From ac815fdfba732e46b930b686aa599df0e3f8d767 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 27 Jan 2022 22:16:43 -0500
Subject: [PATCH] use improved accessors for fixes

---
 src/KOKKOS/fix_deform_kokkos.cpp |  2 +-
 src/fix_deform.cpp               | 49 ++++++++++++--------------------
 src/fix_deform.h                 |  3 +-
 3 files changed, 20 insertions(+), 34 deletions(-)

diff --git a/src/KOKKOS/fix_deform_kokkos.cpp b/src/KOKKOS/fix_deform_kokkos.cpp
index 576e34503c..104ac41188 100644
--- a/src/KOKKOS/fix_deform_kokkos.cpp
+++ b/src/KOKKOS/fix_deform_kokkos.cpp
@@ -319,7 +319,7 @@ void FixDeformKokkos::end_of_step()
     //  if (mask[i] & groupbit)
     //    domain->x2lamda(x[i],x[i]);
 
-    if (nrigid)
+    if (rfix.size() > 0)
       error->all(FLERR,"Cannot (yet) use rigid bodies with fix deform and Kokkos");
       //for (i = 0; i < nrigid; i++)
       //  modify->fix[rfix[i]]->deform(0);
diff --git a/src/fix_deform.cpp b/src/fix_deform.cpp
index 71429ac0f8..68893701a0 100644
--- a/src/fix_deform.cpp
+++ b/src/fix_deform.cpp
@@ -45,7 +45,7 @@ enum{ONE_FROM_ONE,ONE_FROM_TWO,TWO_FROM_ONE};
 /* ---------------------------------------------------------------------- */
 
 FixDeform::FixDeform(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
-rfix(nullptr), irregular(nullptr), set(nullptr)
+irregular(nullptr), set(nullptr)
 {
   if (narg < 4) error->all(FLERR,"Illegal fix deform command");
 
@@ -127,8 +127,8 @@ rfix(nullptr), irregular(nullptr), set(nullptr)
           error->all(FLERR,"Illegal fix deform command");
         if (strstr(arg[iarg+3],"v_") != arg[iarg+3])
           error->all(FLERR,"Illegal fix deform command");
-        delete [] set[index].hstr;
-        delete [] set[index].hratestr;
+        delete[] set[index].hstr;
+        delete[] set[index].hratestr;
         set[index].hstr = utils::strdup(&arg[iarg+2][2]);
         set[index].hratestr = utils::strdup(&arg[iarg+3][2]);
         iarg += 4;
@@ -185,8 +185,8 @@ rfix(nullptr), irregular(nullptr), set(nullptr)
           error->all(FLERR,"Illegal fix deform command");
         if (strstr(arg[iarg+3],"v_") != arg[iarg+3])
           error->all(FLERR,"Illegal fix deform command");
-        delete [] set[index].hstr;
-        delete [] set[index].hratestr;
+        delete[] set[index].hstr;
+        delete[] set[index].hratestr;
         set[index].hstr = utils::strdup(&arg[iarg+2][2]);
         set[index].hratestr = utils::strdup(&arg[iarg+3][2]);
         iarg += 4;
@@ -344,7 +344,6 @@ rfix(nullptr), irregular(nullptr), set(nullptr)
     force_reneighbor = 1;
   next_reneighbor = -1;
 
-  nrigid = 0;
   flip = 0;
 
   if (force_reneighbor) irregular = new Irregular(lmp);
@@ -359,12 +358,11 @@ FixDeform::~FixDeform()
 {
   if (set) {
     for (int i = 0; i < 6; i++) {
-      delete [] set[i].hstr;
-      delete [] set[i].hratestr;
+      delete[] set[i].hstr;
+      delete[] set[i].hratestr;
     }
   }
-  delete [] set;
-  delete [] rfix;
+  delete[] set;
 
   delete irregular;
 
@@ -396,9 +394,8 @@ void FixDeform::init()
   // domain, fix nvt/sllod, compute temp/deform only work on single h_rate
 
   int count = 0;
-  for (int i = 0; i < modify->nfix; i++)
-    if (strcmp(modify->fix[i]->style,"deform") == 0) count++;
-  if (count > 1) error->all(FLERR,"More than one fix deform");
+  if (modify->get_fix_by_style("deform").size() > 1)
+    error->all(FLERR,"More than one fix deform");
 
   // Kspace setting
 
@@ -609,20 +606,12 @@ void FixDeform::init()
   }
 
   // detect if any rigid fixes exist so rigid bodies can be rescaled
-  // rfix[] = indices to each fix rigid
+  // rfix[] = vector with pointers to each fix rigid
 
-  delete [] rfix;
-  nrigid = 0;
-  rfix = nullptr;
+  rfix.clear();
 
-  for (int i = 0; i < modify->nfix; i++)
-    if (modify->fix[i]->rigid_flag) nrigid++;
-  if (nrigid) {
-    rfix = new int[nrigid];
-    nrigid = 0;
-    for (int i = 0; i < modify->nfix; i++)
-      if (modify->fix[i]->rigid_flag) rfix[nrigid++] = i;
-  }
+  for (auto ifix : modify->get_fix_list())
+    if (ifix->rigid_flag) rfix.push_back(ifix);
 }
 
 /* ----------------------------------------------------------------------
@@ -894,9 +883,8 @@ void FixDeform::end_of_step()
       if (mask[i] & groupbit)
         domain->x2lamda(x[i],x[i]);
 
-    if (nrigid)
-      for (i = 0; i < nrigid; i++)
-        modify->fix[rfix[i]]->deform(0);
+    for (auto ifix : rfix)
+      ifix->deform(0);
   }
 
   // reset global and local box to new size/shape
@@ -934,9 +922,8 @@ void FixDeform::end_of_step()
       if (mask[i] & groupbit)
         domain->lamda2x(x[i],x[i]);
 
-    if (nrigid)
-      for (i = 0; i < nrigid; i++)
-        modify->fix[rfix[i]]->deform(1);
+    for (auto ifix : rfix)
+      ifix->deform(1);
   }
 
   // redo KSpace coeffs since box has changed
diff --git a/src/fix_deform.h b/src/fix_deform.h
index c1becf58f9..90aabbd228 100644
--- a/src/fix_deform.h
+++ b/src/fix_deform.h
@@ -45,8 +45,7 @@ class FixDeform : public Fix {
   double *h_rate, *h_ratelo;
   int varflag;                   // 1 if VARIABLE option is used, 0 if not
   int kspace_flag;               // 1 if KSpace invoked, 0 if not
-  int nrigid;                    // number of rigid fixes
-  int *rfix;                     // indices of rigid fixes
+  std::vector<Fix *> rfix;       // pointers to rigid fixes
   class Irregular *irregular;    // for migrating atoms after box flips
 
   double TWOPI;