Merge pull request #1490 from akohlmey/next_version

Step version number for stable release

cmake/CMakeLists.txt

@@ -322,7 +322,7 @@ find_package(OpenMP QUIET)
 # where we assume older GCC semantics. For the time being, we disable OpenMP by default
 # for GCC 9.x and beyond. People may manually turn it on, but need to run the script
 # src/USER-OMP/hack_openmp_for_pgi_gcc9.sh on all sources to make it compatible with gcc 9.
-if ((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 9.0.0))
+if ((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER 8.99.9))
   option(BUILD_OMP "Build with OpenMP support" OFF)
 else()
   option(BUILD_OMP "Build with OpenMP support" ${OpenMP_FOUND})

doc/lammps.1

@@ -1,4 +1,4 @@
-.TH LAMMPS "31 May 2019" "2019-05-31"
+.TH LAMMPS "5 June 2019" "2019-06-05"
 .SH NAME
 .B LAMMPS
 \- Molecular Dynamics Simulator.

doc/src/Commands.txt

@@ -33,6 +33,11 @@ commands in it are used to define a LAMMPS simulation.
    Commands_bond
    Commands_kspace
 
+.. toctree::
+   :maxdepth: 1
+
+   Commands_removed
+
 END_RST -->
 
 <!-- HTML_ONLY -->
@@ -49,5 +54,7 @@ END_RST -->
 "Bond, angle, dihedral, improper commands"_Commands_bond.html
 "KSpace solvers"_Commands_kspace.html  :all(b)
 
+"Removed commands and packages"_Commands_removed.html  :all(b)
+
 <!-- END_HTML_ONLY -->
 

doc/src/Commands_removed.txt

@@ -0,0 +1,66 @@
+"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands.html)
+
+:line
+
+Removed commands and packages :h3
+
+This page lists LAMMPS commands and packages that have been removed from
+the distribution and provides suggestions for alternatives or replacements.
+LAMMPS has special dummy styles implemented, that will stop LAMMPS and
+print a suitable error message in most cases, when a style/command is used
+that has been removed.
+
+Fix ave/spatial and fix ave/spatial/sphere :h4
+
+The fixes ave/spatial and ave/spatial/sphere have been removed from LAMMPS
+since they were superseded by the more general and extensible "chunk
+infrastructure".  Here the system is partitioned in one of many possible
+ways through the "compute chunk/atom"_compute_chunk_atom.html command
+and then averaging is done using "fix ave/chunk"_fix_ave_chunk.html.
+Please refer to the "chunk HOWTO"_Howto_chunk.html section for an overview.
+
+MEAM package :h4
+
+The MEAM package has been removed since it was superseded by the
+"USER-MEAMC package"_Package_details.html#PKG-USER-MEAMC. The code in
+the USER-MEAMC package is a translation of the Fortran code of MEAM into C++,
+which removes several restrictions (e.g. there can be multiple instances
+in hybrid pair styles) and allows for some optimizations leading
+to better performance.  The new pair style "meam/c"_pair_meamc.html has
+the exact same syntax as the old "meam" pair style and thus pair style
+"meam"_pair_meamc.html is an alias to the new style and backward
+compatibility of old inputs is preserved.
+
+REAX package :h4
+
+The REAX package has been removed since it was superseded by the
+"USER-REAXC package"_Package_details.html#PKG-USER-REAXC.  The USER-REAXC
+package has been tested to yield equivalent results to the REAX package,
+offers better performance, supports OpenMP multi-threading via USER-OMP,
+and GPU and threading parallelization through KOKKOS.  The new pair styles
+are not syntax compatible with the removed reax pair style, so input
+files will have to be adapted.
+
+USER-CUDA package :h4
+
+The USER-CUDA package had been removed, since it had been unmaintained
+for a long time and had known bugs and problems.  Significant parts of
+the design were transferred to the
+"KOKKOS package"_Package_details.html#PKG-KOKKOS, which has similar
+performance characteristics on Nvidia GPUs. Both, the KOKKOS
+and the "GPU package"_Package_details.html#PKG-GPU are maintained
+and allow running LAMMPS with GPU acceleration.
+
+restart2data tool :h4
+
+The functionality of the restart2data tool has been folded into the
+LAMMPS executable directly instead of having a separate tool.  A
+combination of the commands "read_restart"_read_restart.html and
+"write_data"_write_data.html can be used to the same effect.  For added
+convenience this conversion can also be triggered by "command line
+flags"_Run_options.html

doc/src/Errors_messages.txt

@@ -610,6 +610,62 @@ This means there is something invalid about the topology definitions. :dd
 
