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modifications to correctly print modified dihedrals, impropers

This commit is contained in:
jrgissing 2018-01-22 23:56:11 -07:00
parent 5e9d257ec2
commit d2da49cdf9
4 changed files with 50 additions and 26 deletions
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56
src/atom_vec.cpp
View File

@ -274,7 +274,7 @@ void AtomVec::write_angle(FILE *fp, int n, tagint **buf, int index)
pack dihedral info for data file
------------------------------------------------------------------------- */
void AtomVec::pack_dihedral(tagint **buf)
int AtomVec::pack_dihedral(tagint **buf)
{
tagint *tag = atom->tag;
int *num_dihedral = atom->num_dihedral;
@ -291,25 +291,31 @@ void AtomVec::pack_dihedral(tagint **buf)
if (newton_bond) {
for (i = 0; i < nlocal; i++)
for (j = 0; j < num_dihedral[i]; j++) {
buf[m][0] = MAX(dihedral_type[i][j],-dihedral_type[i][j]);
buf[m][1] = dihedral_atom1[i][j];
buf[m][2] = dihedral_atom2[i][j];
buf[m][3] = dihedral_atom3[i][j];
buf[m][4] = dihedral_atom4[i][j];
if (buf) {
buf[m][0] = MAX(dihedral_type[i][j],-dihedral_type[i][j]);
buf[m][1] = dihedral_atom1[i][j];
buf[m][2] = dihedral_atom2[i][j];
buf[m][3] = dihedral_atom3[i][j];
buf[m][4] = dihedral_atom4[i][j];
}
m++;
}
} else {
for (i = 0; i < nlocal; i++)
for (j = 0; j < num_dihedral[i]; j++)
if (tag[i] == dihedral_atom2[i][j]) {
buf[m][0] = MAX(dihedral_type[i][j],-dihedral_type[i][j]);
buf[m][1] = dihedral_atom1[i][j];
buf[m][2] = dihedral_atom2[i][j];
buf[m][3] = dihedral_atom3[i][j];
buf[m][4] = dihedral_atom4[i][j];
if (buf) {
buf[m][0] = MAX(dihedral_type[i][j],-dihedral_type[i][j]);
buf[m][1] = dihedral_atom1[i][j];
buf[m][2] = dihedral_atom2[i][j];
buf[m][3] = dihedral_atom3[i][j];
buf[m][4] = dihedral_atom4[i][j];
}
m++;
}
}
return m;
}
/* ----------------------------------------------------------------------
@ -330,7 +336,7 @@ void AtomVec::write_dihedral(FILE *fp, int n, tagint **buf, int index)
pack improper info for data file
------------------------------------------------------------------------- */
void AtomVec::pack_improper(tagint **buf)
int AtomVec::pack_improper(tagint **buf)
{
tagint *tag = atom->tag;
int *num_improper = atom->num_improper;
@ -347,25 +353,31 @@ void AtomVec::pack_improper(tagint **buf)
if (newton_bond) {
for (i = 0; i < nlocal; i++)
for (j = 0; j < num_improper[i]; j++) {
buf[m][0] = MAX(improper_type[i][j],-improper_type[i][j]);
buf[m][1] = improper_atom1[i][j];
buf[m][2] = improper_atom2[i][j];
buf[m][3] = improper_atom3[i][j];
buf[m][4] = improper_atom4[i][j];
if (buf) {
buf[m][0] = MAX(improper_type[i][j],-improper_type[i][j]);
buf[m][1] = improper_atom1[i][j];
buf[m][2] = improper_atom2[i][j];
buf[m][3] = improper_atom3[i][j];
buf[m][4] = improper_atom4[i][j];
}
m++;
}
} else {
for (i = 0; i < nlocal; i++)
for (j = 0; j < num_improper[i]; j++)
if (tag[i] == improper_atom2[i][j]) {
buf[m][0] = MAX(improper_type[i][j],-improper_type[i][j]);
buf[m][1] = improper_atom1[i][j];
buf[m][2] = improper_atom2[i][j];
buf[m][3] = improper_atom3[i][j];
buf[m][4] = improper_atom4[i][j];
if (buf) {
buf[m][0] = MAX(improper_type[i][j],-improper_type[i][j]);
buf[m][1] = improper_atom1[i][j];
buf[m][2] = improper_atom2[i][j];
buf[m][3] = improper_atom3[i][j];
buf[m][4] = improper_atom4[i][j];
}
m++;
}
}
return m;
}
/* ----------------------------------------------------------------------

4
src/atom_vec.h
View File

@ -107,9 +107,9 @@ class AtomVec : protected Pointers {
void write_bond(FILE *, int, tagint **, int);
int pack_angle(tagint **);
void write_angle(FILE *, int, tagint **, int);
void pack_dihedral(tagint **);
int pack_dihedral(tagint **);
void write_dihedral(FILE *, int, tagint **, int);
void pack_improper(tagint **);
int pack_improper(tagint **);
void write_improper(FILE *, int, tagint **, int);
virtual int property_atom(char *) {return -1;}

14
src/write_data.cpp
View File

@ -152,8 +152,8 @@ void WriteData::write(char *file)
if (natoms != atom->natoms && output->thermo->lostflag == ERROR)
error->all(FLERR,"Atom count is inconsistent, cannot write data file");
// sum up bond,angle counts
// may be different than atom->nbonds,nangles if broken/turned-off
// sum up bond,angle,dihedral,improper counts
// may be different than atom->nbonds,nangles, etc. if broken/turned-off
if (atom->molecular == 1 && (atom->nbonds || atom->nbondtypes)) {
nbonds_local = atom->avec->pack_bond(NULL);
@ -164,6 +164,16 @@ void WriteData::write(char *file)
MPI_Allreduce(&nangles_local,&nangles,1,MPI_LMP_BIGINT,MPI_SUM,world);
}
if (atom->molecular == 1 && (atom->ndihedrals || atom->ndihedraltypes)) {
ndihedrals_local = atom->avec->pack_dihedral(NULL);
MPI_Allreduce(&ndihedrals_local,&ndihedrals,1,MPI_LMP_BIGINT,MPI_SUM,world);
}
if (atom->molecular == 1 && (atom->nimpropers || atom->nimpropertypes)) {
nimpropers_local = atom->avec->pack_improper(NULL);
MPI_Allreduce(&nimpropers_local,&nimpropers,1,MPI_LMP_BIGINT,MPI_SUM,world);
}
// open data file
if (me == 0) {

2
src/write_data.h
View File

@ -38,6 +38,8 @@ class WriteData : protected Pointers {
FILE *fp;
bigint nbonds_local,nbonds;
bigint nangles_local,nangles;
bigint ndihedrals_local,ndihedrals;
bigint nimpropers_local,nimpropers;
void header();
void type_arrays();