------------------------------------------------------------------------- */
int FixShake::masscheck(double massone)
{
for (int i = 0; i < nmass; i++)
if (fabs(mass_list[i]-massone) <= MASSDELTA) return 1;
return 0;
}
/* ----------------------------------------------------------------------
update the unconstrained position of each atom
only for SHAKE clusters, else set to 0.0
assumes NVE update, seems to be accurate enough for NVT,NPT,NPH as well
------------------------------------------------------------------------- */
void FixShake::unconstrained_update()
{
double dtfmsq;
if (rmass) {
for (int i = 0; i < nlocal; i++) {
if (shake_flag[i]) {
dtfmsq = dtfsq / rmass[i];
xshake[i][0] = x[i][0] + dtv*v[i][0] + dtfmsq*f[i][0];
xshake[i][1] = x[i][1] + dtv*v[i][1] + dtfmsq*f[i][1];
xshake[i][2] = x[i][2] + dtv*v[i][2] + dtfmsq*f[i][2];
} else xshake[i][2] = xshake[i][1] = xshake[i][0] = 0.0;
}
} else {
for (int i = 0; i < nlocal; i++) {
if (shake_flag[i]) {
dtfmsq = dtfsq / mass[type[i]];
xshake[i][0] = x[i][0] + dtv*v[i][0] + dtfmsq*f[i][0];
xshake[i][1] = x[i][1] + dtv*v[i][1] + dtfmsq*f[i][1];
xshake[i][2] = x[i][2] + dtv*v[i][2] + dtfmsq*f[i][2];
} else xshake[i][2] = xshake[i][1] = xshake[i][0] = 0.0;
}
}
}
/* ----------------------------------------------------------------------
update the unconstrained position of each atom in a rRESPA step
only for SHAKE clusters, else set to 0.0
assumes NVE update, seems to be accurate enough for NVT,NPT,NPH as well
------------------------------------------------------------------------- */
void FixShake::unconstrained_update_respa(int ilevel)
{
// xshake = atom coords after next x update in innermost loop
// depends on rRESPA level
// for levels > 0 this includes more than one velocity update
// xshake = predicted position from call to this routine at level N =
// x + dt0 (v + dtN/m fN + 1/2 dt(N-1)/m f(N-1) + ... + 1/2 dt0/m f0)
// also set dtfsq = dt0*dtN so that shake2,shake3,etc can use it
double ***f_level = ((FixRespa *) modify->fix[ifix_respa])->f_level;
dtfsq = dtf_inner * step_respa[ilevel];
double invmass,dtfmsq;
int jlevel;
if (rmass) {
for (int i = 0; i < nlocal; i++) {
if (shake_flag[i]) {
invmass = 1.0 / rmass[i];
dtfmsq = dtfsq * invmass;
xshake[i][0] = x[i][0] + dtv*v[i][0] + dtfmsq*f[i][0];
xshake[i][1] = x[i][1] + dtv*v[i][1] + dtfmsq*f[i][1];
xshake[i][2] = x[i][2] + dtv*v[i][2] + dtfmsq*f[i][2];
for (jlevel = 0; jlevel < ilevel; jlevel++) {
dtfmsq = dtf_innerhalf * step_respa[jlevel] * invmass;
xshake[i][0] += dtfmsq*f_level[i][jlevel][0];
xshake[i][1] += dtfmsq*f_level[i][jlevel][1];
xshake[i][2] += dtfmsq*f_level[i][jlevel][2];
}
} else xshake[i][2] = xshake[i][1] = xshake[i][0] = 0.0;
}
} else {
for (int i = 0; i < nlocal; i++) {
if (shake_flag[i]) {
invmass = 1.0 / mass[type[i]];
dtfmsq = dtfsq * invmass;
xshake[i][0] = x[i][0] + dtv*v[i][0] + dtfmsq*f[i][0];
xshake[i][1] = x[i][1] + dtv*v[i][1] + dtfmsq*f[i][1];
xshake[i][2] = x[i][2] + dtv*v[i][2] + dtfmsq*f[i][2];
for (jlevel = 0; jlevel < ilevel; jlevel++) {
dtfmsq = dtf_innerhalf * step_respa[jlevel] * invmass;
xshake[i][0] += dtfmsq*f_level[i][jlevel][0];
xshake[i][1] += dtfmsq*f_level[i][jlevel][1];
xshake[i][2] += dtfmsq*f_level[i][jlevel][2];
}
} else xshake[i][2] = xshake[i][1] = xshake[i][0] = 0.0;
}
}
}
/* ---------------------------------------------------------------------- */
void FixShake::shake2(int m)
{
int nlist,list[2];
double v[6];
double invmass0,invmass1;
// local atom IDs and constraint distances
int i0 = atom->map(shake_atom[m][0]);
int i1 = atom->map(shake_atom[m][1]);
double bond1 = bond_distance[shake_type[m][0]];
// r01 = distance vec between atoms, with PBC
double r01[3];
r01[0] = x[i0][0] - x[i1][0];
r01[1] = x[i0][1] - x[i1][1];
r01[2] = x[i0][2] - x[i1][2];
domain->minimum_image(r01);
// s01 = distance vec after unconstrained update, with PBC
double s01[3];
s01[0] = xshake[i0][0] - xshake[i1][0];
s01[1] = xshake[i0][1] - xshake[i1][1];
s01[2] = xshake[i0][2] - xshake[i1][2];
domain->minimum_image(s01);
// scalar distances between atoms
double r01sq = r01[0]*r01[0] + r01[1]*r01[1] + r01[2]*r01[2];
double s01sq = s01[0]*s01[0] + s01[1]*s01[1] + s01[2]*s01[2];
// a,b,c = coeffs in quadratic equation for lamda
if (rmass) {
invmass0 = 1.0/rmass[i0];
invmass1 = 1.0/rmass[i1];
} else {
invmass0 = 1.0/mass[type[i0]];
invmass1 = 1.0/mass[type[i1]];
}
double a = (invmass0+invmass1)*(invmass0+invmass1) * r01sq;
double b = 2.0 * (invmass0+invmass1) *
(s01[0]*r01[0] + s01[1]*r01[1] + s01[2]*r01[2]);
double c = s01sq - bond1*bond1;
// error check
double determ = b*b - 4.0*a*c;
if (determ < 0.0) {
error->warning("Shake determinant < 0.0",0);
determ = 0.0;
}
// exact quadratic solution for lamda
double lamda,lamda1,lamda2;
lamda1 = (-b+sqrt(determ)) / (2.0*a);
lamda2 = (-b-sqrt(determ)) / (2.0*a);
if (fabs(lamda1) <= fabs(lamda2)) lamda = lamda1;
else lamda = lamda2;
// update forces if atom is owned by this processor
lamda /= dtfsq;
if (i0 < nlocal) {
f[i0][0] += lamda*r01[0];
f[i0][1] += lamda*r01[1];
f[i0][2] += lamda*r01[2];
}
if (i1 < nlocal) {
f[i1][0] -= lamda*r01[0];
f[i1][1] -= lamda*r01[1];
f[i1][2] -= lamda*r01[2];
}
if (evflag) {
nlist = 0;
if (i0 < nlocal) list[nlist++] = i0;
if (i1 < nlocal) list[nlist++] = i1;
v[0] = lamda*r01[0]*r01[0];
v[1] = lamda*r01[1]*r01[1];
v[2] = lamda*r01[2]*r01[2];
v[3] = lamda*r01[0]*r01[1];
v[4] = lamda*r01[0]*r01[2];
v[5] = lamda*r01[1]*r01[2];
v_tally(nlist,list,2.0,v);
}
}
/* ---------------------------------------------------------------------- */
void FixShake::shake3(int m)
{
int nlist,list[3];
double v[6];
double invmass0,invmass1,invmass2;
// local atom IDs and constraint distances
int i0 = atom->map(shake_atom[m][0]);
int i1 = atom->map(shake_atom[m][1]);
int i2 = atom->map(shake_atom[m][2]);
double bond1 = bond_distance[shake_type[m][0]];
double bond2 = bond_distance[shake_type[m][1]];
// r01,r02 = distance vec between atoms, with PBC
double r01[3];
r01[0] = x[i0][0] - x[i1][0];
r01[1] = x[i0][1] - x[i1][1];
r01[2] = x[i0][2] - x[i1][2];
domain->minimum_image(r01);
double r02[3];
r02[0] = x[i0][0] - x[i2][0];
r02[1] = x[i0][1] - x[i2][1];
r02[2] = x[i0][2] - x[i2][2];
domain->minimum_image(r02);
// s01,s02 = distance vec after unconstrained update, with PBC
double s01[3];
s01[0] = xshake[i0][0] - xshake[i1][0];
s01[1] = xshake[i0][1] - xshake[i1][1];
s01[2] = xshake[i0][2] - xshake[i1][2];
domain->minimum_image(s01);
double s02[3];
s02[0] = xshake[i0][0] - xshake[i2][0];
s02[1] = xshake[i0][1] - xshake[i2][1];
s02[2] = xshake[i0][2] - xshake[i2][2];
domain->minimum_image(s02);
// scalar distances between atoms
double r01sq = r01[0]*r01[0] + r01[1]*r01[1] + r01[2]*r01[2];
double r02sq = r02[0]*r02[0] + r02[1]*r02[1] + r02[2]*r02[2];
double s01sq = s01[0]*s01[0] + s01[1]*s01[1] + s01[2]*s01[2];
double s02sq = s02[0]*s02[0] + s02[1]*s02[1] + s02[2]*s02[2];
// matrix coeffs and rhs for lamda equations
if (rmass) {
invmass0 = 1.0/rmass[i0];
invmass1 = 1.0/rmass[i1];
invmass2 = 1.0/rmass[i2];
} else {
invmass0 = 1.0/mass[type[i0]];
invmass1 = 1.0/mass[type[i1]];
invmass2 = 1.0/mass[type[i2]];
}
double a11 = 2.0 * (invmass0+invmass1) *
(s01[0]*r01[0] + s01[1]*r01[1] + s01[2]*r01[2]);
double a12 = 2.0 * invmass0 *
(s01[0]*r02[0] + s01[1]*r02[1] + s01[2]*r02[2]);
double a21 = 2.0 * invmass0 *
(s02[0]*r01[0] + s02[1]*r01[1] + s02[2]*r01[2]);
double a22 = 2.0 * (invmass0+invmass2) *
(s02[0]*r02[0] + s02[1]*r02[1] + s02[2]*r02[2]);
// inverse of matrix
double determ = a11*a22 - a12*a21;
if (determ == 0.0) error->one("Shake determinant = 0.0");
double determinv = 1.0/determ;
double a11inv = a22*determinv;
double a12inv = -a12*determinv;
double a21inv = -a21*determinv;
double a22inv = a11*determinv;
// quadratic correction coeffs
double r0102 = (r01[0]*r02[0] + r01[1]*r02[1] + r01[2]*r02[2]);
double quad1_0101 = (invmass0+invmass1)*(invmass0+invmass1) * r01sq;
double quad1_0202 = invmass0*invmass0 * r02sq;
double quad1_0102 = 2.0 * (invmass0+invmass1)*invmass0 * r0102;
double quad2_0202 = (invmass0+invmass2)*(invmass0+invmass2) * r02sq;
double quad2_0101 = invmass0*invmass0 * r01sq;
double quad2_0102 = 2.0 * (invmass0+invmass2)*invmass0 * r0102;
// iterate until converged
double lamda01 = 0.0;
double lamda02 = 0.0;
int niter = 0;
int done = 0;
double quad1,quad2,b1,b2,lamda01_new,lamda02_new;
while (!done && niter < max_iter) {
quad1 = quad1_0101 * lamda01*lamda01 + quad1_0202 * lamda02*lamda02 +
quad1_0102 * lamda01*lamda02;
quad2 = quad2_0101 * lamda01*lamda01 + quad2_0202 * lamda02*lamda02 +
quad2_0102 * lamda01*lamda02;
b1 = bond1*bond1 - s01sq - quad1;
b2 = bond2*bond2 - s02sq - quad2;
lamda01_new = a11inv*b1 + a12inv*b2;
lamda02_new = a21inv*b1 + a22inv*b2;
done = 1;
if (fabs(lamda01_new-lamda01) > tolerance) done = 0;
if (fabs(lamda02_new-lamda02) > tolerance) done = 0;
lamda01 = lamda01_new;
lamda02 = lamda02_new;
niter++;
}
// update forces if atom is owned by this processor
lamda01 = lamda01/dtfsq;
lamda02 = lamda02/dtfsq;
if (i0 < nlocal) {
f[i0][0] += lamda01*r01[0] + lamda02*r02[0];
f[i0][1] += lamda01*r01[1] + lamda02*r02[1];
f[i0][2] += lamda01*r01[2] + lamda02*r02[2];
}
if (i1 < nlocal) {
f[i1][0] -= lamda01*r01[0];
f[i1][1] -= lamda01*r01[1];
f[i1][2] -= lamda01*r01[2];
}
if (i2 < nlocal) {
f[i2][0] -= lamda02*r02[0];
f[i2][1] -= lamda02*r02[1];
f[i2][2] -= lamda02*r02[2];
}
if (evflag) {
nlist = 0;
if (i0 < nlocal) list[nlist++] = i0;
if (i1 < nlocal) list[nlist++] = i1;
if (i2 < nlocal) list[nlist++] = i2;
v[0] = lamda01*r01[0]*r01[0] + lamda02*r02[0]*r02[0];
v[1] = lamda01*r01[1]*r01[1] + lamda02*r02[1]*r02[1];
v[2] = lamda01*r01[2]*r01[2] + lamda02*r02[2]*r02[2];
v[3] = lamda01*r01[0]*r01[1] + lamda02*r02[0]*r02[1];
v[4] = lamda01*r01[0]*r01[2] + lamda02*r02[0]*r02[2];
v[5] = lamda01*r01[1]*r01[2] + lamda02*r02[1]*r02[2];
v_tally(nlist,list,3.0,v);
}
}
/* ---------------------------------------------------------------------- */
void FixShake::shake4(int m)
{
int nlist,list[4];
double v[6];
double invmass0,invmass1,invmass2,invmass3;
// local atom IDs and constraint distances
int i0 = atom->map(shake_atom[m][0]);
int i1 = atom->map(shake_atom[m][1]);
int i2 = atom->map(shake_atom[m][2]);
int i3 = atom->map(shake_atom[m][3]);
double bond1 = bond_distance[shake_type[m][0]];
double bond2 = bond_distance[shake_type[m][1]];
double bond3 = bond_distance[shake_type[m][2]];
// r01,r02,r03 = distance vec between atoms, with PBC
double r01[3];
r01[0] = x[i0][0] - x[i1][0];
r01[1] = x[i0][1] - x[i1][1];
r01[2] = x[i0][2] - x[i1][2];
domain->minimum_image(r01);
double r02[3];
r02[0] = x[i0][0] - x[i2][0];
r02[1] = x[i0][1] - x[i2][1];
r02[2] = x[i0][2] - x[i2][2];
domain->minimum_image(r02);
double r03[3];
r03[0] = x[i0][0] - x[i3][0];
r03[1] = x[i0][1] - x[i3][1];
r03[2] = x[i0][2] - x[i3][2];
domain->minimum_image(r03);
// s01,s02,s03 = distance vec after unconstrained update, with PBC
double s01[3];
s01[0] = xshake[i0][0] - xshake[i1][0];
s01[1] = xshake[i0][1] - xshake[i1][1];
s01[2] = xshake[i0][2] - xshake[i1][2];
domain->minimum_image(s01);
double s02[3];
s02[0] = xshake[i0][0] - xshake[i2][0];
s02[1] = xshake[i0][1] - xshake[i2][1];
s02[2] = xshake[i0][2] - xshake[i2][2];
domain->minimum_image(s02);
double s03[3];
s03[0] = xshake[i0][0] - xshake[i3][0];
s03[1] = xshake[i0][1] - xshake[i3][1];
s03[2] = xshake[i0][2] - xshake[i3][2];
domain->minimum_image(s03);
// scalar distances between atoms
double r01sq = r01[0]*r01[0] + r01[1]*r01[1] + r01[2]*r01[2];
double r02sq = r02[0]*r02[0] + r02[1]*r02[1] + r02[2]*r02[2];
double r03sq = r03[0]*r03[0] + r03[1]*r03[1] + r03[2]*r03[2];
double s01sq = s01[0]*s01[0] + s01[1]*s01[1] + s01[2]*s01[2];
double s02sq = s02[0]*s02[0] + s02[1]*s02[1] + s02[2]*s02[2];
double s03sq = s03[0]*s03[0] + s03[1]*s03[1] + s03[2]*s03[2];
// matrix coeffs and rhs for lamda equations
if (rmass) {
invmass0 = 1.0/rmass[i0];
invmass1 = 1.0/rmass[i1];
invmass2 = 1.0/rmass[i2];
invmass3 = 1.0/rmass[i3];
} else {
invmass0 = 1.0/mass[type[i0]];
invmass1 = 1.0/mass[type[i1]];
invmass2 = 1.0/mass[type[i2]];
invmass3 = 1.0/mass[type[i3]];
}
double a11 = 2.0 * (invmass0+invmass1) *
(s01[0]*r01[0] + s01[1]*r01[1] + s01[2]*r01[2]);
double a12 = 2.0 * invmass0 *
(s01[0]*r02[0] + s01[1]*r02[1] + s01[2]*r02[2]);
double a13 = 2.0 * invmass0 *
(s01[0]*r03[0] + s01[1]*r03[1] + s01[2]*r03[2]);
double a21 = 2.0 * invmass0 *
(s02[0]*r01[0] + s02[1]*r01[1] + s02[2]*r01[2]);
double a22 = 2.0 * (invmass0+invmass2) *
(s02[0]*r02[0] + s02[1]*r02[1] + s02[2]*r02[2]);
double a23 = 2.0 * invmass0 *
(s02[0]*r03[0] + s02[1]*r03[1] + s02[2]*r03[2]);
double a31 = 2.0 * invmass0 *
(s03[0]*r01[0] + s03[1]*r01[1] + s03[2]*r01[2]);
double a32 = 2.0 * invmass0 *
(s03[0]*r02[0] + s03[1]*r02[1] + s03[2]*r02[2]);
double a33 = 2.0 * (invmass0+invmass3) *
(s03[0]*r03[0] + s03[1]*r03[1] + s03[2]*r03[2]);
// inverse of matrix;
double determ = a11*a22*a33 + a12*a23*a31 + a13*a21*a32 -
a11*a23*a32 - a12*a21*a33 - a13*a22*a31;
if (determ == 0.0) error->one("Shake determinant = 0.0");
double determinv = 1.0/determ;
double a11inv = determinv * (a22*a33 - a23*a32);
double a12inv = -determinv * (a12*a33 - a13*a32);
double a13inv = determinv * (a12*a23 - a13*a22);
double a21inv = -determinv * (a21*a33 - a23*a31);
double a22inv = determinv * (a11*a33 - a13*a31);
double a23inv = -determinv * (a11*a23 - a13*a21);
double a31inv = determinv * (a21*a32 - a22*a31);
double a32inv = -determinv * (a11*a32 - a12*a31);
double a33inv = determinv * (a11*a22 - a12*a21);
// quadratic correction coeffs
double r0102 = (r01[0]*r02[0] + r01[1]*r02[1] + r01[2]*r02[2]);
double r0103 = (r01[0]*r03[0] + r01[1]*r03[1] + r01[2]*r03[2]);
double r0203 = (r02[0]*r03[0] + r02[1]*r03[1] + r02[2]*r03[2]);
double quad1_0101 = (invmass0+invmass1)*(invmass0+invmass1) * r01sq;
double quad1_0202 = invmass0*invmass0 * r02sq;
double quad1_0303 = invmass0*invmass0 * r03sq;
double quad1_0102 = 2.0 * (invmass0+invmass1)*invmass0 * r0102;
double quad1_0103 = 2.0 * (invmass0+invmass1)*invmass0 * r0103;
double quad1_0203 = 2.0 * invmass0*invmass0 * r0203;
double quad2_0101 = invmass0*invmass0 * r01sq;
double quad2_0202 = (invmass0+invmass2)*(invmass0+invmass2) * r02sq;
double quad2_0303 = invmass0*invmass0 * r03sq;
double quad2_0102 = 2.0 * (invmass0+invmass2)*invmass0 * r0102;
double quad2_0103 = 2.0 * invmass0*invmass0 * r0103;
double quad2_0203 = 2.0 * (invmass0+invmass2)*invmass0 * r0203;
double quad3_0101 = invmass0*invmass0 * r01sq;
double quad3_0202 = invmass0*invmass0 * r02sq;
double quad3_0303 = (invmass0+invmass3)*(invmass0+invmass3) * r03sq;
double quad3_0102 = 2.0 * invmass0*invmass0 * r0102;
double quad3_0103 = 2.0 * (invmass0+invmass3)*invmass0 * r0103;
double quad3_0203 = 2.0 * (invmass0+invmass3)*invmass0 * r0203;
// iterate until converged
double lamda01 = 0.0;
double lamda02 = 0.0;
double lamda03 = 0.0;
int niter = 0;
int done = 0;
double quad1,quad2,quad3,b1,b2,b3,lamda01_new,lamda02_new,lamda03_new;
while (!done && niter < max_iter) {
quad1 = quad1_0101 * lamda01*lamda01 +
quad1_0202 * lamda02*lamda02 +
quad1_0303 * lamda03*lamda03 +
quad1_0102 * lamda01*lamda02 +
quad1_0103 * lamda01*lamda03 +
quad1_0203 * lamda02*lamda03;
quad2 = quad2_0101 * lamda01*lamda01 +
quad2_0202 * lamda02*lamda02 +
quad2_0303 * lamda03*lamda03 +
quad2_0102 * lamda01*lamda02 +
quad2_0103 * lamda01*lamda03 +
quad2_0203 * lamda02*lamda03;
quad3 = quad3_0101 * lamda01*lamda01 +
quad3_0202 * lamda02*lamda02 +
quad3_0303 * lamda03*lamda03 +
quad3_0102 * lamda01*lamda02 +
quad3_0103 * lamda01*lamda03 +
quad3_0203 * lamda02*lamda03;
b1 = bond1*bond1 - s01sq - quad1;
b2 = bond2*bond2 - s02sq - quad2;
b3 = bond3*bond3 - s03sq - quad3;
lamda01_new = a11inv*b1 + a12inv*b2 + a13inv*b3;
lamda02_new = a21inv*b1 + a22inv*b2 + a23inv*b3;
lamda03_new = a31inv*b1 + a32inv*b2 + a33inv*b3;
done = 1;
if (fabs(lamda01_new-lamda01) > tolerance) done = 0;
if (fabs(lamda02_new-lamda02) > tolerance) done = 0;
if (fabs(lamda03_new-lamda03) > tolerance) done = 0;
lamda01 = lamda01_new;
lamda02 = lamda02_new;
lamda03 = lamda03_new;
niter++;
}
// update forces if atom is owned by this processor
lamda01 = lamda01/dtfsq;
lamda02 = lamda02/dtfsq;
lamda03 = lamda03/dtfsq;
if (i0 < nlocal) {
f[i0][0] += lamda01*r01[0] + lamda02*r02[0] + lamda03*r03[0];
f[i0][1] += lamda01*r01[1] + lamda02*r02[1] + lamda03*r03[1];
f[i0][2] += lamda01*r01[2] + lamda02*r02[2] + lamda03*r03[2];
}
if (i1 < nlocal) {
f[i1][0] -= lamda01*r01[0];
f[i1][1] -= lamda01*r01[1];
f[i1][2] -= lamda01*r01[2];
}
if (i2 < nlocal) {
f[i2][0] -= lamda02*r02[0];
f[i2][1] -= lamda02*r02[1];
f[i2][2] -= lamda02*r02[2];
}
if (i3 < nlocal) {
f[i3][0] -= lamda03*r03[0];
f[i3][1] -= lamda03*r03[1];
f[i3][2] -= lamda03*r03[2];
}
if (evflag) {
nlist = 0;
if (i0 < nlocal) list[nlist++] = i0;
if (i1 < nlocal) list[nlist++] = i1;
if (i2 < nlocal) list[nlist++] = i2;
if (i3 < nlocal) list[nlist++] = i3;
v[0] = lamda01*r01[0]*r01[0]+lamda02*r02[0]*r02[0]+lamda03*r03[0]*r03[0];
v[1] = lamda01*r01[1]*r01[1]+lamda02*r02[1]*r02[1]+lamda03*r03[1]*r03[1];
v[2] = lamda01*r01[2]*r01[2]+lamda02*r02[2]*r02[2]+lamda03*r03[2]*r03[2];
v[3] = lamda01*r01[0]*r01[1]+lamda02*r02[0]*r02[1]+lamda03*r03[0]*r03[1];
v[4] = lamda01*r01[0]*r01[2]+lamda02*r02[0]*r02[2]+lamda03*r03[0]*r03[2];
v[5] = lamda01*r01[1]*r01[2]+lamda02*r02[1]*r02[2]+lamda03*r03[1]*r03[2];
v_tally(nlist,list,4.0,v);
}
}
/* ---------------------------------------------------------------------- */
void FixShake::shake3angle(int m)
{
int nlist,list[3];
double v[6];
double invmass0,invmass1,invmass2;
// local atom IDs and constraint distances
int i0 = atom->map(shake_atom[m][0]);
int i1 = atom->map(shake_atom[m][1]);
int i2 = atom->map(shake_atom[m][2]);
double bond1 = bond_distance[shake_type[m][0]];
double bond2 = bond_distance[shake_type[m][1]];
double bond12 = angle_distance[shake_type[m][2]];
// r01,r02,r12 = distance vec between atoms, with PBC
double r01[3];
r01[0] = x[i0][0] - x[i1][0];
r01[1] = x[i0][1] - x[i1][1];
r01[2] = x[i0][2] - x[i1][2];
domain->minimum_image(r01);
double r02[3];
r02[0] = x[i0][0] - x[i2][0];
r02[1] = x[i0][1] - x[i2][1];
r02[2] = x[i0][2] - x[i2][2];
domain->minimum_image(r02);
double r12[3];
r12[0] = x[i1][0] - x[i2][0];
r12[1] = x[i1][1] - x[i2][1];
r12[2] = x[i1][2] - x[i2][2];
domain->minimum_image(r12);
// s01,s02,s12 = distance vec after unconstrained update, with PBC
double s01[3];
s01[0] = xshake[i0][0] - xshake[i1][0];
s01[1] = xshake[i0][1] - xshake[i1][1];
s01[2] = xshake[i0][2] - xshake[i1][2];
domain->minimum_image(s01);
double s02[3];
s02[0] = xshake[i0][0] - xshake[i2][0];
s02[1] = xshake[i0][1] - xshake[i2][1];
s02[2] = xshake[i0][2] - xshake[i2][2];
domain->minimum_image(s02);
double s12[3];
s12[0] = xshake[i1][0] - xshake[i2][0];
s12[1] = xshake[i1][1] - xshake[i2][1];
s12[2] = xshake[i1][2] - xshake[i2][2];
domain->minimum_image(s12);
// scalar distances between atoms
double r01sq = r01[0]*r01[0] + r01[1]*r01[1] + r01[2]*r01[2];
double r02sq = r02[0]*r02[0] + r02[1]*r02[1] + r02[2]*r02[2];
double r12sq = r12[0]*r12[0] + r12[1]*r12[1] + r12[2]*r12[2];
double s01sq = s01[0]*s01[0] + s01[1]*s01[1] + s01[2]*s01[2];
double s02sq = s02[0]*s02[0] + s02[1]*s02[1] + s02[2]*s02[2];
double s12sq = s12[0]*s12[0] + s12[1]*s12[1] + s12[2]*s12[2];
// matrix coeffs and rhs for lamda equations
if (rmass) {
invmass0 = 1.0/rmass[i0];
invmass1 = 1.0/rmass[i1];
invmass2 = 1.0/rmass[i2];
} else {
invmass0 = 1.0/mass[type[i0]];
invmass1 = 1.0/mass[type[i1]];
invmass2 = 1.0/mass[type[i2]];
}
double a11 = 2.0 * (invmass0+invmass1) *
(s01[0]*r01[0] + s01[1]*r01[1] + s01[2]*r01[2]);
double a12 = 2.0 * invmass0 *
(s01[0]*r02[0] + s01[1]*r02[1] + s01[2]*r02[2]);
double a13 = - 2.0 * invmass1 *
(s01[0]*r12[0] + s01[1]*r12[1] + s01[2]*r12[2]);
double a21 = 2.0 * invmass0 *
(s02[0]*r01[0] + s02[1]*r01[1] + s02[2]*r01[2]);
double a22 = 2.0 * (invmass0+invmass2) *
(s02[0]*r02[0] + s02[1]*r02[1] + s02[2]*r02[2]);
double a23 = 2.0 * invmass2 *
(s02[0]*r12[0] + s02[1]*r12[1] + s02[2]*r12[2]);
double a31 = - 2.0 * invmass1 *
(s12[0]*r01[0] + s12[1]*r01[1] + s12[2]*r01[2]);
double a32 = 2.0 * invmass2 *
(s12[0]*r02[0] + s12[1]*r02[1] + s12[2]*r02[2]);
double a33 = 2.0 * (invmass1+invmass2) *
(s12[0]*r12[0] + s12[1]*r12[1] + s12[2]*r12[2]);
// inverse of matrix
double determ = a11*a22*a33 + a12*a23*a31 + a13*a21*a32 -
a11*a23*a32 - a12*a21*a33 - a13*a22*a31;
if (determ == 0.0) error->one("Shake determinant = 0.0");
double determinv = 1.0/determ;
double a11inv = determinv * (a22*a33 - a23*a32);
double a12inv = -determinv * (a12*a33 - a13*a32);
double a13inv = determinv * (a12*a23 - a13*a22);
double a21inv = -determinv * (a21*a33 - a23*a31);
double a22inv = determinv * (a11*a33 - a13*a31);
double a23inv = -determinv * (a11*a23 - a13*a21);
double a31inv = determinv * (a21*a32 - a22*a31);
double a32inv = -determinv * (a11*a32 - a12*a31);
double a33inv = determinv * (a11*a22 - a12*a21);
// quadratic correction coeffs
double r0102 = (r01[0]*r02[0] + r01[1]*r02[1] + r01[2]*r02[2]);
double r0112 = (r01[0]*r12[0] + r01[1]*r12[1] + r01[2]*r12[2]);
double r0212 = (r02[0]*r12[0] + r02[1]*r12[1] + r02[2]*r12[2]);
double quad1_0101 = (invmass0+invmass1)*(invmass0+invmass1) * r01sq;
double quad1_0202 = invmass0*invmass0 * r02sq;
double quad1_1212 = invmass1*invmass1 * r12sq;
double quad1_0102 = 2.0 * (invmass0+invmass1)*invmass0 * r0102;
double quad1_0112 = - 2.0 * (invmass0+invmass1)*invmass1 * r0112;
double quad1_0212 = - 2.0 * invmass0*invmass1 * r0212;
double quad2_0101 = invmass0*invmass0 * r01sq;
double quad2_0202 = (invmass0+invmass2)*(invmass0+invmass2) * r02sq;
double quad2_1212 = invmass2*invmass2 * r12sq;
double quad2_0102 = 2.0 * (invmass0+invmass2)*invmass0 * r0102;
double quad2_0112 = 2.0 * invmass0*invmass2 * r0112;
double quad2_0212 = 2.0 * (invmass0+invmass2)*invmass2 * r0212;
double quad3_0101 = invmass1*invmass1 * r01sq;
double quad3_0202 = invmass2*invmass2 * r02sq;
double quad3_1212 = (invmass1+invmass2)*(invmass1+invmass2) * r12sq;
double quad3_0102 = - 2.0 * invmass1*invmass2 * r0102;
double quad3_0112 = - 2.0 * (invmass1+invmass2)*invmass1 * r0112;
double quad3_0212 = 2.0 * (invmass1+invmass2)*invmass2 * r0212;
// iterate until converged
double lamda01 = 0.0;
double lamda02 = 0.0;
double lamda12 = 0.0;
int niter = 0;
int done = 0;
double quad1,quad2,quad3,b1,b2,b3,lamda01_new,lamda02_new,lamda12_new;
while (!done && niter < max_iter) {
quad1 = quad1_0101 * lamda01*lamda01 +
quad1_0202 * lamda02*lamda02 +
quad1_1212 * lamda12*lamda12 +
quad1_0102 * lamda01*lamda02 +
quad1_0112 * lamda01*lamda12 +
quad1_0212 * lamda02*lamda12;
quad2 = quad2_0101 * lamda01*lamda01 +
quad2_0202 * lamda02*lamda02 +
quad2_1212 * lamda12*lamda12 +
quad2_0102 * lamda01*lamda02 +
quad2_0112 * lamda01*lamda12 +
quad2_0212 * lamda02*lamda12;
quad3 = quad3_0101 * lamda01*lamda01 +
quad3_0202 * lamda02*lamda02 +
quad3_1212 * lamda12*lamda12 +
quad3_0102 * lamda01*lamda02 +
quad3_0112 * lamda01*lamda12 +
quad3_0212 * lamda02*lamda12;
b1 = bond1*bond1 - s01sq - quad1;
b2 = bond2*bond2 - s02sq - quad2;
b3 = bond12*bond12 - s12sq - quad3;
lamda01_new = a11inv*b1 + a12inv*b2 + a13inv*b3;
lamda02_new = a21inv*b1 + a22inv*b2 + a23inv*b3;
lamda12_new = a31inv*b1 + a32inv*b2 + a33inv*b3;
done = 1;
if (fabs(lamda01_new-lamda01) > tolerance) done = 0;
if (fabs(lamda02_new-lamda02) > tolerance) done = 0;
if (fabs(lamda12_new-lamda12) > tolerance) done = 0;
lamda01 = lamda01_new;
lamda02 = lamda02_new;
lamda12 = lamda12_new;
niter++;
}
// update forces if atom is owned by this processor
lamda01 = lamda01/dtfsq;
lamda02 = lamda02/dtfsq;
lamda12 = lamda12/dtfsq;
if (i0 < nlocal) {
f[i0][0] += lamda01*r01[0] + lamda02*r02[0];
f[i0][1] += lamda01*r01[1] + lamda02*r02[1];
f[i0][2] += lamda01*r01[2] + lamda02*r02[2];
}
if (i1 < nlocal) {
f[i1][0] -= lamda01*r01[0] - lamda12*r12[0];
f[i1][1] -= lamda01*r01[1] - lamda12*r12[1];
f[i1][2] -= lamda01*r01[2] - lamda12*r12[2];
}
if (i2 < nlocal) {
f[i2][0] -= lamda02*r02[0] + lamda12*r12[0];
f[i2][1] -= lamda02*r02[1] + lamda12*r12[1];
f[i2][2] -= lamda02*r02[2] + lamda12*r12[2];
}
if (evflag) {
nlist = 0;
if (i0 < nlocal) list[nlist++] = i0;
if (i1 < nlocal) list[nlist++] = i1;
if (i2 < nlocal) list[nlist++] = i2;
v[0] = lamda01*r01[0]*r01[0]+lamda02*r02[0]*r02[0]+lamda12*r12[0]*r12[0];
v[1] = lamda01*r01[1]*r01[1]+lamda02*r02[1]*r02[1]+lamda12*r12[1]*r12[1];
v[2] = lamda01*r01[2]*r01[2]+lamda02*r02[2]*r02[2]+lamda12*r12[2]*r12[2];
v[3] = lamda01*r01[0]*r01[1]+lamda02*r02[0]*r02[1]+lamda12*r12[0]*r12[1];
v[4] = lamda01*r01[0]*r01[2]+lamda02*r02[0]*r02[2]+lamda12*r12[0]*r12[2];
v[5] = lamda01*r01[1]*r01[2]+lamda02*r02[1]*r02[2]+lamda12*r12[1]*r12[2];
v_tally(nlist,list,3.0,v);
}
}
/* ----------------------------------------------------------------------
print-out bond & angle statistics
------------------------------------------------------------------------- */
void FixShake::stats()
{
int i,j,m,n,iatom,jatom,katom;
double delx,dely,delz;
double r,r1,r2,r3,angle;
// zero out accumulators
int nb = atom->nbondtypes + 1;
int na = atom->nangletypes + 1;
for (i = 0; i < nb; i++) {
b_count[i] = 0;
b_ave[i] = b_max[i] = 0.0;
b_min[i] = BIG;
}
for (i = 0; i < na; i++) {
a_count[i] = 0;
a_ave[i] = a_max[i] = 0.0;
a_min[i] = BIG;
}
// log stats for each bond & angle
// OK to double count since are just averaging
double **x = atom->x;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
if (shake_flag[i] == 0) continue;
// bond stats
n = shake_flag[i];
if (n == 1) n = 3;
iatom = atom->map(shake_atom[i][0]);
for (j = 1; j < n; j++) {
jatom = atom->map(shake_atom[i][j]);
delx = x[iatom][0] - x[jatom][0];
dely = x[iatom][1] - x[jatom][1];
delz = x[iatom][2] - x[jatom][2];
domain->minimum_image(delx,dely,delz);
r = sqrt(delx*delx + dely*dely + delz*delz);
m = shake_type[i][j-1];
b_count[m]++;
b_ave[m] += r;
b_max[m] = MAX(b_max[m],r);
b_min[m] = MIN(b_min[m],r);
}
// angle stats
if (shake_flag[i] == 1) {
iatom = atom->map(shake_atom[i][0]);
jatom = atom->map(shake_atom[i][1]);
katom = atom->map(shake_atom[i][2]);
delx = x[iatom][0] - x[jatom][0];
dely = x[iatom][1] - x[jatom][1];
delz = x[iatom][2] - x[jatom][2];
domain->minimum_image(delx,dely,delz);
r1 = sqrt(delx*delx + dely*dely + delz*delz);
delx = x[iatom][0] - x[katom][0];
dely = x[iatom][1] - x[katom][1];
delz = x[iatom][2] - x[katom][2];
domain->minimum_image(delx,dely,delz);
r2 = sqrt(delx*delx + dely*dely + delz*delz);
delx = x[jatom][0] - x[katom][0];
dely = x[jatom][1] - x[katom][1];
delz = x[jatom][2] - x[katom][2];
domain->minimum_image(delx,dely,delz);
r3 = sqrt(delx*delx + dely*dely + delz*delz);
angle = acos((r1*r1 + r2*r2 - r3*r3) / (2.0*r1*r2));
angle *= 180.0/PI;
m = shake_type[i][2];
a_count[m]++;
a_ave[m] += angle;
a_max[m] = MAX(a_max[m],angle);
a_min[m] = MIN(a_min[m],angle);
}
}
// sum across all procs
MPI_Allreduce(b_count,b_count_all,nb,MPI_INT,MPI_SUM,world);
MPI_Allreduce(b_ave,b_ave_all,nb,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(b_max,b_max_all,nb,MPI_DOUBLE,MPI_MAX,world);
MPI_Allreduce(b_min,b_min_all,nb,MPI_DOUBLE,MPI_MIN,world);
MPI_Allreduce(a_count,a_count_all,na,MPI_INT,MPI_SUM,world);
MPI_Allreduce(a_ave,a_ave_all,na,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(a_max,a_max_all,na,MPI_DOUBLE,MPI_MAX,world);
MPI_Allreduce(a_min,a_min_all,na,MPI_DOUBLE,MPI_MIN,world);
// print stats only for non-zero counts
if (me == 0) {
if (screen) {
fprintf(screen,
"SHAKE stats (type/ave/delta) on step " BIGINT_FORMAT "\n",
update->ntimestep);
for (i = 1; i < nb; i++)
if (b_count_all[i])
fprintf(screen," %d %g %g\n",i,
b_ave_all[i]/b_count_all[i],b_max_all[i]-b_min_all[i]);
for (i = 1; i < na; i++)
if (a_count_all[i])
fprintf(screen," %d %g %g\n",i,
a_ave_all[i]/a_count_all[i],a_max_all[i]-a_min_all[i]);
}
if (logfile) {
fprintf(logfile,
"SHAKE stats (type/ave/delta) on step " BIGINT_FORMAT "\n",
update->ntimestep);
for (i = 0; i < nb; i++)
if (b_count_all[i])
fprintf(logfile," %d %g %g\n",i,
b_ave_all[i]/b_count_all[i],b_max_all[i]-b_min_all[i]);
for (i = 0; i < na; i++)
if (a_count_all[i])
fprintf(logfile," %d %g %g\n",i,
a_ave_all[i]/a_count_all[i],a_max_all[i]-a_min_all[i]);
}
}
// next timestep for stats
next_output += output_every;
}
/* ----------------------------------------------------------------------
find a bond between global tags n1 and n2 stored with local atom i
return -1 if don't find it
return bond index if do find it
------------------------------------------------------------------------- */
int FixShake::bondfind(int i, int n1, int n2)
{
int *tag = atom->tag;
int **bond_atom = atom->bond_atom;
int nbonds = atom->num_bond[i];
int m;
for (m = 0; m < nbonds; m++) {
if (n1 == tag[i] && n2 == bond_atom[i][m]) break;
if (n1 == bond_atom[i][m] && n2 == tag[i]) break;
}
if (m < nbonds) return m;
return -1;
}
/* ----------------------------------------------------------------------
find an angle with global end atoms n1 and n2 stored with local atom i
return -1 if don't find it
return angle index if do find it
------------------------------------------------------------------------- */
int FixShake::anglefind(int i, int n1, int n2)
{
int **angle_atom1 = atom->angle_atom1;
int **angle_atom3 = atom->angle_atom3;
int nangles = atom->num_angle[i];
int m;
for (m = 0; m < nangles; m++) {
if (n1 == angle_atom1[i][m] && n2 == angle_atom3[i][m]) break;
if (n1 == angle_atom3[i][m] && n2 == angle_atom1[i][m]) break;
}
if (m < nangles) return m;
return -1;
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double FixShake::memory_usage()
{
int nmax = atom->nmax;
double bytes = nmax * sizeof(int);
bytes += nmax*4 * sizeof(int);
bytes += nmax*3 * sizeof(int);
bytes += nmax*3 * sizeof(double);
bytes += maxvatom*6 * sizeof(double);
return bytes;
}
/* ----------------------------------------------------------------------
allocate local atom-based arrays
------------------------------------------------------------------------- */
void FixShake::grow_arrays(int nmax)
{
shake_flag = (int *)
memory->srealloc(shake_flag,nmax*sizeof(int),"shake:shake_flag");
shake_atom =
memory->grow_2d_int_array(shake_atom,nmax,4,"shake:shake_atom");
shake_type =
memory->grow_2d_int_array(shake_type,nmax,3,"shake:shake_type");
memory->destroy_2d_double_array(xshake);
xshake = memory->create_2d_double_array(nmax,3,"shake:xshake");
}
/* ----------------------------------------------------------------------
copy values within local atom-based arrays
------------------------------------------------------------------------- */
void FixShake::copy_arrays(int i, int j)
{
int flag = shake_flag[j] = shake_flag[i];
if (flag == 1) {
shake_atom[j][0] = shake_atom[i][0];
shake_atom[j][1] = shake_atom[i][1];
shake_atom[j][2] = shake_atom[i][2];
shake_type[j][0] = shake_type[i][0];
shake_type[j][1] = shake_type[i][1];
shake_type[j][2] = shake_type[i][2];
} else if (flag == 2) {
shake_atom[j][0] = shake_atom[i][0];
shake_atom[j][1] = shake_atom[i][1];
shake_type[j][0] = shake_type[i][0];
} else if (flag == 3) {
shake_atom[j][0] = shake_atom[i][0];
shake_atom[j][1] = shake_atom[i][1];
shake_atom[j][2] = shake_atom[i][2];
shake_type[j][0] = shake_type[i][0];
shake_type[j][1] = shake_type[i][1];
} else if (flag == 4) {
shake_atom[j][0] = shake_atom[i][0];
shake_atom[j][1] = shake_atom[i][1];
shake_atom[j][2] = shake_atom[i][2];
shake_atom[j][3] = shake_atom[i][3];
shake_type[j][0] = shake_type[i][0];
shake_type[j][1] = shake_type[i][1];
shake_type[j][2] = shake_type[i][2];
}
}
/* ----------------------------------------------------------------------
initialize one atom's array values, called when atom is created
------------------------------------------------------------------------- */
void FixShake::set_arrays(int i)
{
shake_flag[i] = 0;
}
/* ----------------------------------------------------------------------
pack values in local atom-based arrays for exchange with another proc
------------------------------------------------------------------------- */
int FixShake::pack_exchange(int i, double *buf)
{
int m = 0;
buf[m++] = shake_flag[i];
int flag = shake_flag[i];
if (flag == 1) {
buf[m++] = shake_atom[i][0];
buf[m++] = shake_atom[i][1];
buf[m++] = shake_atom[i][2];
buf[m++] = shake_type[i][0];
buf[m++] = shake_type[i][1];
buf[m++] = shake_type[i][2];
} else if (flag == 2) {
buf[m++] = shake_atom[i][0];
buf[m++] = shake_atom[i][1];
buf[m++] = shake_type[i][0];
} else if (flag == 3) {
buf[m++] = shake_atom[i][0];
buf[m++] = shake_atom[i][1];
buf[m++] = shake_atom[i][2];
buf[m++] = shake_type[i][0];
buf[m++] = shake_type[i][1];
} else if (flag == 4) {
buf[m++] = shake_atom[i][0];
buf[m++] = shake_atom[i][1];
buf[m++] = shake_atom[i][2];
buf[m++] = shake_atom[i][3];
buf[m++] = shake_type[i][0];
buf[m++] = shake_type[i][1];
buf[m++] = shake_type[i][2];
}
return m;
}
/* ----------------------------------------------------------------------
unpack values in local atom-based arrays from exchange with another proc
------------------------------------------------------------------------- */
int FixShake::unpack_exchange(int nlocal, double *buf)
{
int m = 0;
int flag = shake_flag[nlocal] = static_cast<int> (buf[m++]);
if (flag == 1) {
shake_atom[nlocal][0] = static_cast<int> (buf[m++]);
shake_atom[nlocal][1] = static_cast<int> (buf[m++]);
shake_atom[nlocal][2] = static_cast<int> (buf[m++]);
shake_type[nlocal][0] = static_cast<int> (buf[m++]);
shake_type[nlocal][1] = static_cast<int> (buf[m++]);
shake_type[nlocal][2] = static_cast<int> (buf[m++]);
} else if (flag == 2) {
shake_atom[nlocal][0] = static_cast<int> (buf[m++]);
shake_atom[nlocal][1] = static_cast<int> (buf[m++]);
shake_type[nlocal][0] = static_cast<int> (buf[m++]);
} else if (flag == 3) {
shake_atom[nlocal][0] = static_cast<int> (buf[m++]);
shake_atom[nlocal][1] = static_cast<int> (buf[m++]);
shake_atom[nlocal][2] = static_cast<int> (buf[m++]);
shake_type[nlocal][0] = static_cast<int> (buf[m++]);
shake_type[nlocal][1] = static_cast<int> (buf[m++]);
} else if (flag == 4) {
shake_atom[nlocal][0] = static_cast<int> (buf[m++]);
shake_atom[nlocal][1] = static_cast<int> (buf[m++]);
shake_atom[nlocal][2] = static_cast<int> (buf[m++]);
shake_atom[nlocal][3] = static_cast<int> (buf[m++]);
shake_type[nlocal][0] = static_cast<int> (buf[m++]);
shake_type[nlocal][1] = static_cast<int> (buf[m++]);
shake_type[nlocal][2] = static_cast<int> (buf[m++]);
}
return m;
}
/* ---------------------------------------------------------------------- */
int FixShake::pack_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
m = 0;
if (pbc_flag == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = xshake[j][0];
buf[m++] = xshake[j][1];
buf[m++] = xshake[j][2];
}
} else {
if (domain->triclinic == 0) {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
dz = pbc[2]*domain->zprd;
} else {
dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
dz = pbc[2]*domain->zprd;
}
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = xshake[j][0] + dx;
buf[m++] = xshake[j][1] + dy;
buf[m++] = xshake[j][2] + dz;
}
}
return 3;
}
/* ---------------------------------------------------------------------- */
void FixShake::unpack_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
xshake[i][0] = buf[m++];
xshake[i][1] = buf[m++];
xshake[i][2] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
void FixShake::reset_dt()
{
if (strcmp(update->integrate_style,"verlet") == 0) {
dtv = update->dt;
dtfsq = update->dt * update->dt * force->ftm2v;
} else {
dtv = step_respa[0];
dtf_innerhalf = 0.5 * step_respa[0] * force->ftm2v;
dtf_inner = step_respa[0] * force->ftm2v;
}
}
diff --git a/src/fix_shake.h b/src/fix_shake.h
index fc919aaa1..ef061dc9d 100644
--- a/src/fix_shake.h
+++ b/src/fix_shake.h
@@ -1,119 +1,119 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
FixStyle(shake,FixShake)
#else
#ifndef LMP_FIX_SHAKE_H
#define LMP_FIX_SHAKE_H
-#include "fix.h"
#include "lmptype.h"
+#include "fix.h"
namespace LAMMPS_NS {
class FixShake : public Fix {
public:
FixShake(class LAMMPS *, int, char **);
~FixShake();
int setmask();
void init();
void setup(int);
void pre_neighbor();
void post_force(int);
void post_force_respa(int, int, int);
double memory_usage();
void grow_arrays(int);
void copy_arrays(int, int);
void set_arrays(int);
int pack_exchange(int, double *);
int unpack_exchange(int, double *);
int pack_comm(int, int *, double *, int, int *);
void unpack_comm(int, int, double *);
int dof(int);
void reset_dt();
private:
int me,nprocs;
double PI;
double tolerance; // SHAKE tolerance
int max_iter; // max # of SHAKE iterations
int output_every; // SHAKE stat output every so often
bigint next_output; // timestep for next output
// settings from input command
int *bond_flag,*angle_flag; // bond/angle types to constrain
int *type_flag; // constrain bonds to these types
double *mass_list; // constrain bonds to these masses
int nmass; // # of masses in mass_list
double *bond_distance,*angle_distance; // constraint distances
int ifix_respa; // rRESPA fix needed by SHAKE
int nlevels_respa; // copies of needed rRESPA variables
int *loop_respa;
double *step_respa;
double **x,**v,**f; // local ptrs to atom class quantities
double *mass,*rmass;
int *type;
int nlocal;
// atom-based arrays
int *shake_flag; // 0 if atom not in SHAKE cluster
// 1 = size 3 angle cluster
// 2,3,4 = size of bond-only cluster
int **shake_atom; // global IDs of atoms in cluster
// central atom is 1st
// lowest global ID is 1st for size 2
int **shake_type; // bondtype of each bond in cluster
// for angle cluster, 3rd value
// is angletype
double **xshake; // unconstrained atom coords
int vflag; // virial flag
double dtv,dtfsq; // timesteps for trial move
double dtf_inner,dtf_innerhalf; // timesteps for rRESPA trial move
int *list; // list of clusters to SHAKE
int nlist,maxlist; // size and max-size of list
// stat quantities
int *b_count,*b_count_all; // counts for each bond type
double *b_ave,*b_max,*b_min; // ave/max/min dist for each bond type
double *b_ave_all,*b_max_all,*b_min_all; // MPI summing arrays
int *a_count,*a_count_all; // ditto for angle types
double *a_ave,*a_max,*a_min;
double *a_ave_all,*a_max_all,*a_min_all;
void find_clusters();
int masscheck(double);
void unconstrained_update();
void unconstrained_update_respa(int);
void shake2(int);
void shake3(int);
void shake4(int);
void shake3angle(int);
void stats();
int bondfind(int, int, int);
int anglefind(int, int, int);
};
}
#endif
#endif
diff --git a/src/fix_tmd.cpp b/src/fix_tmd.cpp
index 24cb8bc8f..496b50861 100644
--- a/src/fix_tmd.cpp
+++ b/src/fix_tmd.cpp
@@ -1,561 +1,561 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Paul Crozier (SNL)
Christian Burisch (Bochum Univeristy, Germany)
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "mpi.h"
#include "math.h"
#include "stdlib.h"
#include "string.h"
#include "fix_tmd.h"
-#include "lmptype.h"
#include "atom.h"
#include "update.h"
#include "modify.h"
#include "domain.h"
#include "group.h"
#include "respa.h"
#include "force.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define CHUNK 1000
#define MAXLINE 256
/* ---------------------------------------------------------------------- */
FixTMD::FixTMD(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 6) error->all("Illegal fix tmd command");
rho_stop = atof(arg[3]);
nfileevery = atoi(arg[5]);
if (rho_stop < 0 || nfileevery < 0) error->all("Illegal fix tmd command");
if (nfileevery && narg != 7) error->all("Illegal fix tmd command");
MPI_Comm_rank(world,&me);
// perform initial allocation of atom-based arrays
// register with Atom class
xf = NULL;
xold = NULL;
grow_arrays(atom->nmax);
atom->add_callback(0);
// make sure an atom map exists before reading in target coordinates
if (atom->map_style == 0)
error->all("Cannot use fix TMD unless atom map exists");
// read from arg[4] and store coordinates of final target in xf
readfile(arg[4]);
// open arg[6] statistics file and write header
if (nfileevery) {
if (narg != 7) error->all("Illegal fix tmd command");
if (me == 0) {
fp = fopen(arg[6],"w");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open fix tmd file %s",arg[6]);
error->one(str);
}
fprintf(fp,"%s %s\n","# Step rho_target rho_old gamma_back",
"gamma_forward lambda work_lambda work_analytical");
}
}
masstotal = group->mass(igroup);
// rho_start = initial rho
// xold = initial x or 0.0 if not in group
int *mask = atom->mask;
int *type = atom->type;
int *image = atom->image;
double **x = atom->x;
double *mass = atom->mass;
int nlocal = atom->nlocal;
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
double dx,dy,dz;
int xbox,ybox,zbox;
rho_start = 0.0;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
xbox = (image[i] & 1023) - 512;
ybox = (image[i] >> 10 & 1023) - 512;
zbox = (image[i] >> 20) - 512;
dx = x[i][0] + xbox*xprd - xf[i][0];
dy = x[i][1] + ybox*yprd - xf[i][1];
dz = x[i][2] + zbox*zprd - xf[i][2];
rho_start += mass[type[i]]*(dx*dx + dy*dy + dz*dz);
xold[i][0] = x[i][0] + xbox*xprd;
xold[i][1] = x[i][1] + ybox*yprd;
xold[i][2] = x[i][2] + zbox*zprd;
} else xold[i][0] = xold[i][1] = xold[i][2] = 0.0;
}
double rho_start_total;
MPI_Allreduce(&rho_start,&rho_start_total,1,MPI_DOUBLE,MPI_SUM,world);
rho_start = sqrt(rho_start_total/masstotal);
rho_old = rho_start;
work_lambda = 0.0;
work_analytical = 0.0;
previous_stat = 0;
}
/* ---------------------------------------------------------------------- */
FixTMD::~FixTMD()
{
if (nfileevery && me == 0) fclose(fp);
