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lammps/src/pair_hybrid.cpp
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pair_hybrid.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "math.h"
#include "stdlib.h"
#include "string.h"
#include "ctype.h"
#include "pair_hybrid.h"
#include "atom.h"
#include "force.h"
#include "pair.h"
#include "neighbor.h"
#include "neigh_request.h"
#include "update.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairHybrid::PairHybrid(LAMMPS *lmp) : Pair(lmp)
{
nstyles = 0;
styles = NULL;
keywords = NULL;
multiple = NULL;
}
/* ---------------------------------------------------------------------- */
PairHybrid::~PairHybrid()
{
if (nstyles) {
for (int m = 0; m < nstyles; m++) delete styles[m];
for (int m = 0; m < nstyles; m++) delete [] keywords[m];
}
delete [] styles;
delete [] keywords;
delete [] multiple;
delete [] svector;
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(cutghost);
memory->destroy(nmap);
memory->destroy(map);
}
}
/* ----------------------------------------------------------------------
call each sub-style's compute function
accumulate sub-style global/peratom energy/virial in hybrid
for global vflag = 1:
each sub-style computes own virial[6]
sum sub-style virial[6] to hybrid's virial[6]
for global vflag = 2:
call sub-style with adjusted vflag to prevent it calling
virial_fdotr_compute()
hybrid calls virial_fdotr_compute() on final accumulated f
------------------------------------------------------------------------- */
void PairHybrid::compute(int eflag, int vflag)
{
int i,j,m,n;
// if no_virial_fdotr_compute is set and global component of
// incoming vflag = 2, then
// reset vflag as if global component were 1
// necessary since one or more sub-styles cannot compute virial as F dot r
if (no_virial_fdotr_compute && vflag % 4 == 2) vflag = 1 + vflag/4 * 4;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = eflag_global = vflag_global =
eflag_atom = vflag_atom = 0;
// check if global component of incoming vflag = 2
// if so, reset vflag passed to substyle as if it were 0
// necessary so substyle will not invoke virial_fdotr_compute()
int vflag_substyle;
if (vflag % 4 == 2) vflag_substyle = vflag/4 * 4;
else vflag_substyle = vflag;
for (m = 0; m < nstyles; m++) {
styles[m]->compute(eflag,vflag_substyle);
if (eflag_global) {
eng_vdwl += styles[m]->eng_vdwl;
eng_coul += styles[m]->eng_coul;
}
if (vflag_global) {
for (n = 0; n < 6; n++) virial[n] += styles[m]->virial[n];
}
if (eflag_atom) {
n = atom->nlocal;
if (force->newton_pair) 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_pair) 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];
}
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ---------------------------------------------------------------------- */
void PairHybrid::compute_inner()
{
for (int m = 0; m < nstyles; m++)
if (styles[m]->respa_enable) styles[m]->compute_inner();
}
/* ---------------------------------------------------------------------- */
void PairHybrid::compute_middle()
{
for (int m = 0; m < nstyles; m++)
if (styles[m]->respa_enable) styles[m]->compute_middle();
}
/* ---------------------------------------------------------------------- */
void PairHybrid::compute_outer(int eflag, int vflag)
{
for (int m = 0; m < nstyles; m++)
if (styles[m]->respa_enable) styles[m]->compute_outer(eflag,vflag);
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairHybrid::allocate()
{
allocated = 1;
int n = atom->ntypes;
memory->create(setflag,n+1,n+1,"pair:setflag");
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
memory->create(cutsq,n+1,n+1,"pair:cutsq");
memory->create(cutghost,n+1,n+1,"pair:cutghost");
memory->create(nmap,n+1,n+1,"pair:nmap");
memory->create(map,n+1,n+1,nstyles,"pair:map");
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
nmap[i][j] = 0;
}
/* ----------------------------------------------------------------------
create one pair style for each arg in list
