import lammps-netcdf code as USER-NC-DUMP package

lib/netcdf/Makefile.lammps

@@ -0,0 +1,19 @@
+# Settings that the LAMMPS build will import when a package using the
+# netCDF library is installed. This tries to automate configuration
+# via the nc-config tool, which is part of the netCDF installation.
+
+ifeq ($(shell nc-config --has-pnetcdf),no)
+
+netcdf_SYSINC = $(shell nc-config --cflags)
+netcdf_SYSLIB = $(shell nc-config --libs)
+netcdf_SYSPATH =
+
+endif
+
+ifeq ($(shell nc-config --has-pnetcdf),yes)
+
+netcdf_SYSINC = -DLMP_HAS_PNETCDF $(nc-config --cflags)
+netcdf_SYSLIB = $(shell nc-config --libs)
+netcdf_SYSPATH =
+
+endif

src/Makefile

@@ -57,7 +57,7 @@ PACKUSER = user-atc user-awpmd user-cg-cmm user-colvars \
 
 PACKLIB = compress gpu kim kokkos meam mpiio poems python reax voronoi \
 	  user-atc user-awpmd user-colvars user-h5md user-lb user-molfile \
-	  user-qmmm user-quip user-vtk
+	  user-nc-dump user-qmmm user-quip user-vtk
 
 PACKALL = $(PACKAGE) $(PACKUSER)
 

src/USER-NC-DUMP/Install.sh

@@ -0,0 +1,63 @@
+# Install/unInstall package files in LAMMPS
+# mode = 0/1/2 for uninstall/install/update
+
+mode=$1
+
+# enforce using portable C locale
+LC_ALL=C
+export LC_ALL
+
+# arg1 = file, arg2 = file it depends on
+
+action () {
+  if (test $mode = 0) then
+    rm -f ../$1
+  elif (! cmp -s $1 ../$1) then
+    if (test -z "$2" || test -e ../$2) then
+      cp $1 ..
+      if (test $mode = 2) then
+        echo "  updating src/$1"
+      fi
+    fi
+  elif (test -n "$2") then
+    if (test ! -e ../$2) then
+      rm -f ../$1
+    fi
+  fi
+}
+
+for file in *.cpp *.h; do
+  action $file
+done
+
+# edit 2 Makefile.package files to include/exclude package info
+
+if (test $1 = 1) then
+
+  if (test -e ../Makefile.package) then
+    sed -i -e 's/[^ \t]*netcdf[^ \t]* //g' ../Makefile.package
+    sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(netcdf_SYSINC) |' ../Makefile.package
+    sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(netcdf_SYSLIB) |' ../Makefile.package
+    sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(netcdf_SYSPATH) |' ../Makefile.package
+  fi
+
+  if (test -e ../Makefile.package.settings) then
+    sed -i -e '/^include.*netcdf.*$/d' ../Makefile.package.settings
+    # multiline form needed for BSD sed on Macs
+    sed -i -e '4 i \
+include ..\/..\/lib\/netcdf\/Makefile.lammps
+' ../Makefile.package.settings
+
+  fi
+
+elif (test $1 = 0) then
+
+  if (test -e ../Makefile.package) then
+    sed -i -e 's/[^ \t]*netcdf[^ \t]* //g' ../Makefile.package
+  fi
+
+  if (test -e ../Makefile.package.settings) then
+    sed -i -e '/^include.*netcdf.*$/d' ../Makefile.package.settings
+  fi
+
+fi

src/USER-NC-DUMP/README

@@ -0,0 +1,37 @@
+USER-NC-DUMP
+============
+
+This package provides the nc and (optionally) the nc/mpiio dump styles.
+
+PACKAGE DESCRIPTION
+-------------------
+
+This is a LAMMPS (http://lammps.sandia.gov/) dump style for output into a NetCDF
+database. The database format follows the AMBER NetCDF trajectory convention
+(http://ambermd.org/netcdf/nctraj.xhtml), but includes extensions to this
+convention. These extension are:
+* A variable "cell_origin" (of dimension "frame", "cell_spatial") that contains
+  the bottom left corner of the simulation cell.
+* Any number of additional variables corresponding to per atom scalar, vector
+  or tensor quantities available within LAMMPS. Tensor quantities are written in
+  Voigt notation. An additional dimension "Voigt" of length 6 is created for
+  this purpose.
+* Possibility to output to an HDF5 database.
+
+NetCDF files can be directly visualized with the following tools:
+* Ovito (http://www.ovito.org/). Ovito supports the AMBER convention and all of
+  the above extensions.
+* VMD (http://www.ks.uiuc.edu/Research/vmd/).
+* AtomEye (http://www.libatoms.org/). The libAtoms version of AtomEye contains
+  a NetCDF reader that is not present in the standard distribution of AtomEye.
+
+The person who created these files is Lars Pastewka at
+Karlsruhe Institute of Technology (lars.pastewka@kit.edu).
+Contact him directly if you have questions.
+
+Lars Pastewka  
+Institute for Applied Materials (IAM)  
+Karlsruhe Institute of Technology (KIT)  
+Kaiserstraße 12, 76131 Karlsruhe  
+e-mail: lars.pastewka@kit.edu
+

