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

# 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

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)

# 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.

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