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Merge pull request #1340 from akohlmey/bonus-data-checks

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Bonus data checks and updates. Part 1
This commit is contained in:
Axel Kohlmeyer
2019-02-27 15:10:58 -05:00
committed by GitHub
parent 05774ed894 0efc3765f8
commit eb39866e87
14 changed files with 143 additions and 11 deletions
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40
src/atom.cpp
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@ -58,6 +58,7 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
natoms = 0;
nlocal = nghost = nmax = 0;
ntypes = 0;
nellipsoids = nlines = ntris = nbodies = 0;
nbondtypes = nangletypes = ndihedraltypes = nimpropertypes = 0;
nbonds = nangles = ndihedrals = nimpropers = 0;
@ -738,6 +739,45 @@ int Atom::tag_consecutive()
return 1;
}
/* ----------------------------------------------------------------------
check that bonus data settings are valid
error if number of atoms with ellipsoid/line/tri/body flags
are consistent with global setting.
------------------------------------------------------------------------- */
void Atom::bonus_check()
{
bigint local_ellipsoids = 0, local_lines = 0, local_tris = 0;
bigint local_bodies = 0, num_global;
for (int i = 0; i < nlocal; ++i) {
if (ellipsoid && (ellipsoid[i] >=0)) ++local_ellipsoids;
if (line && (line[i] >=0)) ++local_lines;
if (tri && (tri[i] >=0)) ++local_tris;
if (body && (body[i] >=0)) ++local_bodies;
}
MPI_Allreduce(&local_ellipsoids,&num_global,1,MPI_LMP_BIGINT,MPI_MIN,world);
if (nellipsoids != num_global)
error->all(FLERR,"Inconsistent 'ellipsoids' header value and number of "
"atoms with enabled ellipsoid flags");
MPI_Allreduce(&local_lines,&num_global,1,MPI_LMP_BIGINT,MPI_MIN,world);
if (nlines != num_global)
error->all(FLERR,"Inconsistent 'lines' header value and number of "
"atoms with enabled line flags");
MPI_Allreduce(&local_tris,&num_global,1,MPI_LMP_BIGINT,MPI_MIN,world);
if (ntris != num_global)
error->all(FLERR,"Inconsistent 'tris' header value and number of "
"atoms with enabled tri flags");
MPI_Allreduce(&local_bodies,&num_global,1,MPI_LMP_BIGINT,MPI_MIN,world);
if (nbodies != num_global)
error->all(FLERR,"Inconsistent 'bodies' header value and number of "
"atoms with enabled body flags");
}
/* ----------------------------------------------------------------------
count and return words in a single line
make copy of line before using strtok so as not to change line

6
src/atom.h
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@ -34,6 +34,10 @@ class Atom : protected Pointers {
int tag_enable; // 0/1 if atom ID tags are defined
int molecular; // 0 = atomic, 1 = standard molecular system,
// 2 = molecule template system
bigint nellipsoids; // number of ellipsoids
bigint nlines; // number of lines
bigint ntris; // number of triangles
bigint nbodies; // number of bodies
bigint nbonds,nangles,ndihedrals,nimpropers;
int ntypes,nbondtypes,nangletypes,ndihedraltypes,nimpropertypes;
@ -233,6 +237,8 @@ class Atom : protected Pointers {
void tag_extend();
int tag_consecutive();
void bonus_check();
int parse_data(const char *);
int count_words(const char *);
int count_words(const char *, char *);

2
src/atom_vec_body.cpp
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@ -1286,7 +1286,7 @@ void AtomVecBody::data_atom(double *coord, imageint imagetmp, char **values)
body[nlocal] = atoi(values[2]);
if (body[nlocal] == 0) body[nlocal] = -1;
else if (body[nlocal] == 1) body[nlocal] = 0;
else error->one(FLERR,"Invalid atom type in Atoms section of data file");
else error->one(FLERR,"Invalid bodyflag in Atoms section of data file");
rmass[nlocal] = atof(values[3]);
if (rmass[nlocal] <= 0.0)

4
src/atom_vec_body.h
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@ -92,6 +92,8 @@ class AtomVecBody : public AtomVec {
double radius_body(int, int, int *, double *);
void set_quat(int, double *);
int nlocal_bonus;
private:
tagint *tag;
int *type,*mask;
@ -102,7 +104,7 @@ class AtomVecBody : public AtomVec {
double **angmom,**torque;
int *body;
int nlocal_bonus,nghost_bonus,nmax_bonus;
int nghost_bonus,nmax_bonus;
int intdoubleratio; // sizeof(double) / sizeof(int)
MyPoolChunk<int> *icp;

