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getting there

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This commit is contained in:
Tom Swinburne
2020-04-13 19:28:43 +02:00
parent 39799c62fc
commit 430f2ae6aa
9 changed files with 376 additions and 2212 deletions
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22
src/MAKE/Makefile.mpi
View File

@ -7,13 +7,13 @@ SHELL = /bin/sh
# specify flags and libraries needed for your compiler # specify flags and libraries needed for your compiler
CC = mpicxx CC = mpicxx
CCFLAGS = -g -O3 -std=c++11 CCFLAGS = -g -O3 -std=c++11
SHFLAGS = -fPIC SHFLAGS = -fPIC
DEPFLAGS = -M DEPFLAGS = -M
LINK = mpicxx LINK = mpicxx
LINKFLAGS = -g -O3 LINKFLAGS = -g -O3
LIB = LIB =
SIZE = size SIZE = size
ARCHIVE = ar ARCHIVE = ar
@ -28,7 +28,7 @@ SHLIBFLAGS = -shared
# LAMMPS ifdef settings # LAMMPS ifdef settings
# see possible settings in Section 3.5 of the manual # see possible settings in Section 3.5 of the manual
LMP_INC = -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -DLAMMPS_EXCEPTIONS LMP_INC = -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -DLAMMPS_EXCEPTIONS # -DLAMMPS_CXX98
# MPI library # MPI library
# see discussion in Section 3.4 of the manual # see discussion in Section 3.4 of the manual
@ -40,8 +40,8 @@ LMP_INC = -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -DLAMMPS_EXCEPTIONS
# LIB = name of MPI library # LIB = name of MPI library
MPI_INC = -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 MPI_INC = -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1
MPI_PATH = MPI_PATH =
MPI_LIB = MPI_LIB =
# FFT library # FFT library
# see discussion in Section 2.2 (step 6) of manual # see discussion in Section 2.2 (step 6) of manual
@ -50,9 +50,9 @@ MPI_LIB =
# PATH = path for FFT library # PATH = path for FFT library
# LIB = name of FFT library # LIB = name of FFT library
FFT_INC = FFT_INC =
FFT_PATH = FFT_PATH =
FFT_LIB = FFT_LIB =
# JPEG and/or PNG library # JPEG and/or PNG library
# see discussion in Section 2.2 (step 7) of manual # see discussion in Section 2.2 (step 7) of manual
@ -61,9 +61,9 @@ FFT_LIB =
# PATH = path(s) for JPEG library and/or PNG library # PATH = path(s) for JPEG library and/or PNG library
# LIB = name(s) of JPEG library and/or PNG library # LIB = name(s) of JPEG library and/or PNG library
JPG_INC = JPG_INC =
JPG_PATH = JPG_PATH =
JPG_LIB = JPG_LIB =
# --------------------------------------------------------------------- # ---------------------------------------------------------------------
# build rules and dependencies # build rules and dependencies

