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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11578 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2014-02-26 16:10:13 +00:00
parent cde0125c90
commit 1f01bb69b9
4 changed files with 10 additions and 4 deletions
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2
src/RIGID/fix_rigid_small.cpp
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@ -1392,7 +1392,7 @@ void FixRigidSmall::create_bodies()
for (i = 0; i < nlocal; i++) { for (i = 0; i < nlocal; i++) {
if (!(mask[i] & groupbit)) continue; if (!(mask[i] & groupbit)) continue;
domain->unmap(x[i],image[i],unwrap); domain->unmap(x[i],image[i],unwrap);
buf[m++] = ubuf(bodytag[i]).i; buf[m++] = ubuf(bodytag[i]).d;
buf[m++] = unwrap[0]; buf[m++] = unwrap[0];
buf[m++] = unwrap[1]; buf[m++] = unwrap[1];
buf[m++] = unwrap[2]; buf[m++] = unwrap[2];

2
src/USER-OMP/pair_adp_omp.cpp
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@ -200,7 +200,6 @@ void PairADPOMP::eval(int iifrom, int iito, ThrData * const thr)
if (NEWTON_PAIR) { if (NEWTON_PAIR) {
// reduce per thread density // reduce per thread density
thr->timer(Timer::PAIR);
data_reduce_thr(&(rho[0]), nall, comm->nthreads, 1, tid); data_reduce_thr(&(rho[0]), nall, comm->nthreads, 1, tid);
data_reduce_thr(&(mu[0][0]), nall, comm->nthreads, 3, tid); data_reduce_thr(&(mu[0][0]), nall, comm->nthreads, 3, tid);
data_reduce_thr(&(lambda[0][0]), nall, comm->nthreads, 6, tid); data_reduce_thr(&(lambda[0][0]), nall, comm->nthreads, 6, tid);
@ -218,7 +217,6 @@ void PairADPOMP::eval(int iifrom, int iito, ThrData * const thr)
} else { } else {
// reduce per thread density // reduce per thread density
thr->timer(Timer::PAIR);
data_reduce_thr(&(rho[0]), nlocal, comm->nthreads, 1, tid); data_reduce_thr(&(rho[0]), nlocal, comm->nthreads, 1, tid);
data_reduce_thr(&(mu[0][0]), nlocal, comm->nthreads, 3, tid); data_reduce_thr(&(mu[0][0]), nlocal, comm->nthreads, 3, tid);
data_reduce_thr(&(lambda[0][0]), nlocal, comm->nthreads, 6, tid); data_reduce_thr(&(lambda[0][0]), nlocal, comm->nthreads, 6, tid);

2
src/USER-REAXC/reaxc_forces.cpp
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@ -224,7 +224,7 @@ void Validate_Lists( reax_system *system, storage *workspace, reax_list **lists,
if( numH > 0 ) { if( numH > 0 ) {
hbonds = *lists + HBONDS; hbonds = *lists + HBONDS;
for( i = 0; i < n; ++i ) { for( i = 0; i < N; ++i ) {
Hindex = system->my_atoms[i].Hindex; Hindex = system->my_atoms[i].Hindex;
if( Hindex > -1 ) { if( Hindex > -1 ) {
system->my_atoms[i].num_hbonds = system->my_atoms[i].num_hbonds =

