Refactor t_param to InteractionType

[alexxy/gromacs.git] / src / gromacs / gmxpreprocess / topio.cpp

diff --git a/src/gromacs/gmxpreprocess/topio.cpp b/src/gromacs/gmxpreprocess/topio.cpp
index eb0beb201ff79da20a7147af3b6004a9d8a9da54..ca630939fff2dff1a009d7f29e5b743f6749ef88 100644 (file)
--- a/src/gromacs/gmxpreprocess/topio.cpp
+++ b/src/gromacs/gmxpreprocess/topio.cpp
@@ -88,13 +88,12 @@
 static void gen_pairs(const InteractionTypeParameters &nbs, InteractionTypeParameters *pairs, real fudge, int comb)
 {
     real    scaling;
-    int     ntp       = nbs.nr;
+    int     ntp       = nbs.size();
     int     nnn       = static_cast<int>(std::sqrt(static_cast<double>(ntp)));
     GMX_ASSERT(nnn * nnn == ntp, "Number of pairs of generated non-bonded parameters should be a perfect square");
     int     nrfp      = NRFP(F_LJ);
     int     nrfpA     = interaction_function[F_LJ14].nrfpA;
     int     nrfpB     = interaction_function[F_LJ14].nrfpB;
-    pairs->nr = ntp;
 
     if ((nrfp  != nrfpA) || (nrfpA != nrfpB))
     {
@@ -102,17 +101,18 @@ static void gen_pairs(const InteractionTypeParameters &nbs, InteractionTypeParam
     }
 
     fprintf(stderr, "Generating 1-4 interactions: fudge = %g\n", fudge);
-    snew(pairs->param, pairs->nr);
-    for (int i = 0; (i < ntp); i++)
+    pairs->interactionTypes.clear();
+    int                             i = 0;
+    std::array<int, 2>              atomNumbers;
+    std::array<real, MAXFORCEPARAM> forceParam = {NOTSET};
+    for (const auto &type : nbs.interactionTypes)
     {
-        /* Copy param.a */
-        pairs->param[i].a[0] = i / nnn;
-        pairs->param[i].a[1] = i % nnn;
+        /* Copy type.atoms */
+        atomNumbers = {i / nnn, i % nnn };
         /* Copy normal and FEP parameters and multiply by fudge factor */
-
-
-
-        for (int j = 0; (j < nrfp); j++)
+        gmx::ArrayRef<const real> existingParam = type.forceParam();
+        GMX_RELEASE_ASSERT(2*nrfp <= MAXFORCEPARAM, "Can't have more parameters than half of maximum p  arameter number");
+        for (int j = 0; j < nrfp; j++)
         {
             /* If we are using sigma/epsilon values, only the epsilon values
              * should be scaled, but not sigma.
@@ -127,13 +127,11 @@ static void gen_pairs(const InteractionTypeParameters &nbs, InteractionTypeParam
                 scaling = fudge;
             }
 
-            pairs->param[i].c[j]      = scaling*nbs.param[i].c[j];
-            /* NOTE: this should be clear to the compiler, but some gcc 5.2 versions
-             *  issue false positive warnings for the pairs->param.c[] indexing below.
-             */
-            assert(2*nrfp <= MAXFORCEPARAM);
-            pairs->param[i].c[nrfp+j] = scaling*nbs.param[i].c[j];
+            forceParam[j]      = scaling*existingParam[j];
+            forceParam[nrfp+j] = scaling*existingParam[j];
         }
+        pairs->interactionTypes.emplace_back(InteractionType(atomNumbers, forceParam));
+        i++;
     }
 }