Simplify and optimize coordination numbers

.github/workflows/backend-template.yml

@@ -121,9 +121,6 @@ jobs:
           ref: 'master'
           path: 'devel-tools/packages'
 
-      - name: Test build recipes
-        run: bash devel-tools/check_build_recipes
-
       - name: Build and test standalone library
         run: cmake -P devel-tools/build_test_library.cmake
 

.github/workflows/test-library.yml

@@ -39,9 +39,6 @@ jobs:
       #   run: |
       #     sudo apt -y install ccache
 
-      - name: Test build recipes
-        run: bash devel-tools/check_build_recipes
-
       - name: Convert BibTeX references to code
         shell: bash
         working-directory: doc

devel-tools/generate-namd-makefile.sh

@@ -1,9 +1,11 @@
 #!/bin/bash
 
+set -e
+
 # Generate a file suitable for inclusion by the NAMD Makefile
 
 if [ -f "${2}" ] ; then
-    echo "Usage: ${0} <sources_var_name> <sources_path> <objs_var_name> <obj_path> [... source files ...]" >& 1
+    echo "Usage: ${0} <sources_var_name> <sources_path> <objs_var_name> <obj_path> [... source files ...]" >& 2
     exit 1
 fi
 

devel-tools/generate-vmd-makefile.sh

@@ -0,0 +1,87 @@
+#!/bin/bash
+
+set -e
+
+# Generate the file colvars_files.pl used by VMD (i.e. a poor person's version of a dependency file)
+
+if [ ! -f "${1}" ] ; then
+    echo "Usage: ${0} [... source files ...] [... header files ...]" >& 2
+    exit 1
+fi
+
+all_files=("${@}")
+
+
+canonize_filename() {
+    local file=$1
+    if [ "${file%.cpp}" != "${file}" ] ; then
+        basename "${file%.cpp}.C"
+    else
+        basename "${file}"
+    fi
+}
+
+source_files=()
+header_files=()
+cuda_files=()
+for file in "${all_files[@]}" ; do
+    if [ "${file%.cpp}" != "${file}" ] ; then
+        source_files+=($(canonize_filename "${file}"))
+    elif [ "${file%.C}" != "${file}" ] ; then
+        source_files+=($(canonize_filename "${file}"))
+    elif [ "${file%.h}" != "${file}" ] ; then
+        header_files+=($(canonize_filename "${file}"))
+    elif [ "${file%.cu}" != "${file}" ] ; then
+        echo "Error: building of Colvars CUDA files with VMD is not supported yet" >&2
+        # cuda_files+=($(canonize_filename "${file}"))
+    else
+        echo "Error: file ${file} has an unsupported extension" >&2
+        exit 1
+    fi
+done
+
+cat <<EOF
+# List of files for the Colvars module
+
+our ( \$colvars_defines );
+
+our ( @colvars_cc );
+our ( @colvars_cu );
+our ( @colvars_ccpp );
+our ( @colvars_h );
+
+\$colvars_defines = " -DVMDCOLVARS";
+
+@colvars_cc = ();
+EOF
+
+
+print_list() {
+    local var_name=$1
+    shift
+    local -a files=($(echo "${@}" | tr ' ' '\n' | sort | xargs))
+    echo "@${var_name} = ("
+    for file in "${files[@]:0:${#files[@]}-1}" ; do
+        echo "    '${file}',"
+    done
+    echo "    '${files[${#files[@]}-1]}'"
+    echo "    );"
+}
+
+if [ -n "${cuda_files}" ] ; then
+    print_list "colvars_cu" "${cuda_files[@]}"
+else
+    echo "@colvars_cu = ();"
+fi
+
+if [ -n "${source_files}" ] ; then
+    print_list "colvars_ccpp" "${source_files[@]}"
+else
+    echo "@colvars_ccpp = ();"
+fi
+
+if [ -n "${header_files}" ] ; then
+    print_list "colvars_h" "${header_files[@]}"
+else
+    echo "@colvars_h = ();"
+fi

doc/colvars-refman-main.tex

@@ -1966,6 +1966,19 @@
     12}{%
     This number defines the $m$ exponent for the switching function.}
 