951
src/USER-PAFI/atom_vec_pafi.cpp
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@ -1,951 +0,0 @@
/* ----------------------------------------------------------------------
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: Thomas Swinburne (CNRS & CINaM, Marseille, France)
Please cite the related publication:
T.D. Swinburne and M.-C. Marinica, Unsupervised calculation of free energy barriers in large crystalline systems, Physical Review Letters 2018
------------------------------------------------------------------------- */
#include <cmath>
#include <cstdlib>
#include <cstring>
#include "atom.h"
#include "atom_vec_pafi.h"
#include "comm.h"
#include "domain.h"
#include "error.h"
#include "fix.h"
#include "memory.h"
#include "modify.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
AtomVecPAFI::AtomVecPAFI(LAMMPS *lmp) : AtomVec(lmp)
{
molecular = 0;
mass_type = 1;
comm_x_only = 1;
comm_f_only = 1;
size_forward = 3;
size_reverse = 3;
size_border = 15;
size_velocity = 3;
size_data_atom = 5;//14;
size_data_vel = 4;
xcol_data = 3;
atom->pafi_flag = 1;
}
/* ----------------------------------------------------------------------
grow atom arrays
n = 0 grows arrays by a chunk
n > 0 allocates arrays to size n
------------------------------------------------------------------------- */
void AtomVecPAFI::grow(int n)
{
if (n == 0) grow_nmax();
else nmax = n;
atom->nmax = nmax;
if (nmax < 0 || nmax > MAXSMALLINT)
error->one(FLERR,"Per-processor system is too big");
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");
// allocating mech. quantities
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");
// allocating path quantities
path = memory->grow(atom->path,nmax,3,"atom:path");
norm = memory->grow(atom->norm,nmax,3,"atom:norm");
dnorm = memory->grow(atom->dnorm,nmax,3,"atom:dnorm");
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 AtomVecPAFI::grow_reset()
{
tag = atom->tag; type = atom->type;
mask = atom->mask; image = atom->image;
x = atom->x; v = atom->v; f = atom->f;
path = atom->path; norm = atom->norm; dnorm = atom->dnorm;
}
/* ----------------------------------------------------------------------
copy atom I info to atom J
------------------------------------------------------------------------- */
void AtomVecPAFI::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];
path[j][0] = path[i][0];
path[j][1] = path[i][1];
path[j][2] = path[i][2];
norm[j][0] = norm[i][0];
norm[j][1] = norm[i][1];
norm[j][2] = norm[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,delflag);
}
/* ---------------------------------------------------------------------- */
int AtomVecPAFI::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 AtomVecPAFI::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++] = 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;
}
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++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
} 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;
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];
}
}
}
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecPAFI::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 AtomVecPAFI::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 AtomVecPAFI::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 AtomVecPAFI::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 AtomVecPAFI::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++] = path[j][0];
buf[m++] = path[j][1];
buf[m++] = path[j][2];
buf[m++] = norm[j][0];
buf[m++] = norm[j][1];
buf[m++] = norm[j][2];
buf[m++] = dnorm[j][0];
buf[m++] = dnorm[j][1];
buf[m++] = dnorm[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++] = ubuf(tag[j]).d;
buf[m++] = ubuf(type[j]).d;
buf[m++] = ubuf(mask[j]).d;
buf[m++] = path[j][0];
buf[m++] = path[j][1];
buf[m++] = path[j][2];
buf[m++] = norm[j][0];
buf[m++] = norm[j][1];
buf[m++] = norm[j][2];
buf[m++] = dnorm[j][0];
buf[m++] = dnorm[j][1];
buf[m++] = dnorm[j][2];
}
}
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 AtomVecPAFI::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++] = path[j][0];
buf[m++] = path[j][1];
buf[m++] = path[j][2];
buf[m++] = norm[j][0];
buf[m++] = norm[j][1];
buf[m++] = norm[j][2];
buf[m++] = dnorm[j][0];
buf[m++] = dnorm[j][1];
buf[m++] = dnorm[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];
}
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++] = ubuf(tag[j]).d;
buf[m++] = ubuf(type[j]).d;
buf[m++] = ubuf(mask[j]).d;
buf[m++] = path[j][0];
buf[m++] = path[j][1];
buf[m++] = path[j][2];
buf[m++] = norm[j][0];
buf[m++] = norm[j][1];
buf[m++] = norm[j][2];
buf[m++] = dnorm[j][0];
buf[m++] = dnorm[j][1];
buf[m++] = dnorm[j][2];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
} 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++] = path[j][0];
buf[m++] = path[j][1];
buf[m++] = path[j][2];
buf[m++] = norm[j][0];
buf[m++] = norm[j][1];
buf[m++] = norm[j][2];
buf[m++] = dnorm[j][0];
buf[m++] = dnorm[j][1];
buf[m++] = dnorm[j][2];
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];
}
}
}
}
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 AtomVecPAFI::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++] = path[j][0];
buf[m++] = path[j][1];
buf[m++] = path[j][2];
buf[m++] = norm[j][0];
buf[m++] = norm[j][1];
buf[m++] = norm[j][2];
buf[m++] = dnorm[j][0];
buf[m++] = dnorm[j][1];
buf[m++] = dnorm[j][2];
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecPAFI::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;
path[i][0] = buf[m++];
path[i][1] = buf[m++];
path[i][2] = buf[m++];
norm[i][0] = buf[m++];
norm[i][1] = buf[m++];
norm[i][2] = buf[m++];
dnorm[i][0] = buf[m++];
dnorm[i][1] = buf[m++];
dnorm[i][2] = 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]);
}
/* ---------------------------------------------------------------------- */
void AtomVecPAFI::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;
path[i][0] = buf[m++];
path[i][1] = buf[m++];
path[i][2] = buf[m++];
norm[i][0] = buf[m++];
norm[i][1] = buf[m++];
norm[i][2] = buf[m++];
dnorm[i][0] = buf[m++];
dnorm[i][1] = buf[m++];
dnorm[i][2] = buf[m++];
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = 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 AtomVecPAFI::unpack_border_hybrid(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
path[i][0] = buf[m++];
path[i][1] = buf[m++];
path[i][2] = buf[m++];
norm[i][0] = buf[m++];
norm[i][1] = buf[m++];
norm[i][2] = buf[m++];
dnorm[i][0] = buf[m++];
dnorm[i][1] = buf[m++];
dnorm[i][2] = buf[m++];
}
return m;
}
/* ----------------------------------------------------------------------
pack all atom quantities for shipping to another proc
xyz must be 1st 3 values, so that comm::exchange can test on them
------------------------------------------------------------------------- */
int AtomVecPAFI::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++] = path[i][0];
buf[m++] = path[i][1];
buf[m++] = path[i][2];
buf[m++] = norm[i][0];
buf[m++] = norm[i][1];
buf[m++] = norm[i][2];
buf[m++] = dnorm[i][0];
buf[m++] = dnorm[i][1];
buf[m++] = dnorm[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 AtomVecPAFI::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;
path[nlocal][0] = buf[m++];
path[nlocal][1] = buf[m++];
path[nlocal][2] = buf[m++];
norm[nlocal][0] = buf[m++];
norm[nlocal][1] = buf[m++];
norm[nlocal][2] = buf[m++];
dnorm[nlocal][0] = buf[m++];
dnorm[nlocal][1] = buf[m++];
dnorm[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 AtomVecPAFI::size_restart()
{
int i;
int nlocal = atom->nlocal;
int n = 20 * 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 AtomVecPAFI::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++] = path[i][0];
buf[m++] = path[i][1];
buf[m++] = path[i][2];
buf[m++] = norm[i][0];
buf[m++] = norm[i][1];
buf[m++] = norm[i][2];
buf[m++] = dnorm[i][0];
buf[m++] = dnorm[i][1];
buf[m++] = dnorm[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 AtomVecPAFI::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++];
path[nlocal][0] = buf[m++];
path[nlocal][1] = buf[m++];
path[nlocal][2] = buf[m++];
norm[nlocal][0] = buf[m++];
norm[nlocal][1] = buf[m++];
norm[nlocal][2] = buf[m++];
dnorm[nlocal][0] = buf[m++];
dnorm[nlocal][1] = buf[m++];
dnorm[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 AtomVecPAFI::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;
path[nlocal][0] = 0.0;
path[nlocal][1] = 0.0;
path[nlocal][2] = 0.0;
norm[nlocal][0] = 0.0;
norm[nlocal][1] = 0.0;
norm[nlocal][2] = 0.0;
dnorm[nlocal][0] = 0.0;
dnorm[nlocal][1] = 0.0;
dnorm[nlocal][2] = 0.0;
atom->nlocal++;
}
/* ----------------------------------------------------------------------
unpack one line from Atoms section of data file
initialize other atom quantities
------------------------------------------------------------------------- */
void AtomVecPAFI::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");
x[nlocal][0] = coord[0];
x[nlocal][1] = coord[1];
x[nlocal][2] = coord[2];
path[nlocal][0] = 0.;
path[nlocal][1] = 0.;
path[nlocal][2] = 0.;
norm[nlocal][0] = 0.;
norm[nlocal][1] = 0.;
norm[nlocal][2] = 0.;
dnorm[nlocal][0] = 0.;
dnorm[nlocal][1] = 0.;
dnorm[nlocal][2] = 0.;
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 AtomVecPAFI::data_atom_hybrid(int nlocal, char **values)
{
path[nlocal][0] = atof(values[0]);
path[nlocal][1] = atof(values[1]);
path[nlocal][2] = atof(values[2]);
norm[nlocal][0] = atof(values[3]);
norm[nlocal][1] = atof(values[4]);
norm[nlocal][2] = atof(values[5]);
dnorm[nlocal][0] = atof(values[6]);
dnorm[nlocal][1] = atof(values[7]);
dnorm[nlocal][2] = atof(values[8]);
return 9;
}
/* ----------------------------------------------------------------------
pack atom info for data file including 3 image flags
------------------------------------------------------------------------- */
void AtomVecPAFI::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] = x[i][0];
buf[i][3] = x[i][1];
buf[i][4] = x[i][2];
buf[i][5] = ubuf((image[i] & IMGMASK) - IMGMAX).d;
buf[i][6] = ubuf((image[i] >> IMGBITS & IMGMASK) - IMGMAX).d;
buf[i][7] = ubuf((image[i] >> IMG2BITS) - IMGMAX).d;
}
}
/* ----------------------------------------------------------------------
pack hybrid atom info for data file
------------------------------------------------------------------------- */
int AtomVecPAFI::pack_data_hybrid(int i, double *buf)
{
buf[0] = path[i][0];
buf[1] = path[i][1];
buf[2] = path[i][2];
buf[3] = norm[i][0];
buf[4] = norm[i][1];
buf[5] = norm[i][2];
buf[6] = dnorm[i][0];
buf[7] = dnorm[i][1];
buf[8] = dnorm[i][2];
return 9;
}
/* ----------------------------------------------------------------------
write atom info to data file including 3 image flags
------------------------------------------------------------------------- */
void AtomVecPAFI::write_data(FILE *fp, int n, double **buf)
{
for (int i = 0; i < n; i++)
fprintf(fp,TAGINT_FORMAT \
" %d %-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],buf[i][3],buf[i][4],
(int) ubuf(buf[i][5]).i,(int) ubuf(buf[i][6]).i,
(int) ubuf(buf[i][7]).i);
}
/* ----------------------------------------------------------------------
write hybrid atom info to data file
------------------------------------------------------------------------- */
int AtomVecPAFI::write_data_hybrid(FILE *fp, double *buf)
{
fprintf(fp,"%-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e",
buf[0],buf[1],buf[2],
buf[3],buf[4],buf[5],
buf[6],buf[7],buf[8]);
return 9;
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
------------------------------------------------------------------------- */
bigint AtomVecPAFI::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("path")) bytes += memory->usage(path,nmax,3);
if (atom->memcheck("norm")) bytes += memory->usage(norm,nmax,3);
if (atom->memcheck("dnorm")) bytes += memory->usage(dnorm,nmax,3);
return bytes;
}

