/* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator http://lammps.sandia.gov, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains certain rights in this software. This software is distributed under the GNU General Public License. See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ #include "mpi.h" #include "math.h" #include "string.h" #include "stdlib.h" #include "ctype.h" #include "read_data.h" #include "atom.h" #include "atom_vec.h" #include "atom_vec_ellipsoid.h" #include "atom_vec_line.h" #include "atom_vec_tri.h" #include "force.h" #include "molecule.h" #include "comm.h" #include "update.h" #include "modify.h" #include "fix.h" #include "force.h" #include "pair.h" #include "domain.h" #include "bond.h" #include "angle.h" #include "dihedral.h" #include "improper.h" #include "special.h" #include "error.h" #include "memory.h" using namespace LAMMPS_NS; #define MAXLINE 256 #define LB_FACTOR 1.1 #define CHUNK 1024 #define DELTA 4 // must be 2 or larger #define MAXBODY 20 // max # of lines in one body, also in Atom class // customize for new sections #define NSECTIONS 25 // change when add to header::section_keywords // pair style suffixes to ignore // when matching Pair Coeffs comment to currently-defined pair style const char *suffixes[] = {"/cuda","/gpu","/opt","/omp","/kk", "/coul/cut","/coul/long","/coul/msm", "/coul/dsf","/coul/debye","/coul/charmm", NULL}; /* ---------------------------------------------------------------------- */ ReadData::ReadData(LAMMPS *lmp) : Pointers(lmp) { MPI_Comm_rank(world,&me); line = new char[MAXLINE]; keyword = new char[MAXLINE]; style = new char[MAXLINE]; buffer = new char[CHUNK*MAXLINE]; narg = maxarg = 0; arg = NULL; // customize for new sections // pointers to atom styles that store extra info nellipsoids = 0; avec_ellipsoid = (AtomVecEllipsoid *) atom->style_match("ellipsoid"); nlines = 0; avec_line = (AtomVecLine *) atom->style_match("line"); ntris = 0; avec_tri = (AtomVecTri *) atom->style_match("tri"); nbodies = 0; avec_body = (AtomVecBody *) atom->style_match("body"); } /* ---------------------------------------------------------------------- */ ReadData::~ReadData() { delete [] line; delete [] keyword; delete [] style; delete [] buffer; memory->sfree(arg); for (int i = 0; i < nfix; i++) { delete [] fix_header[i]; delete [] fix_section[i]; } memory->destroy(fix_index); memory->sfree(fix_header); memory->sfree(fix_section); } /* ---------------------------------------------------------------------- */ void ReadData::command(int narg, char **arg) { if (narg < 1) error->all(FLERR,"Illegal read_data command"); // optional args addflag = mergeflag = 0; offset[0] = offset[1] = offset[2] = 0.0; nfix = 0; fix_index = NULL; fix_header = NULL; fix_section = NULL; int iarg = 1; while (iarg < narg) { if (strcmp(arg[iarg],"add") == 0) { addflag = 1; iarg++; } else if (strcmp(arg[iarg],"merge") == 0) { mergeflag = 1; iarg++; } else if (strcmp(arg[iarg],"offset") == 0) { if (iarg+4 > narg) error->all(FLERR,"Illegal read_data command"); offset[0] = force->numeric(FLERR,arg[iarg+1]); offset[1] = force->numeric(FLERR,arg[iarg+2]); offset[2] = force->numeric(FLERR,arg[iarg+3]); iarg += 4; } else if (strcmp(arg[iarg],"fix") == 0) { if (iarg+4 > narg) error->all(FLERR,"Illegal read_data command"); memory->grow(fix_index,nfix+1,"read_data:fix_index"); fix_header = (char **) memory->srealloc(fix_header,(nfix+1)*sizeof(char *), "read_data:fix_header"); fix_section = (char **) memory->srealloc(fix_section,(nfix+1)*sizeof(char *), "read_data:fix_section"); fix_index[nfix] = modify->find_fix(arg[iarg+1]); if (fix_index[nfix] < 0) error->all(FLERR,"Fix ID for read_data does not exist"); if (strcmp(arg[iarg+2],"NULL") == 0) fix_header[nfix] = NULL; else { int n = strlen(arg[iarg+2]) + 1; fix_header[nfix] = new char[n]; strcpy(fix_header[nfix],arg[iarg+2]); } int n = strlen(arg[iarg+3]) + 1; fix_section[nfix] = new char[n]; strcpy(fix_section[nfix],arg[iarg+3]); nfix++; iarg += 4; } else error->all(FLERR,"Illegal read_data command"); } // error checks if (domain->box_exist && !addflag && !mergeflag) error->all(FLERR,"Cannot read_data after simulation box is defined"); if (addflag && mergeflag) error->all(FLERR,"Cannot read_data add and merge"); if (domain->dimension == 2 && offset[2] != 0.0) error->all(FLERR,"Cannot use non-zero z offset in read_data " "for 2d simulation"); if (domain->dimension == 2 && domain->zperiodic == 0) error->all(FLERR,"Cannot run 2d simulation with nonperiodic Z dimension"); // perform 1-pass read if no molecular topoogy in file // perform 2-pass read if molecular topology, // first pass calculates max topology/atom int atomflag,topoflag; int bondflag,angleflag,dihedralflag,improperflag; int ellipsoidflag,lineflag,triflag,bodyflag; atomflag = topoflag = 0; bondflag = angleflag = dihedralflag = improperflag = 0; ellipsoidflag = lineflag = triflag = bodyflag = 0; int firstpass = 1; while (1) { // open file on proc 0 if (me == 0) { if (firstpass && screen) fprintf(screen,"Reading data file ...\n"); open(arg[0]); } else fp = NULL; // read header info header(); // problem setup using info from header // 1st pass only if (firstpass) { domain->box_exist = 1; update->ntimestep = 0; // apply extra settings before grow(), even if no topology in file // deallocate() insures new settings are used for topology arrays // if per-atom topology is in file, another grow() is done below atom->bond_per_atom = atom->extra_bond_per_atom; atom->angle_per_atom = atom->extra_angle_per_atom; atom->dihedral_per_atom = atom->extra_dihedral_per_atom; atom->improper_per_atom = atom->extra_improper_per_atom; int n; if (comm->nprocs == 1) n = static_cast (atom->natoms); else n = static_cast (LB_FACTOR * atom->natoms / comm->nprocs); atom->allocate_type_arrays(); atom->deallocate_topology(); atom->avec->grow(n); domain->print_box(" "); domain->set_initial_box(); domain->set_global_box(); comm->set_proc_grid(); domain->set_local_box(); } // customize for new sections // read rest of file in free format while (strlen(keyword)) { // if special fix matches, it processes section if (nfix) { int i; for (i = 0; i < nfix; i++) if (strcmp(keyword,fix_section[i]) == 0) { if (firstpass) fix(fix_index[i],keyword); else skip_lines(modify->fix[fix_index[i]]-> read_data_skip_lines(keyword)); parse_keyword(0); break; } if (i < nfix) continue; } if (strcmp(keyword,"Atoms") == 0) { atomflag = 1; if (firstpass) { if (me == 0 && !style_match(style,atom->atom_style)) error->warning(FLERR,"Atom style in data file differs " "from currently defined atom style"); atoms(); } else skip_lines(atom->natoms); } else if (strcmp(keyword,"Velocities") == 0) { if (atomflag == 0) error->all(FLERR,"Must read Atoms before Velocities"); if (firstpass) velocities(); else skip_lines(atom->natoms); } else if (strcmp(keyword,"Bonds") == 0) { topoflag = bondflag = 1; if (atom->nbonds == 0) error->all(FLERR,"Invalid data file section: Bonds"); if (atomflag == 0) error->all(FLERR,"Must read Atoms before Bonds"); bonds(firstpass); } else if (strcmp(keyword,"Angles") == 0) { topoflag = angleflag = 1; if (atom->nangles == 0) error->all(FLERR,"Invalid data file section: Angles"); if (atomflag == 0) error->all(FLERR,"Must read Atoms before Angles"); angles(firstpass); } else if (strcmp(keyword,"Dihedrals") == 0) { topoflag = dihedralflag = 1; if (atom->ndihedrals == 0) error->all(FLERR,"Invalid data file section: Dihedrals"); if (atomflag == 0) error->all(FLERR,"Must read Atoms before Dihedrals"); dihedrals(firstpass); } else if (strcmp(keyword,"Impropers") == 0) { topoflag = improperflag = 1; if (atom->nimpropers == 0) error->all(FLERR,"Invalid data file section: Impropers"); if (atomflag == 0) error->all(FLERR,"Must read Atoms before Impropers"); impropers(firstpass); } else if (strcmp(keyword,"Ellipsoids") == 0) { ellipsoidflag = 1; if (!avec_ellipsoid) error->all(FLERR,"Invalid data file section: Ellipsoids"); if (atomflag == 0) error->all(FLERR,"Must read Atoms before Ellipsoids"); if (firstpass) bonus(nellipsoids,(AtomVec *) avec_ellipsoid,"ellipsoids"); else skip_lines(nellipsoids); } else if (strcmp(keyword,"Lines") == 0) { lineflag = 1; if (!avec_line) error->all(FLERR,"Invalid data file section: Lines"); if (atomflag == 0) error->all(FLERR,"Must read Atoms before Lines"); if (firstpass) bonus(nlines,(AtomVec *) avec_line,"lines"); else skip_lines(nlines); } else if (strcmp(keyword,"Triangles") == 0) { triflag = 1; if (!avec_tri) error->all(FLERR,"Invalid data file section: Triangles"); if (atomflag == 0) error->all(FLERR,"Must read Atoms before Triangles"); if (firstpass) bonus(ntris,(AtomVec *) avec_tri,"triangles"); else skip_lines(ntris); } else if (strcmp(keyword,"Bodies") == 0) { bodyflag = 1; if (!avec_body) error->all(FLERR,"Invalid data file section: Bodies"); if (atomflag == 0) error->all(FLERR,"Must read Atoms before Bodies"); bodies(firstpass); } else if (strcmp(keyword,"Masses") == 0) { if (firstpass) mass(); else skip_lines(atom->ntypes); } else if (strcmp(keyword,"Pair Coeffs") == 0) { if (force->pair == NULL) error->all(FLERR,"Must define pair_style before Pair Coeffs"); if (firstpass) { if (me == 0 && !style_match(style,force->pair_style)) error->warning(FLERR,"Pair style in data file differs " "from currently defined pair style"); paircoeffs(); } else skip_lines(atom->ntypes); } else if (strcmp(keyword,"PairIJ Coeffs") == 0) { if (force->pair == NULL) error->all(FLERR,"Must define pair_style before PairIJ Coeffs"); if (firstpass) { if (me == 0 && !style_match(style,force->pair_style)) error->warning(FLERR,"Pair style in data file differs " "from currently defined pair style"); pairIJcoeffs(); } else skip_lines(atom->ntypes*(atom->ntypes+1)/2); } else if (strcmp(keyword,"Bond Coeffs") == 0) { if (atom->avec->bonds_allow == 0) error->all(FLERR,"Invalid data file section: Bond Coeffs"); if (force->bond == NULL) error->all(FLERR,"Must define bond_style before Bond Coeffs"); if (firstpass) { if (me == 0 && !style_match(style,force->bond_style)) error->warning(FLERR,"Bond style in data file differs " "from currently defined bond style"); bondcoeffs(); } else skip_lines(atom->nbondtypes); } else if (strcmp(keyword,"Angle Coeffs") == 0) { if (atom->avec->angles_allow == 0) error->all(FLERR,"Invalid data file section: Angle Coeffs"); if (force->angle == NULL) error->all(FLERR,"Must define angle_style before Angle Coeffs"); if (firstpass) { if (me == 0 && !style_match(style,force->angle_style)) error->warning(FLERR,"Angle style in data file differs " "from currently defined angle style"); anglecoeffs(0); } else skip_lines(atom->nangletypes); } else if (strcmp(keyword,"Dihedral Coeffs") == 0) { if (atom->avec->dihedrals_allow == 0) error->all(FLERR,"Invalid data file section: Dihedral Coeffs"); if (force->dihedral == NULL) error->all(FLERR,"Must define dihedral_style before Dihedral Coeffs"); if (firstpass) { if (me == 0 && !style_match(style,force->dihedral_style)) error->warning(FLERR,"Dihedral style in data file differs " "from currently defined dihedral style"); dihedralcoeffs(0); } else skip_lines(atom->ndihedraltypes); } else if (strcmp(keyword,"Improper Coeffs") == 0) { if (atom->avec->impropers_allow == 0) error->all(FLERR,"Invalid data file section: Improper Coeffs"); if (force->improper == NULL) error->all(FLERR,"Must define improper_style before Improper Coeffs"); if (firstpass) { if (me == 0 && !style_match(style,force->improper_style)) error->warning(FLERR,"Improper style in data file differs " "from currently defined improper style"); impropercoeffs(0); } else skip_lines(atom->nimpropertypes); } else if (strcmp(keyword,"BondBond Coeffs") == 0) { if (atom->avec->angles_allow == 0) error->all(FLERR,"Invalid data file section: BondBond Coeffs"); if (force->angle == NULL) error->all(FLERR,"Must define angle_style before BondBond Coeffs"); if (firstpass) anglecoeffs(1); else skip_lines(atom->nangletypes); } else if (strcmp(keyword,"BondAngle Coeffs") == 0) { if (atom->avec->angles_allow == 0) error->all(FLERR,"Invalid data file section: BondAngle Coeffs"); if (force->angle == NULL) error->all(FLERR,"Must define angle_style before BondAngle Coeffs"); if (firstpass) anglecoeffs(2); else skip_lines(atom->nangletypes); } else if (strcmp(keyword,"MiddleBondTorsion Coeffs") == 0) { if (atom->avec->dihedrals_allow == 0) error->all(FLERR, "Invalid data file section: MiddleBondTorsion Coeffs"); if (force->dihedral == NULL) error->all(FLERR, "Must define dihedral_style before " "MiddleBondTorsion Coeffs"); if (firstpass) dihedralcoeffs(1); else skip_lines(atom->ndihedraltypes); } else if (strcmp(keyword,"EndBondTorsion Coeffs") == 0) { if (atom->avec->dihedrals_allow == 0) error->all(FLERR,"Invalid data file section: EndBondTorsion Coeffs"); if (force->dihedral == NULL) error->all(FLERR, "Must define dihedral_style before EndBondTorsion Coeffs"); if (firstpass) dihedralcoeffs(2); else skip_lines(atom->ndihedraltypes); } else if (strcmp(keyword,"AngleTorsion Coeffs") == 0) { if (atom->avec->dihedrals_allow == 0) error->all(FLERR,"Invalid data file section: AngleTorsion Coeffs"); if (force->dihedral == NULL) error->all(FLERR, "Must define dihedral_style before AngleTorsion Coeffs"); if (firstpass) dihedralcoeffs(3); else skip_lines(atom->ndihedraltypes); } else if (strcmp(keyword,"AngleAngleTorsion Coeffs") == 0) { if (atom->avec->dihedrals_allow == 0) error->all(FLERR, "Invalid data file section: AngleAngleTorsion Coeffs"); if (force->dihedral == NULL) error->all(FLERR, "Must define dihedral_style before " "AngleAngleTorsion Coeffs"); if (firstpass) dihedralcoeffs(4); else skip_lines(atom->ndihedraltypes); } else if (strcmp(keyword,"BondBond13 Coeffs") == 0) { if (atom->avec->dihedrals_allow == 0) error->all(FLERR,"Invalid data file section: BondBond13 Coeffs"); if (force->dihedral == NULL) error->all(FLERR, "Must define dihedral_style before BondBond13 Coeffs"); if (firstpass) dihedralcoeffs(5); else skip_lines(atom->ndihedraltypes); } else if (strcmp(keyword,"AngleAngle Coeffs") == 0) { if (atom->avec->impropers_allow == 0) error->all(FLERR,"Invalid data file section: AngleAngle Coeffs"); if (force->improper == NULL) error->all(FLERR, "Must define improper_style before AngleAngle Coeffs"); if (firstpass) impropercoeffs(1); else skip_lines(atom->nimpropertypes); } else { char str[128]; sprintf(str,"Unknown identifier in data file: %s",keyword); error->all(FLERR,str); } parse_keyword(0); } // error if natoms > 0 yet no atoms were read if (atom->natoms > 0 && atomflag == 0) error->all(FLERR,"No atoms in data file"); // close file if (me == 0) { if (compressed) pclose(fp); else fclose(fp); } // done if this was 2nd pass if (!firstpass) break; // at end of 1st pass, error check for required sections // customize for new sections if ((atom->nbonds && !bondflag) || (atom->nangles && !angleflag) || (atom->ndihedrals && !dihedralflag) || (atom->nimpropers && !improperflag)) error->one(FLERR,"Needed molecular topology not in data file"); if ((nellipsoids && !ellipsoidflag) || (nlines && !lineflag) || (ntris && !triflag) || (nbodies && !bodyflag)) error->one(FLERR,"Needed bonus data not in data file"); // break out of loop if no molecular topology in file // else make 2nd pass if (!topoflag) break; firstpass = 0; // reallocate bond,angle,diehdral,improper arrays via grow() // will use new bond,angle,dihedral,improper per-atom values from 1st pass // will also observe extra settings even if bond/etc topology not in file // leaves other atom arrays unchanged, since already nmax in length atom->deallocate_topology(); atom->avec->grow(atom->nmax); } // create special bond lists for molecular systems if (atom->molecular == 1) { Special special(lmp); special.build(); } // for atom style template systems, count total bonds,angles,etc if (atom->molecular == 2) { Molecule **onemols = atom->avec->onemols; int *molindex = atom->molindex; int *molatom = atom->molatom; int nlocal = atom->nlocal; int imol,iatom; bigint nbonds,nangles,ndihedrals,nimpropers; nbonds = nangles = ndihedrals = nimpropers = 0; for (int i = 0; i < nlocal; i++) { imol = molindex[i]; iatom = molatom[i]; nbonds += onemols[imol]->num_bond[iatom]; nangles += onemols[imol]->num_angle[iatom]; ndihedrals += onemols[imol]->num_dihedral[iatom]; nimpropers += onemols[imol]->num_improper[iatom]; } MPI_Allreduce(&nbonds,&atom->nbonds,1,MPI_LMP_BIGINT,MPI_SUM,world); MPI_Allreduce(&nangles,&atom->nangles,1,MPI_LMP_BIGINT,MPI_SUM,world); MPI_Allreduce(&ndihedrals,&atom->ndihedrals,1,MPI_LMP_BIGINT,MPI_SUM,world); MPI_Allreduce(&nimpropers,&atom->nimpropers,1,MPI_LMP_BIGINT,MPI_SUM,world); if (!force->newton_bond) { atom->nbonds /= 2; atom->nangles /= 3; atom->ndihedrals /= 4; atom->nimpropers /= 4; } if (me == 0) { if (atom->nbonds) { if (screen) fprintf(screen," " BIGINT_FORMAT " template bonds\n",atom->nbonds); if (logfile) fprintf(logfile," " BIGINT_FORMAT " template bonds\n",atom->nbonds); } if (atom->nangles) { if (screen) fprintf(screen," " BIGINT_FORMAT " template angles\n", atom->nangles); if (logfile) fprintf(logfile," " BIGINT_FORMAT " template angles\n", atom->nangles); } if (atom->ndihedrals) { if (screen) fprintf(screen," " BIGINT_FORMAT " template dihedrals\n", atom->nbonds); if (logfile) fprintf(logfile," " BIGINT_FORMAT " template bonds\n", atom->ndihedrals); } if (atom->nimpropers) { if (screen) fprintf(screen," " BIGINT_FORMAT " template impropers\n", atom->nimpropers); if (logfile) fprintf(logfile," " BIGINT_FORMAT " template impropers\n", atom->nimpropers); } } } // for atom style template systems // insure nbondtypes,etc are still consistent with template molecules, // in