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Merge branch 'master' of https://github.com/lammps/lammps into lammps-master

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This commit is contained in:
Jacob Gissinger
2021-06-07 22:48:51 -04:00
parent 26fe17a379 d74d7cfd5f
commit b124de3484
4175 changed files with 127478 additions and 48418 deletions
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81
src/read_data.cpp
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@ -1,6 +1,7 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://lammps.sandia.gov/, Sandia National Laboratories
https://www.lammps.org/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
@ -42,24 +43,25 @@
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 32 // max # of lines in one body
static constexpr int MAXLINE = 256;
static constexpr double LB_FACTOR = 1.1;
static constexpr int CHUNK = 1024;
static constexpr int DELTA = 4; // must be 2 or larger
static constexpr int MAXBODY = 32; // max # of lines in one body
// customize for new sections
#define NSECTIONS 30 // change when add to header::section_keywords
// customize for new sections
// change when add to header::section_keywords
static constexpr int NSECTIONS = 30;
enum{NONE,APPEND,VALUE,MERGE};
// 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",
nullptr};
static const char *suffixes[] = {"/cuda","/gpu","/opt","/omp","/kk",
"/coul/cut","/coul/long","/coul/msm",
"/coul/dsf","/coul/debye","/coul/charmm",
nullptr};
/* ---------------------------------------------------------------------- */
@ -788,8 +790,8 @@ void ReadData::command(int narg, char **arg)
} else skip_lines(nimpropertypes);
}
} else error->all(FLERR,fmt::format("Unknown identifier in data file: {}",
keyword));
} else error->all(FLERR,"Unknown identifier in data file: {}",
keyword);
parse_keyword(0);
}
@ -975,8 +977,7 @@ void ReadData::command(int narg, char **arg)
MPI_Barrier(world);
if (comm->me == 0)
utils::logmesg(lmp,fmt::format(" read_data CPU = {:.3f} seconds\n",
MPI_Wtime()-time1));
utils::logmesg(lmp," read_data CPU = {:.3f} seconds\n",MPI_Wtime()-time1);
}
/* ----------------------------------------------------------------------
@ -1021,7 +1022,7 @@ void ReadData::header(int firstpass)
// skip 1st line of file
if (me == 0) {
char *eof = fgets(line,MAXLINE,fp);
char *eof = utils::fgets_trunc(line,MAXLINE,fp);
if (eof == nullptr) error->one(FLERR,"Unexpected end of data file");
}
@ -1030,7 +1031,7 @@ void ReadData::header(int firstpass)
// read a line and bcast length
if (me == 0) {
if (fgets(line,MAXLINE,fp) == nullptr) n = 0;
if (utils::fgets_trunc(line,MAXLINE,fp) == nullptr) n = 0;
else n = strlen(line) + 1;
}
MPI_Bcast(&n,1,MPI_INT,0,world);
@ -1249,7 +1250,7 @@ void ReadData::header(int firstpass)
for (n = 0; n < NSECTIONS; n++)
if (strcmp(keyword,section_keywords[n]) == 0) break;
if (n == NSECTIONS)
error->all(FLERR,fmt::format("Unknown identifier in data file: {}",keyword));
error->all(FLERR,"Unknown identifier in data file: {}",keyword);
// error checks on header values
// must be consistent with atom style and other header values
@ -1313,7 +1314,7 @@ void ReadData::atoms()
MPI_Allreduce(&n,&sum,1,MPI_LMP_BIGINT,MPI_SUM,world);
bigint nassign = sum - (atom->natoms - natoms);
if (me == 0) utils::logmesg(lmp,fmt::format(" {} atoms\n",nassign));
if (me == 0) utils::logmesg(lmp," {} atoms\n",nassign);
if (sum != atom->natoms)
error->all(FLERR,"Did not assign all atoms correctly");
@ -1367,7 +1368,7 @@ void ReadData::velocities()
atom->map_style = Atom::MAP_NONE;
}
if (me == 0) utils::logmesg(lmp,fmt::format(" {} velocities\n",natoms));
if (me == 0) utils::logmesg(lmp," {} velocities\n",natoms);
}
/* ----------------------------------------------------------------------
@ -1420,7 +1421,7 @@ void ReadData::bonds(int firstpass)
if (addflag == NONE) maxall += atom->extra_bond_per_atom;
if (me == 0)
utils::logmesg(lmp,fmt::format(" {} = max bonds/atom\n",maxall));
utils::logmesg(lmp," {} = max bonds/atom\n",maxall);
if (addflag != NONE) {
if (maxall > atom->bond_per_atom)
@ -1442,7 +1443,7 @@ void ReadData::bonds(int firstpass)
if (!force->newton_bond) factor = 2;
if (me == 0)
utils::logmesg(lmp,fmt::format(" {} bonds\n",sum/factor));
utils::logmesg(lmp," {} bonds\n",sum/factor);
if (sum != factor*nbonds)
error->all(FLERR,"Bonds assigned incorrectly");
@ -1498,7 +1499,7 @@ void ReadData::angles(int firstpass)
if (addflag == NONE) maxall += atom->extra_angle_per_atom;
if (me == 0)
utils::logmesg(lmp,fmt::format(" {} = max angles/atom\n",maxall));
utils::logmesg(lmp," {} = max angles/atom\n",maxall);
if (addflag != NONE) {
if (maxall > atom->angle_per_atom)
@ -1520,7 +1521,7 @@ void ReadData::angles(int firstpass)
if (!force->newton_bond) factor = 3;
if (me == 0)
utils::logmesg(lmp,fmt::format(" {} angles\n",sum/factor));
utils::logmesg(lmp," {} angles\n",sum/factor);
if (sum != factor*nangles)
error->all(FLERR,"Angles assigned incorrectly");
@ -1576,7 +1577,7 @@ void ReadData::dihedrals(int firstpass)
if (addflag == NONE) maxall += atom->extra_dihedral_per_atom;
if (me == 0)
utils::logmesg(lmp,fmt::format(" {} = max dihedrals/atom\n",maxall));
utils::logmesg(lmp," {} = max dihedrals/atom\n",maxall);
if (addflag != NONE) {
if (maxall > atom->dihedral_per_atom)
@ -1598,7 +1599,7 @@ void ReadData::dihedrals(int firstpass)
if (!force->newton_bond) factor = 4;
if (me == 0)
utils::logmesg(lmp,fmt::format(" {} dihedrals\n",sum/factor));
utils::logmesg(lmp," {} dihedrals\n",sum/factor);
if (sum != factor*ndihedrals)
error->all(FLERR,"Dihedrals assigned incorrectly");
@ -1654,7 +1655,7 @@ void ReadData::impropers(int firstpass)
if (addflag == NONE) maxall += atom->extra_improper_per_atom;
if (me == 0)
utils::logmesg(lmp,fmt::format(" {} = max impropers/atom\n",maxall));
utils::logmesg(lmp," {} = max impropers/atom\n",maxall);
if (addflag != NONE) {
if (maxall > atom->improper_per_atom)
@ -1676,7 +1677,7 @@ void ReadData::impropers(int firstpass)
if (!force->newton_bond) factor = 4;
if (me == 0)
utils::logmesg(lmp,fmt::format(" {} impropers\n",sum/factor));
utils::logmesg(lmp," {} impropers\n",sum/factor);
if (sum != factor*nimpropers)
error->all(FLERR,"Impropers assigned incorrectly");
@ -1715,7 +1716,7 @@ void ReadData::bonus(bigint nbonus, AtomVec *ptr, const char *type)
}
if (me == 0)
utils::logmesg(lmp,fmt::format(" {} {}\n",natoms,type));
utils::logmesg(lmp," {} {}\n",natoms,type);
}
/* ----------------------------------------------------------------------
@ -1753,7 +1754,7 @@ void ReadData::bodies(int firstpass, AtomVec *ptr)
m = 0;
while (nchunk < nmax && nline <= CHUNK-MAXBODY) {
eof = fgets(&buffer[m],MAXLINE,fp);
eof = utils::fgets_trunc(&buffer[m],MAXLINE,fp);
if (eof == nullptr) error->one(FLERR,"Unexpected end of data file");
rv = sscanf(&buffer[m],"%d %d %d",&tmp,&ninteger,&ndouble);
if (rv != 3)
@ -1767,7 +1768,7 @@ void ReadData::bodies(int firstpass, AtomVec *ptr)
nword = 0;
while (nword < ninteger) {
eof = fgets(&buffer[m],MAXLINE,fp);
eof = utils::fgets_trunc(&buffer[m],MAXLINE,fp);
if (eof == nullptr) error->one(FLERR,"Unexpected end of data file");
ncount = utils::trim_and_count_words(&buffer[m]);
if (ncount == 0)
@ -1781,7 +1782,7 @@ void ReadData::bodies(int firstpass, AtomVec *ptr)
nword = 0;
while (nword < ndouble) {
eof = fgets(&buffer[m],MAXLINE,fp);
eof = utils::fgets_trunc(&buffer[m],MAXLINE,fp);
if (eof == nullptr) error->one(FLERR,"Unexpected end of data file");
ncount = utils::trim_and_count_words(&buffer[m]);
if (ncount == 0)
@ -1819,7 +1820,7 @@ void ReadData::bodies(int firstpass, AtomVec *ptr)
}
if (me == 0 && firstpass)
utils::logmesg(lmp,fmt::format(" {} bodies\n",natoms));
utils::logmesg(lmp," {} bodies\n",natoms);
}
/* ---------------------------------------------------------------------- */
@ -2135,8 +2136,8 @@ void ReadData::open(char *file)
}
if (fp == nullptr)
error->one(FLERR,fmt::format("Cannot open file {}: {}",
file, utils::getsyserror()));
error->one(FLERR,"Cannot open file {}: {}",
file, utils::getsyserror());
}
/* ----------------------------------------------------------------------
@ -2159,15 +2160,15 @@ void ReadData::parse_keyword(int first)
if (me == 0) {
if (!first) {
if (fgets(line,MAXLINE,fp) == nullptr) eof = 1;
if (utils::fgets_trunc(line,MAXLINE,fp) == nullptr) eof = 1;
}
while (eof == 0 && done == 0) {
int blank = strspn(line," \t\n\r");
if ((blank == (int)strlen(line)) || (line[blank] == '#')) {
if (fgets(line,MAXLINE,fp) == nullptr) eof = 1;
if (utils::fgets_trunc(line,MAXLINE,fp) == nullptr) eof = 1;
} else done = 1;
}
if (fgets(buffer,MAXLINE,fp) == nullptr) {
if (utils::fgets_trunc(buffer,MAXLINE,fp) == nullptr) {
eof = 1;
buffer[0] = '\0';
}
@ -2221,7 +2222,7 @@ void ReadData::skip_lines(bigint n)
if (me) return;
if (n <= 0) return;
char *eof = nullptr;
for (bigint i = 0; i < n; i++) eof = fgets(line,MAXLINE,fp);
for (bigint i = 0; i < n; i++) eof = utils::fgets_trunc(line,MAXLINE,fp);
if (eof == nullptr) error->one(FLERR,"Unexpected end of data file");
}