src/USER-NC-DUMP/dump_nc.h

@@ -0,0 +1,141 @@
+/* ======================================================================
+   LAMMPS NetCDF dump style
+   https://github.com/pastewka/lammps-netcdf
+   Lars Pastewka, lars.pastewka@kit.edu
+
+   Copyright (2011-2013) Fraunhofer IWM
+   Copyright (2014) Karlsruhe Institute of Technology
+
+   This program is free software: you can redistribute it and/or modify
+   it under the terms of the GNU General Public License as published by
+   the Free Software Foundation, either version 2 of the License, or
+   (at your option) any later version.
+
+   This program is distributed in the hope that it will be useful,
+   but WITHOUT ANY WARRANTY; without even the implied warranty of
+   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+   GNU General Public License for more details.
+
+   You should have received a copy of the GNU General Public License
+   along with this program.  If not, see <http://www.gnu.org/licenses/>.
+   ====================================================================== */
+
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under 
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef DUMP_CLASS
+
+DumpStyle(nc,DumpNC)
+
+#else
+
+#ifndef LMP_DUMP_NC_H
+#define LMP_DUMP_NC_H
+
+#include "dump_custom.h"
+
+namespace LAMMPS_NS {
+
+const int NC_FIELD_NAME_MAX = 100;
+const int DUMP_NC_MAX_DIMS  = 100;
+
+class DumpNC : public DumpCustom {
+ public:
+  DumpNC(class LAMMPS *, int, char **);
+  virtual ~DumpNC();
+  virtual void write();
+
+ private:
+  // per-atoms quantities (positions, velocities, etc.)
+  struct nc_perat_t {
+    int dims;                     // number of dimensions
+    int field[DUMP_NC_MAX_DIMS];  // field indices corresponding to the dim.
+    char name[NC_FIELD_NAME_MAX]; // field name
+    int var;                      // NetCDF variable
+
+    bool constant;                // is this property per file (not per frame)
+    int ndumped;                  // number of enties written for this prop.
+  };
+
+  typedef void (DumpNC::*funcptr_t)(void *);
+
+  // per-frame quantities (variables, fixes or computes)
+  struct nc_perframe_t {
+    char name[NC_FIELD_NAME_MAX]; // field name
+    int var;                      // NetCDF variable
+    int type;                     // variable, fix, compute or callback
+    int index;                    // index in fix/compute list
+    funcptr_t compute;            // compute function
+    int dim;                      // dimension
+    char id[NC_FIELD_NAME_MAX];   // variable id
+
+    bigint bigint_data;           // actual data
+    double double_data;           // actual data
+  };
+
+  int framei;                  // current frame index
+  int blocki;                  // current block index
+  int ndata;                   // number of data blocks to expect
+
+  bigint ntotalgr;             // # of atoms
+
+  int n_perat;                 // # of netcdf per-atom properties
+  nc_perat_t *perat;           // per-atom properties
+
+  int n_perframe;              // # of global netcdf (not per-atom) fix props
+  nc_perframe_t *perframe;     // global properties
+
+  bool double_precision;       // write everything as double precision
+
+  bigint n_buffer;             // size of buffer
+  int *int_buffer;             // buffer for passing data to netcdf
+  double *double_buffer;       // buffer for passing data to netcdf
+
+  int ncid;
+
+  int frame_dim;
+  int spatial_dim;
+  int Voigt_dim;
+  int atom_dim;
+  int cell_spatial_dim;
+  int cell_angular_dim;
+  int label_dim;
+
+  int spatial_var;
+  int cell_spatial_var;
+  int cell_angular_var;
+
+  int time_var;
+  int cell_origin_var;
+  int cell_lengths_var;
+  int cell_angles_var;
+
+  virtual void openfile();
+  void closefile();
+  virtual void write_header(bigint);
+  virtual void write_data(int, double *);
+  void write_prmtop();
+
+  virtual int modify_param(int, char **);
+
+  void ncerr(int, const char *, int);
+
+  void compute_step(void *);
+  void compute_elapsed(void *);
+  void compute_elapsed_long(void *);
+};
+
+}
+
+#endif
+#endif

src/USER-NC-DUMP/dump_nc_mpiio.h

@@ -0,0 +1,140 @@
+/* ======================================================================
+   LAMMPS NetCDF dump style
+   https://github.com/pastewka/lammps-netcdf
+   Lars Pastewka, lars.pastewka@kit.edu
+
+   Copyright (2011-2013) Fraunhofer IWM
+   Copyright (2014) Karlsruhe Institute of Technology
+
+   This program is free software: you can redistribute it and/or modify
+   it under the terms of the GNU General Public License as published by
+   the Free Software Foundation, either version 2 of the License, or
+   (at your option) any later version.
+
+   This program is distributed in the hope that it will be useful,
+   but WITHOUT ANY WARRANTY; without even the implied warranty of
+   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+   GNU General Public License for more details.
+
+   You should have received a copy of the GNU General Public License
+   along with this program.  If not, see <http://www.gnu.org/licenses/>.
+   ====================================================================== */
+
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under 
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+#if defined(LMP_HAS_PNETCDF)
+
+#ifdef DUMP_CLASS
+
+DumpStyle(nc/mpiio,DumpNCMPIIO)
+
+#else
+
+#ifndef LMP_DUMP_NC_MPIIO_H
+#define LMP_DUMP_NC_MPIIO_H
+
+#include "dump_custom.h"
+
+namespace LAMMPS_NS {
+
+const int NC_MPIIO_FIELD_NAME_MAX = 100;
+const int DUMP_NC_MPIIO_MAX_DIMS  = 100;
+
+class DumpNCMPIIO : public DumpCustom {
+ public:
+  DumpNCMPIIO(class LAMMPS *, int, char **);
+  virtual ~DumpNCMPIIO();
+  virtual void write();
+
+ private:
+  // per-atoms quantities (positions, velocities, etc.)
+  struct nc_perat_t {
+    int dims;                           // number of dimensions
+    int field[DUMP_NC_MPIIO_MAX_DIMS];  // field indices corresponding to the dim.
+    char name[NC_MPIIO_FIELD_NAME_MAX]; // field name
+    int var;                            // NetCDF variable
+  };
+
+  typedef void (DumpNCMPIIO::*funcptr_t)(void *);
+
+  // per-frame quantities (variables, fixes or computes)
+  struct nc_perframe_t {
+    char name[NC_MPIIO_FIELD_NAME_MAX]; // field name
+    int var;                            // NetCDF variable
+    int type;                           // variable, fix, compute or callback
+    int index;                          // index in fix/compute list
+    funcptr_t compute;                  // compute function
+    int dim;                            // dimension
+    char id[NC_MPIIO_FIELD_NAME_MAX];   // variable id
+
+    bigint bigint_data;                 // actual data
+    double double_data;                 // actual data
+  };
+
+  int framei;                           // current frame index
+  int blocki;                           // current block index
+  int ndata;                            // number of data blocks to expect
+
+  bigint ntotalgr;                      // # of atoms
+
+  int n_perat;                          // # of netcdf per-atom properties
+  nc_perat_t *perat;                    // per-atom properties
+
+  int n_perframe;                       // # of global netcdf (not per-atom) fix props
+  nc_perframe_t *perframe;              // global properties
+
+  bool double_precision;                // write everything as double precision
+
+  bigint n_buffer;                      // size of buffer
+  int *int_buffer;                      // buffer for passing data to netcdf
+  double *double_buffer;                // buffer for passing data to netcdf
+
+  int ncid;
+
+  int frame_dim;
+  int spatial_dim;
+  int Voigt_dim;
+  int atom_dim;
+  int cell_spatial_dim;
+  int cell_angular_dim;
+  int label_dim;
+
+  int spatial_var;
+  int cell_spatial_var;
+  int cell_angular_var;
+
+  int time_var;
+  int cell_origin_var;
+  int cell_lengths_var;
+  int cell_angles_var;
+
+  virtual void openfile();
+  void closefile();
+  void write_time_and_cell();
+  virtual void write_data(int, double *);
+  void write_prmtop();
+
+  virtual int modify_param(int, char **);
+
+  void ncerr(int, const char *, int);
+
+  void compute_step(void *);
+  void compute_elapsed(void *);
+  void compute_elapsed_long(void *);
+};
+
+}
+
+#endif
+#endif
+#endif /* defined(LMP_HAS_PNETCDF) */