91
src/USER-PAFI/atom_vec_pafi.h
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@ -1,91 +0,0 @@
/* -*- c++ -*- ----------------------------------------------------------
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: Thomas Swinburne (CNRS & CINaM, Marseille, France)
Please cite the related publication:
T.D. Swinburne and M.-C. Marinica, Unsupervised calculation of free energy barriers in large crystalline systems, Physical Review Letters 2018
------------------------------------------------------------------------- */
#ifdef ATOM_CLASS
AtomStyle(pafi,AtomVecPAFI)
#else
#ifndef LMP_ATOM_VEC_PAFI_H
#define LMP_ATOM_VEC_PAFI_H
#include "atom_vec.h"
namespace LAMMPS_NS {
class AtomVecPAFI : public AtomVec {
public:
AtomVecPAFI(class LAMMPS *);
void grow(int);
void grow_reset();
void copy(int, int, int);
int pack_comm(int, int *, double *, int, int *);
int pack_comm_vel(int, int *, double *, int, int *);
void unpack_comm(int, int, double *);
void unpack_comm_vel(int, int, double *);
int pack_reverse(int, int, double *);
void unpack_reverse(int, int *, double *);
int pack_border(int, int *, double *, int, int *);
int pack_border_vel(int, int *, double *, int, int *);
int pack_border_hybrid(int, int *, double *);
void unpack_border(int, int, double *);
void unpack_border_vel(int, int, double *);
int unpack_border_hybrid(int, int, double *);
int pack_exchange(int, double *);
int unpack_exchange(double *);
int size_restart();
int pack_restart(int, double *);
int unpack_restart(double *);
void create_atom(int, double *);
virtual void data_atom(double *, imageint, char **);
virtual int data_atom_hybrid(int, char **);
virtual void pack_data(double **);
virtual int pack_data_hybrid(int, double *);
virtual void write_data(FILE *, int, double **);
virtual int write_data_hybrid(FILE *, double *);
bigint memory_usage();
private:
tagint *tag;
int *type,*mask;
imageint *image;
double **x,**v,**f; // lattice quantities
// 0th, 1st and 2nd derivative of reference path w.r.t. to path coordinate r
double **path,**norm,**dnorm;
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Per-processor system is too big
The number of owned atoms plus ghost atoms on a single
processor must fit in 32-bit integer.
E: Invalid atom type in Atoms section of data file
Atom types must range from 1 to specified # of types.
*/

