Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F92094511
atom_vec_wavepacket.cpp
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Sun, Nov 17, 07:32
Size
33 KB
Mime Type
text/x-c
Expires
Tue, Nov 19, 07:32 (2 d)
Engine
blob
Format
Raw Data
Handle
22375432
Attached To
rLAMMPS lammps
atom_vec_wavepacket.cpp
View Options
/* ----------------------------------------------------------------------
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: Ilya Valuev (JIHT, Moscow, Russia)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdlib.h>
#include <string.h>
#include "atom_vec_wavepacket.h"
#include "atom.h"
#include "comm.h"
#include "domain.h"
#include "modify.h"
#include "force.h"
#include "fix.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
AtomVecWavepacket::AtomVecWavepacket(LAMMPS *lmp) : AtomVec(lmp)
{
comm_x_only = comm_f_only = 0;
mass_type = 1;
molecular = 0;
forceclearflag = 1;
size_forward = 4; // coords[3]+radius[1]
size_reverse = 10; // force[3]+erforce[1]+ervelforce[1]+vforce[3]+csforce[2]
size_border = 10; // coords[3]+tag[1]+type[1]+mask[1]+q[1]+spin[1]+eradius[1]+etag[1]
size_velocity = 6; // +velocities[3]+ ervel[1]+cs[2]
size_data_atom = 11; // for input file: 1-tag 2-type 3-q 4-spin 5-eradius 6-etag 7-cs_re 8-cs_im 9-x 10-y 11-z
size_data_vel = 5; // for input file: vx vy vz ervel <??>
xcol_data = 9; // starting column for x data
atom->wavepacket_flag = 1;
atom->electron_flag = 1; // compatible with eff
atom->q_flag = atom->spin_flag = atom->eradius_flag =
atom->ervel_flag = atom->erforce_flag = 1;
atom->cs_flag = atom->csforce_flag = atom->vforce_flag = atom->ervelforce_flag = atom->etag_flag = 1;
}
/* ----------------------------------------------------------------------
grow atom-electron arrays
n = 0 grows arrays by a chunk
n > 0 allocates arrays to size n
------------------------------------------------------------------------- */
void AtomVecWavepacket::grow(int n)
{
if (n == 0) grow_nmax();
else nmax = n;
atom->nmax = nmax;
tag = memory->grow(atom->tag,nmax,"atom:tag");
type = memory->grow(atom->type,nmax,"atom:type");
mask = memory->grow(atom->mask,nmax,"atom:mask");
image = memory->grow(atom->image,nmax,"atom:image");
x = memory->grow(atom->x,nmax,3,"atom:x");
v = memory->grow(atom->v,nmax,3,"atom:v");
f = memory->grow(atom->f,nmax*comm->nthreads,3,"atom:f");
q = memory->grow(atom->q,nmax,"atom:q");
spin = memory->grow(atom->spin,nmax,"atom:spin");
eradius = memory->grow(atom->eradius,nmax,"atom:eradius");
ervel = memory->grow(atom->ervel,nmax,"atom:ervel");
erforce = memory->grow(atom->erforce,nmax*comm->nthreads,"atom:erforce");
cs = memory->grow(atom->cs,2*nmax,"atom:cs");
csforce = memory->grow(atom->csforce,2*nmax,"atom:csforce");
vforce = memory->grow(atom->vforce,3*nmax,"atom:vforce");
ervelforce = memory->grow(atom->ervelforce,nmax,"atom:ervelforce");
etag = memory->grow(atom->etag,nmax,"atom:etag");
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 AtomVecWavepacket::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;
cs = atom->cs;
csforce = atom->csforce;
vforce = atom->vforce;
ervelforce = atom->ervelforce;
etag = atom->etag;
}
/* ----------------------------------------------------------------------
copy atom I info to atom J
------------------------------------------------------------------------- */
void AtomVecWavepacket::copy(int i, int j, int delflag)
{
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];
cs[2*j] = cs[2*i];
cs[2*j+1] = cs[2*i+1];
etag[j] = etag[i];
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j,delflag);
}
/* ---------------------------------------------------------------------- */
void AtomVecWavepacket::force_clear(int n, size_t nbytes)
{