case data file re-defined them if (atom->molecular == 2) atom->avec->onemols[0]->check_attributes(1); } /* ---------------------------------------------------------------------- read free-format header of data file 1st line and blank lines are skipped non-blank lines are checked for header keywords and leading value is read header ends with EOF or non-blank line containing no header keyword if EOF, line is set to blank line else line has first keyword line for rest of file ------------------------------------------------------------------------- */ void ReadData::header() { int n; char *ptr; // customize for new sections const char *section_keywords[NSECTIONS] = {"Atoms","Velocities","Ellipsoids","Lines","Triangles","Bodies", "Bonds","Angles","Dihedrals","Impropers", "Masses","Pair Coeffs","PairIJ Coeffs","Bond Coeffs","Angle Coeffs", "Dihedral Coeffs","Improper Coeffs", "BondBond Coeffs","BondAngle Coeffs","MiddleBondTorsion Coeffs", "EndBondTorsion Coeffs","AngleTorsion Coeffs", "AngleAngleTorsion Coeffs","BondBond13 Coeffs","AngleAngle Coeffs"}; // skip 1st line of file if (me == 0) { char *eof = fgets(line,MAXLINE,fp); if (eof == NULL) error->one(FLERR,"Unexpected end of data file"); } while (1) { // read a line and bcast length if flag is set if (me == 0) { if (fgets(line,MAXLINE,fp) == NULL) n = 0; else n = strlen(line) + 1; } MPI_Bcast(&n,1,MPI_INT,0,world); // if n = 0 then end-of-file so return with blank line if (n == 0) { line[0] = '\0'; return; } MPI_Bcast(line,n,MPI_CHAR,0,world); // trim anything from '#' onward // if line is blank, continue if ((ptr = strchr(line,'#'))) *ptr = '\0'; if (strspn(line," \t\n\r") == strlen(line)) continue; // allow special fixes first chance to match and process the line // if fix matches, continue to next header line if (nfix) { for (n = 0; n < nfix; n++) { if (!fix_header[n]) continue; if (strstr(line,fix_header[n])) { modify->fix[fix_index[n]]->read_data_header(line); break; } } if (n < nfix) continue; } // search line for header keyword and set corresponding variable // customize for new header lines if (strstr(line,"atoms")) { sscanf(line,BIGINT_FORMAT,&atom->natoms); // check for these first // otherwise "triangles" will be matched as "angles" } else if (strstr(line,"ellipsoids")) { if (!avec_ellipsoid) error->all(FLERR,"No ellipsoids allowed with this atom style"); sscanf(line,BIGINT_FORMAT,&nellipsoids); } else if (strstr(line,"lines")) { if (!avec_line) error->all(FLERR,"No lines allowed with this atom style"); sscanf(line,BIGINT_FORMAT,&nlines); } else if (strstr(line,"triangles")) { if (!avec_tri) error->all(FLERR,"No triangles allowed with this atom style"); sscanf(line,BIGINT_FORMAT,&ntris); } else if (strstr(line,"bodies")) { if (!avec_body) error->all(FLERR,"No bodies allowed with this atom style"); sscanf(line,BIGINT_FORMAT,&nbodies); } else if (strstr(line,"bonds")) sscanf(line,BIGINT_FORMAT,&atom->nbonds); else if (strstr(line,"angles")) sscanf(line,BIGINT_FORMAT,&atom->nangles); else if (strstr(line,"dihedrals")) sscanf(line,BIGINT_FORMAT, &atom->ndihedrals); else if (strstr(line,"impropers")) sscanf(line,BIGINT_FORMAT, &atom->nimpropers); else if (strstr(line,"atom types")) sscanf(line,"%d",&atom->ntypes); else if (strstr(line,"bond types")) sscanf(line,"%d",&atom->nbondtypes); else if (strstr(line,"angle types")) sscanf(line,"%d",&atom->nangletypes); else if (strstr(line,"dihedral types")) sscanf(line,"%d",&atom->ndihedraltypes); else if (strstr(line,"improper types")) sscanf(line,"%d",&atom->nimpropertypes); else if (strstr(line,"extra bond per atom")) sscanf(line,"%d",&atom->extra_bond_per_atom); else if (strstr(line,"extra angle per atom")) sscanf(line,"%d",&atom->extra_angle_per_atom); else if (strstr(line,"extra dihedral per atom")) sscanf(line,"%d",&atom->extra_dihedral_per_atom); else if (strstr(line,"extra improper per atom")) sscanf(line,"%d",&atom->extra_improper_per_atom); else if (strstr(line,"extra special per atom")) sscanf(line,"%d",&force->special_extra); else if (strstr(line,"xlo xhi")) sscanf(line,"%lg %lg",&domain->boxlo[0],&domain->boxhi[0]); else if (strstr(line,"ylo yhi")) sscanf(line,"%lg %lg",&domain->boxlo[1],&domain->boxhi[1]); else if (strstr(line,"zlo zhi")) sscanf(line,"%lg %lg",&domain->boxlo[2],&domain->boxhi[2]); else if (strstr(line,"xy xz yz")) { domain->triclinic = 1; sscanf(line,"%lg %lg %lg",&domain->xy,&domain->xz,&domain->yz); } else break; } // error check on total system size if (atom->natoms < 0 || atom->natoms >= MAXBIGINT || atom->nbonds < 0 || atom->nbonds >= MAXBIGINT || atom->nangles < 0 || atom->nangles >= MAXBIGINT || atom->ndihedrals < 0 || atom->ndihedrals >= MAXBIGINT || atom->nimpropers < 0 || atom->nimpropers >= MAXBIGINT) error->all(FLERR,"System in data file is too big"); // check that exiting string is a valid section keyword parse_keyword(1); for (n = 0; n < NSECTIONS; n++) if (strcmp(keyword,section_keywords[n]) == 0) break; if (n == NSECTIONS) { char str[128]; sprintf(str,"Unknown identifier in data file: %s",keyword); error->all(FLERR,str); } // error checks on header values // must be consistent with atom style and other header values if ((atom->nbonds || atom->nbondtypes) && atom->avec->bonds_allow == 0) error->all(FLERR,"No bonds allowed with this atom style"); if ((atom->nangles || atom->nangletypes) && atom->avec->angles_allow == 0) error->all(FLERR,"No angles allowed with this atom style"); if ((atom->ndihedrals || atom->ndihedraltypes) && atom->avec->dihedrals_allow == 0) error->all(FLERR,"No dihedrals allowed with this atom style"); if ((atom->nimpropers || atom->nimpropertypes) && atom->avec->impropers_allow == 0) error->all(FLERR,"No impropers allowed with this atom style"); if (atom->nbonds > 0 && atom->nbondtypes <= 0) error->all(FLERR,"Bonds defined but no bond types"); if (atom->nangles > 0 && atom->nangletypes <= 0) error->all(FLERR,"Angles defined but no angle types"); if (atom->ndihedrals > 0 && atom->ndihedraltypes <= 0) error->all(FLERR,"Dihedrals defined but no dihedral types"); if (atom->nimpropers > 0 && atom->nimpropertypes <= 0) error->all(FLERR,"Impropers defined but no improper types"); if (atom->molecular == 2) { if (atom->nbonds || atom->nangles || atom->ndihedrals || atom->nimpropers) error->all(FLERR,"No molecule topology allowed with atom style template"); } } /* ---------------------------------------------------------------------- read all atoms ------------------------------------------------------------------------- */ void ReadData::atoms() { int nchunk,eof; if (me == 0) { if (screen) fprintf(screen," reading atoms ...