// unregister callbacks to this fix from Atom class
atom->delete_callback(id,0);
// delete locally stored arrays
memory->destroy_2d_double_array(xf);
memory->destroy_2d_double_array(xold);
}
/* ---------------------------------------------------------------------- */
int FixTMD::setmask()
{
int mask = 0;
mask |= INITIAL_INTEGRATE;
mask |= INITIAL_INTEGRATE_RESPA;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixTMD::init()
{
// check that no integrator fix comes after a TMD fix
int flag = 0;
for (int i = 0; i < modify->nfix; i++) {
if (strcmp(modify->fix[i]->style,"tmd") == 0) flag = 1;
if (flag && strcmp(modify->fix[i]->style,"nve") == 0) flag = 2;
if (flag && strcmp(modify->fix[i]->style,"nvt") == 0) flag = 2;
if (flag && strcmp(modify->fix[i]->style,"npt") == 0) flag = 2;
if (flag && strcmp(modify->fix[i]->style,"nph") == 0) flag = 2;
}
if (flag == 2) error->all("Fix tmd must come after integration fixes");
// timesteps
dtv = update->dt;
dtf = update->dt * force->ftm2v;
if (strcmp(update->integrate_style,"respa") == 0)
step_respa = ((Respa *) update->integrate)->step;
}
/* ---------------------------------------------------------------------- */
void FixTMD::initial_integrate(int vflag)
{
double a,b,c,d,e;
double dx,dy,dz,dxkt,dykt,dzkt;
double dxold,dyold,dzold,xback,yback,zback;
double gamma_forward,gamma_back,gamma_max,lambda;
double kt,fr,kttotal,frtotal,dtfm;
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
double *mass = atom->mass;
int *image = atom->image;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int xbox,ybox,zbox;
double delta = update->ntimestep - update->beginstep;
delta /= update->endstep - update->beginstep;
double rho_target = rho_start + delta * (rho_stop - rho_start);
// compute the Lagrange multiplier
a = b = e = 0.0;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dxold = xold[i][0] - xf[i][0];
dyold = xold[i][1] - xf[i][1];
dzold = xold[i][2] - xf[i][2];
xbox = (image[i] & 1023) - 512;
ybox = (image[i] >> 10 & 1023) - 512;
zbox = (image[i] >> 20) - 512;
dx = x[i][0] + xbox*xprd - xf[i][0];
dy = x[i][1] + ybox*yprd - xf[i][1];
dz = x[i][2] + zbox*zprd - xf[i][2];
a += mass[type[i]]*(dxold*dxold + dyold*dyold + dzold*dzold);
b += mass[type[i]]*(dx *dxold + dy *dyold + dz *dzold);
e += mass[type[i]]*(dx *dx + dy *dy + dz *dz);
}
}
double abe[3],abetotal[3];
abe[0] = a; abe[1] = b; abe[2] = e;
MPI_Allreduce(abe,abetotal,3,MPI_DOUBLE,MPI_SUM,world);
a = abetotal[0]/masstotal;
b = 2.0*abetotal[1]/masstotal;
e = abetotal[2]/masstotal;
c = e - rho_old*rho_old;
d = b*b - 4*a*c;
if (d < 0) d = 0;
if (b >= 0) gamma_max = (-b - sqrt(d))/(2*a);
else gamma_max = (-b + sqrt(d))/(2*a);
gamma_back = c/(a*gamma_max);
if (a == 0.0) gamma_back = 0;
c = e - rho_target*rho_target;
d = b*b - 4*a*c;
if (d < 0) d = 0;
if (b >= 0) gamma_max = (-b - sqrt(d))/(2*a);
else gamma_max = (-b + sqrt(d))/(2*a);
gamma_forward = c/(a*gamma_max);
if (a == 0.0) gamma_forward = 0;
fr = kt = 0.0;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dxold = xold[i][0] - xf[i][0];
dyold = xold[i][1] - xf[i][1];
dzold = xold[i][2] - xf[i][2];
xbox = (image[i] & 1023) - 512;
ybox = (image[i] >> 10 & 1023) - 512;
zbox = (image[i] >> 20) - 512;
xback = x[i][0] + xbox*xprd + gamma_back*dxold;
yback = x[i][1] + ybox*yprd + gamma_back*dyold;
zback = x[i][2] + zbox*zprd + gamma_back*dzold;
dxkt = xback - xold[i][0];
dykt = yback - xold[i][1];
dzkt = zback - xold[i][2];
kt += mass[type[i]]*(dxkt*dxkt + dykt*dykt + dzkt*dzkt);
fr += f[i][0]*dxold + f[i][1]*dyold + f[i][2]*dzold;
}
}
double r[2],rtotal[2];
r[0] = fr; r[1] = kt;
MPI_Allreduce(r,rtotal,2,MPI_DOUBLE,MPI_SUM,world);
frtotal = rtotal[0];
kttotal = rtotal[1];
// stat write of mean constraint force based on previous time step constraint
if (nfileevery && me == 0) {
work_analytical +=
(-frtotal - kttotal/dtv/dtf)*(rho_target - rho_old)/rho_old;
lambda = gamma_back*rho_old*masstotal/dtv/dtf;
work_lambda += lambda*(rho_target - rho_old);
if (!(update->ntimestep % nfileevery) &&
(previous_stat != update->ntimestep)) {
fprintf(fp,
BIGINT_FORMAT " %g %g %g %g %g %g %g\n",
update->ntimestep,rho_target,rho_old,
gamma_back,gamma_forward,lambda,work_lambda,work_analytical);
fflush(fp);
previous_stat = update->ntimestep;
}
}
rho_old = rho_target;
// apply the constraint and save constrained positions for next step
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtfm = dtf / mass[type[i]];
dxold = xold[i][0] - xf[i][0];
x[i][0] += gamma_forward*dxold;
v[i][0] += gamma_forward*dxold/dtv;
f[i][0] += gamma_forward*dxold/dtv/dtfm;
dyold = xold[i][1] - xf[i][1];
x[i][1] += gamma_forward*dyold;
v[i][1] += gamma_forward*dyold/dtv;
f[i][1] += gamma_forward*dyold/dtv/dtfm;
dzold = xold[i][2] - xf[i][2];
x[i][2] += gamma_forward*dzold;
v[i][2] += gamma_forward*dzold/dtv;
f[i][2] += gamma_forward*dzold/dtv/dtfm;
xbox = (image[i] & 1023) - 512;
ybox = (image[i] >> 10 & 1023) - 512;
zbox = (image[i] >> 20) - 512;
xold[i][0] = x[i][0] + xbox*xprd;
xold[i][1] = x[i][1] + ybox*yprd;
xold[i][2] = x[i][2] + zbox*zprd;
}
}
}
/* ---------------------------------------------------------------------- */
void FixTMD::initial_integrate_respa(int vflag, int ilevel, int flag)
{
if (flag) return; // only used by NPT,NPH
dtv = step_respa[ilevel];
dtf = step_respa[ilevel] * force->ftm2v;
if (ilevel == 0) initial_integrate(vflag);
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double FixTMD::memory_usage()
{
double bytes = 2*atom->nmax*3 * sizeof(double);
return bytes;
}
/* ----------------------------------------------------------------------
allocate atom-based arrays
------------------------------------------------------------------------- */
void FixTMD::grow_arrays(int nmax)
{
xf = memory->grow_2d_double_array(xf,nmax,3,"fix_tmd:xf");
xold = memory->grow_2d_double_array(xold,nmax,3,"fix_tmd:xold");
}
/* ----------------------------------------------------------------------
copy values within local atom-based arrays
------------------------------------------------------------------------- */
void FixTMD::copy_arrays(int i, int j)
{
xf[j][0] = xf[i][0];
xf[j][1] = xf[i][1];
xf[j][2] = xf[i][2];
xold[j][0] = xold[i][0];
xold[j][1] = xold[i][1];
xold[j][2] = xold[i][2];
}
/* ----------------------------------------------------------------------
pack values in local atom-based arrays for exchange with another proc
------------------------------------------------------------------------- */
int FixTMD::pack_exchange(int i, double *buf)
{
buf[0] = xf[i][0];
buf[1] = xf[i][1];
buf[2] = xf[i][2];
buf[3] = xold[i][0];
buf[4] = xold[i][1];
buf[5] = xold[i][2];
return 6;
}
/* ----------------------------------------------------------------------
unpack values in local atom-based arrays from exchange with another proc
------------------------------------------------------------------------- */
int FixTMD::unpack_exchange(int nlocal, double *buf)
{
xf[nlocal][0] = buf[0];
xf[nlocal][1] = buf[1];
xf[nlocal][2] = buf[2];
xold[nlocal][0] = buf[3];
xold[nlocal][1] = buf[4];
xold[nlocal][2] = buf[5];
return 6;
}
/* ----------------------------------------------------------------------
read target coordinates from file, store with appropriate atom
------------------------------------------------------------------------- */
void FixTMD::readfile(char *file)
{
if (me == 0) {
if (screen) fprintf(screen,"Reading TMD target file %s ...\n",file);
open(file);
}
int *mask = atom->mask;
int nlocal = atom->nlocal;
char *buffer = new char[CHUNK*MAXLINE];
char *ptr,*next,*bufptr;
int i,m,nlines,tag,imageflag,ix,iy,iz;
double x,y,z,xprd,yprd,zprd;
int firstline = 1;
int ncount = 0;
int eof = 0;
xprd = yprd = zprd = -1.0;
while (!eof) {
if (me == 0) {
m = 0;
for (nlines = 0; nlines < CHUNK; nlines++) {
ptr = fgets(&buffer[m],MAXLINE,fp);
if (ptr == NULL) break;
m += strlen(&buffer[m]);
}
if (ptr == NULL) eof = 1;
buffer[m++] = '\n';
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
MPI_Bcast(&nlines,1,MPI_INT,0,world);
MPI_Bcast(&m,1,MPI_INT,0,world);
MPI_Bcast(buffer,m,MPI_CHAR,0,world);
bufptr = buffer;
for (i = 0; i < nlines; i++) {
next = strchr(bufptr,'\n');
*next = '\0';
if (firstline) {
if (strstr(bufptr,"xlo xhi")) {
double lo,hi;
sscanf(bufptr,"%lg %lg",&lo,&hi);
xprd = hi - lo;
bufptr = next + 1;
continue;
} else if (strstr(bufptr,"ylo yhi")) {
double lo,hi;
sscanf(bufptr,"%lg %lg",&lo,&hi);
yprd = hi - lo;
bufptr = next + 1;
continue;
} else if (strstr(bufptr,"zlo zhi")) {
double lo,hi;
sscanf(bufptr,"%lg %lg",&lo,&hi);
zprd = hi - lo;
bufptr = next + 1;
continue;
} else if (atom->count_words(bufptr) == 4) {
if (xprd >= 0.0 || yprd >= 0.0 || zprd >= 0.0)
error->all("Incorrect format in TMD target file");
imageflag = 0;
firstline = 0;
} else if (atom->count_words(bufptr) == 7) {
if (xprd < 0.0 || yprd < 0.0 || zprd < 0.0)
error->all("Incorrect format in TMD target file");
imageflag = 1;
firstline = 0;
} else error->all("Incorrect format in TMD target file");
}
if (imageflag)
sscanf(bufptr,"%d %lg %lg %lg %d %d %d",&tag,&x,&y,&z,&ix,&iy,&iz);
else
sscanf(bufptr,"%d %lg %lg %lg",&tag,&x,&y,&z);
m = atom->map(tag);
if (m >= 0 && m < nlocal && mask[m] & groupbit) {
if (imageflag) {
xf[m][0] = x + ix*xprd;
xf[m][1] = y + iy*yprd;
xf[m][2] = z + iz*zprd;
} else {
xf[m][0] = x;
xf[m][1] = y;
xf[m][2] = z;
}
ncount++;
}
bufptr = next + 1;
}
}
// clean up
delete [] buffer;
if (me == 0) {
if (compressed) pclose(fp);
else fclose(fp);
}
// check that all atoms in group were listed in target file
// set xf = 0.0 for atoms not in group
int gcount = 0;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) gcount++;
else xf[i][0] = xf[i][1] = xf[i][2] = 0.0;
int flag = 0;
if (gcount != ncount) flag = 1;
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall) error->all("TMD target file did not list all group atoms");
}
/* ----------------------------------------------------------------------
proc 0 opens TMD data file
test if gzipped
------------------------------------------------------------------------- */
void FixTMD::open(char *file)
{
compressed = 0;
char *suffix = file + strlen(file) - 3;
if (suffix > file && strcmp(suffix,".gz") == 0) compressed = 1;
if (!compressed) fp = fopen(file,"r");
else {
#ifdef LAMMPS_GZIP
char gunzip[128];
sprintf(gunzip,"gunzip -c %s",file);
fp = popen(gunzip,"r");
#else
error->one("Cannot open gzipped file");
#endif
}
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open file %s",file);
error->one(str);
}
}
/* ---------------------------------------------------------------------- */
void FixTMD::reset_dt()
{
dtv = update->dt;
dtf = update->dt * force->ftm2v;
}
diff --git a/src/fix_ttm.cpp b/src/fix_ttm.cpp
index 4edfba1bb..d486cf49e 100644
--- a/src/fix_ttm.cpp
+++ b/src/fix_ttm.cpp
@@ -1,699 +1,699 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Paul Crozier (SNL)
Carolyn Phillips (University of Michigan)
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "mpi.h"
#include "math.h"
#include "string.h"
#include "stdlib.h"
#include "fix_ttm.h"
-#include "lmptype.h"
#include "atom.h"
#include "force.h"
#include "update.h"
#include "domain.h"
#include "region.h"
#include "respa.h"
#include "comm.h"
#include "random_mars.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MIN(A,B) ((A) < (B)) ? (A) : (B)
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
#define MAXLINE 1024
/* ---------------------------------------------------------------------- */
FixTTM::FixTTM(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 15) error->all("Illegal fix ttm command");
vector_flag = 1;
size_vector = 2;
global_freq = 1;
extvector = 1;
nevery = 1;
restart_peratom = 1;
restart_global = 1;
seed = atoi(arg[3]);
electronic_specific_heat = atof(arg[4]);
electronic_density = atof(arg[5]);
electronic_thermal_conductivity = atof(arg[6]);
gamma_p = atof(arg[7]);
gamma_s = atof(arg[8]);
v_0 = atof(arg[9]);
nxnodes = atoi(arg[10]);
nynodes = atoi(arg[11]);
nznodes = atoi(arg[12]);
fpr = fopen(arg[13],"r");
if (fpr == NULL) {
char str[128];
sprintf(str,"Cannot open file %s",arg[13]);
error->one(str);
}
nfileevery = atoi(arg[14]);
if (nfileevery) {
if (narg != 16) error->all("Illegal fix ttm command");
MPI_Comm_rank(world,&me);
if (me == 0) {
fp = fopen(arg[15],"w");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open fix ttm file %s",arg[15]);
error->one(str);
}
}
}
// error check
if (seed <= 0) error->all("Invalid random number seed in fix ttm command");
if (electronic_specific_heat <= 0.0)
error->all("Fix ttm electronic_specific_heat must be > 0.0");
if (electronic_density <= 0.0)
error->all("Fix ttm electronic_density must be > 0.0");
if (electronic_thermal_conductivity < 0.0)
error->all("Fix ttm electronic_thermal_conductivity must be >= 0.0");
if (gamma_p <= 0.0) error->all("Fix ttm gamma_p must be > 0.0");
if (gamma_s < 0.0) error->all("Fix ttm gamma_s must be >= 0.0");
if (v_0 < 0.0) error->all("Fix ttm v_0 must be >= 0.0");
if (nxnodes <= 0 || nynodes <= 0 || nznodes <= 0)
error->all("Fix ttm number of nodes must be > 0");
v_0_sq = v_0*v_0;
// initialize Marsaglia RNG with processor-unique seed
random = new RanMars(lmp,seed + comm->me);
// allocate per-type arrays for force prefactors
gfactor1 = new double[atom->ntypes+1];
gfactor2 = new double[atom->ntypes+1];
// allocate 3d grid variables
total_nnodes = nxnodes*nynodes*nznodes;
nsum = memory->create_3d_int_array(nxnodes,nynodes,nznodes,"ttm:nsum");
nsum_all = memory->create_3d_int_array(nxnodes,nynodes,nznodes,
"ttm:nsum_all");
T_initial_set = memory->create_3d_int_array(nxnodes,nynodes,nznodes,
"ttm:T_initial_set");
sum_vsq = memory->create_3d_double_array(nxnodes,nynodes,nznodes,
"ttm:sum_vsq");
sum_mass_vsq =
memory->create_3d_double_array(nxnodes,nynodes,nznodes,
"ttm:sum_mass_vsq");
sum_vsq_all = memory->create_3d_double_array(nxnodes,nynodes,nznodes,
"ttm:sum_vsq_all");
sum_mass_vsq_all =
memory->create_3d_double_array(nxnodes,nynodes,nznodes,
"ttm:sum_mass_vsq_all");
T_electron_old =
memory->create_3d_double_array(nxnodes,nynodes,nznodes,
"ttm:T_electron_old");
T_electron =
memory->create_3d_double_array(nxnodes,nynodes,nznodes,"ttm:T_electron");
net_energy_transfer =
memory->create_3d_double_array(nxnodes,nynodes,nznodes,
"TTM:net_energy_transfer");
net_energy_transfer_all =
memory->create_3d_double_array(nxnodes,nynodes,nznodes,
"TTM:net_energy_transfer_all");
flangevin = NULL;
grow_arrays(atom->nmax);
// zero out the flangevin array
for (int i = 0; i < atom->nmax; i++) {
flangevin[i][0] = 0;
flangevin[i][1] = 0;
flangevin[i][2] = 0;
}
atom->add_callback(0);
atom->add_callback(1);
// set initial electron temperatures from user input file
if (me == 0) read_initial_electron_temperatures();
MPI_Bcast(&T_electron[0][0][0],total_nnodes,MPI_DOUBLE,0,world);
}
/* ---------------------------------------------------------------------- */
FixTTM::~FixTTM()
{
if (nfileevery && me == 0) fclose(fp);
delete random;
delete [] gfactor1;
delete [] gfactor2;
memory->destroy_3d_int_array(nsum);
memory->destroy_3d_int_array(nsum_all);
memory->destroy_3d_int_array(T_initial_set);
memory->destroy_3d_double_array(sum_vsq);
memory->destroy_3d_double_array(sum_mass_vsq);
memory->destroy_3d_double_array(sum_vsq_all);
memory->destroy_3d_double_array(sum_mass_vsq_all);
memory->destroy_3d_double_array(T_electron_old);
memory->destroy_3d_double_array(T_electron);
memory->destroy_2d_double_array(flangevin);
memory->destroy_3d_double_array(net_energy_transfer);
memory->destroy_3d_double_array(net_energy_transfer_all);
}
/* ---------------------------------------------------------------------- */
int FixTTM::setmask()
{
int mask = 0;
mask |= POST_FORCE;
mask |= POST_FORCE_RESPA;
mask |= END_OF_STEP;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixTTM::init()
{
if (domain->dimension == 2)
error->all("Cannot use fix ttm with 2d simulation");
if (domain->nonperiodic != 0)
error->all("Cannot use nonperiodic boundares with fix ttm");
if (domain->triclinic)
error->all("Cannot use fix ttm with triclinic box");
// set force prefactors
for (int i = 1; i <= atom->ntypes; i++) {
gfactor1[i] = - gamma_p / force->ftm2v;
gfactor2[i] =
sqrt(24.0*force->boltz*gamma_p/update->dt/force->mvv2e) / force->ftm2v;
}
for (int ixnode = 0; ixnode < nxnodes; ixnode++)
for (int iynode = 0; iynode < nynodes; iynode++)
for (int iznode = 0; iznode < nznodes; iznode++)
net_energy_transfer_all[ixnode][iynode][iznode] = 0;
if (strcmp(update->integrate_style,"respa") == 0)
nlevels_respa = ((Respa *) update->integrate)->nlevels;
}
/* ---------------------------------------------------------------------- */
void FixTTM::setup(int vflag)
{
if (strcmp(update->integrate_style,"verlet") == 0)
post_force_setup(vflag);
else {
((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
post_force_respa_setup(vflag,nlevels_respa-1,0);
((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
}
}
/* ---------------------------------------------------------------------- */
void FixTTM::post_force(int vflag)
{
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double gamma1,gamma2;
// apply damping and thermostat to all atoms in fix group
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
double xscale = (x[i][0] - domain->boxlo[0])/domain->xprd;
double yscale = (x[i][1] - domain->boxlo[1])/domain->yprd;
double zscale = (x[i][2] - domain->boxlo[2])/domain->zprd;
int ixnode = static_cast<int>(xscale*nxnodes);
int iynode = static_cast<int>(yscale*nynodes);
int iznode = static_cast<int>(zscale*nznodes);
while (ixnode > nxnodes-1) ixnode -= nxnodes;
while (iynode > nynodes-1) iynode -= nynodes;
while (iznode > nznodes-1) iznode -= nznodes;
while (ixnode < 0) ixnode += nxnodes;
while (iynode < 0) iynode += nynodes;
while (iznode < 0) iznode += nznodes;
if (T_electron[ixnode][iynode][iznode] < 0)
error->all("Electronic temperature dropped below zero");
double tsqrt = sqrt(T_electron[ixnode][iynode][iznode]);
gamma1 = gfactor1[type[i]];
double vsq = v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2];
if (vsq > v_0_sq) gamma1 *= (gamma_p + gamma_s)/gamma_p;
gamma2 = gfactor2[type[i]] * tsqrt;
flangevin[i][0] = gamma1*v[i][0] + gamma2*(random->uniform()-0.5);
flangevin[i][1] = gamma1*v[i][1] + gamma2*(random->uniform()-0.5);
flangevin[i][2] = gamma1*v[i][2] + gamma2*(random->uniform()-0.5);
f[i][0] += flangevin[i][0];
f[i][1] += flangevin[i][1];
f[i][2] += flangevin[i][2];
}
}
}
/* ---------------------------------------------------------------------- */
void FixTTM::post_force_setup(int vflag)
{
double **f = atom->f;
int *mask = atom->mask;
int nlocal = atom->nlocal;
// apply langevin forces that have been stored from previous run
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
f[i][0] += flangevin[i][0];
f[i][1] += flangevin[i][1];
f[i][2] += flangevin[i][2];
}
}
}
/* ---------------------------------------------------------------------- */
void FixTTM::post_force_respa(int vflag, int ilevel, int iloop)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
}
/* ---------------------------------------------------------------------- */
void FixTTM::post_force_respa_setup(int vflag, int ilevel, int iloop)
{
if (ilevel == nlevels_respa-1) post_force_setup(vflag);
}
/* ---------------------------------------------------------------------- */
void FixTTM::reset_dt()
{
for (int i = 1; i <= atom->ntypes; i++)
gfactor2[i] =
sqrt(24.0*force->boltz*gamma_p/update->dt/force->mvv2e) / force->ftm2v;
}
/* ----------------------------------------------------------------------
read in initial electron temperatures from a user-specified file
only called by proc 0
------------------------------------------------------------------------- */
void FixTTM::read_initial_electron_temperatures()
{
char line[MAXLINE];
for (int ixnode = 0; ixnode < nxnodes; ixnode++)
for (int iynode = 0; iynode < nynodes; iynode++)
for (int iznode = 0; iznode < nznodes; iznode++)
T_initial_set[ixnode][iynode][iznode] = 0;
// read initial electron temperature values from file
int ixnode,iynode,iznode;
double T_tmp;
while (1) {
if (fgets(line,MAXLINE,fpr) == NULL) break;
sscanf(line,"%d %d %d %lg",&ixnode,&iynode,&iznode,&T_tmp);
if (T_tmp < 0.0) error->one("Fix ttm electron temperatures must be > 0.0");
T_electron[ixnode][iynode][iznode] = T_tmp;
T_initial_set[ixnode][iynode][iznode] = 1;
}
for (int ixnode = 0; ixnode < nxnodes; ixnode++)
for (int iynode = 0; iynode < nynodes; iynode++)
for (int iznode = 0; iznode < nznodes; iznode++)
if (T_initial_set[ixnode][iynode][iznode] == 0)
error->one("Initial temperatures not all set in fix ttm");
// close file
fclose(fpr);
}
/* ---------------------------------------------------------------------- */
void FixTTM::end_of_step()
{
double **x = atom->x;
double **v = atom->v;
double *mass = atom->mass;
double *rmass = atom->rmass;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int ixnode = 0; ixnode < nxnodes; ixnode++)
for (int iynode = 0; iynode < nynodes; iynode++)
for (int iznode = 0; iznode < nznodes; iznode++)
net_energy_transfer[ixnode][iynode][iznode] = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
double xscale = (x[i][0] - domain->boxlo[0])/domain->xprd;
double yscale = (x[i][1] - domain->boxlo[1])/domain->yprd;
double zscale = (x[i][2] - domain->boxlo[2])/domain->zprd;
int ixnode = static_cast<int>(xscale*nxnodes);
int iynode = static_cast<int>(yscale*nynodes);
int iznode = static_cast<int>(zscale*nznodes);
while (ixnode > nxnodes-1) ixnode -= nxnodes;
while (iynode > nynodes-1) iynode -= nynodes;
while (iznode > nznodes-1) iznode -= nznodes;
while (ixnode < 0) ixnode += nxnodes;
while (iynode < 0) iynode += nynodes;
while (iznode < 0) iznode += nznodes;
net_energy_transfer[ixnode][iynode][iznode] +=
(flangevin[i][0]*v[i][0] + flangevin[i][1]*v[i][1] +
flangevin[i][2]*v[i][2]);
}
MPI_Allreduce(&net_energy_transfer[0][0][0],
&net_energy_transfer_all[0][0][0],
total_nnodes,MPI_DOUBLE,MPI_SUM,world);
double dx = domain->xprd/nxnodes;
double dy = domain->yprd/nynodes;
double dz = domain->zprd/nznodes;
double del_vol = dx*dy*dz;
// num_inner_timesteps = # of inner steps (thermal solves)
// required this MD step to maintain a stable explicit solve
int num_inner_timesteps = 1;
double inner_dt = update->dt;
double stability_criterion = 1.0 -
2.0*inner_dt/(electronic_specific_heat*electronic_density) *
(electronic_thermal_conductivity*(1.0/dx/dx + 1.0/dy/dy + 1.0/dz/dz));
if (stability_criterion < 0.0) {
inner_dt = 0.5*(electronic_specific_heat*electronic_density) /
(electronic_thermal_conductivity*(1.0/dx/dx + 1.0/dy/dy + 1.0/dz/dz));
num_inner_timesteps = static_cast<int>(update->dt/inner_dt) + 1;
inner_dt = update->dt/double(num_inner_timesteps);
if (num_inner_timesteps > 1000000)
error->warning("Too many inner timesteps in fix ttm",0);
}
for (int ith_inner_timestep = 0; ith_inner_timestep < num_inner_timesteps;
ith_inner_timestep++) {
for (int ixnode = 0; ixnode < nxnodes; ixnode++)
for (int iynode = 0; iynode < nynodes; iynode++)
for (int iznode = 0; iznode < nznodes; iznode++)
T_electron_old[ixnode][iynode][iznode] =
T_electron[ixnode][iynode][iznode];
// compute new electron T profile
for (int ixnode = 0; ixnode < nxnodes; ixnode++)
for (int iynode = 0; iynode < nynodes; iynode++)
for (int iznode = 0; iznode < nznodes; iznode++) {
int right_xnode = ixnode + 1;
int right_ynode = iynode + 1;
int right_znode = iznode + 1;
if (right_xnode == nxnodes) right_xnode = 0;
if (right_ynode == nynodes) right_ynode = 0;
if (right_znode == nznodes) right_znode = 0;
int left_xnode = ixnode - 1;
int left_ynode = iynode - 1;
int left_znode = iznode - 1;
if (left_xnode == -1) left_xnode = nxnodes - 1;
if (left_ynode == -1) left_ynode = nynodes - 1;
if (left_znode == -1) left_znode = nznodes - 1;
T_electron[ixnode][iynode][iznode] =
T_electron_old[ixnode][iynode][iznode] +
inner_dt/(electronic_specific_heat*electronic_density) *
(electronic_thermal_conductivity *
((T_electron_old[right_xnode][iynode][iznode] +
T_electron_old[left_xnode][iynode][iznode] -
2*T_electron_old[ixnode][iynode][iznode])/dx/dx +
(T_electron_old[ixnode][right_ynode][iznode] +
T_electron_old[ixnode][left_ynode][iznode] -
2*T_electron_old[ixnode][iynode][iznode])/dy/dy +
(T_electron_old[ixnode][iynode][right_znode] +
T_electron_old[ixnode][iynode][left_znode] -
2*T_electron_old[ixnode][iynode][iznode])/dz/dz) -
(net_energy_transfer_all[ixnode][iynode][iznode])/del_vol);
}
}
// output nodal temperatures for current timestep
if ((nfileevery) && !(update->ntimestep % nfileevery)) {
// compute atomic Ta for each grid point
for (int ixnode = 0; ixnode < nxnodes; ixnode++)
for (int iynode = 0; iynode < nynodes; iynode++)
for (int iznode = 0; iznode < nznodes; iznode++) {
nsum[ixnode][iynode][iznode] = 0;
nsum_all[ixnode][iynode][iznode] = 0;
sum_vsq[ixnode][iynode][iznode] = 0.0;
sum_mass_vsq[ixnode][iynode][iznode] = 0.0;
sum_vsq_all[ixnode][iynode][iznode] = 0.0;
sum_mass_vsq_all[ixnode][iynode][iznode] = 0.0;
}
double massone;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
double xscale = (x[i][0] - domain->boxlo[0])/domain->xprd;
double yscale = (x[i][1] - domain->boxlo[1])/domain->yprd;
double zscale = (x[i][2] - domain->boxlo[2])/domain->zprd;
int ixnode = static_cast<int>(xscale*nxnodes);
int iynode = static_cast<int>(yscale*nynodes);
int iznode = static_cast<int>(zscale*nznodes);
while (ixnode > nxnodes-1) ixnode -= nxnodes;
while (iynode > nynodes-1) iynode -= nynodes;
while (iznode > nznodes-1) iznode -= nznodes;
while (ixnode < 0) ixnode += nxnodes;
while (iynode < 0) iynode += nynodes;
while (iznode < 0) iznode += nznodes;
double vsq = v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2];
nsum[ixnode][iynode][iznode] += 1;
sum_vsq[ixnode][iynode][iznode] += vsq;
sum_mass_vsq[ixnode][iynode][iznode] += massone*vsq;
}
MPI_Allreduce(&nsum[0][0][0],&nsum_all[0][0][0],total_nnodes,
MPI_INT,MPI_SUM,world);
MPI_Allreduce(&sum_vsq[0][0][0],&sum_vsq_all[0][0][0],total_nnodes,
MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(&sum_mass_vsq[0][0][0],&sum_mass_vsq_all[0][0][0],
total_nnodes,MPI_DOUBLE,MPI_SUM,world);
if (me == 0) {
fprintf(fp,BIGINT_FORMAT,update->ntimestep);
double T_a;
for (int ixnode = 0; ixnode < nxnodes; ixnode++)
for (int iynode = 0; iynode < nynodes; iynode++)
for (int iznode = 0; iznode < nznodes; iznode++) {
T_a = 0;
if (nsum_all[ixnode][iynode][iznode] > 0)
T_a = sum_mass_vsq_all[ixnode][iynode][iznode]/
(3.0*force->boltz*nsum_all[ixnode][iynode][iznode]/force->mvv2e);
fprintf(fp," %f",T_a);
}
fprintf(fp,"\t");
for (int ixnode = 0; ixnode < nxnodes; ixnode++)
for (int iynode = 0; iynode < nynodes; iynode++)
for (int iznode = 0; iznode < nznodes; iznode++)
fprintf(fp,"%f ",T_electron[ixnode][iynode][iznode]);
fprintf(fp,"\n");
}
}
}
/* ----------------------------------------------------------------------
memory usage of 3d grid
------------------------------------------------------------------------- */
double FixTTM::memory_usage()
{
double bytes = 0.0;
bytes += 5*total_nnodes * sizeof(int);
bytes += 14*total_nnodes * sizeof(double);
return bytes;
}
/* ---------------------------------------------------------------------- */
void FixTTM::grow_arrays(int ngrow)
{
flangevin = memory->grow_2d_double_array(flangevin,ngrow,3,"TTM:flangevin");
}
/* ----------------------------------------------------------------------
return the energy of the electronic subsystem or the net_energy transfer
between the subsystems
------------------------------------------------------------------------- */
double FixTTM::compute_vector(int n)
{
double e_energy = 0.0;
double transfer_energy = 0.0;
double dx = domain->xprd/nxnodes;
double dy = domain->yprd/nynodes;
double dz = domain->zprd/nznodes;
double del_vol = dx*dy*dz;
for (int ixnode = 0; ixnode < nxnodes; ixnode++)
for (int iynode = 0; iynode < nynodes; iynode++)
for (int iznode = 0; iznode < nznodes; iznode++) {
e_energy +=
T_electron[ixnode][iynode][iznode]*electronic_specific_heat*
electronic_density*del_vol;
transfer_energy +=
net_energy_transfer_all[ixnode][iynode][iznode]*update->dt;
}
if (n == 0) return e_energy;
if (n == 1) return transfer_energy;
return 0.0;
}
/* ----------------------------------------------------------------------
pack entire state of Fix into one write
------------------------------------------------------------------------- */
void FixTTM::write_restart(FILE *fp)
{
double *rlist = (double *)
memory->smalloc((1+nxnodes*nynodes*nznodes)*sizeof(double),"TTM:rlist");
int n = 0;
rlist[n++] = seed;
for (int ixnode = 0; ixnode < nxnodes; ixnode++)
for (int iynode = 0; iynode < nynodes; iynode++)
for (int iznode = 0; iznode < nznodes; iznode++)
rlist[n++] = T_electron[ixnode][iynode][iznode];
if (comm->me == 0) {
int size = n * sizeof(double);
fwrite(&size,sizeof(int),1,fp);
fwrite(rlist,sizeof(double),n,fp);
}
memory->sfree(rlist);
}
/* ----------------------------------------------------------------------
use state info from restart file to restart the Fix
------------------------------------------------------------------------- */
void FixTTM::restart(char *buf)
{
int n = 0;
double *rlist = (double *) buf;
// the seed must be changed from the initial seed
seed = static_cast<int> (0.5*rlist[n++]);
for (int ixnode = 0; ixnode < nxnodes; ixnode++)
for (int iynode = 0; iynode < nynodes; iynode++)
for (int iznode = 0; iznode < nznodes; iznode++)
T_electron[ixnode][iynode][iznode] = rlist[n++];
delete random;
random = new RanMars(lmp,seed+comm->me);
}
/* ----------------------------------------------------------------------
pack values in local atom-based arrays for restart file
------------------------------------------------------------------------- */
int FixTTM::pack_restart(int i, double *buf)
{
buf[0] = 4;
buf[1] = flangevin[i][0];
buf[2] = flangevin[i][1];
buf[3] = flangevin[i][2];
return 4;
}
/* ----------------------------------------------------------------------
unpack values from atom->extra array to restart the fix
------------------------------------------------------------------------- */
void FixTTM::unpack_restart(int nlocal, int nth)
{
double **extra = atom->extra;
// skip to Nth set of extra values
int m = 0;
for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);
m++;
flangevin[nlocal][0] = extra[nlocal][m++];
flangevin[nlocal][1] = extra[nlocal][m++];
flangevin[nlocal][2] = extra[nlocal][m++];
}
/* ----------------------------------------------------------------------
maxsize of any atom's restart data
------------------------------------------------------------------------- */
int FixTTM::maxsize_restart()
{
return 4;
}
/* ----------------------------------------------------------------------
size of atom nlocal's restart data
------------------------------------------------------------------------- */
int FixTTM::size_restart(int nlocal)
{
return 4;
}
diff --git a/src/group.cpp b/src/group.cpp
index 79a526b5b..b5803ccdb 100644
--- a/src/group.cpp
+++ b/src/group.cpp
@@ -1,1469 +1,1469 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "math.h"
#include "mpi.h"
#include "stdio.h"
#include "string.h"
#include "stdlib.h"
#include "group.h"
-#include "lmptype.h"
#include "domain.h"
#include "atom.h"
#include "force.h"
#include "region.h"
#include "modify.h"
#include "fix.h"
#include "compute.h"
#include "output.h"
#include "dump.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MAX_GROUP 32
enum{TYPE,MOLECULE,ID};
enum{LT,LE,GT,GE,EQ,NEQ,BETWEEN};
#define BIG 1.0e20
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
/* ----------------------------------------------------------------------
initialize group memory
------------------------------------------------------------------------- */
Group::Group(LAMMPS *lmp) : Pointers(lmp)
{
MPI_Comm_rank(world,&me);
names = new char*[MAX_GROUP];
bitmask = new int[MAX_GROUP];
inversemask = new int[MAX_GROUP];
for (int i = 0; i < MAX_GROUP; i++) names[i] = NULL;
for (int i = 0; i < MAX_GROUP; i++) bitmask[i] = 1 << i;
for (int i = 0; i < MAX_GROUP; i++) inversemask[i] = bitmask[i] ^ ~0;
// create "all" group
char *str = (char *) "all";
int n = strlen(str) + 1;
names[0] = new char[n];
strcpy(names[0],str);
ngroup = 1;
}
/* ----------------------------------------------------------------------
free all memory
------------------------------------------------------------------------- */
Group::~Group()
{
for (int i = 0; i < MAX_GROUP; i++) delete [] names[i];
delete [] names;
delete [] bitmask;
delete [] inversemask;
}
/* ----------------------------------------------------------------------
assign atoms to a new or existing group
------------------------------------------------------------------------- */
void Group::assign(int narg, char **arg)
{
int i;
if (domain->box_exist == 0)
error->all("Group command before simulation box is defined");
if (narg < 2) error->all("Illegal group command");
// delete the group if not being used elsewhere
// clear mask of each atom assigned to this group
if (strcmp(arg[1],"delete") == 0) {
int igroup = find(arg[0]);
if (igroup == -1) error->all("Could not find group delete group ID");
if (igroup == 0) error->all("Cannot delete group all");
for (i = 0; i < modify->nfix; i++)
if (modify->fix[i]->igroup == igroup)
error->all("Cannot delete group currently used by a fix");
for (i = 0; i < modify->ncompute; i++)
if (modify->compute[i]->igroup == igroup)
error->all("Cannot delete group currently used by a compute");
for (i = 0; i < output->ndump; i++)
if (output->dump[i]->igroup == igroup)
error->all("Cannot delete group currently used by a dump");
if (atom->firstgroupname && strcmp(arg[0],atom->firstgroupname) == 0)
error->all("Cannot delete group currently used by atom_modify first");
int *mask = atom->mask;
int nlocal = atom->nlocal;
int bits = inversemask[igroup];
for (i = 0; i < nlocal; i++) mask[i] &= bits;
delete [] names[igroup];
names[igroup] = NULL;
ngroup--;
return;
}
// find group in existing list
// add a new group if igroup = -1
int igroup = find(arg[0]);
if (igroup == -1) {
if (ngroup == MAX_GROUP) error->all("Too many groups");
igroup = find_unused();
int n = strlen(arg[0]) + 1;
names[igroup] = new char[n];
strcpy(names[igroup],arg[0]);
ngroup++;
}
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int bit = bitmask[igroup];
// style = region
// add to group if atom is in region
if (strcmp(arg[1],"region") == 0) {
if (narg != 3) error->all("Illegal group command");
int iregion = domain->find_region(arg[2]);
if (iregion == -1) error->all("Group region ID does not exist");
for (i = 0; i < nlocal; i++)
if (domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2]))
mask[i] |= bit;
// style = logical condition
} else if (narg >= 3 &&
(strcmp(arg[2],"<") == 0 || strcmp(arg[2],">") == 0 ||
strcmp(arg[2],"<=") == 0 || strcmp(arg[2],">=") == 0 ||
strcmp(arg[2],"<>") == 0)) {
if (narg < 4 || narg > 5) error->all("Illegal group command");
int category,condition,bound1,bound2;
if (strcmp(arg[1],"type") == 0) category = TYPE;
else if (strcmp(arg[1],"molecule") == 0) category = MOLECULE;
else if (strcmp(arg[1],"id") == 0) category = ID;
else error->all("Illegal group command");
if (strcmp(arg[2],"<") == 0) condition = LT;
else if (strcmp(arg[2],"<=") == 0) condition = LE;
else if (strcmp(arg[2],">") == 0) condition = GT;
else if (strcmp(arg[2],">=") == 0) condition = GE;
else if (strcmp(arg[2],"==") == 0) condition = EQ;
else if (strcmp(arg[2],"!=") == 0) condition = NEQ;
else if (strcmp(arg[2],"<>") == 0) condition = BETWEEN;
else error->all("Illegal group command");
bound1 = atoi(arg[3]);
bound2 = -1;
if (condition == BETWEEN) {
if (narg != 5) error->all("Illegal group command");
bound2 = atoi(arg[4]);
}
int *attribute;
if (category == TYPE) attribute = atom->type;
else if (category == MOLECULE) attribute = atom->molecule;
else if (category == ID) attribute = atom->tag;
// add to group if meets condition
if (condition == LT) {
for (i = 0; i < nlocal; i++) if (attribute[i] < bound1) mask[i] |= bit;
} else if (condition == LE) {
for (i = 0; i < nlocal; i++) if (attribute[i] <= bound1) mask[i] |= bit;
} else if (condition == GT) {
for (i = 0; i < nlocal; i++) if (attribute[i] > bound1) mask[i] |= bit;
} else if (condition == GE) {
for (i = 0; i < nlocal; i++) if (attribute[i] >= bound1) mask[i] |= bit;
} else if (condition == EQ) {
for (i = 0; i < nlocal; i++) if (attribute[i] == bound1) mask[i] |= bit;
} else if (condition == NEQ) {
for (i = 0; i < nlocal; i++) if (attribute[i] != bound1) mask[i] |= bit;
} else if (condition == BETWEEN) {
for (i = 0; i < nlocal; i++)
if (attribute[i] >= bound1 && attribute[i] <= bound2) mask[i] |= bit;
}
// style = list of values
} else if (strcmp(arg[1],"type") == 0 || strcmp(arg[1],"molecule") == 0 ||
strcmp(arg[1],"id") == 0) {
if (narg < 3) error->all("Illegal group command");
int length = narg-2;
int *list = new int[length];
int category;
if (strcmp(arg[1],"type") == 0) category = TYPE;
else if (strcmp(arg[1],"molecule") == 0) category = MOLECULE;
else if (strcmp(arg[1],"id") == 0) category = ID;
else error->all("Illegal group command");
length = narg - 2;
for (int iarg = 2; iarg < narg; iarg++) list[iarg-2] = atoi(arg[iarg]);
int *attribute;
if (category == TYPE) attribute = atom->type;
else if (category == MOLECULE) attribute = atom->molecule;
else if (category == ID) attribute = atom->tag;
// add to group if attribute is any in list
for (int ilist = 0; ilist < length; ilist++)
for (i = 0; i < nlocal; i++)
if (attribute[i] == list[ilist]) mask[i] |= bit;
delete [] list;
// style = subtract
} else if (strcmp(arg[1],"subtract") == 0) {
if (narg < 4) error->all("Illegal group command");
int length = narg-2;
int *list = new int[length];
int jgroup;
for (int iarg = 2; iarg < narg; iarg++) {
jgroup = find(arg[iarg]);
if (jgroup == -1) error->all("Group ID does not exist");
list[iarg-2] = jgroup;
}
// add to group if in 1st group in list
int otherbit = bitmask[list[0]];
for (i = 0; i < nlocal; i++)
if (mask[i] & otherbit) mask[i] |= bit;
// remove atoms if they are in any of the other groups
// AND with inverse mask removes the atom from group
int inverse = inversemask[igroup];
for (int ilist = 1; ilist < length; ilist++) {
otherbit = bitmask[list[ilist]];
for (i = 0; i < nlocal; i++)
if (mask[i] & otherbit) mask[i] &= inverse;
}
delete [] list;
// style = union
} else if (strcmp(arg[1],"union") == 0) {
if (narg < 3) error->all("Illegal group command");
int length = narg-2;
int *list = new int[length];
int jgroup;
for (int iarg = 2; iarg < narg; iarg++) {
jgroup = find(arg[iarg]);
if (jgroup == -1) error->all("Group ID does not exist");
list[iarg-2] = jgroup;
}
// add to group if in any other group in list
int otherbit;
for (int ilist = 0; ilist < length; ilist++) {
otherbit = bitmask[list[ilist]];
for (i = 0; i < nlocal; i++)
if (mask[i] & otherbit) mask[i] |= bit;
}
delete [] list;
// style = intersect
} else if (strcmp(arg[1],"intersect") == 0) {
if (narg < 4) error->all("Illegal group command");
int length = narg-2;
int *list = new int[length];
int jgroup;
for (int iarg = 2; iarg < narg; iarg++) {
jgroup = find(arg[iarg]);
if (jgroup == -1) error->all("Group ID does not exist");
list[iarg-2] = jgroup;
}
// add to group if in all groups in list
int otherbit,ok,ilist;
for (i = 0; i < nlocal; i++) {
ok = 1;
for (ilist = 0; ilist < length; ilist++) {
otherbit = bitmask[list[ilist]];
if ((mask[i] & otherbit) == 0) ok = 0;
}
if (ok) mask[i] |= bit;
}
delete [] list;
// not a valid group style
} else error->all("Illegal group command");
// print stats for changed group
int n;
n = 0;
for (i = 0; i < nlocal; i++) if (mask[i] & bit) n++;
double rlocal = n;
double all;
MPI_Allreduce(&rlocal,&all,1,MPI_DOUBLE,MPI_SUM,world);
if (me == 0) {
if (screen) fprintf(screen,"%.15g atoms in group %s\n",all,names[igroup]);
if (logfile)
fprintf(logfile,"%.15g atoms in group %s\n",all,names[igroup]);
}
}
/* ----------------------------------------------------------------------
add flagged atoms to a new or existing group
------------------------------------------------------------------------- */
void Group::create(char *name, int *flag)
{
int i;
// find group in existing list
// add a new group if igroup = -1
int igroup = find(name);
if (igroup == -1) {
if (ngroup == MAX_GROUP) error->all("Too many groups");
igroup = find_unused();
int n = strlen(name) + 1;
names[igroup] = new char[n];
strcpy(names[igroup],name);
ngroup++;
}
// add atoms to group whose flags are set
int *mask = atom->mask;
int nlocal = atom->nlocal;
int bit = bitmask[igroup];
for (i = 0; i < nlocal; i++)
if (flag[i]) mask[i] |= bit;
}
/* ----------------------------------------------------------------------
return group index if name matches existing group, -1 if no such group
------------------------------------------------------------------------- */
int Group::find(const char *name)
{
for (int igroup = 0; igroup < MAX_GROUP; igroup++)
if (names[igroup] && strcmp(name,names[igroup]) == 0) return igroup;
return -1;
}
/* ----------------------------------------------------------------------
return index of first available group
should never be called when group limit has been reached
------------------------------------------------------------------------- */
int Group::find_unused()
{
for (int igroup = 0; igroup < MAX_GROUP; igroup++)
if (names[igroup] == NULL) return igroup;
return -1;
}
/* ----------------------------------------------------------------------
write group info to a restart file