 The data file header lists bonds but no bond types. :dd
 
+{Bond/react: Cannot use fix bond/react with non-molecular systems} :dt
+
+Only systems with bonds that can be changed can be used. Atom_style
+template does not qualify. :dd
+
+{Bond/react: Rmax cutoff is longer than pairwise cutoff} :dt
+
+This is not allowed because bond creation is done using the pairwise
+neighbor list. :dd
+
+{Bond/react: Molecule template ID for fix bond/react does not exist} :dt
+
+A valid molecule template must have been created with the molecule
+command. :dd
+
+{Bond/react: Reaction templates must contain the same number of atoms} :dt
+
+There should be a one-to-one correspondence between atoms in the
+pre-reacted and post-reacted templates, as specified by the map file. :dd
+
+{Bond/react: Unknown section in map file} :dt
+
+Please ensure reaction map files are properly formatted. :dd
+
+{Bond/react: Atom affected by reaction too close to template edge} :dt
+
+This means an atom which changes type during the reaction is too close
+to an 'edge' atom defined in the superimpose file. This could cause
+incorrect assignment of bonds, angle, etc. Generally, this means you
+must include more atoms in your templates, such that there are at
+least two atoms between each atom involved in the reaction and an edge
+atom. :dd
+
+{Bond/react: Fix bond/react needs ghost atoms from farther away} :dt
+
+This is because a processor needs to superimpose the entire unreacted
+molecule template onto simulation atoms it knows about. The
+comm_modify cutoff command can be used to extend the communication
+range. :dd
+
+{Bond/react: A deleted atom cannot remain bonded to an atom that is not deleted} :dt
+
+Self-explanatory. :dd
+
+{Bond/react special bond generation overflow} :dt
+
+The number of special bonds per-atom created by a reaction exceeds the
+system setting. See the read_data or create_box command for how to
+specify this value. :dd
+
+{Bond/react topology/atom exceed system topology/atom} :dt
+
+The number of bonds, angles etc per-atom created by a reaction exceeds
+the system setting. See the read_data or create_box command for how to
+specify this value. :dd
+
 {Both restart files must use % or neither} :dt
 
 Self-explanatory. :dd

doc/src/Errors_warnings.txt

@@ -82,6 +82,11 @@ bond/angle/dihedral.  LAMMPS computes this by taking the maximum bond
 length, multiplying by the number of bonds in the interaction (e.g. 3
 for a dihedral) and adding a small amount of stretch. :dd
 
+{Bond/react: An atom in 'react #%d' changes bond connectivity but not atom type} :dt
+
+You may want to double-check that all atom types are properly assigned
+in the post-reaction template. :dd
+
 {Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero} :dt
 
 Self-explanatory. :dd

doc/src/Manual.txt

@@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="31 May 2019 version">
+<META NAME="docnumber" CONTENT="5 Jun 2019 version">
 <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
 <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
 </HEAD>
@@ -21,7 +21,7 @@
 :line
 
 LAMMPS Documentation :c,h1
-31 May 2019 version :c,h2
+5 Jun 2019 version :c,h2
 
 "What is a LAMMPS version?"_Manual_version.html
 

doc/src/fix_bond_react.txt

@@ -18,8 +18,8 @@ fix ID group-ID bond/react common_keyword values ...
 
 ID, group-ID are documented in "fix"_fix.html command. Group-ID is ignored. :ulb,l
 bond/react = style name of this fix command :l
-zero or more common keyword/value pairs may be appended directly after 'bond/react' :l
-these apply to all reaction specifications (below) :l
+the common keyword/values may be appended directly after 'bond/react' :l
+this applies to all reaction specifications (below) :l
 common_keyword = {stabilization} :l
   {stabilization} values = {no} or {yes} {group-ID} {xmax}
     {no} = no reaction site stabilization
@@ -136,10 +136,12 @@ words, can be customized for each reaction, or reaction step):
 A check for possible new reaction sites is performed every {Nevery}
 timesteps.
 
