git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11328 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -23,6 +23,7 @@
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#include "atom_vec_ellipsoid.h"
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#include "atom_vec_line.h"
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#include "atom_vec_tri.h"
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#include "molecule.h"
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#include "comm.h"
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#include "update.h"
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#include "modify.h"
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@ -220,25 +221,25 @@ void ReadData::command(int narg, char **arg)
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} else if (strcmp(keyword,"Bonds") == 0) {
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topoflag = bondflag = 1;
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if (atom->avec->bonds_allow == 0)
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if (atom->nbonds == 0)
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error->all(FLERR,"Invalid data file section: Bonds");
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if (atomflag == 0) error->all(FLERR,"Must read Atoms before Bonds");
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bonds(firstpass);
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} else if (strcmp(keyword,"Angles") == 0) {
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topoflag = angleflag = 1;
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if (atom->avec->angles_allow == 0)
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if (atom->nangles == 0)
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error->all(FLERR,"Invalid data file section: Angles");
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if (atomflag == 0) error->all(FLERR,"Must read Atoms before Angles");
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angles(firstpass);
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} else if (strcmp(keyword,"Dihedrals") == 0) {
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topoflag = dihedralflag = 1;
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if (atom->avec->dihedrals_allow == 0)
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if (atom->ndihedrals == 0)
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error->all(FLERR,"Invalid data file section: Dihedrals");
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if (atomflag == 0) error->all(FLERR,"Must read Atoms before Dihedrals");
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dihedrals(firstpass);
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} else if (strcmp(keyword,"Impropers") == 0) {
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topoflag = improperflag = 1;
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if (atom->avec->impropers_allow == 0)
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if (atom->nimpropers == 0)
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error->all(FLERR,"Invalid data file section: Impropers");
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if (atomflag == 0) error->all(FLERR,"Must read Atoms before Impropers");
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impropers(firstpass);
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@ -471,10 +472,83 @@ void ReadData::command(int narg, char **arg)
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// create special bond lists for molecular systems
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if (atom->molecular) {
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if (atom->molecular == 1) {
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Special special(lmp);
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special.build();
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}
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// for atom style template systems, count total bonds,angles,etc
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if (atom->molecular == 2) {
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Molecule **onemols = atom->avec->onemols;
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int *molindex = atom->molindex;
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int *molatom = atom->molatom;
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int nlocal = atom->nlocal;
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int imol,iatom;
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bigint nbonds,nangles,ndihedrals,nimpropers;
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nbonds = nangles = ndihedrals = nimpropers = 0;
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for (int i = 0; i < nlocal; i++) {
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imol = molindex[i];
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iatom = molatom[i];
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nbonds += onemols[imol]->num_bond[iatom];
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nangles += onemols[imol]->num_angle[iatom];
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ndihedrals += onemols[imol]->num_dihedral[iatom];
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nimpropers += onemols[imol]->num_improper[iatom];
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}
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MPI_Allreduce(&nbonds,&atom->nbonds,1,MPI_LMP_BIGINT,MPI_SUM,world);
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MPI_Allreduce(&nangles,&atom->nangles,1,MPI_LMP_BIGINT,MPI_SUM,world);
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MPI_Allreduce(&ndihedrals,&atom->ndihedrals,1,MPI_LMP_BIGINT,MPI_SUM,world);
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MPI_Allreduce(&nimpropers,&atom->nimpropers,1,MPI_LMP_BIGINT,MPI_SUM,world);
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if (!force->newton_bond) {
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atom->nbonds /= 2;
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atom->nangles /= 3;
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atom->ndihedrals /= 4;
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atom->nimpropers /= 4;
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}
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if (me == 0) {
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if (atom->nbonds) {
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if (screen)
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fprintf(screen," " BIGINT_FORMAT " template bonds\n",atom->nbonds);
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if (logfile)
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fprintf(logfile," " BIGINT_FORMAT " template bonds\n",atom->nbonds);
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}
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if (atom->nangles) {
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if (screen)
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fprintf(screen," " BIGINT_FORMAT " template angles\n",
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atom->nangles);
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if (logfile)
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fprintf(logfile," " BIGINT_FORMAT " template angles\n",
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atom->nangles);
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}
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if (atom->ndihedrals) {
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if (screen)
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fprintf(screen," " BIGINT_FORMAT " template dihedrals\n",
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atom->nbonds);
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if (logfile)
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fprintf(logfile," " BIGINT_FORMAT " template bonds\n",
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atom->ndihedrals);
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}
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if (atom->nimpropers) {
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if (screen)