968
src/USER-PAFI/atom_vec_pafipath.cpp
View File

@ -1,968 +0,0 @@
/* ----------------------------------------------------------------------
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: Thomas Swinburne (CNRS & CINaM, Marseille, France)
Please cite the related publication:
T.D. Swinburne and M.-C. Marinica, Unsupervised calculation of free energy barriers in large crystalline systems, Physical Review Letters 2018
------------------------------------------------------------------------- */
#include <cmath>
#include <cstdlib>
#include <cstring>
#include "atom.h"
#include "atom_vec_pafipath.h"
#include "comm.h"
#include "domain.h"
#include "error.h"
#include "fix.h"
#include "memory.h"
#include "modify.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
AtomVecPAFIPATH::AtomVecPAFIPATH(LAMMPS *lmp) : AtomVec(lmp)
{
molecular = 0;
mass_type = 1;
comm_x_only = 1;
comm_f_only = 1;
size_forward = 3;
size_reverse = 3;
size_border = 15;
size_velocity = 3;
size_data_atom = 14;
size_data_vel = 4;
xcol_data = 3;
atom->pafi_flag = 1;
}
/* ----------------------------------------------------------------------
grow atom arrays
n = 0 grows arrays by a chunk
n > 0 allocates arrays to size n
------------------------------------------------------------------------- */
void AtomVecPAFIPATH::grow(int n)
{
if (n == 0) grow_nmax();
else nmax = n;
atom->nmax = nmax;
if (nmax < 0 || nmax > MAXSMALLINT)
error->one(FLERR,"Per-processor system is too big");
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");
// allocating mech. quantities
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");
// allocating path quantities
path = memory->grow(atom->path,nmax,3,"atom:path");
norm = memory->grow(atom->norm,nmax,3,"atom:norm");
dnorm = memory->grow(atom->dnorm,nmax,3,"atom:dnorm");
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 AtomVecPAFIPATH::grow_reset()
{
tag = atom->tag; type = atom->type;
mask = atom->mask; image = atom->image;
x = atom->x; v = atom->v; f = atom->f;
path = atom->path; norm = atom->norm; dnorm = atom->dnorm;
}
/* ----------------------------------------------------------------------
copy atom I info to atom J
------------------------------------------------------------------------- */
void AtomVecPAFIPATH::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];
path[j][0] = path[i][0];
path[j][1] = path[i][1];
path[j][2] = path[i][2];
norm[j][0] = norm[i][0];
norm[j][1] = norm[i][1];
norm[j][2] = norm[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,delflag);
}
/* ---------------------------------------------------------------------- */
int AtomVecPAFIPATH::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 AtomVecPAFIPATH::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++] = 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;
}
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++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
} 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;
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];
}
}
}
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecPAFIPATH::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 AtomVecPAFIPATH::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 AtomVecPAFIPATH::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 AtomVecPAFIPATH::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 AtomVecPAFIPATH::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++] = path[j][0];
buf[m++] = path[j][1];
buf[m++] = path[j][2];
buf[m++] = norm[j][0];
buf[m++] = norm[j][1];
buf[m++] = norm[j][2];
buf[m++] = dnorm[j][0];
buf[m++] = dnorm[j][1];
buf[m++] = dnorm[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++] = ubuf(tag[j]).d;
buf[m++] = ubuf(type[j]).d;
buf[m++] = ubuf(mask[j]).d;
buf[m++] = path[j][0];
buf[m++] = path[j][1];
buf[m++] = path[j][2];
buf[m++] = norm[j][0];
buf[m++] = norm[j][1];
buf[m++] = norm[j][2];
buf[m++] = dnorm[j][0];
buf[m++] = dnorm[j][1];
buf[m++] = dnorm[j][2];
}
}
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 AtomVecPAFIPATH::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++] = path[j][0];
buf[m++] = path[j][1];
buf[m++] = path[j][2];
buf[m++] = norm[j][0];
buf[m++] = norm[j][1];
buf[m++] = norm[j][2];
buf[m++] = dnorm[j][0];
buf[m++] = dnorm[j][1];
buf[m++] = dnorm[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];
}
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++] = ubuf(tag[j]).d;
buf[m++] = ubuf(type[j]).d;
buf[m++] = ubuf(mask[j]).d;
buf[m++] = path[j][0];
buf[m++] = path[j][1];
buf[m++] = path[j][2];
buf[m++] = norm[j][0];
buf[m++] = norm[j][1];
buf[m++] = norm[j][2];
buf[m++] = dnorm[j][0];
buf[m++] = dnorm[j][1];
buf[m++] = dnorm[j][2];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
} 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++] = path[j][0];
buf[m++] = path[j][1];
buf[m++] = path[j][2];
buf[m++] = norm[j][0];
buf[m++] = norm[j][1];
buf[m++] = norm[j][2];
buf[m++] = dnorm[j][0];
buf[m++] = dnorm[j][1];
buf[m++] = dnorm[j][2];
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];
}
}
}
}
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 AtomVecPAFIPATH::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++] = path[j][0];
buf[m++] = path[j][1];
buf[m++] = path[j][2];
buf[m++] = norm[j][0];
buf[m++] = norm[j][1];
buf[m++] = norm[j][2];
buf[m++] = dnorm[j][0];
buf[m++] = dnorm[j][1];
buf[m++] = dnorm[j][2];
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecPAFIPATH::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;
path[i][0] = buf[m++];
path[i][1] = buf[m++];
path[i][2] = buf[m++];
norm[i][0] = buf[m++];
norm[i][1] = buf[m++];
norm[i][2] = buf[m++];
dnorm[i][0] = buf[m++];
dnorm[i][1] = buf[m++];
dnorm[i][2] = 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]);
}
/* ---------------------------------------------------------------------- */
void AtomVecPAFIPATH::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;
path[i][0] = buf[m++];
path[i][1] = buf[m++];
path[i][2] = buf[m++];
norm[i][0] = buf[m++];
norm[i][1] = buf[m++];
norm[i][2] = buf[m++];
dnorm[i][0] = buf[m++];
dnorm[i][1] = buf[m++];
dnorm[i][2] = buf[m++];
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = 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 AtomVecPAFIPATH::unpack_border_hybrid(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
path[i][0] = buf[m++];
path[i][1] = buf[m++];
path[i][2] = buf[m++];
norm[i][0] = buf[m++];
norm[i][1] = buf[m++];
norm[i][2] = buf[m++];
dnorm[i][0] = buf[m++];
dnorm[i][1] = buf[m++];
dnorm[i][2] = buf[m++];
}
return m;
}
/* ----------------------------------------------------------------------
pack all atom quantities for shipping to another proc
xyz must be 1st 3 values, so that comm::exchange can test on them
------------------------------------------------------------------------- */
int AtomVecPAFIPATH::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++] = path[i][0];
buf[m++] = path[i][1];
buf[m++] = path[i][2];
buf[m++] = norm[i][0];
buf[m++] = norm[i][1];
buf[m++] = norm[i][2];
buf[m++] = dnorm[i][0];
buf[m++] = dnorm[i][1];
buf[m++] = dnorm[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 AtomVecPAFIPATH::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;
path[nlocal][0] = buf[m++];
path[nlocal][1] = buf[m++];
path[nlocal][2] = buf[m++];
norm[nlocal][0] = buf[m++];
norm[nlocal][1] = buf[m++];
norm[nlocal][2] = buf[m++];
dnorm[nlocal][0] = buf[m++];
dnorm[nlocal][1] = buf[m++];
dnorm[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 AtomVecPAFIPATH::size_restart()
{
int i;
int nlocal = atom->nlocal;
int n = 20 * 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 AtomVecPAFIPATH::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++] = path[i][0];
buf[m++] = path[i][1];
buf[m++] = path[i][2];
buf[m++] = norm[i][0];
buf[m++] = norm[i][1];
buf[m++] = norm[i][2];
buf[m++] = dnorm[i][0];
buf[m++] = dnorm[i][1];
buf[m++] = dnorm[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 AtomVecPAFIPATH::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++];
path[nlocal][0] = buf[m++];
path[nlocal][1] = buf[m++];
path[nlocal][2] = buf[m++];
norm[nlocal][0] = buf[m++];
norm[nlocal][1] = buf[m++];
norm[nlocal][2] = buf[m++];
dnorm[nlocal][0] = buf[m++];
dnorm[nlocal][1] = buf[m++];
dnorm[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 AtomVecPAFIPATH::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;
path[nlocal][0] = 0.0;
path[nlocal][1] = 0.0;
path[nlocal][2] = 0.0;
norm[nlocal][0] = 0.0;
norm[nlocal][1] = 0.0;
norm[nlocal][2] = 0.0;
dnorm[nlocal][0] = 0.0;
dnorm[nlocal][1] = 0.0;
dnorm[nlocal][2] = 0.0;
atom->nlocal++;
}
/* ----------------------------------------------------------------------
unpack one line from Atoms section of data file
initialize other atom quantities
------------------------------------------------------------------------- */
void AtomVecPAFIPATH::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");
x[nlocal][0] = coord[0];
x[nlocal][1] = coord[1];
x[nlocal][2] = coord[2];
path[nlocal][0] = atof(values[5]);
path[nlocal][1] = atof(values[6]);
path[nlocal][2] = atof(values[7]);
norm[nlocal][0] = atof(values[8]);
norm[nlocal][1] = atof(values[9]);
norm[nlocal][2] = atof(values[10]);
dnorm[nlocal][0] = atof(values[11]);
dnorm[nlocal][1] = atof(values[12]);
dnorm[nlocal][2] = atof(values[13]);
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 AtomVecPAFIPATH::data_atom_hybrid(int nlocal, char **values)
{
path[nlocal][0] = atof(values[0]);
path[nlocal][1] = atof(values[1]);
path[nlocal][2] = atof(values[2]);
norm[nlocal][0] = atof(values[3]);
norm[nlocal][1] = atof(values[4]);
norm[nlocal][2] = atof(values[5]);
dnorm[nlocal][0] = atof(values[6]);
dnorm[nlocal][1] = atof(values[7]);
dnorm[nlocal][2] = atof(values[8]);
return 9;
}
/* ----------------------------------------------------------------------
pack atom info for data file including 3 image flags
------------------------------------------------------------------------- */
void AtomVecPAFIPATH::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] = x[i][0];
buf[i][3] = x[i][1];
buf[i][4] = x[i][2];
buf[i][5] = path[i][0];
buf[i][6] = path[i][1];
buf[i][7] = path[i][2];
buf[i][8] = norm[i][0];
buf[i][9] = norm[i][1];
buf[i][10] = norm[i][2];
buf[i][11] = dnorm[i][0];
buf[i][12] = dnorm[i][1];
buf[i][13] = dnorm[i][2];
buf[i][14] = ubuf((image[i] & IMGMASK) - IMGMAX).d;
buf[i][15] = ubuf((image[i] >> IMGBITS & IMGMASK) - IMGMAX).d;
buf[i][16] = ubuf((image[i] >> IMG2BITS) - IMGMAX).d;
}
}
/* ----------------------------------------------------------------------
pack hybrid atom info for data file
------------------------------------------------------------------------- */
int AtomVecPAFIPATH::pack_data_hybrid(int i, double *buf)
{
buf[0] = path[i][0];
buf[1] = path[i][1];
buf[2] = path[i][2];
buf[3] = norm[i][0];
buf[4] = norm[i][1];
buf[5] = norm[i][2];
buf[6] = dnorm[i][0];
buf[7] = dnorm[i][1];
buf[8] = dnorm[i][2];
return 9;
}
/* ----------------------------------------------------------------------
write atom info to data file including 3 image flags
------------------------------------------------------------------------- */
void AtomVecPAFIPATH::write_data(FILE *fp, int n, double **buf)
{
for (int i = 0; i < n; i++)
fprintf(fp,TAGINT_FORMAT \
" %d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e"
" %-1.16e %-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],buf[i][3],buf[i][4],
buf[i][5],buf[i][6],buf[i][7],
buf[i][8],buf[i][9],buf[i][10],
buf[i][11],buf[i][12],buf[i][13],
(int) ubuf(buf[i][14]).i,(int) ubuf(buf[i][15]).i,
(int) ubuf(buf[i][16]).i);
}
/* ----------------------------------------------------------------------
write hybrid atom info to data file
------------------------------------------------------------------------- */
int AtomVecPAFIPATH::write_data_hybrid(FILE *fp, double *buf)
{
fprintf(fp,"%-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e",
buf[0],buf[1],buf[2],
buf[3],buf[4],buf[5],
buf[6],buf[7],buf[8]);
return 9;
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
------------------------------------------------------------------------- */
bigint AtomVecPAFIPATH::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("path")) bytes += memory->usage(path,nmax,3);
if (atom->memcheck("norm")) bytes += memory->usage(norm,nmax,3);
if (atom->memcheck("dnorm")) bytes += memory->usage(dnorm,nmax,3);
return bytes;
}