-Two conditions must be met for a reaction to occur. First a bonding
-atom pair must be identified. Second, the topology surrounding the
-bonding atom pair must match the topology of the pre-reaction
-template. If both these conditions are met, the reaction site is
+Three physical conditions must be met for a reaction to occur. First,
+a bonding atom pair must be identified within the reaction distance
+cutoffs. Second, the topology surrounding the bonding atom pair must
+match the topology of the pre-reaction template. Finally, any reaction
+constraints listed in the map file (see below) must be satisfied. If
+all of these conditions are met, the reaction site is eligible to be
 modified to match the post-reaction template.
 
 A bonding atom pair will be identified if several conditions are met.
@@ -203,14 +205,24 @@ new types must also be defined during the setup of a given simulation.
 A discussion of correctly handling this is also provided on the
 "molecule"_molecule.html command page.
 
+NOTE: When a reaction occurs, it is possible that the resulting
+topology/atom (e.g. special bonds, dihedrals, etc.) exceeds that of
+the existing system and reaction templates. As when inserting
+molecules, enough space for this increased topology/atom must be
+reserved by using the relevant "extra" keywords to the
+"read_data"_read_data.html or "create_box"_create_box.html commands.
+
 The map file is a text document with the following format:
 
 A map file has a header and a body. The header of map file the
-contains one mandatory keyword and three optional keywords. The
-mandatory keyword is 'equivalences' and the optional keywords are
-'edgeIDs' and 'deleteIDs' and 'customIDs':
+contains one mandatory keyword and four optional keywords. The
+mandatory keyword is 'equivalences':
+
+N {equivalences} = # of atoms N in the reaction molecule templates :pre
+
+The optional keywords are 'edgeIDs', 'deleteIDs', 'customIDs' and
+'constraints':
 
-N {equivalences} = # of atoms N in the reaction molecule templates
 N {edgeIDs} = # of edge atoms N in the pre-reacted molecule template
 N {deleteIDs} = # of atoms N that are specified for deletion
 N {customIDs} = # of atoms N that are specified for a custom update
@@ -244,8 +256,8 @@ A sample map file is given below:
 
 # this is a map file :pre
 
-2 edgeIDs
-7 equivalences :pre
+7 equivalences
+2 edgeIDs :pre
 
 BondingIDs :pre
 
@@ -297,26 +309,25 @@ can allow for the possibility of one or more reverse reactions.
 
 The optional keywords deal with the probability of a given reaction
 occurring as well as the stable equilibration of each reaction site as
-it occurs.
+it occurs:
 
-The {prob} keyword can affect whether an eligible reaction actually
-occurs. The fraction setting must be a value between 0.0 and 1.0. A
-uniform random number between 0.0 and 1.0 is generated and the
+The {prob} keyword can affect whether or not an eligible reaction
+actually occurs. The fraction setting must be a value between 0.0 and
+1.0. A uniform random number between 0.0 and 1.0 is generated and the
 eligible reaction only occurs if the random number is less than the
 fraction. Up to N reactions are permitted to occur, as optionally
 specified by the {max_rxn} keyword.
 
 The {stabilize_steps} keyword allows for the specification of how many
 timesteps a reaction site is stabilized before being returned to the
-overall system thermostat.
-
-In order to produce the most physical behavior, this 'reaction site
-equilibration time' should be tuned to be as small as possible while
-retaining stability for a given system or reaction step. After a
-limited number of case studies, this number has been set to a default
-of 60 timesteps. Ideally, it should be individually tuned for each fix
-reaction step. Note that in some situations, decreasing rather than
-increasing this parameter will result in an increase in stability.
+overall system thermostat. In order to produce the most physical
+behavior, this 'reaction site equilibration time' should be tuned to
+be as small as possible while retaining stability for a given system
+or reaction step. After a limited number of case studies, this number
+has been set to a default of 60 timesteps. Ideally, it should be
+individually tuned for each fix reaction step. Note that in some
+situations, decreasing rather than increasing this parameter will
+result in an increase in stability.
 
