Merge pull request #1361 from akohlmey/collected-small-changes

Collected small changes for the next patch release

.github/PULL_REQUEST_TEMPLATE.md

@@ -4,7 +4,7 @@ _Briefly describe the new feature(s), enhancement(s), or bugfix(es) included in
 
 **Related Issues**
 
-__If this addresses an open GitHub Issue, mention the issue number here. Use the phrases `fixes #221` or `closes #135`, when you want those issues to be automatically closed when the pull request is merged_
+_If this addresses an open GitHub issue for this project, please mention the issue number here, and describe the relation. Use the phrases `fixes #221` or `closes #135`, when you want an issue to be automatically closed when the pull request is merged_
 
 **Author(s)**
 
@@ -16,15 +16,15 @@ By submitting this pull request, I agree, that my contribution will be included
 
 **Backward Compatibility**
 
-_Please state whether any changes in the pull request break backward compatibility for inputs, and - if yes - explain what has been changed and why_
+_Please state whether any changes in the pull request will break backward compatibility for inputs, and - if yes - explain what has been changed and why_
 
 **Implementation Notes**
 
 _Provide any relevant details about how the changes are implemented, how correctness was verified, how other features - if any - in LAMMPS are affected_
 
 **Post Submission Checklist**
 
-_Please check the fields below as they are completed **after** the pull request has been submitted_
+_Please check the fields below as they are completed **after** the pull request has been submitted. Delete lines that don't apply_
 
 - [ ] The feature or features in this pull request is complete
 - [ ] Licensing information is complete

cmake/CMakeLists.txt

@@ -1336,26 +1336,20 @@ set(temp_git_commit "(unknown)")
 set(temp_git_branch "(unknown)")
 set(temp_git_describe "(unknown)")
 set(temp_git_info "false")
-if(GIT_FOUND)
-  execute_process(COMMAND ${GIT_EXECUTABLE} describe HEAD
-    RESULT_VARIABLE temp_in_git_checkout
+if(GIT_FOUND AND EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/../.git)
+  set(temp_git_info "true")
+  execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/../.git rev-parse HEAD
+    OUTPUT_VARIABLE temp_git_commit
+    ERROR_QUIET
+    OUTPUT_STRIP_TRAILING_WHITESPACE)
+  execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/../.git rev-parse --abbrev-ref HEAD
+    OUTPUT_VARIABLE temp_git_branch
+    ERROR_QUIET
+    OUTPUT_STRIP_TRAILING_WHITESPACE)
+  execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/../.git describe --dirty=-modified
+    OUTPUT_VARIABLE temp_git_describe
     ERROR_QUIET
     OUTPUT_STRIP_TRAILING_WHITESPACE)
-  if(temp_in_git_checkout EQUAL 0)
-    set(temp_git_info "true")
-    execute_process(COMMAND ${GIT_EXECUTABLE} rev-parse HEAD
-      OUTPUT_VARIABLE temp_git_commit
-      ERROR_QUIET
-      OUTPUT_STRIP_TRAILING_WHITESPACE)
-    execute_process(COMMAND ${GIT_EXECUTABLE} rev-parse --abbrev-ref HEAD
-      OUTPUT_VARIABLE temp_git_branch
-      ERROR_QUIET
-      OUTPUT_STRIP_TRAILING_WHITESPACE)
-    execute_process(COMMAND ${GIT_EXECUTABLE} describe --dirty=-modified
-      OUTPUT_VARIABLE temp_git_describe
-      ERROR_QUIET
-      OUTPUT_STRIP_TRAILING_WHITESPACE)
-  endif()
 endif()
 
 set(temp "${temp}const bool LAMMPS_NS::LAMMPS::has_git_info = ${temp_git_info};\n")

src/.gitignore

@@ -6,6 +6,7 @@
 
 /style_*.h
 /lmpinstalledpkgs.h
+/lmpgitversion.h
 
 /*_gpu.h
 /*_gpu.cpp

src/Makefile

@@ -171,7 +171,7 @@ gitversion:
 	@echo 'Gathering git version information'
 	@echo '#ifndef LMP_GIT_VERSION_H' >  ${TMPNAME}.lmpgitversion
 	@echo '#define LMP_GIT_VERSION_H' >> ${TMPNAME}.lmpgitversion
-	@if (type git && git describe HEAD ) >> /dev/null 2>> /dev/null ; then \
+	@if (type git && test -e ../.git ) >> /dev/null 2>> /dev/null ; then \
 	  git='true';					\
 	  commit=$$(git rev-parse HEAD);		\
 	  branch=$$(git rev-parse --abbrev-ref HEAD);	\

src/USER-BOCS/fix_bocs.cpp

@@ -697,6 +697,11 @@ int FixBocs::read_F_table( char *filename, int p_basis_type )
                                     "of %d in read_F_table",p_basis_type);
     error->all(FLERR,errmsg);
   }
+  // cleanup
+  for (i = 0; i < N_columns; ++i) {
+    free(data[i]);
+  }
+  free(data);
   return n_entries;
 }
 

src/group.cpp

@@ -207,6 +207,12 @@ void Group::assign(int narg, char **arg)
     else if (strcmp(arg[1],"molecule") == 0) category = MOLECULE;
     else if (strcmp(arg[1],"id") == 0) category = ID;
 
+    if ((category == MOLECULE) && (!atom->molecular))
+      error->all(FLERR,"Group command requires atom attribute molecule");
+
+    if ((category == ID) && (!atom->tag_enable))
+      error->all(FLERR,"Group command requires atom IDs");
+
     // args = logical condition
 
     if (narg > 3 &&
@@ -362,10 +368,13 @@ void Group::assign(int narg, char **arg)
   } else if (strcmp(arg[1],"include") == 0) {
 
     if (narg != 3) error->all(FLERR,"Illegal group command");
-    if (strcmp(arg[2],"molecule") != 0)
-      error->all(FLERR,"Illegal group command");
+    if (strcmp(arg[2],"molecule") == 0) {
+      if (!atom->molecular)
+        error->all(FLERR,"Group command requires atom attribute molecule");
+
+      add_molecules(igroup,bit);
 
-    add_molecules(igroup,bit);
+    } else error->all(FLERR,"Illegal group command");
 
   // style = subtract