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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3551 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2009-12-16 20:27:17 +00:00
parent 664fa43717
commit 823cbd55b3
8 changed files with 220 additions and 649 deletions
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202
src/compute_rdf.cpp Normal file
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@ -0,0 +1,202 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Paul Crozier (SNL), Jeff Greathouse (SNL)
------------------------------------------------------------------------- */
#include "mpi.h"
#include "math.h"
#include "stdlib.h"
#include "compute_rdf.h"
#include "atom.h"
#include "update.h"
#include "force.h"
#include "pair.h"
#include "neighbor.h"
#include "neigh_request.h"
#include "neigh_list.h"
#include "group.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeRDF::ComputeRDF(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg < 8 || (narg-6) % 2) error->all("Illegal compute rdf command");
array_flag = 1;
size_array_rows = 1;
size_array_cols = 1;
extarray = 1;
maxbin = atoi(arg[5]);
npairs = 0;
rdfpair = memory->create_2d_int_array(atom->ntypes+1,atom->ntypes+1,
"rdf:rdfpair");
for (int i = 1; i <= atom->ntypes; i++)
for (int j = 1; j <= atom->ntypes; j++)
rdfpair[i][j] = 0;
int itype,jtype;
for (int i = 6; i < narg; i += 2) {
itype = atoi(arg[i]);
jtype = atoi(arg[i+1]);
if (itype < 1 || jtype < 1 || itype > atom->ntypes || jtype > atom->ntypes)
error->all("Invalid atom type in compute rdf command");
npairs++;
rdfpair[itype][jtype] = npairs;
}
hist = memory->create_2d_double_array(maxbin,npairs+1,"rdf:hist");
array = memory->create_2d_double_array(maxbin,npairs+1,"rdf:array");
int *nrdfatom = new int[atom->ntypes+1];
for (int i = 1; i <= atom->ntypes; i++) nrdfatom[i] = 0;
int *mask = atom->mask;
int *type = atom->type;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) nrdfatom[type[i]]++;
nrdfatoms = new int[atom->ntypes+1];
MPI_Allreduce(&nrdfatom[1],&nrdfatoms[1],atom->ntypes,MPI_INT,MPI_SUM,world);
delete [] nrdfatom;
}
/* ---------------------------------------------------------------------- */
ComputeRDF::~ComputeRDF()
{
memory->destroy_2d_int_array(rdfpair);
memory->destroy_2d_double_array(hist);
delete [] nrdfatoms;
}
/* ---------------------------------------------------------------------- */
void ComputeRDF::init()
{
if (force->pair) delr = force->pair->cutforce / maxbin;
else error->all("Compute rdf requires a pair style be defined");
delrinv = 1.0/delr;
// need an occasional half neighbor list
int irequest = neighbor->request((void *) this);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->compute = 1;
neighbor->requests[irequest]->occasional = 1;
}
/* ---------------------------------------------------------------------- */
void ComputeRDF::init_list(int id, NeighList *ptr)
{
list = ptr;
}
/* ---------------------------------------------------------------------- */
void ComputeRDF::compute_array()
{
invoked_array = update->ntimestep;
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int *type = atom->type;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int nall = atom->nlocal + atom->nghost;
int newton_pair = force->newton_pair;
int i,j,ii,jj,inum,jnum,itype,jtype,ipair,jpair,bin;
double xtmp,ytmp,ztmp,delx,dely,delz,r;
int *ilist,*jlist,*numneigh,**firstneigh;
// invoke half neighbor list (will copy or build if necessary)
neighbor->build_one(list->index);
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// zero the histogram counts
for (int i = 0; i < maxbin; i++)
for (int j = 0; j < npairs; j++)
hist[i][j] = 0;
// tally the RDF
// both atom i and j must be in fix group
// itype,jtype must have been specified by user
// weighting factor must be != 0.0 for this pair
// could be 0 and still be in neigh list for long-range Coulombics
// count the interaction once even if neighbor pair is stored on 2 procs
// if itype = jtype, count the interaction twice
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
if (mask[i] & groupbit) {
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j >= nall) {
if (special_coul[j/nall] == 0.0 && special_lj[j/nall] == 0.0)
continue;
j %= nall;
}
if (mask[j] & groupbit) {
jtype = type[j];
ipair = rdfpair[itype][jtype];
jpair = rdfpair[jtype][itype];
if (!ipair && !jpair) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
r = sqrt(delx*delx + dely*dely + delz*delz);
bin = static_cast<int> (r*delrinv);
if (bin >= maxbin) continue;
if (ipair) hist[bin][ipair-1]++;
if (newton_pair || j < nlocal)
if (jpair) hist[bin][jpair-1]++;