\n"); if (logfile) fprintf(logfile," reading atoms ...\n"); } bigint nread = 0; bigint natoms = atom->natoms; while (nread < natoms) { nchunk = MIN(natoms-nread,CHUNK); eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); if (eof) error->all(FLERR,"Unexpected end of data file"); atom->data_atoms(nchunk,buffer); nread += nchunk; } // check that all atoms were assigned correctly bigint tmp = atom->nlocal; MPI_Allreduce(&tmp,&natoms,1,MPI_LMP_BIGINT,MPI_SUM,world); if (me == 0) { if (screen) fprintf(screen," " BIGINT_FORMAT " atoms\n",natoms); if (logfile) fprintf(logfile," " BIGINT_FORMAT " atoms\n",natoms); } if (natoms != atom->natoms) error->all(FLERR,"Did not assign all atoms correctly"); // check that atom IDs are valid atom->tag_check(); // create global mapping of atoms if (atom->map_style) { atom->map_init(); atom->map_set(); } } /* ---------------------------------------------------------------------- read all velocities to find atoms, must build atom map if not a molecular system ------------------------------------------------------------------------- */ void ReadData::velocities() { int nchunk,eof; if (me == 0) { if (screen) fprintf(screen," reading velocities ...\n"); if (logfile) fprintf(logfile," reading velocities ...\n"); } int mapflag = 0; if (atom->map_style == 0) { mapflag = 1; atom->map_init(); atom->map_set(); } bigint nread = 0; bigint natoms = atom->natoms; while (nread < natoms) { nchunk = MIN(natoms-nread,CHUNK); eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); if (eof) error->all(FLERR,"Unexpected end of data file"); atom->data_vels(nchunk,buffer); nread += nchunk; } if (mapflag) { atom->map_delete(); atom->map_style = 0; } if (me == 0) { if (screen) fprintf(screen," " BIGINT_FORMAT " velocities\n",natoms); if (logfile) fprintf(logfile," " BIGINT_FORMAT " velocities\n",natoms); } } /* ---------------------------------------------------------------------- scan or read all bonds ------------------------------------------------------------------------- */ void ReadData::bonds(int firstpass) { if (me == 0) { if (firstpass) { if (screen) fprintf(screen," scanning bonds ...\n"); if (logfile) fprintf(logfile," scanning bonds ...\n"); } else { if (screen) fprintf(screen," reading bonds ...\n"); if (logfile) fprintf(logfile," reading bonds ...\n"); } } // allocate count if firstpass int nlocal = atom->nlocal; int *count = NULL; if (firstpass) { memory->create(count,nlocal,"read_data:count"); for (int i = 0; i < nlocal; i++) count[i] = 0; } // read and process bonds int nchunk,eof; bigint nread = 0; bigint nbonds = atom->nbonds; while (nread < nbonds) { nchunk = MIN(nbonds-nread,CHUNK); eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); if (eof) error->all(FLERR,"Unexpected end of data file"); atom->data_bonds(nchunk,buffer,count); nread += nchunk; } // if firstpass: tally max bond/atom and return if (firstpass) { int max = 0; for (int i = 0; i < nlocal; i++) max = MAX(max,count[i]); int maxall; MPI_Allreduce(&max,&maxall,1,MPI_INT,MPI_MAX,world); maxall += atom->extra_bond_per_atom; if (me == 0) { if (screen) fprintf(screen," %d = max bonds/atom\n",maxall); if (logfile) fprintf(logfile," %d = max bonds/atom\n",maxall); } atom->bond_per_atom = maxall; memory->destroy(count); return; } // if 2nd pass: check that bonds were assigned correctly bigint n = 0; for (int i = 0; i < nlocal; i++) n += atom->num_bond[i]; bigint sum; MPI_Allreduce(&n,&sum,1,MPI_LMP_BIGINT,MPI_SUM,world); int factor = 1; if (!force->newton_bond) factor = 2; if (me == 0) { if (screen) fprintf(screen," " BIGINT_FORMAT " bonds\n",sum/factor); if (logfile) fprintf(logfile," " BIGINT_FORMAT " bonds\n",sum/factor); } if (sum != factor*atom->nbonds) error->all(FLERR,"Bonds assigned incorrectly"); } /* ---------------------------------------------------------------------- scan or read all angles ------------------------------------------------------------------------- */ void ReadData::angles(int firstpass) { if (me == 0) { if (firstpass) { if (screen) fprintf(screen," scanning angles ...\n"); if (logfile) fprintf(logfile," scanning angles ...\n"); } else { if (screen) fprintf(screen," reading angles ...\n"); if (logfile) fprintf(logfile," reading angles ...\n"); } } // allocate count if firstpass int nlocal = atom->nlocal; int *count = NULL; if (firstpass) { memory->create(count,nlocal,"read_data:count"); for (int i = 0; i < nlocal; i++) count[i] = 0; } // read and process angles int nchunk,eof; bigint nread = 0; bigint nangles = atom->nangles; while (nread < nangles) { nchunk = MIN(nangles-nread,CHUNK); eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); if (eof) error->all(FLERR,"Unexpected end of data file"); atom->data_angles(nchunk,buffer,count); nread += nchunk; } // if firstpass: tally max angle/atom and return if (firstpass) { int max = 0; for (int i = 0; i < nlocal; i++) max = MAX(max,count[i]); int maxall; MPI_Allreduce(&max,&maxall,1,MPI_INT,MPI_MAX,world); maxall += atom->extra_angle_per_atom; if (me == 0) { if (screen) fprintf(screen," %d = max angles/atom\n",maxall); if (logfile) fprintf(logfile," %d = max angles/atom\n",maxall); } atom->angle_per_atom = maxall; memory->destroy(count); return; } // if 2nd pass: check that angles were assigned correctly bigint n = 0; for (int i = 0; i < nlocal; i++) n += atom->num_angle[i]; bigint sum; MPI_Allreduce(&n,&sum,1,MPI_LMP_BIGINT,MPI_SUM,world); int factor = 1; if (!force->newton_bond) factor = 3; if (me == 0) { if (screen) fprintf(screen," " BIGINT_FORMAT " angles\n",sum/factor); if (logfile) fprintf(logfile," " BIGINT_FORMAT " angles\n",sum/factor); } if (sum != factor*atom->nangles) error->all(FLERR,"Angles assigned incorrectly"); } /* ---------------------------------------------------------------------- scan or read all dihedrals ------------------------------------------------------------------------- */ void ReadData::dihedrals(int firstpass) { if (me == 0) { if (firstpass) { if (screen) fprintf(screen," scanning dihedrals ...