------------------------------------------------------------------------- */
void PairHybrid::settings(int narg, char **arg)
{
int i,m,istyle;
if (narg < 1) error->all(FLERR,"Illegal pair_style command");
// delete old lists, since cannot just change settings
if (nstyles) {
for (m = 0; m < nstyles; m++) delete styles[m];
delete [] styles;
for (m = 0; m < nstyles; m++) delete [] keywords[m];
delete [] keywords;
}
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(cutghost);
memory->destroy(nmap);
memory->destroy(map);
}
allocated = 0;
// build list of all known pair styles
build_styles();
// allocate list of sub-styles as big as possibly needed
styles = new Pair*[narg];
keywords = new char*[narg];
multiple = new int[narg];
// allocate each sub-style
// call settings() with set of args that are not pair style names
int iarg,jarg,dummy;
iarg = 0;
nstyles = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"hybrid") == 0)
error->all(FLERR,"Pair style hybrid cannot have hybrid as an argument");
if (strcmp(arg[iarg],"none") == 0)
error->all(FLERR,"Pair style hybrid cannot have none as an argument");
styles[nstyles] = force->new_pair(arg[i],lmp->suffix,dummy);
int n = strlen(arg[iarg]) + 1;
keywords[nstyles] = new char[n];
strcpy(keywords[nstyles],arg[iarg]);
jarg = iarg + 1;
while (jarg < narg && !known_style(arg[jarg])) jarg++;
styles[nstyles]->settings(jarg-iarg-1,&arg[iarg+1]);
iarg = jarg;
nstyles++;
}
// free allstyles
for (int i = 0; i < nallstyles; i++) delete [] allstyles[i];
delete [] allstyles;
// multiple[i] = 1 to N if sub-style used multiple times, else 0
for (int i = 0; i < nstyles; i++) {
int count = 0;
for (int j = 0; j < nstyles; j++) {
if (strcmp(keywords[j],keywords[i]) == 0) count++;
if (j == i) multiple[i] = count;
}
if (count == 1) multiple[i] = 0;
}
// set comm_forward, comm_reverse, comm_reverse_off to max of any sub-style
for (m = 0; m < nstyles; m++) {
if (styles[m]) comm_forward = MAX(comm_forward,styles[m]->comm_forward);
if (styles[m]) comm_reverse = MAX(comm_reverse,styles[m]->comm_reverse);
if (styles[m]) comm_reverse_off = MAX(comm_reverse_off,
styles[m]->comm_reverse_off);
}
// single_enable = 1 if any sub-style is set
// respa_enable = 1 if any sub-style is set
// no_virial_fdotr_compute = 1 if any sub-style is set
// ghostneigh = 1 if any sub-style is set
single_enable = 0;
for (m = 0; m < nstyles; m++)
if (styles[m]->single_enable) single_enable = 1;
for (m = 0; m < nstyles; m++)
if (styles[m]->respa_enable) respa_enable = 1;
for (m = 0; m < nstyles; m++)
if (styles[m]->no_virial_fdotr_compute) no_virial_fdotr_compute = 1;
for (m = 0; m < nstyles; m++)
if (styles[m]->ghostneigh) ghostneigh = 1;
// single_extra = min of all sub-style single_extra
// allocate svector
single_extra = styles[0]->single_extra;
for (m = 1; m < nstyles; m++)
single_extra = MIN(single_extra,styles[m]->single_extra);
if (single_extra) {
delete [] svector;
svector = new double[single_extra];
}
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairHybrid::coeff(int narg, char **arg)
{
if (narg < 3) error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
int ilo,ihi,jlo,jhi;
force->bounds(arg[0],atom->ntypes,ilo,ihi);
force->bounds(arg[1],atom->ntypes,jlo,jhi);
// 3rd arg = pair sub-style name
// 4th arg = pair sub-style index if name used multiple times
// allow for "none" as valid sub-style name
int multflag;
int m;
for (m = 0; m < nstyles; m++) {
multflag = 0;
if (strcmp(arg[2],keywords[m]) == 0) {
if (multiple[m]) {
multflag = 1;
if (narg < 4) error->all(FLERR,"Incorrect args for pair coefficients");
if (!isdigit(arg[3][0]))
error->all(FLERR,"Incorrect args for pair coefficients");
int index = atoi(arg[3]);
if (index == multiple[m]) break;
else continue;
} else break;
}
}
int none = 0;
if (m == nstyles) {
if (strcmp(arg[2],"none") == 0) none = 1;
else error->all(FLERR,"Pair coeff for hybrid has invalid style");
}
// move 1st/2nd args to 2nd/3rd args
// if multflag: move 1st/2nd args to 3rd/4th args
