git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9722 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
338
src/improper_hybrid.cpp
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338
src/improper_hybrid.cpp
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "math.h"
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#include "string.h"
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#include "ctype.h"
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#include "improper_hybrid.h"
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#include "atom.h"
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#include "neighbor.h"
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#include "domain.h"
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#include "comm.h"
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#include "force.h"
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#include "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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#define EXTRA 1000
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/* ---------------------------------------------------------------------- */
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ImproperHybrid::ImproperHybrid(LAMMPS *lmp) : Improper(lmp)
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{
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nstyles = 0;
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}
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/* ---------------------------------------------------------------------- */
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ImproperHybrid::~ImproperHybrid()
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{
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if (nstyles) {
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for (int i = 0; i < nstyles; i++) delete styles[i];
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delete [] styles;
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for (int i = 0; i < nstyles; i++) delete [] keywords[i];
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delete [] keywords;
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}
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if (allocated) {
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memory->destroy(setflag);
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memory->destroy(map);
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delete [] nimproperlist;
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delete [] maximproper;
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for (int i = 0; i < nstyles; i++)
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memory->destroy(improperlist[i]);
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delete [] improperlist;
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}
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}
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/* ---------------------------------------------------------------------- */
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void ImproperHybrid::compute(int eflag, int vflag)
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{
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int i,j,m,n;
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// save ptrs to original improperlist
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int nimproperlist_orig = neighbor->nimproperlist;
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int **improperlist_orig = neighbor->improperlist;
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// if this is re-neighbor step, create sub-style improperlists
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// nimproperlist[] = length of each sub-style list
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// realloc sub-style improperlist if necessary
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// load sub-style improperlist with 5 values from original improperlist
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if (neighbor->ago == 0) {
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for (m = 0; m < nstyles; m++) nimproperlist[m] = 0;
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for (i = 0; i < nimproperlist_orig; i++) {
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m = map[improperlist_orig[i][4]];
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nimproperlist[m]++;
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}
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for (m = 0; m < nstyles; m++) {
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if (nimproperlist[m] > maximproper[m]) {
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memory->destroy(improperlist[m]);
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maximproper[m] = nimproperlist[m] + EXTRA;
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memory->create(improperlist[m],maximproper[m],5,
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"improper_hybrid:improperlist");
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}
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nimproperlist[m] = 0;
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}
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for (i = 0; i < nimproperlist_orig; i++) {
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m = map[improperlist_orig[i][4]];
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if (m < 0) continue;
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n = nimproperlist[m];
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improperlist[m][n][0] = improperlist_orig[i][0];
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improperlist[m][n][1] = improperlist_orig[i][1];
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improperlist[m][n][2] = improperlist_orig[i][2];
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improperlist[m][n][3] = improperlist_orig[i][3];
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improperlist[m][n][4] = improperlist_orig[i][4];
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nimproperlist[m]++;
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}
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}
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// call each sub-style's compute function
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// set neighbor->improperlist to sub-style improperlist before call
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// accumulate sub-style global/peratom energy/virial in hybrid
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if (eflag || vflag) ev_setup(eflag,vflag);
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else evflag = 0;
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for (m = 0; m < nstyles; m++) {
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neighbor->nimproperlist = nimproperlist[m];
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neighbor->improperlist = improperlist[m];
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styles[m]->compute(eflag,vflag);
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if (eflag_global) energy += styles[m]->energy;
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if (vflag_global)
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for (n = 0; n < 6; n++) virial[n] += styles[m]->virial[n];
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if (eflag_atom) {
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n = atom->nlocal;
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if (force->newton_bond) n += atom->nghost;
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double *eatom_substyle = styles[m]->eatom;
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for (i = 0; i < n; i++) eatom[i] += eatom_substyle[i];
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}
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if (vflag_atom) {
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n = atom->nlocal;
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if (force->newton_bond) n += atom->nghost;
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double **vatom_substyle = styles[m]->vatom;
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for (i = 0; i < n; i++)
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for (j = 0; j < 6; j++)
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vatom[i][j] += vatom_substyle[i][j];
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}
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}
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// restore ptrs to original improperlist
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neighbor->nimproperlist = nimproperlist_orig;
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neighbor->improperlist = improperlist_orig;
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}
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/* ---------------------------------------------------------------------- */
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void ImproperHybrid::allocate()
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{
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allocated = 1;
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int n = atom->nimpropertypes;
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memory->create(map,n+1,"improper:map");
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memory->create(setflag,n+1,"improper:setflag");
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for (int i = 1; i <= n; i++) setflag[i] = 0;
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nimproperlist = new int[nstyles];
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maximproper = new int[nstyles];
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improperlist = new int**[nstyles];
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for (int m = 0; m < nstyles; m++) maximproper[m] = 0;
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for (int m = 0; m < nstyles; m++) improperlist[m] = NULL;
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}
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/* ----------------------------------------------------------------------
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create one improper style for each arg in list
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------------------------------------------------------------------------- */
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void ImproperHybrid::settings(int narg, char **arg)
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{
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int i,m,istyle;
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if (narg < 1) error->all(FLERR,"Illegal improper_style command");
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// delete old lists, since cannot just change settings
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if (nstyles) {
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for (int i = 0; i < nstyles; i++) delete styles[i];
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delete [] styles;
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for (int i = 0; i < nstyles; i++) delete [] keywords[i];
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delete [] keywords;
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}
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if (allocated) {
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memory->destroy(setflag);
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memory->destroy(map);
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delete [] nimproperlist;
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delete [] maximproper;
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for (int i = 0; i < nstyles; i++)
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memory->destroy(improperlist[i]);
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delete [] improperlist;
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}
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allocated = 0;
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// count sub-styles by skipping numeric args
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// one exception is 1st arg of style "table", which is non-numeric word
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// need a better way to skip these exceptions
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nstyles = 0;
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i = 0;
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while (i < narg) {
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if (strcmp(arg[i],"table") == 0) i++;
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i++;
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while (i < narg && !isalpha(arg[i][0])) i++;
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nstyles++;
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}
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// allocate list of sub-styles
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styles = new Improper*[nstyles];
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keywords = new char*[nstyles];
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// allocate each sub-style and call its settings() with subset of args
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// define subset of args for a sub-style by skipping numeric args
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// one exception is 1st arg of style "table", which is non-numeric
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// need a better way to skip these exceptions
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int dummy;
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nstyles = 0;
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i = 0;
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while (i < narg) {
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for (m = 0; m < nstyles; m++)
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if (strcmp(arg[i],keywords[m]) == 0)
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error->all(FLERR,"Improper style hybrid cannot use "
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"same improper style twice");
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if (strcmp(arg[i],"hybrid") == 0)
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error->all(FLERR,
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"Improper style hybrid cannot have hybrid as an argument");
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if (strcmp(arg[i],"none") == 0)
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error->all(FLERR,"Improper style hybrid cannot have none as an argument");
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styles[nstyles] = force->new_improper(arg[i],lmp->suffix,dummy);
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keywords[nstyles] = new char[strlen(arg[i])+1];
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strcpy(keywords[nstyles],arg[i]);
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istyle = i;
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if (strcmp(arg[i],"table") == 0) i++;
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i++;
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while (i < narg && !isalpha(arg[i][0])) i++;
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styles[nstyles]->settings(i-istyle-1,&arg[istyle+1]);
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nstyles++;
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}
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}
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/* ----------------------------------------------------------------------
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set coeffs for one type
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---------------------------------------------------------------------- */
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void ImproperHybrid::coeff(int narg, char **arg)
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{
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if (!allocated) allocate();
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int ilo,ihi;
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force->bounds(arg[0],atom->nimpropertypes,ilo,ihi);
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// 2nd arg = improper sub-style name
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// allow for "none" as valid sub-style name
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int m;
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for (m = 0; m < nstyles; m++)
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if (strcmp(arg[1],keywords[m]) == 0) break;
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int none = 0;
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if (m == nstyles) {
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if (strcmp(arg[1],"none") == 0) none = 1;
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else error->all(FLERR,"Improper coeff for hybrid has invalid style");
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}
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// move 1st arg to 2nd arg
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// just copy ptrs, since arg[] points into original input line
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arg[1] = arg[0];
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// invoke sub-style coeff() starting with 1st arg
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if (!none) styles[m]->coeff(narg-1,&arg[1]);
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// set setflag and which type maps to which sub-style
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// if sub-style is none: set hybrid setflag, wipe out map
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for (int i = ilo; i <= ihi; i++) {
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if (none) {
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setflag[i] = 1;
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map[i] = -1;
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} else {
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setflag[i] = styles[m]->setflag[i];
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map[i] = m;
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}
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}
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}
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/* ----------------------------------------------------------------------
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proc 0 writes to restart file
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------------------------------------------------------------------------- */
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void ImproperHybrid::write_restart(FILE *fp)
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{
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fwrite(&nstyles,sizeof(int),1,fp);
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int n;
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for (int m = 0; m < nstyles; m++) {
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n = strlen(keywords[m]) + 1;
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fwrite(&n,sizeof(int),1,fp);
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fwrite(keywords[m],sizeof(char),n,fp);
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}
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}
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/* ----------------------------------------------------------------------
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proc 0 reads from restart file, bcasts
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------------------------------------------------------------------------- */
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void ImproperHybrid::read_restart(FILE *fp)
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{
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int me = comm->me;
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if (me == 0) fread(&nstyles,sizeof(int),1,fp);
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MPI_Bcast(&nstyles,1,MPI_INT,0,world);
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styles = new Improper*[nstyles];
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keywords = new char*[nstyles];
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allocate();
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int n,dummy;
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for (int m = 0; m < nstyles; m++) {
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if (me == 0) fread(&n,sizeof(int),1,fp);
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MPI_Bcast(&n,1,MPI_INT,0,world);
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keywords[m] = new char[n];
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if (me == 0) fread(keywords[m],sizeof(char),n,fp);
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MPI_Bcast(keywords[m],n,MPI_CHAR,0,world);
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styles[m] = force->new_improper(keywords[m],lmp->suffix,dummy);
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}
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}
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/* ----------------------------------------------------------------------
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memory usage
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------------------------------------------------------------------------- */
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double ImproperHybrid::memory_usage()
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{
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double bytes = maxeatom * sizeof(double);
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bytes += maxvatom*6 * sizeof(double);
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for (int m = 0; m < nstyles; m++) bytes += maximproper[m]*5 * sizeof(int);
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for (int m = 0; m < nstyles; m++)
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if (styles[m]) bytes += styles[m]->memory_usage();
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return bytes;
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}
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