forked from lijiext/lammps
use tokenizer to read neb initial replica files
This commit is contained in:
Axel Kohlmeyer
parent
4c13f99b04
commit
080662683d
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@ -32,37 +32,3 @@
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31 2.2000000000000002e+00 7.1662499999999998e+00 1.0032750000000000e+01 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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32 2.2000000000000002e+00 1.0032750000000000e+01 1.0032750000000000e+01 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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@ -5,7 +5,7 @@ LAMMPS data file via write_data, version 4 Jan 2019, timestep = 0
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0.0000000000000000e+00 1.1465999999999999e+01 xlo xhi
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0.0000000000000000e+00 1.1465999999999999e+01 ylo yhi
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0.0000000000000000e+00 2.8664999999999998e+00 zlo zhi
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-1.0000000000000000e+00 10.0664999999999998e+00 zlo zhi
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Masses
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@ -135,24 +135,24 @@ FixNEB::FixNEB(LAMMPS *lmp, int narg, char **arg) :
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else procnext = -1;
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uworld = universe->uworld;
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int *iroots = new int[nreplica];
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MPI_Group uworldgroup,rootgroup;
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if (NEBLongRange) {
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for (int i=0; i<nreplica; i++)
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iroots[i] = universe->root_proc[i];
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int *iroots = new int[nreplica];
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MPI_Group uworldgroup,rootgroup;
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for (int i=0; i<nreplica; i++) iroots[i] = universe->root_proc[i];
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MPI_Comm_group(uworld, &uworldgroup);
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MPI_Group_incl(uworldgroup, nreplica, iroots, &rootgroup);
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MPI_Comm_create(uworld, rootgroup, &rootworld);
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if (rootgroup != MPI_GROUP_NULL) MPI_Group_free(&rootgroup);
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if (uworldgroup != MPI_GROUP_NULL) MPI_Group_free(&uworldgroup);
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delete [] iroots;
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}
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delete [] iroots;
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// create a new compute pe style
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// id = fix-ID + pe, compute group = all
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std::string cmd = id + std::string("_pe");
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id_pe = new char[cmd.size()+1];
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strcpy(id_pe,cmd.c_str());
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modify->add_compute(cmd + " all pe");
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id_pe = utils::strdup(std::string(id)+"_pe");
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modify->add_compute(std::string(id_pe)+" all pe");
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// initialize local storage
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@ -27,6 +27,7 @@
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#include "output.h"
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#include "thermo.h"
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#include "timer.h"
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#include "tokenizer.h"
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#include "universe.h"
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#include "update.h"
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@ -173,12 +174,11 @@ void NEB::run()
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else color = 1;
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MPI_Comm_split(uworld,color,0,&roots);
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int ineb;
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for (ineb = 0; ineb < modify->nfix; ineb++)
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if (strcmp(modify->fix[ineb]->style,"neb") == 0) break;
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if (ineb == modify->nfix) error->all(FLERR,"NEB requires use of fix neb");
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auto fixes = modify->get_fix_by_style("^neb$");
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if (fixes.size() != 1)
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error->all(FLERR,"NEB requires use of exactly one fix neb instance");
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fneb = (FixNEB *) modify->fix[ineb];
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fneb = (FixNEB *) fixes[0];
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if (verbose) numall =7;
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else numall = 4;
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memory->create(all,nreplica,numall,"neb:all");
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@ -376,11 +376,11 @@ void NEB::run()
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void NEB::readfile(char *file, int flag)
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{
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int i,j,m,nchunk,eofflag,nlines;
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int i,nchunk,eofflag,nlines;
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tagint tag;
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char *eof,*start,*next,*buf;
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char line[MAXLINE];
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double xx,yy,zz,delx,dely,delz;
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double delx,dely,delz;
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if (me_universe == 0 && universe->uscreen)