}
}
}
}
// sum histogram across procs
MPI_Allreduce(hist[0],array[0],maxbin*npairs,MPI_DOUBLE,MPI_SUM,world);
}

28
src/fix_com.h → src/compute_rdf.h
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@ -11,27 +11,31 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifndef FIX_COM_H
#define FIX_COM_H
#ifndef COMPUTE_RDF_H
#define COMPUTE_RDF_H
#include "stdio.h"
#include "fix.h"
#include "compute.h"
namespace LAMMPS_NS {
class FixCOM : public Fix {
class ComputeRDF : public Compute {
public:
FixCOM(class LAMMPS *, int, char **);
~FixCOM();
int setmask();
ComputeRDF(class LAMMPS *, int, char **);
~ComputeRDF();
void init();
void setup(int);
void end_of_step();
void init_list(int, class NeighList *);
void compute_array();
private:
int me,first;
FILE *fp;
double masstotal;
int first;
int maxbin; // # of rdf bins
int npairs; // # of rdf pairs
double delr,delrinv; // bin width and its inverse
int **rdfpair; // mapping from 2 types to rdf pair
double **hist; // histogram bins
int *nrdfatoms; // # of atoms of each type in the group
class NeighList *list; // half neighbor list
};
}

92
src/fix_com.cpp
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@ -1,92 +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.
------------------------------------------------------------------------- */
#include "stdlib.h"
#include "fix_com.h"
#include "atom.h"
#include "update.h"
#include "domain.h"
#include "group.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
FixCOM::FixCOM(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg != 5) error->all("Illegal fix com command");
nevery = atoi(arg[3]);
if (nevery <= 0) error->all("Illegal fix com command");
first = 1;
MPI_Comm_rank(world,&me);
if (me == 0) {
fp = fopen(arg[4],"w");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open fix com file %s",arg[4]);
error->one(str);
}
}
if (me == 0) {
fprintf(fp,"# Center-of-mass for group %s\n",group->names[igroup]);
fprintf(fp,"# TimeStep x y z\n");
}
}
/* ---------------------------------------------------------------------- */
FixCOM::~FixCOM()
{
if (me == 0) fclose(fp);
}
/* ---------------------------------------------------------------------- */
int FixCOM::setmask()
{
int mask = 0;
mask |= END_OF_STEP;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixCOM::init()
{
masstotal = group->mass(igroup);
}
/* ---------------------------------------------------------------------- */
void FixCOM::setup(int vflag)
{
if (first) end_of_step();
first = 0;
}
/* ---------------------------------------------------------------------- */
void FixCOM::end_of_step()
{
double xcm[3];
group->xcm(igroup,masstotal,xcm);
if (me == 0) {
fprintf(fp,"%d %g %g %g\n",update->ntimestep,xcm[0],xcm[1],xcm[2]);
fflush(fp);
}
}

93
src/fix_gyration.cpp
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@ -1,93 +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.
------------------------------------------------------------------------- */
#include "stdlib.h"
#include "fix_gyration.h"
#include "atom.h"
#include "update.h"
#include "domain.h"
#include "group.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
FixGyration::FixGyration(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg != 5) error->all("Illegal fix gyration command");
nevery = atoi(arg[3]);
if (nevery <= 0) error->all("Illegal fix gyration command");
first = 1;
MPI_Comm_rank(world,&me);
if (me == 0) {
fp = fopen(arg[4],"w");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open fix gyration file %s",arg[4]);
error->one(str);
}
}
if (me == 0) {
fprintf(fp,"# Radius-of-gyration for group %s\n",group->names[igroup]);
fprintf(fp,"# TimeStep Rg\n");
}
}
/* ---------------------------------------------------------------------- */
FixGyration::~FixGyration()
{
if (me == 0) fclose(fp);
}
/* ---------------------------------------------------------------------- */
int FixGyration::setmask()
{
int mask = 0;
mask |= END_OF_STEP;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixGyration::init()
{
masstotal = group->mass(igroup);
}
/* ---------------------------------------------------------------------- */
void FixGyration::setup(int vflag)
{
if (first) end_of_step();
first = 0;
}
/* ---------------------------------------------------------------------- */
void FixGyration::end_of_step()
{
double xcm[3];
group->xcm(igroup,masstotal,xcm);
double rg = group->gyration(igroup,masstotal,xcm);
if (me == 0) {
fprintf(fp,"%d %g\n",update->ntimestep,rg);
fflush(fp);
}
}

39
src/fix_gyration.h
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@ -1,39 +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.
