sync with current develop
This commit is contained in:
Steve Plimpton
@ -35,10 +35,12 @@
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#include "molecule.h"
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#include "pair.h"
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#include "special.h"
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#include "tokenizer.h"
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#include "update.h"
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#include <cctype>
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#include <cstring>
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#include <unordered_set>
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using namespace LAMMPS_NS;
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@ -49,9 +51,27 @@ static constexpr int DELTA = 4; // must be 2 or larger
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static constexpr int MAXBODY = 32; // max # of lines in one body
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// customize for new sections
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// change when add to header::section_keywords
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static constexpr int NSECTIONS = 25;
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static std::unordered_set<std::string> section_keywords = {
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"Atoms", "Velocities", "Ellipsoids", "Lines", "Triangles", "Bodies",
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"Bonds", "Angles", "Dihedrals", "Impropers",
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"Masses", "Pair Coeffs", "PairIJ 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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};
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// function to check whether a string is a known data section name
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// made a static class member, so it can be called from other classes
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bool ReadData::is_data_section(const std::string &keyword)
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{
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return section_keywords.count(keyword) > 0;
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}
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// clang-format off
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enum{NONE,APPEND,VALUE,MERGE};
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// pair style suffixes to ignore
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@ -79,11 +99,11 @@ ReadData::ReadData(LAMMPS *lmp) : Command(lmp)
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// pointers to atom styles that store bonus info
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nellipsoids = 0;
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avec_ellipsoid = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
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avec_ellipsoid = dynamic_cast<AtomVecEllipsoid *>( atom->style_match("ellipsoid"));
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nlines = 0;
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avec_line = (AtomVecLine *) atom->style_match("line");
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avec_line = dynamic_cast<AtomVecLine *>( atom->style_match("line"));
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ntris = 0;
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avec_tri = (AtomVecTri *) atom->style_match("tri");
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avec_tri = dynamic_cast<AtomVecTri *>( atom->style_match("tri"));
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nbodies = 0;
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avec_body = (AtomVecBody *) atom->style_match("body");
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}
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@ -114,7 +134,7 @@ void ReadData::command(int narg, char **arg)
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if (narg < 1) error->all(FLERR,"Illegal read_data command");
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MPI_Barrier(world);
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double time1 = MPI_Wtime();
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double time1 = platform::walltime();
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// optional args
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@ -266,18 +286,19 @@ void ReadData::command(int narg, char **arg)
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if (iarg+4 > narg)
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error->all(FLERR,"Illegal read_data command");
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memory->grow(fix_index,nfix+1,"read_data:fix_index");
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fix_header = (char **)
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memory->srealloc(fix_header,(nfix+1)*sizeof(char *),
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"read_data:fix_header");
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fix_section = (char **)
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memory->srealloc(fix_section,(nfix+1)*sizeof(char *),
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"read_data:fix_section");
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fix_header = (char **) memory->srealloc(fix_header,(nfix+1)*sizeof(char *),
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"read_data:fix_header");
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fix_section = (char **) memory->srealloc(fix_section,(nfix+1)*sizeof(char *),
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"read_data:fix_section");