 The {update_edges} keyword can increase the number of atoms whose
 atomic charges are updated, when the pre-reaction template contains
@@ -324,11 +335,11 @@ edge atoms. When the value is set to 'charges,' all atoms' atomic
 charges are updated to those specified by the post-reaction template,
 including atoms near the edge of reaction templates. When the value is
 set to 'custom,' an additional section must be included in the map
-file that specifies whether to update charges, on a per-atom basis.
-The format of this section is detailed above. Listing a pre-reaction
-atom ID with a value of 'charges' will force the update of the atom's
-charge, even if it is near a template edge. Atoms not near a template
-edge are unaffected by this setting.
+file that specifies whether or not to update charges, on a per-atom
+basis. The format of this section is detailed above. Listing a
+pre-reaction atom ID with a value of 'charges' will force the update
+of the atom's charge, even if it is near a template edge. Atoms not
+near a template edge are unaffected by this setting.
 
 A few other considerations:
 

doc/src/pair_e3b.txt

@@ -99,7 +99,7 @@ This pair style does not support the "pair_modify"_pair_modify.html
 shift, table, and tail options.
 
 This pair style does not write its information to "binary restart
-files"_restart.html, since it is stored in potential files.  Thus, you
+files"_restart.html.  Thus, you
 need to re-specify the pair_style and pair_coeff commands in an input
 script that reads a restart file.
 

doc/src/variable.txt

@@ -865,7 +865,7 @@ The {is_active()} function allows to query for active settings which
 are grouped by categories. Currently supported categories and
 arguments are:
 
-{package} (argument = {cuda} or {gpu} or {intel} or {kokkos} or {omp})
+{package} (argument = {gpu} or {intel} or {kokkos} or {omp})
 {newton} (argument = {pair} or {bond} or {any})
 {pair} (argument = {single} or {respa} or {manybody} or {tail} or {shift})
 {comm_style} (argument = {brick} or {tiled})
@@ -894,7 +894,7 @@ kspace_style pppm :pre
 
 Example 2: use r-RESPA with inner/outer cutoff, if supported by pair style, otherwise fall back to using pair and reducing the outer time step
 
-timestep $(2.0*(1.0+*is_active(pair,respa))
+timestep $(2.0*(1.0+2.0*is_active(pair,respa))
 if $(is_active(pair,respa)) then "run_style respa 4 3 2 2  improper 1 inner 2 5.5 7.0 outer 3 kspace 4" else "run_style respa 3 3 2  improper 1 pair 2 kspace 3" :pre
 
 The {is_defined()} function allows to query categories like {compute},

doc/utils/sphinx-config/false_positives.txt

@@ -2844,6 +2844,7 @@ unoptimized
 unpadded
 unphysical
 unphysically
+unreacted
 unscaled
 unsets
 unsmoothed

src/USER-MISC/fix_bond_react.cpp

@@ -308,8 +308,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
     onemol->check_attributes(0);
     twomol->check_attributes(0);
     if (onemol->natoms != twomol->natoms)
-      error->all(FLERR,"Post-reacted template must contain the same "
-                       "number of atoms as the pre-reacted template");
+      error->all(FLERR,"Bond/react: Reaction templates must contain the same number of atoms");
     get_molxspecials();
     read(i);
     fclose(fp);
@@ -324,7 +323,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
   delete [] files;
 
   if (atom->molecular != 1)
-    error->all(FLERR,"Cannot use fix bond/react with non-molecular systems");
+    error->all(FLERR,"Bond/react: Cannot use fix bond/react with non-molecular systems");
 
   // check if bonding atoms are 1-2, 1-3, or 1-4 bonded neighbors
   // if so, we don't need non-bonded neighbor list
@@ -472,17 +471,19 @@ FixBondReact::~FixBondReact()
   delete [] guess_branch;
   delete [] pioneer_count;
 
-  char **newarg;
-  newarg = new char*[2];
-  newarg[0] = master_group;
-  newarg[1] = (char *) "delete";
-  group->assign(2,newarg);
-  if (stabilization_flag == 1) {
-    newarg[0] = exclude_group;
+  if (group) {
+    char **newarg;
+    newarg = new char*[2];
+    newarg[0] = master_group;
+    newarg[1] = (char *) "delete";
     group->assign(2,newarg);
-    delete [] exclude_group;
+    if (stabilization_flag == 1) {
+      newarg[0] = exclude_group;
+      group->assign(2,newarg);
+      delete [] exclude_group;
+    }
+    delete [] newarg;
   }
-  delete [] newarg;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -663,7 +664,7 @@ void FixBondReact::init()
   // check cutoff for iatomtype,jatomtype
   for (int i = 0; i < nreacts; i++) {
     if (force->pair == NULL || cutsq[i][1] > force->pair->cutsq[iatomtype[i]][jatomtype[i]])
-      error->all(FLERR,"Fix bond/react cutoff is longer than pairwise cutoff");
+      error->all(FLERR,"Bond/react: Fix bond/react cutoff is longer than pairwise cutoff");
   }
 
