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

simplify things

Browse Source
This commit is contained in:
jrgissing
2022-02-13 15:22:13 -05:00
parent 793cfe05f9
commit 200ea62fd3
2 changed files with 23 additions and 25 deletions
Download Patch File Download Diff File Expand all files Collapse all files

44
src/replicate.cpp
View File

@ -240,7 +240,6 @@ void Replicate::command(int narg, char **arg)
double old_xprd = domain->xprd; double old_xprd = domain->xprd;
double old_yprd = domain->yprd; double old_yprd = domain->yprd;
double old_zprd = domain->zprd; double old_zprd = domain->zprd;
double old_center[3];
for (i = 0; i < 3; i++) { for (i = 0; i < 3; i++) {
old_prd_half[i] = domain->prd_half[i]; old_prd_half[i] = domain->prd_half[i];
old_center[i] = 0.5*(domain->boxlo[i]+domain->boxhi[i]); old_center[i] = 0.5*(domain->boxlo[i]+domain->boxhi[i]);
@ -598,10 +597,6 @@ void Replicate::command(int narg, char **arg)
m = 0; m = 0;
while (m < size_buf_all) { while (m < size_buf_all) {
for (j = 0; j < 3; j++) {
if (buf_all[m+j+1] > old_center[j]) shiftsign[j] = 1;
else shiftsign[j] = -1;
}
image = ((imageint) IMGMAX << IMG2BITS) | image = ((imageint) IMGMAX << IMG2BITS) |
((imageint) IMGMAX << IMGBITS) | IMGMAX; ((imageint) IMGMAX << IMGBITS) | IMGMAX;
if (triclinic == 0) { if (triclinic == 0) {
@ -646,15 +641,15 @@ void Replicate::command(int narg, char **arg)
if (atom->avec->bonds_allow) if (atom->avec->bonds_allow)
for (j = 0; j < atom->num_bond[i]; j++) { for (j = 0; j < atom->num_bond[i]; j++) {
if (bondlist_flag) if (bondlist_flag)
newtag(atom0tag,atom->bond_atom[i][j],shiftsign); newtag(atom0tag,atom->bond_atom[i][j]);
else atom->bond_atom[i][j] += atom_offset; else atom->bond_atom[i][j] += atom_offset;
} }
if (atom->avec->angles_allow) if (atom->avec->angles_allow)
for (j = 0; j < atom->num_angle[i]; j++) { for (j = 0; j < atom->num_angle[i]; j++) {
if (bondlist_flag) { if (bondlist_flag) {
newtag(atom0tag,atom->angle_atom1[i][j],shiftsign); newtag(atom0tag,atom->angle_atom1[i][j]);
newtag(atom0tag,atom->angle_atom2[i][j],shiftsign); newtag(atom0tag,atom->angle_atom2[i][j]);
newtag(atom0tag,atom->angle_atom3[i][j],shiftsign); newtag(atom0tag,atom->angle_atom3[i][j]);
} else { } else {
atom->angle_atom1[i][j] += atom_offset; atom->angle_atom1[i][j] += atom_offset;
atom->angle_atom2[i][j] += atom_offset; atom->angle_atom2[i][j] += atom_offset;
@ -664,10 +659,10 @@ void Replicate::command(int narg, char **arg)
if (atom->avec->dihedrals_allow) if (atom->avec->dihedrals_allow)
for (j = 0; j < atom->num_dihedral[i]; j++) { for (j = 0; j < atom->num_dihedral[i]; j++) {
if (bondlist_flag) { if (bondlist_flag) {
newtag(atom0tag,atom->dihedral_atom1[i][j],shiftsign); newtag(atom0tag,atom->dihedral_atom1[i][j]);
newtag(atom0tag,atom->dihedral_atom2[i][j],shiftsign); newtag(atom0tag,atom->dihedral_atom2[i][j]);
newtag(atom0tag,atom->dihedral_atom3[i][j],shiftsign); newtag(atom0tag,atom->dihedral_atom3[i][j]);
newtag(atom0tag,atom->dihedral_atom4[i][j],shiftsign); newtag(atom0tag,atom->dihedral_atom4[i][j]);
} else { } else {
atom->dihedral_atom1[i][j] += atom_offset; atom->dihedral_atom1[i][j] += atom_offset;
atom->dihedral_atom2[i][j] += atom_offset; atom->dihedral_atom2[i][j] += atom_offset;
@ -678,10 +673,10 @@ void Replicate::command(int narg, char **arg)
if (atom->avec->impropers_allow) if (atom->avec->impropers_allow)
for (j = 0; j < atom->num_improper[i]; j++) { for (j = 0; j < atom->num_improper[i]; j++) {
if (bondlist_flag) { if (bondlist_flag) {
newtag(atom0tag,atom->improper_atom1[i][j],shiftsign); newtag(atom0tag,atom->improper_atom1[i][j]);
newtag(atom0tag,atom->improper_atom2[i][j],shiftsign); newtag(atom0tag,atom->improper_atom2[i][j]);
newtag(atom0tag,atom->improper_atom3[i][j],shiftsign); newtag(atom0tag,atom->improper_atom3[i][j]);
newtag(atom0tag,atom->improper_atom4[i][j],shiftsign); newtag(atom0tag,atom->improper_atom4[i][j]);
} else { } else {
atom->improper_atom1[i][j] += atom_offset; atom->improper_atom1[i][j] += atom_offset;
atom->improper_atom2[i][j] += atom_offset; atom->improper_atom2[i][j] += atom_offset;
@ -867,15 +862,18 @@ void Replicate::command(int narg, char **arg)
reassign bond if > old boxlength / 2 reassign bond if > old boxlength / 2
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
void Replicate::newtag(tagint atom0tag, tagint &tag2bond, double shiftsign[]) { void Replicate::newtag(tagint atom0tag, tagint &tag2bond) {
double del[3]; double del;
int rep2bond[3], repshift[3] = {0, 0, 0}; int repshift,rep2bond[3];
int atom0 = old->map(atom0tag); int atom0 = old->map(atom0tag);
int atom2bond = old->map(tag2bond); int atom2bond = old->map(tag2bond);
for (int i = 0; i < 3; i++) { for (int i = 0; i < 3; i++) {
del[i] = fabs(old->x[atom0][i] - old->x[atom2bond][i]); del = fabs(old->x[atom0][i] - old->x[atom2bond][i]);
if (del[i] > old_prd_half[i]) repshift[i] = shiftsign[i]; if (del > old_prd_half[i]) {
rep2bond[i] = thisrep[i] + repshift[i]; if (old->x[atom0][i] > old_center[i]) repshift = 1;
else repshift = -1;
} else repshift = 0;
rep2bond[i] = thisrep[i] + repshift;
if (rep2bond[i] >= allnrep[i]) rep2bond[i] = 0; if (rep2bond[i] >= allnrep[i]) rep2bond[i] = 0;
if (rep2bond[i] < 0) rep2bond[i] = allnrep[i]-1; if (rep2bond[i] < 0) rep2bond[i] = allnrep[i]-1;
} }

4
src/replicate.h
View File

@ -31,10 +31,10 @@ class Replicate : public Command {
private: private:
Atom *old; Atom *old;
double old_prd_half[3]; double old_prd_half[3], old_center[3];
tagint maxtag; tagint maxtag;
int thisrep[3], allnrep[3]; int thisrep[3], allnrep[3];
void newtag(tagint, tagint &, double[3]); void newtag(tagint, tagint &);
}; };
} // namespace LAMMPS_NS } // namespace LAMMPS_NS