\n"); if (logfile) fprintf(logfile," scanning dihedrals ...\n"); } else { if (screen) fprintf(screen," reading dihedrals ...\n"); if (logfile) fprintf(logfile," reading dihedrals ...\n"); } } // allocate count if firstpass int nlocal = atom->nlocal; int *count = NULL; if (firstpass) { memory->create(count,nlocal,"read_data:count"); for (int i = 0; i < nlocal; i++) count[i] = 0; } // read and process dihedrals int nchunk,eof; bigint nread = 0; bigint ndihedrals = atom->ndihedrals; while (nread < ndihedrals) { nchunk = MIN(ndihedrals-nread,CHUNK); eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); if (eof) error->all(FLERR,"Unexpected end of data file"); atom->data_dihedrals(nchunk,buffer,count); nread += nchunk; } // if firstpass: tally max dihedral/atom and return if (firstpass) { int max = 0; for (int i = 0; i < nlocal; i++) max = MAX(max,count[i]); int maxall; MPI_Allreduce(&max,&maxall,1,MPI_INT,MPI_MAX,world); maxall += atom->extra_dihedral_per_atom; if (me == 0) { if (screen) fprintf(screen," %d = max dihedrals/atom\n",maxall); if (logfile) fprintf(logfile," %d = max dihedrals/atom\n",maxall); } atom->dihedral_per_atom = maxall; memory->destroy(count); return; } // if 2nd pass: check that dihedrals were assigned correctly bigint n = 0; for (int i = 0; i < nlocal; i++) n += atom->num_dihedral[i]; bigint sum; MPI_Allreduce(&n,&sum,1,MPI_LMP_BIGINT,MPI_SUM,world); int factor = 1; if (!force->newton_bond) factor = 4; if (me == 0) { if (screen) fprintf(screen," " BIGINT_FORMAT " dihedrals\n",sum/factor); if (logfile) fprintf(logfile," " BIGINT_FORMAT " dihedrals\n",sum/factor); } if (sum != factor*atom->ndihedrals) error->all(FLERR,"Dihedrals assigned incorrectly"); } /* ---------------------------------------------------------------------- scan or read all impropers ------------------------------------------------------------------------- */ void ReadData::impropers(int firstpass) { if (me == 0) { if (firstpass) { if (screen) fprintf(screen," scanning impropers ...\n"); if (logfile) fprintf(logfile," scanning impropers ...\n"); } else { if (screen) fprintf(screen," reading impropers ...\n"); if (logfile) fprintf(logfile," reading impropers ...\n"); } } // allocate count if firstpass int nlocal = atom->nlocal; int *count = NULL; if (firstpass) { memory->create(count,nlocal,"read_data:count"); for (int i = 0; i < nlocal; i++) count[i] = 0; } // read and process impropers int nchunk,eof; bigint nread = 0; bigint nimpropers = atom->nimpropers; while (nread < nimpropers) { nchunk = MIN(nimpropers-nread,CHUNK); eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); if (eof) error->all(FLERR,"Unexpected end of data file"); atom->data_impropers(nchunk,buffer,count); nread += nchunk; } // if firstpass: tally max improper/atom and return if (firstpass) { int max = 0; for (int i = 0; i < nlocal; i++) max = MAX(max,count[i]); int maxall; MPI_Allreduce(&max,&maxall,1,MPI_INT,MPI_MAX,world); maxall += atom->extra_improper_per_atom; if (me == 0) { if (screen) fprintf(screen," %d = max impropers/atom\n",maxall); if (logfile) fprintf(logfile," %d = max impropers/atom\n",maxall); } atom->improper_per_atom = maxall; memory->destroy(count); return; } // if 2nd pass: check that impropers were assigned correctly bigint n = 0; for (int i = 0; i < nlocal; i++) n += atom->num_improper[i]; bigint sum; MPI_Allreduce(&n,&sum,1,MPI_LMP_BIGINT,MPI_SUM,world); int factor = 1; if (!force->newton_bond) factor = 4; if (me == 0) { if (screen) fprintf(screen," " BIGINT_FORMAT " impropers\n",sum/factor); if (logfile) fprintf(logfile," " BIGINT_FORMAT " impropers\n",sum/factor); } if (sum != factor*atom->nimpropers) error->all(FLERR,"Impropers assigned incorrectly"); } /* ---------------------------------------------------------------------- read all bonus data to find atoms, must build atom map if not a molecular system ------------------------------------------------------------------------- */ void ReadData::bonus(bigint nbonus, AtomVec *ptr, const char *type) { int nchunk,eof; int mapflag = 0; if (atom->map_style == 0) { mapflag = 1; atom->map_init(); atom->map_set(); } bigint nread = 0; bigint natoms = nbonus; while (nread < natoms) { nchunk = MIN(natoms-nread,CHUNK); eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); if (eof) error->all(FLERR,"Unexpected end of data file"); atom->data_bonus(nchunk,buffer,ptr); nread += nchunk; } if (mapflag) { atom->map_delete(); atom->map_style = 0; } if (me == 0) { if (screen) fprintf(screen," " BIGINT_FORMAT " %s\n",natoms,type); if (logfile) fprintf(logfile," " BIGINT_FORMAT " %s\n",natoms,type); } } /* ---------------------------------------------------------------------- read all body data variable amount of info per body, described by ninteger and ndouble to find atoms, must build atom map if not a molecular system if not firstpass, just read but no processing of data ------------------------------------------------------------------------- */ void ReadData::bodies(int firstpass) { int i,m,nchunk,nline,nmax,ninteger,ndouble,tmp,onebody; char *eof; int mapflag = 0; if (atom->map_style == 0 && firstpass) { mapflag = 1; atom->map_init(); atom->map_set(); } // nmax = max # of bodies to read in this chunk // nchunk = actual # read bigint nread = 0; bigint natoms = nbodies; while (nread < natoms) { if (natoms-nread > CHUNK) nmax = CHUNK; else nmax = natoms-nread; if (me == 0) { nchunk = 0; nline = 0; m = 0; while (nchunk < nmax && nline <= CHUNK-MAXBODY) { eof = fgets(&buffer[m],MAXLINE,fp); if (eof == NULL) error->one(FLERR,"Unexpected end of data file"); sscanf(&buffer[m],"%d %d %d",&tmp,&ninteger,&ndouble); m += strlen(&buffer[m]); onebody = 0; if (ninteger) onebody += (ninteger-1)/10 + 1; if (ndouble) onebody += (ndouble-1)/10 + 1; if (onebody+1 > MAXBODY) error->one(FLERR, "Too many lines in one body in data file - boost MAXBODY"); for (i = 0; i < onebody; i++) { eof = fgets(&buffer[m],MAXLINE,fp); if (eof == NULL) error->one(FLERR,"Unexpected end of data file"); m += strlen(&buffer[m]); } nchunk++; nline += onebody+1; } if (buffer[m-1] != '\n') strcpy(&buffer[m++],"\n"); m++; } MPI_Bcast(&nchunk,1,MPI_INT,0,world); MPI_Bcast(&m,1,MPI_INT,0,world); MPI_Bcast(buffer,m,MPI_CHAR,0,world); if (firstpass) atom->data_bodies(nchunk,buffer,avec_body); nread += nchunk; } if (mapflag && firstpass) { atom->map_delete(); atom->map_style = 0; } if (me == 0 && firstpass) { if (screen) fprintf(screen," " BIGINT_FORMAT " bodies\n",natoms); if (logfile) fprintf(logfile," " BIGINT_FORMAT " bodies\n",natoms); } } /* ---------------------------------------------------------------------- */ void ReadData::mass() { char *next; char *buf = new char[atom->ntypes*MAXLINE]; int eof = comm->read_lines_from_file(fp,atom->ntypes,MAXLINE,buf); if (eof) error->all(FLERR,"Unexpected end of data file"); char *original = buf; for (int i = 0; i < atom->ntypes; i++) { next = strchr(buf,'\n'); *next = '\0'; atom->set_mass(buf); buf = next + 1; } delete [] original; } /* ---------------------------------------------------------------------- */ void ReadData::paircoeffs() { char *next; char *buf = new char[atom->ntypes*MAXLINE]; int eof = comm->read_lines_from_file(fp,atom->ntypes,MAXLINE,buf); if (eof) error->all(FLERR,"Unexpected end of data file"); char *original = buf; for (int i = 0; i < atom->ntypes; i++) { next = strchr(buf,'\n'); *next = '\0'; parse_coeffs(buf,NULL,1); if (narg == 0) error->all(FLERR,"Unexpected end of PairCoeffs section"); force->pair->coeff(narg,arg); buf = next + 1; } delete [] original; } /* ---------------------------------------------------------------------- */ void ReadData::pairIJcoeffs() { int i,j; char *next; int nsq = atom->ntypes* (atom->ntypes+1) / 2; char *buf = new char[nsq * MAXLINE]; int eof = comm->read_lines_from_file(fp,nsq,MAXLINE,buf); if (eof) error->all(FLERR,"Unexpected end of data file"); char *original = buf; for (i = 0; i < atom->ntypes; i++) for (j = i; j < atom->ntypes; j++) { next = strchr(buf,'\n'); *next = '\0'; parse_coeffs(buf,NULL,0); if (narg == 0) error->all(FLERR,"Unexpected end of PairCoeffs section"); force->pair->coeff(narg,arg); buf = next + 1; } delete [] original; } /* ---------------------------------------------------------------------- */ void ReadData::bondcoeffs() { char *next; char *buf = new char[atom->nbondtypes*MAXLINE]; int eof = comm->read_lines_from_file(fp,atom->nbondtypes,MAXLINE,buf); if (eof) error->all(FLERR,"Unexpected end of data file"); char *original = buf; for (int i = 0; i < atom->nbondtypes; i++) { next = strchr(buf,'\n'); *next = '\0'; parse_coeffs(buf,NULL,0); if (narg == 0) error->all(FLERR,"Unexpected end of BondCoeffs section"); force->bond->coeff(narg,arg); buf = next + 1; } delete [] original; } /* ---------------------------------------------------------------------- */ void ReadData::anglecoeffs(int which) { char *next; char *buf = new char[atom->nangletypes*MAXLINE]; int eof = comm->read_lines_from_file(fp,atom->nangletypes,MAXLINE,buf); if (eof) error->all(FLERR,"Unexpected end of data file"); char *original = buf; for (int i = 0; i < atom->nangletypes; i++) { next = strchr(buf,'\n'); *next = '\0'; if (which == 0) parse_coeffs(buf,NULL,0); else if (which == 1) parse_coeffs(buf,"bb",0); else if (which == 2) parse_coeffs(buf,"ba",0); if (narg == 0) error->all(FLERR,"Unexpected end of AngleCoeffs section"); force->angle->coeff(narg,arg); buf = next + 1; } delete [] original; } /* ---------------------------------------------------------------------- */ void ReadData::dihedralcoeffs(int which) { char *next; char *buf = new char[atom->ndihedraltypes*MAXLINE]; int eof = comm->read_lines_from_file(fp,atom->ndihedraltypes,MAXLINE,buf); if (eof) error->all(FLERR,"Unexpected end of data file"); char *original = buf; for (int i = 0; i < atom->ndihedraltypes; i++) { next = strchr(buf,'\n'); *next = '\0'; if (which == 0) parse_coeffs(buf,NULL,0); else if (which == 1) parse_coeffs(buf,"mbt",0); else if (which == 2) parse_coeffs(buf,"ebt",0); else if (which == 3) parse_coeffs(buf,"at",0); else if (which == 4) parse_coeffs(buf,"aat",0); else if (which == 5) parse_coeffs(buf,"bb13",0); if (narg == 0) error->all(FLERR,"Unexpected end of DihedralCoeffs section"); force->dihedral->coeff(narg,arg); buf = next + 1; } delete [] original; } /* ---------------------------------------------------------------------- */ void ReadData::impropercoeffs(int which) { char *next; char *buf = new char[atom->nimpropertypes*MAXLINE]; int eof = comm->read_lines_from_file(fp,atom->nimpropertypes,MAXLINE,buf); if (eof) error->all(FLERR,"Unexpected end of data file"); char *original = buf; for (int i = 0; i < atom->nimpropertypes; i++) { next = strchr(buf,'\n'); *next = '\0'; if (which == 0) parse_coeffs(buf,NULL,0); else if (which == 1) parse_coeffs(buf,"aa",0); if (narg == 0) error->all(FLERR,"Unexpected end of ImproperCoeffs section"); force->improper->coeff(narg,arg); buf = next + 