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atom_vec_hybrid.cpp
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Tue, Jun 25, 07:52

atom_vec_hybrid.cpp
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/* ----------------------------------------------------------------------
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 "stdlib.h"
#include "string.h"
#include "atom_vec_hybrid.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;
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 sub-style ptrs and hybrid local ptrs are up to date
// for sub-styles, is in case sub-style reallocs actually realloced
for (int k = 0; k < nstyles; k++) styles[k]->grow_reset();
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;
}
/* ----------------------------------------------------------------------
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];
omega[nlocal][1];
omega[nlocal][2];
}
if (atom->angmom_flag) {
angmom[nlocal][0];
angmom[nlocal][1];
angmom[nlocal][2];
}
// 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;
}

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