8
src/molecule.cpp
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@ -709,6 +709,7 @@ void Molecule::dihedrals(int flag, char *line)
dihedral_atom1[m][num_dihedral[m]] = atom1; dihedral_atom1[m][num_dihedral[m]] = atom1;
dihedral_atom2[m][num_dihedral[m]] = atom2; dihedral_atom2[m][num_dihedral[m]] = atom2;
dihedral_atom3[m][num_dihedral[m]] = atom3; dihedral_atom3[m][num_dihedral[m]] = atom3;
dihedral_atom4[m][num_dihedral[m]] = atom4;
num_dihedral[m]++; num_dihedral[m]++;
if (newton_bond == 0) { if (newton_bond == 0) {
m = atom1-1; m = atom1-1;
@ -716,18 +717,21 @@ void Molecule::dihedrals(int flag, char *line)
dihedral_atom1[m][num_dihedral[m]] = atom1; dihedral_atom1[m][num_dihedral[m]] = atom1;
dihedral_atom2[m][num_dihedral[m]] = atom2; dihedral_atom2[m][num_dihedral[m]] = atom2;
dihedral_atom3[m][num_dihedral[m]] = atom3; dihedral_atom3[m][num_dihedral[m]] = atom3;
dihedral_atom4[m][num_dihedral[m]] = atom4;
num_dihedral[m]++; num_dihedral[m]++;
m = atom3-1; m = atom3-1;
dihedral_type[m][num_dihedral[m]] = itype; dihedral_type[m][num_dihedral[m]] = itype;
dihedral_atom1[m][num_dihedral[m]] = atom1; dihedral_atom1[m][num_dihedral[m]] = atom1;
dihedral_atom2[m][num_dihedral[m]] = atom2; dihedral_atom2[m][num_dihedral[m]] = atom2;
dihedral_atom3[m][num_dihedral[m]] = atom3; dihedral_atom3[m][num_dihedral[m]] = atom3;
dihedral_atom4[m][num_dihedral[m]] = atom4;
num_dihedral[m]++; num_dihedral[m]++;
m = atom4-1; m = atom4-1;
dihedral_type[m][num_dihedral[m]] = itype; dihedral_type[m][num_dihedral[m]] = itype;
dihedral_atom1[m][num_dihedral[m]] = atom1; dihedral_atom1[m][num_dihedral[m]] = atom1;
dihedral_atom2[m][num_dihedral[m]] = atom2; dihedral_atom2[m][num_dihedral[m]] = atom2;
dihedral_atom3[m][num_dihedral[m]] = atom3; dihedral_atom3[m][num_dihedral[m]] = atom3;
dihedral_atom4[m][num_dihedral[m]] = atom4;
num_dihedral[m]++; num_dihedral[m]++;
} }
} else { } else {
@ -790,6 +794,7 @@ void Molecule::impropers(int flag, char *line)
improper_atom1[m][num_improper[m]] = atom1; improper_atom1[m][num_improper[m]] = atom1;
improper_atom2[m][num_improper[m]] = atom2; improper_atom2[m][num_improper[m]] = atom2;
improper_atom3[m][num_improper[m]] = atom3; improper_atom3[m][num_improper[m]] = atom3;
improper_atom4[m][num_improper[m]] = atom4;
num_improper[m]++; num_improper[m]++;
if (newton_bond == 0) { if (newton_bond == 0) {
m = atom1-1; m = atom1-1;
@ -797,18 +802,21 @@ void Molecule::impropers(int flag, char *line)
improper_atom1[m][num_improper[m]] = atom1; improper_atom1[m][num_improper[m]] = atom1;
improper_atom2[m][num_improper[m]] = atom2; improper_atom2[m][num_improper[m]] = atom2;
improper_atom3[m][num_improper[m]] = atom3; improper_atom3[m][num_improper[m]] = atom3;
improper_atom4[m][num_improper[m]] = atom4;
num_improper[m]++; num_improper[m]++;
m = atom3-1; m = atom3-1;
improper_type[m][num_improper[m]] = itype; improper_type[m][num_improper[m]] = itype;
improper_atom1[m][num_improper[m]] = atom1; improper_atom1[m][num_improper[m]] = atom1;
improper_atom2[m][num_improper[m]] = atom2; improper_atom2[m][num_improper[m]] = atom2;
improper_atom3[m][num_improper[m]] = atom3; improper_atom3[m][num_improper[m]] = atom3;
improper_atom4[m][num_improper[m]] = atom4;
num_improper[m]++; num_improper[m]++;
m = atom4-1; m = atom4-1;
improper_type[m][num_improper[m]] = itype; improper_type[m][num_improper[m]] = itype;
improper_atom1[m][num_improper[m]] = atom1; improper_atom1[m][num_improper[m]] = atom1;
improper_atom2[m][num_improper[m]] = atom2; improper_atom2[m][num_improper[m]] = atom2;
improper_atom3[m][num_improper[m]] = atom3; improper_atom3[m][num_improper[m]] = atom3;
improper_atom4[m][num_improper[m]] = atom4;
num_improper[m]++; num_improper[m]++;
} }
} else { } else {