Activate LAMMMPS trajectory files (.lammpstrj)

chemfiles · Mar 18, 2016 · 7237af1 · 7237af1
1 parent 186c978
commit 7237af1
Show file tree

Hide file tree

Showing 6 changed files with 31 additions and 3 deletions.
diff --git a/external/CMakeLists.txt b/external/CMakeLists.txt
@@ -30,6 +30,7 @@ set(VMD_MOLFILE_PLUGINS_ENABLED
     molfiles/src/dcdplugin.c
     molfiles/src/gromacsplugin.cxx
     molfiles/src/pdbplugin.c
+    molfiles/src/lammpsplugin.c
 )
 
 # These plugins are not yet activated, but can be compiled into chemfiles easily
@@ -60,7 +61,6 @@ set(VMD_MOLFILE_PLUGINS_DISABLED
     molfiles/src/grdplugin.cxx
     molfiles/src/gridplugin.cxx
     molfiles/src/jsplugin.c
-    molfiles/src/lammpsplugin.c
     molfiles/src/maeffplugin.cxx
     molfiles/src/mapplugin.cxx
     molfiles/src/mdfplugin.cxx

diff --git a/include/chemfiles/formats/Molfile.hpp b/include/chemfiles/formats/Molfile.hpp
@@ -35,6 +35,7 @@ enum MolfileFormat {
     TRR, ///< Gromacs .trr file format
     XTC, ///< Gromacs .xtc file format
     TRJ, ///< Gromacs .trj file format
+    LAMMPS, ///< Lammps trajectory files
 };
 
 //! A thin wrapper around the vmd plugin functions

diff --git a/src/TrajectoryFactory.cpp b/src/TrajectoryFactory.cpp
@@ -50,6 +50,7 @@ TrajectoryFactory::TrajectoryFactory() : formats_(), extensions_() {
     registration<Molfile<TRR>>(formats_, extensions_);
     registration<Molfile<XTC>>(formats_, extensions_);
     registration<Molfile<TRJ>>(formats_, extensions_);
+    registration<Molfile<LAMMPS>>(formats_, extensions_);
 }
 
 TrajectoryFactory& TrajectoryFactory::get() {

diff --git a/src/formats/Molfile.cpp b/src/formats/Molfile.cpp
@@ -30,6 +30,7 @@ static std::map<MolfileFormat, plugin_data_t> molfile_plugins {
     {TRR, {"TRR", "gromacsplugin", "trr", ".trr", true}},
     {XTC, {"XTC", "gromacsplugin", "xtc", ".xtc", false}},
     {TRJ, {"TRJ", "gromacsplugin", "trj", ".trj", true}},
+    {LAMMPS, {"LAMMPS", "lammpsplugin", "lammpstrj", ".lammpstrj", false}},
 };
 
 struct plugin_reginfo_t {
@@ -103,7 +104,7 @@ void Molfile<F>::read(Frame& frame){
     std::vector<float> coords(3*static_cast<size_t>(natoms_));
     std::vector<float> velocities(0);
 
-    molfile_timestep_t timestep;
+    molfile_timestep_t timestep{};
     timestep.coords = coords.data();
     if (molfile_plugins[F].have_velocities){
         velocities.resize(3*static_cast<size_t>(natoms_));
@@ -254,6 +255,7 @@ namespace chemfiles {
     PLUGINS_FUNCTIONS(gromacsplugin, TRR);
     PLUGINS_FUNCTIONS(gromacsplugin, XTC);
     PLUGINS_FUNCTIONS(gromacsplugin, TRJ);
+    PLUGINS_FUNCTIONS(lammpsplugin, LAMMPS);
 }
 
 #undef PLUGINS_FUNCTIONS
@@ -265,3 +267,4 @@ template class chemfiles::Molfile<GRO>;
 template class chemfiles::Molfile<TRR>;
 template class chemfiles::Molfile<XTC>;
 template class chemfiles::Molfile<TRJ>;
+template class chemfiles::Molfile<LAMMPS>;
diff --git a/tests/data b/tests/data
diff --git a/tests/formats/lammps-molfile.cpp b/tests/formats/lammps-molfile.cpp
@@ -0,0 +1,23 @@
+#include "catch.hpp"
+#include "chemfiles.hpp"
+using namespace chemfiles;
+
+#define LAMMPSDIR SRCDIR "/data/lammps/"
+
+bool roughly(const Vector3D& a, const Vector3D& b, const double eps){
+    return (fabs(a[0] - b[0]) < eps)
+        && (fabs(a[1] - b[1]) < eps)
+        && (fabs(a[2] - b[2]) < eps);
+}
+
+TEST_CASE("Read files in LAMMPS .lammpstrj format using Molfile", "[Molfile]"){
+    Trajectory file(LAMMPSDIR "polymer.lammpstrj");
+    Frame frame = file.read();
+    double eps = 1e-3;
+
+    CHECK(frame.natoms() == 1714);
+    auto positions = frame.positions();
+    CHECK(roughly(positions[0], vector3d(51.8474f, 100.348f, 116.516f), eps));
+    // this one has a non zero image index (1 0 0)
+    CHECK(roughly(positions[1189], vector3d(116.829f, 91.2404f, 79.8858f), eps));
+}