------------------------------------------------------------------------- */
#ifndef FIX_GYRATION_H
#define FIX_GYRATION_H
#include "stdio.h"
#include "fix.h"
namespace LAMMPS_NS {
class FixGyration : public Fix {
public:
FixGyration(class LAMMPS *, int, char **);
~FixGyration();
int setmask();
void init();
void setup(int);
void end_of_step();
private:
int me,first;
FILE *fp;
double masstotal;
};
}
#endif

355
src/fix_msd.cpp
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@ -1,355 +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.
------------------------------------------------------------------------- */
#include "stdlib.h"
#include "string.h"
#include "fix_msd.h"
#include "atom.h"
#include "update.h"
#include "domain.h"
#include "group.h"
#include "modify.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
FixMSD::FixMSD(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 5) error->all("Illegal fix msd command");
nevery = atoi(arg[3]);
if (nevery <= 0) error->all("Illegal fix msd command");
first = 1;
restart_peratom = 1;
MPI_Comm_rank(world,&me);
if (me == 0) {
fp = fopen(arg[4],"w");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open fix msd file %s",arg[4]);
error->one(str);
}
}
if (me == 0) {
fprintf(fp,"# Mean-squared Displacement for group %s\n",
group->names[igroup]);
fprintf(fp,"# TimeStep x y z total\n");
}
// optional args
comflag = 0;
int iarg = 5;
while (iarg < narg) {
if (strcmp(arg[iarg],"com") == 0) {
if (iarg+2 > narg) error->all("Illegal fix msd command");
if (strcmp(arg[iarg+1],"no") == 0) comflag = 0;
else if (strcmp(arg[iarg+1],"yes") == 0) comflag = 1;
else error->all("Illegal fix msd command");
iarg += 2;
} else error->all("Illegal fix msd command");
}
// perform initial allocation of atom-based array
// register with Atom class
xoriginal = NULL;
grow_arrays(atom->nmax);
atom->add_callback(0);
atom->add_callback(1);
// cm = original center of mass
double cm[3];
if (comflag) {
masstotal = group->mass(igroup);
group->xcm(igroup,masstotal,cm);
}
// xoriginal = initial unwrapped positions of atoms
// relative to center of mass if comflag is set
double **x = atom->x;
int *mask = atom->mask;
int *image = atom->image;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
domain->unmap(x[i],image[i],xoriginal[i]);
if (comflag) {
xoriginal[i][0] -= cm[0];
xoriginal[i][1] -= cm[1];
xoriginal[i][2] -= cm[2];
}
} else xoriginal[i][0] = xoriginal[i][1] = xoriginal[i][2] = 0.0;
}
// nmsd = # of atoms in group
nmsd = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) nmsd++;
int nmsd_all;
MPI_Allreduce(&nmsd,&nmsd_all,1,MPI_INT,MPI_SUM,world);
nmsd = nmsd_all;
if (nmsd == 0) error->all("Fix msd group has no atoms");
}
/* ---------------------------------------------------------------------- */
FixMSD::~FixMSD()
{
if (me == 0) fclose(fp);
// unregister callbacks to this fix from Atom class
atom->delete_callback(id,0);
atom->delete_callback(id,1);
// delete locally stored array
memory->destroy_2d_double_array(xoriginal);
}
/* ---------------------------------------------------------------------- */
int FixMSD::setmask()
{
int mask = 0;
mask |= END_OF_STEP;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixMSD::init()
{
// warn if more than one msd fix
int count = 0;
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"msd") == 0) count++;
if (count > 1 && me == 0) error->warning("More than one fix msd");
}
/* ---------------------------------------------------------------------- */
void FixMSD::setup(int vflag)
{
if (first) end_of_step();
first = 0;
}
/* ---------------------------------------------------------------------- */
void FixMSD::end_of_step()
{
// cm = current center of mass
double cm[3];
if (comflag) {
group->mass(igroup);
group->xcm(igroup,masstotal,cm);
}
double **x = atom->x;
int *mask = atom->mask;
int *image = atom->image;
int nlocal = atom->nlocal;
double *h = domain->h;
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
int xbox,ybox,zbox;
double dx,dy,dz;
double msd[4];
msd[0] = msd[1] = msd[2] = msd[3] = 0.0;
// dx,dy,dz = displacement of atom from original position
// relative to center of mass if comflag is set
// for triclinic, need to unwrap current atom coord via h matrix
if (domain->triclinic == 0) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
xbox = (image[i] & 1023) - 512;
ybox = (image[i] >> 10 & 1023) - 512;