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fprintf(screen," " BIGINT_FORMAT " template impropers\n",
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atom->nimpropers);
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if (logfile)
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fprintf(logfile," " BIGINT_FORMAT " template impropers\n",
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atom->nimpropers);
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}
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}
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}
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// for atom style template systems
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// insure nbondtypes,etc are still consistent with template molecules,
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// in case data file re-defined them
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if (atom->molecular == 2) atom->avec->onemols[0]->check_attributes(1);
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}
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/* ----------------------------------------------------------------------
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@ -559,20 +633,20 @@ void ReadData::header()
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// otherwise "triangles" will be matched as "angles"
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} else if (strstr(line,"ellipsoids")) {
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if (!avec_ellipsoid && me == 0)
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error->one(FLERR,"No ellipsoids allowed with this atom style");
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if (!avec_ellipsoid)
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error->all(FLERR,"No ellipsoids allowed with this atom style");
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sscanf(line,BIGINT_FORMAT,&nellipsoids);
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} else if (strstr(line,"lines")) {
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if (!avec_line && me == 0)
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error->one(FLERR,"No lines allowed with this atom style");
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if (!avec_line)
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error->all(FLERR,"No lines allowed with this atom style");
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sscanf(line,BIGINT_FORMAT,&nlines);
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} else if (strstr(line,"triangles")) {
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if (!avec_tri && me == 0)
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error->one(FLERR,"No triangles allowed with this atom style");
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if (!avec_tri)
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error->all(FLERR,"No triangles allowed with this atom style");
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sscanf(line,BIGINT_FORMAT,&ntris);
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} else if (strstr(line,"bodies")) {
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if (!avec_body && me == 0)
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error->one(FLERR,"No bodies allowed with this atom style");
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if (!avec_body)
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error->all(FLERR,"No bodies allowed with this atom style");
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sscanf(line,BIGINT_FORMAT,&nbodies);
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}
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@ -620,44 +694,49 @@ void ReadData::header()
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atom->nbonds < 0 || atom->nbonds >= MAXBIGINT ||
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atom->nangles < 0 || atom->nangles >= MAXBIGINT ||
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atom->ndihedrals < 0 || atom->ndihedrals >= MAXBIGINT ||
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atom->nimpropers < 0 || atom->nimpropers >= MAXBIGINT) {
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if (me == 0) error->one(FLERR,"System in data file is too big");
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}
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atom->nimpropers < 0 || atom->nimpropers >= MAXBIGINT)
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error->all(FLERR,"System in data file is too big");
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// check that exiting string is a valid section keyword
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parse_keyword(1);
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for (n = 0; n < NSECTIONS; n++)
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if (strcmp(keyword,section_keywords[n]) == 0) break;
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if (n == NSECTIONS && me == 0) {
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if (n == NSECTIONS) {
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char str[128];
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sprintf(str,"Unknown identifier in data file: %s",keyword);
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error->one(FLERR,str);
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error->all(FLERR,str);
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}
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// error check on consistency of header values
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// error checks on header values
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// must be consistent with atom style and other header values
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if ((atom->nbonds || atom->nbondtypes) &&
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atom->avec->bonds_allow == 0 && me == 0)
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error->one(FLERR,"No bonds allowed with this atom style");
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atom->avec->bonds_allow == 0)
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error->all(FLERR,"No bonds allowed with this atom style");
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if ((atom->nangles || atom->nangletypes) &&
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atom->avec->angles_allow == 0 && me == 0)
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error->one(FLERR,"No angles allowed with this atom style");
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atom->avec->angles_allow == 0)
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error->all(FLERR,"No angles allowed with this atom style");
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if ((atom->ndihedrals || atom->ndihedraltypes) &&
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atom->avec->dihedrals_allow == 0 && me == 0)
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error->one(FLERR,"No dihedrals allowed with this atom style");
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atom->avec->dihedrals_allow == 0)
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error->all(FLERR,"No dihedrals allowed with this atom style");
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if ((atom->nimpropers || atom->nimpropertypes) &&
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atom->avec->impropers_allow == 0 && me == 0)
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error->one(FLERR,"No impropers allowed with this atom style");
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atom->avec->impropers_allow == 0)
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error->all(FLERR,"No impropers allowed with this atom style");
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if (atom->nbonds > 0 && atom->nbondtypes <= 0)
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error->all(FLERR,"Bonds defined but no bond types");
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if (atom->nangles > 0 && atom->nangletypes <= 0)
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error->all(FLERR,"Angles defined but no angle types");
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if (atom->ndihedrals > 0 && atom->ndihedraltypes <= 0)
