From 1f01bb69b998b0645d841e01485a6412f151dc68 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Wed, 26 Feb 2014 16:10:13 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11578 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- src/RIGID/fix_rigid_small.cpp | 2 +- src/USER-OMP/pair_adp_omp.cpp | 2 -- src/USER-REAXC/reaxc_forces.cpp | 2 +- src/molecule.cpp | 8 ++++++++ 4 files changed, 10 insertions(+), 4 deletions(-) diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp index 19c6d1b403..40c9a9a708 100644 --- a/src/RIGID/fix_rigid_small.cpp +++ b/src/RIGID/fix_rigid_small.cpp @@ -1392,7 +1392,7 @@ void FixRigidSmall::create_bodies() for (i = 0; i < nlocal; i++) { if (!(mask[i] & groupbit)) continue; 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[1]; buf[m++] = unwrap[2]; diff --git a/src/USER-OMP/pair_adp_omp.cpp b/src/USER-OMP/pair_adp_omp.cpp index 56139c8980..41be063200 100644 --- a/src/USER-OMP/pair_adp_omp.cpp +++ b/src/USER-OMP/pair_adp_omp.cpp @@ -200,7 +200,6 @@ void PairADPOMP::eval(int iifrom, int iito, ThrData * const thr) if (NEWTON_PAIR) { // reduce per thread density - thr->timer(Timer::PAIR); data_reduce_thr(&(rho[0]), nall, comm->nthreads, 1, tid); data_reduce_thr(&(mu[0][0]), nall, comm->nthreads, 3, 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 { // reduce per thread density - thr->timer(Timer::PAIR); data_reduce_thr(&(rho[0]), nlocal, comm->nthreads, 1, tid); data_reduce_thr(&(mu[0][0]), nlocal, comm->nthreads, 3, tid); data_reduce_thr(&(lambda[0][0]), nlocal, comm->nthreads, 6, tid); diff --git a/src/USER-REAXC/reaxc_forces.cpp b/src/USER-REAXC/reaxc_forces.cpp index 9fac507f78..d10b2e8e2f 100644 --- a/src/USER-REAXC/reaxc_forces.cpp +++ b/src/USER-REAXC/reaxc_forces.cpp @@ -224,7 +224,7 @@ void Validate_Lists( reax_system *system, storage *workspace, reax_list **lists, if( numH > 0 ) { hbonds = *lists + HBONDS; - for( i = 0; i < n; ++i ) { + for( i = 0; i < N; ++i ) { Hindex = system->my_atoms[i].Hindex; if( Hindex > -1 ) { system->my_atoms[i].num_hbonds = diff --git a/src/molecule.cpp b/src/molecule.cpp index f1b87f4c5b..ea1fa6b73a 100644 --- a/src/molecule.cpp +++ b/src/molecule.cpp @@ -709,6 +709,7 @@ void Molecule::dihedrals(int flag, char *line) dihedral_atom1[m][num_dihedral[m]] = atom1; dihedral_atom2[m][num_dihedral[m]] = atom2; dihedral_atom3[m][num_dihedral[m]] = atom3; + dihedral_atom4[m][num_dihedral[m]] = atom4; num_dihedral[m]++; if (newton_bond == 0) { m = atom1-1; @@ -716,18 +717,21 @@ void Molecule::dihedrals(int flag, char *line) dihedral_atom1[m][num_dihedral[m]] = atom1; dihedral_atom2[m][num_dihedral[m]] = atom2; dihedral_atom3[m][num_dihedral[m]] = atom3; + dihedral_atom4[m][num_dihedral[m]] = atom4; num_dihedral[m]++; m = atom3-1; dihedral_type[m][num_dihedral[m]] = itype; dihedral_atom1[m][num_dihedral[m]] = atom1; dihedral_atom2[m][num_dihedral[m]] = atom2; dihedral_atom3[m][num_dihedral[m]] = atom3; + dihedral_atom4[m][num_dihedral[m]] = atom4; num_dihedral[m]++; m = atom4-1; dihedral_type[m][num_dihedral[m]] = itype; dihedral_atom1[m][num_dihedral[m]] = atom1; dihedral_atom2[m][num_dihedral[m]] = atom2; dihedral_atom3[m][num_dihedral[m]] = atom3; + dihedral_atom4[m][num_dihedral[m]] = atom4; num_dihedral[m]++; } } else { @@ -790,6 +794,7 @@ void Molecule::impropers(int flag, char *line) improper_atom1[m][num_improper[m]] = atom1; improper_atom2[m][num_improper[m]] = atom2; improper_atom3[m][num_improper[m]] = atom3; + improper_atom4[m][num_improper[m]] = atom4; num_improper[m]++; if (newton_bond == 0) { m = atom1-1; @@ -797,18 +802,21 @@ void Molecule::impropers(int flag, char *line) improper_atom1[m][num_improper[m]] = atom1; improper_atom2[m][num_improper[m]] = atom2; improper_atom3[m][num_improper[m]] = atom3; + improper_atom4[m][num_improper[m]] = atom4; num_improper[m]++; m = atom3-1; improper_type[m][num_improper[m]] = itype; improper_atom1[m][num_improper[m]] = atom1; improper_atom2[m][num_improper[m]] = atom2; improper_atom3[m][num_improper[m]] = atom3; + improper_atom4[m][num_improper[m]] = atom4; num_improper[m]++; m = atom4-1; improper_type[m][num_improper[m]] = itype; improper_atom1[m][num_improper[m]] = atom1; improper_atom2[m][num_improper[m]] = atom2; improper_atom3[m][num_improper[m]] = atom3; + improper_atom4[m][num_improper[m]] = atom4; num_improper[m]++; } } else {