Homec4science
Diffusion lammps (lammm-master-deprecated) Browse

lammps/src/MOLECULE/improper_hybrid.cpp
eb04caa0548alammm-master-deprecated

Last Change
Raw File

improper_hybrid.cpp
View Options

/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "math.h"
#include "string.h"
#include "improper_hybrid.h"
#include "atom.h"
#include "neighbor.h"
#include "domain.h"
#include "comm.h"
#include "force.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define EXTRA 1000
/* ---------------------------------------------------------------------- */
ImproperHybrid::ImproperHybrid(LAMMPS *lmp) : Improper(lmp)
{
nstyles = 0;
}
/* ---------------------------------------------------------------------- */
ImproperHybrid::~ImproperHybrid()
{
if (nstyles) {
for (int i = 0; i < nstyles; i++) delete styles[i];
delete [] styles;
for (int i = 0; i < nstyles; i++) delete [] keywords[i];
delete [] keywords;
}
if (allocated) {
memory->destroy(setflag);
memory->destroy(map);
delete [] nimproperlist;
delete [] maximproper;
for (int i = 0; i < nstyles; i++)
memory->destroy(improperlist[i]);
delete [] improperlist;
}
}
/* ---------------------------------------------------------------------- */
void ImproperHybrid::compute(int eflag, int vflag)
{
int i,j,m,n;
// save ptrs to original improperlist
int nimproperlist_orig = neighbor->nimproperlist;
int **improperlist_orig = neighbor->improperlist;
// if this is re-neighbor step, create sub-style improperlists
// nimproperlist[] = length of each sub-style list
// realloc sub-style improperlist if necessary
// load sub-style improperlist with 5 values from original improperlist
if (neighbor->ago == 0) {
for (m = 0; m < nstyles; m++) nimproperlist[m] = 0;
for (i = 0; i < nimproperlist_orig; i++) {
m = map[improperlist_orig[i][4]];
nimproperlist[m]++;
}
for (m = 0; m < nstyles; m++) {
if (nimproperlist[m] > maximproper[m]) {
memory->destroy(improperlist[m]);
maximproper[m] = nimproperlist[m] + EXTRA;
memory->create(improperlist[m],maximproper[m],5,
"improper_hybrid:improperlist");
}
nimproperlist[m] = 0;
}
for (i = 0; i < nimproperlist_orig; i++) {
m = map[improperlist_orig[i][4]];
if (m < 0) continue;
n = nimproperlist[m];
improperlist[m][n][0] = improperlist_orig[i][0];
improperlist[m][n][1] = improperlist_orig[i][1];
improperlist[m][n][2] = improperlist_orig[i][2];
improperlist[m][n][3] = improperlist_orig[i][3];
improperlist[m][n][4] = improperlist_orig[i][4];
nimproperlist[m]++;
}
}
// call each sub-style's compute function
// set neighbor->improperlist to sub-style improperlist before call
// accumulate sub-style global/peratom energy/virial in hybrid
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = 0;
for (m = 0; m < nstyles; m++) {
neighbor->nimproperlist = nimproperlist[m];
neighbor->improperlist = improperlist[m];
styles[m]->compute(eflag,vflag);
if (eflag_global) energy += styles[m]->energy;
if (vflag_global)
for (n = 0; n < 6; n++) virial[n] += styles[m]->virial[n];
if (eflag_atom) {
n = atom->nlocal;
if (force->newton_bond) n += atom->nghost;
double *eatom_substyle = styles[m]->eatom;
for (i = 0; i < n; i++) eatom[i] += eatom_substyle[i];
}
if (vflag_atom) {
n = atom->nlocal;
if (force->newton_bond) n += atom->nghost;
double **vatom_substyle = styles[m]->vatom;
for (i = 0; i < n; i++)
for (j = 0; j < 6; j++)
vatom[i][j] += vatom_substyle[i][j];
}
}
// restore ptrs to original improperlist
neighbor->nimproperlist = nimproperlist_orig;
neighbor->improperlist = improperlist_orig;
}
/* ---------------------------------------------------------------------- */
void ImproperHybrid::allocate()
{
allocated = 1;
int n = atom->nimpropertypes;