2
src/atom_vec_ellipsoid.cpp
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@ -1148,7 +1148,7 @@ void AtomVecEllipsoid::data_atom(double *coord, imageint imagetmp,
ellipsoid[nlocal] = atoi(values[2]);
if (ellipsoid[nlocal] == 0) ellipsoid[nlocal] = -1;
else if (ellipsoid[nlocal] == 1) ellipsoid[nlocal] = 0;
else error->one(FLERR,"Invalid atom type in Atoms section of data file");
else error->one(FLERR,"Invalid ellipsoidflag in Atoms section of data file");
rmass[nlocal] = atof(values[3]);
if (rmass[nlocal] <= 0.0)

4
src/atom_vec_ellipsoid.h
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@ -83,6 +83,8 @@ class AtomVecEllipsoid : public AtomVec {
void set_shape(int, double, double, double);
int nlocal_bonus;
private:
tagint *tag;
int *type,*mask;
@ -92,7 +94,7 @@ class AtomVecEllipsoid : public AtomVec {
double **angmom,**torque;
int *ellipsoid;
int nlocal_bonus,nghost_bonus,nmax_bonus;
int nghost_bonus,nmax_bonus;
void grow_bonus();
void copy_bonus(int, int);

2
src/atom_vec_line.cpp
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@ -1044,7 +1044,7 @@ void AtomVecLine::data_atom(double *coord, imageint imagetmp, char **values)
line[nlocal] = atoi(values[3]);
if (line[nlocal] == 0) line[nlocal] = -1;
else if (line[nlocal] == 1) line[nlocal] = 0;
else error->one(FLERR,"Invalid atom type in Atoms section of data file");
else error->one(FLERR,"Invalid lineflag in Atoms section of data file");
rmass[nlocal] = atof(values[4]);
if (rmass[nlocal] <= 0.0)

4
src/atom_vec_line.h
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@ -83,6 +83,8 @@ class AtomVecLine : public AtomVec {
void set_length(int, double);
int nlocal_bonus;
private:
tagint *tag;
int *type,*mask;
@ -93,7 +95,7 @@ class AtomVecLine : public AtomVec {
double **omega,**torque;
int *line;
int nlocal_bonus,nghost_bonus,nmax_bonus;
int nghost_bonus,nmax_bonus;
void grow_bonus();
void copy_bonus(int, int);

2
src/atom_vec_tri.cpp
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@ -1443,7 +1443,7 @@ void AtomVecTri::data_atom(double *coord, imageint imagetmp, char **values)
tri[nlocal] = atoi(values[3]);
if (tri[nlocal] == 0) tri[nlocal] = -1;
else if (tri[nlocal] == 1) tri[nlocal] = 0;
else error->one(FLERR,"Invalid atom type in Atoms section of data file");
else error->one(FLERR,"Invalid triflag in Atoms section of data file");
rmass[nlocal] = atof(values[4]);
if (rmass[nlocal] <= 0.0)

4
src/atom_vec_tri.h
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@ -85,6 +85,8 @@ class AtomVecTri : public AtomVec {
void set_equilateral(int, double);
int nlocal_bonus;
private:
tagint *tag;
int *type,*mask;
@ -95,7 +97,7 @@ class AtomVecTri : public AtomVec {
double **omega,**angmom,**torque;
int *tri;
int nlocal_bonus,nghost_bonus,nmax_bonus;
int nghost_bonus,nmax_bonus;
void grow_bonus();
void copy_bonus(int, int);

36
src/delete_atoms.cpp
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@ -16,6 +16,10 @@
#include "delete_atoms.h"
#include "atom.h"
#include "atom_vec.h"
#include "atom_vec_ellipsoid.h"
#include "atom_vec_line.h"
#include "atom_vec_tri.h"
#include "atom_vec_body.h"
#include "molecule.h"
#include "comm.h"
#include "domain.h"
@ -121,11 +125,39 @@ void DeleteAtoms::command(int narg, char **arg)
}
// reset atom->natoms and also topology counts
// reset atom->map if it exists
// set nghost to 0 so old ghosts of deleted atoms won't be mapped
bigint nblocal = atom->nlocal;
MPI_Allreduce(&nblocal,&atom->natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);
// reset bonus data counts
AtomVecEllipsoid *avec_ellipsoid =
(AtomVecEllipsoid *) atom->style_match("ellipsoid");
AtomVecLine *avec_line = (AtomVecLine *) atom->style_match("line");
AtomVecTri *avec_tri = (AtomVecTri *) atom->style_match("tri");
AtomVecBody *avec_body = (AtomVecBody *) atom->style_match("body");
bigint nlocal_bonus;
if (atom->nellipsoids > 0) {
nlocal_bonus = avec_ellipsoid->nlocal_bonus;
MPI_Allreduce(&nlocal_bonus,&atom->nellipsoids,1,MPI_LMP_BIGINT,MPI_SUM,world);
}
if (atom->nlines > 0) {
nlocal_bonus = avec_line->nlocal_bonus;
MPI_Allreduce(&nlocal_bonus,&atom->nlines,1,MPI_LMP_BIGINT,MPI_SUM,world);
}
if (atom->ntris > 0) {
nlocal_bonus = avec_tri->nlocal_bonus;
MPI_Allreduce(&nlocal_bonus,&atom->ntris,1,MPI_LMP_BIGINT,MPI_SUM,world);
}
if (atom->nbodies > 0) {
nlocal_bonus = avec_body->nlocal_bonus;
MPI_Allreduce(&nlocal_bonus,&atom->nbodies,1,MPI_LMP_BIGINT,MPI_SUM,world);
}
// reset atom->map if it exists
// set nghost to 0 so old ghosts of deleted atoms won't be mapped
if (atom->map_style) {
atom->nghost = 0;
atom->map_init();

