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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11328 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2014-01-25 22:46:08 +00:00
parent 2f6a46a2be
commit 0ce16af78b
63 changed files with 2943 additions and 798 deletions
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17
src/neighbor.cpp
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@ -756,6 +756,7 @@ void Neighbor::init()
}
// set flags that determine which topology neighboring routines to use
// bonds,etc can only be broken for atom->molecular = 1, not 2
// SHAKE sets bonds and angles negative
// bond_quartic sets bonds to 0
// delete_bonds sets all interactions negative
@ -767,7 +768,7 @@ void Neighbor::init()
bond_off = angle_off = 1;
if (force->bond && force->bond_match("quartic")) bond_off = 1;
if (atom->avec->bonds_allow) {
if (atom->avec->bonds_allow && atom->molecular == 1) {
for (i = 0; i < atom->nlocal; i++) {
if (bond_off) break;
for (m = 0; m < atom->num_bond[i]; m++)
@ -775,7 +776,7 @@ void Neighbor::init()
}
}
if (atom->avec->angles_allow) {
if (atom->avec->angles_allow && atom->molecular == 1) {
for (i = 0; i < atom->nlocal; i++) {
if (angle_off) break;
for (m = 0; m < atom->num_angle[i]; m++)
@ -784,7 +785,7 @@ void Neighbor::init()
}
int dihedral_off = 0;
if (atom->avec->dihedrals_allow) {
if (atom->avec->dihedrals_allow && atom->molecular == 1) {
for (i = 0; i < atom->nlocal; i++) {
if (dihedral_off) break;
for (m = 0; m < atom->num_dihedral[i]; m++)
@ -793,7 +794,7 @@ void Neighbor::init()
}
int improper_off = 0;
if (atom->avec->impropers_allow) {
if (atom->avec->impropers_allow && atom->molecular == 1) {
for (i = 0; i < atom->nlocal; i++) {
if (improper_off) break;
for (m = 0; m < atom->num_improper[i]; m++)
@ -815,15 +816,19 @@ void Neighbor::init()
// set ptrs to topology build functions
if (bond_off) bond_build = &Neighbor::bond_partial;
else if (atom->molecular == 2) bond_build = &Neighbor::bond_template;
else bond_build = &Neighbor::bond_all;
if (angle_off) angle_build = &Neighbor::angle_partial;
else if (atom->molecular == 2) angle_build = &Neighbor::angle_template;
else angle_build = &Neighbor::angle_all;
if (dihedral_off) dihedral_build = &Neighbor::dihedral_partial;
else if (atom->molecular == 2) dihedral_build = &Neighbor::dihedral_template;
else dihedral_build = &Neighbor::dihedral_all;
if (improper_off) improper_build = &Neighbor::improper_partial;
else if (atom->molecular == 2) improper_build = &Neighbor::improper_template;
else improper_build = &Neighbor::improper_all;
// set topology neighbor list counts to 0
@ -912,7 +917,7 @@ void Neighbor::choose_build(int index, NeighRequest *rq)
else pb = &Neighbor::half_bin_no_newton_ghost;
} else if (triclinic == 0) {
pb = &Neighbor::half_bin_newton;
} else if (triclinic == 1)
} else if (triclinic == 1)
pb = &Neighbor::half_bin_newton_tri;
} else if (rq->newton == 1) {
if (triclinic == 0) pb = &Neighbor::half_bin_newton;
@ -1317,7 +1322,7 @@ int Neighbor::check_distance()
/* ----------------------------------------------------------------------
build all perpetual neighbor lists every few timesteps
pairwise & topology lists are created as needed
topology lists only built if topoflag = 1
topology lists only built if topoflag = 1, USER-CUDA calls with topoflag = 0
------------------------------------------------------------------------- */
void Neighbor::build(int topoflag)