91
src/USER-PAFI/atom_vec_pafipath.h
View File

@ -1,91 +0,0 @@
/* -*- c++ -*- ----------------------------------------------------------
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: Thomas Swinburne (CNRS & CINaM, Marseille, France)
Please cite the related publication:
T.D. Swinburne and M.-C. Marinica, Unsupervised calculation of free energy barriers in large crystalline systems, Physical Review Letters 2018
------------------------------------------------------------------------- */
#ifdef ATOM_CLASS
AtomStyle(pafipath,AtomVecPAFIPATH)
#else
#ifndef LMP_ATOM_VEC_PAFIPATH_H
#define LMP_ATOM_VEC_PAFIPATH_H
#include "atom_vec.h"
namespace LAMMPS_NS {
class AtomVecPAFIPATH : public AtomVec {
public:
AtomVecPAFIPATH(class LAMMPS *);
void grow(int);
void grow_reset();
void copy(int, int, int);
int pack_comm(int, int *, double *, int, int *);
int pack_comm_vel(int, int *, double *, int, int *);
void unpack_comm(int, int, double *);
void unpack_comm_vel(int, int, double *);
int pack_reverse(int, int, double *);
void unpack_reverse(int, int *, double *);
int pack_border(int, int *, double *, int, int *);
int pack_border_vel(int, int *, double *, int, int *);
int pack_border_hybrid(int, int *, double *);
void unpack_border(int, int, double *);
void unpack_border_vel(int, int, double *);
int unpack_border_hybrid(int, int, double *);
int pack_exchange(int, double *);
int unpack_exchange(double *);
int size_restart();
int pack_restart(int, double *);
int unpack_restart(double *);
void create_atom(int, double *);
virtual void data_atom(double *, imageint, char **);
virtual int data_atom_hybrid(int, char **);
virtual void pack_data(double **);
virtual int pack_data_hybrid(int, double *);
virtual void write_data(FILE *, int, double **);
virtual int write_data_hybrid(FILE *, double *);
bigint memory_usage();
private:
tagint *tag;
int *type,*mask;
imageint *image;
double **x,**v,**f; // lattice quantities
// 0th, 1st and 2nd derivative of reference path w.r.t. to path coordinate r
double **path,**norm,**dnorm;
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Per-processor system is too big
The number of owned atoms plus ghost atoms on a single
processor must fit in 32-bit integer.
E: Invalid atom type in Atoms section of data file
Atom types must range from 1 to specified # of types.
*/

24
src/atom.cpp
View File

@ -117,12 +117,6 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
eff_plastic_strain_rate = NULL; eff_plastic_strain_rate = NULL;
damage = NULL; damage = NULL;
// USER-PAFI
path = NULL;
norm = NULL;
dnorm = NULL;
// molecular info // molecular info
bond_per_atom = extra_bond_per_atom = 0; bond_per_atom = extra_bond_per_atom = 0;
@ -167,7 +161,6 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
sphere_flag = peri_flag = electron_flag = 0; sphere_flag = peri_flag = electron_flag = 0;
wavepacket_flag = sph_flag = 0; wavepacket_flag = sph_flag = 0;
molecule_flag = 0; molecule_flag = 0;
q_flag = mu_flag = 0; q_flag = mu_flag = 0;
omega_flag = torque_flag = angmom_flag = 0; omega_flag = torque_flag = angmom_flag = 0;
@ -198,10 +191,6 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
eff_plastic_strain_rate_flag = 0; eff_plastic_strain_rate_flag = 0;
damage_flag = 0; damage_flag = 0;
// USER-PAFI
pafi_flag = 0;
// Peridynamic scale factor // Peridynamic scale factor
pdscale = 1.0; pdscale = 1.0;
@ -358,12 +347,6 @@ Atom::~Atom()
memory->destroy(improper_atom3); memory->destroy(improper_atom3);
memory->destroy(improper_atom4); memory->destroy(improper_atom4);
// USER-PAFI
memory->destroy(path);
memory->destroy(norm);
memory->destroy(dnorm);
// delete custom atom arrays // delete custom atom arrays
for (int i = 0; i < nivector; i++) { for (int i = 0; i < nivector; i++) {
@ -439,7 +422,7 @@ void Atom::create_avec(const char *style, int narg, char **arg, int trysuffix)
// customize by adding new flag // customize by adding new flag
sphere_flag = peri_flag = electron_flag = 0; sphere_flag = peri_flag = electron_flag = 0;
wavepacket_flag = sph_flag = pafi_flag = 0; wavepacket_flag = sph_flag = 0;
molecule_flag = 0; molecule_flag = 0;
q_flag = mu_flag = 0; q_flag = mu_flag = 0;
@ -2311,11 +2294,6 @@ void *Atom::extract(char *name)
if (strcmp(name,"dpdTheta") == 0) return (void *) dpdTheta; if (strcmp(name,"dpdTheta") == 0) return (void *) dpdTheta;
if (strcmp(name,"edpd_temp") == 0) return (void *) edpd_temp; if (strcmp(name,"edpd_temp") == 0) return (void *) edpd_temp;
// USER-PAFI
if (strcmp(name,"norm") == 0) return (void *) norm;
if (strcmp(name,"dnorm") == 0) return (void *) dnorm;
if (strcmp(name,"path") == 0) return (void *) path;
return NULL; return NULL;
} }