zbox = (image[i] >> 20) - 512;
if (comflag) {
dx = x[i][0] + xbox*xprd - cm[0] - xoriginal[i][0];
dy = x[i][1] + ybox*yprd - cm[1] - xoriginal[i][1];
dz = x[i][2] + zbox*zprd - cm[2] - xoriginal[i][2];
} else {
dx = x[i][0] + xbox*xprd - xoriginal[i][0];
dy = x[i][1] + ybox*yprd - xoriginal[i][1];
dz = x[i][2] + zbox*zprd - xoriginal[i][2];
}
msd[0] += dx*dx;
msd[1] += dy*dy;
msd[2] += dz*dz;
msd[3] += dx*dx + dy*dy + dz*dz;
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
xbox = (image[i] & 1023) - 512;
ybox = (image[i] >> 10 & 1023) - 512;
zbox = (image[i] >> 20) - 512;
if (comflag) {
dx = x[i][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox -
cm[0] - xoriginal[i][0];
dy = x[i][1] + h[1]*ybox + h[3]*zbox - cm[1] - xoriginal[i][1];
dz = x[i][2] + h[2]*zbox - cm[2] - xoriginal[i][2];
} else {
dx = x[i][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox - xoriginal[i][0];
dy = x[i][1] + h[1]*ybox + h[3]*zbox - xoriginal[i][1];
dz = x[i][2] + h[2]*zbox - xoriginal[i][2];
}
msd[0] += dx*dx;
msd[1] += dy*dy;
msd[2] += dz*dz;
msd[3] += dx*dx + dy*dy + dz*dz;
}
}
double msd_all[4];
MPI_Allreduce(msd,msd_all,4,MPI_DOUBLE,MPI_SUM,world);
msd_all[0] /= nmsd;
msd_all[1] /= nmsd;
msd_all[2] /= nmsd;
msd_all[3] /= nmsd;
if (me == 0) {
fprintf(fp,"%d %g %g %g %g\n",update->ntimestep,
msd_all[0],msd_all[1],msd_all[2],msd_all[3]);
fflush(fp);
}
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
double FixMSD::memory_usage()
{
double bytes = atom->nmax*3 * sizeof(double);
return bytes;
}
/* ----------------------------------------------------------------------
allocate atom-based array
------------------------------------------------------------------------- */
void FixMSD::grow_arrays(int nmax)
{
xoriginal =
memory->grow_2d_double_array(xoriginal,nmax,3,"msd:xoriginal");
}
/* ----------------------------------------------------------------------
copy values within local atom-based array
------------------------------------------------------------------------- */
void FixMSD::copy_arrays(int i, int j)
{
xoriginal[j][0] = xoriginal[i][0];
xoriginal[j][1] = xoriginal[i][1];
xoriginal[j][2] = xoriginal[i][2];
}
/* ----------------------------------------------------------------------
pack values in local atom-based array for exchange with another proc
------------------------------------------------------------------------- */
int FixMSD::pack_exchange(int i, double *buf)
{
buf[0] = xoriginal[i][0];
buf[1] = xoriginal[i][1];
buf[2] = xoriginal[i][2];
return 3;
}
/* ----------------------------------------------------------------------
unpack values in local atom-based array from exchange with another proc
------------------------------------------------------------------------- */
int FixMSD::unpack_exchange(int nlocal, double *buf)
{
xoriginal[nlocal][0] = buf[0];
xoriginal[nlocal][1] = buf[1];
xoriginal[nlocal][2] = buf[2];
return 3;
}
/* ----------------------------------------------------------------------
pack values in local atom-based arrays for restart file
------------------------------------------------------------------------- */
int FixMSD::pack_restart(int i, double *buf)
{
buf[0] = 4;
buf[1] = xoriginal[i][0];
buf[2] = xoriginal[i][1];
buf[3] = xoriginal[i][2];
return 4;
}
/* ----------------------------------------------------------------------
unpack values from atom->extra array to restart the fix
------------------------------------------------------------------------- */
void FixMSD::unpack_restart(int nlocal, int nth)
{
double **extra = atom->extra;
// skip to Nth set of extra values
int m = 0;
for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);
m++;
xoriginal[nlocal][0] = extra[nlocal][m++];
xoriginal[nlocal][1] = extra[nlocal][m++];
xoriginal[nlocal][2] = extra[nlocal][m++];
}
/* ----------------------------------------------------------------------
maxsize of any atom's restart data
------------------------------------------------------------------------- */
int FixMSD::maxsize_restart()
{
return 4;
}
/* ----------------------------------------------------------------------
size of atom nlocal's restart data
------------------------------------------------------------------------- */
int FixMSD::size_restart(int nlocal)
{
return 4;
}

52
src/fix_msd.h
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@ -1,52 +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.
