WIP: Handle boundary conditions internally

.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/compile-gromacs.sh

@@ -45,8 +45,8 @@ compile_gromacs_target() {
     while [ $# -ge 1 ]; do
         if [ "${1,,}" = "debug" ]; then
             GMX_BUILD_TYPE=Debug
-            GMX_BUILD_OPTS+=(-DCMAKE_BUILD_TYPE=Debug -DCMAKE_VERBOSE_MAKEFILE=yes)
-            GMX_BUILD_OPTS+=(-DCOLVARS_DEBUG=ON)
+            GMX_BUILD_OPTS+=(-DCMAKE_VERBOSE_MAKEFILE=yes)
+            GMX_BUILD_OPTS+=(-DCMAKE_CXX_FLAGS="-DCOLVARS_DEBUG=1")
         else
             GMX_INSTALL_DIR=${1}
         fi

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

@@ -1495,15 +1495,16 @@
 
 \cvsubsec{Treatment of periodic boundary conditions}{sec:cvc_pbcs}
 
-In all colvar components described below, the following rules apply concerning periodic boundary
-conditions (PBCs):
+When copying over atomic coordinates from \MDENGINE, Colvars also copies its boundary conditions and unit cell vectors.  Periodic or non-periodic boundary conditions are supported for each direction independently, thus allowing for mixed-periodicity conditions if \MDENGINE{} allows them.  When using triclinic unit cells, tilt factors up to 1/2 are supported by looping over one additional layer of adjacent periodic images around the simulation cell to find the minimum image.  The use of tilt factors beyond 1/2 is \emph{not recommended}, and may lead to slower performance\cvlammpsonly{ (LAMMPS will also print warnings to that sense)}.
+
+For all colvar components implemented by Colvars internal code, the following rules apply:
 \begin{enumerate}
 \item Distance vectors between two coordinates
   $\mathbf{d}_{i,j} = \left(\mathbf{x}_1 - \mathbf{x}_2\right)$, are calculated following the
   minimum-image convention by default, unless \refkey{forceNoPBC}{colvar|cvc|forceNoPBC} is enabled.
   ($\mathbf{x}_1$ and $\mathbf{x}_2$ may be either individual atomic coordinates, or centers of mass
   of two groups.)
-\item For all other functions of individual atomic coordinates,
+\item For all other functions of multiple atomic coordinates,
   $f\left(\mathbf{x}_1, \mathbf{x}_2, \ldots\right)$, it is assumed that all atoms that are part of
   the same group are in the same periodic unit cell (see \ref{sec:colvar_atom_groups_wrapping}).
 \end{enumerate}
@@ -1966,6 +1967,19 @@
     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 +1990,7 @@
     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 +2012,12 @@
     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.
   }
+
 \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.
 
 
 
@@ -8201,6 +8212,9 @@
   The legacy keyword \texttt{disableForces} for atom groups is now deprecated and will be discontinued in a future release.
   Atom groups now have an automated way to save computation if forces are not used, and enabling this option otherwise would lead to incorrect behavior.
 
+\item \textbf{Colvars version 2026-XX-XX or later.}\\
+  Periodic boundary conditions are handled internally, rather than using code by \MDENGINE{} to compute the minimum-image convention (see \ref{sec:cvc_pbcs}).
+
 \end{itemize}
 
 

gromacs/src/applied_forces/colvars/colvarproxygromacs.cpp.patch

@@ -1,14 +1,24 @@
 diff --git a/src/gromacs/applied_forces/colvars/colvarproxygromacs.cpp b/src/gromacs/applied_forces/colvars/colvarproxygromacs.cpp
-index 76b350c611..37e5b53647 100644
+index 76b350c611..3876022dd3 100644
 --- a/src/gromacs/applied_forces/colvars/colvarproxygromacs.cpp
 +++ b/src/gromacs/applied_forces/colvars/colvarproxygromacs.cpp
 @@ -79,9 +79,6 @@ ColvarProxyGromacs::ColvarProxyGromacs(const std::string& colvarsConfigString,
      // Retrieve masses and charges from input file
      updated_masses_ = updated_charges_ = true;
- 
+
 -    // User-scripted forces are not available in GROMACS
 -    have_scripts = false;
 -
      angstrom_value_ = 0.1;
- 
+
      // From Gnu units
+@@ -281,7 +278,8 @@ ColvarProxyGromacs::~ColvarProxyGromacs()
+ }
+
+
+-cvm::rvector ColvarProxyGromacs::position_distance(cvm::atom_pos const& pos1, cvm::atom_pos const& pos2) const
++cvm::rvector ColvarProxyGromacs::position_distance_engine(cvm::atom_pos const& pos1,
++                                                          cvm::atom_pos const& pos2) const
+ {
+     rvec r1, r2, dr;
+     r1[0] = pos1.x;