only called by proc 0
------------------------------------------------------------------------- */
void Group::write_restart(FILE *fp)
{
fwrite(&ngroup,sizeof(int),1,fp);
// use count to not change restart format with deleted groups
// remove this on next major release
int n;
int count = 0;
for (int i = 0; i < MAX_GROUP; i++) {
if (names[i]) n = strlen(names[i]) + 1;
else n = 0;
fwrite(&n,sizeof(int),1,fp);
if (n) {
fwrite(names[i],sizeof(char),n,fp);
count++;
}
if (count == ngroup) break;
}
}
/* ----------------------------------------------------------------------
read group info from a restart file
proc 0 reads, bcast to all procs
------------------------------------------------------------------------- */
void Group::read_restart(FILE *fp)
{
int i,n;
// delete existing group names
// atom masks will be overwritten by reading of restart file
for (i = 0; i < MAX_GROUP; i++) delete [] names[i];
if (me == 0) fread(&ngroup,sizeof(int),1,fp);
MPI_Bcast(&ngroup,1,MPI_INT,0,world);
// use count to not change restart format with deleted groups
// remove this on next major release
int count = 0;
for (i = 0; i < MAX_GROUP; i++) {
if (count == ngroup) {
names[i] = NULL;
continue;
}
if (me == 0) fread(&n,sizeof(int),1,fp);
MPI_Bcast(&n,1,MPI_INT,0,world);
if (n) {
names[i] = new char[n];
if (me == 0) fread(names[i],sizeof(char),n,fp);
MPI_Bcast(names[i],n,MPI_CHAR,0,world);
count++;
} else names[i] = NULL;
}
}
// ----------------------------------------------------------------------
// computations on a group of atoms
// ----------------------------------------------------------------------
/* ----------------------------------------------------------------------
count atoms in group
------------------------------------------------------------------------- */
bigint Group::count(int igroup)
{
int groupbit = bitmask[igroup];
int *mask = atom->mask;
int nlocal = atom->nlocal;
int n = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) n++;
bigint nsingle = n;
bigint nall;
MPI_Allreduce(&nsingle,&nall,1,MPI_LMP_BIGINT,MPI_SUM,world);
return nall;
}
/* ----------------------------------------------------------------------
count atoms in group and region
------------------------------------------------------------------------- */
bigint Group::count(int igroup, int iregion)
{
int groupbit = bitmask[igroup];
Region *region = domain->regions[iregion];
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int n = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) n++;
bigint nsingle = n;
bigint nall;
MPI_Allreduce(&nsingle,&nall,1,MPI_LMP_BIGINT,MPI_SUM,world);
return nall;
}
/* ----------------------------------------------------------------------
compute the total mass of group of atoms
use either per-type mass or per-atom rmass
------------------------------------------------------------------------- */
double Group::mass(int igroup)
{
int groupbit = bitmask[igroup];
double *mass = atom->mass;
double *rmass = atom->rmass;
int *mask = atom->mask;
int *type = atom->type;
int nlocal = atom->nlocal;
double one = 0.0;
if (rmass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) one += rmass[i];
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) one += mass[type[i]];
}
double all;
MPI_Allreduce(&one,&all,1,MPI_DOUBLE,MPI_SUM,world);
return all;
}
/* ----------------------------------------------------------------------
compute the total mass of group of atoms in region
use either per-type mass or per-atom rmass
------------------------------------------------------------------------- */
double Group::mass(int igroup, int iregion)
{
int groupbit = bitmask[igroup];
Region *region = domain->regions[iregion];
double **x = atom->x;
double *mass = atom->mass;
double *rmass = atom->rmass;
int *mask = atom->mask;
int *type = atom->type;
int nlocal = atom->nlocal;
double one = 0.0;
if (rmass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]))
one += rmass[i];
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]))
one += mass[type[i]];
}
double all;
MPI_Allreduce(&one,&all,1,MPI_DOUBLE,MPI_SUM,world);
return all;
}
/* ----------------------------------------------------------------------
compute the total charge of group of atoms
------------------------------------------------------------------------- */
double Group::charge(int igroup)
{
int groupbit = bitmask[igroup];
double *q = atom->q;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double qone = 0.0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) qone += q[i];
double qall;
MPI_Allreduce(&qone,&qall,1,MPI_DOUBLE,MPI_SUM,world);
return qall;
}
/* ----------------------------------------------------------------------
compute the total charge of group of atoms in region
------------------------------------------------------------------------- */
double Group::charge(int igroup, int iregion)
{
int groupbit = bitmask[igroup];
Region *region = domain->regions[iregion];
double **x = atom->x;
double *q = atom->q;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double qone = 0.0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]))
qone += q[i];
double qall;
MPI_Allreduce(&qone,&qall,1,MPI_DOUBLE,MPI_SUM,world);
return qall;
}
/* ----------------------------------------------------------------------
compute the coordinate bounds of the group of atoms
periodic images are not considered, so atoms are NOT unwrapped
------------------------------------------------------------------------- */
void Group::bounds(int igroup, double *minmax)
{
int groupbit = bitmask[igroup];
double extent[6];
extent[0] = extent[2] = extent[4] = BIG;
extent[1] = extent[3] = extent[5] = -BIG;
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
extent[0] = MIN(extent[0],x[i][0]);
extent[1] = MAX(extent[1],x[i][0]);
extent[2] = MIN(extent[2],x[i][1]);
extent[3] = MAX(extent[3],x[i][1]);
extent[4] = MIN(extent[4],x[i][2]);
extent[5] = MAX(extent[5],x[i][2]);
}
}
// compute extent across all procs
// flip sign of MIN to do it in one Allreduce MAX
// set box by extent in shrink-wrapped dims
extent[0] = -extent[0];
extent[2] = -extent[2];
extent[4] = -extent[4];
MPI_Allreduce(extent,minmax,6,MPI_DOUBLE,MPI_MAX,world);
minmax[0] = -minmax[0];
minmax[2] = -minmax[2];
minmax[4] = -minmax[4];
}
/* ----------------------------------------------------------------------
compute the coordinate bounds of the group of atoms in region
periodic images are not considered, so atoms are NOT unwrapped
------------------------------------------------------------------------- */
void Group::bounds(int igroup, double *minmax, int iregion)
{
int groupbit = bitmask[igroup];
Region *region = domain->regions[iregion];
double extent[6];
extent[0] = extent[2] = extent[4] = BIG;
extent[1] = extent[3] = extent[5] = -BIG;
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
extent[0] = MIN(extent[0],x[i][0]);
extent[1] = MAX(extent[1],x[i][0]);
extent[2] = MIN(extent[2],x[i][1]);
extent[3] = MAX(extent[3],x[i][1]);
extent[4] = MIN(extent[4],x[i][2]);
extent[5] = MAX(extent[5],x[i][2]);
}
}
// compute extent across all procs
// flip sign of MIN to do it in one Allreduce MAX
// set box by extent in shrink-wrapped dims
extent[0] = -extent[0];
extent[2] = -extent[2];
extent[4] = -extent[4];
MPI_Allreduce(extent,minmax,6,MPI_DOUBLE,MPI_MAX,world);
minmax[0] = -minmax[0];
minmax[2] = -minmax[2];
minmax[4] = -minmax[4];
}
/* ----------------------------------------------------------------------
compute the center-of-mass coords of group of atoms
masstotal = total mass
return center-of-mass coords in cm[]
must unwrap atoms to compute center-of-mass correctly
------------------------------------------------------------------------- */
void Group::xcm(int igroup, double masstotal, double *cm)
{
int groupbit = bitmask[igroup];
double **x = atom->x;
int *mask = atom->mask;
int *type = atom->type;
int *image = atom->image;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
double cmone[3];
cmone[0] = cmone[1] = cmone[2] = 0.0;
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
int xbox,ybox,zbox;
double massone;
if (rmass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
xbox = (image[i] & 1023) - 512;
ybox = (image[i] >> 10 & 1023) - 512;
zbox = (image[i] >> 20) - 512;
massone = rmass[i];
cmone[0] += (x[i][0] + xbox*xprd) * massone;
cmone[1] += (x[i][1] + ybox*yprd) * massone;
cmone[2] += (x[i][2] + zbox*zprd) * massone;
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
xbox = (image[i] & 1023) - 512;
ybox = (image[i] >> 10 & 1023) - 512;
zbox = (image[i] >> 20) - 512;
massone = mass[type[i]];
cmone[0] += (x[i][0] + xbox*xprd) * massone;
cmone[1] += (x[i][1] + ybox*yprd) * massone;
cmone[2] += (x[i][2] + zbox*zprd) * massone;
}
}
MPI_Allreduce(cmone,cm,3,MPI_DOUBLE,MPI_SUM,world);
if (masstotal > 0.0) {
cm[0] /= masstotal;
cm[1] /= masstotal;
cm[2] /= masstotal;
}
}
/* ----------------------------------------------------------------------
compute the center-of-mass coords of group of atoms in region
mastotal = total mass
return center-of-mass coords in cm[]
must unwrap atoms to compute center-of-mass correctly
------------------------------------------------------------------------- */
void Group::xcm(int igroup, double masstotal, double *cm, int iregion)
{
int groupbit = bitmask[igroup];
Region *region = domain->regions[iregion];
double **x = atom->x;
int *mask = atom->mask;
int *type = atom->type;
int *image = atom->image;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
double cmone[3];
cmone[0] = cmone[1] = cmone[2] = 0.0;
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
int xbox,ybox,zbox;
double massone;
if (rmass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
xbox = (image[i] & 1023) - 512;
ybox = (image[i] >> 10 & 1023) - 512;
zbox = (image[i] >> 20) - 512;
massone = rmass[i];
cmone[0] += (x[i][0] + xbox*xprd) * massone;
cmone[1] += (x[i][1] + ybox*yprd) * massone;
cmone[2] += (x[i][2] + zbox*zprd) * massone;
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
xbox = (image[i] & 1023) - 512;
ybox = (image[i] >> 10 & 1023) - 512;
zbox = (image[i] >> 20) - 512;
massone = mass[type[i]];
cmone[0] += (x[i][0] + xbox*xprd) * massone;
cmone[1] += (x[i][1] + ybox*yprd) * massone;
cmone[2] += (x[i][2] + zbox*zprd) * massone;
}
}
MPI_Allreduce(cmone,cm,3,MPI_DOUBLE,MPI_SUM,world);
if (masstotal > 0.0) {
cm[0] /= masstotal;
cm[1] /= masstotal;
cm[2] /= masstotal;
}
}
/* ----------------------------------------------------------------------
compute the center-of-mass velocity of group of atoms
masstotal = total mass
return center-of-mass velocity in cm[]
------------------------------------------------------------------------- */
void Group::vcm(int igroup, double masstotal, double *cm)
{
int groupbit = bitmask[igroup];
double **v = atom->v;
int *mask = atom->mask;
int *type = atom->type;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
double p[3],massone;
p[0] = p[1] = p[2] = 0.0;
if (rmass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
massone = rmass[i];
p[0] += v[i][0]*massone;
p[1] += v[i][1]*massone;
p[2] += v[i][2]*massone;
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
massone = mass[type[i]];
p[0] += v[i][0]*massone;
p[1] += v[i][1]*massone;
p[2] += v[i][2]*massone;
}
}
MPI_Allreduce(p,cm,3,MPI_DOUBLE,MPI_SUM,world);
if (masstotal > 0.0) {
cm[0] /= masstotal;
cm[1] /= masstotal;
cm[2] /= masstotal;
}
}
/* ----------------------------------------------------------------------
compute the center-of-mass velocity of group of atoms in region
masstotal = total mass
return center-of-mass velocity in cm[]
------------------------------------------------------------------------- */
void Group::vcm(int igroup, double masstotal, double *cm, int iregion)
{
int groupbit = bitmask[igroup];
Region *region = domain->regions[iregion];
double **x = atom->x;
double **v = atom->v;
int *mask = atom->mask;
int *type = atom->type;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
double p[3],massone;
p[0] = p[1] = p[2] = 0.0;
if (rmass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
massone = rmass[i];
p[0] += v[i][0]*massone;
p[1] += v[i][1]*massone;
p[2] += v[i][2]*massone;
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
massone = mass[type[i]];
p[0] += v[i][0]*massone;
p[1] += v[i][1]*massone;
p[2] += v[i][2]*massone;
}
}
MPI_Allreduce(p,cm,3,MPI_DOUBLE,MPI_SUM,world);
if (masstotal > 0.0) {
cm[0] /= masstotal;
cm[1] /= masstotal;
cm[2] /= masstotal;
}
}
/* ----------------------------------------------------------------------
compute the total force on group of atoms
------------------------------------------------------------------------- */
void Group::fcm(int igroup, double *cm)
{
int groupbit = bitmask[igroup];
double **f = atom->f;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double flocal[3];
flocal[0] = flocal[1] = flocal[2] = 0.0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
flocal[0] += f[i][0];
flocal[1] += f[i][1];
flocal[2] += f[i][2];
}
MPI_Allreduce(flocal,cm,3,MPI_DOUBLE,MPI_SUM,world);
}
/* ----------------------------------------------------------------------
compute the total force on group of atoms in region
------------------------------------------------------------------------- */
void Group::fcm(int igroup, double *cm, int iregion)
{
int groupbit = bitmask[igroup];
Region *region = domain->regions[iregion];
double **x = atom->x;
double **f = atom->f;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double flocal[3];
flocal[0] = flocal[1] = flocal[2] = 0.0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
flocal[0] += f[i][0];
flocal[1] += f[i][1];
flocal[2] += f[i][2];
}
MPI_Allreduce(flocal,cm,3,MPI_DOUBLE,MPI_SUM,world);
}
/* ----------------------------------------------------------------------
compute the total kinetic energy of group of atoms and return it
------------------------------------------------------------------------- */
double Group::ke(int igroup)
{
int groupbit = bitmask[igroup];
double **v = atom->v;
int *mask = atom->mask;
int *type = atom->type;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
double one = 0.0;
if (rmass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
one += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
rmass[i];
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
one += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
mass[type[i]];
}
double all;
MPI_Allreduce(&one,&all,1,MPI_DOUBLE,MPI_SUM,world);
all *= 0.5 * force->mvv2e;
return all;
}
/* ----------------------------------------------------------------------
compute the total kinetic energy of group of atoms in region and return it
------------------------------------------------------------------------- */
double Group::ke(int igroup, int iregion)
{
int groupbit = bitmask[igroup];
Region *region = domain->regions[iregion];
double **x = atom->x;
double **v = atom->v;
int *mask = atom->mask;
int *type = atom->type;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
double one = 0.0;
if (rmass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]))
one += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
rmass[i];
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]))
one += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
mass[type[i]];
}
double all;
MPI_Allreduce(&one,&all,1,MPI_DOUBLE,MPI_SUM,world);
all *= 0.5 * force->mvv2e;
return all;
}
/* ----------------------------------------------------------------------
compute the radius-of-gyration of group of atoms
around center-of-mass cm
must unwrap atoms to compute Rg correctly
------------------------------------------------------------------------- */
double Group::gyration(int igroup, double masstotal, double *cm)
{
int groupbit = bitmask[igroup];
double **x = atom->x;
int *mask = atom->mask;
int *type = atom->type;
int *image = atom->image;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
int xbox,ybox,zbox;
double dx,dy,dz,massone;
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
double rg = 0.0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
xbox = (image[i] & 1023) - 512;
ybox = (image[i] >> 10 & 1023) - 512;
zbox = (image[i] >> 20) - 512;
dx = (x[i][0] + xbox*xprd) - cm[0];
dy = (x[i][1] + ybox*yprd) - cm[1];
dz = (x[i][2] + zbox*zprd) - cm[2];
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
rg += (dx*dx + dy*dy + dz*dz) * massone;
}
double rg_all;
MPI_Allreduce(&rg,&rg_all,1,MPI_DOUBLE,MPI_SUM,world);
if (masstotal > 0.0) return sqrt(rg_all/masstotal);
return 0.0;
}
/* ----------------------------------------------------------------------
compute the radius-of-gyration of group of atoms in region
around center-of-mass cm
must unwrap atoms to compute Rg correctly
------------------------------------------------------------------------- */
double Group::gyration(int igroup, double masstotal, double *cm, int iregion)
{
int groupbit = bitmask[igroup];
Region *region = domain->regions[iregion];
double **x = atom->x;
int *mask = atom->mask;
int *type = atom->type;
int *image = atom->image;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
int xbox,ybox,zbox;
double dx,dy,dz,massone;
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
double rg = 0.0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
xbox = (image[i] & 1023) - 512;
ybox = (image[i] >> 10 & 1023) - 512;
zbox = (image[i] >> 20) - 512;
dx = (x[i][0] + xbox*xprd) - cm[0];
dy = (x[i][1] + ybox*yprd) - cm[1];
dz = (x[i][2] + zbox*zprd) - cm[2];
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
rg += (dx*dx + dy*dy + dz*dz) * massone;
}
double rg_all;
MPI_Allreduce(&rg,&rg_all,1,MPI_DOUBLE,MPI_SUM,world);
if (masstotal > 0.0) return sqrt(rg_all/masstotal);
return 0.0;
}
/* ----------------------------------------------------------------------
compute the angular momentum L (lmom) of group
around center-of-mass cm
must unwrap atoms to compute L correctly
------------------------------------------------------------------------- */
void Group::angmom(int igroup, double *cm, double *lmom)
{
int groupbit = bitmask[igroup];
double **x = atom->x;
double **v = atom->v;
int *mask = atom->mask;
int *type = atom->type;
int *image = atom->image;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
int xbox,ybox,zbox;
double dx,dy,dz,massone;
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
double p[3];
p[0] = p[1] = p[2] = 0.0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
xbox = (image[i] & 1023) - 512;
ybox = (image[i] >> 10 & 1023) - 512;
zbox = (image[i] >> 20) - 512;
dx = (x[i][0] + xbox*xprd) - cm[0];
dy = (x[i][1] + ybox*yprd) - cm[1];
dz = (x[i][2] + zbox*zprd) - cm[2];
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
p[0] += massone * (dy*v[i][2] - dz*v[i][1]);
p[1] += massone * (dz*v[i][0] - dx*v[i][2]);
p[2] += massone * (dx*v[i][1] - dy*v[i][0]);
}
MPI_Allreduce(p,lmom,3,MPI_DOUBLE,MPI_SUM,world);
}
/* ----------------------------------------------------------------------
compute the angular momentum L (lmom) of group of atoms in region
around center-of-mass cm
must unwrap atoms to compute L correctly
------------------------------------------------------------------------- */
void Group::angmom(int igroup, double *cm, double *lmom, int iregion)
{
int groupbit = bitmask[igroup];
Region *region = domain->regions[iregion];
double **x = atom->x;
double **v = atom->v;
int *mask = atom->mask;
int *type = atom->type;
int *image = atom->image;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
int xbox,ybox,zbox;
double dx,dy,dz,massone;
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
double p[3];
p[0] = p[1] = p[2] = 0.0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
xbox = (image[i] & 1023) - 512;
ybox = (image[i] >> 10 & 1023) - 512;
zbox = (image[i] >> 20) - 512;
dx = (x[i][0] + xbox*xprd) - cm[0];
dy = (x[i][1] + ybox*yprd) - cm[1];
dz = (x[i][2] + zbox*zprd) - cm[2];
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
p[0] += massone * (dy*v[i][2] - dz*v[i][1]);
p[1] += massone * (dz*v[i][0] - dx*v[i][2]);
p[2] += massone * (dx*v[i][1] - dy*v[i][0]);
}
MPI_Allreduce(p,lmom,3,MPI_DOUBLE,MPI_SUM,world);
}
/* ----------------------------------------------------------------------
compute the torque T (tq) on group
around center-of-mass cm
must unwrap atoms to compute T correctly
------------------------------------------------------------------------- */
void Group::torque(int igroup, double *cm, double *tq)
{
int groupbit = bitmask[igroup];
double **x = atom->x;
double **f = atom->f;
int *mask = atom->mask;
int *image = atom->image;
int nlocal = atom->nlocal;
int xbox,ybox,zbox;
double dx,dy,dz;
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
double tlocal[3];
tlocal[0] = tlocal[1] = tlocal[2] = 0.0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
xbox = (image[i] & 1023) - 512;
ybox = (image[i] >> 10 & 1023) - 512;
zbox = (image[i] >> 20) - 512;
dx = (x[i][0] + xbox*xprd) - cm[0];
dy = (x[i][1] + ybox*yprd) - cm[1];
dz = (x[i][2] + zbox*zprd) - cm[2];
tlocal[0] += dy*f[i][2] - dz*f[i][1];
tlocal[1] += dz*f[i][0] - dx*f[i][2];
tlocal[2] += dx*f[i][1] - dy*f[i][0];
}
MPI_Allreduce(tlocal,tq,3,MPI_DOUBLE,MPI_SUM,world);
}
/* ----------------------------------------------------------------------
compute the torque T (tq) on group of atoms in region
around center-of-mass cm
must unwrap atoms to compute T correctly
------------------------------------------------------------------------- */
void Group::torque(int igroup, double *cm, double *tq, int iregion)
{
int groupbit = bitmask[igroup];
Region *region = domain->regions[iregion];
double **x = atom->x;
double **f = atom->f;
int *mask = atom->mask;
int *image = atom->image;
int nlocal = atom->nlocal;
int xbox,ybox,zbox;
double dx,dy,dz;
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
double tlocal[3];
tlocal[0] = tlocal[1] = tlocal[2] = 0.0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
xbox = (image[i] & 1023) - 512;
ybox = (image[i] >> 10 & 1023) - 512;
zbox = (image[i] >> 20) - 512;
dx = (x[i][0] + xbox*xprd) - cm[0];
dy = (x[i][1] + ybox*yprd) - cm[1];
dz = (x[i][2] + zbox*zprd) - cm[2];
tlocal[0] += dy*f[i][2] - dz*f[i][1];
tlocal[1] += dz*f[i][0] - dx*f[i][2];
tlocal[2] += dx*f[i][1] - dy*f[i][0];
}
MPI_Allreduce(tlocal,tq,3,MPI_DOUBLE,MPI_SUM,world);
}
/* ----------------------------------------------------------------------
compute moment of inertia tensor around center-of-mass cm of group
must unwrap atoms to compute itensor correctly
------------------------------------------------------------------------- */
void Group::inertia(int igroup, double *cm, double itensor[3][3])
{
int i,j;
int groupbit = bitmask[igroup];
double **x = atom->x;
int *mask = atom->mask;
int *type = atom->type;
int *image = atom->image;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
int xbox,ybox,zbox;
double dx,dy,dz,massone;
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
double ione[3][3];
for (i = 0; i < 3; i++)
for (j = 0; j < 3; j++)
ione[i][j] = 0.0;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
xbox = (image[i] & 1023) - 512;
ybox = (image[i] >> 10 & 1023) - 512;
zbox = (image[i] >> 20) - 512;
dx = (x[i][0] + xbox*xprd) - cm[0];
dy = (x[i][1] + ybox*yprd) - cm[1];
dz = (x[i][2] + zbox*zprd) - cm[2];
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
ione[0][0] += massone * (dy*dy + dz*dz);
ione[1][1] += massone * (dx*dx + dz*dz);
ione[2][2] += massone * (dx*dx + dy*dy);
ione[0][1] -= massone * dx*dy;
ione[1][2] -= massone * dy*dz;
ione[0][2] -= massone * dx*dz;
}
ione[1][0] = ione[0][1];
ione[2][1] = ione[1][2];
ione[2][0] = ione[0][2];
MPI_Allreduce(&ione[0][0],&itensor[0][0],9,MPI_DOUBLE,MPI_SUM,world);
}
/* ----------------------------------------------------------------------
compute moment of inertia tensor around cm of group of atoms in region
must unwrap atoms to compute itensor correctly
------------------------------------------------------------------------- */
void Group::inertia(int igroup, double *cm, double itensor[3][3], int iregion)
{
int i,j;
int groupbit = bitmask[igroup];
Region *region = domain->regions[iregion];
double **x = atom->x;
int *mask = atom->mask;
int *type = atom->type;
int *image = atom->image;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
int xbox,ybox,zbox;
double dx,dy,dz,massone;
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
double ione[3][3];
for (i = 0; i < 3; i++)
for (j = 0; j < 3; j++)
ione[i][j] = 0.0;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
xbox = (image[i] & 1023) - 512;
ybox = (image[i] >> 10 & 1023) - 512;
zbox = (image[i] >> 20) - 512;
dx = (x[i][0] + xbox*xprd) - cm[0];
dy = (x[i][1] + ybox*yprd) - cm[1];
dz = (x[i][2] + zbox*zprd) - cm[2];
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
ione[0][0] += massone * (dy*dy + dz*dz);
ione[1][1] += massone * (dx*dx + dz*dz);
ione[2][2] += massone * (dx*dx + dy*dy);
ione[0][1] -= massone * dx*dy;
ione[1][2] -= massone * dy*dz;
ione[0][2] -= massone * dx*dz;
}
ione[1][0] = ione[0][1];
ione[2][1] = ione[1][2];
ione[2][0] = ione[0][2];
MPI_Allreduce(&ione[0][0],&itensor[0][0],9,MPI_DOUBLE,MPI_SUM,world);
}
/* ----------------------------------------------------------------------
compute angular velocity omega from L = Iw, inverting I to solve for w
really not a group operation, but L and I were computed for a group
------------------------------------------------------------------------- */
void Group::omega(double *angmom, double inertia[3][3], double *w)
{
double inverse[3][3];
inverse[0][0] = inertia[1][1]*inertia[2][2] - inertia[1][2]*inertia[2][1];
inverse[0][1] = -(inertia[0][1]*inertia[2][2] - inertia[0][2]*inertia[2][1]);
inverse[0][2] = inertia[0][1]*inertia[1][2] - inertia[0][2]*inertia[1][1];
inverse[1][0] = -(inertia[1][0]*inertia[2][2] - inertia[1][2]*inertia[2][0]);
inverse[1][1] = inertia[0][0]*inertia[2][2] - inertia[0][2]*inertia[2][0];
inverse[1][2] = -(inertia[0][0]*inertia[1][2] - inertia[0][2]*inertia[1][0]);
inverse[2][0] = inertia[1][0]*inertia[2][1] - inertia[1][1]*inertia[2][0];
inverse[2][1] = -(inertia[0][0]*inertia[2][1] - inertia[0][1]*inertia[2][0]);
inverse[2][2] = inertia[0][0]*inertia[1][1] - inertia[0][1]*inertia[1][0];
double determinant = inertia[0][0]*inertia[1][1]*inertia[2][2] +
inertia[0][1]*inertia[1][2]*inertia[2][0] +
inertia[0][2]*inertia[1][0]*inertia[2][1] -
inertia[0][0]*inertia[1][2]*inertia[2][1] -
inertia[0][1]*inertia[1][0]*inertia[2][2] -
inertia[2][0]*inertia[1][1]*inertia[0][2];
if (determinant > 0.0)
for (int i = 0; i < 3; i++)
for (int j = 0; j < 3; j++)
inverse[i][j] /= determinant;
w[0] = inverse[0][0]*angmom[0] + inverse[0][1]*angmom[1] +
inverse[0][2]*angmom[2];
w[1] = inverse[1][0]*angmom[0] + inverse[1][1]*angmom[1] +
inverse[1][2]*angmom[2];
w[2] = inverse[2][0]*angmom[0] + inverse[2][1]*angmom[1] +
inverse[2][2]*angmom[2];
}
diff --git a/src/group.h b/src/group.h
index cc0938f4a..9621aa850 100644
--- a/src/group.h
+++ b/src/group.h
@@ -1,72 +1,72 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifndef LMP_GROUP_H
#define LMP_GROUP_H
+#include "lmptype.h"
#include "stdio.h"
#include "pointers.h"
-#include "lmptype.h"
namespace LAMMPS_NS {
class Group : protected Pointers {
public:
int ngroup; // # of defined groups
char **names; // name of each group
int *bitmask; // one-bit mask for each group
int *inversemask; // inverse mask for each group
Group(class LAMMPS *);
~Group();
void assign(int, char **); // assign atoms to a group
void create(char *, int *); // add flagged atoms to a group
int find(const char *); // lookup name in list of groups
void write_restart(FILE *);
void read_restart(FILE *);
bigint count(int); // count atoms in group
bigint count(int,int); // count atoms in group & region
double mass(int); // total mass of atoms in group
double mass(int,int);
double charge(int); // total charge of atoms in group
double charge(int,int);
void bounds(int, double *); // bounds of atoms in group
void bounds(int, double *, int);
void xcm(int, double, double *); // center-of-mass coords of group
void xcm(int, double, double *, int);
void vcm(int, double, double *); // center-of-mass velocity of group
void vcm(int, double, double *, int);
void fcm(int, double *); // total force on group
void fcm(int, double *, int);
double ke(int); // kinetic energy of group
double ke(int, int);
double gyration(int, double, double *); // radius-of-gyration of group
double gyration(int, double, double *, int);
void angmom(int, double *, double *); // angular momentum of group
void angmom(int, double *, double *, int);
void torque(int, double *, double *); // torque on group
void torque(int, double *, double *, int);
void inertia(int, double *, double [3][3]); // inertia tensor
void inertia(int, double *, double [3][3], int);
void omega(double *, double [3][3], double *); // angular velocity
private:
int me;
int find_unused();
};
}
#endif
diff --git a/src/integrate.cpp b/src/integrate.cpp
index 5b7d8df19..80bf89f67 100644
--- a/src/integrate.cpp
+++ b/src/integrate.cpp
@@ -1,132 +1,132 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "stdlib.h"
#include "integrate.h"
-#include "lmptype.h"
#include "update.h"
#include "modify.h"
#include "compute.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
Integrate::Integrate(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
{
elist_global = elist_atom = NULL;
vlist_global = vlist_atom = NULL;
}
/* ---------------------------------------------------------------------- */
Integrate::~Integrate()
{
delete [] elist_global;
delete [] elist_atom;
delete [] vlist_global;
delete [] vlist_atom;
}
/* ----------------------------------------------------------------------
setup lists of computes for global and per-atom PE and pressure
------------------------------------------------------------------------- */
void Integrate::ev_setup()
{
delete [] elist_global;
delete [] elist_atom;
delete [] vlist_global;
delete [] vlist_atom;
elist_global = elist_atom = NULL;
vlist_global = vlist_atom = NULL;
nelist_global = nelist_atom = 0;
nvlist_global = nvlist_atom = 0;
for (int i = 0; i < modify->ncompute; i++) {
if (modify->compute[i]->peflag) nelist_global++;
if (modify->compute[i]->peatomflag) nelist_atom++;
if (modify->compute[i]->pressflag) nvlist_global++;
if (modify->compute[i]->pressatomflag) nvlist_atom++;
}
if (nelist_global) elist_global = new Compute*[nelist_global];
if (nelist_atom) elist_atom = new Compute*[nelist_atom];
if (nvlist_global) vlist_global = new Compute*[nvlist_global];
if (nvlist_atom) vlist_atom = new Compute*[nvlist_atom];
nelist_global = nelist_atom = 0;
nvlist_global = nvlist_atom = 0;
for (int i = 0; i < modify->ncompute; i++) {
if (modify->compute[i]->peflag)
elist_global[nelist_global++] = modify->compute[i];
if (modify->compute[i]->peatomflag)
elist_atom[nelist_atom++] = modify->compute[i];
if (modify->compute[i]->pressflag)
vlist_global[nvlist_global++] = modify->compute[i];
if (modify->compute[i]->pressatomflag)
vlist_atom[nvlist_atom++] = modify->compute[i];
}
}
/* ----------------------------------------------------------------------
set eflag,vflag for current iteration
invoke matchstep() on all timestep-dependent computes to clear their arrays
eflag/vflag based on computes that need info on this ntimestep
eflag = 0 = no energy computation
eflag = 1 = global energy only
eflag = 2 = per-atom energy only
eflag = 3 = both global and per-atom energy
vflag = 0 = no virial computation (pressure)
vflag = 1 = global virial with pair portion via sum of pairwise interactions
vflag = 2 = global virial with pair portion via F dot r including ghosts
vflag = 4 = per-atom virial only
vflag = 5 or 6 = both global and per-atom virial
------------------------------------------------------------------------- */
void Integrate::ev_set(bigint ntimestep)
{
int i,flag;
flag = 0;
int eflag_global = 0;
for (i = 0; i < nelist_global; i++)
if (elist_global[i]->matchstep(ntimestep)) flag = 1;
if (flag) eflag_global = 1;
flag = 0;
int eflag_atom = 0;
for (i = 0; i < nelist_atom; i++)
if (elist_atom[i]->matchstep(ntimestep)) flag = 1;
if (flag) eflag_atom = 2;
if (eflag_global) update->eflag_global = ntimestep;
if (eflag_atom) update->eflag_atom = ntimestep;
eflag = eflag_global + eflag_atom;
flag = 0;
int vflag_global = 0;
for (i = 0; i < nvlist_global; i++)
if (vlist_global[i]->matchstep(ntimestep)) flag = 1;
if (flag) vflag_global = virial_style;
flag = 0;
int vflag_atom = 0;
for (i = 0; i < nvlist_atom; i++)
if (vlist_atom[i]->matchstep(ntimestep)) flag = 1;
if (flag) vflag_atom = 4;
if (vflag_global) update->vflag_global = ntimestep;
if (vflag_atom) update->vflag_atom = ntimestep;
vflag = vflag_global + vflag_atom;
}
diff --git a/src/integrate.h b/src/integrate.h
index bcbc71192..d869ceac2 100644
--- a/src/integrate.h
+++ b/src/integrate.h
@@ -1,51 +1,51 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifndef LMP_INTEGRATE_H
#define LMP_INTEGRATE_H
-#include "pointers.h"
#include "lmptype.h"
+#include "pointers.h"
namespace LAMMPS_NS {
class Integrate : protected Pointers {
public:
Integrate(class LAMMPS *, int, char **);
virtual ~Integrate();
virtual void init() = 0;
virtual void setup() = 0;
virtual void setup_minimal(int) = 0;
virtual void run(int) = 0;
virtual void cleanup() {}
virtual void reset_dt() {}
virtual double memory_usage() {return 0.0;}
protected:
int eflag,vflag; // flags for energy/virial computation
int virial_style; // compute virial explicitly or implicitly
int nelist_global,nelist_atom; // # of PE,virial computes to check
int nvlist_global,nvlist_atom;
class Compute **elist_global; // lists of PE,virial Computes
class Compute **elist_atom;
class Compute **vlist_global;
class Compute **vlist_atom;
void ev_setup();
void ev_set(bigint);
};
}
#endif
diff --git a/src/library.cpp b/src/library.cpp
index 2b2cc3977..fd58515d2 100644
--- a/src/library.cpp
+++ b/src/library.cpp
@@ -1,411 +1,411 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
// C or Fortran style library interface to LAMMPS
// customize by adding new LAMMPS-specific functions
+#include "lmptype.h"
#include "mpi.h"
#include "string.h"
#include "stdlib.h"
#include "library.h"
-#include "lmptype.h"
#include "lammps.h"
#include "input.h"
#include "atom.h"
#include "domain.h"
#include "update.h"
#include "group.h"
#include "input.h"
#include "variable.h"
#include "modify.h"
#include "compute.h"
#include "fix.h"
using namespace LAMMPS_NS;
/* ----------------------------------------------------------------------
create an instance of LAMMPS and return pointer to it
pass in command-line args and MPI communicator to run on
------------------------------------------------------------------------- */
void lammps_open(int argc, char **argv, MPI_Comm communicator, void **ptr)
{
LAMMPS *lmp = new LAMMPS(argc,argv,communicator);
*ptr = (void *) lmp;
}
/* ----------------------------------------------------------------------
create an instance of LAMMPS and return pointer to it
caller doesn't know MPI communicator, so use MPI_COMM_WORLD
intialize MPI if needed
------------------------------------------------------------------------- */
void lammps_open_no_mpi(int argc, char **argv, void **ptr)
{
int flag;
MPI_Initialized(&flag);
if (!flag) {
int argc = 0;
char **argv = NULL;
MPI_Init(&argc,&argv);
}
MPI_Comm communicator = MPI_COMM_WORLD;
LAMMPS *lmp = new LAMMPS(argc,argv,communicator);
*ptr = (void *) lmp;
}
/* ----------------------------------------------------------------------
destruct an instance of LAMMPS
------------------------------------------------------------------------- */
void lammps_close(void *ptr)
{
LAMMPS *lmp = (LAMMPS *) ptr;
delete lmp;
}
/* ----------------------------------------------------------------------
process an input script in filename str
------------------------------------------------------------------------- */
void lammps_file(void *ptr, char *str)
{
LAMMPS *lmp = (LAMMPS *) ptr;
lmp->input->file(str);
}
/* ----------------------------------------------------------------------
process a single input command in str
------------------------------------------------------------------------- */
char *lammps_command(void *ptr, char *str)
{
LAMMPS *lmp = (LAMMPS *) ptr;
return lmp->input->one(str);
}
/* ----------------------------------------------------------------------
clean-up function to free memory allocated by lib and returned to caller
------------------------------------------------------------------------- */
void lammps_free(void *ptr)
{
free(ptr);
}
/* ----------------------------------------------------------------------
add LAMMPS-specific library functions
all must receive LAMMPS pointer as argument
customize by adding a function here and in library.h header file
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
extract a pointer to an internal LAMMPS global entity
name = desired quantity, e.g. dt or boxyhi or natoms
returns a void pointer to the entity
which the caller can cast to the proper data type
returns a NULL if name not listed below
customize by adding names
------------------------------------------------------------------------- */
void *lammps_extract_global(void *ptr, char *name)
{
LAMMPS *lmp = (LAMMPS *) ptr;
if (strcmp(name,"dt") == 0) return (void *) &lmp->update->dt;
if (strcmp(name,"boxxlo") == 0) return (void *) &lmp->domain->boxlo[0];
if (strcmp(name,"boxxhi") == 0) return (void *) &lmp->domain->boxhi[0];
if (strcmp(name,"boxylo") == 0) return (void *) &lmp->domain->boxlo[1];
if (strcmp(name,"boxyhi") == 0) return (void *) &lmp->domain->boxhi[1];
if (strcmp(name,"boxzlo") == 0) return (void *) &lmp->domain->boxlo[2];
if (strcmp(name,"boxzhi") == 0) return (void *) &lmp->domain->boxhi[2];
if (strcmp(name,"natoms") == 0) return (void *) &lmp->atom->natoms;
if (strcmp(name,"nlocal") == 0) return (void *) &lmp->atom->nlocal;
return NULL;
}
/* ----------------------------------------------------------------------
extract a pointer to an internal LAMMPS atom-based entity
name = desired quantity, e.g. x or mass
returns a void pointer to the entity
which the caller can cast to the proper data type
returns a NULL if Atom::extract() does not recognize the name
customize by adding names to Atom::extract()
------------------------------------------------------------------------- */
void *lammps_extract_atom(void *ptr, char *name)
{
LAMMPS *lmp = (LAMMPS *) ptr;
return lmp->atom->extract(name);
}
/* ----------------------------------------------------------------------
extract a pointer to an internal LAMMPS compute-based entity
id = compute ID
style = 0 for global data, 1 for per-atom data, 2 for local data
type = 0 for scalar, 1 for vector, 2 for array
returns a void pointer to the compute's internal data structure
for the entity which the caller can cast to the proper data type
returns a NULL if id is not recognized or style/type not supported
IMPORTANT: if the compute is not current it will be invoked
LAMMPS cannot easily check if it is valid to invoke the compute,
so caller must insure that it is OK
------------------------------------------------------------------------- */
void *lammps_extract_compute(void *ptr, char *id, int style, int type)
{
LAMMPS *lmp = (LAMMPS *) ptr;
int icompute = lmp->modify->find_compute(id);
if (icompute < 0) return NULL;
Compute *compute = lmp->modify->compute[icompute];
if (style == 0) {
if (type == 0) {
if (!compute->scalar_flag) return NULL;
if (compute->invoked_scalar != lmp->update->ntimestep)
compute->compute_scalar();
return (void *) &compute->scalar;
}
if (type == 1) {
if (!compute->vector_flag) return NULL;
if (compute->invoked_vector != lmp->update->ntimestep)
compute->compute_vector();
return (void *) compute->vector;
}
if (type == 2) {
if (!compute->array_flag) return NULL;
if (compute->invoked_array != lmp->update->ntimestep)
compute->compute_array();
return (void *) compute->array;
}
}
if (style == 1) {
if (!compute->peratom_flag) return NULL;
if (type == 1) {
if (compute->invoked_peratom != lmp->update->ntimestep)
compute->compute_peratom();
return (void *) compute->vector_atom;
}
if (type == 2) {
if (compute->invoked_peratom != lmp->update->ntimestep)
compute->compute_peratom();
return (void *) compute->array_atom;
}
}
if (style == 2) {
if (!compute->local_flag) return NULL;
if (type == 1) {
if (compute->invoked_local != lmp->update->ntimestep)
compute->compute_local();
return (void *) compute->vector_local;
}
if (type == 2) {
if (compute->invoked_local != lmp->update->ntimestep)
compute->compute_local();
return (void *) compute->array_local;
}
}
return NULL;
}
/* ----------------------------------------------------------------------
extract a pointer to an internal LAMMPS fix-based entity
id = fix ID
style = 0 for global data, 1 for per-atom data, 2 for local data
type = 0 for scalar, 1 for vector, 2 for array
i,j = indices needed only to specify which global vector or array value
for global data, returns a pointer to a memory location
which is allocated by this function
which the caller can cast to a (double *) which points to the value
for per-atom or local data, returns a pointer to the
fix's internal data structure for the entity
which the caller can cast to the proper data type
returns a NULL if id is not recognized or style/type not supported
IMPORTANT: for global data,
this function allocates a double to store the value in,
so the caller must free this memory to avoid a leak, e.g.