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fprintf(universe->uscreen,"Reading NEB coordinate file(s) ...\n");
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@ -424,10 +424,7 @@ void NEB::readfile(char *file, int flag)
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}
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char *buffer = new char[CHUNK*MAXLINE];
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char **values = new char*[ATTRIBUTE_PERLINE];
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double fraction = ireplica/(nreplica-1.0);
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double **x = atom->x;
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int nlocal = atom->nlocal;
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@ -435,9 +432,7 @@ void NEB::readfile(char *file, int flag)
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// two versions of read_lines_from_file() for world vs universe bcast
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// count # of atom coords changed so can check for invalid atom IDs in file
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int ncount = 0;
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int nread = 0;
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int ncount = 0, nread = 0;
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while (nread < nlines) {
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nchunk = MIN(nlines-nread,CHUNK);
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if (flag == 0)
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@ -461,49 +456,47 @@ void NEB::readfile(char *file, int flag)
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for (i = 0; i < nchunk; i++) {
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next = strchr(buf,'\n');
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*next = '\0';
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values[0] = strtok(buf," \t\n\r\f");
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for (j = 1; j < nwords; j++)
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values[j] = strtok(nullptr," \t\n\r\f");
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try {
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ValueTokenizer values(buf," \t\n\r\f");
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// adjust atom coord based on replica fraction
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// for flag = 0, interpolate for intermediate and final replicas
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// for flag = 1, replace existing coord with new coord
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// ignore image flags of replica x
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// displacement from first replica is via minimum image convention
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// if x of some replica is across periodic boundary:
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// new x may be outside box
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// will be remapped back into box when simulation starts
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// its image flags will then be adjusted
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// adjust atom coord based on replica fraction
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// for flag = 0, interpolate for intermediate and final replicas
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// for flag = 1, replace existing coord with new coord
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// ignore image flags of replica x
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// displacement from first replica is via minimum image convention
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// if x of some replica is across periodic boundary:
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// new x may be outside box
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// will be remapped back into box when simulation starts
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// its image flags will then be adjusted
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tag = ATOTAGINT(values[0]);
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m = atom->map(tag);
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if (m >= 0 && m < nlocal) {
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ncount++;
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xx = atof(values[1]);
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yy = atof(values[2]);
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zz = atof(values[3]);
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tag = values.next_tagint();
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int m = atom->map(tag);
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if (m >= 0 && m < nlocal) {
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ncount++;
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delx = xx - x[m][0];
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dely = yy - x[m][1];
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delz = zz - x[m][2];
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delx = values.next_double() - x[m][0];
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dely = values.next_double() - x[m][1];
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delz = values.next_double() - x[m][2];
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domain->minimum_image(delx,dely,delz);
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domain->minimum_image(delx,dely,delz);
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if (flag == 0) {
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x[m][0] += fraction*delx;
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x[m][1] += fraction*dely;
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x[m][2] += fraction*delz;
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} else {
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x[m][0] += delx;
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x[m][1] += dely;
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x[m][2] += delz;
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if (flag == 0) {
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x[m][0] += fraction*delx;
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x[m][1] += fraction*dely;
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x[m][2] += fraction*delz;
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} else {