// just copy ptrs, since arg[] points into original input line
arg[2+multflag] = arg[1];
arg[1+multflag] = arg[0];
// invoke sub-style coeff() starting with 1st remaining arg
if (!none) styles[m]->coeff(narg-1-multflag,&arg[1+multflag]);
// if sub-style only allows one pair coeff call (with * * and type mapping)
// then unset setflag/map assigned to that style before setting it below
// in case pair coeff for this sub-style is being called for 2nd time
if (!none && styles[m]->one_coeff)
for (int i = 1; i <= atom->ntypes; i++)
for (int j = i; j <= atom->ntypes; j++)
if (nmap[i][j] && map[i][j][0] == m) {
setflag[i][j] = 0;
nmap[i][j] = 0;
}
// set setflag and which type pairs map to which sub-style
// if sub-style is none: set hybrid setflag, wipe out map
// else: set hybrid setflag & map only if substyle setflag is set
// previous mappings are wiped out
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
if (none) {
setflag[i][j] = 1;
nmap[i][j] = 0;
count++;
} else if (styles[m]->setflag[i][j]) {
setflag[i][j] = 1;
nmap[i][j] = 1;
map[i][j][0] = m;
count++;
}
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairHybrid::init_style()
{
int i,m,itype,jtype,used,istyle,skip;
// error if a sub-style is not used
int ntypes = atom->ntypes;
for (istyle = 0; istyle < nstyles; istyle++) {
used = 0;
for (itype = 1; itype <= ntypes; itype++)
for (jtype = itype; jtype <= ntypes; jtype++)
for (m = 0; m < nmap[itype][jtype]; m++)
if (map[itype][jtype][m] == istyle) used = 1;
if (used == 0) error->all(FLERR,"Pair hybrid sub-style is not used");
}
// each sub-style makes its neighbor list request(s)
for (istyle = 0; istyle < nstyles; istyle++) styles[istyle]->init_style();
// create skip lists for each pair neigh request
// any kind of list can have its skip flag set at this stage
for (i = 0; i < neighbor->nrequest; i++) {
if (!neighbor->requests[i]->pair) continue;
// istyle = associated sub-style
for (istyle = 0; istyle < nstyles; istyle++)
if (styles[istyle] == neighbor->requests[i]->requestor) break;
// allocate iskip and ijskip
// initialize so as to skip all pair types
// set ijskip = 0 if type pair matches any entry in sub-style map
// set ijskip = 0 if mixing will assign type pair to this sub-style
// will occur if type pair is currently unassigned
// and both I,I and J,J are assigned to single sub-style
// and sub-style for both I,I and J,J match istyle
// set iskip = 1 only if all ijskip for itype are 1
int *iskip = new int[ntypes+1];
int **ijskip;
memory->create(ijskip,ntypes+1,ntypes+1,"pair_hybrid:ijskip");
for (itype = 1; itype <= ntypes; itype++)
for (jtype = 1; jtype <= ntypes; jtype++)
ijskip[itype][jtype] = 1;
for (itype = 1; itype <= ntypes; itype++)
for (jtype = itype; jtype <= ntypes; jtype++) {
for (m = 0; m < nmap[itype][jtype]; m++)
if (map[itype][jtype][m] == istyle)
ijskip[itype][jtype] = ijskip[jtype][itype] = 0;
if (nmap[itype][jtype] == 0 &&
nmap[itype][itype] == 1 && map[itype][itype][0] == istyle &&
nmap[jtype][jtype] == 1 && map[jtype][jtype][0] == istyle)
ijskip[itype][jtype] = ijskip[jtype][itype] = 0;
}
for (itype = 1; itype <= ntypes; itype++) {
iskip[itype] = 1;
for (jtype = 1; jtype <= ntypes; jtype++)
if (ijskip[itype][jtype] == 0) iskip[itype] = 0;
}
// if any skipping occurs
// set request->skip and copy iskip and ijskip into request
// else delete iskip and ijskip
skip = 0;
for (itype = 1; itype <= ntypes; itype++)
for (jtype = 1; jtype <= ntypes; jtype++)
if (ijskip[itype][jtype] == 1) skip = 1;
if (skip) {
neighbor->requests[i]->skip = 1;
neighbor->requests[i]->iskip = iskip;
neighbor->requests[i]->ijskip = ijskip;
} else {
delete [] iskip;
memory->destroy(ijskip);
}
}
// combine sub-style neigh list requests and create new ones if needed
modify_requests();
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairHybrid::init_one(int i, int j)
{
// if I,J is not set explicitly:
// perform mixing only if I,I sub-style = J,J sub-style
// also require I,I and J,J are both assigned to single sub-style
