diff --git a/doc/src/pair_nb3b_harmonic.txt b/doc/src/pair_nb3b_harmonic.txt
index 86a535acf3c691e206bdadda9df52de0ff59a9a0..3f7066c82663bc128198f2bdeea0d6b8ea279bfd 100644
--- a/doc/src/pair_nb3b_harmonic.txt
+++ b/doc/src/pair_nb3b_harmonic.txt
@@ -80,10 +80,12 @@ For a given entry, if the first three arguments are all different,
then the entry is for the {K} and {theta_0} parameters (the cutoff in
this case is irrelevant).
-It is {not} required that the potential file contain entries for all
-of the elements listed in the pair_coeff command. It can also contain
-entries for additional elements not being used in a particular
-simulation; LAMMPS ignores those entries.
+It is required that the potential file contains entries for {all}
+permutations of the elements listed in the pair_coeff command.
+If certain combinations are not parameterized the corresponding
+parameters should be set to zero. The potential file can also
+contain entries for additional elements which are not used in
+a particular simulation; LAMMPS ignores those entries.
:line
diff --git a/src/USER-INTEL/intel_preprocess.h b/src/USER-INTEL/intel_preprocess.h
index d5cf6f5be2cee5cb5b15c876d08cdd5da81441b0..1f6225dc440188a80371a32b59ca0f0e90a40c18 100644
--- a/src/USER-INTEL/intel_preprocess.h
+++ b/src/USER-INTEL/intel_preprocess.h
@@ -248,12 +248,6 @@ enum {TIME_PACK, TIME_HOST_NEIGHBOR, TIME_HOST_PAIR, TIME_OFFLOAD_NEIGHBOR,
#else
-#define IP_PRE_omp_range(ifrom, ito, tid, inum, nthreads) \
- { \
- ifrom = 0; \
- ito = inum; \
- }
-
#define IP_PRE_omp_range_id(ifrom, ito, tid, inum, nthreads) \
{ \
tid = 0; \
@@ -299,15 +293,6 @@ enum {TIME_PACK, TIME_HOST_NEIGHBOR, TIME_HOST_PAIR, TIME_OFFLOAD_NEIGHBOR,
ito = inum; \
}
-#define IP_PRE_omp_range_id_vec(ifrom, ip, ito, tid, inum, \
- nthreads, vecsize) \
- { \
- tid = 0; \
- ifrom = 0; \
- ito = inum; \
- ip = vecsize; \
- }
-
#endif
#define IP_PRE_fdotr_acc_force_l5(lf, lt, minlocal, nthreads, f_start, \
diff --git a/src/USER-OMP/fix_qeq_reax_omp.cpp b/src/USER-OMP/fix_qeq_reax_omp.cpp
index 3ca193be74d3bb1f46d6ee411928971000e6caa0..df586132d4aad785d017c45068436222292c68a2 100644
--- a/src/USER-OMP/fix_qeq_reax_omp.cpp
+++ b/src/USER-OMP/fix_qeq_reax_omp.cpp
@@ -172,6 +172,7 @@ void FixQEqReaxOMP::compute_H()
H.firstnbr[ai] = num_nbrs;
num_nbrs += numneigh[ai];
}
+ m_fill = num_nbrs;
// fill in the H matrix
diff --git a/src/USER-OMP/pair_reaxc_omp.cpp b/src/USER-OMP/pair_reaxc_omp.cpp
index 91fa3d38c7f3d0310fb5e7e69729ff4c3bdc90e6..45c4bce0c08f9c8d8bb993dcde5261daf3753741 100644
--- a/src/USER-OMP/pair_reaxc_omp.cpp
+++ b/src/USER-OMP/pair_reaxc_omp.cpp
@@ -84,10 +84,11 @@ PairReaxCOMP::PairReaxCOMP(LAMMPS *lmp) : PairReaxC(lmp), ThrOMP(lmp, THR_PAIR)
PairReaxCOMP::~PairReaxCOMP()
{
- reax_list * bonds = lists+BONDS;
- for (int i=0; i<bonds->num_intrs; ++i)
- sfree(bonds->select.bond_list[i].bo_data.CdboReduction, "CdboReduction");
-
+ if (setup_flag) {
+ reax_list * bonds = lists+BONDS;
+ for (int i=0; i<bonds->num_intrs; ++i)
+ sfree(bonds->select.bond_list[i].bo_data.CdboReduction, "CdboReduction");
+ }
memory->destroy(num_nbrs_offset);
#ifdef OMP_TIMING
diff --git a/src/atom.cpp b/src/atom.cpp
index df4db0a84205a8499ad78e85123ff72cd09b3c49..e46b1a72426bf8b9db25d9dd8487c49f4826f8df 100644
--- a/src/atom.cpp
+++ b/src/atom.cpp
@@ -1514,12 +1514,13 @@ void Atom::set_mass(double *values)
}
/* ----------------------------------------------------------------------
- check that all masses have been set
+ check that all per-atom-type masses have been set
------------------------------------------------------------------------- */
void Atom::check_mass(const char *file, int line)
{
if (mass == NULL) return;
+ if (rmass_flag) return;
for (int itype = 1; itype <= ntypes; itype++)
if (mass_setflag[itype] == 0)
error->all(file,line,"Not all per-type masses are set");
diff --git a/src/info.cpp b/src/info.cpp
index 6a7f70b39df559e368b72b533d1cde6213701640..9fcc24fde9ca1e757501ea3acf99c33f1f5a9a10 100644
--- a/src/info.cpp
+++ b/src/info.cpp
@@ -1,5 +1,4 @@
/* ----------------------------------------------------------------------
- fputs
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
diff --git a/src/molecule.cpp b/src/molecule.cpp
index 76b28e3d470611f56c9f33d367a6a8f6b53736fc..e0e9ec8aaf1cb3925a3318fa872edfc82b733e62 100644
--- a/src/molecule.cpp
+++ b/src/molecule.cpp
@@ -219,7 +219,7 @@ void Molecule::compute_mass()
if (massflag) return;
massflag = 1;
- if (!rmassflag) atom->check_mass(FLERR);
+ atom->check_mass(FLERR);
masstotal = 0.0;
for (int i = 0; i < natoms; i++) {
@@ -243,7 +243,7 @@ void Molecule::compute_com()
if (!comflag) {
comflag = 1;
- if (!rmassflag) atom->check_mass(FLERR);
+ atom->check_mass(FLERR);
double onemass;
com[0] = com[1] = com[2] = 0.0;
@@ -308,7 +308,7 @@ void Molecule::compute_inertia()
if (!inertiaflag) {
inertiaflag = 1;
- if (!rmassflag) atom->check_mass(FLERR);
+ atom->check_mass(FLERR);
double onemass,dx,dy,dz;
for (int i = 0; i < 6; i++) itensor[i] = 0.0;