+\item %
+  \labelkey{colvar|coordNum|group1CenterOnly}
+  \keydef
+    {group1CenterOnly}{%
+    \texttt{coordNum}}{%
+    Use only \texttt{group1}'s center of
+    mass}{%
+    boolean}{%
+    \texttt{off}}{%
+    If this option is \texttt{on}, only contacts between the center of mass of \texttt{group1} and atoms of \texttt{group2} are calculated (by default, the sum extends over all pairs of atoms in \texttt{group1} and \texttt{group2}).
+    If \texttt{group1} is a \texttt{dummyAtom}, this option is set to \texttt{yes} by default.
+}
+
 \item %
   \labelkey{colvar|coordNum|group2CenterOnly}
   \keydef
@@ -1976,7 +1989,7 @@
     boolean}{%
     \texttt{off}}{%
     If this option is \texttt{on}, only contacts between each atoms in \texttt{group1} and the center of mass of     \texttt{group2} are calculated (by default, the sum extends over all pairs of atoms in \texttt{group1} and \texttt{group2}).
-If \texttt{group2} is a \texttt{dummyAtom}, this option is set to \texttt{yes} by default.
+    If \texttt{group2} is a \texttt{dummyAtom}, this option is set to \texttt{yes} by default.
 }
 
 \item %
@@ -1998,15 +2011,24 @@
     positive integer}{%
     100}{This controls the pairlist feature, dictating how many steps are taken between regenerating pair  lists if the tolerance is greater than 0.
   }
+
+\item %
+  \labelkey{colvar|coordNum|useInternalPBC}%
+  \keydef{useInternalPBC}{%
+    \texttt{coordNum}}{%
+    Use the PBC functions from the Colvars library (as opposed to MD engine)}{%
+    boolean}{%
+    engine-dependent}{%
+    If this keyword is set to \texttt{yes}, Colvars will use internal code to compute mininum-image distances, instead of calling the function used by \MDENGINE{}: enabling this flag may speed up computation.
+    \cvvmdonly{In VMD, the default value of this flag is true.} 
+    \cvlammpsonly{Please note that, unlike the LAMMPS function, the current internal code is not robust against large tilt factors: use this feature only for unit cells near an orthogonal shape.}
+    }
+
 \end{cvcoptions}
 
-This component returns a dimensionless number, which ranges from
-approximately 0 (all interatomic distances are much larger than the
-cutoff) to $N_{\mathtt{group1}} \times N_{\mathtt{group2}}$ (all distances
-are less than the cutoff), or $N_{\mathtt{group1}}$ if
-\texttt{group2CenterOnly} is used.  For performance reasons, at least
-one of \texttt{group1} and \texttt{group2} should be of limited size or \texttt{group2CenterOnly} should be used: the cost of the loop over all pairs grows as $N_{\mathtt{group1}} \times N_{\mathtt{group2}}$.
-Setting $\mathtt{tolerance} > 0$ ameliorates this to some degree, although every pair is still checked to regenerate the pair  list.
+This component returns a dimensionless number, which ranges from 0 (all interatomic distances are much larger than the cutoff) to $N_{\mathtt{group1}} \times N_{\mathtt{group2}}$ (all possible pairwise distances are much smaller than the cutoff).
+The computational cost also grows with the number of pairwise distances calculated, unless either \texttt{group1CenterOnly} or \texttt{group2CenterOnly} are used.
+Setting $\mathtt{tolerance} > 0$ could mitigate this by looping over pairs less frequently than every step.
 
 
 

misc_interfaces/stubs/colvarproxy_stub.cpp

@@ -24,6 +24,9 @@
 colvarproxy_stub::colvarproxy_stub()
 {
   version_int = get_version_from_string(COLVARPROXY_VERSION);
+
+  use_internal_pbc_ = true;
+
   b_simulation_running = false;
 
   // both fields are taken from data structures already available

src/colvar.cpp

@@ -21,6 +21,7 @@
 #include "colvarbias.h"
 #include "colvars_memstream.h"
 #include "colvarcomp_torchann.h"
+#include "colvarcomp_coordnums.h"
 
 std::map<std::string, std::function<colvar::cvc *()>> colvar::global_cvc_map =
     std::map<std::string, std::function<colvar::cvc *()>>();