memset(&erforce[n],0,nbytes);
}
/* ---------------------------------------------------------------------- */
// this will be used as partial pack for unsplit Hartree packets (v, ervel not regarded as separate variables)
int AtomVecWavepacket::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];
}
} 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];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
// this is a complete pack of all 'position' variables of AWPMD
int AtomVecWavepacket::pack_comm_vel(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz,dvx,dvy,dvz;
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++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
buf[m++] = ervel[j];
buf[m++] = cs[2*j];
buf[m++] = cs[2*j+1];
}
} 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;
}
if (!deform_vremap) {
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++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
buf[m++] = ervel[j];
buf[m++] = cs[2*j];
buf[m++] = cs[2*j+1];
}
} else {
dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
dvz = pbc[2]*h_rate[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++] = eradius[j];
if (mask[i] & deform_groupbit) {
buf[m++] = v[j][0] + dvx;
buf[m++] = v[j][1] + dvy;
buf[m++] = v[j][2] + dvz;
} else {
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
buf[m++] = ervel[j];
buf[m++] = cs[2*j];
buf[m++] = cs[2*j+1];
}
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecWavepacket::pack_comm_hybrid(int n, int *list, double *buf)
{
int i,j,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = eradius[j];
buf[m++] = ervel[j];
buf[m++] = cs[2*j];
buf[m++] = cs[2*j+1];
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecWavepacket::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++];
}
}
/* ---------------------------------------------------------------------- */
void AtomVecWavepacket::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++];
eradius[i] = buf[m++];
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
ervel[i] = buf[m++];
cs[2*i] = buf[m++];
cs[2*i+1] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecWavepacket::unpack_comm_hybrid(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++){
eradius[i] = buf[m++];
ervel[i] = buf[m++];
cs[2*i] = buf[m++];
cs[2*i+1] = buf[m++];
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecWavepacket::pack_reverse(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) { //10
buf[m++] = f[i][0];
buf[m++] = f[i][1];
buf[m++] = f[i][2];
buf[m++] = erforce[i];
buf[m++] = ervelforce[i];
buf[m++] = vforce[3*i];
buf[m++] = vforce[3*i+1];
buf[m++] = vforce[3*i+2];
buf[m++] = csforce[2*i];
buf[m++] = csforce[2*i+1];
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecWavepacket::pack_reverse_hybrid(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++){
buf[m++] = erforce[i];
buf[m++] = ervelforce[i];
buf[m++] = vforce[3*i];
buf[m++] = vforce[3*i+1];
buf[m++] = vforce[3*i+2];
buf[m++] = csforce[2*i];
buf[m++] = csforce[2*i+1];
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecWavepacket::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++];
ervelforce[j] += buf[m++];
vforce[3*j] += buf[m++];
vforce[3*j+1] += buf[m++];
vforce[3*j+2] += buf[m++];
csforce[2*j] += buf[m++];
csforce[2*j+1] += buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecWavepacket::unpack_reverse_hybrid(int n, int *list, double *buf)
{
int i,j,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
erforce[j] += buf[m++];
ervelforce[j] += buf[m++];
vforce[3*j] += buf[m++];
vforce[3*j+1] += buf[m++];
vforce[3*j+2] += buf[m++];
csforce[2*j] += buf[m++];
csforce[2*j+1] += buf[m++];
}
return m;
}
/* ---------------------------------------------------------------------- */