22
src/read_data.cpp
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@ -396,7 +396,8 @@ void ReadData::command(int narg, char **arg)
// values in this data file
natoms = ntypes = 0;
natoms = 0;
ntypes = 0;
nbonds = nangles = ndihedrals = nimpropers = 0;
nbondtypes = nangletypes = ndihedraltypes = nimpropertypes = 0;
@ -993,18 +994,29 @@ void ReadData::header(int firstpass)
if (!avec_ellipsoid)
error->all(FLERR,"No ellipsoids allowed with this atom style");
sscanf(line,BIGINT_FORMAT,&nellipsoids);
if (addflag == NONE) atom->nellipsoids = nellipsoids;
else if (firstpass) atom->nellipsoids += nellipsoids;
} else if (strstr(line,"lines")) {
if (!avec_line)
error->all(FLERR,"No lines allowed with this atom style");
sscanf(line,BIGINT_FORMAT,&nlines);
if (addflag == NONE) atom->nlines = nlines;
else if (firstpass) atom->nlines += nlines;
} else if (strstr(line,"triangles")) {
if (!avec_tri)
error->all(FLERR,"No triangles allowed with this atom style");
sscanf(line,BIGINT_FORMAT,&ntris);
if (addflag == NONE) atom->ntris = ntris;
else if (firstpass) atom->ntris += ntris;
} else if (strstr(line,"bodies")) {
if (!avec_body)
error->all(FLERR,"No bodies allowed with this atom style");
sscanf(line,BIGINT_FORMAT,&nbodies);
if (addflag == NONE) atom->nbodies = nbodies;
else if (firstpass) atom->nbodies += nbodies;
} else if (strstr(line,"bonds")) {
sscanf(line,BIGINT_FORMAT,&nbonds);
@ -1084,6 +1096,10 @@ void ReadData::header(int firstpass)
// error check on total system size
if (atom->natoms < 0 || atom->natoms >= MAXBIGINT ||
atom->nellipsoids < 0 || atom->nellipsoids >= MAXBIGINT ||
atom->nlines < 0 || atom->nlines >= MAXBIGINT ||
atom->ntris < 0 || atom->ntris >= MAXBIGINT ||
atom->nbodies < 0 || atom->nbodies >= MAXBIGINT ||
atom->nbonds < 0 || atom->nbonds >= MAXBIGINT ||
atom->nangles < 0 || atom->nangles >= MAXBIGINT ||
atom->ndihedrals < 0 || atom->ndihedrals >= MAXBIGINT ||
@ -1174,6 +1190,10 @@ void ReadData::atoms()
atom->tag_check();
// check that bonus data has been reserved as needed
atom->bonus_check();
// create global mapping of atoms
if (atom->map_style) {

15
src/set.cpp
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@ -964,6 +964,21 @@ void Set::set(int keyword)
count++;
}
// update bonus data numbers
if (keyword == SHAPE) {
bigint nlocal_bonus = avec_ellipsoid->nlocal_bonus;
MPI_Allreduce(&nlocal_bonus,&atom->nellipsoids,1,
MPI_LMP_BIGINT,MPI_SUM,world);
}
if (keyword == LENGTH) {
bigint nlocal_bonus = avec_line->nlocal_bonus;
MPI_Allreduce(&nlocal_bonus,&atom->nlines,1,MPI_LMP_BIGINT,MPI_SUM,world);
}
if (keyword == TRI) {
bigint nlocal_bonus = avec_tri->nlocal_bonus;
MPI_Allreduce(&nlocal_bonus,&atom->ntris,1,MPI_LMP_BIGINT,MPI_SUM,world);
}
// clear up per-atom memory if allocated
memory->destroy(vec1);

11
src/write_data.cpp
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@ -177,6 +177,17 @@ void WriteData::write(char *file)
MPI_Allreduce(&nimpropers_local,&nimpropers,1,MPI_LMP_BIGINT,MPI_SUM,world);
}
// check for bonus data.
if (me == 0) {
if ((atom->nellipsoids > 0)
|| (atom->nlines > 0)
|| (atom->ntris > 0)
|| (atom->nbodies > 0))
error->warning(FLERR,"System has ellipsoids, lines, triangles, or bodies. "
"Those are not yet supported by write_data. The data file "
"will thus be incomplete.");
}
// open data file
if (me == 0) {