This repository has been merged into the main LAMMPS repository. Development here
has ceased, please head to the LAMMPS repository for a current version. dump nc
and dump nc/mpiio can be found in the USER-NETCDF directory:
https://github.com/lammps/lammps/tree/master/src/USER-NETCDF
The files in this directory are a user-contributed package for LAMMPS.
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
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.
Syntax:
dump ID group-ID nc|nc/mpiio N file args
dump_modify ID keyword values
with
args = list of atom attributes
keyword = append or double or global
- append yes: append output to existing NetCDF file
- append yes at frame: append out to existing NetCDF file and start writing to frame given; if negative frame is counted from the end of file.
- double yes|no: output data as double instead of single precision
- global = list of global (not per atom, but per frame) quantities can be variables, compute or fix data prefixed with v_, c_ and f_, respectively.
The list of atom attributes is identical to the 'custom' dump style. The 'nc' dump style uses the standard NetCDF library and collects all data onto a single processor before writing. The 'nc/mpiio' dump style uses parallel-netcdf and MPI-IO and has better performance on a larger number of processors. Note that 'nc' outputs all atoms sorted by tag while 'nc/mpiio' outputs in order of the MPI rank.
Example 1:
dump 1 all nc 100 traj.nc type x y z vx vy vz
dump_modify 1 append yes at -1 global c_thermo_pe c_thermo_temp c_thermo_press
Example 2:
dump 1 all nc/mpiio 1000 traj.nc id type x y z
In your LAMMPS src directory type:
git clone https://github.com/pastewka/lammps-netcdf.git USER-DUMP-NC
make yes-user-dump-nc
Note that LAMMPS needs to be linked to NetCDF (for 'dump nc') and Parallel netCDF (for 'dump nc/mpiio'). This requires a modification of your favorite makefile. Please add
EXTRA_INC += $(shell nc-config --cflags) -I/path/to/parallel-netcdf/include
EXTRA_LIB += $(shell nc-config --libs) -L/path/to/parallel-netcdf/lib -lpnetcdf
to the respective EXTRA_INC, EXTRA_LIB section of the makefile.
NetCDF: http://www.unidata.ucar.edu/software/netcdf/
Parallel netCDF: http://trac.mcs.anl.gov/projects/parallel-netcdf/
This is package is known to work with LAMMPS 15Aug14.