// will be used for Hartree unsplit version (the etag is added however)
int AtomVecWavepacket::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++] = ubuf(tag[j]).d;
buf[m++] = ubuf(type[j]).d;
buf[m++] = ubuf(mask[j]).d;
buf[m++] = q[j];
buf[m++] = ubuf(spin[j]).d;
buf[m++] = eradius[j];
buf[m++] = ubuf(etag[j]).d;
}
} 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++] = ubuf(tag[j]).d;
buf[m++] = ubuf(type[j]).d;
buf[m++] = ubuf(mask[j]).d;
buf[m++] = q[j];
buf[m++] = ubuf(spin[j]).d;
buf[m++] = eradius[j];
buf[m++] = ubuf(etag[j]).d;
}
}
if (atom->nextra_border)
for (int iextra = 0; iextra < atom->nextra_border; iextra++)
m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]);
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecWavepacket::pack_border_vel(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz,dvx,dvy,dvz;
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++] = ubuf(tag[j]).d;
buf[m++] = ubuf(type[j]).d;
buf[m++] = ubuf(mask[j]).d;
buf[m++] = q[j];
buf[m++] = ubuf(spin[j]).d;
buf[m++] = eradius[j];
buf[m++] = ubuf(etag[j]).d;
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
buf[m++] = ervel[j];
buf[m++] = cs[2*j];
buf[m++] = cs[2*j+1];
}
} 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];
}
if (domain->triclinic == 0) {
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++] = ubuf(tag[j]).d;
buf[m++] = ubuf(type[j]).d;
buf[m++] = ubuf(mask[j]).d;
buf[m++] = q[j];
buf[m++] = ubuf(spin[j]).d;
buf[m++] = eradius[j];
buf[m++] = ubuf(etag[j]).d;
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
buf[m++] = ervel[j];
buf[m++] = cs[2*j];
buf[m++] = cs[2*j+1];
}
} else {
dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
dvz = pbc[2]*h_rate[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++] = ubuf(tag[j]).d;
buf[m++] = ubuf(type[j]).d;
buf[m++] = ubuf(mask[j]).d;
buf[m++] = q[j];
buf[m++] = ubuf(spin[j]).d;
buf[m++] = eradius[j];
buf[m++] = ubuf(etag[j]).d;
if (mask[i] & deform_groupbit) {
buf[m++] = v[j][0] + dvx;
buf[m++] = v[j][1] + dvy;
buf[m++] = v[j][2] + dvz;
} else {
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
buf[m++] = ervel[j];
buf[m++] = cs[2*j];
buf[m++] = cs[2*j+1];
}
}
}
if (atom->nextra_border)
for (int iextra = 0; iextra < atom->nextra_border; iextra++)
m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]);
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecWavepacket::pack_border_hybrid(int n, int *list, double *buf)
{
int i,j,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = q[j];
buf[m++] = ubuf(spin[j]).d;
buf[m++] = eradius[j];
buf[m++] = ubuf(etag[j]).d;
buf[m++] = ervel[j];
buf[m++] = cs[2*j];
buf[m++] = cs[2*j+1];
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecWavepacket::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] = (tagint) ubuf(buf[m++]).i;
type[i] = (int) ubuf(buf[m++]).i;
mask[i] = (int) ubuf(buf[m++]).i;
q[i] = buf[m++];
spin[i] = (int) ubuf(buf[m++]).i;
eradius[i] = buf[m++];
etag[i] = (int) ubuf(buf[m++]).i;
}
if (atom->nextra_border)
for (int iextra = 0; iextra < atom->nextra_border; iextra++)
m += modify->fix[atom->extra_border[iextra]]->
unpack_border(n,first,&buf[m]);
}
/* ---------------------------------------------------------------------- */
void AtomVecWavepacket::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] = (tagint) ubuf(buf[m++]).i;
type[i] = (int) ubuf(buf[m++]).i;
mask[i] = (int) ubuf(buf[m++]).i;
q[i] = buf[m++];
spin[i] = (int) ubuf(buf[m++]).i;
eradius[i] = buf[m++];
etag[i] = (int) ubuf(buf[m++]).i;
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
ervel[i] = buf[m++];
cs[2*i] = buf[m++];
cs[2*i+1] = buf[m++];
}
if (atom->nextra_border)
