Use ListOfLists for atom to constraint mapping

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

diff --git a/src/gromacs/gmxpreprocess/grompp.cpp b/src/gromacs/gmxpreprocess/grompp.cpp
index 735b5c37d67350b6bc66e4970ed13fe00d2276ff..21f967e02a1c4764183ee2337d0cde5630b3d0ee 100644 (file)
--- a/src/gromacs/gmxpreprocess/grompp.cpp
+++ b/src/gromacs/gmxpreprocess/grompp.cpp
@@ -102,6 +102,7 @@
 #include "gromacs/utility/futil.h"
 #include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/keyvaluetreebuilder.h"
+#include "gromacs/utility/listoflists.h"
 #include "gromacs/utility/mdmodulenotification.h"
 #include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/snprintf.h"
@@ -1426,7 +1427,7 @@ static bool haveDecoupledModeInMol(const gmx_moltype_t&           molt,
 
     const t_atom* atom = molt.atoms.atom;
 
-    t_blocka atomToConstraints =
+    const auto atomToConstraints =
             gmx::make_at2con(molt, iparams, gmx::FlexibleConstraintTreatment::Exclude);
 
     bool haveDecoupledMode = false;
@@ -1456,23 +1457,21 @@ static bool haveDecoupledModeInMol(const gmx_moltype_t&           molt,
                 int a1 = il.iatoms[1 + i + 1];
                 int a2 = il.iatoms[1 + i + 2];
                 if ((atom[a0].m > atom[a2].m * massFactorThreshold || atom[a2].m > atom[a0].m * massFactorThreshold)
-                    && atomToConstraints.index[a0 + 1] - atomToConstraints.index[a0] == 1
-                    && atomToConstraints.index[a2 + 1] - atomToConstraints.index[a2] == 1
-                    && atomToConstraints.index[a1 + 1] - atomToConstraints.index[a1] >= 3)
+                    && atomToConstraints[a0].ssize() == 1 && atomToConstraints[a2].ssize() == 1
+                    && atomToConstraints[a1].ssize() >= 3)
                 {
-                    int constraint0 = atomToConstraints.a[atomToConstraints.index[a0]];
-                    int constraint2 = atomToConstraints.a[atomToConstraints.index[a2]];
+                    int constraint0 = atomToConstraints[a0][0];
+                    int constraint2 = atomToConstraints[a2][0];
 
                     bool foundAtom0 = false;
                     bool foundAtom2 = false;
-                    for (int conIndex = atomToConstraints.index[a1];
-                         conIndex < atomToConstraints.index[a1 + 1]; conIndex++)
+                    for (const int constraint : atomToConstraints[a1])
                     {
-                        if (atomToConstraints.a[conIndex] == constraint0)
+                        if (constraint == constraint0)
                         {
                             foundAtom0 = true;
                         }
-                        if (atomToConstraints.a[conIndex] == constraint2)
+                        if (constraint == constraint2)
                         {
                             foundAtom2 = true;
                         }
@@ -1486,8 +1485,6 @@ static bool haveDecoupledModeInMol(const gmx_moltype_t&           molt,
         }
     }
 
-    done_blocka(&atomToConstraints);
-
     return haveDecoupledMode;
 }