Updated name of intemolecular exclusions function

A follow-up commit for change I35073ad69752e22968c0e2821e2fdf9f0c465b2a
changes names as it was suggested in the review.

Change-Id: If6b12c1d04973556d85a1c01d6f3cbb9b8b4d5f5

diff --git a/src/gromacs/domdec/domdec_topology.cpp b/src/gromacs/domdec/domdec_topology.cpp
index 2140716d12a57dc6ecb7919abbcda0c4819efa3e..91da3d3357e6a160ddc71ee3e747e03ea076c7a1 100644 (file)
--- a/src/gromacs/domdec/domdec_topology.cpp
+++ b/src/gromacs/domdec/domdec_topology.cpp
@@ -1995,7 +1995,7 @@ static int make_local_bondeds_excls(gmx_domdec_t *dd,
                         make_exclusions_zone(dd, zones, mtop->moltype, cginfo,
                                              excl_t, izone, cg0t,
                                              cg1t,
-                                             mtop->intermolecularExclusions);
+                                             mtop->intermolecularExclusionGroup);
                     }
                     else
                     {

diff --git a/src/gromacs/mdrun/mimic.cpp b/src/gromacs/mdrun/mimic.cpp
index 75141946183488d81b6f9b710383f1dab81a7908..62ef97ac80dd7a0177ed4ae9ae6311757fd2b295 100644 (file)
--- a/src/gromacs/mdrun/mimic.cpp
+++ b/src/gromacs/mdrun/mimic.cpp
@@ -225,9 +225,9 @@ void gmx::Integrator::do_mimic()
         ir->nsteps = mimicCommunicator.getStepNumber();
     }
 
-    ir->nstxout_compressed               = 0;
-    groups                               = &top_global->groups;
-    top_global->intermolecularExclusions = genQmmmIndices(*top_global);
+    ir->nstxout_compressed                   = 0;
+    groups                                   = &top_global->groups;
+    top_global->intermolecularExclusionGroup = genQmmmIndices(*top_global);
 
     /* Initial values */
     init_rerun(fplog, cr, outputProvider, ir, oenv, mdrunOptions,

diff --git a/src/gromacs/mdrun/rerun.cpp b/src/gromacs/mdrun/rerun.cpp
index 815fbc5908581d63aefd5637424cd43aaaa762f7..db5d1e255b6c40afa5e5eb7802a251e4ac28a938 100644 (file)
--- a/src/gromacs/mdrun/rerun.cpp
+++ b/src/gromacs/mdrun/rerun.cpp
@@ -280,7 +280,7 @@ void gmx::Integrator::do_rerun()
     groups                 = &top_global->groups;
     if (ir->eI == eiMimic)
     {
-        top_global->intermolecularExclusions = genQmmmIndices(*top_global);
+        top_global->intermolecularExclusionGroup = genQmmmIndices(*top_global);
     }
 
     /* Initial values */

diff --git a/src/gromacs/topology/mtop_util.cpp b/src/gromacs/topology/mtop_util.cpp
index 86895d7981836d81dc755403e8ca96c0b75bffb5..0ed126bb0207ae5e38a4133babe5cd5b9ded564f 100644 (file)
--- a/src/gromacs/topology/mtop_util.cpp
+++ b/src/gromacs/topology/mtop_util.cpp
@@ -1051,10 +1051,10 @@ static void copyExclsFromMtop(const gmx_mtop_t &mtop,
 /*! \brief Updates inter-molecular exclusion lists
  *
  * This function updates inter-molecular exclusions to exclude all
- * non-bonded interactions between QM atoms
+ * non-bonded interactions between a given list of atoms
  *
  * \param[inout]    excls   existing exclusions in local topology
- * \param[in]       ids     list of global QM atoms IDs
+ * \param[in]       ids     list of global IDs of atoms
  */
 static void addMimicExclusions(t_blocka                      *excls,
                                const gmx::ArrayRef<const int> ids)
@@ -1121,10 +1121,10 @@ static void gen_local_top(const gmx_mtop_t  &mtop,
     copyIdefFromMtop(mtop, &top->idef, freeEnergyInteractionsAtEnd, bMergeConstr);
     copyCgsFromMtop(mtop, &top->cgs);
     copyExclsFromMtop(mtop, &top->excls);
-    if (!mtop.intermolecularExclusions.empty())
+    if (!mtop.intermolecularExclusionGroup.empty())
     {
         addMimicExclusions(&top->excls,
-                           mtop.intermolecularExclusions);
+                           mtop.intermolecularExclusionGroup);
     }
 }
 

diff --git a/src/gromacs/topology/topology.h b/src/gromacs/topology/topology.h
index 63969db13d995a635805517fe49df51cdbe9fbc8..4c7da94216bf16f47466c0198b7dbce4404273e9 100644 (file)
--- a/src/gromacs/topology/topology.h
+++ b/src/gromacs/topology/topology.h
@@ -163,7 +163,7 @@ struct gmx_mtop_t //NOLINT(clang-analyzer-optin.performance.Padding)
     /*! \brief List of global atom indices of atoms between which
      * non-bonded interactions must be excluded.
      */
-    std::vector<int>                  intermolecularExclusions;
+    std::vector<int>                  intermolecularExclusionGroup;
 
     /* Derived data  below */
     //! Indices for each molblock entry for fast lookup of atom properties