for (int iextra = 0; iextra < atom->nextra_border; iextra++)
m += modify->fix[atom->extra_border[iextra]]->
unpack_border(n,first,&buf[m]);
}
/* ---------------------------------------------------------------------- */
int AtomVecWavepacket::unpack_border_hybrid(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
q[i] = buf[m++];
spin[i] = (int) ubuf(buf[m++]).i;
eradius[i] = buf[m++];
etag[i] = (int) ubuf(buf[m++]).i;
ervel[i] = buf[m++];
cs[2*i] = buf[m++];
cs[2*i+1] = buf[m++];
}
return 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 AtomVecWavepacket::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++] = ubuf(tag[i]).d;
buf[m++] = ubuf(type[i]).d;
buf[m++] = ubuf(mask[i]).d;
buf[m++] = ubuf(image[i]).d;
buf[m++] = q[i];
buf[m++] = ubuf(spin[i]).d;
buf[m++] = eradius[i];
buf[m++] = ervel[i];
buf[m++] = ubuf(etag[i]).d;
buf[m++] = cs[2*i];
buf[m++] = cs[2*i+1];
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 AtomVecWavepacket::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] = (tagint) ubuf(buf[m++]).i;
type[nlocal] = (int) ubuf(buf[m++]).i;
mask[nlocal] = (int) ubuf(buf[m++]).i;
image[nlocal] = (imageint) ubuf(buf[m++]).i;
q[nlocal] = buf[m++];
spin[nlocal] = (int) ubuf(buf[m++]).i;
eradius[nlocal] = buf[m++];
ervel[nlocal] = buf[m++];
etag[nlocal] = (int) ubuf(buf[m++]).i;
cs[2*nlocal] = buf[m++];
cs[2*nlocal+1] = 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 AtomVecWavepacket::size_restart()
{
int i;
int nlocal = atom->nlocal;
int n = 18 * 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 AtomVecWavepacket::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++] = ubuf(tag[i]).d;
buf[m++] = ubuf(type[i]).d;
buf[m++] = ubuf(mask[i]).d;
buf[m++] = ubuf(image[i]).d;
buf[m++] = v[i][0];
buf[m++] = v[i][1];
buf[m++] = v[i][2];
buf[m++] = q[i];
buf[m++] = ubuf(spin[i]).d;
buf[m++] = eradius[i];
buf[m++] = ervel[i];
buf[m++] = ubuf(etag[i]).d;
buf[m++] = cs[2*i];
buf[m++] = cs[2*i+1];
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 AtomVecWavepacket::unpack_restart(double *buf)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) {
grow(0);
if (atom->nextra_store)
memory->grow(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] = (tagint) ubuf(buf[m++]).i;
type[nlocal] = (int) ubuf(buf[m++]).i;
mask[nlocal] = (int) ubuf(buf[m++]).i;
image[nlocal] = (imageint) ubuf(buf[m++]).i;
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
q[nlocal] = buf[m++];
spin[nlocal] = (int) ubuf(buf[m++]).i;
eradius[nlocal] = buf[m++];
ervel[nlocal] = buf[m++];
etag[nlocal] = (int) ubuf(buf[m++]).i;
cs[2*nlocal] = buf[m++];
cs[2*nlocal+1] = 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
AWPMD: creates a proton
------------------------------------------------------------------------- */
void AtomVecWavepacket::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] = ((imageint) IMGMAX << IMG2BITS) |
((imageint) IMGMAX << IMGBITS) | IMGMAX;
v[nlocal][0] = 0.0;
v[nlocal][1] = 0.0;
v[nlocal][2] = 0.0;
q[nlocal] = 1.;
spin[nlocal] = 0;
eradius[nlocal] = 0.0;
ervel[nlocal] = 0.0;
etag[nlocal] = 0;
cs[2*nlocal] = 0.;
cs[2*nlocal+1] = 0.;
atom->nlocal++;
}
/* ----------------------------------------------------------------------
unpack one line from Atoms section of data file
initialize other atom quantities
AWPMD: 0-tag 1-type 2-q 3-spin 4-eradius 5-etag 6-cs_re 7-cs_im
------------------------------------------------------------------------- */
void AtomVecWavepacket::data_atom(double *coord, imageint imagetmp,
char **values)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
tag[nlocal] = ATOTAGINT(values[0]);
type[nlocal] = atoi(values[1]);
if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
