git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5947 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -19,6 +19,7 @@
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#include "read_data.h"
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#include "atom.h"
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#include "atom_vec.h"
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#include "atom_vec_ellipsoid.h"
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#include "comm.h"
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#include "update.h"
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#include "force.h"
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@ -39,7 +40,8 @@ using namespace LAMMPS_NS;
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#define CHUNK 1024
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#define DELTA 4 // must be 2 or larger
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#define NSECTIONS 22 // change when add to header::section_keywords
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// customize for new sections
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#define NSECTIONS 23 // change when add to header::section_keywords
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#define MIN(a,b) ((a) < (b) ? (a) : (b))
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#define MAX(a,b) ((a) > (b) ? (a) : (b))
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@ -54,6 +56,12 @@ ReadData::ReadData(LAMMPS *lmp) : Pointers(lmp)
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buffer = new char[CHUNK*MAXLINE];
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narg = maxarg = 0;
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arg = NULL;
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// customize for new sections
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// pointers to atom styles that store extra info
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nellipsoids = 0;
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avec_ellipsoid = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
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}
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/* ---------------------------------------------------------------------- */
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@ -128,8 +136,8 @@ void ReadData::command(int narg, char **arg)
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comm->set_procs();
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domain->set_local_box();
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// customize for new sections
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// read rest of file in free format
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// if add a section keyword, add to header::section_keywords and NSECTIONS
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int atomflag = 0;
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@ -140,6 +148,12 @@ void ReadData::command(int narg, char **arg)
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} else if (strcmp(keyword,"Velocities") == 0) {
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if (atomflag == 0) error->all("Must read Atoms before Velocities");
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velocities();
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} else if (strcmp(keyword,"Ellipsoids") == 0) {
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if (!avec_ellipsoid)
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error->all("Invalid data file section: Ellipsoids");
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if (atomflag == 0) error->all("Must read Atoms before Ellipsoids");
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ellipsoids();
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} else if (strcmp(keyword,"Bonds") == 0) {
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if (atom->avec->bonds_allow == 0)
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error->all("Invalid data file section: Bonds");
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@ -287,14 +301,17 @@ void ReadData::header(int flag)
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int n;
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char *ptr;
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// customize for new sections
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char *section_keywords[NSECTIONS] =
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{"Atoms","Velocities","Bonds","Angles","Dihedrals","Impropers","Masses",
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"Pair Coeffs","Bond Coeffs","Angle Coeffs",
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{"Atoms","Velocities","Ellipsoids",
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"Bonds","Angles","Dihedrals","Impropers",
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"Masses","Pair Coeffs","Bond Coeffs","Angle Coeffs",
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"Dihedral Coeffs","Improper Coeffs",
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"BondBond Coeffs","BondAngle Coeffs","MiddleBondTorsion Coeffs",
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"EndBondTorsion Coeffs","AngleTorsion Coeffs",
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"AngleAngleTorsion Coeffs","BondBond13 Coeffs","AngleAngle Coeffs"};
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// skip 1st line of file
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if (me == 0) {
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@ -302,6 +319,8 @@ void ReadData::header(int flag)
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if (eof == NULL) error->one("Unexpected end of data file");
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}
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// customize for new header lines
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while (1) {
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// read a line and bcast length if flag is set
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@ -351,6 +370,12 @@ void ReadData::header(int flag)
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else if (strstr(line,"extra bond per atom"))
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sscanf(line,"%d",&atom->extra_bond_per_atom);
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else if (strstr(line,"ellipsoids")) {
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if (!avec_ellipsoid)
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error->all("No ellipsoids allowed with this atom style");
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sscanf(line,BIGINT_FORMAT,&nellipsoids);
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}
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else if (strstr(line,"xlo xhi"))
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sscanf(line,"%lg %lg",&domain->boxlo[0],&domain->boxhi[0]);
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else if (strstr(line,"ylo yhi"))
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@ -543,6 +568,57 @@ void ReadData::velocities()
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}
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}
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/* ----------------------------------------------------------------------
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read all ellipsoids
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to find atoms, must build atom map if not a molecular system
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------------------------------------------------------------------------- */
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void ReadData::ellipsoids()
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{
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int i,m,nchunk;
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int mapflag = 0;
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if (atom->map_style == 0) {
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mapflag = 1;
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atom->map_style = 1;
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atom->map_init();
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atom->map_set();
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}
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bigint nread = 0;
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bigint natoms = nellipsoids;
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while (nread < natoms) {
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if (natoms-nread > CHUNK) nchunk = CHUNK;
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else nchunk = natoms-nread;
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if (me == 0) {
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char *eof;
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m = 0;
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for (i = 0; i < nchunk; i++) {
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eof = fgets(&buffer[m],MAXLINE,fp);
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if (eof == NULL) error->one("Unexpected end of data file");
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m += strlen(&buffer[m]);
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}
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buffer[m++] = '\n';
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}