   // need a half neighbor list, built every Nevery steps
@@ -1172,7 +1173,7 @@ void FixBondReact::superimpose_algorithm()
         // let's go ahead and catch the simplest of hangs
         //if (hang_catch > onemol->natoms*4)
         if (hang_catch > atom->nlocal*30) {
-          error->one(FLERR,"Excessive iteration of superimpose algorithm");
+          error->one(FLERR,"Bond/react: Excessive iteration of superimpose algorithm");
         }
       }
     }
@@ -1285,7 +1286,7 @@ void FixBondReact::make_a_guess()
 
   for (int i = 0; i < nxspecial[atom->map(glove[pion][1])][0]; i++) {
     if (atom->map(xspecial[atom->map(glove[pion][1])][i]) < 0) {
-      error->all(FLERR,"Fix bond/react needs ghost atoms from further away1"); // parallel issues.
+      error->all(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away1"); // parallel issues.
     }
     if (i_limit_tags[(int)atom->map(xspecial[atom->map(glove[pion][1])][i])] != 0) {
       status = GUESSFAIL;
@@ -1396,7 +1397,7 @@ void FixBondReact::check_a_neighbor()
 
             //another check for ghost atoms. perhaps remove the one in make_a_guess
             if (atom->map(glove[(int)onemol_xspecial[pion][neigh]-1][1]) < 0) {
-              error->all(FLERR,"Fix bond/react needs ghost atoms from further away2");
+              error->all(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away2");
             }
 
             for (int j = 0; j < onemol_nxspecial[onemol_xspecial[pion][neigh]-1][0]; j++) {
@@ -1448,7 +1449,7 @@ void FixBondReact::check_a_neighbor()
 
         //another check for ghost atoms. perhaps remove the one in make_a_guess
         if (atom->map(glove[(int)onemol_xspecial[pion][neigh]-1][1]) < 0) {
-          error->all(FLERR,"Fix bond/react needs ghost atoms from further away3");
+          error->all(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away3");
         }
 
         for (int ii = 0; ii < onemol_nxspecial[onemol_xspecial[pion][neigh]-1][0]; ii++) {
@@ -1490,7 +1491,7 @@ void FixBondReact::crosscheck_the_neighbor()
         glove[onemol_xspecial[pion][trace]-1][0] == 0) {
 
       if (avail_guesses == MAXGUESS) {
-        error->warning(FLERR,"Fix bond/react failed because MAXGUESS set too small. ask developer for info");
+        error->warning(FLERR,"Bond/react: Fix bond/react failed because MAXGUESS set too small. ask developer for info");
         status = GUESSFAIL;
         return;
       }
@@ -1559,7 +1560,7 @@ void FixBondReact::inner_crosscheck_loop()
 
   //another check for ghost atoms. perhaps remove the one in make_a_guess
   if (atom->map(glove[(int)onemol_xspecial[pion][neigh]-1][1]) < 0) {
-    error->all(FLERR,"Fix bond/react needs ghost atoms from further away4");
+    error->all(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away4");
   }
 
   if (guess_branch[avail_guesses-1] == 0) avail_guesses--;
@@ -1720,7 +1721,7 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
   // if atoms change types, but aren't landlocked, that's bad
   for (int i = 0; i < twomol->natoms; i++) {
     if (twomol->type[i] != onemol->type[equivalences[i][1][myrxn]-1] && landlocked_atoms[i][myrxn] == 0)
-      error->one(FLERR,"Atom affected by reaction too close to template edge");
+      error->one(FLERR,"Bond/react: Atom affected by reaction too close to template edge");
   }
 
