Add support for reading Gromacs TNG trajectory files

README.md

@@ -72,13 +72,18 @@ the following libraries:
 * NetCDF
 * BLAS
 * LAPACK
-* ARPACK (now bundled with CPPTRAJ)
-* Bzip2
 * Gzip
+* Bzip2
 * Parallel NetCDF (-mpi build only, for NetCDF trajectory output in parallel)
 * CUDA (-cuda build only)
-* FFTW (mostly optional; required for PME functionality)
-* [helPME](https://github.com/andysim/helpme) (optional; required for PME functionality)
+* FFTW (mostly optional; required for PME functionality and very large FFTs)
+
+CPPTRAJ also makes use of the following libraries that are bundled with CPPTRAJ. External ones can be used in place of these if desired.
+
+* ARPACK; without this diagonalization of sparse matrices in `diagmatrix` will be slow
+* [helPME](https://github.com/andysim/helpme), required for PME functionality
+* XDR for reading GROMACS XTC trajectories
+* TNG for reading GROMACS TNG trajectories
 
 `./configure gnu` should be adequate to set up compilation for most systems.
 For systems without BLAS/LAPACK/ARPACK and/or NetCDF libraries installed,
@@ -92,21 +97,24 @@ be specified to enable OpenMP parallelization, e.g. `./configure -openmp gnu`.
 An MPI-parallelized version of CPPTRAJ can also be built using the `-mpi` flag.
 CPPTRAJ can be built with both MPI and OpenMP; when running this build users
 should take care to properly set OMP_NUM_THREADS if using more than 1 MPI
-thread per node. A CUDA build is now also available via the `-cuda` flag.
-By default CPPTRAJ will be configured for multiple shader models; to restrict
-the CUDA build to a single shader model use the SHADER_MODEL environment variable.
-Any combination of `-cuda`, `-mpi`, and `-openmp` may be used.
-
-The configure script by default sets everything up to link dynamically. The
-`-static` flag can be used to force static linking. If linking errors are
-encountered you may need to specify library locations using the `--with-LIB=`
-options. For example, to use NetCDF compiled in `/opt/netcdf` use the option
-`--with-netcdf=/opt/netcdf`. Alternatively, individual libraries can be
-disabled with the `-no<LIB>` options. The `-libstatic` flag
-can be used to static link only libraries that have been specified.
+process per node (the number of processes * threads should not be greater than
+the number of physical cores on the machine).
+
+A CUDA build is now also available via the `-cuda` configure flag. However, currently
+only a few commands benefit from this (see the manual for details). By default CPPTRAJ
+will be configured for multiple shader models; to restrict the CUDA build to a single
+shader model set the SHADER_MODEL environment variable before running `configure`.
+
+Any combination of `-cuda`, `-mpi`, and `-openmp` may be used. The configure script by
+default sets everything up to link dynamically. The `-static` flag can be used to force
+static linking. If linking errors are encountered you may need to specify library locations
+using the `--with-LIB=` options. For example, to use NetCDF compiled in `/opt/netcdf`
+use the option `--with-netcdf=/opt/netcdf`. Alternatively, individual libraries can be
+disabled with the `-no<LIB>` options. The `-libstatic` flag can be used to static link
+only libraries that have been specified.
 
 After `configure` has been successfully run, `make install` will
-compile and place the cpptraj binary in the `bin/` subdirectory. Note that
+compile and place the cpptraj binary in the `$CPPTRAJHOME/bin` subdirectory. Note that
 on multithreaded systems `make -j X install` (where X is an integer > 1
 and less than the max # cores on your system) will run much faster.
 After installation, It is highly recommended that `make check` be run as
@@ -203,6 +211,8 @@ External libraries bundled with CPPTRAJ
 
 * CPPTRAJ uses the [ARPACK](https://www.caam.rice.edu//software/ARPACK/) library to calculate eigenvalues/eigenvectors from large sparse matrices.
 
-* CPPTRAJ uses the [xdrfile](http://www.gromacs.org/Developer\_Zone/Programming\_Guide/XTC\_Library) library for reading XTC file; specifically a somewhat updated version from [MDTRAJ](https://github.com/mdtraj/mdtraj) that includes some bugfixes and enhancements. See `src/xdrfile/README` for details.
+* CPPTRAJ uses the [xdrfile](http://www.gromacs.org/Developer\_Zone/Programming\_Guide/XTC\_Library) library for reading XTC files; specifically a somewhat updated version from [MDTRAJ](https://github.com/mdtraj/mdtraj) that includes some bugfixes and enhancements. See `src/xdrfile/README` for details.
+
+* CPPTRAJ uses the [GROMACS TNG](https://github.com/gromacs/tng) library for reading TNG files. See `sec/tng/README` for details.
 