if (setflag[i][j] == 0) {
if (nmap[i][i] != 1 || nmap[j][j] != 1 || map[i][i][0] != map[j][j][0])
error->one(FLERR,"All pair coeffs are not set");
nmap[i][j] = 1;
map[i][j][0] = map[i][i][0];
}
// call init/mixing for all sub-styles of I,J
// set cutsq in sub-style just as Pair::init() does via call to init_one()
// set cutghost for I,J and J,I just as sub-style does
// sum tail corrections for I,J
// return max cutoff of all sub-styles assigned to I,J
// if no sub-styles assigned to I,J (pair_coeff none), cutmax = 0.0 returned
double cutmax = 0.0;
cutghost[i][j] = cutghost[j][i] = 0.0;
if (tail_flag) etail_ij = ptail_ij = 0.0;
nmap[j][i] = nmap[i][j];
for (int k = 0; k < nmap[i][j]; k++) {
map[j][i][k] = map[i][j][k];
double cut = styles[map[i][j][k]]->init_one(i,j);
styles[map[i][j][k]]->cutsq[i][j] =
styles[map[i][j][k]]->cutsq[j][i] = cut*cut;
if (styles[map[i][j][k]]->ghostneigh)
cutghost[i][j] = cutghost[j][i] =
MAX(cutghost[i][j],styles[map[i][j][k]]->cutghost[i][j]);
if (tail_flag) {
etail_ij += styles[map[i][j][k]]->etail_ij;
ptail_ij += styles[map[i][j][k]]->ptail_ij;
}
cutmax = MAX(cutmax,cut);
}
return cutmax;
}
/* ----------------------------------------------------------------------
combine sub-style neigh list requests and create new ones if needed
------------------------------------------------------------------------- */
void PairHybrid::modify_requests()
{
int i,j;
NeighRequest *irq,*jrq;
// loop over pair requests only
// if list is skip list and not copy, look for non-skip list of same kind
// if one exists, point at that one via otherlist
// else make new non-skip request of same kind and point at that one
// don't bother to set ID for new request, since pair hybrid ignores list
// only exception is half_from_full:
// ignore it, turn off skip, since it will derive from its skip parent
// after possible new request creation, unset skip flag and otherlist
// for these derived lists: granhistory, rRESPA inner/middle
// this prevents neighbor from treating them as skip lists
// copy list check is for pair style = hybrid/overlay
// which invokes this routine
for (i = 0; i < neighbor->nrequest; i++) {
if (!neighbor->requests[i]->pair) continue;
irq = neighbor->requests[i];
if (irq->skip == 0 || irq->copy) continue;
if (irq->half_from_full) {
irq->skip = 0;
continue;
}
for (j = 0; j < neighbor->nrequest; j++) {
if (!neighbor->requests[j]->pair) continue;
jrq = neighbor->requests[j];
if (irq->same_kind(jrq) && jrq->skip == 0) break;
}
if (j < neighbor->nrequest) irq->otherlist = j;
else {
int newrequest = neighbor->request(this);
neighbor->requests[newrequest]->copy_request(irq);
irq->otherlist = newrequest;
}
if (irq->granhistory || irq->respainner || irq->respamiddle) {
irq->skip = 0;
irq->otherlist = -1;
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairHybrid::write_restart(FILE *fp)
{
fwrite(&nstyles,sizeof(int),1,fp);
// each sub-style writes its settings, but no coeff info
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);
styles[m]->write_restart_settings(fp);
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairHybrid::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 Pair*[nstyles];
keywords = new char*[nstyles];
// each sub-style is created via new_pair()
// each reads its settings, but no coeff info
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_pair(keywords[m],lmp->suffix,dummy);
styles[m]->read_restart_settings(fp);
}
}
/* ----------------------------------------------------------------------
call sub-style to compute single interaction
error if sub-style does not support single() call
since overlay could have multiple sub-styles, sum results explicitly
------------------------------------------------------------------------- */
double PairHybrid::single(int i, int j, int itype, int jtype,
double rsq, double factor_coul, double factor_lj,
double &fforce)
{
if (nmap[itype][jtype] == 0)