   // additionally, if a bond changes type, but neither involved atom is landlocked, bad
@@ -1736,7 +1737,7 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
             onemol_batom = onemol->bond_atom[onemol_atomi-1][m];
             if (onemol_batom == equivalences[twomol_atomj-1][1][myrxn]) {
               if (twomol->bond_type[i][j] != onemol->bond_type[onemol_atomi-1][m]) {
-                error->one(FLERR,"Bond type affected by reaction too close to template edge");
+                error->one(FLERR,"Bond/react: Bond type affected by reaction too close to template edge");
               }
             }
           }
@@ -1746,7 +1747,7 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
               onemol_batom = onemol->bond_atom[onemol_atomj-1][m];
               if (onemol_batom == equivalences[i][1][myrxn]) {
                 if (twomol->bond_type[i][j] != onemol->bond_type[onemol_atomj-1][m]) {
-                  error->one(FLERR,"Bond type affected by reaction too close to template edge");
+                  error->one(FLERR,"Bond/react: Bond type affected by reaction too close to template edge");
                 }
               }
             }
@@ -1762,7 +1763,7 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
       int ii = reverse_equiv[i][1][myrxn] - 1;
       for (int j = 0; j < twomol_nxspecial[ii][0]; j++) {
         if (delete_atoms[equivalences[twomol_xspecial[ii][j]-1][1][myrxn]-1][myrxn] == 0) {
-         error->one(FLERR,"A deleted atom cannot remain bonded to an atom that is not deleted");
+         error->one(FLERR,"Bond/react: A deleted atom cannot remain bonded to an atom that is not deleted");
         }
       }
     }
@@ -1773,7 +1774,7 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
     for (int i = 0; i < twomol->natoms; i++) {
       if (twomol_nxspecial[i][0] != onemol_nxspecial[equivalences[i][1][myrxn]-1][0] && landlocked_atoms[i][myrxn] == 0) {
         char str[128];
-        sprintf(str,"An atom in 'react #%d' changes bond connectivity but not atom type",myrxn+1);
+        sprintf(str,"Bond/react: An atom in 'react #%d' changes bond connectivity but not atom type",myrxn+1);
         error->warning(FLERR,str);
         break;
       }
@@ -2261,7 +2262,7 @@ void FixBondReact::update_everything()
           if (landlocked_atoms[j][rxnID] == 1) {
             for (int k = 0; k < nspecial[atom->map(update_mega_glove[jj+1][i])][2]; k++) {
               if (atom->map(special[atom->map(update_mega_glove[jj+1][i])][k]) < 0) {
-                error->all(FLERR,"Fix bond/react needs ghost atoms from further away - most likely too many processors");
+                error->all(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away - most likely too many processors");
               }
             }
           }
@@ -2322,6 +2323,8 @@ void FixBondReact::update_everything()
                   nspecial[atom->map(update_mega_glove[jj+1][i])][1]++;
                   nspecial[atom->map(update_mega_glove[jj+1][i])][2]++;
                 }
+                if (nspecial[atom->map(update_mega_glove[jj+1][i])][2] > atom->maxspecial)
+                  error->one(FLERR,"Bond/react special bond generation overflow");
                 for (int n = nspecial[atom->map(update_mega_glove[jj+1][i])][2]-1; n > insert_num; n--) {
                   special[atom->map(update_mega_glove[jj+1][i])][n] = special[atom->map(update_mega_glove[jj+1][i])][n-1];
                 }
@@ -2383,6 +2386,8 @@ void FixBondReact::update_everything()
                 bond_type[atom->map(update_mega_glove[jj+1][i])][insert_num] = twomol->bond_type[j][p];
                 bond_atom[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->bond_atom[j][p]-1][1][rxnID]][i];
                 num_bond[atom->map(update_mega_glove[jj+1][i])]++;
+                if (num_bond[atom->map(update_mega_glove[jj+1][i])] > atom->bond_per_atom)
+                  error->one(FLERR,"Bond/react topology/atom exceed system topology/atom");
                 delta_bonds++;
               }
             }
@@ -2457,6 +2462,8 @@ void FixBondReact::update_everything()
                   angle_atom2[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->angle_atom2[j][p]-1][1][rxnID]][i];
                   angle_atom3[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->angle_atom3[j][p]-1][1][rxnID]][i];
                   num_angle[atom->map(update_mega_glove[jj+1][i])]++;
+                  if (num_angle[atom->map(update_mega_glove[jj+1][i])] > atom->angle_per_atom)
+                    error->one(FLERR,"Bond/react topology/atom exceed system topology/atom");
                   delta_angle++;
                 }
               }
@@ -2538,6 +2545,8 @@ void FixBondReact::update_everything()
                   dihedral_atom3[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->dihedral_atom3[j][p]-1][1][rxnID]][i];
                   dihedral_atom4[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->dihedral_atom4[j][p]-1][1][rxnID]][i];
                   num_dihedral[atom->map(update_mega_glove[jj+1][i])]++;
+                  if (num_dihedral[atom->map(update_mega_glove[jj+1][i])] > atom->dihedral_per_atom)
+                    error->one(FLERR,"Bond/react topology/atom exceed system topology/atom");
                   delta_dihed++;
                 }
               }
@@ -2619,6 +2628,8 @@ void FixBondReact::update_everything()
                   improper_atom3[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->improper_atom3[j][p]-1][1][rxnID]][i];
                   improper_atom4[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->improper_atom4[j][p]-1][1][rxnID]][i];
                   num_improper[atom->map(update_mega_glove[jj+1][i])]++;
+                  if (num_improper[atom->map(update_mega_glove[jj+1][i])] > atom->improper_per_atom)
+                    error->one(FLERR,"Bond/react topology/atom exceed system topology/atom");
                   delta_imprp++;
                 }
               }
@@ -2716,7 +2727,7 @@ void FixBondReact::read(int myrxn)
 