memory->create(map,n+1,"improper:map");
memory->create(setflag,n+1,"improper:setflag");
for (int i = 1; i <= n; i++) setflag[i] = 0;
nimproperlist = new int[nstyles];
maximproper = new int[nstyles];
improperlist = new int**[nstyles];
for (int m = 0; m < nstyles; m++) maximproper[m] = 0;
for (int m = 0; m < nstyles; m++) improperlist[m] = NULL;
}
/* ----------------------------------------------------------------------
create one improper style for each arg in list
------------------------------------------------------------------------- */
void ImproperHybrid::settings(int narg, char **arg)
{
nstyles = narg;
styles = new Improper*[nstyles];
keywords = new char*[nstyles];
int dummy;
for (int m = 0; m < nstyles; m++) {
for (int i = 0; i < m; i++)
if (strcmp(arg[m],arg[i]) == 0)
error->all(FLERR,
"Improper style hybrid cannot use same improper style twice");
if (strcmp(arg[m],"hybrid") == 0)
error->all(FLERR,
"Improper style hybrid cannot have hybrid as an argument");
if (strcmp(arg[m],"none") == 0)
error->all(FLERR,"Improper style hybrid cannot have none as an argument");
styles[m] = force->new_improper(arg[m],lmp->suffix,dummy);
keywords[m] = new char[strlen(arg[m])+1];
strcpy(keywords[m],arg[m]);
}
}
/* ----------------------------------------------------------------------
set coeffs for one type
---------------------------------------------------------------------- */
void ImproperHybrid::coeff(int narg, char **arg)
{
if (!allocated) allocate();
int ilo,ihi;
force->bounds(arg[0],atom->nimpropertypes,ilo,ihi);
// 2nd arg = improper sub-style name
// allow for "none" as valid sub-style name
int m;
for (m = 0; m < nstyles; m++)
if (strcmp(arg[1],keywords[m]) == 0) break;
int none = 0;
if (m == nstyles) {
if (strcmp(arg[1],"none") == 0) none = 1;
else error->all(FLERR,"Improper coeff for hybrid has invalid style");
}
// move 1st arg to 2nd arg
// just copy ptrs, since arg[] points into original input line
arg[1] = arg[0];
// invoke sub-style coeff() starting with 1st arg
if (!none) styles[m]->coeff(narg-1,&arg[1]);
// set setflag and which type maps to which sub-style
// if sub-style is none: set hybrid setflag, wipe out map
for (int i = ilo; i <= ihi; i++) {
if (none) {
setflag[i] = 1;
map[i] = -1;
} else {
setflag[i] = styles[m]->setflag[i];
map[i] = m;
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void ImproperHybrid::write_restart(FILE *fp)
{
fwrite(&nstyles,sizeof(int),1,fp);
int n;
for (int m = 0; m < nstyles; m++) {
n = strlen(keywords[m]) + 1;
fwrite(&n,sizeof(int),1,fp);
fwrite(keywords[m],sizeof(char),n,fp);
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void ImproperHybrid::read_restart(FILE *fp)
{
int me = comm->me;
if (me == 0) fread(&nstyles,sizeof(int),1,fp);
MPI_Bcast(&nstyles,1,MPI_INT,0,world);
styles = new Improper*[nstyles];
keywords = new char*[nstyles];
allocate();
int n,dummy;
for (int m = 0; m < nstyles; m++) {
if (me == 0) fread(&n,sizeof(int),1,fp);
MPI_Bcast(&n,1,MPI_INT,0,world);
keywords[m] = new char[n];
if (me == 0) fread(keywords[m],sizeof(char),n,fp);
MPI_Bcast(keywords[m],n,MPI_CHAR,0,world);
styles[m] = force->new_improper(keywords[m],lmp->suffix,dummy);
}
}
/* ----------------------------------------------------------------------
memory usage
------------------------------------------------------------------------- */
double ImproperHybrid::memory_usage()
{
double bytes = maxeatom * sizeof(double);
bytes += maxvatom*6 * sizeof(double);
for (int m = 0; m < nstyles; m++) bytes += maximproper[m]*5 * sizeof(int);
for (int m = 0; m < nstyles; m++)
if (styles[m]) bytes += styles[m]->memory_usage();
return bytes;
}
c4science · Help