double *dptr = (double *) lammps_extract_fix();
double value = *dptr;
free(dptr);
IMPORTANT: LAMMPS cannot easily check when info extracted from
the fix is valid, so caller must insure that it is OK
------------------------------------------------------------------------- */
void *lammps_extract_fix(void *ptr, char *id, int style, int type,
int i, int j)
{
LAMMPS *lmp = (LAMMPS *) ptr;
int ifix = lmp->modify->find_fix(id);
if (ifix < 0) return NULL;
Fix *fix = lmp->modify->fix[ifix];
if (style == 0) {
double *dptr = (double *) malloc(sizeof(double));
if (type == 0) {
if (!fix->scalar_flag) return NULL;
*dptr = fix->compute_scalar();
return (void *) dptr;
}
if (type == 1) {
if (!fix->vector_flag) return NULL;
*dptr = fix->compute_vector(i);
return (void *) dptr;
}
if (type == 2) {
if (!fix->array_flag) return NULL;
*dptr = fix->compute_array(i,j);
return (void *) dptr;
}
}
if (style == 1) {
if (!fix->peratom_flag) return NULL;
if (type == 1) return (void *) fix->vector_atom;
if (type == 2) return (void *) fix->array_atom;
}
if (style == 2) {
if (!fix->local_flag) return NULL;
if (type == 1) return (void *) fix->vector_local;
if (type == 2) return (void *) fix->array_local;
}
return NULL;
}
/* ----------------------------------------------------------------------
extract a pointer to an internal LAMMPS evaluated variable
name = variable name, must be equal-style or atom-style variable
group = group ID for evaluating an atom-style variable, else NULL
for equal-style variable, returns a pointer to a memory location
which is allocated by this function
which the caller can cast to a (double *) which points to the value
for atom-style variable, returns a pointer to the
vector of per-atom values on each processor,
which the caller can cast to the proper data type
returns a NULL if name is not recognized or not equal-style or atom-style
IMPORTANT: for both equal-style and atom-style variables,
this function allocates memory to store the variable data in
so the caller must free this memory to avoid a leak
e.g. for equal-style variables
double *dptr = (double *) lammps_extract_variable();
double value = *dptr;
free(dptr);
e.g. for atom-style variables
double *vector = (double *) lammps_extract_variable();
use the vector values
free(vector);
IMPORTANT: LAMMPS cannot easily check when it is valid to evaluate
the variable or any fixes or computes or thermodynamic info it references,
so caller must insure that it is OK
------------------------------------------------------------------------- */
void *lammps_extract_variable(void *ptr, char *name, char *group)
{
LAMMPS *lmp = (LAMMPS *) ptr;
int ivar = lmp->input->variable->find(name);
if (ivar < 0) return NULL;
if (lmp->input->variable->equalstyle(ivar)) {
double *dptr = (double *) malloc(sizeof(double));
*dptr = lmp->input->variable->compute_equal(ivar);
return (void *) dptr;
}
if (lmp->input->variable->atomstyle(ivar)) {
int igroup = lmp->group->find(group);
if (igroup < 0) return NULL;
int nlocal = lmp->atom->nlocal;
double *vector = (double *) malloc(nlocal*sizeof(double));
lmp->input->variable->compute_atom(ivar,igroup,vector,1,0);
return (void *) vector;
}
return NULL;
}
/* ---------------------------------------------------------------------- */
int lammps_get_natoms(void *ptr)
{
LAMMPS *lmp = (LAMMPS *) ptr;
if (lmp->atom->natoms > MAXSMALLINT) return 0;
int natoms = static_cast<int> (lmp->atom->natoms);
return natoms;
}
/* ---------------------------------------------------------------------- */
void lammps_get_coords(void *ptr, double *coords)
{
LAMMPS *lmp = (LAMMPS *) ptr;
// error if tags are not defined or not consecutive
if (lmp->atom->tag_enable == 0 || lmp->atom->tag_consecutive() == 0) return;
if (lmp->atom->natoms > MAXSMALLINT) return;
int natoms = static_cast<int> (lmp->atom->natoms);
double *copy = new double[3*natoms];
for (int i = 0; i < 3*natoms; i++) copy[i] = 0.0;
double **x = lmp->atom->x;
int *tag = lmp->atom->tag;
int nlocal = lmp->atom->nlocal;
int id,offset;
for (int i = 0; i < nlocal; i++) {
id = tag[i];
offset = 3*(id-1);
copy[offset+0] = x[i][0];
copy[offset+1] = x[i][1];
copy[offset+2] = x[i][2];
}
MPI_Allreduce(copy,coords,3*natoms,MPI_DOUBLE,MPI_SUM,lmp->world);
delete [] copy;
}
/* ---------------------------------------------------------------------- */
void lammps_put_coords(void *ptr, double *coords)
{
LAMMPS *lmp = (LAMMPS *) ptr;
// error if no map defined by LAMMPS
if (lmp->atom->map_style == 0) return;
if (lmp->atom->natoms > MAXSMALLINT) return;
int natoms = static_cast<int> (lmp->atom->natoms);
double **x = lmp->atom->x;
int m,offset;
for (int i = 0; i < natoms; i++) {
if ((m = lmp->atom->map(i+1)) >= 0) {
offset = 3*i;
x[m][0] = coords[offset+0];
x[m][1] = coords[offset+1];
x[m][2] = coords[offset+2];
}
}
}
diff --git a/src/lmptype.h b/src/lmptype.h
index af2bf465d..a1f6662fe 100644
--- a/src/lmptype.h
+++ b/src/lmptype.h
@@ -1,114 +1,111 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
// define integer data types used by LAMMPS and associated size limits
-// smallint = variables for system on 1 processor (nlocal, nmax, etc)
+// smallint = variables for on-procesor system (nlocal, nmax, etc)
// tagint = variables for atom IDs (tag)
// bigint = variables for total system (natoms, ntimestep, etc)
// smallint must be an int, as defined by C compiler
// tagint can be 32-bit or 64-bit int, must be >= smallint
// NOTE: 64-bit tagint is not yet supported
// bigint can be 32-bit or 64-bit int, must be >= tagint
-// MAXSMALLINT = max value of a smallint
-// MAXTAGINT = max value of a tagint
-// MAXBIGINT = max value of a bigint
-
-// MPI_LMP_TAGINT = MPI data type corresponding to tagint
-// MPI_LMP_BIGINT = MPI data type corresponding to bigint
+// MPI_LMP_TAGINT = MPI data type corresponding to a tagint
+// MPI_LMP_BIGINT = MPI data type corresponding to a bigint
// NOTE: if your machine/MPI does not support "long long" ints,
-// but only "long" ints, then you will need to set
-// MPI_LONG_LONG to MPI_LONG and atoll to atol
+// but only "long" ints, then you will need to change
+// MPI_LONG_LONG to MPI_LONG, and atoll to atol
#ifndef LMP_LMPTYPE_H
#define LMP_LMPTYPE_H
-#include "limits.h"
#define __STDC_LIMIT_MACROS
-#include "stdint.h"
#define __STDC_FORMAT_MACROS
+
+#include "limits.h"
+#include "stdint.h"
#include "inttypes.h"
namespace LAMMPS_NS {
// default settings
// 32-bit smallint and tagint, 64-bit bigint
typedef int smallint;
typedef int tagint;
typedef int64_t bigint;
#define MAXSMALLINT INT_MAX
#define MAXTAGINT INT_MAX
#define MAXBIGINT INT64_MAX
#define MPI_LMP_TAGINT MPI_INT
#define MPI_LMP_BIGINT MPI_LONG_LONG
#define TAGINT_FORMAT "%d"
#define BIGINT_FORMAT "%" PRId64
#define ATOTAGINT atoi
#define ATOBIGINT atoll
// for molecular problems that exceed 2 billion (2^31) atoms
// 32-bit smallint, 64-bit tagint and bigint
// NOTE: 64-bit tagint is not yet supported
/*
typedef int smallint;
typedef int64_t tagint;
typedef int64_t bigint;
#define MAXSMALLINT INT_MAX
#define MAXTAGINT INT64_MAX
#define MAXBIGINT INT64_MAX
#define MPI_LMP_TAGINT MPI_LONG_LONG
#define MPI_LMP_BIGINT MPI_LONG_LONG
#define TAGINT_FORMAT "%" PRId64
#define BIGINT_FORMAT "%" PRId64
#define ATOTAGINT atoll
#define ATOBIGINT atoll
*/
// for machines that do not support 64-bit ints
// 32-bit smallint and tagint and bigint
/*
typedef int smallint;
typedef int tagint;
typedef int bigint;
#define MAXSMALLINT INT_MAX
#define MAXTAGINT INT_MAX
#define MAXBIGINT INT_MAX
#define MPI_LMP_TAGINT MPI_INT
#define MPI_LMP_BIGINT MPI_INT
#define TAGINT_FORMAT "%d"
#define BIGINT_FORMAT "%d"
#define ATOTAGINT atoi
#define ATOBIGINT atoi
*/
}
#endif
diff --git a/src/memory.cpp b/src/memory.cpp
index df8cff685..b7e4c4dc4 100644
--- a/src/memory.cpp
+++ b/src/memory.cpp
@@ -1,441 +1,441 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "mpi.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "memory.h"
-#include "lmptype.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
Memory::Memory(LAMMPS *lmp) : Pointers(lmp) {}
/* ----------------------------------------------------------------------
safe malloc
------------------------------------------------------------------------- */
void *Memory::smalloc(int n, const char *name)
{
if (n == 0) return NULL;
void *ptr = malloc(n);
if (ptr == NULL) {
char str[128];
sprintf(str,"Failed to allocate %d bytes for array %s",n,name);
error->one(str);
}
return ptr;
}
/* ----------------------------------------------------------------------
safe free
------------------------------------------------------------------------- */
void Memory::sfree(void *ptr)
{
if (ptr == NULL) return;
free(ptr);
}
/* ----------------------------------------------------------------------
safe realloc
------------------------------------------------------------------------- */
void *Memory::srealloc(void *ptr, int n, const char *name)
{
if (n == 0) {
sfree(ptr);
return NULL;
}
ptr = realloc(ptr,n);
if (ptr == NULL) {
char str[128];
sprintf(str,"Failed to reallocate %d bytes for array %s",n,name);
error->one(str);
}
return ptr;
}
/* ----------------------------------------------------------------------
create a 1d double array with index from nlo to nhi inclusive
------------------------------------------------------------------------- */
double *Memory::create_1d_double_array(int nlo, int nhi, const char *name)
{
int n = nhi - nlo + 1;
double *array = (double *) smalloc(n*sizeof(double),name);
return array-nlo;
}
/* ----------------------------------------------------------------------
free a 1d double array with index offset
------------------------------------------------------------------------- */
void Memory::destroy_1d_double_array(double *array, int offset)
{
if (array == NULL) return;
sfree(array + offset);
}
/* ----------------------------------------------------------------------
create a 2d double array
------------------------------------------------------------------------- */
double **Memory::create_2d_double_array(int n1, int n2, const char *name)
{
double *data = (double *) smalloc(n1*n2*sizeof(double),name);
double **array = (double **) smalloc(n1*sizeof(double *),name);
int n = 0;
for (int i = 0; i < n1; i++) {
array[i] = &data[n];
n += n2;
}
return array;
}
/* ----------------------------------------------------------------------
free a 2d double array
------------------------------------------------------------------------- */
void Memory::destroy_2d_double_array(double **array)
{
if (array == NULL) return;
sfree(array[0]);
sfree(array);
}
/* ----------------------------------------------------------------------
grow or shrink 1st dim of a 2d double array
last dim must stay the same
if either dim is 0, return NULL
------------------------------------------------------------------------- */
double **Memory::grow_2d_double_array(double **array,
int n1, int n2, const char *name)
{
if (array == NULL) return create_2d_double_array(n1,n2,name);
double *data = (double *) srealloc(array[0],n1*n2*sizeof(double),name);
array = (double **) srealloc(array,n1*sizeof(double *),name);
int n = 0;
for (int i = 0; i < n1; i++) {
array[i] = &data[n];
n += n2;
}
return array;
}
/* ----------------------------------------------------------------------
create a 2d int array
if either dim is 0, return NULL
------------------------------------------------------------------------- */
int **Memory::create_2d_int_array(int n1, int n2, const char *name)
{
if (n1 == 0 || n2 == 0) return NULL;
int *data = (int *) smalloc(n1*n2*sizeof(int),name);
int **array = (int **) smalloc(n1*sizeof(int *),name);
int n = 0;
for (int i = 0; i < n1; i++) {
array[i] = &data[n];
n += n2;
}
return array;
}
/* ----------------------------------------------------------------------
free a 2d int array
------------------------------------------------------------------------- */
void Memory::destroy_2d_int_array(int **array)
{
if (array == NULL) return;
sfree(array[0]);
sfree(array);
}
/* ----------------------------------------------------------------------
grow or shrink 1st dim of a 2d int array
last dim must stay the same
if either dim is 0, return NULL
------------------------------------------------------------------------- */
int **Memory::grow_2d_int_array(int **array, int n1, int n2, const char *name)
{
if (n1 == 0 || n2 == 0) {
destroy_2d_int_array(array);
return NULL;
}
if (array == NULL) return create_2d_int_array(n1,n2,name);
int *data = (int *) srealloc(array[0],n1*n2*sizeof(int),name);
array = (int **) srealloc(array,n1*sizeof(int *),name);
int n = 0;
for (int i = 0; i < n1; i++) {
array[i] = &data[n];
n += n2;
}
return array;
}
/* ----------------------------------------------------------------------
create a 2d double array with 2nd index from n2lo to n2hi inclusive
------------------------------------------------------------------------- */
double **Memory::create_2d_double_array(int n1, int n2lo, int n2hi,
const char *name)
{
int n2 = n2hi - n2lo + 1;
double **array = create_2d_double_array(n1,n2,name);
for (int i = 0; i < n1; i++) array[i] -= n2lo;
return array;
}
/* ----------------------------------------------------------------------
free a 2d double array with 2nd index offset
------------------------------------------------------------------------- */
void Memory::destroy_2d_double_array(double **array, int offset)
{
if (array == NULL) return;
sfree(&array[0][offset]);
sfree(array);
}
/* ----------------------------------------------------------------------
create a 3d double array
------------------------------------------------------------------------- */
double ***Memory::create_3d_double_array(int n1, int n2, int n3,
const char *name)
{
int i,j;
double *data = (double *) smalloc(n1*n2*n3*sizeof(double),name);
double **plane = (double **) smalloc(n1*n2*sizeof(double *),name);
double ***array = (double ***) smalloc(n1*sizeof(double **),name);
int n = 0;
for (i = 0; i < n1; i++) {
array[i] = &plane[i*n2];
for (j = 0; j < n2; j++) {
plane[i*n2+j] = &data[n];
n += n3;
}
}
return array;
}
/* ----------------------------------------------------------------------
free a 3d double array
------------------------------------------------------------------------- */
void Memory::destroy_3d_double_array(double ***array)
{
if (array == NULL) return;
sfree(array[0][0]);
sfree(array[0]);
sfree(array);
}
/* ----------------------------------------------------------------------
grow or shrink 1st dim of a 3d double array
last 2 dims must stay the same
if any dim is 0, return NULL
------------------------------------------------------------------------- */
double ***Memory::grow_3d_double_array(double ***array,
int n1, int n2, int n3,
const char *name)
{
int i,j;
if (n1 == 0 || n2 == 0 || n3 == 0) {
destroy_3d_double_array(array);
return NULL;
}
if (array == NULL) return create_3d_double_array(n1,n2,n3,name);
double *data = (double *) srealloc(array[0][0],n1*n2*n3*sizeof(double),name);
double **plane = (double **) srealloc(array[0],n1*n2*sizeof(double *),name);
array = (double ***) srealloc(array,n1*sizeof(double **),name);
int n = 0;
for (i = 0; i < n1; i++) {
array[i] = &plane[i*n2];
for (j = 0; j < n2; j++) {
plane[i*n2+j] = &data[n];
n += n3;
}
}
return array;
}
/* ----------------------------------------------------------------------
create a 3d double array with 1st index from n1lo to n1hi inclusive
------------------------------------------------------------------------- */
double ***Memory::create_3d_double_array(int n1lo, int n1hi,
int n2, int n3, const char *name)
{
int n1 = n1hi - n1lo + 1;
double ***array = create_3d_double_array(n1,n2,n3,name);
return array-n1lo;
}
/* ----------------------------------------------------------------------
free a 3d double array with 1st index offset
------------------------------------------------------------------------- */
void Memory::destroy_3d_double_array(double ***array, int offset)
{
if (array) destroy_3d_double_array(array + offset);
}
/* ----------------------------------------------------------------------
create a 3d double array with
1st index from n1lo to n1hi inclusive,
2nd index from n2lo to n2hi inclusive,
3rd index from n3lo to n3hi inclusive
------------------------------------------------------------------------- */
double ***Memory::create_3d_double_array(int n1lo, int n1hi,
int n2lo, int n2hi,
int n3lo, int n3hi, const char *name)
{
int n1 = n1hi - n1lo + 1;
int n2 = n2hi - n2lo + 1;
int n3 = n3hi - n3lo + 1;
double ***array = create_3d_double_array(n1,n2,n3,name);
for (int i = 0; i < n1*n2; i++) array[0][i] -= n3lo;
for (int i = 0; i < n1; i++) array[i] -= n2lo;
return array-n1lo;
}
/* ----------------------------------------------------------------------
free a 3d double array with all 3 indices offset
------------------------------------------------------------------------- */
void Memory::destroy_3d_double_array(double ***array, int n1_offset,
int n2_offset, int n3_offset)
{
if (array == NULL) return;
sfree(&array[n1_offset][n2_offset][n3_offset]);
sfree(&array[n1_offset][n2_offset]);
sfree(array + n1_offset);
}
/* ----------------------------------------------------------------------
create a 3d int array
------------------------------------------------------------------------- */
int ***Memory::create_3d_int_array(int n1, int n2, int n3, const char *name)
{
int i,j;
int *data = (int *) smalloc(n1*n2*n3*sizeof(int),name);
int **plane = (int **) smalloc(n1*n2*sizeof(int *),name);
int ***array = (int ***) smalloc(n1*sizeof(int **),name);
int n = 0;
for (i = 0; i < n1; i++) {
array[i] = &plane[i*n2];
for (j = 0; j < n2; j++) {
plane[i*n2+j] = &data[n];
n += n3;
}
}
return array;
}
/* ----------------------------------------------------------------------
free a 3d int array
------------------------------------------------------------------------- */
void Memory::destroy_3d_int_array(int ***array)
{
if (array == NULL) return;
sfree(array[0][0]);
sfree(array[0]);
sfree(array);
}
/* ----------------------------------------------------------------------
create a 4d double array
------------------------------------------------------------------------- */
double ****Memory::create_4d_double_array(int n1, int n2, int n3, int n4,
const char *name)
{
int i,j,k;
double *data = (double *) smalloc(n1*n2*n3*n4*sizeof(double),name);
double **cube = (double **) smalloc(n1*n2*n3*sizeof(double *),name);
double ***plane = (double ***) smalloc(n1*n2*sizeof(double **),name);
double ****array = (double ****) smalloc(n1*sizeof(double ***),name);
int n = 0;
for (i = 0; i < n1; i++) {
array[i] = &plane[i*n2];
for (j = 0; j < n2; j++) {
plane[i*n2+j] = &cube[i*n2*n3+j*n3];
for (k = 0; k < n3; k++) {
cube[i*n2*n3+j*n3+k] = &data[n];
n += n4;
}
}
}
return array;
}
/* ----------------------------------------------------------------------
free a 4d double array
------------------------------------------------------------------------- */
void Memory::destroy_4d_double_array(double ****array)
{
if (array == NULL) return;
sfree(array[0][0][0]);
sfree(array[0][0]);
sfree(array[0]);
sfree(array);
}
diff --git a/src/min.cpp b/src/min.cpp
index 255bdfb60..b7c51cb48 100644
--- a/src/min.cpp
+++ b/src/min.cpp
@@ -1,765 +1,765 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Aidan Thompson (SNL)
improved CG and backtrack ls, added quadratic ls
Sources: Numerical Recipes frprmn routine
"Conjugate Gradient Method Without the Agonizing Pain" by
JR Shewchuk, http://www-2.cs.cmu.edu/~jrs/jrspapers.html#cg
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "math.h"
#include "stdlib.h"
#include "string.h"
#include "min.h"
-#include "lmptype.h"
#include "atom.h"
#include "domain.h"
#include "comm.h"
#include "update.h"
#include "modify.h"
#include "fix_minimize.h"
#include "compute.h"
#include "neighbor.h"
#include "force.h"
#include "pair.h"
#include "bond.h"
#include "angle.h"
#include "dihedral.h"
#include "improper.h"
#include "kspace.h"
#include "output.h"
#include "thermo.h"
#include "timer.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MIN(A,B) ((A) < (B)) ? (A) : (B)
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
/* ---------------------------------------------------------------------- */
Min::Min(LAMMPS *lmp) : Pointers(lmp)
{
dmax = 0.1;
searchflag = 0;
linestyle = 0;
elist_global = elist_atom = NULL;
vlist_global = vlist_atom = NULL;
nextra_global = 0;
fextra = NULL;
nextra_atom = 0;
xextra_atom = fextra_atom = NULL;
extra_peratom = extra_nlen = NULL;
extra_max = NULL;
requestor = NULL;
}
/* ---------------------------------------------------------------------- */
Min::~Min()
{
delete [] elist_global;
delete [] elist_atom;
delete [] vlist_global;
delete [] vlist_atom;
delete [] fextra;
memory->sfree(xextra_atom);
memory->sfree(fextra_atom);
memory->sfree(extra_peratom);
memory->sfree(extra_nlen);
memory->sfree(extra_max);
memory->sfree(requestor);
}
/* ---------------------------------------------------------------------- */
void Min::init()
{
// create fix needed for storing atom-based quantities
// will delete it at end of run
char **fixarg = new char*[3];
fixarg[0] = (char *) "MINIMIZE";
fixarg[1] = (char *) "all";
fixarg[2] = (char *) "MINIMIZE";
modify->add_fix(3,fixarg);
delete [] fixarg;
fix_minimize = (FixMinimize *) modify->fix[modify->nfix-1];
// clear out extra global and per-atom dof
// will receive requests for new per-atom dof during pair init()
// can then add vectors to fix_minimize in setup()
nextra_global = 0;
delete [] fextra;
fextra = NULL;
nextra_atom = 0;
memory->sfree(xextra_atom);
memory->sfree(fextra_atom);
memory->sfree(extra_peratom);
memory->sfree(extra_nlen);
memory->sfree(extra_max);
memory->sfree(requestor);
xextra_atom = fextra_atom = NULL;
extra_peratom = extra_nlen = NULL;
extra_max = NULL;
requestor = NULL;
// virial_style:
// 1 if computed explicitly by pair->compute via sum over pair interactions
// 2 if computed implicitly by pair->virial_compute via sum over ghost atoms
if (force->newton_pair) virial_style = 2;
else virial_style = 1;
// setup lists of computes for global and per-atom PE and pressure
ev_setup();
// set flags for what arrays to clear in force_clear()
// need to clear torques,erforce if arrays exists
torqueflag = 0;
if (atom->torque_flag) torqueflag = 1;
erforceflag = 0;
if (atom->erforce_flag) erforceflag = 1;
// orthogonal vs triclinic simulation box
triclinic = domain->triclinic;
// reset reneighboring criteria if necessary
neigh_every = neighbor->every;
neigh_delay = neighbor->delay;
neigh_dist_check = neighbor->dist_check;
if (neigh_every != 1 || neigh_delay != 0 || neigh_dist_check != 1) {
if (comm->me == 0)
error->warning("Resetting reneighboring criteria during minimization");
}
neighbor->every = 1;
neighbor->delay = 0;
neighbor->dist_check = 1;
niter = neval = 0;
// style-specific initialization
init_style();
}
/* ----------------------------------------------------------------------
setup before run
------------------------------------------------------------------------- */
void Min::setup()
{
if (comm->me == 0 && screen) fprintf(screen,"Setting up minimization ...\n");
// setup extra global dof due to fixes
// cannot be done in init() b/c update init() is before modify init()
nextra_global = modify->min_dof();
if (nextra_global) fextra = new double[nextra_global];
// compute for potential energy
int id = modify->find_compute("thermo_pe");
if (id < 0) error->all("Minimization could not find thermo_pe compute");
pe_compute = modify->compute[id];
// style-specific setup does two tasks
// setup extra global dof vectors
// setup extra per-atom dof vectors due to requests from Pair classes
// cannot be done in init() b/c update init() is before modify/pair init()
setup_style();
// ndoftotal = total dof for entire minimization problem
// dof for atoms, extra per-atom, extra global
bigint ndofme = 3*atom->nlocal;
for (int m = 0; m < nextra_atom; m++)
ndofme += extra_peratom[m]*atom->nlocal;
MPI_Allreduce(&ndofme,&ndoftotal,1,MPI_LMP_BIGINT,MPI_SUM,world);
ndoftotal += nextra_global;
// setup domain, communication and neighboring
// acquire ghosts
// build neighbor lists
atom->setup();
if (triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
domain->reset_box();
comm->setup();
if (neighbor->style) neighbor->setup_bins();
comm->exchange();
if (atom->sortfreq > 0) atom->sort();
comm->borders();
if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
neighbor->build();
neighbor->ncalls = 0;
// remove these restriction eventually
if (nextra_global && searchflag == 0)
error->all("Cannot use a damped dynamics min style with fix box/relax");
if (nextra_atom && searchflag == 0)
error->all("Cannot use a damped dynamics min style with per-atom DOF");
// atoms may have migrated in comm->exchange()
reset_vectors();
// compute all forces
ev_set(update->ntimestep);
force_clear();
modify->setup_pre_force(vflag);
if (force->pair) force->pair->compute(eflag,vflag);
if (atom->molecular) {
if (force->bond) force->bond->compute(eflag,vflag);
if (force->angle) force->angle->compute(eflag,vflag);
if (force->dihedral) force->dihedral->compute(eflag,vflag);
if (force->improper) force->improper->compute(eflag,vflag);
}
if (force->kspace) {
force->kspace->setup();
force->kspace->compute(eflag,vflag);
}
if (force->newton) comm->reverse_comm();
// update per-atom minimization variables stored by pair styles
if (nextra_atom)
for (int m = 0; m < nextra_atom; m++)
requestor[m]->min_xf_get(m);
modify->setup(vflag);
output->setup(1);
// stats for Finish to print
ecurrent = pe_compute->compute_scalar();
if (nextra_global) ecurrent += modify->min_energy(fextra);
if (output->thermo->normflag) ecurrent /= atom->natoms;
einitial = ecurrent;
fnorm2_init = sqrt(fnorm_sqr());
fnorminf_init = fnorm_inf();
}
/* ----------------------------------------------------------------------
setup without output or one-time post-init setup
flag = 0 = just force calculation
flag = 1 = reneighbor and force calculation
------------------------------------------------------------------------- */
void Min::setup_minimal(int flag)
{
// setup domain, communication and neighboring
// acquire ghosts
// build neighbor lists
if (flag) {
if (triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
domain->reset_box();
comm->setup();
if (neighbor->style) neighbor->setup_bins();
comm->exchange();
comm->borders();
if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
neighbor->build();
neighbor->ncalls = 0;
}
// atoms may have migrated in comm->exchange()
reset_vectors();
// compute all forces
ev_set(update->ntimestep);
force_clear();
modify->setup_pre_force(vflag);
if (force->pair) force->pair->compute(eflag,vflag);
if (atom->molecular) {
if (force->bond) force->bond->compute(eflag,vflag);
if (force->angle) force->angle->compute(eflag,vflag);
if (force->dihedral) force->dihedral->compute(eflag,vflag);
if (force->improper) force->improper->compute(eflag,vflag);
}
if (force->kspace) {
force->kspace->setup();
force->kspace->compute(eflag,vflag);
}
if (force->newton) comm->reverse_comm();
// update per-atom minimization variables stored by pair styles
if (nextra_atom)
for (int m = 0; m < nextra_atom; m++)
requestor[m]->min_xf_get(m);
modify->setup(vflag);
// stats for Finish to print
ecurrent = pe_compute->compute_scalar();
if (nextra_global) ecurrent += modify->min_energy(fextra);
if (output->thermo->normflag) ecurrent /= atom->natoms;
einitial = ecurrent;
fnorm2_init = sqrt(fnorm_sqr());
fnorminf_init = fnorm_inf();
}
/* ----------------------------------------------------------------------
perform minimization, calling iterate() for N steps
------------------------------------------------------------------------- */
void Min::run(int n)
{
// minimizer iterations
int iter_start = niter;
stop_condition = iterate(n);
stopstr = stopstrings(stop_condition);
// if early exit from iterate loop:
// set update->nsteps to niter for Finish stats to print
// set output->next values to this timestep
// call energy_force() to insure vflag is set when forces computed
// output->write does final output for thermo, dump, restart files
// add ntimestep to all computes that store invocation times
// since are hardwiring call to thermo/dumps and computes may not be ready
if (stop_condition) {
update->nsteps = niter;
if (update->restrict_output == 0) {
for (int idump = 0; idump < output->ndump; idump++)
output->next_dump[idump] = update->ntimestep;
output->next_dump_any = update->ntimestep;
if (output->restart_every) output->next_restart = update->ntimestep;
}
output->next_thermo = update->ntimestep;
modify->addstep_compute_all(update->ntimestep);
ecurrent = energy_force(0);
output->write(update->ntimestep);
}
}
/* ---------------------------------------------------------------------- */
void Min::cleanup()
{
// stats for Finish to print
efinal = ecurrent;
fnorm2_final = sqrt(fnorm_sqr());
fnorminf_final = fnorm_inf();
// reset reneighboring criteria
neighbor->every = neigh_every;
neighbor->delay = neigh_delay;
neighbor->dist_check = neigh_dist_check;
// delete fix at end of run, so its atom arrays won't persist
modify->delete_fix("MINIMIZE");
}
/* ----------------------------------------------------------------------
evaluate potential energy and forces
may migrate atoms due to reneighboring
return new energy, which should include nextra_global dof
return negative gradient stored in atom->f
return negative gradient for nextra_global dof in fextra
------------------------------------------------------------------------- */
double Min::energy_force(int resetflag)
{
// check for reneighboring
// always communicate since minimizer moved atoms
int nflag = neighbor->decide();
if (nflag == 0) {
timer->stamp();
comm->forward_comm();
timer->stamp(TIME_COMM);
} else {
if (modify->n_min_pre_exchange) modify->min_pre_exchange();
if (triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
if (domain->box_change) {
domain->reset_box();
comm->setup();
if (neighbor->style) neighbor->setup_bins();
}
timer->stamp();
comm->exchange();
if (atom->sortfreq > 0 &&
update->ntimestep >= atom->nextsort) atom->sort();
comm->borders();
if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
timer->stamp(TIME_COMM);
neighbor->build();
timer->stamp(TIME_NEIGHBOR);
}
ev_set(update->ntimestep);
force_clear();
if (modify->n_min_pre_force) modify->min_pre_force(vflag);
timer->stamp();
if (force->pair) {
force->pair->compute(eflag,vflag);
timer->stamp(TIME_PAIR);
}
if (atom->molecular) {
if (force->bond) force->bond->compute(eflag,vflag);
if (force->angle) force->angle->compute(eflag,vflag);
if (force->dihedral) force->dihedral->compute(eflag,vflag);
if (force->improper) force->improper->compute(eflag,vflag);
timer->stamp(TIME_BOND);
}
if (force->kspace) {
force->kspace->compute(eflag,vflag);
timer->stamp(TIME_KSPACE);
}
if (force->newton) {
comm->reverse_comm();
timer->stamp(TIME_COMM);
}
// update per-atom minimization variables stored by pair styles
if (nextra_atom)
for (int m = 0; m < nextra_atom; m++)
requestor[m]->min_xf_get(m);
// fixes that affect minimization
if (modify->n_min_post_force) modify->min_post_force(vflag);
// compute potential energy of system
// normalize if thermo PE does
double energy = pe_compute->compute_scalar();
if (nextra_global) energy += modify->min_energy(fextra);
if (output->thermo->normflag) energy /= atom->natoms;
// if reneighbored, atoms migrated
// if resetflag = 1, update x0 of atoms crossing PBC
// reset vectors used by lo-level minimizer
if (nflag) {
if (resetflag) fix_minimize->reset_coords();
reset_vectors();
}
return energy;
}
/* ----------------------------------------------------------------------
clear force on own & ghost atoms
setup and clear other arrays as needed
------------------------------------------------------------------------- */
void Min::force_clear()
{
int i;
// clear global force array
// nall includes ghosts only if either newton flag is set
int nall;
if (force->newton) nall = atom->nlocal + atom->nghost;
else nall = atom->nlocal;
double **f = atom->f;
for (i = 0; i < nall; i++) {
f[i][0] = 0.0;
f[i][1] = 0.0;
f[i][2] = 0.0;
}
if (torqueflag) {
double **torque = atom->torque;
for (i = 0; i < nall; i++) {
torque[i][0] = 0.0;
torque[i][1] = 0.0;
torque[i][2] = 0.0;
}
}
if (erforceflag) {
double *erforce = atom->erforce;
for (i = 0; i < nall; i++)
erforce[i] = 0.0;
}
}
/* ----------------------------------------------------------------------
pair style makes request to add a per-atom variables to minimization
requestor stores callback to pair class to invoke during min
to get current variable and forces on it and to update the variable
return flag that pair can use if it registers multiple variables
------------------------------------------------------------------------- */
int Min::request(Pair *pair, int peratom, double maxvalue)
{
int n = nextra_atom + 1;
xextra_atom = (double **) memory->srealloc(xextra_atom,n*sizeof(double *),
"min:xextra_atom");
fextra_atom = (double **) memory->srealloc(fextra_atom,n*sizeof(double *),
"min:fextra_atom");
extra_peratom = (int *) memory->srealloc(extra_peratom,n*sizeof(int),
"min:extra_peratom");
extra_nlen = (int *) memory->srealloc(extra_nlen,n*sizeof(int),
"min:extra_nlen");
extra_max = (double *) memory->srealloc(extra_max,n*sizeof(double),
"min:extra_max");
requestor = (Pair **) memory->srealloc(requestor,n*sizeof(Pair *),
"min:requestor");
requestor[nextra_atom] = pair;
extra_peratom[nextra_atom] = peratom;
extra_max[nextra_atom] = maxvalue;
nextra_atom++;
return nextra_atom-1;
}
/* ---------------------------------------------------------------------- */
void Min::modify_params(int narg, char **arg)
{
if (narg == 0) error->all("Illegal min_modify command");
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"dmax") == 0) {
if (iarg+2 > narg) error->all("Illegal min_modify command");
dmax = atof(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"line") == 0) {
if (iarg+2 > narg) error->all("Illegal min_modify command");
if (strcmp(arg[iarg+1],"backtrack") == 0) linestyle = 0;
else if (strcmp(arg[iarg+1],"quadratic") == 0) linestyle = 1;
else error->all("Illegal min_modify command");
iarg += 2;
} else error->all("Illegal min_modify command");
}
}
/* ----------------------------------------------------------------------
setup lists of computes for global and per-atom PE and pressure
------------------------------------------------------------------------- */
void Min::ev_setup()
{
delete [] elist_global;
delete [] elist_atom;
delete [] vlist_global;
delete [] vlist_atom;
elist_global = elist_atom = NULL;
vlist_global = vlist_atom = NULL;
nelist_global = nelist_atom = 0;
nvlist_global = nvlist_atom = 0;
for (int i = 0; i < modify->ncompute; i++) {
if (modify->compute[i]->peflag) nelist_global++;
if (modify->compute[i]->peatomflag) nelist_atom++;
if (modify->compute[i]->pressflag) nvlist_global++;
if (modify->compute[i]->pressatomflag) nvlist_atom++;
}
if (nelist_global) elist_global = new Compute*[nelist_global];
if (nelist_atom) elist_atom = new Compute*[nelist_atom];
if (nvlist_global) vlist_global = new Compute*[nvlist_global];
if (nvlist_atom) vlist_atom = new Compute*[nvlist_atom];
nelist_global = nelist_atom = 0;
nvlist_global = nvlist_atom = 0;
for (int i = 0; i < modify->ncompute; i++) {
if (modify->compute[i]->peflag)
elist_global[nelist_global++] = modify->compute[i];
if (modify->compute[i]->peatomflag)
elist_atom[nelist_atom++] = modify->compute[i];
if (modify->compute[i]->pressflag)
vlist_global[nvlist_global++] = modify->compute[i];
if (modify->compute[i]->pressatomflag)
vlist_atom[nvlist_atom++] = modify->compute[i];
}
}
/* ----------------------------------------------------------------------
set eflag,vflag for current iteration
invoke matchstep() on all timestep-dependent computes to clear their arrays
eflag/vflag based on computes that need info on this ntimestep
always set eflag_global = 1, since need energy every iteration
eflag = 0 = no energy computation
eflag = 1 = global energy only
eflag = 2 = per-atom energy only
eflag = 3 = both global and per-atom energy
vflag = 0 = no virial computation (pressure)
vflag = 1 = global virial with pair portion via sum of pairwise interactions
vflag = 2 = global virial with pair portion via F dot r including ghosts
vflag = 4 = per-atom virial only
vflag = 5 or 6 = both global and per-atom virial
------------------------------------------------------------------------- */
void Min::ev_set(bigint ntimestep)
{
int i,flag;
int eflag_global = 1;
for (i = 0; i < nelist_global; i++)
elist_global[i]->matchstep(ntimestep);
flag = 0;
int eflag_atom = 0;
for (i = 0; i < nelist_atom; i++)
if (elist_atom[i]->matchstep(ntimestep)) flag = 1;
if (flag) eflag_atom = 2;
if (eflag_global) update->eflag_global = update->ntimestep;
if (eflag_atom) update->eflag_atom = update->ntimestep;
eflag = eflag_global + eflag_atom;
flag = 0;
int vflag_global = 0;
for (i = 0; i < nvlist_global; i++)
if (vlist_global[i]->matchstep(ntimestep)) flag = 1;
if (flag) vflag_global = virial_style;
flag = 0;
int vflag_atom = 0;
for (i = 0; i < nvlist_atom; i++)
if (vlist_atom[i]->matchstep(ntimestep)) flag = 1;
if (flag) vflag_atom = 4;
if (vflag_global) update->vflag_global = update->ntimestep;
if (vflag_atom) update->vflag_atom = update->ntimestep;
vflag = vflag_global + vflag_atom;
}
/* ----------------------------------------------------------------------
compute and return ||force||_2^2
------------------------------------------------------------------------- */
double Min::fnorm_sqr()
{
int i,n;
double *fatom;
double local_norm2_sqr = 0.0;
for (i = 0; i < nvec; i++) local_norm2_sqr += fvec[i]*fvec[i];
if (nextra_atom) {
for (int m = 0; m < nextra_atom; m++) {
fatom = fextra_atom[m];
n = extra_nlen[m];
for (i = 0; i < n; i++)
local_norm2_sqr += fatom[i]*fatom[i];
}
}
double norm2_sqr = 0.0;
MPI_Allreduce(&local_norm2_sqr,&norm2_sqr,1,MPI_DOUBLE,MPI_SUM,world);
if (nextra_global)
for (i = 0; i < nextra_global; i++)
norm2_sqr += fextra[i]*fextra[i];
return norm2_sqr;
}
/* ----------------------------------------------------------------------
compute and return ||force||_inf
------------------------------------------------------------------------- */
double Min::fnorm_inf()
{
int i,n;
double *fatom;
double local_norm_inf = 0.0;
for (i = 0; i < nvec; i++)
local_norm_inf = MAX(fabs(fvec[i]),local_norm_inf);
if (nextra_atom) {
for (int m = 0; m < nextra_atom; m++) {
fatom = fextra_atom[m];
n = extra_nlen[m];
for (i = 0; i < n; i++)
local_norm_inf = MAX(fabs(fatom[i]),local_norm_inf);
}
}
double norm_inf = 0.0;
MPI_Allreduce(&local_norm_inf,&norm_inf,1,MPI_DOUBLE,MPI_MAX,world);
if (nextra_global)
for (i = 0; i < nextra_global; i++)
norm_inf = MAX(fabs(fextra[i]),norm_inf);
return norm_inf;
}
/* ----------------------------------------------------------------------
possible stop conditions
------------------------------------------------------------------------- */
char *Min::stopstrings(int n)
{
char *strings[] = {"max iterations",
"max force evaluations",
"energy tolerance",
"force tolerance",
"search direction is not downhill",
"linesearch alpha is zero",
"forces are zero",
"quadratic factors are zero",
"trust region too small",
"HFTN minimizer error"};
return strings[n];
}
diff --git a/src/min.h b/src/min.h
index 7b0990333..de0d596c3 100644
--- a/src/min.h
+++ b/src/min.h
@@ -1,108 +1,108 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifndef LMP_MIN_H
#define LMP_MIN_H
-#include "pointers.h"
#include "lmptype.h"
+#include "pointers.h"
namespace LAMMPS_NS {
class Min : protected Pointers {
public:
double einitial,efinal,eprevious;
double fnorm2_init,fnorminf_init,fnorm2_final,fnorminf_final;
double alpha_final;
int niter,neval;
int stop_condition;
char *stopstr;
int searchflag; // 0 if damped dynamics, 1 if sub-cycles on local search
Min(class LAMMPS *);
virtual ~Min();
void init();
void setup();
void setup_minimal(int);
void run(int);
void cleanup();
int request(class Pair *, int, double);
double memory_usage() {return 0.0;}
void modify_params(int, char **);
double fnorm_sqr();
double fnorm_inf();
virtual void init_style() {}
virtual void setup_style() = 0;
virtual void reset_vectors() = 0;
virtual int iterate(int) = 0;
protected:
int eflag,vflag; // flags for energy/virial computation
int virial_style; // compute virial explicitly or implicitly
double dmax; // max dist to move any atom in one step
int linestyle; // 0 = backtrack, 1 = quadratic
int nelist_global,nelist_atom; // # of PE,virial computes to check
int nvlist_global,nvlist_atom;
class Compute **elist_global; // lists of PE,virial Computes
class Compute **elist_atom;
class Compute **vlist_global;
class Compute **vlist_atom;
int pairflag;
int torqueflag,erforceflag;
int triclinic; // 0 if domain is orthog, 1 if triclinic
int narray; // # of arrays stored by fix_minimize
class FixMinimize *fix_minimize; // fix that stores auxiliary data
class Compute *pe_compute; // compute for potential energy
double ecurrent; // current potential energy
bigint ndoftotal; // total dof for entire problem
int nvec; // local atomic dof = length of xvec
double *xvec; // variables for atomic dof, as 1d vector
double *fvec; // force vector for atomic dof, as 1d vector
int nextra_global; // # of extra global dof due to fixes
double *fextra; // force vector for extra global dof
// xextra is stored by fix
int nextra_atom; // # of extra per-atom variables
double **xextra_atom; // ptr to the variable
double **fextra_atom; // ptr to the force on the variable
int *extra_peratom; // # of values in variable, e.g. 3 in x
int *extra_nlen; // total local length of variable, e.g 3*nlocal
double *extra_max; // max allowed change per iter for atom's var
class Pair **requestor; // Pair that stores/manipulates the variable
int neigh_every,neigh_delay,neigh_dist_check; // neighboring params
double energy_force(int);
void force_clear();
double compute_force_norm_sqr();
double compute_force_norm_inf();
void ev_setup();
void ev_set(bigint);
char *stopstrings(int);
};
}
#endif
diff --git a/src/min_cg.cpp b/src/min_cg.cpp
index 9ad87904f..9ef3c8c4a 100644
--- a/src/min_cg.cpp
+++ b/src/min_cg.cpp
@@ -1,187 +1,187 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "mpi.h"
#include "math.h"
#include "string.h"
#include "min_cg.h"
-#include "lmptype.h"
#include "atom.h"
#include "update.h"
#include "output.h"
#include "timer.h"
using namespace LAMMPS_NS;
// EPS_ENERGY = minimum normalization for energy tolerance
#define EPS_ENERGY 1.0e-8
// same as in other min classes
enum{MAXITER,MAXEVAL,ETOL,FTOL,DOWNHILL,ZEROALPHA,ZEROFORCE,ZEROQUAD};
#define MIN(A,B) ((A) < (B)) ? (A) : (B)
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
/* ---------------------------------------------------------------------- */
MinCG::MinCG(LAMMPS *lmp) : MinLineSearch(lmp) {}
/* ----------------------------------------------------------------------
minimization via conjugate gradient iterations
------------------------------------------------------------------------- */
int MinCG::iterate(int maxiter)
{
int i,m,n,fail,ntimestep;
double beta,gg,dot[2],dotall[2];
double *fatom,*gatom,*hatom;
// nlimit = max # of CG iterations before restarting
// set to ndoftotal unless too big
int nlimit = static_cast<int> (MIN(MAXSMALLINT,ndoftotal));
// initialize working vectors
for (i = 0; i < nvec; i++) h[i] = g[i] = fvec[i];
if (nextra_atom)
for (m = 0; m < nextra_atom; m++) {
fatom = fextra_atom[m];
gatom = gextra_atom[m];
hatom = hextra_atom[m];
n = extra_nlen[m];
for (i = 0; i < n; i++) hatom[i] = gatom[i] = fatom[i];
}
if (nextra_global)
for (i = 0; i < nextra_global; i++) hextra[i] = gextra[i] = fextra[i];
gg = fnorm_sqr();
for (int iter = 0; iter < maxiter; iter++) {
ntimestep = ++update->ntimestep;
niter++;
// line minimization along direction h from current atom->x
eprevious = ecurrent;
fail = (this->*linemin)(ecurrent,alpha_final);
if (fail) return fail;
// function evaluation criterion
if (neval >= update->max_eval) return MAXEVAL;
// energy tolerance criterion
if (fabs(ecurrent-eprevious) <
update->etol * 0.5*(fabs(ecurrent) + fabs(eprevious) + EPS_ENERGY))
return ETOL;
// force tolerance criterion
dot[0] = dot[1] = 0.0;
for (i = 0; i < nvec; i++) {
dot[0] += fvec[i]*fvec[i];
dot[1] += fvec[i]*g[i];
}
if (nextra_atom)
for (m = 0; m < nextra_atom; m++) {
fatom = fextra_atom[m];
gatom = gextra_atom[m];
n = extra_nlen[m];
for (i = 0; i < n; i++) {
dot[0] += fatom[i]*fatom[i];
dot[1] += fatom[i]*gatom[i];
}
}
MPI_Allreduce(dot,dotall,2,MPI_DOUBLE,MPI_SUM,world);
if (nextra_global)
for (i = 0; i < nextra_global; i++) {
dotall[0] += fextra[i]*fextra[i];
dotall[1] += fextra[i]*gextra[i];
}
if (dotall[0] < update->ftol*update->ftol) return FTOL;
// update new search direction h from new f = -Grad(x) and old g
// this is Polak-Ribieri formulation
// beta = dotall[0]/gg would be Fletcher-Reeves
// reinitialize CG every ndof iterations by setting beta = 0.0
beta = MAX(0.0,(dotall[0] - dotall[1])/gg);
if ((niter+1) % nlimit == 0) beta = 0.0;
gg = dotall[0];
for (i = 0; i < nvec; i++) {
g[i] = fvec[i];
h[i] = g[i] + beta*h[i];
}
if (nextra_atom)
for (m = 0; m < nextra_atom; m++) {
fatom = fextra_atom[m];
gatom = gextra_atom[m];
hatom = hextra_atom[m];
n = extra_nlen[m];
for (i = 0; i < n; i++) {
gatom[i] = fatom[i];
hatom[i] = gatom[i] + beta*hatom[i];
}
}
if (nextra_global)
for (i = 0; i < nextra_global; i++) {
gextra[i] = fextra[i];
hextra[i] = gextra[i] + beta*hextra[i];
}
// reinitialize CG if new search direction h is not downhill
dot[0] = 0.0;
for (i = 0; i < nvec; i++) dot[0] += g[i]*h[i];
if (nextra_atom)
for (m = 0; m < nextra_atom; m++) {
gatom = gextra_atom[m];
hatom = hextra_atom[m];
n = extra_nlen[m];
for (i = 0; i < n; i++) dot[0] += gatom[i]*hatom[i];
}
MPI_Allreduce(dot,dotall,1,MPI_DOUBLE,MPI_SUM,world);
if (nextra_global)
for (i = 0; i < nextra_global; i++)
dotall[0] += gextra[i]*hextra[i];
if (dotall[0] <= 0.0) {
for (i = 0; i < nvec; i++) h[i] = g[i];
if (nextra_atom)
for (m = 0; m < nextra_atom; m++) {
gatom = gextra_atom[m];
hatom = hextra_atom[m];
n = extra_nlen[m];
for (i = 0; i < n; i++) hatom[i] = gatom[i];
}
if (nextra_global)
for (i = 0; i < nextra_global; i++) hextra[i] = gextra[i];
}
// output for thermo, dump, restart files
if (output->next == ntimestep) {
timer->stamp();
output->write(ntimestep);
timer->stamp(TIME_OUTPUT);
}
}
return MAXITER;
}
diff --git a/src/min_quickmin.cpp b/src/min_quickmin.cpp
index 6fb15b175..ec59fd20f 100644
--- a/src/min_quickmin.cpp
+++ b/src/min_quickmin.cpp
@@ -1,240 +1,240 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "mpi.h"
#include "math.h"
#include "min_quickmin.h"
-#include "lmptype.h"
#include "universe.h"
#include "atom.h"
#include "force.h"
#include "update.h"
#include "output.h"
#include "timer.h"
#include "error.h"
using namespace LAMMPS_NS;
// EPS_ENERGY = minimum normalization for energy tolerance
#define EPS_ENERGY 1.0e-8
// same as in other min classes
enum{MAXITER,MAXEVAL,ETOL,FTOL,DOWNHILL,ZEROALPHA,ZEROFORCE,ZEROQUAD};
#define MIN(A,B) ((A) < (B)) ? (A) : (B)
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
#define DELAYSTEP 5
/* ---------------------------------------------------------------------- */
MinQuickMin::MinQuickMin(LAMMPS *lmp) : Min(lmp) {}
/* ---------------------------------------------------------------------- */
void MinQuickMin::init_style()
{
dt = update->dt;
}
/* ---------------------------------------------------------------------- */
void MinQuickMin::setup_style()
{
double **v = atom->v;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
v[i][0] = v[i][1] = v[i][2] = 0.0;
}
/* ----------------------------------------------------------------------
set current vector lengths and pointers
called after atoms have migrated
------------------------------------------------------------------------- */
void MinQuickMin::reset_vectors()
{
// atomic dof
nvec = 3 * atom->nlocal;
if (nvec) xvec = atom->x[0];
if (nvec) fvec = atom->f[0];