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if (is_data_section(arg[iarg+3]))
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error->all(FLERR,"Custom data section name {} for fix {} collides with existing "
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"data section",arg[iarg+3],arg[iarg+1]);
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fix_index[nfix] = modify->find_fix(arg[iarg+1]);
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if (fix_index[nfix] < 0)
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error->all(FLERR,"Fix ID for read_data does not exist");
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if (fix_index[nfix] < 0) error->all(FLERR,"Fix ID for read_data does not exist");
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if (strcmp(arg[iarg+2],"NULL") == 0) fix_header[nfix] = nullptr;
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else fix_header[nfix] = utils::strdup(arg[iarg+2]);
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fix_section[nfix] = utils::strdup(arg[iarg+3]);
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if (strcmp(arg[iarg+3],"NULL") == 0) fix_section[nfix] = utils::strdup(arg[iarg+1]);
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else fix_section[nfix] = utils::strdup(arg[iarg+3]);
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nfix++;
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iarg += 4;
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@ -308,10 +329,14 @@ void ReadData::command(int narg, char **arg)
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// check if data file is available and readable
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if (!utils::file_is_readable(arg[0]))
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if (!platform::file_is_readable(arg[0]))
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error->all(FLERR,fmt::format("Cannot open file {}: {}",
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arg[0], utils::getsyserror()));
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// reset so we can warn about reset image flags exactly once per data file
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atom->reset_image_flag[0] = atom->reset_image_flag[1] = atom->reset_image_flag[2] = false;
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// first time system initialization
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if (addflag == NONE) {
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@ -426,7 +451,7 @@ void ReadData::command(int narg, char **arg)
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nlocal_previous = atom->nlocal;
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int firstpass = 1;
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while (1) {
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while (true) {
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// open file on proc 0
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@ -517,6 +542,7 @@ void ReadData::command(int narg, char **arg)
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"from currently defined atom style");
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atoms();
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} else skip_lines(natoms);
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} else if (strcmp(keyword,"Velocities") == 0) {
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if (atomflag == 0)
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error->all(FLERR,"Must read Atoms before Velocities");
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@ -525,52 +551,50 @@ 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 (nbonds == 0)
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error->all(FLERR,"Invalid data file section: Bonds");
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if (nbonds == 0) 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 (nangles == 0)
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error->all(FLERR,"Invalid data file section: Angles");
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if (nangles == 0) 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 (ndihedrals == 0)
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error->all(FLERR,"Invalid data file section: Dihedrals");
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if (ndihedrals == 0) 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 (nimpropers == 0)
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error->all(FLERR,"Invalid data file section: Impropers");
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if (nimpropers == 0) 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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} else if (strcmp(keyword,"Ellipsoids") == 0) {
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ellipsoidflag = 1;
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if (!avec_ellipsoid)
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error->all(FLERR,"Invalid data file section: Ellipsoids");
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if (atomflag == 0)
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error->all(FLERR,"Must read Atoms before Ellipsoids");
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if (!avec_ellipsoid) error->all(FLERR,"Invalid data file section: Ellipsoids");
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if (atomflag == 0) error->all(FLERR,"Must read Atoms before Ellipsoids");
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if (firstpass)
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bonus(nellipsoids,(AtomVec *) avec_ellipsoid,"ellipsoids");
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else skip_lines(nellipsoids);
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} else if (strcmp(keyword,"Lines") == 0) {
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lineflag = 1;
