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Merge pull request #887 from akohlmey/create-bonds-single-bugfix

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Fix bug in create_bonds single/bond
This commit is contained in:
Steve Plimpton
2018-05-07 10:37:00 -06:00
committed by GitHub
parent 1ea5b9eabb 366aaf2450
commit bc0c405bfa
1 changed files with 33 additions and 18 deletions
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51
src/create_bonds.cpp
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@ -323,9 +323,13 @@ void CreateBonds::single_bond()
// check that 2 atoms exist
const int nlocal = atom->nlocal;
const int idx1 = atom->map(batom1);
const int idx2 = atom->map(batom2);
int count = 0;
if (atom->map(batom1) >= 0) count++;
if (atom->map(batom2) >= 0) count++;
if ((idx1 >= 0) && (idx1 < nlocal)) count++;
if ((idx2 >= 0) && (idx2 < nlocal)) count++;
int allcount;
MPI_Allreduce(&count,&allcount,1,MPI_INT,MPI_SUM,world);
@ -338,7 +342,7 @@ void CreateBonds::single_bond()
int **bond_type = atom->bond_type;
tagint **bond_atom = atom->bond_atom;
if ((m = atom->map(batom1)) >= 0) {
if ((m = idx1) >= 0) {
if (num_bond[m] == atom->bond_per_atom)
error->one(FLERR,"New bond exceeded bonds per atom in create_bonds");
bond_type[m][num_bond[m]] = btype;
@ -349,7 +353,7 @@ void CreateBonds::single_bond()
if (force->newton_bond) return;
if ((m = atom->map(batom2)) >= 0) {
if ((m = idx2) >= 0) {
if (num_bond[m] == atom->bond_per_atom)
error->one(FLERR,"New bond exceeded bonds per atom in create_bonds");
bond_type[m][num_bond[m]] = btype;
@ -366,10 +370,15 @@ void CreateBonds::single_angle()
// check that 3 atoms exist
const int nlocal = atom->nlocal;
const int idx1 = atom->map(aatom1);
const int idx2 = atom->map(aatom2);
const int idx3 = atom->map(aatom3);
int count = 0;
if (atom->map(aatom1) >= 0) count++;
if (atom->map(aatom2) >= 0) count++;
if (atom->map(aatom3) >= 0) count++;
if ((idx1 >= 0) && (idx1 < nlocal)) count++;
if ((idx2 >= 0) && (idx2 < nlocal)) count++;
if ((idx3 >= 0) && (idx3 < nlocal)) count++;
int allcount;
MPI_Allreduce(&count,&allcount,1,MPI_INT,MPI_SUM,world);
@ -384,7 +393,7 @@ void CreateBonds::single_angle()
tagint **angle_atom2 = atom->angle_atom2;
tagint **angle_atom3 = atom->angle_atom3;
if ((m = atom->map(aatom2)) >= 0) {
if ((m = idx2) >= 0) {
if (num_angle[m] == atom->angle_per_atom)
error->one(FLERR,"New angle exceeded angles per atom in create_bonds");
angle_type[m][num_angle[m]] = atype;
@ -397,7 +406,7 @@ void CreateBonds::single_angle()
if (force->newton_bond) return;
if ((m = atom->map(aatom1)) >= 0) {
if ((m = idx1) >= 0) {
if (num_angle[m] == atom->angle_per_atom)
error->one(FLERR,"New angle exceeded angles per atom in create_bonds");
angle_type[m][num_angle[m]] = atype;
@ -407,7 +416,7 @@ void CreateBonds::single_angle()
num_angle[m]++;
}
if ((m = atom->map(aatom3)) >= 0) {
if ((m = idx3) >= 0) {
if (num_angle[m] == atom->angle_per_atom)
error->one(FLERR,"New angle exceeded angles per atom in create_bonds");
angle_type[m][num_angle[m]] = atype;
@ -426,11 +435,17 @@ void CreateBonds::single_dihedral()
// check that 4 atoms exist
const int nlocal = atom->nlocal;
const int idx1 = atom->map(datom1);
const int idx2 = atom->map(datom2);
const int idx3 = atom->map(datom3);
const int idx4 = atom->map(datom4);
int count = 0;
if (atom->map(datom1) >= 0) count++;
if (atom->map(datom2) >= 0) count++;
if (atom->map(datom3) >= 0) count++;
if (atom->map(datom4) >= 0) count++;
if ((idx1 >= 0) && (idx1 < nlocal)) count++;
if ((idx2 >= 0) && (idx2 < nlocal)) count++;
if ((idx3 >= 0) && (idx3 < nlocal)) count++;
if ((idx4 >= 0) && (idx4 < nlocal)) count++;
int allcount;
MPI_Allreduce(&count,&allcount,1,MPI_INT,MPI_SUM,world);
@ -446,7 +461,7 @@ void CreateBonds::single_dihedral()
tagint **dihedral_atom3 = atom->dihedral_atom3;
tagint **dihedral_atom4 = atom->dihedral_atom4;
if ((m = atom->map(datom2)) >= 0) {
if ((m = idx2) >= 0) {
if (num_dihedral[m] == atom->dihedral_per_atom)
error->one(FLERR,
"New dihedral exceeded dihedrals per atom in create_bonds");
@ -461,7 +476,7 @@ void CreateBonds::single_dihedral()
if (force->newton_bond) return;
if ((m = atom->map(datom1)) >= 0) {
if ((m = idx1) >= 0) {
if (num_dihedral[m] == atom->dihedral_per_atom)
error->one(FLERR,
"New dihedral exceeded dihedrals per atom in create_bonds");
@ -473,7 +488,7 @@ void CreateBonds::single_dihedral()
num_dihedral[m]++;
}
if ((m = atom->map(datom3)) >= 0) {
if ((m = idx3) >= 0) {
if (num_dihedral[m] == atom->dihedral_per_atom)
error->one(FLERR,
"New dihedral exceeded dihedrals per atom in create_bonds");
@ -485,7 +500,7 @@ void CreateBonds::single_dihedral()
num_dihedral[m]++;
}
if ((m = atom->map(datom4)) >= 0) {
if ((m = idx4) >= 0) {
if (num_dihedral[m] == atom->dihedral_per_atom)
error->one(FLERR,
"New dihedral exceeded dihedrals per atom in create_bonds");