}
/* ----------------------------------------------------------------------
minimization via QuickMin damped dynamics
/* ---------------------------------------------------------------------- */
int MinQuickMin::iterate(int maxiter)
{
bigint ntimestep;
double vmax,vdotf,vdotfall,fdotf,fdotfall,scale;
double dtvone,dtv,dtfm;
int flag,flagall;
alpha_final = 0.0;
bigint last_negative = update->ntimestep;
for (int iter = 0; iter < maxiter; iter++) {
ntimestep = ++update->ntimestep;
niter++;
// zero velocity if anti-parallel to force
// else project velocity in direction of force
double **v = atom->v;
double **f = atom->f;
int nlocal = atom->nlocal;
vdotf = 0.0;
for (int i = 0; i < nlocal; i++)
vdotf += v[i][0]*f[i][0] + v[i][1]*f[i][1] + v[i][2]*f[i][2];
MPI_Allreduce(&vdotf,&vdotfall,1,MPI_DOUBLE,MPI_SUM,world);
// sum vdotf over replicas, if necessary
// this communicator would be invalid for multiprocess replicas
if (update->multireplica == 1) {
vdotf = vdotfall;
MPI_Allreduce(&vdotf,&vdotfall,1,MPI_DOUBLE,MPI_SUM,universe->uworld);
}
if (vdotfall < 0.0) {
last_negative = ntimestep;
for (int i = 0; i < nlocal; i++)
v[i][0] = v[i][1] = v[i][2] = 0.0;
} else {
fdotf = 0.0;
for (int i = 0; i < nlocal; i++)
fdotf += f[i][0]*f[i][0] + f[i][1]*f[i][1] + f[i][2]*f[i][2];
MPI_Allreduce(&fdotf,&fdotfall,1,MPI_DOUBLE,MPI_SUM,world);
// sum fdotf over replicas, if necessary
// this communicator would be invalid for multiprocess replicas
if (update->multireplica == 1) {
fdotf = fdotfall;
MPI_Allreduce(&fdotf,&fdotfall,1,MPI_DOUBLE,MPI_SUM,universe->uworld);
}
if (fdotfall == 0.0) scale = 0.0;
else scale = vdotfall/fdotfall;
for (int i = 0; i < nlocal; i++) {
v[i][0] = scale * f[i][0];
v[i][1] = scale * f[i][1];
v[i][2] = scale * f[i][2];
}
}
// limit timestep so no particle moves further than dmax
double *rmass = atom->rmass;
double *mass = atom->mass;
int *type = atom->type;
dtvone = dt;
for (int i = 0; i < nlocal; i++) {
vmax = MAX(fabs(v[i][0]),fabs(v[i][1]));
vmax = MAX(vmax,fabs(v[i][2]));
if (dtvone*vmax > dmax) dtvone = dmax/vmax;
}
MPI_Allreduce(&dtvone,&dtv,1,MPI_DOUBLE,MPI_MIN,world);
// min dtv over replicas, if necessary
// this communicator would be invalid for multiprocess replicas
if (update->multireplica == 1) {
dtvone = dtv;
MPI_Allreduce(&dtvone,&dtv,1,MPI_DOUBLE,MPI_MIN,universe->uworld);
}
// Euler integration step
double **x = atom->x;
if (rmass) {
for (int i = 0; i < nlocal; i++) {
dtfm = dtv / rmass[i];
x[i][0] += dtv * v[i][0];
x[i][1] += dtv * v[i][1];
x[i][2] += dtv * v[i][2];
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
}
} else {
for (int i = 0; i < nlocal; i++) {
dtfm = dtv / mass[type[i]];
x[i][0] += dtv * v[i][0];
x[i][1] += dtv * v[i][1];
x[i][2] += dtv * v[i][2];
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
}
}
eprevious = ecurrent;
ecurrent = energy_force(0);
neval++;
// energy tolerance criterion
// only check after DELAYSTEP elapsed since velocties reset to 0
// sync across replicas if running multi-replica minimization
if (update->etol > 0.0 && ntimestep-last_negative > DELAYSTEP) {
if (update->multireplica == 0) {
if (fabs(ecurrent-eprevious) <
update->etol * 0.5*(fabs(ecurrent) + fabs(eprevious) + EPS_ENERGY))
return ETOL;
} else {
if (fabs(ecurrent-eprevious) <
update->etol * 0.5*(fabs(ecurrent) + fabs(eprevious) + EPS_ENERGY))
flag = 0;
else flag = 1;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,universe->uworld);
if (flagall == 0) return ETOL;
}
}
// force tolerance criterion
// sync across replicas if running multi-replica minimization
if (update->ftol > 0.0) {
fdotf = fnorm_sqr();
if (update->multireplica == 0) {
if (fdotf < update->ftol*update->ftol) return FTOL;
} else {
if (fdotf < update->ftol*update->ftol) flag = 0;
else flag = 1;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,universe->uworld);
if (flagall == 0) return FTOL;
}
}
// output for thermo, dump, restart files
if (output->next == ntimestep) {
timer->stamp();
output->write(ntimestep);
timer->stamp(TIME_OUTPUT);
}
}
return MAXITER;
}
diff --git a/src/modify.h b/src/modify.h
index f211167a1..56d94d63b 100644
--- a/src/modify.h
+++ b/src/modify.h
@@ -1,138 +1,138 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifndef LMP_MODIFY_H
#define LMP_MODIFY_H
+#include "lmptype.h"
#include "stdio.h"
#include "pointers.h"
-#include "lmptype.h"
namespace LAMMPS_NS {
class Modify : protected Pointers {
public:
int nfix,maxfix;
int n_initial_integrate,n_post_integrate,n_pre_exchange,n_pre_neighbor;
int n_pre_force,n_post_force;
int n_final_integrate,n_end_of_step,n_thermo_energy;
int n_initial_integrate_respa,n_post_integrate_respa;
int n_pre_force_respa,n_post_force_respa,n_final_integrate_respa;
int n_min_pre_exchange,n_min_pre_force,n_min_post_force,n_min_energy;
int restart_pbc_any; // 1 if any fix sets restart_pbc
int nfix_restart_global; // stored fix global info from restart file
int nfix_restart_peratom; // stored fix peratom info from restart file
class Fix **fix; // list of fixes
int *fmask; // bit mask for when each fix is applied
int ncompute,maxcompute; // list of computes
class Compute **compute;
Modify(class LAMMPS *);
~Modify();
void init();
void setup(int);
void setup_pre_force(int);
void initial_integrate(int);
void post_integrate();
void pre_decide();
void pre_exchange();
void pre_neighbor();
void pre_force(int);
void post_force(int);
void final_integrate();
void end_of_step();
double thermo_energy();
void post_run();
void setup_pre_force_respa(int, int);
void initial_integrate_respa(int, int, int);
void post_integrate_respa(int, int);
void pre_force_respa(int, int, int);
void post_force_respa(int, int, int);
void final_integrate_respa(int, int);
void setup_min_pre_force(int);
void min_pre_exchange();
void min_pre_force(int);
void min_post_force(int);
double min_energy(double *);
void min_store();
void min_step(double, double *);
void min_clearstore();
void min_pushstore();
void min_popstore();
int min_reset_ref();
double max_alpha(double *);
int min_dof();
void add_fix(int, char **);
void modify_fix(int, char **);
void delete_fix(const char *);
int find_fix(const char *);
void add_compute(int, char **);
void modify_compute(int, char **);
void delete_compute(char *);
int find_compute(char *);
void clearstep_compute();
void addstep_compute(bigint);
void addstep_compute_all(bigint);
void write_restart(FILE *);
int read_restart(FILE *);
void restart_deallocate();
double memory_usage();
private:
// lists of fixes to apply at different stages of timestep
int *list_initial_integrate,*list_post_integrate;
int *list_pre_exchange,*list_pre_neighbor;
int *list_pre_force,*list_post_force;
int *list_final_integrate,*list_end_of_step,*list_thermo_energy;
int *list_initial_integrate_respa,*list_post_integrate_respa;
int *list_pre_force_respa,*list_post_force_respa;
int *list_final_integrate_respa;
int *list_min_pre_exchange,*list_min_pre_force;
int *list_min_post_force,*list_min_energy;
int *end_of_step_every;
int n_timeflag; // list of computes that store time invocation
int *list_timeflag;
char **id_restart_global; // stored fix global info
char **style_restart_global; // from read-in restart file
char **state_restart_global;
char **id_restart_peratom; // stored fix peratom info
char **style_restart_peratom; // from read-in restart file
int *index_restart_peratom;
int index_permanent; // fix/compute index returned to library call
void list_init(int, int &, int *&);
void list_init_end_of_step(int, int &, int *&);
void list_init_thermo_energy(int, int &, int *&);
void list_init_compute();
};
}
#endif
diff --git a/src/neigh_bond.cpp b/src/neigh_bond.cpp
index e89c31cf3..2ef6b8950 100644
--- a/src/neigh_bond.cpp
+++ b/src/neigh_bond.cpp
@@ -1,400 +1,400 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "neighbor.h"
#include "lmptype.h"
+#include "neighbor.h"
#include "atom.h"
#include "force.h"
#include "update.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define BONDDELTA 10000
/* ---------------------------------------------------------------------- */
void Neighbor::bond_all()
{
int i,m,atom1;
int nlocal = atom->nlocal;
int *num_bond = atom->num_bond;
int **bond_atom = atom->bond_atom;
int **bond_type = atom->bond_type;
int *tag = atom->tag;
int newton_bond = force->newton_bond;
nbondlist = 0;
for (i = 0; i < nlocal; i++)
for (m = 0; m < num_bond[i]; m++) {
atom1 = atom->map(bond_atom[i][m]);
if (atom1 == -1) {
char str[128];
sprintf(str,
"Bond atoms %d %d missing on proc %d at step " BIGINT_FORMAT,
tag[i],bond_atom[i][m],me,update->ntimestep);
error->one(str);
}
if (newton_bond || i < atom1) {
if (nbondlist == maxbond) {
maxbond += BONDDELTA;
bondlist = memory->grow_2d_int_array(bondlist,maxbond,3,
"neighbor:bondlist");
}
bondlist[nbondlist][0] = i;
bondlist[nbondlist][1] = atom1;
bondlist[nbondlist][2] = bond_type[i][m];
nbondlist++;
}
}
}
/* ---------------------------------------------------------------------- */
void Neighbor::bond_partial()
{
int i,m,atom1;
int nlocal = atom->nlocal;
int *num_bond = atom->num_bond;
int **bond_atom = atom->bond_atom;
int **bond_type = atom->bond_type;
int *tag = atom->tag;
int newton_bond = force->newton_bond;
nbondlist = 0;
for (i = 0; i < nlocal; i++)
for (m = 0; m < num_bond[i]; m++) {
if (bond_type[i][m] <= 0) continue;
atom1 = atom->map(bond_atom[i][m]);
if (atom1 == -1) {
char str[128];
sprintf(str,
"Bond atoms %d %d missing on proc %d at step " BIGINT_FORMAT,
tag[i],bond_atom[i][m],me,update->ntimestep);
error->one(str);
}
if (newton_bond || i < atom1) {
if (nbondlist == maxbond) {
maxbond += BONDDELTA;
bondlist = memory->grow_2d_int_array(bondlist,maxbond,3,
"neighbor:bondlist");
}
bondlist[nbondlist][0] = i;
bondlist[nbondlist][1] = atom1;
bondlist[nbondlist][2] = bond_type[i][m];
nbondlist++;
}
}
}
/* ---------------------------------------------------------------------- */
void Neighbor::angle_all()
{
int i,m,atom1,atom2,atom3;
int nlocal = atom->nlocal;
int *num_angle = atom->num_angle;
int **angle_atom1 = atom->angle_atom1;
int **angle_atom2 = atom->angle_atom2;
int **angle_atom3 = atom->angle_atom3;
int **angle_type = atom->angle_type;
int newton_bond = force->newton_bond;
nanglelist = 0;
for (i = 0; i < nlocal; i++)
for (m = 0; m < num_angle[i]; m++) {
atom1 = atom->map(angle_atom1[i][m]);
atom2 = atom->map(angle_atom2[i][m]);
atom3 = atom->map(angle_atom3[i][m]);
if (atom1 == -1 || atom2 == -1 || atom3 == -1) {
char str[128];
sprintf(str,
"Angle atoms %d %d %d missing on proc %d at step "
BIGINT_FORMAT,
angle_atom1[i][m],angle_atom2[i][m],angle_atom3[i][m],
me,update->ntimestep);
error->one(str);
}
if (newton_bond || (i <= atom1 && i <= atom2 && i <= atom3)) {
if (nanglelist == maxangle) {
maxangle += BONDDELTA;
anglelist = memory->grow_2d_int_array(anglelist,maxangle,4,
"neighbor:anglelist");
}
anglelist[nanglelist][0] = atom1;
anglelist[nanglelist][1] = atom2;
anglelist[nanglelist][2] = atom3;
anglelist[nanglelist][3] = angle_type[i][m];
nanglelist++;
}
}
}
/* ---------------------------------------------------------------------- */
void Neighbor::angle_partial()
{
int i,m,atom1,atom2,atom3;
int nlocal = atom->nlocal;
int *num_angle = atom->num_angle;
int **angle_atom1 = atom->angle_atom1;
int **angle_atom2 = atom->angle_atom2;
int **angle_atom3 = atom->angle_atom3;
int **angle_type = atom->angle_type;
int newton_bond = force->newton_bond;
nanglelist = 0;
for (i = 0; i < nlocal; i++)
for (m = 0; m < num_angle[i]; m++) {
if (angle_type[i][m] <= 0) continue;
atom1 = atom->map(angle_atom1[i][m]);
atom2 = atom->map(angle_atom2[i][m]);
atom3 = atom->map(angle_atom3[i][m]);
if (atom1 == -1 || atom2 == -1 || atom3 == -1) {
char str[128];
sprintf(str,
"Angle atoms %d %d %d missing on proc %d at step "
BIGINT_FORMAT,
angle_atom1[i][m],angle_atom2[i][m],angle_atom3[i][m],
me,update->ntimestep);
error->one(str);
}
if (newton_bond || (i <= atom1 && i <= atom2 && i <= atom3)) {
if (nanglelist == maxangle) {
maxangle += BONDDELTA;
anglelist = memory->grow_2d_int_array(anglelist,maxangle,4,
"neighbor:anglelist");
}
anglelist[nanglelist][0] = atom1;
anglelist[nanglelist][1] = atom2;
anglelist[nanglelist][2] = atom3;
anglelist[nanglelist][3] = angle_type[i][m];
nanglelist++;
}
}
}
/* ---------------------------------------------------------------------- */
void Neighbor::dihedral_all()
{
int i,m,atom1,atom2,atom3,atom4;
int nlocal = atom->nlocal;
int *num_dihedral = atom->num_dihedral;
int **dihedral_atom1 = atom->dihedral_atom1;
int **dihedral_atom2 = atom->dihedral_atom2;
int **dihedral_atom3 = atom->dihedral_atom3;
int **dihedral_atom4 = atom->dihedral_atom4;
int **dihedral_type = atom->dihedral_type;
int newton_bond = force->newton_bond;
ndihedrallist = 0;
for (i = 0; i < nlocal; i++)
for (m = 0; m < num_dihedral[i]; m++) {
atom1 = atom->map(dihedral_atom1[i][m]);
atom2 = atom->map(dihedral_atom2[i][m]);
atom3 = atom->map(dihedral_atom3[i][m]);
atom4 = atom->map(dihedral_atom4[i][m]);
if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
char str[128];
sprintf(str,
"Dihedral atoms %d %d %d %d missing on proc %d at step "
BIGINT_FORMAT,
dihedral_atom1[i][m],dihedral_atom2[i][m],
dihedral_atom3[i][m],dihedral_atom4[i][m],
me,update->ntimestep);
error->one(str);
}
if (newton_bond ||
(i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)) {
if (ndihedrallist == maxdihedral) {
maxdihedral += BONDDELTA;
dihedrallist =
memory->grow_2d_int_array(dihedrallist,maxdihedral,5,
"neighbor:dihedrallist");
}
dihedrallist[ndihedrallist][0] = atom1;
dihedrallist[ndihedrallist][1] = atom2;
dihedrallist[ndihedrallist][2] = atom3;
dihedrallist[ndihedrallist][3] = atom4;
dihedrallist[ndihedrallist][4] = dihedral_type[i][m];
ndihedrallist++;
}
}
}
/* ---------------------------------------------------------------------- */
void Neighbor::dihedral_partial()
{
int i,m,atom1,atom2,atom3,atom4;
int nlocal = atom->nlocal;
int *num_dihedral = atom->num_dihedral;
int **dihedral_atom1 = atom->dihedral_atom1;
int **dihedral_atom2 = atom->dihedral_atom2;
int **dihedral_atom3 = atom->dihedral_atom3;
int **dihedral_atom4 = atom->dihedral_atom4;
int **dihedral_type = atom->dihedral_type;
int newton_bond = force->newton_bond;
ndihedrallist = 0;
for (i = 0; i < nlocal; i++)
for (m = 0; m < num_dihedral[i]; m++) {
if (dihedral_type[i][m] <= 0) continue;
atom1 = atom->map(dihedral_atom1[i][m]);
atom2 = atom->map(dihedral_atom2[i][m]);
atom3 = atom->map(dihedral_atom3[i][m]);
atom4 = atom->map(dihedral_atom4[i][m]);
if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
char str[128];
sprintf(str,
"Dihedral atoms %d %d %d %d missing on proc %d at step "
BIGINT_FORMAT,
dihedral_atom1[i][m],dihedral_atom2[i][m],
dihedral_atom3[i][m],dihedral_atom4[i][m],
me,update->ntimestep);
error->one(str);
}
if (newton_bond ||
(i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)) {
if (ndihedrallist == maxdihedral) {
maxdihedral += BONDDELTA;
dihedrallist =
memory->grow_2d_int_array(dihedrallist,maxdihedral,5,
"neighbor:dihedrallist");
}
dihedrallist[ndihedrallist][0] = atom1;
dihedrallist[ndihedrallist][1] = atom2;
dihedrallist[ndihedrallist][2] = atom3;
dihedrallist[ndihedrallist][3] = atom4;
dihedrallist[ndihedrallist][4] = dihedral_type[i][m];
ndihedrallist++;
}
}
}
/* ---------------------------------------------------------------------- */
void Neighbor::improper_all()
{
int i,m,atom1,atom2,atom3,atom4;
int nlocal = atom->nlocal;
int *num_improper = atom->num_improper;
int **improper_atom1 = atom->improper_atom1;
int **improper_atom2 = atom->improper_atom2;
int **improper_atom3 = atom->improper_atom3;
int **improper_atom4 = atom->improper_atom4;
int **improper_type = atom->improper_type;
int newton_bond = force->newton_bond;
nimproperlist = 0;
for (i = 0; i < nlocal; i++)
for (m = 0; m < num_improper[i]; m++) {
atom1 = atom->map(improper_atom1[i][m]);
atom2 = atom->map(improper_atom2[i][m]);
atom3 = atom->map(improper_atom3[i][m]);
atom4 = atom->map(improper_atom4[i][m]);
if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
char str[128];
sprintf(str,
"Improper atoms %d %d %d %d missing on proc %d at step "
BIGINT_FORMAT,
improper_atom1[i][m],improper_atom2[i][m],
improper_atom3[i][m],improper_atom4[i][m],
me,update->ntimestep);
error->one(str);
}
if (newton_bond ||
(i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)) {
if (nimproperlist == maximproper) {
maximproper += BONDDELTA;
improperlist =
memory->grow_2d_int_array(improperlist,maximproper,5,
"neighbor:improperlist");
}
improperlist[nimproperlist][0] = atom1;
improperlist[nimproperlist][1] = atom2;
improperlist[nimproperlist][2] = atom3;
improperlist[nimproperlist][3] = atom4;
improperlist[nimproperlist][4] = improper_type[i][m];
nimproperlist++;
}
}
}
/* ---------------------------------------------------------------------- */
void Neighbor::improper_partial()
{
int i,m,atom1,atom2,atom3,atom4;
int nlocal = atom->nlocal;
int *num_improper = atom->num_improper;
int **improper_atom1 = atom->improper_atom1;
int **improper_atom2 = atom->improper_atom2;
int **improper_atom3 = atom->improper_atom3;
int **improper_atom4 = atom->improper_atom4;
int **improper_type = atom->improper_type;
int newton_bond = force->newton_bond;
nimproperlist = 0;
for (i = 0; i < nlocal; i++)
for (m = 0; m < num_improper[i]; m++) {
if (improper_type[i][m] <= 0) continue;
atom1 = atom->map(improper_atom1[i][m]);
atom2 = atom->map(improper_atom2[i][m]);
atom3 = atom->map(improper_atom3[i][m]);
atom4 = atom->map(improper_atom4[i][m]);
if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
char str[128];
sprintf(str,
"Improper atoms %d %d %d %d missing on proc %d at step "
BIGINT_FORMAT,
improper_atom1[i][m],improper_atom2[i][m],
improper_atom3[i][m],improper_atom4[i][m],
me,update->ntimestep);
error->one(str);
}
if (newton_bond ||
(i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)) {
if (nimproperlist == maximproper) {
maximproper += BONDDELTA;
improperlist =
memory->grow_2d_int_array(improperlist,maximproper,5,
"neighbor:improperlist");
}
improperlist[nimproperlist][0] = atom1;
improperlist[nimproperlist][1] = atom2;
improperlist[nimproperlist][2] = atom3;
improperlist[nimproperlist][3] = atom4;
improperlist[nimproperlist][4] = improper_type[i][m];
nimproperlist++;
}
}
}
diff --git a/src/neighbor.cpp b/src/neighbor.cpp
index e97a11d64..7240fde42 100644
--- a/src/neighbor.cpp
+++ b/src/neighbor.cpp
@@ -1,1671 +1,1671 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author (triclinic and multi-neigh) : Pieter in 't Veld (SNL)
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "mpi.h"
#include "math.h"
#include "stdlib.h"
#include "string.h"
#include "neighbor.h"
-#include "lmptype.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "atom.h"
#include "atom_vec.h"
#include "comm.h"
#include "force.h"
#include "pair.h"
#include "domain.h"
#include "group.h"
#include "modify.h"
#include "fix.h"
#include "compute.h"
#include "update.h"
#include "respa.h"
#include "output.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define RQDELTA 1
#define EXDELTA 1
#define LB_FACTOR 1.5
#define SMALL 1.0e-6
#define BIG 1.0e20
#define CUT2BIN_RATIO 100
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
enum{NSQ,BIN,MULTI}; // also in neigh_list.cpp
//#define NEIGH_LIST_DEBUG 1
/* ---------------------------------------------------------------------- */
Neighbor::Neighbor(LAMMPS *lmp) : Pointers(lmp)
{
MPI_Comm_rank(world,&me);
MPI_Comm_size(world,&nprocs);
style = BIN;
every = 1;
delay = 10;
dist_check = 1;
pgsize = 100000;
oneatom = 2000;
binsizeflag = 0;
build_once = 0;
cutneighsq = NULL;
cuttype = NULL;
cuttypesq = NULL;
fixchecklist = NULL;
// coords at last neighboring
maxhold = 0;
xhold = NULL;
// binning
maxhead = 0;
binhead = NULL;
maxbin = 0;
bins = NULL;
// pair exclusion list info
includegroup = 0;
nex_type = maxex_type = 0;
ex1_type = ex2_type = NULL;
ex_type = NULL;
nex_group = maxex_group = 0;
ex1_group = ex2_group = ex1_bit = ex2_bit = NULL;
nex_mol = maxex_mol = 0;
ex_mol_group = ex_mol_bit = NULL;
// pair lists
maxlocal = 0;
nblist = nglist = nslist = 0;
nlist = 0;
lists = NULL;
pair_build = NULL;
stencil_create = NULL;
blist = glist = slist = NULL;
nrequest = maxrequest = 0;
requests = NULL;
old_style = BIN;
old_triclinic = 0;
old_nrequest = 0;
old_requests = NULL;
// bond lists
maxbond = 0;
bondlist = NULL;
maxangle = 0;
anglelist = NULL;
maxdihedral = 0;
dihedrallist = NULL;
maximproper = 0;
improperlist = NULL;
}
/* ---------------------------------------------------------------------- */
Neighbor::~Neighbor()
{
memory->destroy_2d_double_array(cutneighsq);
delete [] cuttype;
delete [] cuttypesq;
delete [] fixchecklist;
memory->destroy_2d_double_array(xhold);
memory->sfree(binhead);
memory->sfree(bins);
memory->sfree(ex1_type);
memory->sfree(ex2_type);
memory->destroy_2d_int_array(ex_type);
memory->sfree(ex1_group);
memory->sfree(ex2_group);
delete [] ex1_bit;
delete [] ex2_bit;
memory->sfree(ex_mol_group);
delete [] ex_mol_bit;
for (int i = 0; i < nlist; i++) delete lists[i];
delete [] lists;
delete [] pair_build;
delete [] stencil_create;
delete [] blist;
delete [] glist;
delete [] slist;
for (int i = 0; i < nrequest; i++) delete requests[i];
memory->sfree(requests);
for (int i = 0; i < old_nrequest; i++) delete old_requests[i];
memory->sfree(old_requests);
memory->destroy_2d_int_array(bondlist);
memory->destroy_2d_int_array(anglelist);
memory->destroy_2d_int_array(dihedrallist);
memory->destroy_2d_int_array(improperlist);
}
/* ---------------------------------------------------------------------- */
void Neighbor::init()
{
int i,j,m,n;
ncalls = ndanger = 0;
dimension = domain->dimension;
triclinic = domain->triclinic;
newton_pair = force->newton_pair;
// error check
if (delay > 0 && (delay % every) != 0)
error->all("Neighbor delay must be 0 or multiple of every setting");
if (pgsize < 10*oneatom)
error->all("Neighbor page size must be >= 10x the one atom setting");
// ------------------------------------------------------------------
// settings
// set neighbor cutoffs (force cutoff + skin)
// trigger determines when atoms migrate and neighbor lists are rebuilt
// needs to be non-zero for migration distance check
// even if pair = NULL and no neighbor lists are used
// cutneigh = force cutoff + skin if cutforce > 0, else cutneigh = 0
triggersq = 0.25*skin*skin;
boxcheck = 0;
if (domain->box_change && (domain->xperiodic || domain->yperiodic ||
(dimension == 3 && domain->zperiodic)))
boxcheck = 1;
n = atom->ntypes;
if (cutneighsq == NULL) {
cutneighsq = memory->create_2d_double_array(n+1,n+1,"neigh:cutneighsq");
cuttype = new double[n+1];
cuttypesq = new double[n+1];
}
double cutoff,delta,cut;
cutneighmin = BIG;
cutneighmax = 0.0;
for (i = 1; i <= n; i++) {
cuttype[i] = cuttypesq[i] = 0.0;
for (j = 1; j <= n; j++) {
if (force->pair) cutoff = sqrt(force->pair->cutsq[i][j]);
else cutoff = 0.0;
if (cutoff > 0.0) delta = skin;
else delta = 0.0;
cut = cutoff + delta;
cutneighsq[i][j] = cut*cut;
cuttype[i] = MAX(cuttype[i],cut);
cuttypesq[i] = MAX(cuttypesq[i],cut*cut);
cutneighmin = MIN(cutneighmin,cut);
cutneighmax = MAX(cutneighmax,cut);
}
}
cutneighmaxsq = cutneighmax * cutneighmax;
// check other classes that can induce reneighboring in decide()
// don't check if build_once is set
restart_check = 0;
if (output->restart_every) restart_check = 1;
delete [] fixchecklist;
fixchecklist = NULL;
fixchecklist = new int[modify->nfix];
fix_check = 0;
for (i = 0; i < modify->nfix; i++)
if (modify->fix[i]->force_reneighbor)
fixchecklist[fix_check++] = i;
must_check = 0;
if (restart_check || fix_check) must_check = 1;
if (build_once) must_check = 0;
// set special_flag for 1-2, 1-3, 1-4 neighbors
// flag[0] is not used, flag[1] = 1-2, flag[2] = 1-3, flag[3] = 1-4
// flag = 0 if both LJ/Coulomb special values are 0.0
// flag = 1 if both LJ/Coulomb special values are 1.0
// flag = 2 otherwise or if KSpace solver is enabled
// pairwise portion of KSpace solver uses all 1-2,1-3,1-4 neighbors
if (force->special_lj[1] == 0.0 && force->special_coul[1] == 0.0)
special_flag[1] = 0;
else if (force->special_lj[1] == 1.0 && force->special_coul[1] == 1.0)
special_flag[1] = 1;
else special_flag[1] = 2;
if (force->special_lj[2] == 0.0 && force->special_coul[2] == 0.0)
special_flag[2] = 0;
else if (force->special_lj[2] == 1.0 && force->special_coul[2] == 1.0)
special_flag[2] = 1;
else special_flag[2] = 2;
if (force->special_lj[3] == 0.0 && force->special_coul[3] == 0.0)
special_flag[3] = 0;
else if (force->special_lj[3] == 1.0 && force->special_coul[3] == 1.0)
special_flag[3] = 1;
else special_flag[3] = 2;
if (force->kspace) special_flag[1] = special_flag[2] = special_flag[3] = 2;
// maxwt = max multiplicative factor on atom indices stored in neigh list
maxwt = 0;
if (special_flag[1] == 2) maxwt = 2;
if (special_flag[2] == 2) maxwt = 3;
if (special_flag[3] == 2) maxwt = 4;
// rRESPA cutoffs
int respa = 0;
if (update->whichflag == 1 && strcmp(update->integrate_style,"respa") == 0) {
if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;
}
if (respa) {
double *cut_respa = ((Respa *) update->integrate)->cutoff;
cut_inner_sq = (cut_respa[1] + skin) * (cut_respa[1] + skin);
cut_middle_sq = (cut_respa[3] + skin) * (cut_respa[3] + skin);
cut_middle_inside_sq = (cut_respa[0] - skin) * (cut_respa[0] - skin);
}
// ------------------------------------------------------------------
// xhold, bins, exclusion lists
// free xhold and bins if not needed for this run
if (dist_check == 0) {
memory->destroy_2d_double_array(xhold);
maxhold = 0;
xhold = NULL;
}
if (style == NSQ) {
memory->sfree(bins);
memory->sfree(binhead);
maxbin = maxhead = 0;
binhead = NULL;
bins = NULL;
}
// 1st time allocation of xhold and bins
if (dist_check) {
if (maxhold == 0) {
maxhold = atom->nmax;
xhold = memory->create_2d_double_array(maxhold,3,"neigh:xhold");
}
}
if (style != NSQ) {
if (maxbin == 0) {
maxbin = atom->nmax;
bins = (int *) memory->smalloc(maxbin*sizeof(int),"bins");
}
}
// exclusion lists for type, group, molecule settings from neigh_modify
n = atom->ntypes;
if (nex_type == 0 && nex_group == 0 && nex_mol == 0) exclude = 0;
else exclude = 1;
if (nex_type) {
memory->destroy_2d_int_array(ex_type);
ex_type = (int **) memory->create_2d_int_array(n+1,n+1,"neigh:ex_type");
for (i = 1; i <= n; i++)
for (j = 1; j <= n; j++)
ex_type[i][j] = 0;
for (i = 0; i < nex_type; i++) {
if (ex1_type[i] <= 0 || ex1_type[i] > n ||
ex2_type[i] <= 0 || ex2_type[i] > n)
error->all("Invalid atom type in neighbor exclusion list");
ex_type[ex1_type[i]][ex2_type[i]] = 1;
ex_type[ex2_type[i]][ex1_type[i]] = 1;
}
}
if (nex_group) {
delete [] ex1_bit;
delete [] ex2_bit;
ex1_bit = new int[nex_group];
ex2_bit = new int[nex_group];
for (i = 0; i < nex_group; i++) {
ex1_bit[i] = group->bitmask[ex1_group[i]];
ex2_bit[i] = group->bitmask[ex2_group[i]];
}
}
if (nex_mol) {
delete [] ex_mol_bit;
ex_mol_bit = new int[nex_mol];
for (i = 0; i < nex_mol; i++)
ex_mol_bit[i] = group->bitmask[ex_mol_group[i]];
}
// ------------------------------------------------------------------
// pairwise lists
// test if pairwise lists need to be re-created
// no need to re-create if:
// neigh style and triclinic has not changed and
// current requests = old requests
int same = 1;
if (style != old_style) same = 0;
if (triclinic != old_triclinic) same = 0;
if (nrequest != old_nrequest) same = 0;
else
for (i = 0; i < nrequest; i++)
if (requests[i]->identical(old_requests[i]) == 0) same = 0;
#ifdef NEIGH_LIST_DEBUG
if (comm->me == 0) printf("SAME flag %d\n",same);
#endif
// if old and new are not the same, create new pairwise lists
if (!same) {
// delete old lists and create new ones
for (i = 0; i < nlist; i++) delete lists[i];
delete [] lists;
delete [] pair_build;
delete [] stencil_create;
nlist = nrequest;
lists = new NeighList*[nlist];
pair_build = new PairPtr[nlist];
stencil_create = new StencilPtr[nlist];
// create individual lists, one per request
// copy dnum setting from request to list
// pass list ptr back to requestor (except for Command class)
for (i = 0; i < nlist; i++) {
lists[i] = new NeighList(lmp,pgsize);
lists[i]->index = i;
lists[i]->dnum = requests[i]->dnum;
if (requests[i]->pair) {
Pair *pair = (Pair *) requests[i]->requestor;
pair->init_list(requests[i]->id,lists[i]);
} else if (requests[i]->fix) {
Fix *fix = (Fix *) requests[i]->requestor;
fix->init_list(requests[i]->id,lists[i]);
} else if (requests[i]->compute) {
Compute *compute = (Compute *) requests[i]->requestor;
compute->init_list(requests[i]->id,lists[i]);
}
}
// detect lists that are connected to other lists
// if-then-else sequence is important
// since don't want to re-process skip or copy lists further down
// copy: point this list at request->otherlist, could be a skip list
// skip: point this list at request->otherlist, copy skip info from request
// half_from_full: point this list at preceeding full list
// granhistory: set preceeding list's listgranhistory to this list
// also set precedding list's ptr to FixShearHistory
// respaouter: point this list at preceeding 1/2 inner/middle lists
// pair and half: if there is a full non-occasional non-skip list
// change this list to half_from_full and point at the full list
// parent could be copy list or pair or fix
// fix/compute requests:
// kind of request = half or full, occasional or not doesn't matter
// if request = half and non-skip pair half/respaouter exists,
// become copy of that list
// if request = full and non-skip pair full exists,
// become copy of that list
// if request = half and non-skip pair full exists,
// become half_from_full of that list
// if no matches, do nothing, fix/compute list will be built directly
// ok if parent is copy list
for (i = 0; i < nlist; i++) {
if (requests[i]->copy)
lists[i]->listcopy = lists[requests[i]->otherlist];
else if (requests[i]->skip) {
lists[i]->listskip = lists[requests[i]->otherlist];
lists[i]->copy_skip_info(requests[i]->iskip,requests[i]->ijskip);
} else if (requests[i]->half_from_full)
lists[i]->listfull = lists[i-1];
else if (requests[i]->granhistory) {
lists[i-1]->listgranhistory = lists[i];
for (int ifix = 0; ifix < modify->nfix; ifix++)
if (strcmp(modify->fix[ifix]->style,"SHEAR_HISTORY") == 0)
lists[i-1]->fix_history = (FixShearHistory *) modify->fix[ifix];
} else if (requests[i]->respaouter) {
if (requests[i-1]->respainner) {
lists[i]->respamiddle = 0;
lists[i]->listinner = lists[i-1];
} else {
lists[i]->respamiddle = 1;
lists[i]->listmiddle = lists[i-1];
lists[i]->listinner = lists[i-2];
}
} else if (requests[i]->pair && requests[i]->half) {
for (j = 0; j < nlist; j++)
if (requests[j]->full && requests[j]->occasional == 0 &&
requests[j]->skip == 0) break;
if (j < nlist) {
requests[i]->half = 0;
requests[i]->half_from_full = 1;
lists[i]->listfull = lists[j];
}
} else if (requests[i]->fix || requests[i]->compute) {
for (j = 0; j < nlist; j++) {
if (requests[i]->half && requests[j]->pair &&
requests[j]->skip == 0 && requests[j]->half) break;
if (requests[i]->full && requests[j]->pair &&
requests[j]->skip == 0 && requests[j]->full) break;
if (requests[i]->half && requests[j]->pair &&
requests[j]->skip == 0 && requests[j]->respaouter) break;
}
if (j < nlist) {
requests[i]->copy = 1;
lists[i]->listcopy = lists[j];
} else {
for (j = 0; j < nlist; j++) {
if (requests[i]->half && requests[j]->pair &&
requests[j]->skip == 0 && requests[j]->full) break;
}
if (j < nlist) {
requests[i]->half = 0;
requests[i]->half_from_full = 1;
lists[i]->listfull = lists[j];
}
}
}
}
// set ptrs to pair_build and stencil_create functions for each list
// ptrs set to NULL if not set explicitly
for (i = 0; i < nlist; i++) {
choose_build(i,requests[i]);
if (style != NSQ) choose_stencil(i,requests[i]);
else stencil_create[i] = NULL;
}
// set each list's build/grow/stencil flags based on neigh request
// buildflag = 1 if its pair_build() invoked every reneighbor
// growflag = 1 if it stores atom-based arrays and pages
// stencilflag = 1 if it stores stencil arrays
for (i = 0; i < nlist; i++) {
lists[i]->buildflag = 1;
if (pair_build[i] == NULL) lists[i]->buildflag = 0;
if (requests[i]->occasional) lists[i]->buildflag = 0;
lists[i]->growflag = 1;
if (requests[i]->copy) lists[i]->growflag = 0;
lists[i]->stencilflag = 1;
if (style == NSQ) lists[i]->stencilflag = 0;
if (stencil_create[i] == NULL) lists[i]->stencilflag = 0;
}
#ifdef NEIGH_LIST_DEBUG
for (i = 0; i < nlist; i++) lists[i]->print_attributes();
#endif
// allocate atom arrays and 1st pages of lists that store them
maxlocal = atom->nmax;
for (i = 0; i < nlist; i++)
if (lists[i]->growflag) {
lists[i]->grow(maxlocal);
lists[i]->add_pages();
}
// setup 3 vectors of pairwise neighbor lists
// blist = lists whose pair_build() is invoked every reneighbor
// glist = lists who store atom arrays which are used every reneighbor
// slist = lists who store stencil arrays which are used every reneighbor
// blist and glist vectors are used by neighbor::build()
// slist vector is used by neighbor::setup_bins()
nblist = nglist = nslist = 0;
delete [] blist;
delete [] glist;
delete [] slist;
blist = new int[nlist];
glist = new int[nlist];
slist = new int[nlist];
for (i = 0; i < nlist; i++) {
if (lists[i]->buildflag) blist[nblist++] = i;
if (lists[i]->growflag && requests[i]->occasional == 0)
glist[nglist++] = i;
if (lists[i]->stencilflag && requests[i]->occasional == 0)
slist[nslist++] = i;
}
#ifdef NEIGH_LIST_DEBUG
print_lists_of_lists();
#endif
// reorder build vector if necessary
// relevant for lists that copy/skip/half-full from parent
// the derived list must appear in blist after the parent list
// no occasional lists are in build vector
// swap two lists within blist when dependency is mis-ordered
// done when entire pass thru blist results in no swaps
int done = 0;
while (!done) {
done = 1;
for (i = 0; i < nblist; i++) {
NeighList *ptr = NULL;
if (lists[blist[i]]->listfull) ptr = lists[blist[i]]->listfull;
if (lists[blist[i]]->listcopy) ptr = lists[blist[i]]->listcopy;
if (lists[blist[i]]->listskip) ptr = lists[blist[i]]->listskip;
if (ptr == NULL) continue;
for (m = 0; m < nlist; m++)
if (ptr == lists[m]) break;
for (j = 0; j < nblist; j++)
if (m == blist[j]) break;
if (j < i) continue;
int tmp = blist[i];
blist[i] = blist[j];
blist[j] = tmp;
done = 0;
break;
}
}
#ifdef NEIGH_LIST_DEBUG
print_lists_of_lists();
#endif
}
// delete old requests
// copy current requests and style to old for next run
for (i = 0; i < old_nrequest; i++) delete old_requests[i];
memory->sfree(old_requests);
old_nrequest = nrequest;
old_requests = requests;
nrequest = maxrequest = 0;
requests = NULL;
old_style = style;
old_triclinic = triclinic;
// ------------------------------------------------------------------
// topology lists
// 1st time allocation of topology lists
if (atom->molecular && atom->nbonds && maxbond == 0) {
if (nprocs == 1) maxbond = atom->nbonds;
else maxbond = static_cast<int> (LB_FACTOR * atom->nbonds / nprocs);
bondlist = memory->create_2d_int_array(maxbond,3,"neigh:bondlist");
}
if (atom->molecular && atom->nangles && maxangle == 0) {
if (nprocs == 1) maxangle = atom->nangles;
else maxangle = static_cast<int> (LB_FACTOR * atom->nangles / nprocs);
anglelist = memory->create_2d_int_array(maxangle,4,"neigh:anglelist");
}
if (atom->molecular && atom->ndihedrals && maxdihedral == 0) {
if (nprocs == 1) maxdihedral = atom->ndihedrals;
else maxdihedral = static_cast<int>
(LB_FACTOR * atom->ndihedrals / nprocs);
dihedrallist =
memory->create_2d_int_array(maxdihedral,5,"neigh:dihedrallist");
}
if (atom->molecular && atom->nimpropers && maximproper == 0) {
if (nprocs == 1) maximproper = atom->nimpropers;
else maximproper = static_cast<int>
(LB_FACTOR * atom->nimpropers / nprocs);
improperlist =
memory->create_2d_int_array(maximproper,5,"neigh:improperlist");
}
// set flags that determine which topology neighboring routines to use
// SHAKE sets bonds and angles negative
// bond_quartic sets bonds to 0
// delete_bonds sets all interactions negative
int bond_off = 0;
int angle_off = 0;
for (i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"shake") == 0)
bond_off = angle_off = 1;
if (force->bond && force->bond_match("quartic")) bond_off = 1;
if (atom->avec->bonds_allow) {
for (i = 0; i < atom->nlocal; i++) {
if (bond_off) break;
for (m = 0; m < atom->num_bond[i]; m++)
if (atom->bond_type[i][m] <= 0) bond_off = 1;
}
}
if (atom->avec->angles_allow) {
for (i = 0; i < atom->nlocal; i++) {
if (angle_off) break;
for (m = 0; m < atom->num_angle[i]; m++)
if (atom->angle_type[i][m] <= 0) angle_off = 1;
}
}
int dihedral_off = 0;
if (atom->avec->dihedrals_allow) {
for (i = 0; i < atom->nlocal; i++) {
if (dihedral_off) break;
for (m = 0; m < atom->num_dihedral[i]; m++)
if (atom->dihedral_type[i][m] <= 0) dihedral_off = 1;
}
}
int improper_off = 0;
if (atom->avec->impropers_allow) {
for (i = 0; i < atom->nlocal; i++) {
if (improper_off) break;
for (m = 0; m < atom->num_improper[i]; m++)
if (atom->improper_type[i][m] <= 0) improper_off = 1;
}
}
// set ptrs to topology build functions
if (bond_off) bond_build = &Neighbor::bond_partial;
else bond_build = &Neighbor::bond_all;
if (angle_off) angle_build = &Neighbor::angle_partial;
else angle_build = &Neighbor::angle_all;
if (dihedral_off) dihedral_build = &Neighbor::dihedral_partial;
else dihedral_build = &Neighbor::dihedral_all;
if (improper_off) improper_build = &Neighbor::improper_partial;
else improper_build = &Neighbor::improper_all;
// set topology neighbor list counts to 0
// in case all are turned off but potential is still defined
nbondlist = nanglelist = ndihedrallist = nimproperlist = 0;
}
/* ---------------------------------------------------------------------- */
int Neighbor::request(void *requestor)
{
if (nrequest == maxrequest) {
maxrequest += RQDELTA;
requests = (NeighRequest **)
memory->srealloc(requests,maxrequest*sizeof(NeighRequest *),
"neighbor:requests");
}
requests[nrequest] = new NeighRequest(lmp);
requests[nrequest]->requestor = requestor;
nrequest++;
return nrequest-1;
}
/* ----------------------------------------------------------------------
determine which pair_build function each neigh list needs
based on settings of neigh request
copy -> copy_from function
skip -> granular function if gran with granhistory
respa function if respaouter
skip_from function for everything else
half_from_full, half, full, gran, respaouter ->
choose by newton and rq->newton and tri settings
style NSQ options = newton off, newton on
style BIN options = newton off, newton on and not tri, newton on and tri
stlye MULTI options = same options as BIN
if none of these, ptr = NULL since pair_build is not invoked for this list
use "else if" b/c skip,copy can be set in addition to half,full,etc
------------------------------------------------------------------------- */
void Neighbor::choose_build(int index, NeighRequest *rq)
{
PairPtr pb = NULL;
if (rq->copy) pb = &Neighbor::copy_from;
else if (rq->skip) {
if (rq->gran && lists[index]->listgranhistory)
pb = &Neighbor::skip_from_granular;
else if (rq->respaouter) pb = &Neighbor::skip_from_respa;
else pb = &Neighbor::skip_from;
} else if (rq->half_from_full) {
if (newton_pair == 0) pb = &Neighbor::half_from_full_no_newton;
else if (newton_pair == 1) pb = &Neighbor::half_from_full_newton;
} else if (rq->half) {
if (style == NSQ) {
if (rq->newton == 0) {
if (newton_pair == 0)
pb = &Neighbor::half_nsq_no_newton;
else if (newton_pair == 1)
pb = &Neighbor::half_nsq_newton;
} else if (rq->newton == 1) {
pb = &Neighbor::half_nsq_newton;
} else if (rq->newton == 2) {
pb = &Neighbor::half_nsq_no_newton;
}
} else if (style == BIN) {
if (rq->newton == 0) {
if (newton_pair == 0) pb = &Neighbor::half_bin_no_newton;
else if (triclinic == 0) pb = &Neighbor::half_bin_newton;
else if (triclinic == 1) pb = &Neighbor::half_bin_newton_tri;
} else if (rq->newton == 1) {
if (triclinic == 0) pb = &Neighbor::half_bin_newton;
else if (triclinic == 1) pb = &Neighbor::half_bin_newton_tri;
} else if (rq->newton == 2) {
pb = &Neighbor::half_bin_no_newton;
}
} else if (style == MULTI) {
if (rq->newton == 0) {
if (newton_pair == 0) pb = &Neighbor::half_multi_no_newton;
else if (triclinic == 0) pb = &Neighbor::half_multi_newton;
else if (triclinic == 1) pb = &Neighbor::half_multi_newton_tri;
} else if (rq->newton == 1) {
if (triclinic == 0) pb = &Neighbor::half_multi_newton;
else if (triclinic == 1) pb = &Neighbor::half_multi_newton_tri;
} else if (rq->newton == 2) {
pb = &Neighbor::half_multi_no_newton;
}
}
} else if (rq->full) {
if (style == NSQ) pb = &Neighbor::full_nsq;
else if (style == BIN) pb = &Neighbor::full_bin;
else if (style == MULTI) pb = &Neighbor::full_multi;
} else if (rq->gran) {
if (style == NSQ) {
if (newton_pair == 0) pb = &Neighbor::granular_nsq_no_newton;
else if (newton_pair == 1) pb = &Neighbor::granular_nsq_newton;
} else if (style == BIN) {
if (newton_pair == 0) pb = &Neighbor::granular_bin_no_newton;
else if (triclinic == 0) pb = &Neighbor::granular_bin_newton;
else if (triclinic == 1) pb = &Neighbor::granular_bin_newton_tri;
} else if (style == MULTI)
error->all("Neighbor multi not yet enabled for granular");
} else if (rq->respaouter) {
if (style == NSQ) {
if (newton_pair == 0) pb = &Neighbor::respa_nsq_no_newton;
else if (newton_pair == 1) pb = &Neighbor::respa_nsq_newton;
} else if (style == BIN) {
if (newton_pair == 0) pb = &Neighbor::respa_bin_no_newton;
else if (triclinic == 0) pb = &Neighbor::respa_bin_newton;
else if (triclinic == 1) pb = &Neighbor::respa_bin_newton_tri;
} else if (style == MULTI)
error->all("Neighbor multi not yet enabled for rRESPA");
}
pair_build[index] = pb;
}
/* ----------------------------------------------------------------------
determine which stencil_create function each neigh list needs
based on settings of neigh request, only called if style != NSQ
skip or copy or half_from_full -> no stencil
half, gran, respaouter, full -> choose by newton and tri and dimension
if none of these, ptr = NULL since this list needs no stencils
use "else if" b/c skip,copy can be set in addition to half,full,etc
------------------------------------------------------------------------- */
void Neighbor::choose_stencil(int index, NeighRequest *rq)
{
StencilPtr sc = NULL;
if (rq->skip || rq->copy || rq->half_from_full) sc = NULL;
else if (rq->half || rq->gran || rq->respaouter) {
if (style == BIN) {
if (rq->newton == 0) {
if (newton_pair == 0) {
if (dimension == 2)
sc = &Neighbor::stencil_half_bin_2d_no_newton;
else if (dimension == 3)
sc = &Neighbor::stencil_half_bin_3d_no_newton;
} else if (triclinic == 0) {
if (dimension == 2)
sc = &Neighbor::stencil_half_bin_2d_newton;
else if (dimension == 3)
sc = &Neighbor::stencil_half_bin_3d_newton;
} else if (triclinic == 1) {
if (dimension == 2)
sc = &Neighbor::stencil_half_bin_2d_newton_tri;
else if (dimension == 3)
sc = &Neighbor::stencil_half_bin_3d_newton_tri;
}
} else if (rq->newton == 1) {
if (triclinic == 0) {
if (dimension == 2)
sc = &Neighbor::stencil_half_bin_2d_newton;
else if (dimension == 3)
sc = &Neighbor::stencil_half_bin_3d_newton;
} else if (triclinic == 1) {
if (dimension == 2)
sc = &Neighbor::stencil_half_bin_2d_newton_tri;
else if (dimension == 3)
sc = &Neighbor::stencil_half_bin_3d_newton_tri;
}
} else if (rq->newton == 2) {
if (dimension == 2)
sc = &Neighbor::stencil_half_bin_2d_no_newton;
else if (dimension == 3)
sc = &Neighbor::stencil_half_bin_3d_no_newton;
}
} else if (style == MULTI) {
if (rq->newton == 0) {
if (newton_pair == 0) {
if (dimension == 2)
sc = &Neighbor::stencil_half_multi_2d_no_newton;
else if (dimension == 3)
sc = &Neighbor::stencil_half_multi_3d_no_newton;
} else if (triclinic == 0) {
if (dimension == 2)
sc = &Neighbor::stencil_half_multi_2d_newton;
else if (dimension == 3)
sc = &Neighbor::stencil_half_multi_3d_newton;
} else if (triclinic == 1) {
if (dimension == 2)
sc = &Neighbor::stencil_half_multi_2d_newton_tri;
else if (dimension == 3)
sc = &Neighbor::stencil_half_multi_3d_newton_tri;
}
} else if (rq->newton == 1) {
if (triclinic == 0) {
if (dimension == 2)
sc = &Neighbor::stencil_half_multi_2d_newton;
else if (dimension == 3)
sc = &Neighbor::stencil_half_multi_3d_newton;
} else if (triclinic == 1) {
if (dimension == 2)
sc = &Neighbor::stencil_half_multi_2d_newton_tri;
else if (dimension == 3)
sc = &Neighbor::stencil_half_multi_3d_newton_tri;
}
} else if (rq->newton == 2) {
if (dimension == 2)
sc = &Neighbor::stencil_half_multi_2d_no_newton;
else if (dimension == 3)
sc = &Neighbor::stencil_half_multi_3d_no_newton;
}
}
} else if (rq->full) {
if (style == BIN) {
if (dimension == 2) sc = &Neighbor::stencil_full_bin_2d;
else if (dimension == 3) sc = &Neighbor::stencil_full_bin_3d;
} else if (style == MULTI) {
if (dimension == 2) sc = &Neighbor::stencil_full_multi_2d;
else if (dimension == 3) sc = &Neighbor::stencil_full_multi_3d;
}
}
stencil_create[index] = sc;
}
/* ---------------------------------------------------------------------- */
void Neighbor::print_lists_of_lists()
{
if (comm->me == 0) {
printf("Build lists = %d: ",nblist);
for (int i = 0; i < nblist; i++) printf("%d ",blist[i]);
printf("\n");
printf("Grow lists = %d: ",nglist);
for (int i = 0; i < nglist; i++) printf("%d ",glist[i]);
printf("\n");
printf("Stencil lists = %d: ",nslist);
for (int i = 0; i < nslist; i++) printf("%d ",slist[i]);
printf("\n");
}
}
/* ---------------------------------------------------------------------- */
int Neighbor::decide()
{
if (must_check) {
int n = update->ntimestep;
if (restart_check && n == output->next_restart) return 1;
for (int i = 0; i < fix_check; i++)
if (n == modify->fix[fixchecklist[i]]->next_reneighbor) return 1;
}
ago++;
if (ago >= delay && ago % every == 0) {
if (build_once) return 0;
if (dist_check == 0) return 1;
return check_distance();
} else return 0;
}
/* ----------------------------------------------------------------------
if any atom moved trigger distance (half of neighbor skin) return 1
shrink trigger distance if box size has changed
conservative shrink procedure:
compute distance each of 8 corners of box has moved since last reneighbor
reduce skin distance by sum of 2 largest of the 8 values
new trigger = 1/2 of reduced skin distance
for orthogonal box, only need 2 lo/hi corners
for triclinic, need all 8 corners since deformations can displace all 8
------------------------------------------------------------------------- */
int Neighbor::check_distance()
{
double delx,dely,delz,rsq;
double delta,deltasq,delta1,delta2;
if (boxcheck) {
if (triclinic == 0) {
delx = bboxlo[0] - boxlo_hold[0];
dely = bboxlo[1] - boxlo_hold[1];
delz = bboxlo[2] - boxlo_hold[2];
delta1 = sqrt(delx*delx + dely*dely + delz*delz);
delx = bboxhi[0] - boxhi_hold[0];
dely = bboxhi[1] - boxhi_hold[1];
delz = bboxhi[2] - boxhi_hold[2];
delta2 = sqrt(delx*delx + dely*dely + delz*delz);
delta = 0.5 * (skin - (delta1+delta2));
deltasq = delta*delta;
} else {
domain->box_corners();
delta1 = delta2 = 0.0;
for (int i = 0; i < 8; i++) {
delx = corners[i][0] - corners_hold[i][0];
dely = corners[i][1] - corners_hold[i][1];
delz = corners[i][2] - corners_hold[i][2];
delta = sqrt(delx*delx + dely*dely + delz*delz);
if (delta > delta1) delta1 = delta;
else if (delta > delta2) delta2 = delta;
}
delta = 0.5 * (skin - (delta1+delta2));
deltasq = delta*delta;
}
} else deltasq = triggersq;
double **x = atom->x;
int nlocal = atom->nlocal;
if (includegroup) nlocal = atom->nfirst;
int flag = 0;
for (int i = 0; i < nlocal; i++) {
delx = x[i][0] - xhold[i][0];
dely = x[i][1] - xhold[i][1];
delz = x[i][2] - xhold[i][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq > deltasq) flag = 1;
}
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_MAX,world);
if (flagall && ago == MAX(every,delay)) ndanger++;
return flagall;
}
/* ----------------------------------------------------------------------
build all perpetual neighbor lists every few timesteps
pairwise & topology lists are created as needed
------------------------------------------------------------------------- */