   // skip 1st line of file
   eof = fgets(line,MAXLINE,fp);
-  if (eof == NULL) error->one(FLERR,"Unexpected end of superimpose file");
+  if (eof == NULL) error->one(FLERR,"Bond/react: Unexpected end of superimpose file");
 
   // read header lines
   // skip blank lines or lines that start with "#"
@@ -2770,7 +2781,7 @@ void FixBondReact::read(int myrxn)
       DeleteAtoms(line, myrxn);
     } else if (strcmp(keyword,"Constraints") == 0) {
       Constraints(line, myrxn);
-    } else error->one(FLERR,"Unknown section in superimpose file");
+    } else error->one(FLERR,"Bond/react: Unknown section in map file");
 
     parse_keyword(1,line,keyword);
 
@@ -2778,13 +2789,13 @@ void FixBondReact::read(int myrxn)
 
   // error check
   if (bondflag == 0 || equivflag == 0)
-    error->all(FLERR,"Superimpose file missing BondingIDs or Equivalences section\n");
+    error->all(FLERR,"Bond/react: Map file missing BondingIDs or Equivalences section\n");
 
   if (update_edges_flag[myrxn] == 2 && customedgesflag == 0)
-    error->all(FLERR,"Map file must have a Custom Edges section when using 'update_edges custom'\n");
+    error->all(FLERR,"Bond/react: Map file must have a Custom Edges section when using 'update_edges custom'\n");
 
   if (update_edges_flag[myrxn] != 2 && customedgesflag == 1)
-    error->all(FLERR,"Specify 'update_edges custom' to include Custom Edges section in map file\n");
+    error->all(FLERR,"Bond/react: Specify 'update_edges custom' to include Custom Edges section in map file\n");
 }
 
 void FixBondReact::EdgeIDs(char *line, int myrxn)
@@ -2830,7 +2841,7 @@ void FixBondReact::CustomEdges(char *line, int myrxn)
     else if (strcmp(edgemode,"charges") == 0)
       custom_edges[tmp-1][myrxn] = 1;
     else
-      error->one(FLERR,"Illegal value in 'Custom Edges' section of map file");
+      error->one(FLERR,"Bond/react: Illegal value in 'Custom Edges' section of map file");
   }
   delete [] edgemode;
 }
@@ -2861,7 +2872,7 @@ void FixBondReact::Constraints(char *line, int myrxn)
       constraints[myrxn][3] = tmp[2]*tmp[2]; // using square of distance
       constraints[myrxn][4] = tmp[3]*tmp[3];
     } else
-      error->one(FLERR,"Illegal constraint type in 'Constraints' section of map file");
+      error->one(FLERR,"Bond/react: Illegal constraint type in 'Constraints' section of map file");
   }
   delete [] constraint_type;
 }
@@ -2871,7 +2882,7 @@ void FixBondReact::open(char *file)
   fp = fopen(file,"r");
   if (fp == NULL) {
     char str[128];
-    snprintf(str,128,"Cannot open superimpose file %s",file);
+    snprintf(str,128,"Bond/react: Cannot open map file %s",file);
     error->one(FLERR,str);
   }
 }
@@ -2884,7 +2895,7 @@ void FixBondReact::readline(char *line)
     else n = strlen(line) + 1;
   }
   MPI_Bcast(&n,1,MPI_INT,0,world);
-  if (n == 0) error->all(FLERR,"Unexpected end of superimpose file");
+  if (n == 0) error->all(FLERR,"Bond/react: Unexpected end of map file");
   MPI_Bcast(line,n,MPI_CHAR,0,world);
 }
 