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if (!avec_line)
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error->all(FLERR,"Invalid data file section: Lines");
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if (!avec_line) error->all(FLERR,"Invalid data file section: Lines");
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if (atomflag == 0) error->all(FLERR,"Must read Atoms before Lines");
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if (firstpass) bonus(nlines,(AtomVec *) avec_line,"lines");
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else skip_lines(nlines);
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} else if (strcmp(keyword,"Triangles") == 0) {
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triflag = 1;
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if (!avec_tri)
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error->all(FLERR,"Invalid data file section: Triangles");
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if (!avec_tri) error->all(FLERR,"Invalid data file section: Triangles");
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if (atomflag == 0) error->all(FLERR,"Must read Atoms before Triangles");
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if (firstpass) bonus(ntris,(AtomVec *) avec_tri,"triangles");
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else skip_lines(ntris);
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} else if (strcmp(keyword,"Bodies") == 0) {
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bodyflag = 1;
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if (!avec_body)
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@ -651,6 +675,7 @@ void ReadData::command(int narg, char **arg)
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error->all(FLERR,"Must define angle_style before BondBond Coeffs");
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if (firstpass) anglecoeffs(1);
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else skip_lines(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(FLERR,"Invalid data file section: BondAngle Coeffs");
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@ -668,46 +693,41 @@ void ReadData::command(int narg, char **arg)
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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(FLERR,
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"Invalid data file section: MiddleBondTorsion Coeffs");
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error->all(FLERR,"Invalid data file section: MiddleBondTorsion Coeffs");
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if (force->dihedral == nullptr)
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error->all(FLERR,
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"Must define dihedral_style before "
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"MiddleBondTorsion Coeffs");
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error->all(FLERR,"Must define dihedral_style before MiddleBondTorsion Coeffs");
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if (firstpass) dihedralcoeffs(1);
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else skip_lines(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(FLERR,"Invalid data file section: EndBondTorsion Coeffs");
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if (force->dihedral == nullptr)
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error->all(FLERR,
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"Must define dihedral_style before EndBondTorsion Coeffs");
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error->all(FLERR,"Must define dihedral_style before EndBondTorsion Coeffs");
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if (firstpass) dihedralcoeffs(2);
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else skip_lines(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(FLERR,"Invalid data file section: AngleTorsion Coeffs");
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if (force->dihedral == nullptr)
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error->all(FLERR,
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"Must define dihedral_style before AngleTorsion Coeffs");
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error->all(FLERR,"Must define dihedral_style before AngleTorsion Coeffs");
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if (firstpass) dihedralcoeffs(3);
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else skip_lines(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(FLERR,
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"Invalid data file section: AngleAngleTorsion Coeffs");
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error->all(FLERR,"Invalid data file section: AngleAngleTorsion Coeffs");
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if (force->dihedral == nullptr)
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error->all(FLERR,
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"Must define dihedral_style before "
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"AngleAngleTorsion Coeffs");
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error->all(FLERR,"Must define dihedral_style before AngleAngleTorsion Coeffs");
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if (firstpass) dihedralcoeffs(4);
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else skip_lines(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(FLERR,"Invalid data file section: BondBond13 Coeffs");
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if (force->dihedral == nullptr)
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error->all(FLERR,
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"Must define dihedral_style before BondBond13 Coeffs");
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error->all(FLERR,"Must define dihedral_style before BondBond13 Coeffs");
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if (firstpass) dihedralcoeffs(5);
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else skip_lines(ndihedraltypes);
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@ -715,8 +735,7 @@ void ReadData::command(int narg, char **arg)
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if (atom->avec->impropers_allow == 0)
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error->all(FLERR,"Invalid data file section: AngleAngle Coeffs");
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if (force->improper == nullptr)
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error->all(FLERR,
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"Must define improper_style before AngleAngle Coeffs");
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error->all(FLERR,"Must define improper_style before AngleAngle Coeffs");
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if (firstpass) impropercoeffs(1);
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else skip_lines(nimpropertypes);
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@ -747,7 +766,7 @@ void ReadData::command(int narg, char **arg)
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// close file
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if (me == 0) {
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if (compressed) pclose(fp);
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if (compressed) platform::pclose(fp);
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else fclose(fp);
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fp = nullptr;
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}
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@ -859,7 +878,7 @@ void ReadData::command(int narg, char **arg)
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if (addflag != NONE) {
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if (domain->triclinic) domain->x2lamda(atom->nlocal);
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Irregular *irregular = new Irregular(lmp);
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auto irregular = new Irregular(lmp);
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irregular->migrate_atoms(1);
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delete irregular;
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if (domain->triclinic) domain->lamda2x(atom->nlocal);
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@ -875,7 +894,7 @@ void ReadData::command(int narg, char **arg)
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if (domain->nonperiodic == 2) {
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if (domain->triclinic) domain->x2lamda(atom->nlocal);
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domain->reset_box();
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Irregular *irregular = new Irregular(lmp);
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auto irregular = new Irregular(lmp);
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irregular->migrate_atoms(1);
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delete irregular;
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if (domain->triclinic) domain->lamda2x(atom->nlocal);
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@ -884,30 +903,34 @@ void ReadData::command(int narg, char **arg)
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bigint nblocal = atom->nlocal;
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MPI_Allreduce(&nblocal,&natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);
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if (natoms != atom->natoms)
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error->all(FLERR,
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"Read_data shrink wrap did not assign all atoms correctly");
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error->all(FLERR,"Read_data shrink wrap did not assign all atoms correctly");
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}
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// restore old styles, when reading with nocoeff flag given
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if (coeffflag == 0) {
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if (force->pair) delete force->pair;
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delete force->pair;
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delete[] force->pair_style;
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force->pair = saved_pair;
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force->pair_style = saved_pair_style;
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if (force->bond) delete force->bond;
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delete force->bond;
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delete[] force->bond_style;
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force->bond = saved_bond;
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force->bond_style = saved_bond_style;
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if (force->angle) delete force->angle;
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delete force->angle;
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delete[] force->angle_style;
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force->angle = saved_angle;
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force->angle_style = saved_angle_style;
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if (force->dihedral) delete force->dihedral;
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delete force->dihedral;
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delete[] force->dihedral_style;
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force->dihedral = saved_dihedral;
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force->dihedral_style = saved_dihedral_style;
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if (force->improper) delete force->improper;
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delete force->improper;
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delete[] force->improper_style;
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force->improper = saved_improper;
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force->improper_style = saved_improper_style;
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@ -920,7 +943,7 @@ void ReadData::command(int narg, char **arg)
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MPI_Barrier(world);
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if (comm->me == 0)
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utils::logmesg(lmp," read_data CPU = {:.3f} seconds\n",MPI_Wtime()-time1);
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utils::logmesg(lmp," read_data CPU = {:.3f} seconds\n",platform::walltime()-time1);
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}
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/* ----------------------------------------------------------------------
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@ -949,17 +972,6 @@ void ReadData::header(int firstpass)
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atom->nimpropertypes = extra_improper_types;
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}
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// customize for new sections
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const char *section_keywords[NSECTIONS] =
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{"Atoms","Velocities","Ellipsoids","Lines","Triangles","Bodies",
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"Bonds","Angles","Dihedrals","Impropers",
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"Masses","Pair Coeffs","PairIJ 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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@ -967,7 +979,7 @@ void ReadData::header(int firstpass)
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if (eof == nullptr) error->one(FLERR,"Unexpected end of data file");
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}
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while (1) {
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while (true) {
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// read a line and bcast length
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@ -1008,119 +1020,80 @@ void ReadData::header(int firstpass)
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// search line for header keyword and set corresponding variable
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// customize for new header lines
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// check for triangles before angles so "triangles" not matched as "angles"
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int extra_flag_value = 0;
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int rv;
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auto words = utils::split_words(line);
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|
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if (utils::strmatch(line,"^\\s*\\d+\\s+atoms\\s")) {
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rv = sscanf(line,BIGINT_FORMAT,&natoms);
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if (rv != 1)
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error->all(FLERR,"Could not parse 'atoms' line in data file header");
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natoms = utils::bnumeric(FLERR, words[0], false, lmp);
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if (addflag == NONE) atom->natoms = natoms;
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else if (firstpass) atom->natoms += natoms;
|
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} else if (utils::strmatch(line,"^\\s*\\d+\\s+ellipsoids\\s")) {
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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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rv = sscanf(line,BIGINT_FORMAT,&nellipsoids);
|
||||
if (rv != 1)
|
||||
error->all(FLERR,"Could not parse 'ellipsoids' line in data file header");
|
||||
if (!avec_ellipsoid) error->all(FLERR,"No ellipsoids allowed with this atom style");
|
||||
nellipsoids = utils::bnumeric(FLERR, words[0], false, lmp);
|
||||
if (addflag == NONE) atom->nellipsoids = nellipsoids;
|
||||
else if (firstpass) atom->nellipsoids += nellipsoids;
|
||||
|
||||
} else if (utils::strmatch(line,"^\\s*\\d+\\s+lines\\s")) {
|
||||
if (!avec_line)
|
||||
error->all(FLERR,"No lines allowed with this atom style");
|
||||
rv = sscanf(line,BIGINT_FORMAT,&nlines);
|
||||
if (rv != 1)
|
||||
error->all(FLERR,"Could not parse 'lines' line in data file header");
|
||||
if (!avec_line) error->all(FLERR,"No lines allowed with this atom style");
|
||||
nlines = utils::bnumeric(FLERR, words[0], false, lmp);
|
||||
if (addflag == NONE) atom->nlines = nlines;
|
||||
else if (firstpass) atom->nlines += nlines;
|
||||
|
||||
} else if (utils::strmatch(line,"^\\s*\\d+\\s+triangles\\s")) {
|
||||
if (!avec_tri)
|
||||
error->all(FLERR,"No triangles allowed with this atom style");
|
||||
rv = sscanf(line,BIGINT_FORMAT,&ntris);
|
||||
if (rv != 1)
|
||||
error->all(FLERR,"Could not parse 'triangles' line in data file header");
|
||||
if (!avec_tri) error->all(FLERR,"No triangles allowed with this atom style");
|
||||
ntris = utils::bnumeric(FLERR, words[0], false, lmp);
|
||||
if (addflag == NONE) atom->ntris = ntris;
|
||||
else if (firstpass) atom->ntris += ntris;
|
||||
|
||||
} else if (utils::strmatch(line,"^\\s*\\d+\\s+bodies\\s")) {
|
||||
if (!avec_body)
|
||||
error->all(FLERR,"No bodies allowed with this atom style");
|
||||
rv = sscanf(line,BIGINT_FORMAT,&nbodies);
|
||||
if (rv != 1)
|
||||
error->all(FLERR,"Could not parse 'bodies' line in data file header");
|
||||
if (!avec_body) error->all(FLERR,"No bodies allowed with this atom style");
|
||||
nbodies = utils::bnumeric(FLERR, words[0], false, lmp);
|
||||
if (addflag == NONE) atom->nbodies = nbodies;
|
||||
else if (firstpass) atom->nbodies += nbodies;
|
||||
|
||||
} else if (utils::strmatch(line,"^\\s*\\d+\\s+bonds\\s")) {
|
||||
rv = sscanf(line,BIGINT_FORMAT,&nbonds);
|
||||
if (rv != 1)
|
||||
error->all(FLERR,"Could not parse 'bonds' line in data file header");
|
||||
nbonds = utils::bnumeric(FLERR, words[0], false, lmp);
|
||||
if (addflag == NONE) atom->nbonds = nbonds;
|
||||
else if (firstpass) atom->nbonds += nbonds;
|
||||
|
||||
} else if (utils::strmatch(line,"^\\s*\\d+\\s+angles\\s")) {
|
||||
rv = sscanf(line,BIGINT_FORMAT,&nangles);
|
||||
if (rv != 1)
|
||||
error->all(FLERR,"Could not parse 'angles' line in data file header");
|
||||
nangles = utils::bnumeric(FLERR, words[0], false, lmp);
|
||||
if (addflag == NONE) atom->nangles = nangles;
|
||||
else if (firstpass) atom->nangles += nangles;
|
||||
|
||||
} else if (utils::strmatch(line,"^\\s*\\d+\\s+dihedrals\\s")) {
|
||||
rv = sscanf(line,BIGINT_FORMAT,&ndihedrals);
|
||||
if (rv != 1)
|
||||
error->all(FLERR,"Could not parse 'dihedrals' line in data file header");
|
||||
ndihedrals = utils::bnumeric(FLERR, words[0], false, lmp);
|
||||
if (addflag == NONE) atom->ndihedrals = ndihedrals;
|
||||
else if (firstpass) atom->ndihedrals += ndihedrals;
|
||||
|
||||
} else if (utils::strmatch(line,"^\\s*\\d+\\s+impropers\\s")) {
|
||||
rv = sscanf(line,BIGINT_FORMAT,&nimpropers);
|
||||
if (rv != 1)
|
||||
error->all(FLERR,"Could not parse 'impropers' line in data file header");
|
||||
nimpropers = utils::bnumeric(FLERR, words[0], false, lmp);
|
||||
if (addflag == NONE) atom->nimpropers = nimpropers;
|
||||
else if (firstpass) atom->nimpropers += nimpropers;
|
||||
|
||||
// Atom class type settings are only set by first data file
|
||||
|
||||
} else if (utils::strmatch(line,"^\\s*\\d+\\s+atom\\s+types\\s")) {
|
||||
rv = sscanf(line,"%d",&ntypes);
|
||||
if (rv != 1)
|
||||
error->all(FLERR,"Could not parse 'atom types' line "
|
||||
"in data file header");
|
||||
ntypes = utils::inumeric(FLERR, words[0], false, lmp);
|
||||
if (addflag == NONE) atom->ntypes = ntypes + extra_atom_types;
|
||||
|
||||
} else if (utils::strmatch(line,"\\s*\\d+\\s+bond\\s+types\\s")) {
|
||||
rv = sscanf(line,"%d",&nbondtypes);
|
||||
if (rv != 1)
|
||||
error->all(FLERR,"Could not parse 'bond types' line "
|
||||
"in data file header");
|
||||
nbondtypes = utils::inumeric(FLERR, words[0], false, lmp);
|
||||
if (addflag == NONE) atom->nbondtypes = nbondtypes + extra_bond_types;
|
||||
|
||||
} else if (utils::strmatch(line,"^\\s*\\d+\\s+angle\\s+types\\s")) {
|
||||
rv = sscanf(line,"%d",&nangletypes);
|
||||
if (rv != 1)
|
||||
error->all(FLERR,"Could not parse 'angle types' line "
|
||||
"in data file header");
|
||||
nangletypes = utils::inumeric(FLERR, words[0], false, lmp);
|
||||
if (addflag == NONE) atom->nangletypes = nangletypes + extra_angle_types;
|
||||
|
||||
} else if (utils::strmatch(line,"^\\s*\\d+\\s+dihedral\\s+types\\s")) {
|
||||
rv = sscanf(line,"%d",&ndihedraltypes);
|
||||
if (rv != 1)
|
||||
error->all(FLERR,"Could not parse 'dihedral types' line "
|
||||
"in data file header");
|
||||
if (addflag == NONE)
|
||||
atom->ndihedraltypes = ndihedraltypes + extra_dihedral_types;
|
||||
ndihedraltypes = utils::inumeric(FLERR, words[0], false, lmp);
|
||||
if (addflag == NONE) atom->ndihedraltypes = ndihedraltypes + extra_dihedral_types;
|
||||
|
||||
} else if (utils::strmatch(line,"^\\s*\\d+\\s+improper\\s+types\\s")) {
|
||||
rv = sscanf(line,"%d",&nimpropertypes);
|
||||
if (rv != 1)
|
||||
error->all(FLERR,"Could not parse 'improper types' line "
|
||||
"in data file header");
|
||||
if (addflag == NONE)
|
||||
atom->nimpropertypes = nimpropertypes + extra_improper_types;
|
||||
nimpropertypes = utils::inumeric(FLERR, words[0], false, lmp);
|
||||
if (addflag == NONE) atom->nimpropertypes = nimpropertypes + extra_improper_types;
|
||||
|
||||
// these settings only used by first data file
|
||||
// also, these are obsolescent. we parse them to maintain backward
|
||||
@ -1129,45 +1102,41 @@ void ReadData::header(int firstpass)
|
||||
// the input and the data file, we use the larger of the two.
|
||||
|
||||
} else if (strstr(line,"extra bond per atom")) {
|
||||
if (addflag == NONE) sscanf(line,"%d",&extra_flag_value);
|
||||
if (addflag == NONE) extra_flag_value = utils::inumeric(FLERR, words[0], false, lmp);
|
||||
atom->extra_bond_per_atom = MAX(atom->extra_bond_per_atom,extra_flag_value);
|
||||
} else if (strstr(line,"extra angle per atom")) {
|
||||
if (addflag == NONE) sscanf(line,"%d",&extra_flag_value);
|
||||
if (addflag == NONE) extra_flag_value = utils::inumeric(FLERR, words[0], false, lmp);
|
||||
atom->extra_angle_per_atom = MAX(atom->extra_angle_per_atom,extra_flag_value);
|
||||
} else if (strstr(line,"extra dihedral per atom")) {
|
||||
if (addflag == NONE) sscanf(line,"%d",&extra_flag_value);
|
||||
if (addflag == NONE) extra_flag_value = utils::inumeric(FLERR, words[0], false, lmp);
|
||||
atom->extra_dihedral_per_atom = MAX(atom->extra_dihedral_per_atom,extra_flag_value);
|
||||
} else if (strstr(line,"extra improper per atom")) {
|
||||
if (addflag == NONE) sscanf(line,"%d",&extra_flag_value);
|
||||
if (addflag == NONE) extra_flag_value = utils::inumeric(FLERR, words[0], false, lmp);
|
||||
atom->extra_improper_per_atom = MAX(atom->extra_improper_per_atom,extra_flag_value);
|
||||
} else if (strstr(line,"extra special per atom")) {
|
||||
if (addflag == NONE) sscanf(line,"%d",&extra_flag_value);
|
||||
if (addflag == NONE) extra_flag_value = utils::inumeric(FLERR, words[0], false, lmp);
|
||||
force->special_extra = MAX(force->special_extra,extra_flag_value);
|
||||
|
||||
// local copy of box info
|
||||
// so can treat differently for first vs subsequent data files
|
||||
|
||||
} else if (utils::strmatch(line,"^\\s*\\f+\\s+\\f+\\s+xlo\\s+xhi\\s")) {
|
||||
rv = sscanf(line,"%lg %lg",&boxlo[0],&boxhi[0]);
|
||||
if (rv != 2)
|
||||
error->all(FLERR,"Could not parse 'xlo xhi' line in data file header");
|
||||
boxlo[0] = utils::numeric(FLERR, words[0], false, lmp);
|
||||
boxhi[0] = utils::numeric(FLERR, words[1], false, lmp);
|
||||
|
||||
} else if (utils::strmatch(line,"^\\s*\\f+\\s+\\f+\\s+ylo\\s+yhi\\s")) {
|
||||
rv = sscanf(line,"%lg %lg",&boxlo[1],&boxhi[1]);
|
||||
if (rv != 2)
|
||||
error->all(FLERR,"Could not parse 'ylo yhi' line in data file header");
|
||||
boxlo[1] = utils::numeric(FLERR, words[0], false, lmp);
|
||||
boxhi[1] = utils::numeric(FLERR, words[1], false, lmp);
|
||||
|
||||
} else if (utils::strmatch(line,"^\\s*\\f+\\s+\\f+\\s+zlo\\s+zhi\\s")) {
|
||||
rv = sscanf(line,"%lg %lg",&boxlo[2],&boxhi[2]);
|
||||
if (rv != 2)
|
||||
error->all(FLERR,"Could not parse 'zlo zhi' line in data file header");
|
||||
boxlo[2] = utils::numeric(FLERR, words[0], false, lmp);
|
||||
boxhi[2] = utils::numeric(FLERR, words[1], false, lmp);
|
||||
|
||||
} else if (utils::strmatch(line,"^\\s*\\f+\\s+\\f+\\s+\\f+"
|
||||
"\\s+xy\\s+xz\\s+yz\\s")) {
|
||||
} else if (utils::strmatch(line,"^\\s*\\f+\\s+\\f+\\s+\\f+\\s+xy\\s+xz\\s+yz\\s")) {
|
||||
triclinic = 1;
|
||||
rv = sscanf(line,"%lg %lg %lg",&xy,&xz,&yz);
|
||||
if (rv != 3)
|
||||
error->all(FLERR,"Could not parse 'xy xz yz' line in data file header");
|
||||
xy = utils::numeric(FLERR, words[0], false, lmp);
|
||||
xz = utils::numeric(FLERR, words[1], false, lmp);
|
||||
yz = utils::numeric(FLERR, words[2], false, lmp);
|
||||
|
||||
} else break;
|
||||
}
|
||||
@ -1188,9 +1157,7 @@ void ReadData::header(int firstpass)
|
||||
// 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)
|
||||
if (!is_data_section(keyword))
|
||||
error->all(FLERR,"Unknown identifier in data file: {}",keyword);
|
||||
|
||||
// error checks on header values
|
||||
@ -1244,6 +1211,22 @@ void ReadData::atoms()
|
||||
nread += nchunk;
|
||||
}
|
||||
|
||||
// warn if we have read data with non-zero image flags for non-periodic boundaries.
|
||||
// we may want to turn this into an error at some point, since this essentially
|
||||
// creates invalid position information that works by accident most of the time.
|
||||
|
||||
if (comm->me == 0) {
|
||||
if (atom->reset_image_flag[0])
|
||||
error->warning(FLERR,"Non-zero imageflag(s) in x direction for "
|
||||
"non-periodic boundary reset to zero");
|
||||
if (atom->reset_image_flag[1])
|
||||
error->warning(FLERR,"Non-zero imageflag(s) in y direction for "
|
||||
"non-periodic boundary reset to zero");
|
||||
if (atom->reset_image_flag[2])
|
||||
error->warning(FLERR,"Non-zero imageflag(s) in z direction for "
|
||||
"non-periodic boundary reset to zero");
|
||||
}
|
||||
|
||||
// check that all atoms were assigned correctly
|
||||
|
||||
bigint n = atom->nlocal;
|
||||
@ -1327,7 +1310,7 @@ void ReadData::bonds(int firstpass)
|
||||
int *count = nullptr;
|
||||
if (firstpass) {
|
||||
memory->create(count,nlocal,"read_data:count");
|
||||
memset(count,0,nlocal*sizeof(int));
|
||||
if (count) memset(count,0,nlocal*sizeof(int));
|
||||
}
|
||||
|
||||
// read and process bonds
|
||||
@ -1401,7 +1384,7 @@ void ReadData::angles(int firstpass)
|
||||
int *count = nullptr;
|
||||
if (firstpass) {
|
||||
memory->create(count,nlocal,"read_data:count");
|
||||
memset(count,0,nlocal*sizeof(int));
|
||||
if (count) memset(count,0,nlocal*sizeof(int));
|
||||
}
|
||||
|
||||
// read and process angles
|
||||
@ -1475,7 +1458,7 @@ void ReadData::dihedrals(int firstpass)
|
||||
int *count = nullptr;
|
||||
if (firstpass) {
|
||||
memory->create(count,nlocal,"read_data:count");
|
||||
memset(count,0,nlocal*sizeof(int));
|
||||
if (count) memset(count,0,nlocal*sizeof(int));
|
||||
}
|
||||
|
||||
// read and process dihedrals
|
||||
@ -1549,7 +1532,7 @@ void ReadData::impropers(int firstpass)
|
||||
int *count = nullptr;
|
||||
if (firstpass) {
|
||||
memory->create(count,nlocal,"read_data:count");
|
||||
memset(count,0,nlocal*sizeof(int));
|
||||
if (count) memset(count,0,nlocal*sizeof(int));
|
||||
}
|
||||
|
||||
// read and process impropers
|
||||
@ -1644,12 +1627,12 @@ void ReadData::bonus(bigint nbonus, AtomVec *ptr, const char *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 past data, but no processing of data
|
||||
if not firstpass, just read past body data and only process body header
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void ReadData::bodies(int firstpass, AtomVec *ptr)
|
||||
{
|
||||
int m,nchunk,nline,nmax,ninteger,ndouble,nword,ncount,onebody,tmp,rv;
|
||||
int m,nchunk,nline,nmax,ninteger,ndouble,nword,ncount,onebody;
|
||||
char *eof;
|
||||
|
||||
int mapflag = 0;
|
||||
@ -1663,11 +1646,11 @@ void ReadData::bodies(int firstpass, AtomVec *ptr)
|
||||
// nchunk = actual # read
|
||||
|
||||
bigint nread = 0;
|
||||
bigint natoms = nbodies;
|
||||
bigint nblocks = nbodies;
|
||||
|
||||
while (nread < natoms) {
|
||||
if (natoms-nread > CHUNK) nmax = CHUNK;
|
||||
else nmax = natoms-nread;
|
||||
while (nread < nblocks) {
|
||||
if (nblocks-nread > CHUNK) nmax = CHUNK;
|
||||
else nmax = nblocks-nread;
|
||||
|
||||
if (me == 0) {
|
||||
nchunk = 0;
|
||||
@ -1676,11 +1659,25 @@ void ReadData::bodies(int firstpass, AtomVec *ptr)
|
||||
|
||||
while (nchunk < nmax && nline <= CHUNK-MAXBODY) {
|
||||
eof = utils::fgets_trunc(&buffer[m],MAXLINE,fp);
|
||||
const char *buf = &buffer[m];
|
||||
if (eof == nullptr) error->one(FLERR,"Unexpected end of data file");
|
||||
rv = sscanf(&buffer[m],"%d %d %d",&tmp,&ninteger,&ndouble);
|
||||
if (rv != 3)
|
||||
error->one(FLERR,"Incorrect format in Bodies section of data file");
|
||||
m += strlen(&buffer[m]);
|
||||
try {
|
||||
auto values = ValueTokenizer(utils::trim_comment(buf));
|
||||
tagint tagdata = values.next_tagint() + id_offset;
|
||||
ninteger = values.next_int();
|
||||
ndouble = values.next_double();
|
||||
if (tagdata <= 0 || tagdata > atom->map_tag_max)
|
||||
throw TokenizerException("Invalid atom ID in body header", utils::trim(buf));
|
||||
if (ninteger < 0)
|
||||
throw TokenizerException("Invalid number of integers", utils::trim(buf));
|
||||
if (ndouble < 0)
|
||||
throw TokenizerException("Invalid number of doubles", utils::trim(buf));
|
||||
if (values.has_next())
|
||||
throw TokenizerException("Too many tokens in body header", utils::trim(buf));
|
||||
} catch (TokenizerException &e) {
|
||||
error->one(FLERR,std::string(e.what()) + " while reading Bodies section of data file");
|
||||
}
|
||||
m += strlen(buf);
|
||||
|
||||
// read lines one at a time into buffer and count words
|
||||
// count to ninteger and ndouble until have enough lines
|
||||
@ -1716,8 +1713,7 @@ void ReadData::bodies(int firstpass, AtomVec *ptr)
|
||||
error->one(FLERR,"Too many values in body lines in data file");
|
||||
|
||||
if (onebody+1 > MAXBODY)
|
||||
error->one(FLERR,
|
||||
"Too many lines in one body in data file - boost MAXBODY");
|
||||
error->one(FLERR,"Too many lines in one body in data file - boost MAXBODY");
|
||||
|
||||
nchunk++;
|
||||
nline += onebody+1;
|
||||
@ -1741,7 +1737,7 @@ void ReadData::bodies(int firstpass, AtomVec *ptr)
|
||||
}
|
||||
|
||||
if (me == 0 && firstpass)
|
||||
utils::logmesg(lmp," {} bodies\n",natoms);
|
||||
utils::logmesg(lmp," {} bodies\n",nblocks);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
@ -1749,7 +1745,7 @@ void ReadData::bodies(int firstpass, AtomVec *ptr)
|
||||
void ReadData::mass()
|
||||
{
|
||||
char *next;
|
||||
char *buf = new char[ntypes*MAXLINE];
|
||||
auto buf = new char[ntypes*MAXLINE];
|
||||
|
||||
int eof = utils::read_lines_from_file(fp,ntypes,MAXLINE,buf,me,world);
|
||||
if (eof) error->all(FLERR,"Unexpected end of data file");
|
||||
@ -1769,7 +1765,7 @@ void ReadData::mass()
|
||||
void ReadData::paircoeffs()
|
||||
{
|
||||
char *next;
|
||||
char *buf = new char[ntypes*MAXLINE];
|
||||
auto buf = new char[ntypes*MAXLINE];
|
||||
|
||||
int eof = utils::read_lines_from_file(fp,ntypes,MAXLINE,buf,me,world);
|
||||
if (eof) error->all(FLERR,"Unexpected end of data file");
|
||||
@ -1795,7 +1791,7 @@ void ReadData::pairIJcoeffs()
|
||||
char *next;
|
||||
|
||||
int nsq = ntypes * (ntypes+1) / 2;
|
||||
char *buf = new char[nsq * MAXLINE];
|
||||
auto buf = new char[nsq * MAXLINE];
|
||||
|
||||
int eof = utils::read_lines_from_file(fp,nsq,MAXLINE,buf,me,world);
|
||||
if (eof) error->all(FLERR,"Unexpected end of data file");
|
||||
@ -1821,7 +1817,7 @@ void ReadData::bondcoeffs()
|
||||
if (!nbondtypes) return;
|
||||
|
||||
char *next;
|
||||
char *buf = new char[nbondtypes*MAXLINE];
|
||||
auto buf = new char[nbondtypes*MAXLINE];
|
||||
|
||||
int eof = utils::read_lines_from_file(fp,nbondtypes,MAXLINE,buf,me,world);
|
||||
if (eof) error->all(FLERR,"Unexpected end of data file");
|
||||
@ -1846,7 +1842,7 @@ void ReadData::anglecoeffs(int which)
|
||||
if (!nangletypes) return;
|
||||
|
||||
char *next;
|
||||
char *buf = new char[nangletypes*MAXLINE];
|
||||
auto buf = new char[nangletypes*MAXLINE];
|
||||
|
||||
int eof = utils::read_lines_from_file(fp,nangletypes,MAXLINE,buf,me,world);
|
||||
if (eof) error->all(FLERR,"Unexpected end of data file");
|
||||
@ -1873,7 +1869,7 @@ void ReadData::dihedralcoeffs(int which)
|
||||
if (!ndihedraltypes) return;
|
||||
|
||||
char *next;
|
||||
char *buf = new char[ndihedraltypes*MAXLINE];
|
||||
auto buf = new char[ndihedraltypes*MAXLINE];
|
||||
|
||||
int eof = utils::read_lines_from_file(fp,ndihedraltypes,MAXLINE,buf,me,world);
|
||||
if (eof) error->all(FLERR,"Unexpected end of data file");
|
||||
@ -1903,7 +1899,7 @@ void ReadData::impropercoeffs(int which)
|
||||
if (!nimpropertypes) return;
|
||||
|
||||
char *next;
|
||||
char *buf = new char[nimpropertypes*MAXLINE];
|
||||
auto buf = new char[nimpropertypes*MAXLINE];
|
||||
|
||||
int eof = utils::read_lines_from_file(fp,nimpropertypes,MAXLINE,buf,me,world);
|
||||
if (eof) error->all(FLERR,"Unexpected end of data file");
|
||||
@ -1958,34 +1954,20 @@ int ReadData::reallocate(int **pcount, int cmax, int amax)
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 opens data file
|
||||
test if gzipped
|
||||
test if compressed
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void ReadData::open(char *file)
|
||||
void ReadData::open(const std::string &file)
|
||||
{
|
||||
if (utils::strmatch(file,"\\.gz$")) {
|
||||
if (platform::has_compress_extension(file)) {
|
||||
compressed = 1;
|
||||
|
||||
#ifdef LAMMPS_GZIP
|
||||
auto gunzip = fmt::format("gzip -c -d {}",file);
|
||||
|
||||
#ifdef _WIN32
|
||||
fp = _popen(gunzip.c_str(),"rb");
|
||||
#else
|
||||
fp = popen(gunzip.c_str(),"r");
|
||||
#endif
|
||||
|
||||
#else
|
||||
error->one(FLERR,"Cannot open gzipped file without gzip support");
|
||||
#endif
|
||||
fp = platform::compressed_read(file);
|
||||
if (!fp) error->one(FLERR,"Cannot open compressed file {}", file);
|
||||
} else {
|
||||
compressed = 0;
|
||||
fp = fopen(file,"r");
|
||||
fp = fopen(file.c_str(),"r");
|
||||
if (!fp) error->one(FLERR,"Cannot open file {}: {}", file, utils::getsyserror());
|
||||
}
|
||||
|
||||
if (fp == nullptr)
|
||||
error->one(FLERR,"Cannot open file {}: {}",
|
||||
file, utils::getsyserror());
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
|
||||
Reference in New Issue
Block a user