7
src/atom.h
View File

@ -111,13 +111,6 @@ class Atom : protected Pointers {
double *edpd_cv; // heat capacity double *edpd_cv; // heat capacity
int cc_species; int cc_species;
// USER-PAFI package
int pafi_flag;
double **path;
double **norm;
double **dnorm;
// molecular info // molecular info
int **nspecial; // 0,1,2 = cumulative # of 1-2,1-3,1-4 neighs int **nspecial; // 0,1,2 = cumulative # of 1-2,1-3,1-4 neighs

429
src/library.cpp
View File

@ -1490,24 +1490,8 @@ void lammps_scatter_atoms_subset(void *ptr, char *name,
#endif #endif
/* ----------------------------------------------------------------------
Contributing author: Thomas Swinburne (CNRS & CINaM, Marseille, France)
gather the named per atom fix and return it in user-allocated data
(extract_fix was found to give errors when running lammps in parallel)
data will be ordered by atom ID
requirement for consecutive atom IDs (1 to N)
id = fix ID
count: number of entries per atom
Fills 1d data, which must be pre-allocated to length of count * Natoms, where Natoms is as queried by get_natoms()
method:
alloc and zero count*Natom length vector
loop over nlocal to fill vector with my values
Allreduce to sum vector into data across all procs
------------------------------------------------------------------------- */
#if defined(LAMMPS_BIGBIG) #if defined(LAMMPS_BIGBIG)
void lammps_gather_peratom_fix(void *ptr, char * /*id */, int /*count*/, void * /*data*/) void lammps_gather_peratom_fix(void *ptr, char * /*id */, int /*type*/, int /*count*/, void * /*data*/)
{ {
LAMMPS *lmp = (LAMMPS *) ptr; LAMMPS *lmp = (LAMMPS *) ptr;
@ -1516,7 +1500,7 @@ void lammps_gather_peratom_fix(void *ptr, char * /*id */, int /*count*/, void *
END_CAPTURE END_CAPTURE
} }
#else #else
void lammps_gather_peratom_fix(void *ptr, char *id, int count, void *data) void lammps_gather_peratom_fix(void *ptr, char *id, int type, int count, void *data)
{ {
LAMMPS *lmp = (LAMMPS *) ptr; LAMMPS *lmp = (LAMMPS *) ptr;
@ -1526,7 +1510,7 @@ void lammps_gather_peratom_fix(void *ptr, char *id, int count, void *data)
int ifix = lmp->modify->find_fix(id); int ifix = lmp->modify->find_fix(id);
if (ifix < 0) { if (ifix < 0) {
lmp->error->warning(FLERR,"lammps_gather_pertatom_fix: unknown fix id"); lmp->error->warning(FLERR,"lammps_gather_peratom_fix: unknown fix id");
return; return;
} }
@ -1547,31 +1531,57 @@ void lammps_gather_peratom_fix(void *ptr, char *id, int count, void *data)
// copy = Natom length vector of per-atom values // copy = Natom length vector of per-atom values
// use atom ID to insert each atom's values into copy // use atom ID to insert each atom's values into copy
// MPI_Allreduce with MPI_SUM to merge into data, ordered by atom ID // MPI_Allreduce with MPI_SUM to merge into data, ordered by atom ID
if (type==0) {
int *vector = NULL;
int **array = NULL;
if (count == 1) vector = (int *) fix->vector_atom; //vptr;
else array = (int **) fix->array_atom; //vptr;
double *vector = NULL; int *copy;
double **array = NULL; lmp->memory->create(copy,count*natoms,"lib/gather:copy");
if (count == 1) vector = (double *) fix->vector_atom; //vptr; for (i = 0; i < count*natoms; i++) copy[i] = 0;
else array = (double **) fix->array_atom; //vptr;
double *copy; tagint *tag = lmp->atom->tag;
lmp->memory->create(copy,count*natoms,"lib/gather:copy"); int nlocal = lmp->atom->nlocal;
for (i = 0; i < count*natoms; i++) copy[i] = 0.0;
tagint *tag = lmp->atom->tag; if (count == 1) {
int nlocal = lmp->atom->nlocal; for (i = 0; i < nlocal; i++)
copy[tag[i]-1] = vector[i];
if (count == 1) { } else {
for (i = 0; i < nlocal; i++) for (i = 0; i < nlocal; i++) {
copy[tag[i]-1] = vector[i]; offset = count*(tag[i]-1);
} else { for (j = 0; j < count; j++)
for (i = 0; i < nlocal; i++) { copy[offset++] = array[i][j];
offset = count*(tag[i]-1); }
for (j = 0; j < count; j++)
copy[offset++] = array[i][j];
} }
MPI_Allreduce(copy,data,count*natoms,MPI_INT,MPI_SUM,lmp->world);
lmp->memory->destroy(copy);
} else {
double *vector = NULL;
double **array = NULL;
if (count == 1) vector = (double *) fix->vector_atom; //vptr;
else array = (double **) fix->array_atom; //vptr;
double *copy;
lmp->memory->create(copy,count*natoms,"lib/gather:copy");
for (i = 0; i < count*natoms; i++) copy[i] = 0.0;
tagint *tag = lmp->atom->tag;
int nlocal = lmp->atom->nlocal;
if (count == 1) {
for (i = 0; i < nlocal; i++)
copy[tag[i]-1] = vector[i];
} else {
for (i = 0; i < nlocal; i++) {
offset = count*(tag[i]-1);
for (j = 0; j < count; j++)
copy[offset++] = array[i][j];
}
}
MPI_Allreduce(copy,data,count*natoms,MPI_DOUBLE,MPI_SUM,lmp->world);
lmp->memory->destroy(copy);
} }
MPI_Allreduce(copy,data,count*natoms,MPI_DOUBLE,MPI_SUM,lmp->world);
lmp->memory->destroy(copy);
} }
END_CAPTURE END_CAPTURE
} }
@ -1595,8 +1605,8 @@ void lammps_gather_peratom_fix(void *ptr, char *id, int count, void *data)
Allreduce to sum vector into data across all procs Allreduce to sum vector into data across all procs
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#if defined(LAMMPS_BIGBIG) #if defined(LAMMPS_BIGBIG)
void lammps_gather_peratom_fix_subset(void *ptr, char * /*id */, int /*count*/, void lammps_gather_peratom_fix_subset(void *ptr, char * /*id */, int /*type*/,
int /*ndata*/, int * /*ids*/, void * /*data*/) int /*count*/, int /*ndata*/, int * /*ids*/, void * /*data*/)
{ {
LAMMPS *lmp = (LAMMPS *) ptr; LAMMPS *lmp = (LAMMPS *) ptr;
@ -1605,7 +1615,7 @@ void lammps_gather_peratom_fix_subset(void *ptr, char * /*id */, int /*count*/,
END_CAPTURE END_CAPTURE
} }
#else #else