1; } delete [] original; } /* ---------------------------------------------------------------------- read fix section, pass lines to fix to process n = index of fix ------------------------------------------------------------------------- */ void ReadData::fix(int ifix, char *keyword) { int nchunk,eof; bigint nline = modify->fix[ifix]->read_data_skip_lines(keyword); bigint nread = 0; while (nread < nline) { nchunk = MIN(nline-nread,CHUNK); eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer); if (eof) error->all(FLERR,"Unexpected end of data file"); modify->fix[ifix]->read_data_section(keyword,nchunk,buffer); nread += nchunk; } } /* ---------------------------------------------------------------------- reallocate the count vector from cmax to amax+1 and return new length zero new locations ------------------------------------------------------------------------- */ int ReadData::reallocate(int **pcount, int cmax, int amax) { int *count = *pcount; memory->grow(count,amax+1,"read_data:count"); for (int i = cmax; i <= amax; i++) count[i] = 0; *pcount = count; return amax+1; } /* ---------------------------------------------------------------------- proc 0 opens data file test if gzipped ------------------------------------------------------------------------- */ void ReadData::open(char *file) { compressed = 0; char *suffix = file + strlen(file) - 3; if (suffix > file && strcmp(suffix,".gz") == 0) compressed = 1; if (!compressed) fp = fopen(file,"r"); else { #ifdef LAMMPS_GZIP char gunzip[128]; sprintf(gunzip,"gzip -c -d %s",file); #ifdef _WIN32 fp = _popen(gunzip,"rb"); #else fp = popen(gunzip,"r"); #endif #else error->one(FLERR,"Cannot open gzipped file"); #endif } if (fp == NULL) { char str[128]; sprintf(str,"Cannot open file %s",file); error->one(FLERR,str); } } /* ---------------------------------------------------------------------- grab next keyword read lines until one is non-blank keyword is all text on line w/out leading & trailing white space optional style can be appended after comment char '#' read one additional line (assumed blank) if any read hits EOF, set keyword to empty if first = 1, line variable holds non-blank line that ended header ------------------------------------------------------------------------- */ void ReadData::parse_keyword(int first) { int eof = 0; // proc 0 reads upto non-blank line plus 1 following line // eof is set to 1 if any read hits end-of-file if (me == 0) { if (!first) { if (fgets(line,MAXLINE,fp) == NULL) eof = 1; } while (eof == 0 && strspn(line," \t\n\r") == strlen(line)) { if (fgets(line,MAXLINE,fp) == NULL) eof = 1; } if (fgets(buffer,MAXLINE,fp) == NULL) eof = 1; } // if eof, set keyword empty and return MPI_Bcast(&eof,1,MPI_INT,0,world); if (eof) { keyword[0] = '\0'; return; } // bcast keyword line to all procs int n; if (me == 0) n = strlen(line) + 1; MPI_Bcast(&n,1,MPI_INT,0,world); MPI_Bcast(line,n,MPI_CHAR,0,world); // store optional "style" following comment char '#' after keyword char *ptr; if ((ptr = strchr(line,'#'))) { *ptr++ = '\0'; while (*ptr == ' ' || *ptr == '\t') ptr++; int stop = strlen(ptr) - 1; while (ptr[stop] == ' ' || ptr[stop] == '\t' || ptr[stop] == '\n' || ptr[stop] == '\r') stop--; ptr[stop+1] = '\0'; strcpy(style,ptr); } else style[0] = '\0'; // copy non-whitespace portion of line into keyword int start = strspn(line," \t\n\r"); int stop = strlen(line) - 1; while (line[stop] == ' ' || line[stop] == '\t' || line[stop] == '\n' || line[stop] == '\r') stop--; line[stop+1] = '\0'; strcpy(keyword,&line[start]); } /* ---------------------------------------------------------------------- proc 0 reads N lines from file could be skipping Natoms lines, so use bigints ------------------------------------------------------------------------- */ void ReadData::skip_lines(bigint n) { if (me) return; char *eof; for (bigint i = 0; i < n; i++) eof = fgets(line,MAXLINE,fp); if (eof == NULL) error->one(FLERR,"Unexpected end of data file"); } /* ---------------------------------------------------------------------- parse a line of coeffs into words, storing them in narg,arg trim anything from '#' onward word strings remain in line, are not copied if addstr != NULL, add addstr as extra arg for class2 angle/dihedral/improper if 2nd word starts with letter, then is hybrid style, add addstr after it else add addstr before 2nd word if dupflag, duplicate 1st word, so pair_coeff "2" becomes "2 2" ------------------------------------------------------------------------- */ void ReadData::parse_coeffs(char *line, const char *addstr, int dupflag) { char *ptr; if ((ptr = strchr(line,'#'))) *ptr = '\0'; narg = 0; char *word = strtok(line," \t\n\r\f"); while (word) { if (narg == maxarg) { maxarg += DELTA; arg = (char **) memory->srealloc(arg,maxarg*sizeof(char *),"read_data:arg"); } if (addstr && narg == 1 && !islower(word[0])) arg[narg++] = (char *) addstr; arg[narg++] = word; if (addstr && narg == 2 && islower(word[0])) arg[narg++] = (char *) addstr; if (dupflag && narg == 1) arg[narg++] = word; word = strtok(NULL," \t\n\r\f"); } } /* ---------------------------------------------------------------------- compare two style strings if they both exist one = comment in data file section, two = currently-defined style ignore suffixes listed in suffixes array at top of file ------------------------------------------------------------------------- */ int ReadData::style_match(const char *one, const char *two) { int i,delta,len,len1,len2; if ((one == NULL) || (two == NULL)) return 1; len1 = strlen(one); len2 = strlen(two); for (i = 0; suffixes[i] != NULL; i++) { len = strlen(suffixes[i]); if ((delta = len1 - len) > 0) if (strcmp(one+delta,suffixes[i]) == 0) len1 = delta; if ((delta = len2 - len) > 0) if (strcmp(two+delta,suffixes[i]) == 0) len2 = delta; } if ((len1 == 0) || (len1 == len2) || (strncmp(one,two,len1) == 0)) return 1; return 0; }