From 32b967ed9c2871507291d5c85ab80baaa42d104e Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 13 Jun 2017 16:26:49 -0400
Subject: [PATCH] add rigid body overlap warnings to change_box and
 delete_atoms

---
 src/change_box.cpp     |  3 +++
 src/delete_atoms.cpp   | 21 +++++++++++++++------
 src/displace_atoms.cpp |  2 +-
 3 files changed, 19 insertions(+), 7 deletions(-)

diff --git a/src/change_box.cpp b/src/change_box.cpp
index add1fe1d0a..c6ec078a01 100644
--- a/src/change_box.cpp
+++ b/src/change_box.cpp
@@ -316,6 +316,9 @@ void ChangeBox::command(int narg, char **arg)
 
     } else if (ops[m].style == REMAP) {
 
+      if (modify->check_rigid_group_overlap(groupbit))
+        error->warning(FLERR,"Attempting to remap atoms in rigid bodies");
+
       // convert atoms to lamda coords, using last box state
       // convert atoms back to box coords, using current box state
       // save current box state
diff --git a/src/delete_atoms.cpp b/src/delete_atoms.cpp
index 116c2a2f1e..85bd6f88dd 100644
--- a/src/delete_atoms.cpp
+++ b/src/delete_atoms.cpp
@@ -69,6 +69,15 @@ void DeleteAtoms::command(int narg, char **arg)
   else if (strcmp(arg[0],"porosity") == 0) delete_porosity(narg,arg);
   else error->all(FLERR,"Illegal delete_atoms command");
 
+  if (allflag) {
+    int igroup = group->find("all");
+    if ((igroup >= 0) && modify->check_rigid_group_overlap(group->bitmask[igroup]))
+      error->warning(FLERR,"Attempting to delete atoms in rigid bodies");
+  } else {
+    if (modify->check_rigid_list_overlap(dlist))
+      error->warning(FLERR,"Attempting to delete atoms in rigid bodies");
+  }
+
   // if allflag = 1, just reset atom->nlocal
   // else delete atoms one by one
 
@@ -89,16 +98,16 @@ void DeleteAtoms::command(int narg, char **arg)
     int i = 0;
     while (i < nlocal) {
       if (dlist[i]) {
-	avec->copy(nlocal-1,i,1);
-	dlist[i] = dlist[nlocal-1];
-	nlocal--;
+        avec->copy(nlocal-1,i,1);
+        dlist[i] = dlist[nlocal-1];
+        nlocal--;
       } else i++;
     }
-    
+
     atom->nlocal = nlocal;
     memory->destroy(dlist);
   }
-  
+
   // if non-molecular system and compress flag set,
   // reset atom tags to be contiguous
   // set all atom IDs to 0, call tag_extend()
@@ -201,7 +210,7 @@ void DeleteAtoms::delete_group(int narg, char **arg)
     allflag = 1;
     return;
   }
-  
+
   // allocate and initialize deletion list
 
   int nlocal = atom->nlocal;
diff --git a/src/displace_atoms.cpp b/src/displace_atoms.cpp
index 9efb9c8f65..a9aa5cf855 100644
--- a/src/displace_atoms.cpp
+++ b/src/displace_atoms.cpp
@@ -76,7 +76,7 @@ void DisplaceAtoms::command(int narg, char **arg)
   groupbit = group->bitmask[igroup];
 
   if (modify->check_rigid_group_overlap(groupbit))
-    error->warning(FLERR,"Displacing atoms in rigid bodies");
+    error->warning(FLERR,"Attempting to displace atoms in rigid bodies");
 
   int style = -1;
   if (strcmp(arg[1],"move") == 0) style = MOVE;