gromacs/src/applied_forces/colvars/colvarproxygromacs.h.patch

@@ -0,0 +1,15 @@
+diff --git a/src/gromacs/applied_forces/colvars/colvarproxygromacs.h b/src/gromacs/applied_forces/colvars/colvarproxygromacs.h
+index 32b1e8d0d7..3c0a0dee9a 100644
+--- a/src/gromacs/applied_forces/colvars/colvarproxygromacs.h
++++ b/src/gromacs/applied_forces/colvars/colvarproxygromacs.h
+@@ -146,8 +146,8 @@ public:
+      */
+     int check_atom_id(int atomNumber) override;
+
+-    //! Compute the minimum distance with respect to the PBC between 2 atoms.
+-    cvm::rvector position_distance(cvm::atom_pos const& pos1, cvm::atom_pos const& pos2) const override;
++    //! Compute the minimum distance with respect to the PBCs between 2 positions using GROMACS code
++    cvm::rvector position_distance_engine(cvm::atom_pos const& pos1, cvm::atom_pos const& pos2) const override;
+ };
+
+ } // namespace gmx

gromacs/src/applied_forces/colvars/colvarsforceprovider.cpp.patch

@@ -0,0 +1,55 @@
+diff --git a/src/gromacs/applied_forces/colvars/colvarsforceprovider.cpp b/src/gromacs/applied_forces/colvars/colvarsforceprovider.cpp
+index 5860eed790..bc34e6ccaa 100644
+--- a/src/gromacs/applied_forces/colvars/colvarsforceprovider.cpp
++++ b/src/gromacs/applied_forces/colvars/colvarsforceprovider.cpp
+@@ -337,15 +337,47 @@ void ColvarsForceProvider::calculateForces(const ForceProviderInput& forceProvid
+                                            ForceProviderOutput*      forceProviderOutput)
+ {
+
+-    // Construct t_pbc struct
+-    set_pbc(&gmxPbc_, pbcType_, forceProviderInput.box_);
++    auto const& box = forceProviderInput.box_;
++
++    // Set PBC struct for use in ColvarProxyGromacs::position_distance()
++    set_pbc(&gmxPbc_, pbcType_, box);
++
++    // Share PBCs with the library as well
++    switch (pbcType_)
++    {
++        case PbcType::Unset:
++            GMX_RELEASE_ASSERT(false, "PBC type not set when being used by ColvarsForceProvider.");
++            break;
++        case PbcType::XY:
++            boundaries_.set_boundaries(true,
++                                       true,
++                                       false,
++                                       cvm::rvector{ box[0][0], box[0][1], box[0][2] },
++                                       cvm::rvector{ box[1][0], box[1][1], box[1][2] },
++                                       cvm::rvector{ 0.0, 0.0, 0.0 });
++            break;
++        case PbcType::Xyz:
++            boundaries_.set_boundaries(true,
++                                       true,
++                                       true,
++                                       cvm::rvector{ box[0][0], box[0][1], box[0][2] },
++                                       cvm::rvector{ box[1][0], box[1][1], box[1][2] },
++                                       cvm::rvector{ box[2][0], box[2][1], box[2][2] });
++            break;
++        case PbcType::Screw:
++            boundaries_.reset();
++            boundaries_.set_type(cvm::system_boundary_conditions::types::unsupported);
++            break;
++        case PbcType::No: boundaries_.reset(); break;
++        default:
++            GMX_RELEASE_ASSERT(false, "Invalid pbcType in ColvarsForceProvider::calculateForces");
++    }
+
+     const MpiComm& mpiComm = forceProviderInput.mpiComm_;
+     // Local atom coords
+     const gmx::ArrayRef<const gmx::RVec> x = forceProviderInput.x_;
+     // Local atom coords (coerced into into old gmx type)
+     const rvec* xPointer = &(x.data()->as_vec());
+-    const auto& box      = forceProviderInput.box_;
+
+     colvars->it = forceProviderInput.step_;
+

gromacs/update_patches_from_git.sh

@@ -0,0 +1,21 @@
+#!/bin/bash
+
+GROMACS_SOURCE=${1}
+if [ -n "${GROMACS_SOURCE}" ] ; then
+    GROMACS_SOURCE=$(git -C ${GROMACS_SOURCE} rev-parse --show-toplevel)
+fi
+
+if [ $? != 0 ] || [ ! -s ${GROMACS_SOURCE}/src/gromacs/version.h.cmakein ] ; then
+    echo >&2
+    echo "Usage: $0 <path_to_GROMACS_tree>" >& 2
+    exit 1
+fi
+
+COLVARS_SOURCE=$(dirname $(realpath $0))
+COLVARS_SOURCE=$(git -C ${COLVARS_SOURCE} rev-parse --show-toplevel)
+
+modified_files=($(git -C ${GROMACS_SOURCE} ls-files -m src/gromacs/applied_forces/colvars))
+
+for file in ${modified_files[@]} ; do
+    git -C ${GROMACS_SOURCE} diff ${file} > ${COLVARS_SOURCE}/gromacs/src/${file#src\/gromacs\/}.patch
+done