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MPI_Bcast(&m,1,MPI_INT,0,world);
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MPI_Bcast(buffer,m,MPI_CHAR,0,world);
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atom->data_bonus(nchunk,buffer,avec_ellipsoid);
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nread += nchunk;
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}
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if (mapflag) {
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atom->map_delete();
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atom->map_style = 0;
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}
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if (me == 0) {
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if (screen) fprintf(screen," " BIGINT_FORMAT " ellipsoids\n",natoms);
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if (logfile) fprintf(logfile," " BIGINT_FORMAT " ellipsoids\n",natoms);
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}
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}
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/* ---------------------------------------------------------------------- */
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void ReadData::bonds()
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@ -933,6 +1009,7 @@ void ReadData::scan(int &bond_per_atom, int &angle_per_atom,
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int natoms = static_cast<int> (atom->natoms);
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bond_per_atom = angle_per_atom = dihedral_per_atom = improper_per_atom = 0;
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// customize for new sections
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// allocate topology counting vector
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// initially, array length = 1 to natoms
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// will grow via reallocate() if atom IDs > natoms
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@ -947,32 +1024,33 @@ void ReadData::scan(int &bond_per_atom, int &angle_per_atom,
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else if (strcmp(keyword,"Atoms") == 0) skip_lines(natoms);
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else if (strcmp(keyword,"Velocities") == 0) skip_lines(natoms);
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else if (strcmp(keyword,"Pair Coeffs") == 0) {
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else if (strcmp(keyword,"Ellipsoids") == 0) {
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if (!avec_ellipsoid)
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error->all("Invalid data file section: Ellipsoids");
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skip_lines(nellipsoids);
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} else if (strcmp(keyword,"Pair Coeffs") == 0) {
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if (force->pair == NULL)
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error->all("Must define pair_style before Pair Coeffs");
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skip_lines(atom->ntypes);
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} else if (strcmp(keyword,"Bond Coeffs") == 0) {
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if (atom->avec->bonds_allow == 0)
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error->all("Invalid data file section: Bond Coeffs");
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if (force->bond == NULL)
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error->all("Must define bond_style before Bond Coeffs");
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skip_lines(atom->nbondtypes);
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} else if (strcmp(keyword,"Angle Coeffs") == 0) {
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if (atom->avec->angles_allow == 0)
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error->all("Invalid data file section: Angle Coeffs");
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if (force->angle == NULL)
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error->all("Must define angle_style before Angle Coeffs");
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skip_lines(atom->nangletypes);
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} else if (strcmp(keyword,"Dihedral Coeffs") == 0) {
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skip_lines(atom->ndihedraltypes);
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if (atom->avec->dihedrals_allow == 0)
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error->all("Invalid data file section: Dihedral Coeffs");
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if (force->dihedral == NULL)
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error->all("Must define dihedral_style before Dihedral Coeffs");
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} else if (strcmp(keyword,"Improper Coeffs") == 0) {
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if (atom->avec->impropers_allow == 0)
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error->all("Invalid data file section: Improper Coeffs");
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@ -986,49 +1064,42 @@ void ReadData::scan(int &bond_per_atom, int &angle_per_atom,
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if (force->angle == NULL)
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error->all("Must define angle_style before BondBond Coeffs");
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skip_lines(atom->nangletypes);
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} else if (strcmp(keyword,"BondAngle Coeffs") == 0) {
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if (atom->avec->angles_allow == 0)
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error->all("Invalid data file section: BondAngle Coeffs");
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if (force->angle == NULL)
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error->all("Must define angle_style before BondAngle Coeffs");
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skip_lines(atom->nangletypes);
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} else if (strcmp(keyword,"MiddleBondTorsion Coeffs") == 0) {
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if (atom->avec->dihedrals_allow == 0)
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error->all("Invalid data file section: MiddleBondTorsion Coeffs");
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if (force->dihedral == NULL)
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error->all("Must define dihedral_style before MiddleBondTorsion Coeffs");
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skip_lines(atom->ndihedraltypes);
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} else if (strcmp(keyword,"EndBondTorsion Coeffs") == 0) {
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if (atom->avec->dihedrals_allow == 0)
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error->all("Invalid data file section: EndBondTorsion Coeffs");
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if (force->dihedral == NULL)
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error->all("Must define dihedral_style before EndBondTorsion Coeffs");
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skip_lines(atom->ndihedraltypes);
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} else if (strcmp(keyword,"AngleTorsion Coeffs") == 0) {
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if (atom->avec->dihedrals_allow == 0)
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error->all("Invalid data file section: AngleTorsion Coeffs");
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if (force->dihedral == NULL)
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error->all("Must define dihedral_style before AngleTorsion Coeffs");
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skip_lines(atom->ndihedraltypes);
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} else if (strcmp(keyword,"AngleAngleTorsion Coeffs") == 0) {
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if (atom->avec->dihedrals_allow == 0)
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error->all("Invalid data file section: AngleAngleTorsion Coeffs");
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if (force->dihedral == NULL)
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error->all("Must define dihedral_style before AngleAngleTorsion Coeffs");
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skip_lines(atom->ndihedraltypes);
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} else if (strcmp(keyword,"BondBond13 Coeffs") == 0) {
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if (atom->avec->dihedrals_allow == 0)
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error->all("Invalid data file section: BondBond13 Coeffs");
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if (force->dihedral == NULL)
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error->all("Must define dihedral_style before BondBond13 Coeffs");
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skip_lines(atom->ndihedraltypes);
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} else if (strcmp(keyword,"AngleAngle Coeffs") == 0) {
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if (atom->avec->impropers_allow == 0)
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error->all("Invalid data file section: AngleAngle Coeffs");
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