error->one(FLERR,"Invalid atom type in Atoms section of data file");
q[nlocal] = atof(values[2]);
spin[nlocal] = atoi(values[3]);
eradius[nlocal] = atof(values[4]);
if (eradius[nlocal] < 0.0)
error->one(FLERR,"Invalid eradius in Atoms section of data file");
etag[nlocal] = atoi(values[5]);
cs[2*nlocal] = atoi(values[6]);
cs[2*nlocal+1] = atof(values[7]);
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 AtomVecWavepacket::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(FLERR,"Invalid eradius in Atoms section of data file");
etag[nlocal] = atoi(values[3]);
cs[2*nlocal] = atoi(values[4]);
cs[2*nlocal+1] = atof(values[5]);
v[nlocal][0] = 0.0;
v[nlocal][1] = 0.0;
v[nlocal][2] = 0.0;
ervel[nlocal] = 0.0;
return 3;
}
/* ----------------------------------------------------------------------
unpack one line from Velocities section of data file
------------------------------------------------------------------------- */
void AtomVecWavepacket::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 AtomVecWavepacket::data_vel_hybrid(int m, char **values)
{
ervel[m] = atof(values[0]);
return 1;
}
/* ----------------------------------------------------------------------
pack atom info for data file including 3 image flags
------------------------------------------------------------------------- */
void AtomVecWavepacket::pack_data(double **buf)
{
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
buf[i][0] = ubuf(tag[i]).d;
buf[i][1] = ubuf(type[i]).d;
buf[i][2] = q[i];
buf[i][3] = ubuf(spin[i]).d;
buf[i][4] = eradius[i];
buf[i][5] = ubuf(etag[i]).d;
buf[i][6] = cs[2*i];
buf[i][7] = cs[2*i+1];
buf[i][8] = x[i][0];
buf[i][9] = x[i][1];
buf[i][10] = x[i][2];
buf[i][11] = ubuf((image[i] & IMGMASK) - IMGMAX).d;
buf[i][12] = ubuf((image[i] >> IMGBITS & IMGMASK) - IMGMAX).d;
buf[i][13] = ubuf((image[i] >> IMG2BITS) - IMGMAX).d;
}
}
/* ----------------------------------------------------------------------
pack hybrid atom info for data file
------------------------------------------------------------------------- */
int AtomVecWavepacket::pack_data_hybrid(int i, double *buf)
{
buf[0] = q[i];
buf[1] = ubuf(spin[i]).d;
buf[2] = eradius[i];
buf[3] = ubuf(etag[i]).d;
buf[4] = cs[2*i];
buf[5] = cs[2*i+1];
return 6;
}
/* ----------------------------------------------------------------------
write atom info to data file including 3 image flags
------------------------------------------------------------------------- */
void AtomVecWavepacket::write_data(FILE *fp, int n, double **buf)
{
for (int i = 0; i < n; i++)
fprintf(fp,TAGINT_FORMAT
" %d %-1.16e %d %-1.16e %d %-1.16e %-1.16e %-1.16e "
"%-1.16e %-1.16e %d %d %d\n",
(tagint) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).i,
buf[i][2],(int) ubuf(buf[i][3]).i,buf[i][4],
(int) ubuf(buf[i][5]).i,buf[i][6],buf[i][8],
buf[i][8],buf[i][9],buf[i][10],
(int) ubuf(buf[i][11]).i,(int) ubuf(buf[i][12]).i,
(int) ubuf(buf[i][13]).i);
}
/* ----------------------------------------------------------------------
write hybrid atom info to data file
------------------------------------------------------------------------- */
int AtomVecWavepacket::write_data_hybrid(FILE *fp, double *buf)
{
fprintf(fp," %-1.16e %d %-1.16e %d %-1.16e %-1.16e",
buf[0],(int) ubuf(buf[1]).i,buf[2],(int) ubuf(buf[3]).i,
buf[4],buf[5]);
return 6;
}
/* ----------------------------------------------------------------------
pack velocity info for data file
------------------------------------------------------------------------- */
void AtomVecWavepacket::pack_vel(double **buf)
{
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
buf[i][0] = ubuf(tag[i]).d;
buf[i][1] = v[i][0];
buf[i][2] = v[i][1];
buf[i][3] = v[i][2];
buf[i][4] = ervel[i];
}
}