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x[m][0] += delx;
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x[m][1] += dely;
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x[m][2] += delz;
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}
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}
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} catch (std::exception &e) {
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error->universe_one(FLERR,"Incorrectly formatted NEB file: " + std::string(e.what()));
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}
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buf = next + 1;
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}
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nread += nchunk;
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}
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@ -522,9 +515,7 @@ void NEB::readfile(char *file, int flag)
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}
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// clean up
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delete [] buffer;
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delete [] values;
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delete[] buffer;
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if (flag == 0) {
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if (me_universe == 0) {
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@ -56,7 +56,7 @@ FixNEBSpin::FixNEBSpin(LAMMPS *lmp, int narg, char **arg) :
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counts(nullptr), displacements(nullptr)
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{
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if (narg < 4) error->all(FLERR,"Illegal fix neb_spin command");
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if (narg < 4) error->all(FLERR,"Illegal fix neb/spin command");
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kspring = utils::numeric(FLERR,arg[3],false,lmp);
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if (kspring <= 0.0) error->all(FLERR,"Illegal fix neb command");
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@ -77,16 +77,16 @@ FixNEBSpin::FixNEBSpin(LAMMPS *lmp, int narg, char **arg) :
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int iarg = 4;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"parallel") == 0) {
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error->all(FLERR,"Illegal fix neb command");
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error->all(FLERR,"Illegal fix neb/spin command");
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iarg += 2;
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} else if (strcmp(arg[iarg],"perp") == 0) {
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error->all(FLERR,"Illegal fix neb command");
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error->all(FLERR,"Illegal fix neb/spin command");
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iarg += 2;
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} else if (strcmp (arg[iarg],"end") == 0) {
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iarg += 3;
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} else if (strcmp (arg[iarg],"lattice") == 0) {
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iarg += 2;
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} else error->all(FLERR,"Illegal fix neb command");
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} else error->all(FLERR,"Illegal fix neb/spin command");
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}
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// nreplica = number of partitions
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@ -107,16 +107,18 @@ FixNEBSpin::FixNEBSpin(LAMMPS *lmp, int narg, char **arg) :
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else procnext = -1;
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uworld = universe->uworld;
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int *iroots = new int[nreplica];
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MPI_Group uworldgroup,rootgroup;
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if (NEBLongRange) {
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for (int i=0; i<nreplica; i++)
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iroots[i] = universe->root_proc[i];
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int *iroots = new int[nreplica];
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MPI_Group uworldgroup,rootgroup;
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for (int i=0; i<nreplica; i++) iroots[i] = universe->root_proc[i];
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MPI_Comm_group(uworld, &uworldgroup);
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MPI_Group_incl(uworldgroup, nreplica, iroots, &rootgroup);
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MPI_Comm_create(uworld, rootgroup, &rootworld);
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if (rootgroup != MPI_GROUP_NULL) MPI_Group_free(&rootgroup);
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if (uworldgroup != MPI_GROUP_NULL) MPI_Group_free(&uworldgroup);
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delete [] iroots;
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}
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delete [] iroots;
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// create a new compute pe style
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// id = fix-ID + pe, compute group = all
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@ -38,6 +38,7 @@
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#include "output.h"
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#include "thermo.h"
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#include "timer.h"
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#include "tokenizer.h"
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#include "universe.h"
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#include "update.h"
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@ -147,6 +148,7 @@ void NEBSpin::command(int narg, char **arg)
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verbose=false;
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if (strcmp(arg[narg-1],"verbose") == 0) verbose=true;
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// run the NEB calculation
