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new option *add keep* added to read_dump

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This commit is contained in:
Steven J. Plimpton
2018-03-27 10:08:58 -06:00
parent 24e48760da
commit e8b8428f6b
2 changed files with 51 additions and 29 deletions
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39
src/read_dump.cpp
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@ -50,6 +50,7 @@ using namespace LAMMPS_NS;
enum{ID,TYPE,X,Y,Z,VX,VY,VZ,Q,IX,IY,IZ,FX,FY,FZ};
enum{UNSET,NOSCALE_NOWRAP,NOSCALE_WRAP,SCALE_NOWRAP,SCALE_WRAP};
enum{NOADD,YESADD,KEEPADD};
/* ---------------------------------------------------------------------- */
@ -366,7 +367,7 @@ void ReadDump::header(int fieldinfo)
// triclinic_snap < 0 means no box info in file
if (triclinic_snap < 0 && boxflag > 0)
error->all(FLERR,"No box information in dump. You have to use 'box no'");
error->all(FLERR,"No box information in dump, must use 'box no'");
if (triclinic_snap >= 0) {
if ((triclinic_snap && !triclinic) ||
(!triclinic_snap && triclinic))
@ -479,9 +480,9 @@ void ReadDump::atoms()
nread += nchunk;
}
// if addflag set, add tags to new atoms if possible
// if addflag = YESADD, assign IDs to new snapshot atoms
if (addflag) {
if (addflag == YESADD) {
bigint nblocal = atom->nlocal;
MPI_Allreduce(&nblocal,&atom->natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);
if (atom->natoms < 0 || atom->natoms >= MAXBIGINT)
@ -623,7 +624,7 @@ int ReadDump::fields_and_keywords(int narg, char **arg)
replaceflag = 1;
purgeflag = 0;
trimflag = 0;
addflag = 0;
addflag = NOADD;
for (int i = 0; i < nfield; i++) fieldlabel[i] = NULL;
scaleflag = 0;
wrapflag = 1;
@ -655,8 +656,9 @@ int ReadDump::fields_and_keywords(int narg, char **arg)
iarg += 2;
} else if (strcmp(arg[iarg],"add") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal read_dump command");
if (strcmp(arg[iarg+1],"yes") == 0) addflag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) addflag = 0;
if (strcmp(arg[iarg+1],"yes") == 0) addflag = YESADD;
else if (strcmp(arg[iarg+1],"no") == 0) addflag = NOADD;
else if (strcmp(arg[iarg+1],"keep") == 0) addflag = KEEPADD;
else error->all(FLERR,"Illegal read_dump command");
iarg += 2;
} else if (strcmp(arg[iarg],"label") == 0) {
@ -695,6 +697,8 @@ int ReadDump::fields_and_keywords(int narg, char **arg)
if (purgeflag && (replaceflag || trimflag))
error->all(FLERR,"If read_dump purges it cannot replace or trim");
if (addflag == KEEPADD && atom->tag_enable == 0)
error->all(FLERR,"Read_dump cannot add keep with atom IDs disabled");
return narg-iarg;
}
@ -740,12 +744,13 @@ void ReadDump::process_atoms(int n)
{
int i,m,ifield,itype;
int xbox,ybox,zbox;
tagint tag;
tagint mtag;
double **x = atom->x;
double **v = atom->v;
double *q = atom->q;
double **f = atom->f;
tagint *tag = atom->tag;
imageint *image = atom->image;
int nlocal = atom->nlocal;
tagint map_tag_max = atom->map_tag_max;
@ -758,8 +763,8 @@ void ReadDump::process_atoms(int n)
// NOTE: atom ID in fields is stored as double, not as ubuf
// so can only cast it to tagint, thus cannot be full 64-bit ID
tag = static_cast<tagint> (fields[i][0]);
if (tag <= map_tag_max) m = atom->map(tag);
mtag = static_cast<tagint> (fields[i][0]);
if (mtag <= map_tag_max) m = atom->map(mtag);
else m = -1;
if (m < 0 || m >= nlocal) continue;
@ -835,8 +840,15 @@ void ReadDump::process_atoms(int n)
// create any atoms in chunk that no processor owned
// add atoms in round-robin sequence on processors
// cannot do it geometrically b/c dump coords may not be in simulation box
// check that dump file snapshot has atom type field
if (!addflag) return;
if (addflag == NOADD) return;
int tflag = 0;
for (ifield = 0; ifield < nfield; ifield++)
if (fieldtype[ifield] == TYPE) tflag = 1;
if (!tflag)
error->all(FLERR,"Cannot add atoms if dump file does not store atom type");
MPI_Allreduce(ucflag,ucflag_all,n,MPI_INT,MPI_SUM,world);
@ -881,6 +893,7 @@ void ReadDump::process_atoms(int n)
atom->avec->create_atom(itype,one);
nadd++;
tag = atom->tag;
v = atom->v;
q = atom->q;
image = atom->image;
@ -889,8 +902,12 @@ void ReadDump::process_atoms(int n)
xbox = ybox = zbox = 0;
for (ifield = 1; ifield < nfield; ifield++) {
for (ifield = 0; ifield < nfield; ifield++) {
switch (fieldtype[ifield]) {
case ID:
if (addflag == KEEPADD)
tag[m] = static_cast<tagint> (fields[i][ifield]);
break;
case VX:
v[m][0] = fields[i][ifield];
break;