Merge pull request #547 from akohlmey/collected-bugfixes

Collected small bugfixes and updates

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
 

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,  \

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
 

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

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");

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

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;