void Neighbor::build()
{
int i;
ago = 0;
ncalls++;
// store current atom positions and box size if needed
if (dist_check) {
double **x = atom->x;
int nlocal = atom->nlocal;
if (includegroup) nlocal = atom->nfirst;
if (nlocal > maxhold) {
maxhold = atom->nmax;
memory->destroy_2d_double_array(xhold);
xhold = memory->create_2d_double_array(maxhold,3,"neigh:xhold");
}
for (i = 0; i < nlocal; i++) {
xhold[i][0] = x[i][0];
xhold[i][1] = x[i][1];
xhold[i][2] = x[i][2];
}
if (boxcheck) {
if (triclinic == 0) {
boxlo_hold[0] = bboxlo[0];
boxlo_hold[1] = bboxlo[1];
boxlo_hold[2] = bboxlo[2];
boxhi_hold[0] = bboxhi[0];
boxhi_hold[1] = bboxhi[1];
boxhi_hold[2] = bboxhi[2];
} else {
domain->box_corners();
corners = domain->corners;
for (i = 0; i < 8; i++) {
corners_hold[i][0] = corners[i][0];
corners_hold[i][1] = corners[i][1];
corners_hold[i][2] = corners[i][2];
}
}
}
}
// if necessary, extend atom arrays in pairwise lists
// only for lists with growflag set and which are used every reneighbor
if (atom->nlocal > maxlocal) {
maxlocal = atom->nmax;
for (i = 0; i < nglist; i++) lists[glist[i]]->grow(maxlocal);
}
// extend atom bin list if necessary
if (style != NSQ && atom->nmax > maxbin) {
maxbin = atom->nmax;
memory->sfree(bins);
bins = (int *) memory->smalloc(maxbin*sizeof(int),"bins");
}
// check that pairwise lists with special bond weighting will not overflow
if (atom->molecular && maxwt && nblist) {
bigint max = maxwt * static_cast<bigint> (atom->nlocal + atom->nghost);
if (max > MAXSMALLINT)
error->one("Weighted neighbor list values are too big");
}
// invoke building of pair and molecular neighbor lists
// only for pairwise lists with buildflag set
for (i = 0; i < nblist; i++)
(this->*pair_build[blist[i]])(lists[blist[i]]);
if (atom->molecular) {
if (force->bond) (this->*bond_build)();
if (force->angle) (this->*angle_build)();
if (force->dihedral) (this->*dihedral_build)();
if (force->improper) (this->*improper_build)();
}
}
/* ----------------------------------------------------------------------
build a single occasional pairwise neighbor list indexed by I
called by other classes
------------------------------------------------------------------------- */
void Neighbor::build_one(int i)
{
// update stencils and grow atom arrays and bins as needed
// only for relevant settings of stencilflag and growflag
// do not reset maxlocal to atom->nmax, since not all lists are being grown
if (lists[i]->stencilflag) {
lists[i]->stencil_allocate(smax,style);
(this->*stencil_create[i])(lists[i],sx,sy,sz);
}
if (lists[i]->growflag) lists[i]->grow(maxlocal);
if (style != NSQ && atom->nmax > maxbin) {
maxbin = atom->nmax;
memory->sfree(bins);
bins = (int *) memory->smalloc(maxbin*sizeof(int),"bins");
}
// this condition can cause LAMMPS to crash
// no easy workaround b/c all neighbor lists really need to be rebuilt
// solution is for input script to check more often for rebuild, so warn
int flag = 0;
if (dist_check) flag = check_distance();
if (flag && me == 0)
error->warning("Building an occasional neighobr list when "
"atoms may have moved too far");
(this->*pair_build[i])(lists[i]);
}
/* ----------------------------------------------------------------------
setup neighbor binning parameters
bin numbering in each dimension is global:
0 = 0.0 to binsize, 1 = binsize to 2*binsize, etc
nbin-1,nbin,etc = bbox-binsize to bbox, bbox to bbox+binsize, etc
-1,-2,etc = -binsize to 0.0, -2*binsize to -binsize, etc
code will work for any binsize
since next(xyz) and stencil extend as far as necessary
binsize = 1/2 of cutoff is roughly optimal
for orthogonal boxes:
a dim must be filled exactly by integer # of bins
in periodic, procs on both sides of PBC must see same bin boundary
in non-periodic, coord2bin() still assumes this by use of nbin xyz
for triclinic boxes:
tilted simulation box cannot contain integer # of bins
stencil & neigh list built differently to account for this
mbinlo = lowest global bin any of my ghost atoms could fall into
mbinhi = highest global bin any of my ghost atoms could fall into
mbin = number of bins I need in a dimension
------------------------------------------------------------------------- */
void Neighbor::setup_bins()
{
// bbox lo/hi = bounding box of entire domain
// bbox = size of bbox of entire domain
// bsubbox lo/hi = bounding box of my subdomain extended by comm->cutghost
// for triclinic:
// bbox bounds all 8 corners of tilted box
// subdomain is in lamda coords
// include dimension-dependent extension via comm->cutghost
// domain->bbox() converts lamda extent to box coords and computes bbox
double bbox[3],bsubboxlo[3],bsubboxhi[3];
double *cutghost = comm->cutghost;
if (triclinic == 0) {
bboxlo = domain->boxlo;
bboxhi = domain->boxhi;
bsubboxlo[0] = domain->sublo[0] - cutghost[0];
bsubboxlo[1] = domain->sublo[1] - cutghost[1];
bsubboxlo[2] = domain->sublo[2] - cutghost[2];
bsubboxhi[0] = domain->subhi[0] + cutghost[0];
bsubboxhi[1] = domain->subhi[1] + cutghost[1];
bsubboxhi[2] = domain->subhi[2] + cutghost[2];
} else {
bboxlo = domain->boxlo_bound;
bboxhi = domain->boxhi_bound;
double lo[3],hi[3];
lo[0] = domain->sublo_lamda[0] - cutghost[0];
lo[1] = domain->sublo_lamda[1] - cutghost[1];
lo[2] = domain->sublo_lamda[2] - cutghost[2];
hi[0] = domain->subhi_lamda[0] + cutghost[0];
hi[1] = domain->subhi_lamda[1] + cutghost[1];
hi[2] = domain->subhi_lamda[2] + cutghost[2];
domain->bbox(lo,hi,bsubboxlo,bsubboxhi);
}
bbox[0] = bboxhi[0] - bboxlo[0];
bbox[1] = bboxhi[1] - bboxlo[1];
bbox[2] = bboxhi[2] - bboxlo[2];
// optimal bin size is roughly 1/2 the cutoff
// for BIN style, binsize = 1/2 of max neighbor cutoff
// for MULTI style, binsize = 1/2 of min neighbor cutoff
// special case of all cutoffs = 0.0, binsize = box size
double binsize_optimal;
if (binsizeflag) binsize_optimal = binsize_user;
else if (style == BIN) binsize_optimal = 0.5*cutneighmax;
else binsize_optimal = 0.5*cutneighmin;
if (binsize_optimal == 0.0) binsize_optimal = bbox[0];
double binsizeinv = 1.0/binsize_optimal;
// test for too many global bins in any dimension due to huge global domain
if (bbox[0]*binsizeinv > MAXSMALLINT || bbox[1]*binsizeinv > MAXSMALLINT ||
bbox[2]*binsizeinv > MAXSMALLINT)
error->all("Domain too large for neighbor bins");
// create actual bins
// always have one bin even if cutoff > bbox
// for 2d, nbinz = 1
nbinx = static_cast<int> (bbox[0]*binsizeinv);
nbiny = static_cast<int> (bbox[1]*binsizeinv);
if (dimension == 3) nbinz = static_cast<int> (bbox[2]*binsizeinv);
else nbinz = 1;
if (nbinx == 0) nbinx = 1;
if (nbiny == 0) nbiny = 1;
if (nbinz == 0) nbinz = 1;
// compute actual bin size for nbins to fit into box exactly
// error if actual bin size << cutoff, since will create a zillion bins
// this happens when nbin = 1 and box size << cutoff
// typically due to non-periodic, flat system in a particular dim
// in that extreme case, should use NSQ not BIN neighbor style
binsizex = bbox[0]/nbinx;
binsizey = bbox[1]/nbiny;
binsizez = bbox[2]/nbinz;
bininvx = 1.0 / binsizex;
bininvy = 1.0 / binsizey;
bininvz = 1.0 / binsizez;
if (binsize_optimal*bininvx > CUT2BIN_RATIO ||
binsize_optimal*bininvy > CUT2BIN_RATIO ||
binsize_optimal*bininvz > CUT2BIN_RATIO)
error->all("Cannot use neighbor bins - box size << cutoff");
// mbinlo/hi = lowest and highest global bins my ghost atoms could be in
// coord = lowest and highest values of coords for my ghost atoms
// static_cast(-1.5) = -1, so subract additional -1
// add in SMALL for round-off safety
int mbinxhi,mbinyhi,mbinzhi;
double coord;
coord = bsubboxlo[0] - SMALL*bbox[0];
mbinxlo = static_cast<int> ((coord-bboxlo[0])*bininvx);
if (coord < bboxlo[0]) mbinxlo = mbinxlo - 1;
coord = bsubboxhi[0] + SMALL*bbox[0];
mbinxhi = static_cast<int> ((coord-bboxlo[0])*bininvx);
coord = bsubboxlo[1] - SMALL*bbox[1];
mbinylo = static_cast<int> ((coord-bboxlo[1])*bininvy);
if (coord < bboxlo[1]) mbinylo = mbinylo - 1;
coord = bsubboxhi[1] + SMALL*bbox[1];
mbinyhi = static_cast<int> ((coord-bboxlo[1])*bininvy);
if (dimension == 3) {
coord = bsubboxlo[2] - SMALL*bbox[2];
mbinzlo = static_cast<int> ((coord-bboxlo[2])*bininvz);
if (coord < bboxlo[2]) mbinzlo = mbinzlo - 1;
coord = bsubboxhi[2] + SMALL*bbox[2];
mbinzhi = static_cast<int> ((coord-bboxlo[2])*bininvz);
}
// extend bins by 1 to insure stencil extent is included
// if 2d, only 1 bin in z
mbinxlo = mbinxlo - 1;
mbinxhi = mbinxhi + 1;
mbinx = mbinxhi - mbinxlo + 1;
mbinylo = mbinylo - 1;
mbinyhi = mbinyhi + 1;
mbiny = mbinyhi - mbinylo + 1;
if (dimension == 3) {
mbinzlo = mbinzlo - 1;
mbinzhi = mbinzhi + 1;
} else mbinzlo = mbinzhi = 0;
mbinz = mbinzhi - mbinzlo + 1;
// memory for bin ptrs
bigint bbin = mbinx*mbiny*mbinz;
if (bbin > MAXSMALLINT) error->one("Too many neighbor bins");
mbins = bbin;
if (mbins > maxhead) {
maxhead = mbins;
memory->sfree(binhead);
binhead = (int *) memory->smalloc(maxhead*sizeof(int),"neigh:binhead");
}
// create stencil of bins to search over in neighbor list construction
// sx,sy,sz = max range of stencil in each dim
// smax = max possible size of entire 3d stencil
// stencil is empty if cutneighmax = 0.0
sx = static_cast<int> (cutneighmax*bininvx);
if (sx*binsizex < cutneighmax) sx++;
sy = static_cast<int> (cutneighmax*bininvy);
if (sy*binsizey < cutneighmax) sy++;
sz = static_cast<int> (cutneighmax*bininvz);
if (sz*binsizez < cutneighmax) sz++;
if (dimension == 2) sz = 0;
smax = (2*sx+1) * (2*sy+1) * (2*sz+1);
// create stencils for pairwise neighbor lists
// only done for lists with stencilflag and buildflag set
for (int i = 0; i < nslist; i++) {
lists[slist[i]]->stencil_allocate(smax,style);
(this->*stencil_create[slist[i]])(lists[slist[i]],sx,sy,sz);
}
}
/* ----------------------------------------------------------------------
compute closest distance between central bin (0,0,0) and bin (i,j,k)
------------------------------------------------------------------------- */
double Neighbor::bin_distance(int i, int j, int k)
{
double delx,dely,delz;
if (i > 0) delx = (i-1)*binsizex;
else if (i == 0) delx = 0.0;
else delx = (i+1)*binsizex;
if (j > 0) dely = (j-1)*binsizey;
else if (j == 0) dely = 0.0;
else dely = (j+1)*binsizey;
if (k > 0) delz = (k-1)*binsizez;
else if (k == 0) delz = 0.0;
else delz = (k+1)*binsizez;
return (delx*delx + dely*dely + delz*delz);
}
/* ----------------------------------------------------------------------
set neighbor style and skin distance
------------------------------------------------------------------------- */
void Neighbor::set(int narg, char **arg)
{
if (narg != 2) error->all("Illegal neighbor command");
skin = atof(arg[0]);
if (skin < 0.0) error->all("Illegal neighbor command");
if (strcmp(arg[1],"nsq") == 0) style = NSQ;
else if (strcmp(arg[1],"bin") == 0) style = BIN;
else if (strcmp(arg[1],"multi") == 0) style = MULTI;
else error->all("Illegal neighbor command");
}
/* ----------------------------------------------------------------------
modify parameters of the pair-wise neighbor build
------------------------------------------------------------------------- */
void Neighbor::modify_params(int narg, char **arg)
{
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"every") == 0) {
if (iarg+2 > narg) error->all("Illegal neigh_modify command");
every = atoi(arg[iarg+1]);
if (every <= 0) error->all("Illegal neigh_modify command");
iarg += 2;
} else if (strcmp(arg[iarg],"delay") == 0) {
if (iarg+2 > narg) error->all("Illegal neigh_modify command");
delay = atoi(arg[iarg+1]);
if (delay < 0) error->all("Illegal neigh_modify command");
iarg += 2;
} else if (strcmp(arg[iarg],"check") == 0) {
if (iarg+2 > narg) error->all("Illegal neigh_modify command");
if (strcmp(arg[iarg+1],"yes") == 0) dist_check = 1;
else if (strcmp(arg[iarg+1],"no") == 0) dist_check = 0;
else error->all("Illegal neigh_modify command");
iarg += 2;
} else if (strcmp(arg[iarg],"once") == 0) {
if (iarg+2 > narg) error->all("Illegal neigh_modify command");
if (strcmp(arg[iarg+1],"yes") == 0) build_once = 1;
else if (strcmp(arg[iarg+1],"no") == 0) build_once = 0;
else error->all("Illegal neigh_modify command");
iarg += 2;
} else if (strcmp(arg[iarg],"page") == 0) {
if (iarg+2 > narg) error->all("Illegal neigh_modify command");
pgsize = atoi(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"one") == 0) {
if (iarg+2 > narg) error->all("Illegal neigh_modify command");
oneatom = atoi(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"binsize") == 0) {
if (iarg+2 > narg) error->all("Illegal neigh_modify command");
binsize_user = atof(arg[iarg+1]);
if (binsize_user <= 0.0) binsizeflag = 0;
else binsizeflag = 1;
iarg += 2;
} else if (strcmp(arg[iarg],"include") == 0) {
if (iarg+2 > narg) error->all("Illegal neigh_modify command");
includegroup = group->find(arg[iarg+1]);
if (includegroup < 0)
error->all("Invalid group ID in neigh_modify command");
if (includegroup && (atom->firstgroupname == NULL ||
strcmp(arg[iarg+1],atom->firstgroupname) != 0))
error->all("Neigh_modify include group != atom_modify first group");
iarg += 2;
} else if (strcmp(arg[iarg],"exclude") == 0) {
if (iarg+2 > narg) error->all("Illegal neigh_modify command");
if (strcmp(arg[iarg+1],"type") == 0) {
if (iarg+4 > narg) error->all("Illegal neigh_modify command");
if (nex_type == maxex_type) {
maxex_type += EXDELTA;
ex1_type = (int *) memory->srealloc(ex1_type,maxex_type*sizeof(int),
"neigh:ex1_type");
ex2_type = (int *) memory->srealloc(ex2_type,maxex_type*sizeof(int),
"neigh:ex2_type");
}
ex1_type[nex_type] = atoi(arg[iarg+2]);
ex2_type[nex_type] = atoi(arg[iarg+3]);
nex_type++;
iarg += 4;
} else if (strcmp(arg[iarg+1],"group") == 0) {
if (iarg+4 > narg) error->all("Illegal neigh_modify command");
if (nex_group == maxex_group) {
maxex_group += EXDELTA;
ex1_group =
(int *) memory->srealloc(ex1_group,maxex_group*sizeof(int),
"neigh:ex1_group");
ex2_group =
(int *) memory->srealloc(ex2_group,maxex_group*sizeof(int),
"neigh:ex2_group");
}
ex1_group[nex_group] = group->find(arg[iarg+2]);
ex2_group[nex_group] = group->find(arg[iarg+3]);
if (ex1_group[nex_group] == -1 || ex2_group[nex_group] == -1)
error->all("Invalid group ID in neigh_modify command");
nex_group++;
iarg += 4;
} else if (strcmp(arg[iarg+1],"molecule") == 0) {
if (iarg+3 > narg) error->all("Illegal neigh_modify command");
if (atom->molecule_flag == 0) {
char *str = (char *)
"Neigh_modify exclude molecule requires atom attribute molecule";
error->all(str);
}
if (nex_mol == maxex_mol) {
maxex_mol += EXDELTA;
ex_mol_group =
(int *) memory->srealloc(ex_mol_group,maxex_mol*sizeof(int),
"neigh:ex_mol_group");
}
ex_mol_group[nex_mol] = group->find(arg[iarg+2]);
if (ex_mol_group[nex_mol] == -1)
error->all("Invalid group ID in neigh_modify command");
nex_mol++;
iarg += 3;
} else if (strcmp(arg[iarg+1],"none") == 0) {
nex_type = nex_group = nex_mol = 0;
iarg += 2;
} else error->all("Illegal neigh_modify command");
} else error->all("Illegal neigh_modify command");
}
}
/* ----------------------------------------------------------------------
bin owned and ghost atoms
------------------------------------------------------------------------- */
void Neighbor::bin_atoms()
{
int i,ibin;
for (i = 0; i < mbins; i++) binhead[i] = -1;
// bin in reverse order so linked list will be in forward order
// also puts ghost atoms at end of list, which is necessary
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
if (includegroup) {
int bitmask = group->bitmask[includegroup];
for (i = nall-1; i >= nlocal; i--) {
if (mask[i] & bitmask) {
ibin = coord2bin(x[i]);
bins[i] = binhead[ibin];
binhead[ibin] = i;
}
}
for (i = atom->nfirst-1; i >= 0; i--) {
ibin = coord2bin(x[i]);
bins[i] = binhead[ibin];
binhead[ibin] = i;
}
} else {
for (i = nall-1; i >= 0; i--) {
ibin = coord2bin(x[i]);
bins[i] = binhead[ibin];
binhead[ibin] = i;
}
}
}
/* ----------------------------------------------------------------------
convert atom coords into local bin #
for orthogonal, only ghost atoms will have coord >= bboxhi or coord < bboxlo
take special care to insure ghosts are in correct bins even w/ roundoff
hi ghost atoms = nbin,nbin+1,etc
owned atoms = 0 to nbin-1
lo ghost atoms = -1,-2,etc
this is necessary so that both procs on either side of PBC
treat a pair of atoms straddling the PBC in a consistent way
for triclinic, doesn't matter since stencil & neigh list built differently
------------------------------------------------------------------------- */
int Neighbor::coord2bin(double *x)
{
int ix,iy,iz;
if (x[0] >= bboxhi[0])
ix = static_cast<int> ((x[0]-bboxhi[0])*bininvx) + nbinx;
else if (x[0] >= bboxlo[0]) {
ix = static_cast<int> ((x[0]-bboxlo[0])*bininvx);
ix = MIN(ix,nbinx-1);
} else
ix = static_cast<int> ((x[0]-bboxlo[0])*bininvx) - 1;
if (x[1] >= bboxhi[1])
iy = static_cast<int> ((x[1]-bboxhi[1])*bininvy) + nbiny;
else if (x[1] >= bboxlo[1]) {
iy = static_cast<int> ((x[1]-bboxlo[1])*bininvy);
iy = MIN(iy,nbiny-1);
} else
iy = static_cast<int> ((x[1]-bboxlo[1])*bininvy) - 1;
if (x[2] >= bboxhi[2])
iz = static_cast<int> ((x[2]-bboxhi[2])*bininvz) + nbinz;
else if (x[2] >= bboxlo[2]) {
iz = static_cast<int> ((x[2]-bboxlo[2])*bininvz);
iz = MIN(iz,nbinz-1);
} else
iz = static_cast<int> ((x[2]-bboxlo[2])*bininvz) - 1;
return (iz-mbinzlo)*mbiny*mbinx + (iy-mbinylo)*mbinx + (ix-mbinxlo);
}
/* ----------------------------------------------------------------------
test if atom pair i,j is excluded from neighbor list
due to type, group, molecule settings from neigh_modify command
return 1 if should be excluded, 0 if included
------------------------------------------------------------------------- */
int Neighbor::exclusion(int i, int j, int itype, int jtype,
int *mask, int *molecule)
{
int m;
if (nex_type && ex_type[itype][jtype]) return 1;
if (nex_group) {
for (m = 0; m < nex_group; m++) {
if (mask[i] & ex1_bit[m] && mask[j] & ex2_bit[m]) return 1;
if (mask[i] & ex2_bit[m] && mask[j] & ex1_bit[m]) return 1;
}
}
if (nex_mol) {
for (m = 0; m < nex_mol; m++)
if (mask[i] & ex_mol_bit[m] && mask[j] & ex_mol_bit[m] &&
molecule[i] == molecule[j]) return 1;
}
return 0;
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
------------------------------------------------------------------------- */
double Neighbor::memory_usage()
{
double bytes = 0.0;
bytes += maxhold*3 * sizeof(double);
if (style != NSQ) {
bytes += maxbin * sizeof(int);
bytes += maxhead * sizeof(int);
}
for (int i = 0; i < nlist; i++) bytes += lists[i]->memory_usage();
bytes += maxbond*3 * sizeof(int);
bytes += maxangle*4 * sizeof(int);
bytes += maxdihedral*5 * sizeof(int);
bytes += maximproper*5 * sizeof(int);
return bytes;
}
diff --git a/src/output.h b/src/output.h
index 9e0c72acb..d8ce61e52 100644
--- a/src/output.h
+++ b/src/output.h
@@ -1,71 +1,71 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifndef LMP_OUTPUT_H
#define LMP_OUTPUT_H
-#include "pointers.h"
#include "lmptype.h"
+#include "pointers.h"
namespace LAMMPS_NS {
class Output : protected Pointers {
public:
bigint next; // next timestep for any kind of output
bigint next_thermo; // next timestep for thermo output
int thermo_every; // thermo output every this many steps
bigint last_thermo; // last timestep thermo was output
char *var_thermo; // variable name for thermo frequency
int ivar_thermo; // variable index for thermo frequency
class Thermo *thermo; // Thermodynamic computations
int ndump; // # of Dumps defined
int max_dump; // max size of Dump list
bigint next_dump_any; // next timestep for any Dump
int *every_dump; // output of each Dump every this many steps
bigint *next_dump; // next timestep to do each Dump
bigint *last_dump; // last timestep each snapshot was output
char **var_dump; // variable name for dump frequency
int *ivar_dump; // variable index for dump frequency
class Dump **dump; // list of defined Dumps
bigint next_restart; // next timestep to write a restart file
int restart_every; // write a restart file every this many steps
bigint last_restart; // last timestep a restart file was output
int restart_toggle; // 0 if use restart1 as prefix
// 1 if use restart1 as file, 2 for restart2
char *restart1,*restart2; // names for restart files
class WriteRestart *restart; // Restart output
Output(class LAMMPS *);
~Output();
void init();
void setup(int); // initial output before run/min
void write(bigint); // output for current timestep
void write_dump(bigint); // force output of dump snapshots
void write_restart(bigint); // force output of a restart file
void add_dump(int, char **); // add a Dump to Dump list
void modify_dump(int, char **); // modify a Dump
void delete_dump(char *); // delete a Dump from Dump list
void create_thermo(int, char **); // create a thermo style
void create_restart(int, char **); // create Restart and restart files
void memory_usage(); // print out memory usage
};
}
#endif
diff --git a/src/read_data.cpp b/src/read_data.cpp
index c1a3f010e..50a5f347d 100644
--- a/src/read_data.cpp
+++ b/src/read_data.cpp
@@ -1,1378 +1,1378 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "math.h"
#include "mpi.h"
#include "string.h"
#include "stdlib.h"
#include "read_data.h"
-#include "lmptype.h"
#include "atom.h"
#include "atom_vec.h"
#include "comm.h"
#include "update.h"
#include "force.h"
#include "pair.h"
#include "domain.h"
#include "bond.h"
#include "angle.h"
#include "dihedral.h"
#include "improper.h"
#include "error.h"
#include "memory.h"
#include "special.h"
using namespace LAMMPS_NS;
#define MAXLINE 256
#define LB_FACTOR 1.1
#define CHUNK 1024
#define DELTA 4 // must be 2 or larger
#define NSECTIONS 22 // change when add to header::section_keywords
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
/* ---------------------------------------------------------------------- */
ReadData::ReadData(LAMMPS *lmp) : Pointers(lmp)
{
MPI_Comm_rank(world,&me);
line = new char[MAXLINE];
keyword = new char[MAXLINE];
buffer = new char[CHUNK*MAXLINE];
narg = maxarg = 0;
arg = NULL;
}
/* ---------------------------------------------------------------------- */
ReadData::~ReadData()
{
delete [] line;
delete [] keyword;
delete [] buffer;
memory->sfree(arg);
}
/* ---------------------------------------------------------------------- */
void ReadData::command(int narg, char **arg)
{
if (narg != 1) error->all("Illegal read_data command");
if (domain->box_exist)
error->all("Cannot read_data after simulation box is defined");
if (domain->dimension == 2 && domain->zperiodic == 0)
error->all("Cannot run 2d simulation with nonperiodic Z dimension");
// scan data file to determine max topology needed per atom
// allocate initial topology arrays
if (atom->molecular) {
if (me == 0) {
if (screen) fprintf(screen,"Scanning data file ...\n");
open(arg[0]);
header(0);
scan(atom->bond_per_atom,atom->angle_per_atom,
atom->dihedral_per_atom,atom->improper_per_atom);
if (compressed) pclose(fp);
else fclose(fp);
atom->bond_per_atom += atom->extra_bond_per_atom;
}
MPI_Bcast(&atom->bond_per_atom,1,MPI_INT,0,world);
MPI_Bcast(&atom->angle_per_atom,1,MPI_INT,0,world);
MPI_Bcast(&atom->dihedral_per_atom,1,MPI_INT,0,world);
MPI_Bcast(&atom->improper_per_atom,1,MPI_INT,0,world);
} else
atom->bond_per_atom = atom->angle_per_atom =
atom->dihedral_per_atom = atom->improper_per_atom = 0;
// read header info
if (me == 0) {
if (screen) fprintf(screen,"Reading data file ...\n");
open(arg[0]);
}
header(1);
domain->box_exist = 1;
// problem setup using info from header
update->ntimestep = 0;
int n;
if (comm->nprocs == 1) n = static_cast<int> (atom->natoms);
else n = static_cast<int> (LB_FACTOR * atom->natoms / comm->nprocs);
atom->allocate_type_arrays();
atom->avec->grow(n);
n = atom->nmax;
domain->print_box(" ");
domain->set_initial_box();
domain->set_global_box();
comm->set_procs();
domain->set_local_box();
// read rest of file in free format
// if add a section keyword, add to header::section_keywords and NSECTIONS
int atomflag = 0;
while (strlen(keyword)) {
if (strcmp(keyword,"Atoms") == 0) {
atoms();
atomflag = 1;
} else if (strcmp(keyword,"Velocities") == 0) {
if (atomflag == 0) error->all("Must read Atoms before Velocities");
velocities();
} else if (strcmp(keyword,"Bonds") == 0) {
if (atom->avec->bonds_allow == 0)
error->all("Invalid data file section: Bonds");
if (atomflag == 0) error->all("Must read Atoms before Bonds");
bonds();
} else if (strcmp(keyword,"Angles") == 0) {
if (atom->avec->angles_allow == 0)
error->all("Invalid data file section: Angles");
if (atomflag == 0) error->all("Must read Atoms before Angles");
angles();
} else if (strcmp(keyword,"Dihedrals") == 0) {
if (atom->avec->dihedrals_allow == 0)
error->all("Invalid data file section: Dihedrals");
if (atomflag == 0) error->all("Must read Atoms before Dihedrals");
dihedrals();
} else if (strcmp(keyword,"Impropers") == 0) {
if (atom->avec->impropers_allow == 0)
error->all("Invalid data file section: Impropers");
if (atomflag == 0) error->all("Must read Atoms before Impropers");
impropers();
} else if (strcmp(keyword,"Masses") == 0) {
mass();
} else if (strcmp(keyword,"Shapes") == 0) {
shape();
} else if (strcmp(keyword,"Dipoles") == 0) {
dipole();
} else if (strcmp(keyword,"Pair Coeffs") == 0) {
if (force->pair == NULL)
error->all("Must define pair_style before Pair Coeffs");
paircoeffs();
} else if (strcmp(keyword,"Bond Coeffs") == 0) {
if (atom->avec->bonds_allow == 0)
error->all("Invalid data file section: Bond Coeffs");
if (force->bond == NULL)
error->all("Must define bond_style before Bond Coeffs");
bondcoeffs();
} else if (strcmp(keyword,"Angle Coeffs") == 0) {
if (atom->avec->angles_allow == 0)
error->all("Invalid data file section: Angle Coeffs");
if (force->angle == NULL)
error->all("Must define angle_style before Angle Coeffs");
anglecoeffs(0);
} else if (strcmp(keyword,"Dihedral Coeffs") == 0) {
if (atom->avec->dihedrals_allow == 0)
error->all("Invalid data file section: Dihedral Coeffs");
if (force->dihedral == NULL)
error->all("Must define dihedral_style before Dihedral Coeffs");
dihedralcoeffs(0);
} else if (strcmp(keyword,"Improper Coeffs") == 0) {
if (atom->avec->impropers_allow == 0)
error->all("Invalid data file section: Improper Coeffs");
if (force->improper == NULL)
error->all("Must define improper_style before Improper Coeffs");
impropercoeffs(0);
} else if (strcmp(keyword,"BondBond Coeffs") == 0) {
if (atom->avec->angles_allow == 0)
error->all("Invalid data file section: BondBond Coeffs");
if (force->angle == NULL)
error->all("Must define angle_style before BondBond Coeffs");
anglecoeffs(1);
} else if (strcmp(keyword,"BondAngle Coeffs") == 0) {
if (atom->avec->angles_allow == 0)
error->all("Invalid data file section: BondAngle Coeffs");
if (force->angle == NULL)
error->all("Must define angle_style before BondAngle Coeffs");
anglecoeffs(2);
} else if (strcmp(keyword,"MiddleBondTorsion Coeffs") == 0) {
if (atom->avec->dihedrals_allow == 0)
error->all("Invalid data file section: MiddleBondTorsion Coeffs");
if (force->dihedral == NULL)
error->all("Must define dihedral_style before MiddleBondTorsion Coeffs");
dihedralcoeffs(1);
} else if (strcmp(keyword,"EndBondTorsion Coeffs") == 0) {
if (atom->avec->dihedrals_allow == 0)
error->all("Invalid data file section: EndBondTorsion Coeffs");
if (force->dihedral == NULL)
error->all("Must define dihedral_style before EndBondTorsion Coeffs");
dihedralcoeffs(2);
} else if (strcmp(keyword,"AngleTorsion Coeffs") == 0) {
if (atom->avec->dihedrals_allow == 0)
error->all("Invalid data file section: AngleTorsion Coeffs");
if (force->dihedral == NULL)
error->all("Must define dihedral_style before AngleTorsion Coeffs");
dihedralcoeffs(3);
} else if (strcmp(keyword,"AngleAngleTorsion Coeffs") == 0) {
if (atom->avec->dihedrals_allow == 0)
error->all("Invalid data file section: AngleAngleTorsion Coeffs");
if (force->dihedral == NULL)
error->all("Must define dihedral_style before AngleAngleTorsion Coeffs");
dihedralcoeffs(4);
} else if (strcmp(keyword,"BondBond13 Coeffs") == 0) {
if (atom->avec->dihedrals_allow == 0)
error->all("Invalid data file section: BondBond13 Coeffs");
if (force->dihedral == NULL)
error->all("Must define dihedral_style before BondBond13 Coeffs");
dihedralcoeffs(5);
} else if (strcmp(keyword,"AngleAngle Coeffs") == 0) {
if (atom->avec->impropers_allow == 0)
error->all("Invalid data file section: AngleAngle Coeffs");
if (force->improper == NULL)
error->all("Must define improper_style before AngleAngle Coeffs");
impropercoeffs(1);
} else {
char str[128];
sprintf(str,"Unknown identifier in data file: %s",keyword);
error->all(str);
}
parse_keyword(0,1);
}
// close file
if (me == 0) {
if (compressed) pclose(fp);
else fclose(fp);
}
// error if natoms > 0 yet no atoms were read
if (atom->natoms > 0 && atomflag == 0) error->all("No atoms in data file");
// create bond topology now that system is defined
if (atom->molecular) {
Special special(lmp);
special.build();
}
}
/* ----------------------------------------------------------------------
read free-format header of data file
if flag = 0, only called by proc 0
if flag = 1, called by all procs so bcast lines as read them
1st line and blank lines are skipped
non-blank lines are checked for header keywords and leading value is read
header ends with EOF or non-blank line containing no header keyword
if EOF, line is set to blank line
else line has first keyword line for rest of file
------------------------------------------------------------------------- */
void ReadData::header(int flag)
{
int n;
char *ptr;
char *section_keywords[NSECTIONS] =
{"Atoms","Velocities","Bonds","Angles","Dihedrals","Impropers",
"Masses","Shapes","Dipoles",
"Pair Coeffs","Bond Coeffs","Angle Coeffs",
"Dihedral Coeffs","Improper Coeffs",
"BondBond Coeffs","BondAngle Coeffs","MiddleBondTorsion Coeffs",
"EndBondTorsion Coeffs","AngleTorsion Coeffs",
"AngleAngleTorsion Coeffs","BondBond13 Coeffs","AngleAngle Coeffs"};
// skip 1st line of file
if (me == 0) {
char *eof = fgets(line,MAXLINE,fp);
if (eof == NULL) error->one("Unexpected end of data file");
}
while (1) {
// read a line and bcast length if flag is set
if (me == 0) {
if (fgets(line,MAXLINE,fp) == NULL) n = 0;
else n = strlen(line) + 1;
}
if (flag) MPI_Bcast(&n,1,MPI_INT,0,world);
// if n = 0 then end-of-file so return with blank line
if (n == 0) {
line[0] = '\0';
return;
}
// bcast line if flag is set
if (flag) MPI_Bcast(line,n,MPI_CHAR,0,world);
// trim anything from '#' onward
// if line is blank, continue
if (ptr = strchr(line,'#')) *ptr = '\0';
if (strspn(line," \t\n\r") == strlen(line)) continue;
// search line for header keyword and set corresponding variable
if (strstr(line,"atoms")) sscanf(line,BIGINT_FORMAT,&atom->natoms);
else if (strstr(line,"bonds")) sscanf(line,BIGINT_FORMAT,&atom->nbonds);
else if (strstr(line,"angles")) sscanf(line,BIGINT_FORMAT,&atom->nangles);
else if (strstr(line,"dihedrals")) sscanf(line,BIGINT_FORMAT,
&atom->ndihedrals);
else if (strstr(line,"impropers")) sscanf(line,BIGINT_FORMAT,
&atom->nimpropers);
else if (strstr(line,"atom types")) sscanf(line,"%d",&atom->ntypes);
else if (strstr(line,"bond types")) sscanf(line,"%d",&atom->nbondtypes);
else if (strstr(line,"angle types")) sscanf(line,"%d",&atom->nangletypes);
else if (strstr(line,"dihedral types"))
sscanf(line,"%d",&atom->ndihedraltypes);
else if (strstr(line,"improper types"))
sscanf(line,"%d",&atom->nimpropertypes);
else if (strstr(line,"extra bond per atom"))
sscanf(line,"%d",&atom->extra_bond_per_atom);
else if (strstr(line,"xlo xhi"))
sscanf(line,"%lg %lg",&domain->boxlo[0],&domain->boxhi[0]);
else if (strstr(line,"ylo yhi"))
sscanf(line,"%lg %lg",&domain->boxlo[1],&domain->boxhi[1]);
else if (strstr(line,"zlo zhi"))
sscanf(line,"%lg %lg",&domain->boxlo[2],&domain->boxhi[2]);
else if (strstr(line,"xy xz yz")) {
domain->triclinic = 1;
sscanf(line,"%lg %lg %lg",&domain->xy,&domain->xz,&domain->yz);
} else break;
}
// error check on total system size
if (atom->natoms < 0 || atom->natoms > MAXBIGINT ||
atom->nbonds < 0 || atom->nbonds > MAXBIGINT ||
atom->nangles < 0 || atom->nangles > MAXBIGINT ||
atom->ndihedrals < 0 || atom->ndihedrals > MAXBIGINT ||
atom->nimpropers < 0 || atom->nimpropers > MAXBIGINT) {
if (flag == 0) error->one("System in data file is too big");
else error->all("System in data file is too big");
}
// check that exiting string is a valid section keyword
parse_keyword(1,flag);
for (n = 0; n < NSECTIONS; n++)
if (strcmp(keyword,section_keywords[n]) == 0) break;
if (n == NSECTIONS) {
char str[128];
sprintf(str,"Unknown identifier in data file: %s",keyword);
error->all(str);
}
// error check on consistency of header values
if ((atom->nbonds || atom->nbondtypes) &&
atom->avec->bonds_allow == 0)
error->one("No bonds allowed with this atom style");
if ((atom->nangles || atom->nangletypes) &&
atom->avec->angles_allow == 0)
error->one("No angles allowed with this atom style");
if ((atom->ndihedrals || atom->ndihedraltypes) &&
atom->avec->dihedrals_allow == 0)
error->one("No dihedrals allowed with this atom style");
if ((atom->nimpropers || atom->nimpropertypes) &&
atom->avec->impropers_allow == 0)
error->one("No impropers allowed with this atom style");
if (atom->nbonds > 0 && atom->nbondtypes <= 0)
error->one("Bonds defined but no bond types");
if (atom->nangles > 0 && atom->nangletypes <= 0)
error->one("Angles defined but no angle types");
if (atom->ndihedrals > 0 && atom->ndihedraltypes <= 0)
error->one("Dihedrals defined but no dihedral types");
if (atom->nimpropers > 0 && atom->nimpropertypes <= 0)
error->one("Impropers defined but no improper types");
}
/* ----------------------------------------------------------------------
read all atoms
------------------------------------------------------------------------- */
void ReadData::atoms()
{
int i,m,nchunk;
bigint nread = 0;
bigint natoms = atom->natoms;
while (nread < natoms) {
if (natoms-nread > CHUNK) nchunk = CHUNK;
else nchunk = natoms-nread;
if (me == 0) {
char *eof;
m = 0;
for (i = 0; i < nchunk; i++) {
eof = fgets(&buffer[m],MAXLINE,fp);
if (eof == NULL) error->one("Unexpected end of data file");
m += strlen(&buffer[m]);
}
buffer[m++] = '\n';
}
MPI_Bcast(&m,1,MPI_INT,0,world);
MPI_Bcast(buffer,m,MPI_CHAR,0,world);
atom->data_atoms(nchunk,buffer);
nread += nchunk;
}
// check that all atoms were assigned correctly
bigint tmp = atom->nlocal;
MPI_Allreduce(&tmp,&natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);
if (me == 0) {
if (screen) fprintf(screen," " BIGINT_FORMAT " atoms\n",natoms);
if (logfile) fprintf(logfile," " BIGINT_FORMAT " atoms\n",natoms);
}
if (natoms != atom->natoms) error->all("Did not assign all atoms correctly");
// if any atom ID < 0, error
// if all atom IDs = 0, tag_enable = 0
// if any atom ID > 0, error if any atom ID == 0
// not checking if atom IDs > natoms or are unique
int nlocal = atom->nlocal;
int *tag = atom->tag;
int flag = 0;
for (int i = 0; i < nlocal; i++)
if (tag[i] < 0) flag = 1;
int flag_all;
MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world);
if (flag_all)
error->all("Invalid atom ID in Atoms section of data file");
flag = 0;
for (int i = 0; i < nlocal; i++)
if (tag[i] > 0) flag = 1;
MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_MAX,world);
if (flag_all == 0) atom->tag_enable = 0;
if (atom->tag_enable) {
flag = 0;
for (int i = 0; i < nlocal; i++)
if (tag[i] == 0) flag = 1;
MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world);
if (flag_all)
error->all("Invalid atom ID in Atoms section of data file");
}
// create global mapping
if (atom->map_style) {
atom->map_init();
atom->map_set();
}
}
/* ----------------------------------------------------------------------
read all velocities
to find atoms, must build atom map if not a molecular system
------------------------------------------------------------------------- */
void ReadData::velocities()
{
int i,m,nchunk;
int mapflag = 0;
if (atom->map_style == 0) {
mapflag = 1;
atom->map_style = 1;
atom->map_init();
atom->map_set();
}
bigint nread = 0;
bigint natoms = atom->natoms;
while (nread < natoms) {
if (natoms-nread > CHUNK) nchunk = CHUNK;
else nchunk = natoms-nread;
if (me == 0) {
char *eof;
m = 0;
for (i = 0; i < nchunk; i++) {
eof = fgets(&buffer[m],MAXLINE,fp);
if (eof == NULL) error->one("Unexpected end of data file");
m += strlen(&buffer[m]);
}
buffer[m++] = '\n';
}
MPI_Bcast(&m,1,MPI_INT,0,world);
MPI_Bcast(buffer,m,MPI_CHAR,0,world);
atom->data_vels(nchunk,buffer);
nread += nchunk;
}
if (mapflag) {
atom->map_delete();
atom->map_style = 0;
}
if (me == 0) {
if (screen) fprintf(screen," " BIGINT_FORMAT " velocities\n",natoms);
if (logfile) fprintf(logfile," " BIGINT_FORMAT " velocities\n",natoms);
}
}
/* ---------------------------------------------------------------------- */
void ReadData::bonds()
{
int i,m,nchunk;
bigint nread = 0;
bigint nbonds = atom->nbonds;
while (nread < nbonds) {
nchunk = MIN(nbonds-nread,CHUNK);
if (me == 0) {
char *eof;
m = 0;
for (i = 0; i < nchunk; i++) {
eof = fgets(&buffer[m],MAXLINE,fp);
if (eof == NULL) error->one("Unexpected end of data file");
m += strlen(&buffer[m]);
}
buffer[m++] = '\n';
}
MPI_Bcast(&m,1,MPI_INT,0,world);
MPI_Bcast(buffer,m,MPI_CHAR,0,world);
atom->data_bonds(nchunk,buffer);
nread += nchunk;
}
// check that bonds were assigned correctly
int nlocal = atom->nlocal;
bigint sum;
bigint n = 0;
for (i = 0; i < nlocal; i++) n += atom->num_bond[i];
MPI_Allreduce(&n,&sum,1,MPI_LMP_BIGINT,MPI_SUM,world);
int factor = 1;
if (!force->newton_bond) factor = 2;
if (me == 0) {
if (screen) fprintf(screen," " BIGINT_FORMAT " bonds\n",sum/factor);
if (logfile) fprintf(logfile," " BIGINT_FORMAT " bonds\n",sum/factor);
}
if (sum != factor*atom->nbonds) error->all("Bonds assigned incorrectly");
}
/* ---------------------------------------------------------------------- */
void ReadData::angles()
{
int i,m,nchunk;
bigint nread = 0;
bigint nangles = atom->nangles;
while (nread < nangles) {
nchunk = MIN(nangles-nread,CHUNK);
if (me == 0) {
char *eof;
m = 0;
for (i = 0; i < nchunk; i++) {
eof = fgets(&buffer[m],MAXLINE,fp);
if (eof == NULL) error->one("Unexpected end of data file");
m += strlen(&buffer[m]);
}
buffer[m++] = '\n';
}
MPI_Bcast(&m,1,MPI_INT,0,world);
MPI_Bcast(buffer,m,MPI_CHAR,0,world);
atom->data_angles(nchunk,buffer);
nread += nchunk;
}
// check that ang
int nlocal = atom->nlocal;
bigint sum;
bigint n = 0;
for (i = 0; i < nlocal; i++) n += atom->num_angle[i];
MPI_Allreduce(&n,&sum,1,MPI_LMP_BIGINT,MPI_SUM,world);
int factor = 1;
if (!force->newton_bond) factor = 3;
if (me == 0) {
if (screen) fprintf(screen," " BIGINT_FORMAT " angles\n",sum/factor);
if (logfile) fprintf(logfile," " BIGINT_FORMAT " angles\n",sum/factor);
}
if (sum != factor*atom->nangles) error->all("Angles assigned incorrectly");
}
/* ---------------------------------------------------------------------- */
void ReadData::dihedrals()
{
int i,m,nchunk;
bigint nread = 0;
bigint ndihedrals = atom->ndihedrals;
while (nread < ndihedrals) {
nchunk = MIN(ndihedrals-nread,CHUNK);
if (me == 0) {
char *eof;
m = 0;
for (i = 0; i < nchunk; i++) {
eof = fgets(&buffer[m],MAXLINE,fp);
if (eof == NULL) error->one("Unexpected end of data file");
m += strlen(&buffer[m]);
}
buffer[m++] = '\n';
}
MPI_Bcast(&m,1,MPI_INT,0,world);
MPI_Bcast(buffer,m,MPI_CHAR,0,world);
atom->data_dihedrals(nchunk,buffer);
nread += nchunk;
}
// check that dihedrals were assigned correctly
int nlocal = atom->nlocal;
bigint sum;
bigint n = 0;
for (i = 0; i < nlocal; i++) n += atom->num_dihedral[i];
MPI_Allreduce(&n,&sum,1,MPI_LMP_BIGINT,MPI_SUM,world);
int factor = 1;
if (!force->newton_bond) factor = 4;
if (me == 0) {
if (screen) fprintf(screen," " BIGINT_FORMAT " dihedrals\n",sum/factor);
if (logfile) fprintf(logfile," " BIGINT_FORMAT " dihedrals\n",sum/factor);
}
if (sum != factor*atom->ndihedrals)
error->all("Dihedrals assigned incorrectly");
}
/* ---------------------------------------------------------------------- */
void ReadData::impropers()
{
int i,m,nchunk;
bigint nread = 0;
bigint nimpropers = atom->nimpropers;
while (nread < nimpropers) {
nchunk = MIN(nimpropers-nread,CHUNK);
if (me == 0) {
char *eof;
m = 0;
for (i = 0; i < nchunk; i++) {
eof = fgets(&buffer[m],MAXLINE,fp);
if (eof == NULL) error->one("Unexpected end of data file");
m += strlen(&buffer[m]);
}
buffer[m++] = '\n';
}
MPI_Bcast(&m,1,MPI_INT,0,world);
MPI_Bcast(buffer,m,MPI_CHAR,0,world);
atom->data_impropers(nchunk,buffer);
nread += nchunk;
}
// check that impropers were assigned correctly
int nlocal = atom->nlocal;
bigint sum;
bigint n = 0;
for (i = 0; i < nlocal; i++) n += atom->num_improper[i];
MPI_Allreduce(&n,&sum,1,MPI_LMP_BIGINT,MPI_SUM,world);
int factor = 1;
if (!force->newton_bond) factor = 4;
if (me == 0) {
if (screen) fprintf(screen," " BIGINT_FORMAT " impropers\n",sum/factor);
if (logfile) fprintf(logfile," " BIGINT_FORMAT " impropers\n",sum/factor);
}
if (sum != factor*atom->nimpropers)
error->all("Impropers assigned incorrectly");
}
/* ---------------------------------------------------------------------- */
void ReadData::mass()
{
int i,m;
char *buf = new char[atom->ntypes*MAXLINE];
char *original = buf;
if (me == 0) {
char *eof;
m = 0;
for (i = 0; i < atom->ntypes; i++) {
eof = fgets(&buf[m],MAXLINE,fp);
if (eof == NULL) error->one("Unexpected end of data file");
m += strlen(&buf[m]);
buf[m-1] = '\0';
}
}
MPI_Bcast(&m,1,MPI_INT,0,world);
MPI_Bcast(buf,m,MPI_CHAR,0,world);
for (i = 0; i < atom->ntypes; i++) {
atom->set_mass(buf);
buf += strlen(buf) + 1;
}
delete [] original;
}
/* ---------------------------------------------------------------------- */
void ReadData::shape()
{
int i,m;
char *buf = new char[atom->ntypes*MAXLINE];
char *original = buf;
if (me == 0) {
char *eof;
m = 0;
for (i = 0; i < atom->ntypes; i++) {
eof = fgets(&buf[m],MAXLINE,fp);
if (eof == NULL) error->one("Unexpected end of data file");
m += strlen(&buf[m]);
buf[m-1] = '\0';
}
}
MPI_Bcast(&m,1,MPI_INT,0,world);
MPI_Bcast(buf,m,MPI_CHAR,0,world);
for (i = 0; i < atom->ntypes; i++) {
atom->set_shape(buf);
buf += strlen(buf) + 1;
}
delete [] original;
}
/* ---------------------------------------------------------------------- */
void ReadData::dipole()
{
int i,m;
char *buf = new char[atom->ntypes*MAXLINE];
char *original = buf;
if (me == 0) {
char *eof;
m = 0;
for (i = 0; i < atom->ntypes; i++) {
eof = fgets(&buf[m],MAXLINE,fp);
if (eof == NULL) error->one("Unexpected end of data file");
m += strlen(&buf[m]);
buf[m-1] = '\0';
}
}
MPI_Bcast(&m,1,MPI_INT,0,world);
MPI_Bcast(buf,m,MPI_CHAR,0,world);
for (i = 0; i < atom->ntypes; i++) {
atom->set_dipole(buf);
buf += strlen(buf) + 1;
}
delete [] original;
}
/* ---------------------------------------------------------------------- */
void ReadData::paircoeffs()
{
int i,m;
char *buf = new char[atom->ntypes*MAXLINE];
char *original = buf;
if (me == 0) {
char *eof;
m = 0;
for (i = 0; i < atom->ntypes; i++) {
eof = fgets(&buf[m],MAXLINE,fp);
if (eof == NULL) error->one("Unexpected end of data file");
m += strlen(&buf[m]);
buf[m-1] = '\0';
}
}
MPI_Bcast(&m,1,MPI_INT,0,world);
MPI_Bcast(buf,m,MPI_CHAR,0,world);
for (i = 0; i < atom->ntypes; i++) {
m = strlen(buf) + 1;
parse_coeffs(buf,NULL,1);
force->pair->coeff(narg,arg);
buf += m;
}
delete [] original;
}
/* ---------------------------------------------------------------------- */
void ReadData::bondcoeffs()
{
int i,m;
char *buf = new char[atom->nbondtypes*MAXLINE];
char *original = buf;
if (me == 0) {
char *eof;
m = 0;
for (i = 0; i < atom->nbondtypes; i++) {
eof = fgets(&buf[m],MAXLINE,fp);
if (eof == NULL) error->one("Unexpected end of data file");
m += strlen(&buf[m]);
buf[m-1] = '\0';
}
}
MPI_Bcast(&m,1,MPI_INT,0,world);
MPI_Bcast(buf,m,MPI_CHAR,0,world);
for (i = 0; i < atom->nbondtypes; i++) {
m = strlen(buf) + 1;
parse_coeffs(buf,NULL,0);
force->bond->coeff(narg,arg);
buf += m;
}
delete [] original;
}
/* ---------------------------------------------------------------------- */
void ReadData::anglecoeffs(int which)
{
int i,m;
char *buf = new char[atom->nangletypes*MAXLINE];
char *original = buf;
if (me == 0) {
char *eof;
m = 0;
for (i = 0; i < atom->nangletypes; i++) {
eof = fgets(&buf[m],MAXLINE,fp);
if (eof == NULL) error->one("Unexpected end of data file");
m += strlen(&buf[m]);
buf[m-1] = '\0';
}
}
MPI_Bcast(&m,1,MPI_INT,0,world);
MPI_Bcast(buf,m,MPI_CHAR,0,world);
for (i = 0; i < atom->nangletypes; i++) {
m = strlen(buf) + 1;
if (which == 0) parse_coeffs(buf,NULL,0);
else if (which == 1) parse_coeffs(buf,"bb",0);
else if (which == 2) parse_coeffs(buf,"ba",0);
force->angle->coeff(narg,arg);
buf += m;
}
delete [] original;
}
/* ---------------------------------------------------------------------- */
void ReadData::dihedralcoeffs(int which)
{
int i,m;
char *buf = new char[atom->ndihedraltypes*MAXLINE];
char *original = buf;
if (me == 0) {
char *eof;
m = 0;
for (i = 0; i < atom->ndihedraltypes; i++) {
eof = fgets(&buf[m],MAXLINE,fp);
if (eof == NULL) error->one("Unexpected end of data file");
m += strlen(&buf[m]);
buf[m-1] = '\0';
}
}
MPI_Bcast(&m,1,MPI_INT,0,world);
MPI_Bcast(buf,m,MPI_CHAR,0,world);
for (i = 0; i < atom->ndihedraltypes; i++) {
m = strlen(buf) + 1;
if (which == 0) parse_coeffs(buf,NULL,0);
else if (which == 1) parse_coeffs(buf,"mbt",0);
else if (which == 2) parse_coeffs(buf,"ebt",0);
else if (which == 3) parse_coeffs(buf,"at",0);
else if (which == 4) parse_coeffs(buf,"aat",0);
else if (which == 5) parse_coeffs(buf,"bb13",0);
force->dihedral->coeff(narg,arg);
buf += m;
}
delete [] original;
}
/* ---------------------------------------------------------------------- */
void ReadData::impropercoeffs(int which)
{
int i,m;
char *buf = new char[atom->nimpropertypes*MAXLINE];
char *original = buf;
if (me == 0) {
char *eof;
m = 0;
for (i = 0; i < atom->nimpropertypes; i++) {
eof = fgets(&buf[m],MAXLINE,fp);
if (eof == NULL) error->one("Unexpected end of data file");
m += strlen(&buf[m]);
buf[m-1] = '\0';
}
}
MPI_Bcast(&m,1,MPI_INT,0,world);
MPI_Bcast(buf,m,MPI_CHAR,0,world);
for (i = 0; i < atom->nimpropertypes; i++) {
m = strlen(buf) + 1;
if (which == 0) parse_coeffs(buf,NULL,0);
else if (which == 1) parse_coeffs(buf,"aa",0);
force->improper->coeff(narg,arg);
buf += m;
}
delete [] original;
}
/* ----------------------------------------------------------------------
proc 0 scans the data file for topology maximums
------------------------------------------------------------------------- */
void ReadData::scan(int &bond_per_atom, int &angle_per_atom,
int &dihedral_per_atom, int &improper_per_atom)
{
int i,tmp1,tmp2,atom1,atom2,atom3,atom4;
char *eof;
if (atom->natoms > MAXSMALLINT)
error->all("Molecular data file has too many atoms");
int natoms = static_cast<int> (atom->natoms);
bond_per_atom = angle_per_atom = dihedral_per_atom = improper_per_atom = 0;
// allocate topology counting vector
// initially, array length = 1 to natoms
// will grow via reallocate() if atom IDs > natoms
int cmax = natoms + 1;
int *count = (int *) memory->smalloc(cmax*sizeof(int),"read_data:count");
while (strlen(keyword)) {
if (strcmp(keyword,"Masses") == 0) skip_lines(atom->ntypes);
else if (strcmp(keyword,"Dipoles") == 0) skip_lines(atom->ntypes);
else if (strcmp(keyword,"Atoms") == 0) skip_lines(natoms);
else if (strcmp(keyword,"Velocities") == 0) skip_lines(natoms);
else if (strcmp(keyword,"Pair Coeffs") == 0) {
if (force->pair == NULL)
error->all("Must define pair_style before Pair Coeffs");
skip_lines(atom->ntypes);
} else if (strcmp(keyword,"Bond Coeffs") == 0) {
if (atom->avec->bonds_allow == 0)
error->all("Invalid data file section: Bond Coeffs");
if (force->bond == NULL)
error->all("Must define bond_style before Bond Coeffs");
skip_lines(atom->nbondtypes);
} else if (strcmp(keyword,"Angle Coeffs") == 0) {
if (atom->avec->angles_allow == 0)
error->all("Invalid data file section: Angle Coeffs");
if (force->angle == NULL)
error->all("Must define angle_style before Angle Coeffs");
skip_lines(atom->nangletypes);
} else if (strcmp(keyword,"Dihedral Coeffs") == 0) {
skip_lines(atom->ndihedraltypes);
if (atom->avec->dihedrals_allow == 0)
