git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14823 f3b2605a-c512-4ea7-a41b-209d697bcdaa

lib/colvars/colvaratoms.cpp

@@ -634,9 +634,11 @@ int cvm::atom_group::parse_fitting_options(std::string const &group_conf)
       if (get_keyval(group_conf, "refPositionsCol", ref_pos_col, std::string(""))) {
         // if provided, use PDB column to select coordinates
         bool found = get_keyval(group_conf, "refPositionsColValue", ref_pos_col_value, 0.0);
-        if (found && ref_pos_col_value == 0.0)
+        if (found && ref_pos_col_value == 0.0) {
           cvm::error("Error: refPositionsColValue, "
                      "if provided, must be non-zero.\n", INPUT_ERROR);
+          return COLVARS_ERROR;
+        }
       } else {
         // if not, rely on existing atom indices for the group
         group_for_fit->create_sorted_ids();

lib/colvars/colvarcomp_distances.cpp

@@ -862,14 +862,20 @@ colvar::rmsd::rmsd(std::string const &conf)
       } else {
         // if not, rely on existing atom indices for the group
         atoms.create_sorted_ids();
+        ref_pos.resize(atoms.size());
       }
 
-      ref_pos.resize(atoms.size());
       cvm::load_coords(ref_pos_file.c_str(), ref_pos, atoms.sorted_ids,
                         ref_pos_col, ref_pos_col_value);
     }
   }
 
+  if (ref_pos.size() != atoms.size()) {
+    cvm::error("Error: found " + cvm::to_str(ref_pos.size()) +
+                    " reference positions; expected " + cvm::to_str(atoms.size()));
+    return;
+  }
+
   if (atoms.b_user_defined_fit) {
     cvm::log("WARNING: explicit fitting parameters were provided for atom group \"atoms\".");
   } else {
@@ -1062,6 +1068,12 @@ colvar::eigenvector::eigenvector(std::string const &conf)
     }
   }
 
+  if (ref_pos.size() != atoms.size()) {
+    cvm::error("Error: reference positions were not provided, or do not "
+                      "match the number of requested atoms.\n");
+    return;
+  }
+
   // save for later the geometric center of the provided positions (may not be the origin)
   cvm::rvector ref_pos_center(0.0, 0.0, 0.0);
   for (size_t i = 0; i < atoms.size(); i++) {

lib/colvars/colvarmodule.cpp

@@ -31,6 +31,8 @@ colvarmodule::colvarmodule(colvarproxy *proxy_in)
   cvm::log(cvm::line_marker);
   cvm::log("Initializing the collective variables module, version "+
            cvm::to_str(COLVARS_VERSION)+".\n");
+  cvm::log("Please cite Fiorin et al, Mol Phys 2013 in any publication "
+           "based on this calculation.\n");
 
   // set initial default values
 

lib/colvars/colvarmodule.h

@@ -4,7 +4,7 @@
 #define COLVARMODULE_H
 
 #ifndef COLVARS_VERSION
-#define COLVARS_VERSION "2016-02-28"
+#define COLVARS_VERSION "2016-03-08"
 #endif
 
 #ifndef COLVARS_DEBUG

lib/kim/Makefile.lammps

@@ -15,6 +15,12 @@
 
 # Settings that the LAMMPS build will import when this package is installed
 
-kim_SYSINC  = $(shell kim-api-build-config --includes)
-kim_SYSLIB  = $(shell kim-api-build-config --ldlibs)
-kim_SYSPATH = $(shell kim-api-build-config --ldflags)
+
+KIM_CONFIG_HELPER = kim-api-build-config
+ifeq ($(shell $(KIM_CONFIG_HELPER) --version 2> /dev/null),)
+  $(error $(KIM_CONFIG_HELPER) utility is not available.  Something is wrong with your KIM API package setup)
+endif
+
+kim_SYSINC  = $(shell $(KIM_CONFIG_HELPER) --includes)
+kim_SYSLIB  = $(shell $(KIM_CONFIG_HELPER) --ldlibs)
+kim_SYSPATH = $(shell $(KIM_CONFIG_HELPER) --ldflags)

lib/kim/pair-kim.release.info

@@ -1,6 +1,6 @@
-This package (pair-kim-v1.7.2) created from commit
+This package (pair-kim-v1.7.2+1) created from commit
 
-ff907f94d1ae99114c12155f7f175ab63aa32b39
+ced1275c5fd5b382cb9bd39e44ed1324c7c85e99
 
 of the pair-kim git repository
-By Ryan S. Elliott (relliott@umn.edu) on Sun Jun 28 20:16:30 EDT 2015.
+By Ryan S. Elliott (relliott@umn.edu) on Mon Feb 22 14:59:53 CST 2016.

lib/meam/Makefile.g95

@@ -44,6 +44,7 @@ lib: 	$(OBJ)
 %.o:%.F
 	$(F90) $(F90FLAGS) -c $<
 
+include .depend
 # ------ CLEAN ------
 
 clean:

lib/meam/Makefile.gfortran

@@ -47,6 +47,10 @@ lib: 	$(OBJ)
 %.o:%.F
 	$(F90) $(F90FLAGS) -c $<
 
+%.o:%.c
+	$(CC) $(F90FLAGS) -c $<
+
+include .depend
 # ------ CLEAN ------
 
 clean:

lib/meam/Makefile.ifort

@@ -44,6 +44,7 @@ lib: 	$(OBJ)
 %.o:%.F
 	$(F90) $(F90FLAGS) -c $<
 
+include .depend
 # ------ CLEAN ------
 
 clean:

lib/meam/Makefile.mingw32-cross

@@ -55,6 +55,10 @@ $(LIB):  $(OBJ)
 $(DIR)%.o:%.F
 	$(F90) $(F90FLAGS) -c $< -o $@
 
+$(DIR)%.o:%.c
+	$(F90) $(F90FLAGS) -c $< -o $@
+
+include .depend
 # ------ CLEAN ------
 
 clean:

lib/meam/Makefile.mingw64-cross

@@ -55,6 +55,10 @@ $(LIB):  $(OBJ)
 $(DIR)%.o:%.F
 	$(F90) $(F90FLAGS) -c $< -o $@
 
+$(DIR)%.o:%.c
+	$(F90) $(F90FLAGS) -c $< -o $@
+
+include .depend
 # ------ CLEAN ------
 
 clean:

lib/meam/Makefile.pgf90

@@ -44,6 +44,7 @@ lib: 	$(OBJ)
 %.o:%.F
 	$(F90) $(F90FLAGS) -c $<
 
+include .depend
 # ------ CLEAN ------
 
 clean:

lib/meam/Makefile.tbird

@@ -46,6 +46,7 @@ lib: 	$(OBJ)
 %.o:%.F
 	$(F90) $(F90FLAGS) -c $<
 
+include .depend
 # ------ CLEAN ------
 
 clean: