ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Merge remote-tracking branch 'origin/master' into refactor-table-reading

Browse Source
This commit is contained in:
Richard Berger
2020-06-05 16:41:05 -04:00
parent 2203e1e9e5 12386945d5
commit 4f804f58e3
55 changed files with 587 additions and 867 deletions
Download Patch File Download Diff File Expand all files Collapse all files

168
src/read_data.cpp
View File

@ -814,36 +814,18 @@ void ReadData::command(int narg, char **arg)
}
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);
}
std::string mesg;
if (atom->nbonds)
mesg += fmt::format(" {} template bonds\n",atom->nbonds);
if (atom->nangles)
mesg += fmt::format(" {} template angles\n",atom->nangles);
if (atom->ndihedrals)
mesg += fmt::format(" {} template dihedrals\n",atom->ndihedrals);
if (atom->nimpropers)
mesg += fmt::format(" {} template impropers\n",atom->nimpropers);
utils::logmesg(lmp,mesg);
}
}
@ -913,14 +895,10 @@ void ReadData::command(int narg, char **arg)
// total time
MPI_Barrier(world);
double time2 = MPI_Wtime();
if (comm->me == 0) {
if (screen)
fprintf(screen," read_data CPU = %g secs\n",time2-time1);
if (logfile)
fprintf(logfile," read_data CPU = %g secs\n",time2-time1);
}
if (comm->me == 0)
utils::logmesg(lmp,fmt::format(" read_data CPU = {:.3f} secs\n",
MPI_Wtime()-time1));
}
/* ----------------------------------------------------------------------
@ -1224,10 +1202,7 @@ void ReadData::atoms()
{
int nchunk,eof;
if (me == 0) {
if (screen) fprintf(screen," reading atoms ...\n");
if (logfile) fprintf(logfile," reading atoms ...\n");
}
if (me == 0) utils::logmesg(lmp," reading atoms ...\n");
bigint nread = 0;
@ -1246,10 +1221,7 @@ void ReadData::atoms()
MPI_Allreduce(&n,&sum,1,MPI_LMP_BIGINT,MPI_SUM,world);
bigint nassign = sum - (atom->natoms - natoms);
if (me == 0) {
if (screen) fprintf(screen," " BIGINT_FORMAT " atoms\n",nassign);
if (logfile) fprintf(logfile," " BIGINT_FORMAT " atoms\n",nassign);
}
if (me == 0) utils::logmesg(lmp,fmt::format(" {} atoms\n",nassign));
if (sum != atom->natoms)
error->all(FLERR,"Did not assign all atoms correctly");
@ -1279,10 +1251,7 @@ void ReadData::velocities()
{
int nchunk,eof;
if (me == 0) {
if (screen) fprintf(screen," reading velocities ...\n");
if (logfile) fprintf(logfile," reading velocities ...\n");
}
if (me == 0) utils::logmesg(lmp," reading velocities ...\n");
int mapflag = 0;
if (atom->map_style == 0) {
@ -1306,10 +1275,7 @@ void ReadData::velocities()
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);
}
if (me == 0) utils::logmesg(lmp,fmt::format(" {} velocities\n",natoms));
}
/* ----------------------------------------------------------------------
@ -1321,13 +1287,8 @@ void ReadData::bonds(int firstpass)
int nchunk,eof;
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");
}
if (firstpass) utils::logmesg(lmp," scanning bonds ...\n");
else utils::logmesg(lmp," reading bonds ...\n");
}
// allocate count if firstpass
@ -1362,10 +1323,8 @@ void ReadData::bonds(int firstpass)
MPI_Allreduce(&max,&maxall,1,MPI_INT,MPI_MAX,world);
if (addflag == NONE) 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);
}
if (me == 0)
utils::logmesg(lmp,fmt::format(" {} = max bonds/atom\n",maxall));
if (addflag != NONE) {
if (maxall > atom->bond_per_atom)
@ -1386,10 +1345,8 @@ void ReadData::bonds(int firstpass)
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 (me == 0)