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run();
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}
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@ -166,12 +168,11 @@ void NEBSpin::run()
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// search for neb_spin fix, allocate it
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int ineb;
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for (ineb = 0; ineb < modify->nfix; ineb++)
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if (strcmp(modify->fix[ineb]->style,"neb/spin") == 0) break;
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if (ineb == modify->nfix) error->all(FLERR,"NEBSpin requires use of fix neb/spin");
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auto fixes = modify->get_fix_by_style("^neb/spin");
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if (fixes.size() != 1)
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error->all(FLERR,"NEBSpin requires use of exactly one fix neb/spin instance");
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fneb = (FixNEBSpin *) modify->fix[ineb];
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fneb = (FixNEBSpin *) fixes[0];
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if (verbose) numall =7;
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else numall = 4;
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memory->create(all,nreplica,numall,"neb:all");
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@ -370,12 +371,11 @@ void NEBSpin::run()
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void NEBSpin::readfile(char *file, int flag)
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{
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int i,j,m,nchunk,eofflag,nlines;
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int i,nchunk,eofflag,nlines;
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tagint tag;
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char *eof,*start,*next,*buf;
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char line[MAXLINE];
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double xx,yy,zz;
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double musp,spx,spy,spz;
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double musp,xx,yy,zz,spx,spy,spz;
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if (me_universe == 0 && universe->uscreen)
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fprintf(universe->uscreen,"Reading NEBSpin coordinate file(s) ...\n");
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@ -393,10 +393,12 @@ void NEBSpin::readfile(char *file, int flag)
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start = &line[strspn(line," \t\n\v\f\r")];
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if (*start != '\0' && *start != '#') break;
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}
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sscanf(line,"%d",&nlines);
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int rv = sscanf(line,"%d",&nlines);
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if (rv != 1) nlines = -1;
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}
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MPI_Bcast(&nlines,1,MPI_INT,0,uworld);
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if (nlines < 0)
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error->universe_all(FLERR,"Incorrectly formatted NEB file");
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} else {
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if (me == 0) {
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if (ireplica) {
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@ -407,17 +409,17 @@ void NEBSpin::readfile(char *file, int flag)
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start = &line[strspn(line," \t\n\v\f\r")];
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if (*start != '\0' && *start != '#') break;
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}
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sscanf(line,"%d",&nlines);
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int rv = sscanf(line,"%d",&nlines);
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if (rv != 1) nlines = -1;
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} else nlines = 0;
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}
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MPI_Bcast(&nlines,1,MPI_INT,0,world);
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if (nlines < 0)
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error->all(FLERR,"Incorrectly formatted NEB file");
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}
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char *buffer = new char[CHUNK*MAXLINE];
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char **values = new char*[ATTRIBUTE_PERLINE];
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double fraction = ireplica/(nreplica-1.0);
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double **x = atom->x;
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double **sp = atom->sp;
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double spinit[3],spfinal[3];
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@ -427,11 +429,7 @@ void NEBSpin::readfile(char *file, int flag)
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// two versions of read_lines_from_file() for world vs universe bcast
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// count # of atom coords changed so can check for invalid atom IDs in file
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int ncount = 0;
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int temp_flag,rot_flag;
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temp_flag = rot_flag = 0;
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int nread = 0;
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int ncount=0, nread=0, temp_flag=0, rot_flag=0;
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while (nread < nlines) {
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nchunk = MIN(nlines-nread,CHUNK);
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if (flag == 0)
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@ -444,7 +442,7 @@ void NEBSpin::readfile(char *file, int flag)
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buf = buffer;
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next = strchr(buf,'\n');