------------------------------------------------------------------------- */
#ifndef FIX_MSD_H
#define FIX_MSD_H
#include "stdio.h"
#include "fix.h"
namespace LAMMPS_NS {
class FixMSD : public Fix {
public:
FixMSD(class LAMMPS *, int, char **);
~FixMSD();
int setmask();
void init();
void setup(int);
void end_of_step();
double memory_usage();
void grow_arrays(int);
void copy_arrays(int, int);
int pack_exchange(int, double *);
int unpack_exchange(int, double *);
int pack_restart(int, double *);
void unpack_restart(int, int);
int size_restart(int);
int maxsize_restart();
private:
int me,first,comflag;
FILE *fp;
double masstotal;
int nmsd; // # of atoms in group
double **xoriginal; // original coords of atoms
};
}
#endif

8
src/style.h
View File

@ -90,6 +90,7 @@ CommandStyle(write_restart,WriteRestart)
#include "compute_pe.h"
#include "compute_pe_atom.h"
#include "compute_pressure.h"
#include "compute_rdf.h"
#include "compute_reduce.h"
#include "compute_reduce_region.h"
#include "compute_erotate_sphere.h"
@ -120,6 +121,7 @@ ComputeStyle(msd,ComputeMSD)
ComputeStyle(pe,ComputePE)
ComputeStyle(pe/atom,ComputePEAtom)
ComputeStyle(pressure,ComputePressure)
ComputeStyle(rdf,ComputeRDF)
ComputeStyle(reduce,ComputeReduce)
ComputeStyle(reduce/region,ComputeReduceRegion)
ComputeStyle(erotate/sphere,ComputeERotateSphere)
@ -165,7 +167,6 @@ DumpStyle(xyz,DumpXYZ)
#include "fix_ave_spatial.h"
#include "fix_ave_time.h"
#include "fix_box_relax.h"
#include "fix_com.h"
#include "fix_coord_original.h"
#include "fix_deform.h"
#include "fix_deposit.h"
@ -175,13 +176,11 @@ DumpStyle(xyz,DumpXYZ)
#include "fix_enforce2d.h"
#include "fix_evaporate.h"
#include "fix_gravity.h"
#include "fix_gyration.h"
#include "fix_heat.h"
#include "fix_indent.h"
#include "fix_langevin.h"
#include "fix_lineforce.h"
#include "fix_minimize.h"
#include "fix_msd.h"
#include "fix_momentum.h"
#include "fix_move.h"
#include "fix_nph.h"
@ -228,7 +227,6 @@ FixStyle(ave/histo,FixAveHisto)
FixStyle(ave/spatial,FixAveSpatial)
FixStyle(ave/time,FixAveTime)
FixStyle(box/relax,FixBoxRelax)
FixStyle(com,FixCOM)
FixStyle(coord/original,FixCoordOriginal)
FixStyle(deform,FixDeform)
FixStyle(deposit,FixDeposit)
@ -238,7 +236,6 @@ FixStyle(efield,FixEfield)
FixStyle(enforce2d,FixEnforce2D)
FixStyle(evaporate,FixEvaporate)
FixStyle(gravity,FixGravity)
FixStyle(gyration,FixGyration)
FixStyle(heat,FixHeat)
FixStyle(indent,FixIndent)
FixStyle(langevin,FixLangevin)
@ -246,7 +243,6 @@ FixStyle(lineforce,FixLineForce)
FixStyle(MINIMIZE,FixMinimize)
FixStyle(momentum,FixMomentum)
FixStyle(move,FixMove)
FixStyle(msd,FixMSD)
FixStyle(nph,FixNPH)
FixStyle(npt,FixNPT)
FixStyle(npt/sphere,FixNPTSphere)