 * The reciprocal part of the PME calculation is handled by the [helPME](https://github.com/andysim/helpme) library by Andy Simmonett.

configure

@@ -45,7 +45,7 @@ UsageFull() {
   echo "    --with-<lib>=<DIR> : Use library in specified directory."
   echo "    -l<lib>=<FILE>     : Use specified library file."
   echo "    -no<lib>           : Disable library."
-  echo "    Libraries: netcdf pnetcdf zlib bzlib blas lapack arpack fftw3 readline sanderlib xdrfile"
+  echo "    Libraries: netcdf pnetcdf zlib bzlib blas lapack arpack fftw3 readline sanderlib xdrfile tng"
   echo "    Note: pnetcdf is needed for writing NetCDF trajectories with MPI."
   echo "  LINKING OPTIONS"
   echo "    -static        : Use static linking."
@@ -142,22 +142,25 @@ CPPTRAJLIB=''
 
 # ----- External Libraries -----------------------
 # Total number of external libraries
-NLIB=13
+NLIB=14
 # Library indices
 # Original: FFT ARPACK LAPACK BLAS NETCDF PARANC BZIP ZIP READLINE XDRFILE
+# Libraries containing definition of a function should appear *after*
+# any source files or object files which use it.
 LNETCDF=0
 LPARANC=1    # Parallel NetCDF
 LBZIP=2
-LZIP=3
-LARPACK=4
-LLAPACK=5
-LBLAS=6
-LFFTW3=7
-LREADLINE=8
-LXDRFILE=9
-LSANDER=10
-LTIMER=11
-LCUDA=12
+LTNGFILE=3   # This has to come before ZLIB since it depends on ZLIB
+LZIP=4
+LARPACK=5
+LLAPACK=6
+LBLAS=7
+LFFTW3=8
+LREADLINE=9
+LXDRFILE=10
+LSANDER=11
+LTIMER=12
+LCUDA=13
 
 # LIB_STAT = Library status:
 #   off       : Do not use library.
@@ -281,6 +284,15 @@ LIB_D_ON[$LCUDA]='-DCUDA'
 LIB_DOFF[$LCUDA]=''
 LIB_TYPE[$LCUDA]='cpp'
 
+LIB_STAT[$LTNGFILE]='bundled'
+LIB_CKEY[$LTNGFILE]='tng'
+LIB_HOME[$LTNGFILE]='tng'
+LIB_FLAG[$LTNGFILE]='-ltng_io'
+LIB_STTC[$LTNGFILE]='libtng_io.a'
+LIB_D_ON[$LTNGFILE]='-DHAS_TNGFILE'
+LIB_DOFF[$LTNGFILE]=''
+LIB_TYPE[$LTNGFILE]='ld'
+
 for ((i=0; i < $NLIB; i++)) ; do
   LIB_LINK[$i]='dynamic'
 done
@@ -579,6 +591,21 @@ EOF
   TestProgram "  Checking Xdrfile" "$CXX" "$CXXFLAGS ${LIB_INCL[$LXDRFILE]}" testp.cpp "${LIB_FLAG[$LXDRFILE]}"
 }
 
+TestTngfile() {
+  cat > testp.cpp <<EOF
+#include <tng/tng_io.h>
+tng_trajectory_t traj_;
+bool Unused(const char* fname) {
+  tng_function_status stat = tng_util_trajectory_open(fname, 'r', &traj_);
+  if (stat != TNG_SUCCESS)
+    return false;
+  return true;
+}
+int main() { return 0; }
+EOF
+  TestProgram "  Checking TNG" "$CXX" "$CXXFLAGS ${LIB_INCL[$LTNGFILE]}" testp.cpp "${LIB_FLAG[$LTNGFILE]}"
+}
+
 TestSanderlib() {
   cat > testp.cpp <<EOF
 #include "sander.h"
@@ -640,6 +667,7 @@ TestLibraries() {
   if [ "${LIB_TEST[$LFFTW3]}" = 'yes'    ] ; then TestFFTW3 ; fi
   if [ "${LIB_TEST[$LREADLINE]}" = 'yes' ] ; then TestReadline ; fi
   if [ "${LIB_TEST[$LXDRFILE]}" = 'yes'  ] ; then TestXdrfile ; fi
+  if [ "${LIB_TEST[$LTNGFILE]}" = 'yes'  ] ; then TestTngfile ; fi
   if [ "${LIB_TEST[$LSANDER]}" = 'yes'   ] ; then TestSanderlib ; fi
   if [ "${LIB_TEST[$LCUDA]}" = 'yes'     ] ; then TestCuda ; fi
 }
@@ -876,7 +904,7 @@ SetupLibraries() {
             lhdir="$ladir"
           fi
           if [ "${LIB_LINK[$i]}" = 'static' ] ; then
-            if [ -z "${LIB_STTC[$i]}" ] ; then
+            if [ -z "${LIB_STTC[$i]}" -o ! -f "$lhdir/${LIB_STTC[$i]}" ] ; then
               WrnMsg "Cannot link '${LIB_CKEY[$i]}' statically."
               lflag="-L$lhdir ${LIB_FLAG[$i]}"
             else
@@ -917,6 +945,12 @@ SetupLibraries() {
       LIB_INCL[$i]="$linc"
     fi
   done
+  # Take care of any library dependencies.
+  if [ "${LIB_STAT[$LZIP]}" = 'off' -a "${LIB_STAT[$LTNGFILE]}" != 'off' ] ; then
+    # TNG depends on libz
+    echo "Warning: TNG depends on libz; disabling TNG."
+    LIB_STAT[$LTNGFILE]='off'
+  fi
 }
 
 #-------------------------------------------------------------------------------
@@ -2044,6 +2078,12 @@ if [ "${LIB_STAT[$LXDRFILE]}" = 'bundled' ] ; then
 else
   XDRFILE_TARGET='noxdrfile'
 fi
+# TNG
+if [ "${LIB_STAT[$LTNGFILE]}" = 'bundled' ] ; then
+  TNGFILE_TARGET=${LIB_FLAG[$LTNGFILE]}
+else
+  TNGFILE_TARGET='notngfile'
+fi
 # Arpack
 if [ "${LIB_STAT[$LARPACK]}" = 'bundled' ] ; then
   ARPACK_TARGET=${LIB_FLAG[$LARPACK]}
@@ -2091,6 +2131,8 @@ READLINE_LIB=${LIB_FLAG[$LREADLINE]}
 
 XDRFILE_TARGET=$XDRFILE_TARGET
 
+TNGFILE_TARGET=$TNGFILE_TARGET
+
 ARPACK_TARGET=$ARPACK_TARGET
 
 FFT_TARGET=$FFT_TARGET
@@ -2114,6 +2156,9 @@ cat > $external_config <<EOF
 # configured using: $CONFIGURECMD
 EOF
 BuildRules $external_config nvcc cc f77
+if [ "${LIB_STAT[$LZIP]}" != 'off' ] ; then
+  echo "ZLIB_FLAG=${LIB_FLAG[$LZIP]}" >> $external_config
+fi
 
 # ----- Create directories if necessary ----------
 if [ ! -e "$CPPTRAJBIN" ] ; then

devtools/Template.sh

@@ -181,7 +181,7 @@ elif [ "$TYPE" = 'Traj' ] ; then
     void Info();
     int readVelocity(int, Frame&);
     int readForce(int, Frame&);
-    int processWriteArgs(ArgList&);
+    int processWriteArgs(ArgList&, DataSetList const&);
     int processReadArgs(ArgList&);
     // -------------------------------------------
 #   ifdef MPI
@@ -273,7 +273,7 @@ void $CLASS::WriteHelp() {
 }
 
 /** Process write arguments. */
-int $CLASS::processWriteArgs(ArgList& argIn) {
+int $CLASS::processWriteArgs(ArgList& argIn, DataSetList const& DSLin) {
 
   return 0;
 }

doc/cpptraj.lyx

@@ -12013,7 +12013,7 @@ Cpptraj currently understands the following trajectory file formats:
 \begin_layout Standard
 \align center
 \begin_inset Tabular
-<lyxtabular version="3" rows="20" columns="4">
+<lyxtabular version="3" rows="21" columns="4">
 <features tabularvalignment="middle">
 <column alignment="center" valignment="top" width="25text%">
 <column alignment="center" valignment="top" width="25text%">
@@ -12571,6 +12571,44 @@ xtc
 <cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
 \begin_inset Text
 
+\begin_layout Plain Layout
+Gromacs TNG
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+tng
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+.tng
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Read Only
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
 \begin_layout Plain Layout
 CIF
 \end_layout

lgtm.yml

@@ -1,6 +1,7 @@
 path_classifiers:
   test:
     - "src/readline/*"
+    - "src/tng/*"
 extraction:
   cpp:
     prepare:

src/Constants.h

@@ -65,5 +65,15 @@ namespace Constants {
     * itself is derived from sqrt(1 / ((AMU_TO_KG * NA) / (1000 * CAL_TO_J))).
     */
   const double AMBERTIME_TO_PS = 20.455;
+  /// Pico prefix
+  const double PICO = 1e-12;
+  /// Convert Gromacs force units (kJ / mol * nm) to Amber units (kcal / mol * Ang)
+  const double GMX_FRC_TO_AMBER = ANG_TO_NM * J_TO_CAL;
+  /// Convert Amber force units to Gromacs
+  const double AMBER_FRC_TO_GMX = NM_TO_ANG * CAL_TO_J;
+  /// Convert Gromacs velocity units (nm / ps) to Amber units (Ang / (1/20.455)ps).
+  const double GMX_VEL_TO_AMBER = NM_TO_ANG / AMBERTIME_TO_PS;
+  /// Convert Amber velocity units to Gromacs
+  const double AMBER_VEL_TO_GMX = ANG_TO_NM * AMBERTIME_TO_PS;
 }
 #endif

src/Cpptraj.cpp

@@ -223,6 +223,9 @@ std::string Cpptraj::Defines() {
 #ifdef NO_XDRFILE
   defined_str.append(" -DNO_XDRFILE");
 #endif
+#ifdef HAS_TNGFILE
+  defined_str.append(" -DHAS_TNGFILE");
+#endif
 #if defined(USE_SANDERLIB) && !defined(LIBCPPTRAJ)
   defined_str.append(" -DUSE_SANDERLIB");
 #endif

src/Makefile

@@ -17,7 +17,7 @@ install: $(INSTALL_TARGETS)
 install_cpptraj: cpptraj$(SFX)$(EXE)
 	mv cpptraj$(SFX)$(EXE) $(CPPTRAJBIN)
 
-cpptraj$(SFX)$(EXE): $(OBJECTS) $(FFT_TARGET) $(READLINE_TARGET) $(CUDA_TARGET) $(XDRFILE_TARGET) $(ARPACK_TARGET)
+cpptraj$(SFX)$(EXE): $(OBJECTS) $(FFT_TARGET) $(READLINE_TARGET) $(CUDA_TARGET) $(XDRFILE_TARGET) $(ARPACK_TARGET) $(TNGFILE_TARGET)
 	$(CXX) -o cpptraj$(SFX)$(EXE) $(OBJECTS) $(CUDA_TARGET) $(FFT_TARGET) $(READLINE_LIB) $(CPPTRAJ_LIB) $(LDFLAGS)
 
 # libcpptraj ---------------------------
@@ -27,7 +27,7 @@ cpptraj$(SFX)$(EXE): $(OBJECTS) $(FFT_TARGET) $(READLINE_TARGET) $(CUDA_TARGET)
 
 libcpptraj: $(LIBCPPTRAJ_TARGET)
 
-$(CPPTRAJLIB)/libcpptraj$(SHARED_SUFFIX): $(LIBCPPTRAJ_OBJECTS) $(FFT_TARGET) $(CUDA_TARGET) $(XDRFILE_TARGET) $(ARPACK_TARGET)
+$(CPPTRAJLIB)/libcpptraj$(SHARED_SUFFIX): $(LIBCPPTRAJ_OBJECTS) $(FFT_TARGET) $(CUDA_TARGET) $(XDRFILE_TARGET) $(ARPACK_TARGET) $(TNGFILE_TARGET)
 	$(CXX) -shared -o $(CPPTRAJLIB)/libcpptraj$(SHARED_SUFFIX) $(LIBCPPTRAJ_OBJECTS) $(FFT_TARGET) $(CUDA_TARGET) $(CPPTRAJ_LIB) $(LDFLAGS)
 
 # Static libraries ---------------------
@@ -72,6 +72,9 @@ xdrfile/libxdrfile.a: ../external.config.h
 arpack/libarpack.a: ../external.config.h
 	cd arpack && $(MAKE) install
 
+tng/libtng_io.a: ../external.config.h
+	cd tng && $(MAKE) all
+
 noreadline:
 	@echo ""
 	@echo "Skipping bundled READLINE build"
@@ -82,6 +85,11 @@ noxdrfile:
 	@echo "Skipping bundled XDRFILE build"
 	@echo ""
 
+notngfile:
+	@echo ""
+	@echo "Skipping bundled TNG build"
+	@echo ""
+
 noarpack:
 	@echo ""
 	@echo "Skipping bundled ARPACK build"
@@ -107,6 +115,7 @@ clean:
 	cd xdrfile && $(MAKE) clean
 	cd arpack && $(MAKE) clean
 	cd cuda_kernels && $(MAKE) clean
+	cd tng && $(MAKE) clean
 
 uninstall:
 	$(DEL_FILE) $(CPPTRAJBIN)/cpptraj$(SFX)$(EXE)