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error->all(FLERR,"Dihedrals defined but no dihedral types");
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if (atom->nimpropers > 0 && atom->nimpropertypes <= 0)
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error->all(FLERR,"Impropers defined but no improper types");
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if (atom->nbonds > 0 && atom->nbondtypes <= 0 && me == 0)
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error->one(FLERR,"Bonds defined but no bond types");
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if (atom->nangles > 0 && atom->nangletypes <= 0 && me == 0)
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error->one(FLERR,"Angles defined but no angle types");
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if (atom->ndihedrals > 0 && atom->ndihedraltypes <= 0 && me == 0)
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error->one(FLERR,"Dihedrals defined but no dihedral types");
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if (atom->nimpropers > 0 && atom->nimpropertypes <= 0 && me == 0)
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error->one(FLERR,"Impropers defined but no improper types");
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if (atom->molecular == 2) {
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if (atom->nbonds || atom->nangles || atom->ndihedrals || atom->nimpropers)
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error->all(FLERR,"No molecule topology allowed with atom style template");
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}
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}
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/* ----------------------------------------------------------------------
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@ -803,7 +882,7 @@ void ReadData::bonds(int firstpass)
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if (screen) fprintf(screen," %d = max bonds/atom\n",maxall);
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if (logfile) fprintf(logfile," %d = max bonds/atom\n",maxall);
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}
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atom->bond_per_atom = maxall;
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atom->bond_per_atom = maxall + atom->extra_bond_per_atom;
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memory->destroy(count);
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return;
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}
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@ -877,7 +956,7 @@ void ReadData::angles(int firstpass)
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if (screen) fprintf(screen," %d = max angles/atom\n",maxall);
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if (logfile) fprintf(logfile," %d = max angles/atom\n",maxall);
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}
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atom->angle_per_atom = maxall;
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atom->angle_per_atom = maxall + atom->extra_angle_per_atom;
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memory->destroy(count);
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return;
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}
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@ -951,7 +1030,7 @@ void ReadData::dihedrals(int firstpass)
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if (screen) fprintf(screen," %d = max dihedrals/atom\n",maxall);
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if (logfile) fprintf(logfile," %d = max dihedrals/atom\n",maxall);
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}
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atom->dihedral_per_atom = maxall;
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atom->dihedral_per_atom = maxall + atom->extra_dihedral_per_atom;
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memory->destroy(count);
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return;
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}
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@ -1025,7 +1104,7 @@ void ReadData::impropers(int firstpass)
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if (screen) fprintf(screen," %d = max impropers/atom\n",maxall);
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if (logfile) fprintf(logfile," %d = max impropers/atom\n",maxall);
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}
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atom->improper_per_atom = maxall;
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atom->improper_per_atom = maxall + atom->extra_improper_per_atom;
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memory->destroy(count);
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return;
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}
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@ -1095,7 +1174,7 @@ void ReadData::bonus(bigint nbonus, AtomVec *ptr, const char *type)
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void ReadData::bodies(int firstpass)
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{
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int i,m,nchunk,nmax,ninteger,ndouble,tmp,onebody;
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int i,m,nchunk,nline,nmax,ninteger,ndouble,tmp,onebody;
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char *eof;
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int mapflag = 0;
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@ -1117,10 +1196,10 @@ void ReadData::bodies(int firstpass)
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if (me == 0) {
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nchunk = 0;
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nlines = 0;
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nline = 0;
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m = 0;
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while (nchunk < nmax && nlines <= CHUNK-MAXBODY) {
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while (nchunk < nmax && nline <= CHUNK-MAXBODY) {
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eof = fgets(&buffer[m],MAXLINE,fp);
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if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
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sscanf(&buffer[m],"%d %d %d",&tmp,&ninteger,&ndouble);
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@ -1140,7 +1219,7 @@ void ReadData::bodies(int firstpass)
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}
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nchunk++;
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nlines += onebody+1;
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nline += onebody+1;
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}
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if (buffer[m-1] != '\n') strcpy(&buffer[m++],"\n");
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@ -1334,11 +1413,11 @@ void ReadData::fix(int ifix, char *keyword)
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{
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int nchunk,eof;
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bigint nlines = modify->fix[ifix]->read_data_skip_lines(keyword);
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bigint nline = modify->fix[ifix]->read_data_skip_lines(keyword);
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bigint nread = 0;
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while (nread < nlines) {
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nchunk = MIN(nlines-nread,CHUNK);
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while (nread < nline) {
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nchunk = MIN(nline-nread,CHUNK);
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eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
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if (eof) error->all(FLERR,"Unexpected end of data file");
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modify->fix[ifix]->read_data_section(keyword,nchunk,buffer);
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