# 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

USER-NC-DUMP

============

This package provides the nc and (optionally) the nc/mpiio dump styles.

See the doc page for dump nc or dump nc/mpiio command for how to use them.

Compiling these dump styles requires having the netCDF library installed

on your system. See lib/netcdf/README for additional details.

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

/* ======================================================================

   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_NETCDF)

#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

#endif /* defined(LMP_HAS_NETCDF) */