utils::logmesg(lmp,fmt::format(" {} bonds\n",sum/factor));
if (sum != factor*nbonds)
error->all(FLERR,"Bonds assigned incorrectly");
@ -1404,13 +1361,8 @@ void ReadData::angles(int firstpass)
int nchunk,eof;
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");
}
if (firstpass) utils::logmesg(lmp," scanning angles ...\n");
else utils::logmesg(lmp," reading angles ...\n");
}
// allocate count if firstpass
@ -1445,10 +1397,8 @@ void ReadData::angles(int firstpass)
MPI_Allreduce(&max,&maxall,1,MPI_INT,MPI_MAX,world);
if (addflag == NONE) 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);
}
if (me == 0)
utils::logmesg(lmp,fmt::format(" {} = max angles/atom\n",maxall));
if (addflag != NONE) {
if (maxall > atom->angle_per_atom)
@ -1469,10 +1419,8 @@ void ReadData::angles(int firstpass)
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 (me == 0)
utils::logmesg(lmp,fmt::format(" {} angles\n",sum/factor));
if (sum != factor*nangles)
error->all(FLERR,"Angles assigned incorrectly");
@ -1487,13 +1435,8 @@ void ReadData::dihedrals(int firstpass)
int nchunk,eof;
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");
}
if (firstpass) utils::logmesg(lmp," scanning dihedrals ...\n");
else utils::logmesg(lmp," reading dihedrals ...\n");
}
// allocate count if firstpass
@ -1528,10 +1471,8 @@ void ReadData::dihedrals(int firstpass)
MPI_Allreduce(&max,&maxall,1,MPI_INT,MPI_MAX,world);
if (addflag == NONE) 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);
}
if (me == 0)
utils::logmesg(lmp,fmt::format(" {} = max dihedrals/atom\n",maxall));
if (addflag != NONE) {
if (maxall > atom->dihedral_per_atom)
@ -1552,10 +1493,8 @@ void ReadData::dihedrals(int firstpass)
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 (me == 0)
utils::logmesg(lmp,fmt::format(" {} dihedrals\n",sum/factor));
if (sum != factor*ndihedrals)
error->all(FLERR,"Dihedrals assigned incorrectly");
@ -1570,13 +1509,8 @@ void ReadData::impropers(int firstpass)
int nchunk,eof;
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");
}
if (firstpass) utils::logmesg(lmp," scanning impropers ...\n");
else utils::logmesg(lmp," reading impropers ...\n");
}
// allocate count if firstpass
@ -1611,10 +1545,8 @@ void ReadData::impropers(int firstpass)
MPI_Allreduce(&max,&maxall,1,MPI_INT,MPI_MAX,world);
if (addflag == NONE) 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);
}
if (me == 0)
utils::logmesg(lmp,fmt::format(" {} = max impropers/atom\n",maxall));
if (addflag != NONE) {
if (maxall > atom->improper_per_atom)
@ -1635,10 +1567,8 @@ void ReadData::impropers(int firstpass)
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 (me == 0)
utils::logmesg(lmp,fmt::format(" {} impropers\n",sum/factor));
if (sum != factor*nimpropers)
error->all(FLERR,"Impropers assigned incorrectly");
@ -1676,10 +1606,8 @@ void ReadData::bonus(bigint nbonus, AtomVec *ptr, const char *type)
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);
}
if (me == 0)
utils::logmesg(lmp,fmt::format(" {} {}\n",natoms,type));
}
/* ----------------------------------------------------------------------
@ -1782,10 +1710,8 @@ void ReadData::bodies(int firstpass, AtomVec *ptr)
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);
}
if (me == 0 && firstpass)
utils::logmesg(lmp,fmt::format(" {} bodies\n",natoms));
}
/* ---------------------------------------------------------------------- */