src/USER-MISC/fix_bond_react.h

@@ -189,47 +189,65 @@ Self-explanatory.  Check the input script syntax and compare to the
 documentation for the command.  You can use -echo screen as a
 command-line option when running LAMMPS to see the offending line.
 
-E: Invalid exclude group name
+E: Bond/react: Cannot use fix bond/react with non-molecular systems
 
-Exclude group name should not previously be defined.
-
-E: Cannot use fix bond/react with non-molecular systems
-
-Only systems with bonds that can be changed can be used.  Atom_style
+Only systems with bonds that can be changed can be used. Atom_style
 template does not qualify.
 
-E: Fix bond/react cutoff is longer than pairwise cutoff
+E: Bond/react: Rmax cutoff is longer than pairwise cutoff
 
-This is not allowed because bond creation is done using the
-pairwise neighbor list.
+This is not allowed because bond creation is done using the pairwise
+neighbor list.
 
-E: Molecule template ID for fix bond/react does not exist
+E: Bond/react: Molecule template ID for fix bond/react does not exist
 
-A valid molecule template must have been created with the molecule command.
+A valid molecule template must have been created with the molecule
+command.
 
-E: Superimpose file errors:
+E: Bond/react: Reaction templates must contain the same number of atoms
 
-Please ensure superimpose file is properly formatted.
+There should be a one-to-one correspondence between atoms in the
+pre-reacted and post-reacted templates, as specified by the map file.
 
-E: Atom affected by reaction too close to template edge
+E: Bond/react: Unknown section in map file
+
+Please ensure reaction map files are properly formatted.
+
+E: Bond/react: Atom affected by reaction too close to template edge
 
 This means an atom which changes type during the reaction is too close
-to an 'edge' atom defined in the superimpose file. This could cause incorrect
-assignment of bonds, angle, etc. Generally, this means you must include
-more atoms in your templates, such that there are at least two atoms
-between each atom involved in the reaction and an edge atom.
+to an 'edge' atom defined in the superimpose file. This could cause
+incorrect assignment of bonds, angle, etc. Generally, this means you
+must include more atoms in your templates, such that there are at
+least two atoms between each atom involved in the reaction and an edge
+atom.
 
-E: Fix bond/react needs ghost atoms from farther away
+E: Bond/react: Fix bond/react needs ghost atoms from farther away
 
 This is because a processor needs to superimpose the entire unreacted
-molecule template onto simulation atoms it can 'see.' The comm_modify cutoff
-command can be used to extend the communication range.
+molecule template onto simulation atoms it knows about. The
+comm_modify cutoff command can be used to extend the communication
+range.
 
-E: Excessive iteration of superimpose algorithm
+E: Bond/react: A deleted atom cannot remain bonded to an atom that is not deleted
 
-You may have discovered a bug! But first, please double check that your
-molecule template atom types, bond types, etc. are consistent with your simulation,
-and that all atoms affected by a reaction are sufficently separated from edge atoms.
-If this issue persists, please contact the developer.
+Self-explanatory.
+
+W: Bond/react: An atom in 'react #%d' changes bond connectivity but not atom type
+
+You may want to double-check that all atom types are properly assigned
+in the post-reaction template.
+
+E: Bond/react special bond generation overflow
+
+The number of special bonds per-atom created by a reaction exceeds the
+system setting. See the read_data or create_box command for how to
+specify this value.
+
+E: Bond/react topology/atom exceed system topology/atom
+
+The number of bonds, angles etc per-atom created by a reaction exceeds
+the system setting. See the read_data or create_box command for how to
+specify this value.
 
 */

src/version.h

@@ -1 +1 @@
-#define LAMMPS_VERSION "31 May 2019"
+#define LAMMPS_VERSION "5 Jun 2019"