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*next = '\0';
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int nwords = utils::trim_and_count_words(buf);
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int nwords = utils::count_words(utils::trim_comment(buf));
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*next = '\n';
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if (nwords != ATTRIBUTE_PERLINE)
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@ -455,75 +453,77 @@ void NEBSpin::readfile(char *file, int flag)
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for (i = 0; i < nchunk; i++) {
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next = strchr(buf,'\n');
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*next = '\0';
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values[0] = strtok(buf," \t\n\r\f");
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for (j = 1; j < nwords; j++)
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values[j] = strtok(nullptr," \t\n\r\f");
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try {
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ValueTokenizer values(buf," \t\n\r\f");
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// adjust spin coord based on replica fraction
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// for flag = 0, interpolate for intermediate and final replicas
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// for flag = 1, replace existing coord with new coord
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// ignore image flags of final x
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// for interpolation:
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// new x is displacement from old x via minimum image convention
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// if final x is across periodic boundary:
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// new x may be outside box
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// will be remapped back into box when simulation starts
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// its image flags will then be adjusted
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// adjust spin coord based on replica fraction
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// for flag = 0, interpolate for intermediate and final replicas
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// for flag = 1, replace existing coord with new coord
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// ignore image flags of final x
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// for interpolation:
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// new x is displacement from old x via minimum image convention
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// if final x is across periodic boundary:
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// new x may be outside box
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// will be remapped back into box when simulation starts
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// its image flags will then be adjusted
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tag = ATOTAGINT(values[0]);
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m = atom->map(tag);
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if (m >= 0 && m < nlocal) {
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ncount++;
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musp = atof(values[1]);
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xx = atof(values[2]);
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yy = atof(values[3]);
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zz = atof(values[4]);
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spx = atof(values[5]);
|
||||
spy = atof(values[6]);
|
||||
spz = atof(values[7]);
|
||||
tag = values.next_tagint();
|
||||
int m = atom->map(tag);
|
||||
if (m >= 0 && m < nlocal) {
|
||||
ncount++;
|
||||
|
||||
if (flag == 0) {
|
||||
musp = values.next_double();
|
||||
xx = values.next_double();
|
||||
yy = values.next_double();
|
||||
zz = values.next_double();
|
||||
spx = values.next_double();
|
||||
spy = values.next_double();
|
||||
spz = values.next_double();
|
||||
|
||||
spinit[0] = sp[m][0];
|
||||
spinit[1] = sp[m][1];
|
||||
spinit[2] = sp[m][2];
|
||||
spfinal[0] = spx;
|
||||
spfinal[1] = spy;
|
||||
spfinal[2] = spz;
|
||||
if (flag == 0) {
|
||||
|
||||
// interpolate intermediate spin states
|
||||
spinit[0] = sp[m][0];
|
||||
spinit[1] = sp[m][1];
|
||||
spinit[2] = sp[m][2];
|
||||
spfinal[0] = spx;
|
||||
spfinal[1] = spy;
|
||||
spfinal[2] = spz;
|
||||
|
||||
sp[m][3] = musp;
|
||||
if (fraction == 0.0) {
|
||||
sp[m][0] = spinit[0];
|
||||
sp[m][1] = spinit[1];
|
||||
sp[m][2] = spinit[2];
|
||||
} else if (fraction == 1.0) {
|
||||
sp[m][0] = spfinal[0];
|
||||
sp[m][1] = spfinal[1];
|
||||
sp[m][2] = spfinal[2];
|
||||
// interpolate intermediate spin states
|
||||
|
||||
sp[m][3] = musp;
|
||||
if (fraction == 0.0) {
|
||||
sp[m][0] = spinit[0];
|
||||
sp[m][1] = spinit[1];
|
||||
sp[m][2] = spinit[2];
|
||||
} else if (fraction == 1.0) {
|
||||
sp[m][0] = spfinal[0];
|
||||
sp[m][1] = spfinal[1];
|
||||
sp[m][2] = spfinal[2];
|
||||
} else {
|
||||
temp_flag = initial_rotation(spinit,spfinal,fraction);
|
||||
rot_flag = MAX(temp_flag,rot_flag);
|
||||
sp[m][0] = spfinal[0];
|
||||
sp[m][1] = spfinal[1];
|
||||
sp[m][2] = spfinal[2];
|
||||
}
|
||||
} else {
|
||||
temp_flag = initial_rotation(spinit,spfinal,fraction);
|
||||
rot_flag = MAX(temp_flag,rot_flag);
|
||||
sp[m][0] = spfinal[0];
|
||||
sp[m][1] = spfinal[1];
|
||||
sp[m][2] = spfinal[2];
|
||||
sp[m][3] = musp;
|
||||
x[m][0] = xx;
|
||||
x[m][1] = yy;
|
||||
x[m][2] = zz;
|
||||
sp[m][0] = spx;
|
||||
sp[m][1] = spy;
|
||||
sp[m][2] = spz;
|
||||
}
|
||||
} else {
|
||||
sp[m][3] = musp;
|
||||
x[m][0] = xx;
|
||||
x[m][1] = yy;
|
||||
x[m][2] = zz;
|
||||
sp[m][0] = spx;
|
||||
sp[m][1] = spy;
|
||||
sp[m][2] = spz;
|
||||
}
|
||||
} catch (std::exception &e) {
|
||||
error->universe_one(FLERR,"Incorrectly formatted NEB file: " + std::string(e.what()));
|
||||
}
|
||||
|
||||
buf = next + 1;
|
||||
}
|
||||
|
||||
nread += nchunk;
|
||||
}
|
||||
|
||||
|
|
@ -549,9 +549,7 @@ void NEBSpin::readfile(char *file, int flag)
|
|||
}
|
||||
|
||||
// clean up
|
||||
|
||||
delete[] buffer;
|
||||
delete[] values;
|
||||
|
||||
if (flag == 0) {
|
||||
if (me_universe == 0) {
|
||||
|
|
|
|||
Loading…
Reference in New Issue