void lammps_gather_peratom_fix_subset(void *ptr, char *id, int count, void lammps_gather_peratom_fix_subset(void *ptr, char *id, int type, int count,
int ndata, int *ids, void *data) int ndata, int *ids, void *data)
{ {
LAMMPS *lmp = (LAMMPS *) ptr; LAMMPS *lmp = (LAMMPS *) ptr;
@ -1617,7 +1627,7 @@ void lammps_gather_peratom_fix_subset(void *ptr, char *id, int count,
int ifix = lmp->modify->find_fix(id); int ifix = lmp->modify->find_fix(id);
if (ifix < 0) { if (ifix < 0) {
lmp->error->warning(FLERR,"lammps_gather_pertatom_fix: unknown fix id"); lmp->error->warning(FLERR,"lammps_gather_peratom_fix_subset: unknown fix id");
return; return;
} }
@ -1631,49 +1641,330 @@ void lammps_gather_peratom_fix_subset(void *ptr, char *id, int count,
if (lmp->atom->natoms > MAXSMALLINT) flag = 1; if (lmp->atom->natoms > MAXSMALLINT) flag = 1;
if (flag) { if (flag) {
if (lmp->comm->me == 0) if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"Library error in lammps_gather_peratom_fix"); lmp->error->warning(FLERR,"Library error in lammps_gather_peratom_fix_subset");
return; return;
} }
// copy = Natom length vector of per-atom values // copy = Natom length vector of per-atom values
// use atom ID to insert each atom's values into copy // use atom ID to insert each atom's values into copy
// MPI_Allreduce with MPI_SUM to merge into data, ordered by atom ID // MPI_Allreduce with MPI_SUM to merge into data, ordered by atom ID
if (type==0) {
int *vector = NULL;
int **array = NULL;
if (count == 1) vector = (int *) fix->vector_atom; //vptr;
else array = (int **) fix->array_atom; //vptr;
double *vector = NULL; int *copy;
double **array = NULL; lmp->memory->create(copy,count*ndata,"lib/gather:copy");
if (count == 1) vector = (double *) fix->vector_atom; //vptr; for (i = 0; i < count*ndata; i++) copy[i] = 0;
else array = (double **) fix->array_atom; //vptr;
double *copy; tagint *tag = lmp->atom->tag;
lmp->memory->create(copy,count*natoms,"lib/gather:copy"); int nlocal = lmp->atom->nlocal;
for (i = 0; i < count*natoms; i++) copy[i] = 0.0;
tagint *tag = lmp->atom->tag; if (count == 1) {
int nlocal = lmp->atom->nlocal; for (i = 0; i < ndata; i++) {
aid = ids[i];
if (count == 1) { if ((m = lmp->atom->map(aid)) >= 0 && m < nlocal)
for (i = 0; i < ndata; i++) { copy[i] = vector[m];
aid = ids[i]; }
if ((m = lmp->atom->map(aid)) >= 0 && m < nlocal) } else {
copy[i] = vector[m]; for (i = 0; i < ndata; i++) {
} aid = ids[i];
} else { if ((m = lmp->atom->map(aid)) >= 0 && m < nlocal) {
for (i = 0; i < ndata; i++) { offset = count*i;
aid = ids[i]; for (j = 0; j < count; j++)
if ((m = lmp->atom->map(aid)) >= 0 && m < nlocal) { copy[offset++] = array[m][j];
offset = count*i; }
for (j = 0; j < count; j++)
copy[offset++] = array[m][j];
} }
} }
MPI_Allreduce(copy,data,count*ndata,MPI_INT,MPI_SUM,lmp->world);
lmp->memory->destroy(copy);
} else {
double *vector = NULL;
double **array = NULL;
if (count == 1) vector = (double *) fix->vector_atom; //vptr;
else array = (double **) fix->array_atom; //vptr;
double *copy;
lmp->memory->create(copy,count*ndata,"lib/gather:copy");
for (i = 0; i < count*ndata; i++) copy[i] = 0.0;
tagint *tag = lmp->atom->tag;
int nlocal = lmp->atom->nlocal;
if (count == 1) {
for (i = 0; i < ndata; i++) {
aid = ids[i];
if ((m = lmp->atom->map(aid)) >= 0 && m < nlocal)
copy[i] = vector[m];
}
} else {
for (i = 0; i < ndata; i++) {
aid = ids[i];
if ((m = lmp->atom->map(aid)) >= 0 && m < nlocal) {
offset = count*i;
for (j = 0; j < count; j++)
copy[offset++] = array[m][j];
}
}
}
MPI_Allreduce(copy,data,count*ndata,MPI_DOUBLE,MPI_SUM,lmp->world);
lmp->memory->destroy(copy);
} }
MPI_Allreduce(copy,data,count*natoms,MPI_DOUBLE,MPI_SUM,lmp->world);
lmp->memory->destroy(copy);
} }
END_CAPTURE END_CAPTURE
} }
#endif #endif
/* ----------------------------------------------------------------------
scatter the named atom-based entity in data to all atoms
data is ordered by atom ID
requirement for consecutive atom IDs (1 to N)
see scatter_atoms_subset() to scatter data for some (or all) atoms, unordered
name = desired quantity, e.g. x or charge
type = 0 for integer values, 1 for double values
count = # of per-atom values, e.g. 1 for type or charge, 3 for x or f
use count = 3 with "image" for xyz to be packed into single image flag
data = atom-based values in 1d data, ordered by count, then by atom ID
e.g. x[0][0],x[0][1],x[0][2],x[1][0],x[1][1],x[1][2],x[2][0],...
data must be correct length = count*Natoms, as queried by get_natoms()
method:
loop over Natoms, if I own atom ID, set its values from data
------------------------------------------------------------------------- */
#if defined(LAMMPS_BIGBIG)
void lammps_scatter_peratom_fix(void *ptr, char * /*id */, int /*type*/, int /*count*/, void * /*data*/)
{
LAMMPS *lmp = (LAMMPS *) ptr;
BEGIN_CAPTURE
{
lmp->error->all(FLERR,"Library function lammps_scatter_peratom_fix() "
"is not compatible with -DLAMMPS_BIGBIG");
}
END_CAPTURE
}
#else
void lammps_scatter_peratom_fix(void *ptr, char *id, int type, int count, void *data)
{
LAMMPS *lmp = (LAMMPS *) ptr;
BEGIN_CAPTURE
{
int i,j,m,offset;
int ifix = lmp->modify->find_fix(id);
if (ifix < 0) {
lmp->error->warning(FLERR,"lammps_scatter_peratom_fix: unknown fix id");
return;
}
// error if tags are not defined or not consecutive or no atom map
// NOTE: test that name = image or ids is not a 64-bit int in code?
int flag = 0;
if (lmp->atom->tag_enable == 0 || lmp->atom->tag_consecutive() == 0)
flag = 1;
if (lmp->atom->natoms > MAXSMALLINT) flag = 1;
if (lmp->atom->map_style == 0) flag = 1;
if (flag) {
if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"Library error in lammps_scatter_peratom_fix");