/* ----------------------------------------------------------------------
pack hybrid velocity info for data file
------------------------------------------------------------------------- */
int AtomVecWavepacket::pack_vel_hybrid(int i, double *buf)
{
buf[0] = ervel[i];
return 1;
}
/* ----------------------------------------------------------------------
write velocity info to data file
------------------------------------------------------------------------- */
void AtomVecWavepacket::write_vel(FILE *fp, int n, double **buf)
{
for (int i = 0; i < n; i++)
fprintf(fp,TAGINT_FORMAT " %-1.16e %-1.16e %-1.16e %-1.16e\n",
(tagint) ubuf(buf[i][0]).i,buf[i][1],buf[i][2],buf[i][3],buf[i][4]);
}
/* ----------------------------------------------------------------------
write hybrid velocity info to data file
------------------------------------------------------------------------- */
int AtomVecWavepacket::write_vel_hybrid(FILE *fp, double *buf)
{
fprintf(fp," %-1.16e",buf[0]);
return 1;
}
/* ----------------------------------------------------------------------
assign an index to named atom property and return index
return -1 if name is unknown to this atom style
------------------------------------------------------------------------- */
int AtomVecWavepacket::property_atom(char *name)
{
if (strcmp(name,"spin") == 0) return 0;
if (strcmp(name,"eradius") == 0) return 1;
if (strcmp(name,"ervel") == 0) return 2;
if (strcmp(name,"erforce") == 0) return 3;
return -1;
}
/* ----------------------------------------------------------------------
pack per-atom data into buf for ComputePropertyAtom
index maps to data specific to this atom style
------------------------------------------------------------------------- */
void AtomVecWavepacket::pack_property_atom(int index, double *buf,
int nvalues, int groupbit)
{
int *mask = atom->mask;
int nlocal = atom->nlocal;
int n = 0;
if (index == 0) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = spin[i];
else buf[n] = 0.0;
n += nvalues;
}
} else if (index == 1) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = eradius[i];
else buf[n] = 0.0;
n += nvalues;
}
} else if (index == 2) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = ervel[i];
else buf[n] = 0.0;
n += nvalues;
}
} else if (index == 3) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = erforce[i];
else buf[n] = 0.0;
n += nvalues;
}
}
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
------------------------------------------------------------------------- */
bigint AtomVecWavepacket::memory_usage()
{
bigint bytes = 0;
if (atom->memcheck("tag")) bytes += memory->usage(tag,nmax);
if (atom->memcheck("type")) bytes += memory->usage(type,nmax);
if (atom->memcheck("mask")) bytes += memory->usage(mask,nmax);
if (atom->memcheck("image")) bytes += memory->usage(image,nmax);
if (atom->memcheck("x")) bytes += memory->usage(x,nmax,3);
if (atom->memcheck("v")) bytes += memory->usage(v,nmax,3);
if (atom->memcheck("f")) bytes += memory->usage(f,nmax*comm->nthreads,3);
if (atom->memcheck("q")) bytes += memory->usage(q,nmax);
if (atom->memcheck("spin")) bytes += memory->usage(spin,nmax);
if (atom->memcheck("eradius")) bytes += memory->usage(eradius,nmax);
if (atom->memcheck("ervel")) bytes += memory->usage(ervel,nmax);
if (atom->memcheck("erforce"))
bytes += memory->usage(erforce,nmax*comm->nthreads);
if (atom->memcheck("ervelforce")) bytes += memory->usage(ervelforce,nmax);
if (atom->memcheck("cs")) bytes += memory->usage(cs,2*nmax);
if (atom->memcheck("csforce")) bytes += memory->usage(csforce,2*nmax);
if (atom->memcheck("vforce")) bytes += memory->usage(vforce,3*nmax);
if (atom->memcheck("etag")) bytes += memory->usage(etag,nmax);
return bytes;
}
Event Timeline
Log In to Comment