add delete_atoms "variable" option

doc/src/delete_atoms.rst

@@ -10,7 +10,7 @@ Syntax
 
    delete_atoms style args keyword value ...
 
-* style = *group* or *region* or *overlap* or *porosity*
+* style = *group* or *region* or *overlap* or *porosity* or *variable*
 
   .. parsed-literal::
 
@@ -26,6 +26,7 @@ Syntax
                      or NULL to only impose the group criterion
          fraction = delete this fraction of atoms
          seed = random number seed (positive integer)
+       *variable* args = variable-name
 
 * zero or more keyword/value pairs may be appended
 * keyword = *compress* or *bond* or *mol*
@@ -47,6 +48,7 @@ Examples
    delete_atoms overlap 0.5 solvent colloid
    delete_atoms porosity all cube 0.1 482793 bond yes
    delete_atoms porosity polymer cube 0.1 482793 bond yes
+   detele_atoms variable checkers
 
 Description
 """""""""""
@@ -91,6 +93,13 @@ guarantee that the exact fraction of atoms will be deleted, or that
 the same atoms will be deleted when running on different numbers of
 processors.
 
+For style *variable*, all atoms for which the atom-style variable with
+the given name evaluates to non-zero will be deleted. Additional atoms
+can be deleted if they are in a molecule for which one or more atoms
+were deleted within the region; see the *mol* keyword discussion below.
+This options allows to apply complex selections of atoms not covered
+by the options listed above.
+
 If the *compress* keyword is set to *yes*, then after atoms are
 deleted, then atom IDs are re-assigned so that they run from 1 to the
 number of atoms in the system.  Note that this is not done for

src/delete_atoms.cpp

@@ -24,6 +24,8 @@
 #include "domain.h"
 #include "error.h"
 #include "force.h"
+#include "input.h"
+#include "variable.h"
 #include "group.h"
 #include "memory.h"
 #include "modify.h"
@@ -69,7 +71,8 @@ void DeleteAtoms::command(int narg, char **arg)
   else if (strcmp(arg[0],"region") == 0) delete_region(narg,arg);
   else if (strcmp(arg[0],"overlap") == 0) delete_overlap(narg,arg);
   else if (strcmp(arg[0],"porosity") == 0) delete_porosity(narg,arg);
-  else error->all(FLERR,"Illegal delete_atoms command");
+  else if (strcmp(arg[0],"variable") == 0) delete_variable(narg,arg);
+  else error->all(FLERR,"Unknown delete_atoms sub-command: {}", arg[0]);
 
   if (allflag) {
     int igroup = group->find("all");
@@ -453,6 +456,38 @@ void DeleteAtoms::delete_porosity(int narg, char **arg)
   delete random;
 }
 
+/* ----------------------------------------------------------------------
+   delete all as flagged by non-zero atom style variable
+------------------------------------------------------------------------- */
+
+void DeleteAtoms::delete_variable(int narg, char **arg)
+{
+  if (narg < 2) utils::missing_cmd_args(FLERR,"delete_atoms variable", error);
+
+  int ivar = input->variable->find(arg[1]);
+  if (ivar < 0) error->all(FLERR, "Variable name {} for delete_atoms does not exist", arg[1]);
+  if (!input->variable->atomstyle(ivar))
+    error->all(FLERR,"Variable {} for delete_atoms is invalid style", arg[1]);
+
+  // consume remaining options
+
+  options(narg-2,&arg[2]);
+
+  // aflag = evaluation of per-atom variable
+
+  const int nlocal = atom->nlocal;
+  double *aflag;
+  memory->create(dlist,nlocal,"delete_atoms:dlist");
+  memory->create(aflag,nlocal,"group:aflag");
+  input->variable->compute_atom(ivar,0,aflag,1,0);
+
+  // delete if per-atom variable evaluated to non-zero
+
+  for (int i = 0; i < nlocal; i++) dlist[i] = (aflag[i] == 0.0) ? 0 : 1;
+
+  memory->destroy(aflag);
+}
+
 /* ----------------------------------------------------------------------
    delete all topology interactions that include deleted atoms
 ------------------------------------------------------------------------- */

src/delete_atoms.h

@@ -39,6 +39,7 @@ class DeleteAtoms : public Command {
   void delete_region(int, char **);
   void delete_overlap(int, char **);
   void delete_porosity(int, char **);
+  void delete_variable(int, char **);
 
   void delete_bond();
   void delete_molecule();