error->all("Invalid data file section: Dihedral Coeffs");
if (force->dihedral == NULL)
error->all("Must define dihedral_style before Dihedral Coeffs");
} else if (strcmp(keyword,"Improper Coeffs") == 0) {
if (atom->avec->impropers_allow == 0)
error->all("Invalid data file section: Improper Coeffs");
if (force->improper == NULL)
error->all("Must define improper_style before Improper Coeffs");
skip_lines(atom->nimpropertypes);
} else if (strcmp(keyword,"BondBond Coeffs") == 0) {
if (atom->avec->angles_allow == 0)
error->all("Invalid data file section: BondBond Coeffs");
if (force->angle == NULL)
error->all("Must define angle_style before BondBond Coeffs");
skip_lines(atom->nangletypes);
} else if (strcmp(keyword,"BondAngle Coeffs") == 0) {
if (atom->avec->angles_allow == 0)
error->all("Invalid data file section: BondAngle Coeffs");
if (force->angle == NULL)
error->all("Must define angle_style before BondAngle Coeffs");
skip_lines(atom->nangletypes);
} else if (strcmp(keyword,"MiddleBondTorsion Coeffs") == 0) {
if (atom->avec->dihedrals_allow == 0)
error->all("Invalid data file section: MiddleBondTorsion Coeffs");
if (force->dihedral == NULL)
error->all("Must define dihedral_style before MiddleBondTorsion Coeffs");
skip_lines(atom->ndihedraltypes);
} else if (strcmp(keyword,"EndBondTorsion Coeffs") == 0) {
if (atom->avec->dihedrals_allow == 0)
error->all("Invalid data file section: EndBondTorsion Coeffs");
if (force->dihedral == NULL)
error->all("Must define dihedral_style before EndBondTorsion Coeffs");
skip_lines(atom->ndihedraltypes);
} else if (strcmp(keyword,"AngleTorsion Coeffs") == 0) {
if (atom->avec->dihedrals_allow == 0)
error->all("Invalid data file section: AngleTorsion Coeffs");
if (force->dihedral == NULL)
error->all("Must define dihedral_style before AngleTorsion Coeffs");
skip_lines(atom->ndihedraltypes);
} else if (strcmp(keyword,"AngleAngleTorsion Coeffs") == 0) {
if (atom->avec->dihedrals_allow == 0)
error->all("Invalid data file section: AngleAngleTorsion Coeffs");
if (force->dihedral == NULL)
error->all("Must define dihedral_style before AngleAngleTorsion Coeffs");
skip_lines(atom->ndihedraltypes);
} else if (strcmp(keyword,"BondBond13 Coeffs") == 0) {
if (atom->avec->dihedrals_allow == 0)
error->all("Invalid data file section: BondBond13 Coeffs");
if (force->dihedral == NULL)
error->all("Must define dihedral_style before BondBond13 Coeffs");
skip_lines(atom->ndihedraltypes);
} else if (strcmp(keyword,"AngleAngle Coeffs") == 0) {
if (atom->avec->impropers_allow == 0)
error->all("Invalid data file section: AngleAngle Coeffs");
if (force->improper == NULL)
error->all("Must define improper_style before AngleAngle Coeffs");
skip_lines(atom->nimpropertypes);
} else if (strcmp(keyword,"Bonds") == 0) {
for (i = 1; i < cmax; i++) count[i] = 0;
if (force->newton_bond)
for (i = 0; i < atom->nbonds; i++) {
eof = fgets(line,MAXLINE,fp);
if (eof == NULL) error->one("Unexpected end of data file");
sscanf(line,"%d %d %d %d",&tmp1,&tmp2,&atom1,&atom2);
if (atom1 >= cmax) cmax = reallocate(&count,cmax,atom1);
count[atom1]++;
}
else
for (i = 0; i < atom->nbonds; i++) {
eof = fgets(line,MAXLINE,fp);
if (eof == NULL) error->one("Unexpected end of data file");
sscanf(line,"%d %d %d %d",&tmp1,&tmp2,&atom1,&atom2);
int amax = MAX(atom1,atom2);
if (amax >= cmax) cmax = reallocate(&count,cmax,amax);
count[atom1]++;
count[atom2]++;
}
for (i = 1; i < cmax; i++) bond_per_atom = MAX(bond_per_atom,count[i]);
if (screen) fprintf(screen," %d = max bonds/atom\n",bond_per_atom);
if (logfile) fprintf(logfile," %d = max bonds/atom\n",bond_per_atom);
} else if (strcmp(keyword,"Angles") == 0) {
for (i = 1; i < cmax; i++) count[i] = 0;
if (force->newton_bond)
for (i = 0; i < atom->nangles; i++) {
eof = fgets(line,MAXLINE,fp);
if (eof == NULL) error->one("Unexpected end of data file");
sscanf(line,"%d %d %d %d %d",&tmp1,&tmp2,&atom1,&atom2,&atom3);
if (atom2 >= cmax) cmax = reallocate(&count,cmax,atom2);
count[atom2]++;
}
else
for (i = 0; i < atom->nangles; i++) {
eof = fgets(line,MAXLINE,fp);
if (eof == NULL) error->one("Unexpected end of data file");
sscanf(line,"%d %d %d %d %d",&tmp1,&tmp2,&atom1,&atom2,&atom3);
int amax = MAX(atom1,atom2);
amax = MAX(amax,atom3);
if (amax >= cmax) cmax = reallocate(&count,cmax,amax);
count[atom1]++;
count[atom2]++;
count[atom3]++;
}
for (i = 1; i < cmax; i++) angle_per_atom = MAX(angle_per_atom,count[i]);
if (screen) fprintf(screen," %d = max angles/atom\n",angle_per_atom);
if (logfile) fprintf(logfile," %d = max angles/atom\n",angle_per_atom);
} else if (strcmp(keyword,"Dihedrals") == 0) {
for (i = 1; i < cmax; i++) count[i] = 0;
if (force->newton_bond)
for (i = 0; i < atom->ndihedrals; i++) {
eof = fgets(line,MAXLINE,fp);
if (eof == NULL) error->one("Unexpected end of data file");
sscanf(line,"%d %d %d %d %d %d",
&tmp1,&tmp2,&atom1,&atom2,&atom3,&atom4);
if (atom2 >= cmax) cmax = reallocate(&count,cmax,atom2);
count[atom2]++;
}
else
for (i = 0; i < atom->ndihedrals; i++) {
eof = fgets(line,MAXLINE,fp);
if (eof == NULL) error->one("Unexpected end of data file");
sscanf(line,"%d %d %d %d %d %d",
&tmp1,&tmp2,&atom1,&atom2,&atom3,&atom4);
int amax = MAX(atom1,atom2);
amax = MAX(amax,atom3);
amax = MAX(amax,atom4);
if (amax >= cmax) cmax = reallocate(&count,cmax,amax);
count[atom1]++;
count[atom2]++;
count[atom3]++;
count[atom4]++;
}
for (i = 1; i < cmax; i++)
dihedral_per_atom = MAX(dihedral_per_atom,count[i]);
if (screen)
fprintf(screen," %d = max dihedrals/atom\n",dihedral_per_atom);
if (logfile)
fprintf(logfile," %d = max dihedrals/atom\n",dihedral_per_atom);
} else if (strcmp(keyword,"Impropers") == 0) {
for (i = 1; i < cmax; i++) count[i] = 0;
if (force->newton_bond)
for (i = 0; i < atom->nimpropers; i++) {
eof = fgets(line,MAXLINE,fp);
if (eof == NULL) error->one("Unexpected end of data file");
sscanf(line,"%d %d %d %d %d %d",
&tmp1,&tmp2,&atom1,&atom2,&atom3,&atom4);
if (atom2 >= cmax) cmax = reallocate(&count,cmax,atom2);
count[atom2]++;
}
else
for (i = 0; i < atom->nimpropers; i++) {
eof = fgets(line,MAXLINE,fp);
if (eof == NULL) error->one("Unexpected end of data file");
sscanf(line,"%d %d %d %d %d %d",
&tmp1,&tmp2,&atom1,&atom2,&atom3,&atom4);
int amax = MAX(atom1,atom2);
amax = MAX(amax,atom3);
amax = MAX(amax,atom4);
if (amax >= cmax) cmax = reallocate(&count,cmax,amax);
count[atom1]++;
count[atom2]++;
count[atom3]++;
count[atom4]++;
}
for (i = 1; i < cmax; i++)
improper_per_atom = MAX(improper_per_atom,count[i]);
if (screen)
fprintf(screen," %d = max impropers/atom\n",improper_per_atom);
if (logfile)
fprintf(logfile," %d = max impropers/atom\n",improper_per_atom);
} else {
char str[128];
sprintf(str,"Unknown identifier in data file: %s",keyword);
error->one(str);
}
parse_keyword(0,0);
}
// free topology counting vector
memory->sfree(count);
// error check that topology was specified in file
if ((atom->nbonds && !bond_per_atom) ||
(atom->nangles && !angle_per_atom) ||
(atom->ndihedrals && !dihedral_per_atom) ||
(atom->nimpropers && !improper_per_atom))
error->one("Needed topology not in data file");
}
/* ----------------------------------------------------------------------
reallocate the count vector from cmax to amax+1 and return new length
zero new locations
------------------------------------------------------------------------- */
int ReadData::reallocate(int **pcount, int cmax, int amax)
{
int *count = *pcount;
count = (int *)
memory->srealloc(count,(amax+1)*sizeof(int),"read_data:count");
for (int i = cmax; i <= amax; i++) count[i] = 0;
*pcount = count;
return amax+1;
}
/* ----------------------------------------------------------------------
proc 0 opens data file
test if gzipped
------------------------------------------------------------------------- */
void ReadData::open(char *file)
{
compressed = 0;
char *suffix = file + strlen(file) - 3;
if (suffix > file && strcmp(suffix,".gz") == 0) compressed = 1;
if (!compressed) fp = fopen(file,"r");
else {
#ifdef LAMMPS_GZIP
char gunzip[128];
sprintf(gunzip,"gunzip -c %s",file);
fp = popen(gunzip,"r");
#else
error->one("Cannot open gzipped file");
#endif
}
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open file %s",file);
error->one(str);
}
}
/* ----------------------------------------------------------------------
grab next keyword
read lines until one is non-blank
keyword is all text on line w/out leading & trailing white space
read one additional line (assumed blank)
if any read hits EOF, set keyword to empty
if first = 1, line variable holds non-blank line that ended header
if flag = 0, only proc 0 is calling so no bcast
else flag = 1, bcast keyword line to all procs
------------------------------------------------------------------------- */
void ReadData::parse_keyword(int first, int flag)
{
int eof = 0;
// proc 0 reads upto non-blank line plus 1 following line
// eof is set to 1 if any read hits end-of-file
if (me == 0) {
if (!first) {
if (fgets(line,MAXLINE,fp) == NULL) eof = 1;
}
while (eof == 0 && strspn(line," \t\n\r") == strlen(line)) {
if (fgets(line,MAXLINE,fp) == NULL) eof = 1;
}
if (fgets(buffer,MAXLINE,fp) == NULL) eof = 1;
}
// if eof, set keyword empty and return
if (flag) MPI_Bcast(&eof,1,MPI_INT,0,world);
if (eof) {
keyword[0] = '\0';
return;
}
// bcast keyword line to all procs
if (flag) {
int n;
if (me == 0) n = strlen(line) + 1;
MPI_Bcast(&n,1,MPI_INT,0,world);
MPI_Bcast(line,n,MPI_CHAR,0,world);
}
// copy non-whitespace portion of line into keyword
int start = strspn(line," \t\n\r");
int stop = strlen(line) - 1;
while (line[stop] == ' ' || line[stop] == '\t'
|| line[stop] == '\n' || line[stop] == '\r') stop--;
line[stop+1] = '\0';
strcpy(keyword,&line[start]);
}
/* ----------------------------------------------------------------------
proc 0 reads N lines from file
------------------------------------------------------------------------- */
void ReadData::skip_lines(int n)
{
char *eof;
for (int i = 0; i < n; i++) eof = fgets(line,MAXLINE,fp);
if (eof == NULL) error->one("Unexpected end of data file");
}
/* ----------------------------------------------------------------------
parse a line of coeffs into words, storing them in narg,arg
trim anything from '#' onward
word strings remain in line, are not copied
if addstr != NULL, add addstr as 2nd arg for class2 angle/dihedral/improper
if dupflag, duplicate 1st word, so pair_coeff "2" becomes "2 2"
------------------------------------------------------------------------- */
void ReadData::parse_coeffs(char *line, char *addstr, int dupflag)
{
char *ptr;
if (ptr = strchr(line,'#')) *ptr = '\0';
narg = 0;
char *word = strtok(line," \t\n\r\f");
while (word) {
if (narg == maxarg) {
maxarg += DELTA;
arg = (char **)
memory->srealloc(arg,maxarg*sizeof(char *),"read_data:arg");
}
arg[narg++] = word;
if (addstr && narg == 1) arg[narg++] = addstr;
if (dupflag && narg == 1) arg[narg++] = word;
word = strtok(NULL," \t\n\r\f");
}
}
diff --git a/src/read_restart.cpp b/src/read_restart.cpp
index 51b478306..6c34cf896 100644
--- a/src/read_restart.cpp
+++ b/src/read_restart.cpp
@@ -1,848 +1,848 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "mpi.h"
#include "string.h"
#include "stdlib.h"
#include "sys/types.h"
#include "dirent.h"
#include "read_restart.h"
-#include "lmptype.h"
#include "atom.h"
#include "atom_vec.h"
#include "domain.h"
#include "comm.h"
#include "irregular.h"
#include "update.h"
#include "modify.h"
#include "fix.h"
#include "fix_read_restart.h"
#include "group.h"
#include "force.h"
#include "pair.h"
#include "bond.h"
#include "angle.h"
#include "dihedral.h"
#include "improper.h"
#include "special.h"
#include "universe.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
// same as write_restart.cpp
enum{VERSION,SMALLINT,TAGINT,BIGINT,
UNITS,NTIMESTEP,DIMENSION,NPROCS,PROCGRID_0,PROCGRID_1,PROCGRID_2,
NEWTON_PAIR,NEWTON_BOND,XPERIODIC,YPERIODIC,ZPERIODIC,
BOUNDARY_00,BOUNDARY_01,BOUNDARY_10,BOUNDARY_11,BOUNDARY_20,BOUNDARY_21,
ATOM_STYLE,NATOMS,NTYPES,
NBONDS,NBONDTYPES,BOND_PER_ATOM,
NANGLES,NANGLETYPES,ANGLE_PER_ATOM,
NDIHEDRALS,NDIHEDRALTYPES,DIHEDRAL_PER_ATOM,
NIMPROPERS,NIMPROPERTYPES,IMPROPER_PER_ATOM,
BOXLO_0,BOXHI_0,BOXLO_1,BOXHI_1,BOXLO_2,BOXHI_2,
SPECIAL_LJ_1,SPECIAL_LJ_2,SPECIAL_LJ_3,
SPECIAL_COUL_1,SPECIAL_COUL_2,SPECIAL_COUL_3,
XY,XZ,YZ};
enum{MASS,SHAPE,DIPOLE};
enum{PAIR,BOND,ANGLE,DIHEDRAL,IMPROPER};
#define LB_FACTOR 1.1
/* ---------------------------------------------------------------------- */
ReadRestart::ReadRestart(LAMMPS *lmp) : Pointers(lmp) {}
/* ---------------------------------------------------------------------- */
void ReadRestart::command(int narg, char **arg)
{
if (narg != 1) error->all("Illegal read_restart command");
if (domain->box_exist)
error->all("Cannot read_restart after simulation box is defined");
MPI_Comm_rank(world,&me);
MPI_Comm_size(world,&nprocs);
// if filename contains "*", search dir for latest restart file
char *file = new char[strlen(arg[0]) + 16];
if (strchr(arg[0],'*')) file_search(arg[0],file);
else strcpy(file,arg[0]);
// check if filename contains "%"
int multiproc;
if (strchr(file,'%')) multiproc = 1;
else multiproc = 0;
// open single restart file or base file for multiproc case
if (me == 0) {
if (screen) fprintf(screen,"Reading restart file ...\n");
char *hfile;
if (multiproc) {
hfile = new char[strlen(file) + 16];
char *ptr = strchr(file,'%');
*ptr = '\0';
sprintf(hfile,"%s%s%s",file,"base",ptr+1);
*ptr = '%';
} else hfile = file;
fp = fopen(hfile,"rb");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open restart file %s",hfile);
error->one(str);
}
if (multiproc) delete [] hfile;
}
// read header info and create atom style and simulation box
header();
domain->box_exist = 1;
// problem setup using info from header
int n;
if (nprocs == 1) n = static_cast<int> (atom->natoms);
else n = static_cast<int> (LB_FACTOR * atom->natoms / nprocs);
atom->allocate_type_arrays();
atom->avec->grow(n);
n = atom->nmax;
domain->print_box(" ");
domain->set_initial_box();
domain->set_global_box();
comm->set_procs();
domain->set_local_box();
// read groups, ntype-length arrays, force field, fix info from file
// nextra = max # of extra quantities stored with each atom
group->read_restart(fp);
type_arrays();
force_fields();
int nextra = modify->read_restart(fp);
atom->nextra_store = nextra;
atom->extra = memory->create_2d_double_array(n,nextra,"atom:extra");
// single file:
// nprocs_file = # of chunks in file
// proc 0 reads chunks one at a time and bcasts it to other procs
// each proc unpacks the atoms, saving ones in it's sub-domain
// check for atom in sub-domain differs for orthogonal vs triclinic box
// close restart file when done
AtomVec *avec = atom->avec;
int maxbuf = 0;
double *buf = NULL;
int m;
if (multiproc == 0) {
int triclinic = domain->triclinic;
double *x,lamda[3];
double *coord,*sublo,*subhi;
if (triclinic == 0) {
sublo = domain->sublo;
subhi = domain->subhi;
} else {
sublo = domain->sublo_lamda;
subhi = domain->subhi_lamda;
}
for (int iproc = 0; iproc < nprocs_file; iproc++) {
if (me == 0) fread(&n,sizeof(int),1,fp);
MPI_Bcast(&n,1,MPI_INT,0,world);
if (n > maxbuf) {
maxbuf = n;
memory->sfree(buf);
buf = (double *) memory->smalloc(maxbuf*sizeof(double),
"read_restart:buf");
}
if (n > 0) {
if (me == 0) fread(buf,sizeof(double),n,fp);
MPI_Bcast(buf,n,MPI_DOUBLE,0,world);
}
m = 0;
while (m < n) {
x = &buf[m+1];
if (triclinic) {
domain->x2lamda(x,lamda);
coord = lamda;
} else coord = x;
if (coord[0] >= sublo[0] && coord[0] < subhi[0] &&
coord[1] >= sublo[1] && coord[1] < subhi[1] &&
coord[2] >= sublo[2] && coord[2] < subhi[2]) {
m += avec->unpack_restart(&buf[m]);
}
else m += static_cast<int> (buf[m]);
}
}
if (me == 0) fclose(fp);
// one file per proc:
// nprocs_file = # of files
// each proc reads 1/P fraction of files, keeping all atoms in the files
// perform irregular comm to migrate atoms to correct procs
// close restart file when done
} else {
if (me == 0) fclose(fp);
char *perproc = new char[strlen(file) + 16];
char *ptr = strchr(file,'%');
for (int iproc = me; iproc < nprocs_file; iproc += nprocs) {
*ptr = '\0';
sprintf(perproc,"%s%d%s",file,iproc,ptr+1);
*ptr = '%';
fp = fopen(perproc,"rb");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open restart file %s",perproc);
error->one(str);
}
fread(&n,sizeof(int),1,fp);
if (n > maxbuf) {
maxbuf = n;
memory->sfree(buf);
buf = (double *) memory->smalloc(maxbuf*sizeof(double),
"read_restart:buf");
}
if (n > 0) fread(buf,sizeof(double),n,fp);
m = 0;
while (m < n) m += avec->unpack_restart(&buf[m]);
fclose(fp);
}
delete [] perproc;
// create a temporary fix to hold and migrate extra atom info
// necessary b/c irregular will migrate atoms
if (nextra) {
char cextra[8],fixextra[8];
sprintf(cextra,"%d",nextra);
sprintf(fixextra,"%d",modify->nfix_restart_peratom);
char **newarg = new char*[5];
newarg[0] = (char *) "_read_restart";
newarg[1] = (char *) "all";
newarg[2] = (char *) "READ_RESTART";
newarg[3] = cextra;
newarg[4] = fixextra;
modify->add_fix(5,newarg);
delete [] newarg;
}
// move atoms to new processors via irregular()
// in case read by different proc than wrote restart file
// first do map_init() since irregular->migrate_atoms() will do map_clear()
if (atom->map_style) atom->map_init();
if (domain->triclinic) domain->x2lamda(atom->nlocal);
Irregular *irregular = new Irregular(lmp);
irregular->migrate_atoms();
delete irregular;
if (domain->triclinic) domain->lamda2x(atom->nlocal);
// put extra atom info held by fix back into atom->extra
// destroy temporary fix
if (nextra) {
memory->destroy_2d_double_array(atom->extra);
atom->extra = memory->create_2d_double_array(atom->nmax,nextra,
"atom:extra");
int ifix = modify->find_fix("_read_restart");
FixReadRestart *fix = (FixReadRestart *) modify->fix[ifix];
int *count = fix->count;
double **extra = fix->extra;
double **atom_extra = atom->extra;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
for (int j = 0; j < count[i]; j++)
atom_extra[i][j] = extra[i][j];
modify->delete_fix("_read_restart");
}
}
// clean-up memory
delete [] file;
memory->sfree(buf);
// check that all atoms were assigned to procs
bigint natoms;
bigint nblocal = atom->nlocal;
MPI_Allreduce(&nblocal,&natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);
if (me == 0) {
if (screen) fprintf(screen," " BIGINT_FORMAT " atoms\n",natoms);
if (logfile) fprintf(logfile," " BIGINT_FORMAT " atoms\n",natoms);
}
if (natoms != atom->natoms) error->all("Did not assign all atoms correctly");
if (me == 0) {
if (atom->nbonds) {
if (screen) fprintf(screen," " BIGINT_FORMAT " bonds\n",atom->nbonds);
if (logfile) fprintf(logfile," " BIGINT_FORMAT " bonds\n",atom->nbonds);
}
if (atom->nangles) {
if (screen) fprintf(screen," " BIGINT_FORMAT " angles\n",
atom->nangles);
if (logfile) fprintf(logfile," " BIGINT_FORMAT " angles\n",
atom->nangles);
}
if (atom->ndihedrals) {
if (screen) fprintf(screen," " BIGINT_FORMAT " dihedrals\n",
atom->ndihedrals);
if (logfile) fprintf(logfile," " BIGINT_FORMAT " dihedrals\n",
atom->ndihedrals);
}
if (atom->nimpropers) {
if (screen) fprintf(screen," " BIGINT_FORMAT " impropers\n",
atom->nimpropers);
if (logfile) fprintf(logfile," " BIGINT_FORMAT " impropers\n",
atom->nimpropers);
}
}
// check if tags are being used
// create global mapping and bond topology now that system is defined
int flag = 0;
for (int i = 0; i < atom->nlocal; i++)
if (atom->tag[i] > 0) flag = 1;
int flag_all;
MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_MAX,world);
if (flag_all == 0) atom->tag_enable = 0;
if (atom->map_style) {
atom->map_init();
atom->map_set();
}
if (atom->molecular) {
Special special(lmp);
special.build();
}
}
/* ----------------------------------------------------------------------
search for all files matching infile which contains a "*"
replace "*" with latest timestep value to create outfile name
search dir referenced by initial pathname of file
if infile also contains "%", need to use "base" when search directory
------------------------------------------------------------------------- */
void ReadRestart::file_search(char *infile, char *outfile)
{
char *ptr;
// separate infile into dir + filename
char *dirname = new char[strlen(infile) + 1];
char *filename = new char[strlen(infile) + 1];
if (strchr(infile,'/')) {
ptr = strrchr(infile,'/');
*ptr = '\0';
strcpy(dirname,infile);
strcpy(filename,ptr+1);
*ptr = '/';
} else {
strcpy(dirname,"./");
strcpy(filename,infile);
}
// if filename contains "%" replace "%" with "base"
char *pattern = new char[strlen(filename) + 16];
if (ptr = strchr(filename,'%')) {
*ptr = '\0';
sprintf(pattern,"%s%s%s",filename,"base",ptr+1);
*ptr = '%';
} else strcpy(pattern,filename);
// scan all files in directory, searching for files that match pattern
// maxnum = largest int that matches "*"
int n = strlen(pattern) + 16;
char *begin = new char[n];
char *middle = new char[n];
char *end = new char[n];
ptr = strchr(pattern,'*');
*ptr = '\0';
strcpy(begin,pattern);
strcpy(end,ptr+1);
int nbegin = strlen(begin);
int maxnum = -1;
if (me == 0) {
struct dirent *ep;
DIR *dp = opendir(dirname);
if (dp == NULL)
error->one("Cannot open dir to search for restart file");
while (ep = readdir(dp)) {
if (strstr(ep->d_name,begin) != ep->d_name) continue;
if ((ptr = strstr(&ep->d_name[nbegin],end)) == NULL) continue;
if (strlen(end) == 0) ptr = ep->d_name + strlen(ep->d_name);
*ptr = '\0';
if (strlen(&ep->d_name[nbegin]) < n) {
strcpy(middle,&ep->d_name[nbegin]);
if (atoi(middle) > maxnum) maxnum = atoi(middle);
}
}
closedir(dp);
if (maxnum < 0) error->one("Found no restart file matching pattern");
}
// create outfile with maxint substituted for "*"
// use original infile, not pattern, since need to retain "%" in filename
ptr = strchr(infile,'*');
*ptr = '\0';
sprintf(outfile,"%s%d%s",infile,maxnum,ptr+1);
*ptr = '*';
// clean up
delete [] dirname;
delete [] filename;
delete [] pattern;
delete [] begin;
delete [] middle;
delete [] end;
}
/* ----------------------------------------------------------------------
read header of restart file
------------------------------------------------------------------------- */
void ReadRestart::header()
{
int px,py,pz;
int xperiodic,yperiodic,zperiodic;
int boundary[3][2];
// read flags and values until flag = -1
int flag = read_int();
while (flag >= 0) {
// check restart file version, warn if different
if (flag == VERSION) {
char *version = read_char();
if (strcmp(version,universe->version) != 0 && me == 0) {
error->warning("Restart file version does not match LAMMPS version");
if (screen) fprintf(screen," restart file = %s, LAMMPS = %s\n",
version,universe->version);
}
delete [] version;
// check lmptype.h sizes, error if different
} else if (flag == SMALLINT) {
int size = read_int();
if (size != sizeof(smallint))
error->all("Smallint setting in lmptype.h is not compatible");
} else if (flag == TAGINT) {
int size = read_int();
if (size != sizeof(tagint))
error->all("Tagint setting in lmptype.h is not compatible");
} else if (flag == BIGINT) {
int size = read_int();
if (size != sizeof(bigint))
error->all("Bigint setting in lmptype.h is not compatible");
// reset unit_style only if different
// so that timestep,neighbor-skin are not changed
} else if (flag == UNITS) {
char *style = read_char();
if (strcmp(style,update->unit_style) != 0) update->set_units(style);
delete [] style;
} else if (flag == NTIMESTEP) {
update->ntimestep = read_bigint();
// set dimension from restart file
} else if (flag == DIMENSION) {
int dimension = read_int();
domain->dimension = dimension;
if (domain->dimension == 2 && domain->zperiodic == 0)
error->all("Cannot run 2d simulation with nonperiodic Z dimension");
// read nprocs from restart file, warn if different
} else if (flag == NPROCS) {
nprocs_file = read_int();
if (nprocs_file != comm->nprocs && me == 0)
error->warning("Restart file used different # of processors");
// don't set procgrid, warn if different
} else if (flag == PROCGRID_0) {
px = read_int();
} else if (flag == PROCGRID_1) {
py = read_int();
} else if (flag == PROCGRID_2) {
pz = read_int();
if (comm->user_procgrid[0] != 0 &&
(px != comm->user_procgrid[0] || py != comm->user_procgrid[1] ||
pz != comm->user_procgrid[2]) && me == 0)
error->warning("Restart file used different 3d processor grid");
// don't set newton_pair, leave input script value unchanged
// set newton_bond from restart file
// warn if different and input script settings are not default
} else if (flag == NEWTON_PAIR) {
int newton_pair_file = read_int();
if (force->newton_pair != 1) {
if (newton_pair_file != force->newton_pair && me == 0)
error->warning("Restart file used different newton pair setting, "
"using input script value");
}
} else if (flag == NEWTON_BOND) {
int newton_bond_file = read_int();
if (force->newton_bond != 1) {
if (newton_bond_file != force->newton_bond && me == 0)
error->warning("Restart file used different newton bond setting, "
"using restart file value");
}
force->newton_bond = newton_bond_file;
if (force->newton_pair || force->newton_bond) force->newton = 1;
else force->newton = 0;
// set boundary settings from restart file
// warn if different and input script settings are not default
} else if (flag == XPERIODIC) {
xperiodic = read_int();
} else if (flag == YPERIODIC) {
yperiodic = read_int();
} else if (flag == ZPERIODIC) {
zperiodic = read_int();
} else if (flag == BOUNDARY_00) {
boundary[0][0] = read_int();
} else if (flag == BOUNDARY_01) {
boundary[0][1] = read_int();
} else if (flag == BOUNDARY_10) {
boundary[1][0] = read_int();
} else if (flag == BOUNDARY_11) {
boundary[1][1] = read_int();
} else if (flag == BOUNDARY_20) {
boundary[2][0] = read_int();
} else if (flag == BOUNDARY_21) {
boundary[2][1] = read_int();
if (domain->boundary[0][0] || domain->boundary[0][1] ||
domain->boundary[1][0] || domain->boundary[1][1] ||
domain->boundary[2][0] || domain->boundary[2][1]) {
if (boundary[0][0] != domain->boundary[0][0] ||
boundary[0][1] != domain->boundary[0][1] ||
boundary[1][0] != domain->boundary[1][0] ||
boundary[1][1] != domain->boundary[1][1] ||
boundary[2][0] != domain->boundary[2][0] ||
boundary[2][1] != domain->boundary[2][1]) {
if (me == 0)
error->warning("Restart file used different boundary settings, "
"using restart file values");
}
}
domain->boundary[0][0] = boundary[0][0];
domain->boundary[0][1] = boundary[0][1];
domain->boundary[1][0] = boundary[1][0];
domain->boundary[1][1] = boundary[1][1];
domain->boundary[2][0] = boundary[2][0];
domain->boundary[2][1] = boundary[2][1];
domain->periodicity[0] = domain->xperiodic = xperiodic;
domain->periodicity[1] = domain->yperiodic = yperiodic;
domain->periodicity[2] = domain->zperiodic = zperiodic;
domain->nonperiodic = 0;
if (xperiodic == 0 || yperiodic == 0 || zperiodic == 0) {
domain->nonperiodic = 1;
if (boundary[0][0] >= 2 || boundary[0][1] >= 2 ||
boundary[1][0] >= 2 || boundary[1][1] >= 2 ||
boundary[2][0] >= 2 || boundary[2][1] >= 2)
domain->nonperiodic = 2;
}
// create new AtomVec class
// if style = hybrid, read additional sub-class arguments
} else if (flag == ATOM_STYLE) {
char *style = read_char();
int nwords = 0;
char **words = NULL;
if (strcmp(style,"hybrid") == 0) {
nwords = read_int();
words = new char*[nwords];
for (int i = 0; i < nwords; i++) words[i] = read_char();
}
atom->create_avec(style,nwords,words);
for (int i = 0; i < nwords; i++) delete [] words[i];
delete [] words;
delete [] style;
} else if (flag == NATOMS) {
atom->natoms = read_bigint();
} else if (flag == NTYPES) {
atom->ntypes = read_int();
} else if (flag == NBONDS) {
atom->nbonds = read_bigint();
} else if (flag == NBONDTYPES) {
atom->nbondtypes = read_int();
} else if (flag == BOND_PER_ATOM) {
atom->bond_per_atom = read_int();
} else if (flag == NANGLES) {
atom->nangles = read_bigint();
} else if (flag == NANGLETYPES) {
atom->nangletypes = read_int();
} else if (flag == ANGLE_PER_ATOM) {
atom->angle_per_atom = read_int();
} else if (flag == NDIHEDRALS) {
atom->ndihedrals = read_bigint();
} else if (flag == NDIHEDRALTYPES) {
atom->ndihedraltypes = read_int();
} else if (flag == DIHEDRAL_PER_ATOM) {
atom->dihedral_per_atom = read_int();
} else if (flag == NIMPROPERS) {
atom->nimpropers = read_bigint();
} else if (flag == NIMPROPERTYPES) {
atom->nimpropertypes = read_int();
} else if (flag == IMPROPER_PER_ATOM) {
atom->improper_per_atom = read_int();
} else if (flag == BOXLO_0) {
domain->boxlo[0] = read_double();
} else if (flag == BOXHI_0) {
domain->boxhi[0] = read_double();
} else if (flag == BOXLO_1) {
domain->boxlo[1] = read_double();
} else if (flag == BOXHI_1) {
domain->boxhi[1] = read_double();
} else if (flag == BOXLO_2) {
domain->boxlo[2] = read_double();
} else if (flag == BOXHI_2) {
domain->boxhi[2] = read_double();
} else if (flag == SPECIAL_LJ_1) {
force->special_lj[1] = read_double();
} else if (flag == SPECIAL_LJ_2) {
force->special_lj[2] = read_double();
} else if (flag == SPECIAL_LJ_3) {
force->special_lj[3] = read_double();
} else if (flag == SPECIAL_COUL_1) {
force->special_coul[1] = read_double();
} else if (flag == SPECIAL_COUL_2) {
force->special_coul[2] = read_double();
} else if (flag == SPECIAL_COUL_3) {
force->special_coul[3] = read_double();
} else if (flag == XY) {
domain->triclinic = 1;
domain->xy = read_double();
} else if (flag == XZ) {
domain->triclinic = 1;
domain->xz = read_double();
} else if (flag == YZ) {
domain->triclinic = 1;
domain->yz = read_double();
} else error->all("Invalid flag in header section of restart file");
flag = read_int();
}
}
/* ---------------------------------------------------------------------- */
void ReadRestart::type_arrays()
{
int flag = read_int();
while (flag >= 0) {
if (flag == MASS) {
double *mass = new double[atom->ntypes+1];
if (me == 0) fread(&mass[1],sizeof(double),atom->ntypes,fp);
MPI_Bcast(&mass[1],atom->ntypes,MPI_DOUBLE,0,world);
atom->set_mass(mass);
delete [] mass;
} else if (flag == SHAPE) {
double **shape =
memory->create_2d_double_array(atom->ntypes+1,3,"restart:shape");
if (me == 0) fread(&shape[1][0],sizeof(double),atom->ntypes*3,fp);
MPI_Bcast(&shape[1][0],atom->ntypes*3,MPI_DOUBLE,0,world);
atom->set_shape(shape);
memory->destroy_2d_double_array(shape);
} else if (flag == DIPOLE) {
double *dipole = new double[atom->ntypes+1];
if (me == 0) fread(&dipole[1],sizeof(double),atom->ntypes,fp);
MPI_Bcast(&dipole[1],atom->ntypes,MPI_DOUBLE,0,world);
atom->set_dipole(dipole);
delete [] dipole;
} else error->all("Invalid flag in type arrays section of restart file");
flag = read_int();
}
}
/* ---------------------------------------------------------------------- */
void ReadRestart::force_fields()
{
int n;
char *style;
int flag = read_int();
while (flag >= 0) {
if (flag == PAIR) {
if (me == 0) fread(&n,sizeof(int),1,fp);
MPI_Bcast(&n,1,MPI_INT,0,world);
style = new char[n];
if (me == 0) fread(style,sizeof(char),n,fp);
MPI_Bcast(style,n,MPI_CHAR,0,world);
force->create_pair(style);
delete [] style;
force->pair->read_restart(fp);
} else if (flag == BOND) {
if (me == 0) fread(&n,sizeof(int),1,fp);
MPI_Bcast(&n,1,MPI_INT,0,world);
style = new char[n];
if (me == 0) fread(style,sizeof(char),n,fp);
MPI_Bcast(style,n,MPI_CHAR,0,world);
force->create_bond(style);
delete [] style;
force->bond->read_restart(fp);
} else if (flag == ANGLE) {
if (me == 0) fread(&n,sizeof(int),1,fp);
MPI_Bcast(&n,1,MPI_INT,0,world);
style = new char[n];
if (me == 0) fread(style,sizeof(char),n,fp);
MPI_Bcast(style,n,MPI_CHAR,0,world);
force->create_angle(style);
delete [] style;
force->angle->read_restart(fp);
} else if (flag == DIHEDRAL) {
if (me == 0) fread(&n,sizeof(int),1,fp);
MPI_Bcast(&n,1,MPI_INT,0,world);
style = new char[n];
if (me == 0) fread(style,sizeof(char),n,fp);
MPI_Bcast(style,n,MPI_CHAR,0,world);
force->create_dihedral(style);
delete [] style;
force->dihedral->read_restart(fp);
} else if (flag == IMPROPER) {
if (me == 0) fread(&n,sizeof(int),1,fp);
MPI_Bcast(&n,1,MPI_INT,0,world);
style = new char[n];
if (me == 0) fread(style,sizeof(char),n,fp);
MPI_Bcast(style,n,MPI_CHAR,0,world);
force->create_improper(style);
delete [] style;
force->improper->read_restart(fp);
} else error->all("Invalid flag in force field section of restart file");
flag = read_int();
}
}
/* ----------------------------------------------------------------------
read an int from restart file and bcast it
------------------------------------------------------------------------- */
int ReadRestart::read_int()
{
int value;
if (me == 0) fread(&value,sizeof(int),1,fp);
MPI_Bcast(&value,1,MPI_INT,0,world);
return value;
}
/* ----------------------------------------------------------------------
read a double from restart file and bcast it
------------------------------------------------------------------------- */
double ReadRestart::read_double()
{
double value;
if (me == 0) fread(&value,sizeof(double),1,fp);
MPI_Bcast(&value,1,MPI_DOUBLE,0,world);
return value;
}
/* ----------------------------------------------------------------------
read a char str from restart file and bcast it
str is allocated here, ptr is returned, caller must deallocate
------------------------------------------------------------------------- */
char *ReadRestart::read_char()
{
int n;
if (me == 0) fread(&n,sizeof(int),1,fp);
MPI_Bcast(&n,1,MPI_INT,0,world);
char *value = new char[n];
if (me == 0) fread(value,sizeof(char),n,fp);
MPI_Bcast(value,n,MPI_CHAR,0,world);
return value;
}
/* ----------------------------------------------------------------------
read a bigint from restart file and bcast it
------------------------------------------------------------------------- */
bigint ReadRestart::read_bigint()
{
bigint value;
if (me == 0) fread(&value,sizeof(bigint),1,fp);
MPI_Bcast(&value,1,MPI_LMP_BIGINT,0,world);
return value;
}
diff --git a/src/read_restart.h b/src/read_restart.h
index d5364a144..16d2e675d 100644
--- a/src/read_restart.h
+++ b/src/read_restart.h
@@ -1,53 +1,53 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef COMMAND_CLASS
CommandStyle(read_restart,ReadRestart)
#else
#ifndef LMP_READ_RESTART_H
#define LMP_READ_RESTART_H
+#include "lmptype.h"
#include "stdio.h"
#include "pointers.h"
-#include "lmptype.h"
namespace LAMMPS_NS {
class ReadRestart : protected Pointers {
public:
ReadRestart(class LAMMPS *);
void command(int, char **);
private:
int me,nprocs,nprocs_file;
FILE *fp;
int nfix_restart_global,nfix_restart_peratom;
void file_search(char *, char *);
void header();
void type_arrays();
void force_fields();
int read_int();
double read_double();
char *read_char();
bigint read_bigint();
};
}
#endif
#endif
diff --git a/src/region.h b/src/region.h
index c4a1e18a7..e32d7ff1c 100644
--- a/src/region.h
+++ b/src/region.h
@@ -1,73 +1,73 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifndef LMP_REGION_H
#define LMP_REGION_H
-#include "pointers.h"
#include "lmptype.h"
+#include "pointers.h"
namespace LAMMPS_NS {
class Region : protected Pointers {
public:
char *id,*style;
int interior; // 1 for interior, 0 for exterior
int scaleflag; // 1 for lattice, 0 for box
double xscale,yscale,zscale; // scale factors for box/lattice units
double extent_xlo,extent_xhi; // bounding box on region
double extent_ylo,extent_yhi;
double extent_zlo,extent_zhi;
int bboxflag; // 1 if bounding box is computable
// contact = particle near region surface
struct Contact {
double r; // distance between particle & surf, r > 0.0
double delx,dely,delz; // vector from surface pt to particle
};
Contact *contact; // list of contacts
int cmax; // max # of contacts possible with region
Region(class LAMMPS *, int, char **);
virtual ~Region();
void init();
virtual int dynamic_check();
int match(double, double, double);
int surface(double, double, double, double);
virtual int inside(double, double, double) = 0;
virtual int surface_interior(double *, double) = 0;
virtual int surface_exterior(double *, double) = 0;
protected:
void add_contact(int, double *, double, double, double);
void options(int, char **);
private:
int dynamic; // 1 if region changes over time
int moveflag,rotateflag;
double point[3],axis[3],runit[3];
char *xstr,*ystr,*zstr,*tstr;
int xvar,yvar,zvar,tvar;
double dx,dy,dz,theta;
bigint laststep;
void forward_transform(double &, double &, double &);
void inverse_transform(double &, double &, double &);
void rotate(double &, double &, double &, double);
};
}
#endif
diff --git a/src/replicate.cpp b/src/replicate.cpp
index d0a15af91..503f59c26 100644
--- a/src/replicate.cpp
+++ b/src/replicate.cpp
@@ -1,416 +1,416 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "stdlib.h"
#include "string.h"
#include "replicate.h"
-#include "lmptype.h"
#include "atom.h"
#include "atom_vec.h"
#include "atom_vec_hybrid.h"
#include "force.h"
#include "domain.h"
#include "comm.h"
#include "special.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define LB_FACTOR 1.1
#define EPSILON 1.0e-6
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
/* ---------------------------------------------------------------------- */
Replicate::Replicate(LAMMPS *lmp) : Pointers(lmp) {}
/* ---------------------------------------------------------------------- */
void Replicate::command(int narg, char **arg)
{
int i,j,m,n;
if (domain->box_exist == 0)
error->all("Replicate command before simulation box is defined");
if (narg != 3) error->all("Illegal replicate command");
int me = comm->me;
int nprocs = comm->nprocs;
if (me == 0 && screen) fprintf(screen,"Replicating atoms ...\n");
// nrep = total # of replications
int nx = atoi(arg[0]);
int ny = atoi(arg[1]);
int nz = atoi(arg[2]);
int nrep = nx*ny*nz;
// error and warning checks
if (nx <= 0 || ny <= 0 || nz <= 0) error->all("Illegal replicate command");
if (domain->dimension == 2 && nz != 1)
error->all("Cannot replicate 2d simulation in z dimension");
if ((nx > 1 && domain->xperiodic == 0) ||
(ny > 1 && domain->yperiodic == 0) ||
(nz > 1 && domain->zperiodic == 0))
error->warning("Replicating in a non-periodic dimension");
if (atom->nextra_grow || atom->nextra_restart || atom->nextra_store)
error->all("Cannot replicate with fixes that store atom quantities");
// maxtag = largest atom tag across all existing atoms
int maxtag = 0;
for (i = 0; i < atom->nlocal; i++) maxtag = MAX(atom->tag[i],maxtag);
int maxtag_all;
MPI_Allreduce(&maxtag,&maxtag_all,1,MPI_INT,MPI_MAX,world);
maxtag = maxtag_all;
// maxmol = largest molecule tag across all existing atoms
int maxmol = 0;
if (atom->molecular) {
for (i = 0; i < atom->nlocal; i++) maxmol = MAX(atom->molecule[i],maxmol);
int maxmol_all;
MPI_Allreduce(&maxmol,&maxmol_all,1,MPI_INT,MPI_MAX,world);
maxmol = maxmol_all;
}
// unmap existing atoms via image flags
for (i = 0; i < atom->nlocal; i++)
domain->unmap(atom->x[i],atom->image[i]);
// communication buffer for all my atom's info
// max_size = largest buffer needed by any proc
// must do before new Atom class created,
// since size_restart() uses atom->nlocal
int max_size;
int send_size = atom->avec->size_restart();
MPI_Allreduce(&send_size,&max_size,1,MPI_INT,MPI_MAX,world);
double *buf =
(double *) memory->smalloc(max_size*sizeof(double),"replicate:buf");
// old = original atom class
// atom = new replicated atom class
// if old atom style was hybrid, pass sub-style names to create_avec
Atom *old = atom;
atom = new Atom(lmp);
atom->settings(old);
int nstyles = 0;
char **keywords = NULL;
if (strcmp(old->atom_style,"hybrid") == 0) {
AtomVecHybrid *avec_hybrid = (AtomVecHybrid *) old->avec;
nstyles = avec_hybrid->nstyles;
keywords = avec_hybrid->keywords;
}
atom->create_avec(old->atom_style,nstyles,keywords);
// check that new system will not be too large
// if molecular and N > MAXTAGINT, error
// if atomic and new N > MAXTAGINT, turn off tags for existing and new atoms
// new system cannot exceed MAXBIGINT
if (atom->molecular && (nrep*old->natoms < 0 || nrep*old->natoms > MAXTAGINT))
error->all("Replicated molecular system atom IDs are too big");
if (nrep*old->natoms < 0 || nrep*old->natoms > MAXTAGINT)
atom->tag_enable = 0;
if (atom->tag_enable == 0)
for (int i = 0; i < atom->nlocal; i++)
atom->tag[i] = 0;
if (nrep*old->natoms < 0 || nrep*old->natoms > MAXBIGINT ||
nrep*old->nbonds < 0 || nrep*old->nbonds > MAXBIGINT ||
nrep*old->nangles < 0 || nrep*old->nangles > MAXBIGINT ||
nrep*old->ndihedrals < 0 || nrep*old->ndihedrals > MAXBIGINT ||
nrep*old->nimpropers < 0 || nrep*old->nimpropers > MAXBIGINT)
error->all("Replicated system is too big");
// assign atom and topology counts in new class from old one
atom->natoms = old->natoms * nrep;
atom->nbonds = old->nbonds * nrep;
atom->nangles = old->nangles * nrep;
atom->ndihedrals = old->ndihedrals * nrep;
atom->nimpropers = old->nimpropers * nrep;
atom->ntypes = old->ntypes;
atom->nbondtypes = old->nbondtypes;
atom->nangletypes = old->nangletypes;
atom->ndihedraltypes = old->ndihedraltypes;
atom->nimpropertypes = old->nimpropertypes;
atom->bond_per_atom = old->bond_per_atom;
atom->angle_per_atom = old->angle_per_atom;
atom->dihedral_per_atom = old->dihedral_per_atom;
atom->improper_per_atom = old->improper_per_atom;
// store old simulation box
int triclinic = domain->triclinic;
double old_xprd = domain->xprd;
double old_yprd = domain->yprd;
double old_zprd = domain->zprd;
double old_xy = domain->xy;
double old_xz = domain->xz;
double old_yz = domain->yz;
// setup new simulation box
domain->boxhi[0] = domain->boxlo[0] + nx*old_xprd;
domain->boxhi[1] = domain->boxlo[1] + ny*old_yprd;
domain->boxhi[2] = domain->boxlo[2] + nz*old_zprd;
if (triclinic) {
domain->xy *= ny;
domain->xz *= nz;
domain->yz *= nz;
}
// new problem setup using new box boundaries
if (nprocs == 1) n = static_cast<int> (atom->natoms);
else n = static_cast<int> (LB_FACTOR * atom->natoms / nprocs);
atom->allocate_type_arrays();
atom->avec->grow(n);
n = atom->nmax;
domain->print_box(" ");
domain->set_initial_box();
domain->set_global_box();
comm->set_procs();
domain->set_local_box();
// copy type arrays to new atom class
if (atom->mass) {
for (int itype = 1; itype <= atom->ntypes; itype++) {
atom->mass_setflag[itype] = old->mass_setflag[itype];
if (atom->mass_setflag[itype]) atom->mass[itype] = old->mass[itype];
}
}
if (atom->shape) {
for (int itype = 1; itype <= atom->ntypes; itype++) {
atom->shape_setflag[itype] = old->shape_setflag[itype];
if (atom->shape_setflag[itype]) {
atom->shape[itype][0] = old->shape[itype][0];
atom->shape[itype][1] = old->shape[itype][1];
atom->shape[itype][2] = old->shape[itype][2];
}
}
}
if (atom->dipole) {
for (int itype = 1; itype <= atom->ntypes; itype++) {
atom->dipole_setflag[itype] = old->dipole_setflag[itype];
if (atom->dipole_setflag[itype])
atom->dipole[itype] = old->dipole[itype];
}
}
// set bounds for my proc
// if periodic and I am lo/hi proc, adjust bounds by EPSILON
// insures all replicated atoms will be owned even with round-off
double sublo[3],subhi[3];
if (triclinic == 0) {
sublo[0] = domain->sublo[0]; subhi[0] = domain->subhi[0];
sublo[1] = domain->sublo[1]; subhi[1] = domain->subhi[1];
sublo[2] = domain->sublo[2]; subhi[2] = domain->subhi[2];
} else {
sublo[0] = domain->sublo_lamda[0]; subhi[0] = domain->subhi_lamda[0];
sublo[1] = domain->sublo_lamda[1]; subhi[1] = domain->subhi_lamda[1];
sublo[2] = domain->sublo_lamda[2]; subhi[2] = domain->subhi_lamda[2];
}
if (domain->xperiodic) {
if (comm->myloc[0] == 0) sublo[0] -= EPSILON;
if (comm->myloc[0] == comm->procgrid[0]-1) subhi[0] += EPSILON;
}
if (domain->yperiodic) {
if (comm->myloc[1] == 0) sublo[1] -= EPSILON;
if (comm->myloc[1] == comm->procgrid[1]-1) subhi[1] += EPSILON;
}
if (domain->zperiodic) {
if (comm->myloc[2] == 0) sublo[2] -= EPSILON;
if (comm->myloc[2] == comm->procgrid[2]-1) subhi[2] += EPSILON;
}
// loop over all procs
// if this iteration of loop is me:
// pack my unmapped atom data into buf
// bcast it to all other procs
// performs 3d replicate loop with while loop over atoms in buf
// x = new replicated position, remapped into simulation box
// unpack atom into new atom class from buf if I own it
// adjust tag, mol #, coord, topology info as needed
AtomVec *old_avec = old->avec;
AtomVec *avec = atom->avec;
int ix,iy,iz,image,atom_offset,mol_offset;
double x[3],lamda[3];
double *coord;
int tag_enable = atom->tag_enable;
for (int iproc = 0; iproc < nprocs; iproc++) {
if (me == iproc) {
n = 0;
for (i = 0; i < old->nlocal; i++) n += old_avec->pack_restart(i,&buf[n]);
}
MPI_Bcast(&n,1,MPI_INT,iproc,world);
MPI_Bcast(buf,n,MPI_DOUBLE,iproc,world);
for (ix = 0; ix < nx; ix++) {
for (iy = 0; iy < ny; iy++) {
for (iz = 0; iz < nz; iz++) {
// while loop over one proc's atom list
m = 0;
while (m < n) {
image = (512 << 20) | (512 << 10) | 512;
if (triclinic == 0) {
x[0] = buf[m+1] + ix*old_xprd;
x[1] = buf[m+2] + iy*old_yprd;
x[2] = buf[m+3] + iz*old_zprd;
} else {
x[0] = buf[m+1] + ix*old_xprd + iy*old_xy + iz*old_xz;
x[1] = buf[m+2] + iy*old_yprd + iz*old_yz;
x[2] = buf[m+3] + iz*old_zprd;
}
domain->remap(x,image);
if (triclinic) {
domain->x2lamda(x,lamda);
coord = lamda;
} else coord = x;
if (coord[0] >= sublo[0] && coord[0] < subhi[0] &&
coord[1] >= sublo[1] && coord[1] < subhi[1] &&
coord[2] >= sublo[2] && coord[2] < subhi[2]) {
m += avec->unpack_restart(&buf[m]);
i = atom->nlocal - 1;
if (tag_enable)
atom_offset = iz*ny*nx*maxtag + iy*nx*maxtag + ix*maxtag;
else atom_offset = 0;
mol_offset = iz*ny*nx*maxmol + iy*nx*maxmol + ix*maxmol;
atom->x[i][0] = x[0];
atom->x[i][1] = x[1];
atom->x[i][2] = x[2];
atom->tag[i] += atom_offset;
atom->image[i] = image;
if (atom->molecular) {
if (atom->molecule[i] > 0)
atom->molecule[i] += mol_offset;
if (atom->avec->bonds_allow)
for (j = 0; j < atom->num_bond[i]; j++)
atom->bond_atom[i][j] += atom_offset;
if (atom->avec->angles_allow)
for (j = 0; j < atom->num_angle[i]; j++) {
atom->angle_atom1[i][j] += atom_offset;
atom->angle_atom2[i][j] += atom_offset;
atom->angle_atom3[i][j] += atom_offset;
}
if (atom->avec->dihedrals_allow)
for (j = 0; j < atom->num_dihedral[i]; j++) {
atom->dihedral_atom1[i][j] += atom_offset;
atom->dihedral_atom2[i][j] += atom_offset;
atom->dihedral_atom3[i][j] += atom_offset;
atom->dihedral_atom4[i][j] += atom_offset;
}
if (atom->avec->impropers_allow)
for (j = 0; j < atom->num_improper[i]; j++) {
atom->improper_atom1[i][j] += atom_offset;
atom->improper_atom2[i][j] += atom_offset;
atom->improper_atom3[i][j] += atom_offset;
atom->improper_atom4[i][j] += atom_offset;
}
}
} else m += static_cast<int> (buf[m]);
}
}
}
}
} // end of proc loop
// free communication buffer and old atom class
memory->sfree(buf);
delete old;
// check that all atoms were assigned to procs
bigint natoms;
bigint nblocal = atom->nlocal;
MPI_Allreduce(&nblocal,&natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);
if (me == 0) {
if (screen) fprintf(screen," " BIGINT_FORMAT " atoms\n",natoms);
if (logfile) fprintf(logfile," " BIGINT_FORMAT " atoms\n",natoms);
}
if (natoms != atom->natoms)
error->all("Replicate did not assign all atoms correctly");
if (me == 0) {
if (atom->nbonds) {
if (screen) fprintf(screen," " BIGINT_FORMAT " bonds\n",atom->nbonds);
if (logfile) fprintf(logfile," " BIGINT_FORMAT " bonds\n",atom->nbonds);
}
if (atom->nangles) {
if (screen) fprintf(screen," " BIGINT_FORMAT " angles\n",
atom->nangles);
if (logfile) fprintf(logfile," " BIGINT_FORMAT " angles\n",
atom->nangles);
}
if (atom->ndihedrals) {
if (screen) fprintf(screen," " BIGINT_FORMAT " dihedrals\n",
atom->ndihedrals);
if (logfile) fprintf(logfile," " BIGINT_FORMAT " dihedrals\n",
atom->ndihedrals);
}
if (atom->nimpropers) {
if (screen) fprintf(screen," " BIGINT_FORMAT " impropers\n",
atom->nimpropers);
if (logfile) fprintf(logfile," " BIGINT_FORMAT " impropers\n",
atom->nimpropers);
}
}
// create global mapping and bond topology now that system is defined
if (atom->map_style) {
atom->nghost = 0;
atom->map_init();
atom->map_set();
}
if (atom->molecular) {
Special special(lmp);
special.build();
}
}
diff --git a/src/run.cpp b/src/run.cpp
index e5a1b318e..7ed02bd2b 100644
--- a/src/run.cpp
+++ b/src/run.cpp
@@ -1,252 +1,252 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "stdlib.h"