return;
}
Fix *fix = lmp->modify->fix[ifix];
int natoms = static_cast<int> (lmp->atom->natoms);
if (type == 0) {
int *vector = NULL;
int **array = NULL;
if (count == 1) vector = (int *) fix->vector_atom;
else array = (int **) fix->array_atom;
int *dptr = (int *) data;
if (count == 1) {
for (i = 0; i < natoms; i++)
if ((m = lmp->atom->map(i+1)) >= 0)
vector[m] = dptr[i];
} else {
for (i = 0; i < natoms; i++)
if ((m = lmp->atom->map(i+1)) >= 0) {
offset = count*i;
for (j = 0; j < count; j++)
array[m][j] = dptr[offset++];
}
}
} else {
double *vector = NULL;
double **array = NULL;
if (count == 1) vector = (double *) fix->vector_atom;
else array = (double **) fix->array_atom;
double *dptr = (double *) data;
if (count == 1) {
for (i = 0; i < natoms; i++)
if ((m = lmp->atom->map(i+1)) >= 0)
vector[m] = dptr[i];
} else {
for (i = 0; i < natoms; i++) {
if ((m = lmp->atom->map(i+1)) >= 0) {
offset = count*i;
for (j = 0; j < count; j++)
array[m][j] = dptr[offset++];
}
}
}
}
}
END_CAPTURE
}
#endif
/* ----------------------------------------------------------------------
scatter the named atom-based entity in data to a subset of atoms
data is ordered by provided atom IDs
no requirement for consecutive atom IDs (1 to N)
see scatter_atoms() to scatter data for all atoms, ordered by consecutive IDs
name = desired quantity, e.g. x or charge
type = 0 for integer values, 1 for double values
count = # of per-atom values, e.g. 1 for type or charge, 3 for x or f
use count = 3 with "image" for xyz to be packed into single image flag
ndata = # of atoms in ids and data (could be all atoms)
ids = list of Ndata atom IDs to scatter data to
data = atom-based values in 1d data, ordered by count, then by atom ID
e.g. x[0][0],x[0][1],x[0][2],x[1][0],x[1][1],x[1][2],x[2][0],...
data must be correct length = count*Ndata
method:
loop over Ndata, if I own atom ID, set its values from data
------------------------------------------------------------------------- */
#if defined(LAMMPS_BIGBIG)
void lammps_scatter_peratom_fix_subset(void *ptr, char * /*name */,
int /*type*/, int /*count*/,
int /*ndata*/, int * /*ids*/, void * /*data*/)
{
LAMMPS *lmp = (LAMMPS *) ptr;
BEGIN_CAPTURE
{
lmp->error->all(FLERR,"Library function lammps_scatter_atoms_subset() "
"is not compatible with -DLAMMPS_BIGBIG");
}
END_CAPTURE
}
#else
void lammps_scatter_peratom_fix_subset(void *ptr, char *name,
int type, int count,
int ndata, int *ids, void *data)
{
LAMMPS *lmp = (LAMMPS *) ptr;
BEGIN_CAPTURE
{
int i,j,m,offset;
tagint id;
// error if tags are not defined or no atom map
// NOTE: test that name = image or ids is not a 64-bit int in code?
int flag = 0;
if (lmp->atom->tag_enable == 0) flag = 1;
if (lmp->atom->natoms > MAXSMALLINT) flag = 1;
if (lmp->atom->map_style == 0) flag = 1;
if (flag) {
if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"Library error in lammps_scatter_atoms_subset");
return;
}
void *vptr = lmp->atom->extract(name);
if(vptr == NULL) {
lmp->error->warning(FLERR,
"lammps_scatter_atoms_subset: unknown property name");
return;
}
// copy = Natom length vector of per-atom values
// use atom ID to insert each atom's values into copy
// MPI_Allreduce with MPI_SUM to merge into data, ordered by atom ID
if (type == 0) {
int *vector = NULL;
int **array = NULL;
const int imgpack = (count == 3) && (strcmp(name,"image") == 0);
if ((count == 1) || imgpack) vector = (int *) vptr;
else array = (int **) vptr;
int *dptr = (int *) data;
if (count == 1) {
for (i = 0; i < ndata; i++) {
id = ids[i];
if ((m = lmp->atom->map(id)) >= 0)
vector[m] = dptr[i];
}
} else if (imgpack) {
for (i = 0; i < ndata; i++) {
id = ids[i];
if ((m = lmp->atom->map(id)) >= 0) {
offset = count*i;
int image = dptr[offset++] + IMGMAX;
image += (dptr[offset++] + IMGMAX) << IMGBITS;
image += (dptr[offset++] + IMGMAX) << IMG2BITS;
vector[m] = image;
}
}
} else {
for (i = 0; i < ndata; i++) {
id = ids[i];
if ((m = lmp->atom->map(id)) >= 0) {
offset = count*i;
for (j = 0; j < count; j++)
array[m][j] = dptr[offset++];
}
}
}
} else {
double *vector = NULL;
double **array = NULL;
if (count == 1) vector = (double *) vptr;
else array = (double **) vptr;
double *dptr = (double *) data;
if (count == 1) {
for (i = 0; i < ndata; i++) {
id = ids[i];
if ((m = lmp->atom->map(id)) >= 0)
vector[m] = dptr[i];
}
} else {
for (i = 0; i < ndata; i++) {
id = ids[i];
if ((m = lmp->atom->map(id)) >= 0) {
offset = count*i;
for (j = 0; j < count; j++)
array[m][j] = dptr[offset++];
}
}
}
}
}
END_CAPTURE
}
#endif
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
create N atoms and assign them to procs based on coords create N atoms and assign them to procs based on coords
id = atom IDs (optional, NULL will generate 1 to N) id = atom IDs (optional, NULL will generate 1 to N)

5
src/library.h
View File

@ -69,7 +69,10 @@ void lammps_gather_atoms_subset(void *, char *, int, int, int, int *, void *);
void lammps_scatter_atoms(void *, char *, int, int, void *); void lammps_scatter_atoms(void *, char *, int, int, void *);
void lammps_scatter_atoms_subset(void *, char *, int, int, int, int *, void *); void lammps_scatter_atoms_subset(void *, char *, int, int, int, int *, void *);
void lammps_gather_peratom_fix(void *, char *, int, void *); void lammps_gather_peratom_fix(void *, char *, int, int, void *);
void lammps_gather_peratom_fix_subset(void *, char *, int, int, int, int *, void *);
void lammps_scatter_peratom_fix(void *, char *, int, int, void *);
void lammps_scatter_peratom_fix_subset(void *, char *, int, int, int, int *, void *);
#if defined(LAMMPS_BIGBIG) #if defined(LAMMPS_BIGBIG)