error->one(FLERR,"Invoked pair single on pair style none");
double fone;
fforce = 0.0;
double esum = 0.0;
for (int m = 0; m < nmap[itype][jtype]; m++) {
if (rsq < styles[map[itype][jtype][m]]->cutsq[itype][jtype]) {
if (styles[map[itype][jtype][m]]->single_enable == 0)
error->one(FLERR,"Pair hybrid sub-style does not support single call");
esum += styles[map[itype][jtype][m]]->
single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fone);
fforce += fone;
// copy substyle extra values into hybrid's svector
if (single_extra && styles[map[itype][jtype][m]]->single_extra)
for (m = 0; m < single_extra; m++)
svector[m] = styles[map[itype][jtype][m]]->svector[m];
}
}
return esum;
}
/* ----------------------------------------------------------------------
modify parameters of the pair style
call modify_params of PairHybrid
also pass command args to each sub-style of hybrid
------------------------------------------------------------------------- */
void PairHybrid::modify_params(int narg, char **arg)
{
Pair::modify_params(narg,arg);
for (int m = 0; m < nstyles; m++) styles[m]->modify_params(narg,arg);
}
/* ----------------------------------------------------------------------
extract a ptr to a particular quantity stored by pair
pass request thru to sub-styles
return first non-NULL result except for cut_coul request
for cut_coul, insure all non-NULL results are equal since required by Kspace
------------------------------------------------------------------------- */
void *PairHybrid::extract(const char *str, int &dim)
{
void *cutptr = NULL;
void *ptr;
double cutvalue;
for (int m = 0; m < nstyles; m++) {
ptr = styles[m]->extract(str,dim);
if (ptr && strcmp(str,"cut_coul") == 0) {
double *p_newvalue = (double *) ptr;
double newvalue = *p_newvalue;
if (cutptr && newvalue != cutvalue)
error->all(FLERR,
"Coulomb cutoffs of pair hybrid sub-styles do not match");
cutptr = ptr;
cutvalue = newvalue;
} else if (ptr) return ptr;
}
if (strcmp(str,"cut_coul") == 0) return cutptr;
return NULL;
}
/* ---------------------------------------------------------------------- */
void PairHybrid::reset_dt()
{
for (int m = 0; m < nstyles; m++) styles[m]->reset_dt();
}
/* ----------------------------------------------------------------------
check if itype,jtype maps to sub-style
------------------------------------------------------------------------- */
int PairHybrid::check_ijtype(int itype, int jtype, char *substyle)
{
for (int m = 0; m < nmap[itype][jtype]; m++)
if (strcmp(keywords[map[itype][jtype][m]],substyle) == 0) return 1;
return 0;
}
/* ----------------------------------------------------------------------
allstyles = list of all pair styles in this LAMMPS executable
------------------------------------------------------------------------- */
void PairHybrid::build_styles()
{
nallstyles = 0;
#define PAIR_CLASS
#define PairStyle(key,Class) nallstyles++;
#include "style_pair.h"
#undef PairStyle
#undef PAIR_CLASS
allstyles = new char*[nallstyles];
int n;
nallstyles = 0;
#define PAIR_CLASS
#define PairStyle(key,Class) \
n = strlen(#key) + 1; \
allstyles[nallstyles] = new char[n]; \
strcpy(allstyles[nallstyles],#key); \
nallstyles++;
#include "style_pair.h"
#undef PairStyle
#undef PAIR_CLASS
}
/* ----------------------------------------------------------------------
allstyles = list of all known pair styles
------------------------------------------------------------------------- */
int PairHybrid::known_style(char *str)
{
for (int i = 0; i < nallstyles; i++)
if (strcmp(str,allstyles[i]) == 0) return 1;
return 0;
}
/* ----------------------------------------------------------------------
memory usage of each sub-style
------------------------------------------------------------------------- */
double PairHybrid::memory_usage()
{
double bytes = maxeatom * sizeof(double);
bytes += maxvatom*6 * sizeof(double);
for (int m = 0; m < nstyles; m++) bytes += styles[m]->memory_usage();
return bytes;
}
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