#include "string.h"
#include "run.h"
-#include "lmptype.h"
#include "domain.h"
#include "update.h"
#include "integrate.h"
#include "modify.h"
#include "output.h"
#include "finish.h"
#include "input.h"
#include "timer.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
#define MAXLINE 2048
/* ---------------------------------------------------------------------- */
Run::Run(LAMMPS *lmp) : Pointers(lmp) {}
/* ---------------------------------------------------------------------- */
void Run::command(int narg, char **arg)
{
if (narg < 1) error->all("Illegal run command");
if (domain->box_exist == 0)
error->all("Run command before simulation box is defined");
bigint nsteps_input = ATOBIGINT(arg[0]);
// parse optional args
int uptoflag = 0;
int startflag = 0;
int stopflag = 0;
bigint start,stop;
int preflag = 1;
int postflag = 1;
int nevery = 0;
int ncommands = 0;
int first,last;
int iarg = 1;
while (iarg < narg) {
if (strcmp(arg[iarg],"upto") == 0) {
if (iarg+1 > narg) error->all("Illegal run command");
uptoflag = 1;
iarg += 1;
} else if (strcmp(arg[iarg],"start") == 0) {
if (iarg+2 > narg) error->all("Illegal run command");
startflag = 1;
start = ATOBIGINT(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"stop") == 0) {
if (iarg+2 > narg) error->all("Illegal run command");
stopflag = 1;
stop = ATOBIGINT(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"pre") == 0) {
if (iarg+2 > narg) error->all("Illegal run command");
if (strcmp(arg[iarg+1],"no") == 0) preflag = 0;
else if (strcmp(arg[iarg+1],"yes") == 0) preflag = 1;
else error->all("Illegal run command");
iarg += 2;
} else if (strcmp(arg[iarg],"post") == 0) {
if (iarg+2 > narg) error->all("Illegal run command");
if (strcmp(arg[iarg+1],"no") == 0) postflag = 0;
else if (strcmp(arg[iarg+1],"yes") == 0) postflag = 1;
else error->all("Illegal run command");
iarg += 2;
// all remaining args are commands
// first,last = arg index of first/last commands
// set ncommands = 0 if single command and it is NULL
} else if (strcmp(arg[iarg],"every") == 0) {
if (iarg+3 > narg) error->all("Illegal run command");
nevery = atoi(arg[iarg+1]);
if (nevery <= 0) error->all("Illegal run command");
first = iarg+2;
last = narg-1;
ncommands = last-first + 1;
if (ncommands == 1 && strcmp(arg[first],"NULL") == 0) ncommands = 0;
iarg = narg;
} else error->all("Illegal run command");
}
// set nsteps as integer, using upto value if specified
int nsteps;
if (!uptoflag) {
if (nsteps_input < 0 || nsteps_input > MAXSMALLINT)
error->all("Invalid run command N value");
nsteps = static_cast<int> (nsteps_input);
} else {
bigint delta = nsteps_input - update->ntimestep;
if (delta < 0 || delta > MAXSMALLINT)
error->all("Invalid run command upto value");
nsteps = static_cast<int> (delta);
}
// error check
if (startflag) {
if (start < 0 || start > MAXBIGINT)
error->all("Invalid run command start/stop value");
if (start > update->ntimestep)
error->all("Run command start value is after start of run");
}
if (stopflag) {
if (stop < 0 || stop > MAXBIGINT)
error->all("Invalid run command start/stop value");
if (stop < update->ntimestep + nsteps)
error->all("Run command stop value is before end of run");
}
// if nevery, make copies of arg strings that are commands
// required because re-parsing commands via input->one() will wipe out args
char **commands = NULL;
if (nevery && ncommands > 0) {
commands = new char*[ncommands];
ncommands = 0;
for (int i = first; i <= last; i++) {
int n = strlen(arg[i]) + 1;
commands[ncommands] = new char[n];
strcpy(commands[ncommands],arg[i]);
ncommands++;
}
}
// perform a single run
// use start/stop to set begin/end step
// if pre or 1st run, do System init/setup,
// else just init timer and setup output
// if post, do full Finish, else just print time
update->whichflag = 1;
if (nevery == 0) {
update->nsteps = nsteps;
update->firststep = update->ntimestep;
update->laststep = update->ntimestep + nsteps;
if (update->laststep < 0 || update->laststep > MAXBIGINT)
error->all("Too many timesteps");
if (startflag) update->beginstep = start;
else update->beginstep = update->firststep;
if (stopflag) update->endstep = stop;
else update->endstep = update->laststep;
if (preflag || update->first_update == 0) {
lmp->init();
update->integrate->setup();
} else {
timer->init();
output->setup(0);
}
timer->barrier_start(TIME_LOOP);
update->integrate->run(nsteps);
timer->barrier_stop(TIME_LOOP);
update->integrate->cleanup();
Finish finish(lmp);
finish.end(postflag);
// perform multiple runs optionally interleaved with invocation command(s)
// use start/stop to set begin/end step
// if pre or 1st iteration of multiple runs, do System init/setup,
// else just init timer and setup output
// if post or last iteration, do full Finish, else just print time
} else {
int iter = 0;
int nleft = nsteps;
while (nleft > 0 || iter == 0) {
nsteps = MIN(nleft,nevery);
update->nsteps = nsteps;
update->firststep = update->ntimestep;
update->laststep = update->ntimestep + nsteps;
if (update->laststep < 0 || update->laststep > MAXBIGINT)
error->all("Too many timesteps");
if (startflag) update->beginstep = start;
else update->beginstep = update->firststep;
if (stopflag) update->endstep = stop;
else update->endstep = update->laststep;
if (preflag || iter == 0) {
lmp->init();
update->integrate->setup();
} else {
timer->init();
output->setup(0);
}
timer->barrier_start(TIME_LOOP);
update->integrate->run(nsteps);
timer->barrier_stop(TIME_LOOP);
update->integrate->cleanup();
Finish finish(lmp);
if (postflag || nleft <= nsteps) finish.end(1);
else finish.end(0);
// wrap command invocation with clearstep/addstep
// since a command may invoke computes via variables
if (ncommands) {
modify->clearstep_compute();
for (int i = 0; i < ncommands; i++)
char *command = input->one(commands[i]);
modify->addstep_compute(update->ntimestep + nevery);
}
nleft -= nsteps;
iter++;
}
}
update->whichflag = 0;
update->firststep = update->laststep = 0;
update->beginstep = update->endstep = 0;
if (commands) {
for (int i = 0; i < ncommands; i++) delete [] commands[i];
delete [] commands;
}
}
diff --git a/src/thermo.h b/src/thermo.h
index 8b954ebb8..0d000b0e1 100644
--- a/src/thermo.h
+++ b/src/thermo.h
@@ -1,179 +1,179 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifndef LMP_THERMO_H
#define LMP_THERMO_H
-#include "pointers.h"
#include "lmptype.h"
+#include "pointers.h"
namespace LAMMPS_NS {
class Thermo : protected Pointers {
friend class WriteRestart; // accesses lostflag
friend class MinCG; // accesses compute_pe
public:
char *style;
int normflag; // 0 if do not normalize by atoms, 1 if normalize
int modified; // 1 if thermo_modify has been used, else 0
Thermo(class LAMMPS *, int, char **);
~Thermo();
void init();
bigint lost_check();
void modify_params(int, char **);
void header();
void compute(int);
int evaluate_keyword(char *, double *);
private:
int me;
char *line;
int nfield,nfield_initial;
char **keyword;
int *vtype;
char **format,**format_user;
char *format_float_one_def,*format_float_multi_def;
char *format_int_one_def,*format_int_multi_def;
char *format_float_user,*format_int_user,*format_bigint_user;
char format_multi[128];
char format_bigint_one_def[8],format_bigint_multi_def[8];
int normvalue; // use this for normflag unless natoms = 0
int normuserflag; // 0 if user has not set, 1 if has
int normuser;
int firststep;
int lostflag,lostbefore;
int flushflag,lineflag;
double last_tpcpu,last_spcpu;
double last_time;
bigint last_step;
bigint natoms;
// data used by routines that compute single values
int ivalue; // integer value to print
double dvalue; // double value to print
bigint bivalue; // big integer value to print
int ifield; // which field in thermo output is being computed
int *field2index; // which compute,fix,variable calcs this field
int *argindex1; // indices into compute,fix scalar,vector
int *argindex2;
// data for keyword-specific Compute objects
// index = where they are in computes list
// id = ID of Compute objects
// Compute * = ptrs to the Compute objects
int index_temp,index_press_scalar,index_press_vector,index_pe;
char *id_temp,*id_press,*id_pe;
class Compute *temperature,*pressure,*pe;
int ncompute; // # of Compute objects called by thermo
char **id_compute; // their IDs
int *compute_which; // 0/1 if should call scalar() or vector()
class Compute **computes; // list of ptrs to the Compute objects
int nfix; // # of Fix objects called by thermo
char **id_fix; // their IDs
class Fix **fixes; // list of ptrs to the Fix objects
int nvariable; // # of variables evaulated by thermo
char **id_variable; // list of variable names
int *variables; // list of Variable indices
// private methods
void allocate();
void deallocate();
void parse_fields(char *);
int add_compute(const char *, int);
int add_fix(const char *);
int add_variable(const char *);
typedef void (Thermo::*FnPtr)();
void addfield(const char *, FnPtr, int);
FnPtr *vfunc; // list of ptrs to functions
void compute_compute(); // functions that compute a single value
void compute_fix(); // via calls to Compute,Fix,Variable classes
void compute_variable();
// functions that compute a single value
// customize a new keyword by adding a method prototype
void compute_step();
void compute_elapsed();
void compute_elapsed_long();
void compute_dt();
void compute_cpu();
void compute_tpcpu();
void compute_spcpu();
void compute_atoms();
void compute_temp();
void compute_press();
void compute_pe();
void compute_ke();
void compute_etotal();
void compute_enthalpy();
void compute_evdwl();
void compute_ecoul();
void compute_epair();
void compute_ebond();
void compute_eangle();
void compute_edihed();
void compute_eimp();
void compute_emol();
void compute_elong();
void compute_etail();
void compute_vol();
void compute_lx();
void compute_ly();
void compute_lz();
void compute_xlo();
void compute_xhi();
void compute_ylo();
void compute_yhi();
void compute_zlo();
void compute_zhi();
void compute_xy();
void compute_xz();
void compute_yz();
void compute_xlat();
void compute_ylat();
void compute_zlat();
void compute_pxx();
void compute_pyy();
void compute_pzz();
void compute_pxy();
void compute_pyz();
void compute_pxz();
void compute_fmax();
void compute_fnorm();
};
}
#endif
diff --git a/src/update.h b/src/update.h
index 75edc7e2f..b713c4c11 100644
--- a/src/update.h
+++ b/src/update.h
@@ -1,60 +1,60 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifndef LMP_UPDATE_H
#define LMP_UPDATE_H
-#include "pointers.h"
#include "lmptype.h"
+#include "pointers.h"
namespace LAMMPS_NS {
class Update : protected Pointers {
public:
double dt; // timestep
double etol,ftol; // minimizer tolerances on energy/force
bigint ntimestep; // current step (dynamics or min iterations)
int nsteps; // # of steps to run (dynamics or min iter)
int whichflag; // 0 for unset, 1 for dynamics, 2 for min
bigint firststep,laststep; // 1st & last step of this run
bigint beginstep,endstep; // 1st and last step of multiple runs
int first_update; // 0 before initial update, 1 after
int max_eval; // max force evaluations for minimizer
int restrict_output; // 1 if output should not write dump/restart
int setupflag; // set when setup() is computing forces
int multireplica; // 1 if min across replicas, else 0
bigint eflag_global,eflag_atom; // timestep global/peratom eng is tallied on
bigint vflag_global,vflag_atom; // ditto for virial
char *unit_style;
class Integrate *integrate;
char *integrate_style;
class Min *minimize;
char *minimize_style;
Update(class LAMMPS *);
~Update();
void init();
void set_units(const char *);
void create_integrate(int, char **);
void create_minimize(int, char **);
void reset_timestep(int, char **);
double memory_usage();
};
}
#endif
diff --git a/src/velocity.cpp b/src/velocity.cpp
index 06032e648..77545a86f 100644
--- a/src/velocity.cpp
+++ b/src/velocity.cpp
@@ -1,799 +1,799 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "mpi.h"
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "velocity.h"
-#include "lmptype.h"
#include "atom.h"
#include "update.h"
#include "domain.h"
#include "lattice.h"
#include "input.h"
#include "variable.h"
#include "force.h"
#include "modify.h"
#include "compute.h"
#include "compute_temp.h"
#include "random_park.h"
#include "group.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
enum{CREATE,SET,SCALE,RAMP,ZERO};
enum{ALL,LOCAL,GEOM};
enum{NONE,CONSTANT,EQUAL,ATOM};
#define WARMUP 100
#define SMALL 0.001
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
/* ---------------------------------------------------------------------- */
Velocity::Velocity(LAMMPS *lmp) : Pointers(lmp) {}
/* ---------------------------------------------------------------------- */
void Velocity::command(int narg, char **arg)
{
if (narg < 2) error->all("Illegal velocity command");
if (domain->box_exist == 0)
error->all("Velocity command before simulation box is defined");
if (atom->natoms == 0)
error->all("Velocity command with no atoms existing");
// atom masses must all be set
atom->check_mass();
// identify group
igroup = group->find(arg[0]);
if (igroup == -1) error->all("Could not find velocity group ID");
groupbit = group->bitmask[igroup];
// identify style
if (strcmp(arg[1],"create") == 0) style = CREATE;
else if (strcmp(arg[1],"set") == 0) style = SET;
else if (strcmp(arg[1],"scale") == 0) style = SCALE;
else if (strcmp(arg[1],"ramp") == 0) style = RAMP;
else if (strcmp(arg[1],"zero") == 0) style = ZERO;
else error->all("Illegal velocity command");
// set defaults
temperature = NULL;
dist_flag = 0;
sum_flag = 0;
momentum_flag = 1;
rotation_flag = 0;
loop_flag = ALL;
scale_flag = 1;
// read options from end of input line
// change defaults as options specify
if (style == CREATE) options(narg-4,&arg[4]);
else if (style == SET) options(narg-5,&arg[5]);
else if (style == SCALE) options(narg-3,&arg[3]);
else if (style == RAMP) options(narg-8,&arg[8]);
else if (style == ZERO) options(narg-3,&arg[3]);
// initialize velocities based on style
// create() invoked differently, so can be called externally
if (style == CREATE) {
double t_desired = atof(arg[2]);
int seed = atoi(arg[3]);
create(t_desired,seed);
}
else if (style == SET) set(narg-2,&arg[2]);
else if (style == SCALE) scale(narg-2,&arg[2]);
else if (style == RAMP) ramp(narg-2,&arg[2]);
else if (style == ZERO) zero(narg-2,&arg[2]);
}
/* ----------------------------------------------------------------------
initialization of defaults before calling velocity methods externaly
------------------------------------------------------------------------- */
void Velocity::init_external(char *extgroup)
{
igroup = group->find(extgroup);
if (igroup == -1) error->all("Could not find velocity group ID");
groupbit = group->bitmask[igroup];
temperature = NULL;
dist_flag = 0;
sum_flag = 0;
momentum_flag = 1;
rotation_flag = 0;
loop_flag = ALL;
scale_flag = 1;
}
/* ---------------------------------------------------------------------- */
void Velocity::create(double t_desired, int seed)
{
int i;
if (seed <= 0) error->all("Illegal velocity create command");
// if temperature = NULL, create a new ComputeTemp with the velocity group
int tflag = 0;
if (temperature == NULL) {
char **arg = new char*[3];
arg[0] = (char *) "velocity_temp";
arg[1] = group->names[igroup];
arg[2] = (char *) "temp";
temperature = new ComputeTemp(lmp,3,arg);
tflag = 1;
delete [] arg;
}
// initialize temperature computation
// warn if groups don't match
if (igroup != temperature->igroup && comm->me == 0)
error->warning("Mismatch between velocity and compute groups");
temperature->init();
// store a copy of current velocities
double **v = atom->v;
int nlocal = atom->nlocal;
double **vhold = memory->create_2d_double_array(nlocal,3,"velocity:vnew");
for (i = 0; i < nlocal; i++) {
vhold[i][0] = v[i][0];
vhold[i][1] = v[i][1];
vhold[i][2] = v[i][2];
}
// create new velocities, in uniform or gaussian distribution
// loop option determines looping style, ALL is default
// ALL = loop over all natoms, only set those I own via atom->map
// cannot do this if atom IDs do not span 1-Natoms (some were deleted)
// will produce same V, independent of P, if atoms were read-in
// will NOT produce same V, independent of P, if used create_atoms
// LOCAL = only loop over my atoms, adjust RNG to be proc-specific
// will never produce same V, independent of P
// GEOM = only loop over my atoms
// choose RNG for each atom based on its xyz coord (geometry)
// via random->reset()
// will always produce same V, independent of P
// adjust by factor for atom mass
// for 2d, set Vz to 0.0
double *rmass = atom->rmass;
double *mass = atom->mass;
int *type = atom->type;
int *mask = atom->mask;
int dimension = domain->dimension;
int m;
double vx,vy,vz,factor;
RanPark *random;
if (loop_flag == ALL) {
// create an atom map if one doesn't exist already
int mapflag = 0;
if (atom->map_style == 0) {
mapflag = 1;
atom->map_style = 1;
atom->nghost = 0;
atom->map_init();
atom->map_set();
}
// error check
if (atom->natoms > MAXSMALLINT)
error->all("Too big a problem to use velocity create loop all");
if (atom->tag_enable == 0)
error->all("Cannot use velocity create loop all unless atoms have IDs");
if (atom->tag_consecutive() == 0)
error->all("Atom IDs must be consecutive for velocity create loop all");
// loop over all atoms in system
// generate RNGs for all atoms, only assign to ones I own
// use either per-type mass or per-atom rmass
random = new RanPark(lmp,seed);
int natoms = static_cast<int> (atom->natoms);
for (i = 1; i <= natoms; i++) {
if (dist_flag == 0) {
vx = random->uniform();
vy = random->uniform();
vz = random->uniform();
} else {
vx = random->gaussian();
vy = random->gaussian();
vz = random->gaussian();
}
m = atom->map(i);
if (m >= 0 && m < nlocal) {
if (mask[m] & groupbit) {
if (rmass) factor = 1.0/sqrt(rmass[m]);
else factor = 1.0/sqrt(mass[type[m]]);
v[m][0] = vx * factor;
v[m][1] = vy * factor;
if (dimension == 3) v[m][2] = vz * factor;
else v[m][2] = 0.0;
}
}
}
// delete temporary atom map
if (mapflag) {
atom->map_delete();
atom->map_style = 0;
}
} else if (loop_flag == LOCAL) {
random = new RanPark(lmp,seed + comm->me);
for (i = 0; i < WARMUP; i++) random->uniform();
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (dist_flag == 0) {
vx = random->uniform();
vy = random->uniform();
vz = random->uniform();
} else {
vx = random->gaussian();
vy = random->gaussian();
vz = random->gaussian();
}
if (rmass) factor = 1.0/sqrt(rmass[i]);
else factor = 1.0/sqrt(mass[type[i]]);
v[i][0] = vx * factor;
v[i][1] = vy * factor;
if (dimension == 3) v[i][2] = vz * factor;
else v[i][2] = 0.0;
}
}
} else if (loop_flag == GEOM) {
random = new RanPark(lmp,1);
double **x = atom->x;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
random->reset(seed,x[i]);
if (dist_flag == 0) {
vx = random->uniform();
vy = random->uniform();
vz = random->uniform();
} else {
vx = random->gaussian();
vy = random->gaussian();
vz = random->gaussian();
}
if (rmass) factor = 1.0/sqrt(rmass[i]);
else factor = 1.0/sqrt(mass[type[i]]);
v[i][0] = vx * factor;
v[i][1] = vy * factor;
if (dimension == 3) v[i][2] = vz * factor;
else v[i][2] = 0.0;
}
}
}
// apply momentum and rotation zeroing
if (momentum_flag) zero_momentum();
if (rotation_flag) zero_rotation();
// scale temp to desired value
double t = temperature->compute_scalar();
rescale(t,t_desired);
// if sum_flag set, add back in previous velocities
if (sum_flag) {
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
v[i][0] += vhold[i][0];
v[i][1] += vhold[i][1];
v[i][2] += vhold[i][2];
}
}
}
// free local memory
// if temperature was created, delete it
memory->destroy_2d_double_array(vhold);
delete random;
if (tflag) delete temperature;
}
/* ---------------------------------------------------------------------- */
void Velocity::set(int narg, char **arg)
{
int xstyle,ystyle,zstyle,varflag;
double vx,vy,vz;
char *xstr,*ystr,*zstr;
int xvar,yvar,zvar;
// parse 3 args
xstyle = ystyle = zstyle = CONSTANT;
xstr = ystr = zstr = NULL;
if (strstr(arg[0],"v_") == arg[0]) {
int n = strlen(&arg[0][2]) + 1;
xstr = new char[n];
strcpy(xstr,&arg[0][2]);
} else if (strcmp(arg[0],"NULL") == 0) xstyle = NONE;
else vx = atof(arg[0]);
if (strstr(arg[1],"v_") == arg[1]) {
int n = strlen(&arg[1][2]) + 1;
ystr = new char[n];
strcpy(ystr,&arg[1][2]);
} else if (strcmp(arg[1],"NULL") == 0) ystyle = NONE;
else vy = atof(arg[1]);
if (strstr(arg[2],"v_") == arg[2]) {
int n = strlen(&arg[2][2]) + 1;
zstr = new char[n];
strcpy(zstr,&arg[2][2]);
} else if (strcmp(arg[2],"NULL") == 0) zstyle = NONE;
else vz = atof(arg[2]);
// set and apply scale factors
xscale = yscale = zscale = 1.0;
if (xstyle && !xstr) {
if (scale_flag && domain->lattice == NULL)
error->all("Use of velocity with undefined lattice");
if (scale_flag) xscale = domain->lattice->xlattice;
vx *= xscale;
}
if (ystyle && !ystr) {
if (scale_flag && domain->lattice == NULL)
error->all("Use of velocity with undefined lattice");
if (scale_flag) yscale = domain->lattice->ylattice;
vy *= yscale;
}
if (zstyle && !zstr) {
if (scale_flag && domain->lattice == NULL)
error->all("Use of velocity with undefined lattice");
if (scale_flag) zscale = domain->lattice->zlattice;
vz *= zscale;
}
// check variables
if (xstr) {
xvar = input->variable->find(xstr);
if (xvar < 0) error->all("Variable name for velocity set does not exist");
if (input->variable->equalstyle(xvar)) xstyle = EQUAL;
else if (input->variable->atomstyle(xvar)) xstyle = ATOM;
else error->all("Variable for velocity set is invalid style");
}
if (ystr) {
yvar = input->variable->find(ystr);
if (yvar < 0) error->all("Variable name for velocity set does not exist");
if (input->variable->equalstyle(yvar)) ystyle = EQUAL;
else if (input->variable->atomstyle(yvar)) ystyle = ATOM;
else error->all("Variable for velocity set is invalid style");
}
if (zstr) {
zvar = input->variable->find(zstr);
if (zvar < 0) error->all("Variable name for velocity set does not exist");
if (input->variable->equalstyle(zvar)) zstyle = EQUAL;
else if (input->variable->atomstyle(zvar)) zstyle = ATOM;
else error->all("Variable for velocity set is invalid style");
}
if (xstyle == ATOM || ystyle == ATOM || zstyle == ATOM)
varflag = ATOM;
else if (xstyle == EQUAL || ystyle == EQUAL || zstyle == EQUAL)
varflag = EQUAL;
else varflag = CONSTANT;
// error check for 2d models
if (domain->dimension == 2) {
if (zstyle == CONSTANT && vz != 0.0)
error->all("Cannot set non-zero z velocity for 2d simulation");
if (zstyle == EQUAL || zstyle == ATOM)
error->all("Cannot set varaible z velocity for 2d simulation");
}
// allocate vfield array if necessary
double **vfield = NULL;
if (varflag == ATOM)
vfield = memory->create_2d_double_array(atom->nlocal,3,"velocity:vfield");
// set velocities via constants
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (varflag == CONSTANT) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (sum_flag == 0) {
if (xstyle) v[i][0] = vx;
if (ystyle) v[i][1] = vy;
if (zstyle) v[i][2] = vz;
} else {
if (xstyle) v[i][0] += vx;
if (ystyle) v[i][1] += vy;
if (zstyle) v[i][2] += vz;
}
}
}
// set velocities via variables
} else {
if (xstyle == EQUAL) vx = input->variable->compute_equal(xvar);
else if (xstyle == ATOM)
input->variable->compute_atom(xvar,igroup,&vfield[0][0],3,0);
if (ystyle == EQUAL) vy = input->variable->compute_equal(yvar);
else if (ystyle == ATOM)
input->variable->compute_atom(yvar,igroup,&vfield[0][1],3,0);
if (zstyle == EQUAL) vz = input->variable->compute_equal(zvar);
else if (zstyle == ATOM)
input->variable->compute_atom(zvar,igroup,&vfield[0][2],3,0);
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (sum_flag == 0) {
if (xstyle == ATOM) v[i][0] = vfield[i][0];
else if (xstyle) v[i][0] = vx;
if (ystyle == ATOM) v[i][1] = vfield[i][1];
else if (ystyle) v[i][1] = vy;
if (zstyle == ATOM) v[i][2] = vfield[i][2];
else if (zstyle) v[i][2] = vz;
} else {
if (xstyle == ATOM) v[i][0] += vfield[i][0];
else if (xstyle) v[i][0] += vx;
if (ystyle == ATOM) v[i][1] += vfield[i][1];
else if (ystyle) v[i][1] += vy;
if (zstyle == ATOM) v[i][2] += vfield[i][2];
else if (zstyle) v[i][2] += vz;
}
}
}
// clean up
delete [] xstr;
delete [] ystr;
delete [] zstr;
memory->destroy_2d_double_array(vfield);
}
/* ----------------------------------------------------------------------
rescale velocities of a group after computing its temperature
------------------------------------------------------------------------- */
void Velocity::scale(int narg, char **arg)
{
double t_desired = atof(arg[0]);
// if temperature = NULL, create a new ComputeTemp with the velocity group
int tflag = 0;
if (temperature == NULL) {
char **arg = new char*[3];
arg[0] = (char *) "velocity_temp";
arg[1] = group->names[igroup];
arg[2] = (char *) "temp";
temperature = new ComputeTemp(lmp,3,arg);
tflag = 1;
delete [] arg;
}
// initialize temperature computation
// warn if groups don't match
if (igroup != temperature->igroup && comm->me == 0)
error->warning("Mismatch between velocity and compute groups");
temperature->init();
// scale temp to desired value
double t = temperature->compute_scalar();
rescale(t,t_desired);
// if temperature was created, delete it
if (tflag) delete temperature;
}
/* ----------------------------------------------------------------------
apply a ramped set of velocities
------------------------------------------------------------------------- */
void Velocity::ramp(int narg, char **arg)
{
// set scale factors
if (scale_flag && domain->lattice == NULL)
error->all("Use of velocity with undefined lattice");
if (scale_flag) {
xscale = domain->lattice->xlattice;
yscale = domain->lattice->ylattice;
zscale = domain->lattice->zlattice;
}
else xscale = yscale = zscale = 1.0;
// parse args
int v_dim;
if (strcmp(arg[0],"vx") == 0) v_dim = 0;
else if (strcmp(arg[0],"vy") == 0) v_dim = 1;
else if (strcmp(arg[0],"vz") == 0) v_dim = 2;
else error->all("Illegal velocity command");
if (v_dim == 2 && domain->dimension == 2)
error->all("Velocity ramp in z for a 2d problem");
double v_lo,v_hi;
if (v_dim == 0) {
v_lo = xscale*atof(arg[1]);
v_hi = xscale*atof(arg[2]);
} else if (v_dim == 1) {
v_lo = yscale*atof(arg[1]);
v_hi = yscale*atof(arg[2]);
} else if (v_dim == 2) {
v_lo = zscale*atof(arg[1]);
v_hi = zscale*atof(arg[2]);
}
int coord_dim;
if (strcmp(arg[3],"x") == 0) coord_dim = 0;
else if (strcmp(arg[3],"y") == 0) coord_dim = 1;
else if (strcmp(arg[3],"z") == 0) coord_dim = 2;
else error->all("Illegal velocity command");
double coord_lo,coord_hi;
if (coord_dim == 0) {
coord_lo = xscale*atof(arg[4]);
coord_hi = xscale*atof(arg[5]);
} else if (coord_dim == 1) {
coord_lo = yscale*atof(arg[4]);
coord_hi = yscale*atof(arg[5]);
} else if (coord_dim == 2) {
coord_lo = zscale*atof(arg[4]);
coord_hi = zscale*atof(arg[5]);
}
// vramp = ramped velocity component for v_dim
// add or set based on sum_flag
double **x = atom->x;
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double fraction,vramp;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
fraction = (x[i][coord_dim] - coord_lo) / (coord_hi - coord_lo);
fraction = MAX(fraction,0.0);
fraction = MIN(fraction,1.0);
vramp = v_lo + fraction*(v_hi - v_lo);
if (sum_flag) v[i][v_dim] += vramp;
else v[i][v_dim] = vramp;
}
}
/* ----------------------------------------------------------------------
zero linear or angular momentum of a group
------------------------------------------------------------------------- */
void Velocity::zero(int narg, char **arg)
{
if (strcmp(arg[0],"linear") == 0) zero_momentum();
else if (strcmp(arg[0],"angular") == 0) zero_rotation();
else error->all("Illegal velocity command");
}
/* ----------------------------------------------------------------------
rescale velocities of group atoms to t_new from t_old
------------------------------------------------------------------------- */
void Velocity::rescale(double t_old, double t_new)
{
if (t_old == 0.0) error->all("Attempting to rescale a 0.0 temperature");
double factor = sqrt(t_new/t_old);
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
v[i][0] *= factor;
v[i][1] *= factor;
v[i][2] *= factor;
}
}
/* ----------------------------------------------------------------------
zero the linear momentum of a group of atoms by adjusting v by -Vcm
------------------------------------------------------------------------- */
void Velocity::zero_momentum()
{
// cannot have 0 atoms in group
if (group->count(igroup) == 0)
error->all("Cannot zero momentum of 0 atoms");
// compute velocity of center-of-mass of group
double masstotal = group->mass(igroup);
double vcm[3];
group->vcm(igroup,masstotal,vcm);
// adjust velocities by vcm to zero linear momentum
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
v[i][0] -= vcm[0];
v[i][1] -= vcm[1];
v[i][2] -= vcm[2];
}
}
/* ----------------------------------------------------------------------
zero the angular momentum of a group of atoms by adjusting v by -(w x r)
------------------------------------------------------------------------- */
void Velocity::zero_rotation()
{
int i;
// cannot have 0 atoms in group
if (group->count(igroup) == 0)
error->all("Cannot zero momentum of 0 atoms");
// compute omega (angular velocity) of group around center-of-mass
double xcm[3],angmom[3],inertia[3][3],omega[3];
double masstotal = group->mass(igroup);
group->xcm(igroup,masstotal,xcm);
group->angmom(igroup,xcm,angmom);
group->inertia(igroup,xcm,inertia);
group->omega(angmom,inertia,omega);
// adjust velocities to zero omega
// vnew_i = v_i - w x r_i
// must use unwrapped coords to compute r_i correctly
double **x = atom->x;
double **v = atom->v;
int *mask = atom->mask;
int *image = atom->image;
int nlocal = atom->nlocal;
int xbox,ybox,zbox;
double dx,dy,dz;
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
xbox = (image[i] & 1023) - 512;
ybox = (image[i] >> 10 & 1023) - 512;
zbox = (image[i] >> 20) - 512;
dx = (x[i][0] + xbox*xprd) - xcm[0];
dy = (x[i][1] + ybox*yprd) - xcm[1];
dz = (x[i][2] + zbox*zprd) - xcm[2];
v[i][0] -= omega[1]*dz - omega[2]*dy;
v[i][1] -= omega[2]*dx - omega[0]*dz;
v[i][2] -= omega[0]*dy - omega[1]*dx;
}
}
/* ----------------------------------------------------------------------
parse optional parameters at end of velocity input line
------------------------------------------------------------------------- */
void Velocity::options(int narg, char **arg)
{
if (narg < 0) error->all("Illegal velocity command");
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"dist") == 0) {
if (iarg+2 > narg) error->all("Illegal velocity command");
if (strcmp(arg[iarg+1],"uniform") == 0) dist_flag = 0;
else if (strcmp(arg[iarg+1],"gaussian") == 0) dist_flag = 1;
else error->all("Illegal velocity command");
iarg += 2;
} else if (strcmp(arg[iarg],"sum") == 0) {
if (iarg+2 > narg) error->all("Illegal velocity command");
if (strcmp(arg[iarg+1],"no") == 0) sum_flag = 0;
else if (strcmp(arg[iarg+1],"yes") == 0) sum_flag = 1;
else error->all("Illegal velocity command");
iarg += 2;
} else if (strcmp(arg[iarg],"mom") == 0) {
if (iarg+2 > narg) error->all("Illegal velocity command");
if (strcmp(arg[iarg+1],"no") == 0) momentum_flag = 0;
else if (strcmp(arg[iarg+1],"yes") == 0) momentum_flag = 1;
else error->all("Illegal velocity command");
iarg += 2;
} else if (strcmp(arg[iarg],"rot") == 0) {
if (iarg+2 > narg) error->all("Illegal velocity command");
if (strcmp(arg[iarg+1],"no") == 0) rotation_flag = 0;
else if (strcmp(arg[iarg+1],"yes") == 0) rotation_flag = 1;
else error->all("Illegal velocity command");
iarg += 2;
} else if (strcmp(arg[iarg],"temp") == 0) {
if (iarg+2 > narg) error->all("Illegal velocity command");
int icompute;
for (icompute = 0; icompute < modify->ncompute; icompute++)
if (strcmp(arg[iarg+1],modify->compute[icompute]->id) == 0) break;
if (icompute == modify->ncompute)
error->all("Could not find velocity temperature ID");
temperature = modify->compute[icompute];
if (temperature->tempflag == 0)
error->all("Velocity temperature ID does not compute temperature");
iarg += 2;
} else if (strcmp(arg[iarg],"loop") == 0) {
if (iarg+2 > narg) error->all("Illegal velocity command");
if (strcmp(arg[iarg+1],"all") == 0) loop_flag = ALL;
else if (strcmp(arg[iarg+1],"local") == 0) loop_flag = LOCAL;
else if (strcmp(arg[iarg+1],"geom") == 0) loop_flag = GEOM;
else error->all("Illegal velocity command");
iarg += 2;
} else if (strcmp(arg[iarg],"units") == 0) {
if (iarg+2 > narg) error->all("Illegal velocity command");
if (strcmp(arg[iarg+1],"box") == 0) scale_flag = 0;
else if (strcmp(arg[iarg+1],"lattice") == 0) scale_flag = 1;
else error->all("Illegal velocity command");
iarg += 2;
} else error->all("Illegal velocity command");
}
}
diff --git a/src/write_restart.cpp b/src/write_restart.cpp
index 2f2f73a20..0b8bfac43 100644
--- a/src/write_restart.cpp
+++ b/src/write_restart.cpp
@@ -1,512 +1,512 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
+#include "lmptype.h"
#include "mpi.h"
#include "string.h"
#include "write_restart.h"
-#include "lmptype.h"
#include "atom.h"
#include "atom_vec.h"
#include "atom_vec_hybrid.h"
#include "group.h"
#include "force.h"
#include "pair.h"
#include "bond.h"
#include "angle.h"
#include "dihedral.h"
#include "improper.h"
#include "update.h"
#include "neighbor.h"
#include "domain.h"
#include "modify.h"
#include "universe.h"
#include "comm.h"
#include "output.h"
#include "thermo.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MIN(A,B) ((A) < (B)) ? (A) : (B)
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
// same as read_restart.cpp and tools/restart2data.cpp
enum{VERSION,SMALLINT,TAGINT,BIGINT,
UNITS,NTIMESTEP,DIMENSION,NPROCS,PROCGRID_0,PROCGRID_1,PROCGRID_2,
NEWTON_PAIR,NEWTON_BOND,XPERIODIC,YPERIODIC,ZPERIODIC,
BOUNDARY_00,BOUNDARY_01,BOUNDARY_10,BOUNDARY_11,BOUNDARY_20,BOUNDARY_21,
ATOM_STYLE,NATOMS,NTYPES,
NBONDS,NBONDTYPES,BOND_PER_ATOM,
NANGLES,NANGLETYPES,ANGLE_PER_ATOM,
NDIHEDRALS,NDIHEDRALTYPES,DIHEDRAL_PER_ATOM,
NIMPROPERS,NIMPROPERTYPES,IMPROPER_PER_ATOM,
BOXLO_0,BOXHI_0,BOXLO_1,BOXHI_1,BOXLO_2,BOXHI_2,
SPECIAL_LJ_1,SPECIAL_LJ_2,SPECIAL_LJ_3,
SPECIAL_COUL_1,SPECIAL_COUL_2,SPECIAL_COUL_3,
XY,XZ,YZ};
enum{MASS,SHAPE,DIPOLE};
enum{PAIR,BOND,ANGLE,DIHEDRAL,IMPROPER};
enum{IGNORE,WARN,ERROR}; // same as thermo.cpp
/* ---------------------------------------------------------------------- */
WriteRestart::WriteRestart(LAMMPS *lmp) : Pointers(lmp)
{
MPI_Comm_rank(world,&me);
MPI_Comm_size(world,&nprocs);
}
/* ----------------------------------------------------------------------
called as write_restart command in input script
------------------------------------------------------------------------- */
void WriteRestart::command(int narg, char **arg)
{
if (domain->box_exist == 0)
error->all("Write_restart command before simulation box is defined");
if (narg != 1) error->all("Illegal write_restart command");
// if filename contains a "*", replace with current timestep
char *ptr;
int n = strlen(arg[0]) + 16;
char *file = new char[n];
if (ptr = strchr(arg[0],'*')) {
*ptr = '\0';
sprintf(file,"%s" BIGINT_FORMAT "%s",arg[0],update->ntimestep,ptr+1);
} else strcpy(file,arg[0]);
// init entire system since comm->exchange is done
// comm::init needs neighbor::init needs pair::init needs kspace::init, etc
if (comm->me == 0 && screen)
fprintf(screen,"System init for write_restart ...\n");
lmp->init();
// move atoms to new processors before writing file
// enforce PBC before in case atoms are outside box
// call borders() to rebuild atom map since exchange() destroys map
if (domain->triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
domain->reset_box();
comm->setup();
comm->exchange();
comm->borders();
if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
write(file);
delete [] file;
}
/* ----------------------------------------------------------------------
called from command() and directly from output within run/minimize loop
file = final file name to write, except may contain a "%"
------------------------------------------------------------------------- */
void WriteRestart::write(char *file)
{
// special case where reneighboring is not done in integrator
// on timestep restart file is written (due to build_once being set)
// if box is changing, must be reset, else restart file will have
// wrong box size and atoms will be lost when restart file is read
// other calls to pbc and domain and comm are not made,
// b/c they only make sense if reneighboring is actually performed
if (neighbor->build_once) domain->reset_box();
// natoms = sum of nlocal = value to write into restart file
// if unequal and thermo lostflag is "error", don't write restart file
bigint nblocal = atom->nlocal;
MPI_Allreduce(&nblocal,&natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);
if (natoms != atom->natoms && output->thermo->lostflag == ERROR)
error->all("Atom count is inconsistent, cannot write restart file");
// check if filename contains "%"
int multiproc;
if (strchr(file,'%')) multiproc = 1;
else multiproc = 0;
// open single restart file or base file for multiproc case
if (me == 0) {
char *hfile;
if (multiproc) {
hfile = new char[strlen(file) + 16];
char *ptr = strchr(file,'%');
*ptr = '\0';
sprintf(hfile,"%s%s%s",file,"base",ptr+1);
*ptr = '%';
} else hfile = file;
fp = fopen(hfile,"wb");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open restart file %s",hfile);
error->one(str);
}
if (multiproc) delete [] hfile;
}
// proc 0 writes header, groups, ntype-length arrays, force field
// all procs write fix info
if (me == 0) {
header();
group->write_restart(fp);
type_arrays();
force_fields();
}
modify->write_restart(fp);
// communication buffer for all my atom's info
// max_size = largest buffer needed by any proc
int max_size;
int send_size = atom->avec->size_restart();
MPI_Allreduce(&send_size,&max_size,1,MPI_INT,MPI_MAX,world);
double *buf;
if (me == 0)
buf = (double *)
memory->smalloc(max_size*sizeof(double),"write_restart:buf");
else
buf = (double *)
memory->smalloc(send_size*sizeof(double),"write_restart:buf");
// pack my atom data into buf
AtomVec *avec = atom->avec;
int n = 0;
for (int i = 0; i < atom->nlocal; i++) n += avec->pack_restart(i,&buf[n]);
// if any fix requires it, remap each atom's coords via PBC
// is because fix changes atom coords (excepting an integrate fix)
// just remap in buffer, not actual atoms
if (modify->restart_pbc_any) {
int triclinic = domain->triclinic;
double *lo,*hi,*period;
if (triclinic == 0) {
lo = domain->boxlo;
hi = domain->boxhi;
period = domain->prd;
} else {
lo = domain->boxlo_lamda;
hi = domain->boxhi_lamda;
period = domain->prd_lamda;
}
int xperiodic = domain->xperiodic;
int yperiodic = domain->yperiodic;
int zperiodic = domain->zperiodic;
double *x;
int m = 0;
for (int i = 0; i < atom->nlocal; i++) {
x = &buf[m+1];
if (triclinic) domain->x2lamda(x,x);
if (xperiodic) {
if (x[0] < lo[0]) x[0] += period[0];
if (x[0] >= hi[0]) x[0] -= period[0];
x[0] = MAX(x[0],lo[0]);
}
if (yperiodic) {
if (x[1] < lo[1]) x[1] += period[1];
if (x[1] >= hi[1]) x[1] -= period[1];
x[1] = MAX(x[1],lo[1]);
}
if (zperiodic) {
if (x[2] < lo[2]) x[2] += period[2];
if (x[2] >= hi[2]) x[2] -= period[2];
x[2] = MAX(x[2],lo[2]);
}
if (triclinic) domain->lamda2x(x,x);
m += static_cast<int> (buf[m]);
}
}
// if single file:
// write one chunk of atoms per proc to file
// proc 0 pings each proc, receives its chunk, writes to file
// all other procs wait for ping, send their chunk to proc 0
// else if one file per proc:
// each proc opens its own file and writes its chunk directly
if (multiproc == 0) {
int tmp,recv_size;
MPI_Status status;
MPI_Request request;
if (me == 0) {
for (int iproc = 0; iproc < nprocs; iproc++) {
if (iproc) {
MPI_Irecv(buf,max_size,MPI_DOUBLE,iproc,0,world,&request);
MPI_Send(&tmp,0,MPI_INT,iproc,0,world);
MPI_Wait(&request,&status);
MPI_Get_count(&status,MPI_DOUBLE,&recv_size);
} else recv_size = send_size;
fwrite(&recv_size,sizeof(int),1,fp);
fwrite(buf,sizeof(double),recv_size,fp);
}
fclose(fp);
} else {
MPI_Recv(&tmp,0,MPI_INT,0,0,world,&status);
MPI_Rsend(buf,send_size,MPI_DOUBLE,0,0,world);
}
} else {
if (me == 0) fclose(fp);
char *perproc = new char[strlen(file) + 16];
char *ptr = strchr(file,'%');
*ptr = '\0';
sprintf(perproc,"%s%d%s",file,me,ptr+1);
*ptr = '%';
fp = fopen(perproc,"wb");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open restart file %s",perproc);
error->one(str);
}
delete [] perproc;
fwrite(&send_size,sizeof(int),1,fp);
fwrite(buf,sizeof(double),send_size,fp);
fclose(fp);
}
memory->sfree(buf);
}
/* ----------------------------------------------------------------------
proc 0 writes out problem description
------------------------------------------------------------------------- */
void WriteRestart::header()
{
write_char(VERSION,universe->version);
write_int(SMALLINT,sizeof(smallint));
write_int(TAGINT,sizeof(tagint));
write_int(BIGINT,sizeof(bigint));
write_char(UNITS,update->unit_style);
write_bigint(NTIMESTEP,update->ntimestep);
write_int(DIMENSION,domain->dimension);
write_int(NPROCS,nprocs);
write_int(PROCGRID_0,comm->procgrid[0]);
write_int(PROCGRID_1,comm->procgrid[1]);
write_int(PROCGRID_2,comm->procgrid[2]);
write_int(NEWTON_PAIR,force->newton_pair);
write_int(NEWTON_BOND,force->newton_bond);
write_int(XPERIODIC,domain->xperiodic);
write_int(YPERIODIC,domain->yperiodic);
write_int(ZPERIODIC,domain->zperiodic);
write_int(BOUNDARY_00,domain->boundary[0][0]);
write_int(BOUNDARY_01,domain->boundary[0][1]);
write_int(BOUNDARY_10,domain->boundary[1][0]);
write_int(BOUNDARY_11,domain->boundary[1][1]);
write_int(BOUNDARY_20,domain->boundary[2][0]);
write_int(BOUNDARY_21,domain->boundary[2][1]);
// atom_style must be written before atom class values
// so read_restart can create class before reading class values
// if style = hybrid, also write sub-class styles
write_char(ATOM_STYLE,atom->atom_style);
if (strcmp(atom->atom_style,"hybrid") == 0) {
AtomVecHybrid *avec_hybrid = (AtomVecHybrid *) atom->avec;
int nstyles = avec_hybrid->nstyles;
char **keywords = avec_hybrid->keywords;
fwrite(&nstyles,sizeof(int),1,fp);
for (int i = 0; i < nstyles; i++) {
int n = strlen(keywords[i]) + 1;
fwrite(&n,sizeof(int),1,fp);
fwrite(keywords[i],sizeof(char),n,fp);
}
}
write_bigint(NATOMS,natoms);
write_int(NTYPES,atom->ntypes);
write_bigint(NBONDS,atom->nbonds);
write_int(NBONDTYPES,atom->nbondtypes);
write_int(BOND_PER_ATOM,atom->bond_per_atom);
write_bigint(NANGLES,atom->nangles);
write_int(NANGLETYPES,atom->nangletypes);
write_int(ANGLE_PER_ATOM,atom->angle_per_atom);
write_bigint(NDIHEDRALS,atom->ndihedrals);
write_int(NDIHEDRALTYPES,atom->ndihedraltypes);
write_int(DIHEDRAL_PER_ATOM,atom->dihedral_per_atom);
write_bigint(NIMPROPERS,atom->nimpropers);
write_int(NIMPROPERTYPES,atom->nimpropertypes);
write_int(IMPROPER_PER_ATOM,atom->improper_per_atom);
write_double(BOXLO_0,domain->boxlo[0]);
write_double(BOXHI_0,domain->boxhi[0]);
write_double(BOXLO_1,domain->boxlo[1]);
write_double(BOXHI_1,domain->boxhi[1]);
write_double(BOXLO_2,domain->boxlo[2]);
write_double(BOXHI_2,domain->boxhi[2]);
write_double(SPECIAL_LJ_1,force->special_lj[1]);
write_double(SPECIAL_LJ_2,force->special_lj[2]);
write_double(SPECIAL_LJ_3,force->special_lj[3]);
write_double(SPECIAL_COUL_1,force->special_coul[1]);
write_double(SPECIAL_COUL_2,force->special_coul[2]);
write_double(SPECIAL_COUL_3,force->special_coul[3]);
if (domain->triclinic) {
write_double(XY,domain->xy);
write_double(XZ,domain->xz);
write_double(YZ,domain->yz);
}
// -1 flag signals end of header
int flag = -1;
fwrite(&flag,sizeof(int),1,fp);
}
/* ----------------------------------------------------------------------
proc 0 writes out any type-based arrays that are defined
------------------------------------------------------------------------- */
void WriteRestart::type_arrays()
{
if (atom->mass) {
int flag = MASS;
fwrite(&flag,sizeof(int),1,fp);
fwrite(&atom->mass[1],sizeof(double),atom->ntypes,fp);
}
if (atom->shape) {
int flag = SHAPE;
fwrite(&flag,sizeof(int),1,fp);
fwrite(&atom->shape[1][0],sizeof(double),atom->ntypes*3,fp);
}
if (atom->dipole) {
int flag = DIPOLE;
fwrite(&flag,sizeof(int),1,fp);
fwrite(&atom->dipole[1],sizeof(double),atom->ntypes,fp);
}
// -1 flag signals end of type arrays
int flag = -1;
fwrite(&flag,sizeof(int),1,fp);
}
/* ----------------------------------------------------------------------
proc 0 writes out and force field styles and data that are defined
------------------------------------------------------------------------- */
void WriteRestart::force_fields()
{
if (force->pair) {
int flag = PAIR;
fwrite(&flag,sizeof(int),1,fp);
int n = strlen(force->pair_style) + 1;
fwrite(&n,sizeof(int),1,fp);
fwrite(force->pair_style,sizeof(char),n,fp);
force->pair->write_restart(fp);
}
if (atom->avec->bonds_allow && force->bond) {
int flag = BOND;
fwrite(&flag,sizeof(int),1,fp);
int n = strlen(force->bond_style) + 1;
fwrite(&n,sizeof(int),1,fp);
fwrite(force->bond_style,sizeof(char),n,fp);
force->bond->write_restart(fp);
}
if (atom->avec->angles_allow && force->angle) {
int flag = ANGLE;
fwrite(&flag,sizeof(int),1,fp);
int n = strlen(force->angle_style) + 1;
fwrite(&n,sizeof(int),1,fp);
fwrite(force->angle_style,sizeof(char),n,fp);
force->angle->write_restart(fp);
}
if (atom->avec->dihedrals_allow && force->dihedral) {
int flag = DIHEDRAL;
fwrite(&flag,sizeof(int),1,fp);
int n = strlen(force->dihedral_style) + 1;
fwrite(&n,sizeof(int),1,fp);
fwrite(force->dihedral_style,sizeof(char),n,fp);
force->dihedral->write_restart(fp);
}
if (atom->avec->impropers_allow && force->improper) {
int flag = IMPROPER;
fwrite(&flag,sizeof(int),1,fp);
int n = strlen(force->improper_style) + 1;
fwrite(&n,sizeof(int),1,fp);
fwrite(force->improper_style,sizeof(char),n,fp);
force->improper->write_restart(fp);
}
// -1 flag signals end of force field info
int flag = -1;
fwrite(&flag,sizeof(int),1,fp);
}
/* ----------------------------------------------------------------------
write a flag and an int into restart file
------------------------------------------------------------------------- */
void WriteRestart::write_int(int flag, int value)
{
fwrite(&flag,sizeof(int),1,fp);
fwrite(&value,sizeof(int),1,fp);
}
/* ----------------------------------------------------------------------
write a flag and a double into restart file
------------------------------------------------------------------------- */
void WriteRestart::write_double(int flag, double value)
{
fwrite(&flag,sizeof(int),1,fp);
fwrite(&value,sizeof(double),1,fp);
}
/* ----------------------------------------------------------------------
write a flag and a char str into restart file
------------------------------------------------------------------------- */
void WriteRestart::write_char(int flag, char *value)
{
fwrite(&flag,sizeof(int),1,fp);
int n = strlen(value) + 1;
fwrite(&n,sizeof(int),1,fp);
fwrite(value,sizeof(char),n,fp);
}
/* ----------------------------------------------------------------------
write a flag and a bigint into restart file
------------------------------------------------------------------------- */
void WriteRestart::write_bigint(int flag, bigint value)
{
fwrite(&flag,sizeof(int),1,fp);
fwrite(&value,sizeof(bigint),1,fp);
}
diff --git a/src/write_restart.h b/src/write_restart.h
index db729ec01..8a849e825 100644
--- a/src/write_restart.h
+++ b/src/write_restart.h
@@ -1,53 +1,53 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef COMMAND_CLASS
CommandStyle(write_restart,WriteRestart)
#else
#ifndef LMP_WRITE_RESTART_H
#define LMP_WRITE_RESTART_H
+#include "lmptype.h"
#include "stdio.h"
#include "pointers.h"
-#include "lmptype.h"
namespace LAMMPS_NS {
class WriteRestart : protected Pointers {
public:
WriteRestart(class LAMMPS *);
void command(int, char **);
void write(char *);
private:
int me,nprocs;
FILE *fp;
bigint natoms; // natoms (sum of nlocal) to write into file
void header();
void type_arrays();
void force_fields();
void write_int(int, int);
void write_double(int, double);
void write_char(int, char *);
void write_bigint(int, bigint);
};
}
#endif
#endif