import dump nc and dump nc/mpiio from lammps-netcdf as USER-NC-DUMP package by lars pastewka (69cb8317) · Commits · 郑智淋 / lammps

doc/src/dump_nc.txt

0 → 100644

+64 −0

Original line number	Diff line number	Diff line
		"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c

		:link(lws,http://lammps.sandia.gov)
		:link(ld,Manual.html)
		:link(lc,Section_commands.html#comm)

		:line

		dump nc command :h3
		dump nc/mpiio command :h3

		[Syntax:]

		dump ID group-ID nc N file.nc args
		dump ID group-ID nc/mpiio N file.nc args :pre

		ID = user-assigned name for the dump :ulb,l
		group-ID = ID of the group of atoms to be imaged :l
		{nc} or {nc/mpiio} = style of dump command (other styles {atom} or {cfg} or {dcd} or {xtc} or {xyz} or {local} or {custom} are discussed on the "dump"_dump.html doc page) :l
		N = dump every this many timesteps :l
		file.nc = name of file to write to :l
		args = list of per atom data elements to dump, same as for the 'custom' dump style. :l,ule

		[Examples:]

		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 :pre

		dump 1 all nc/mpiio 1000 traj.nc id type x y z :pre

		[Description:]

		Dump a snapshot of atom coordinates every N timesteps in Amber-style
		NetCDF file format. NetCDF files are binary, portable and self-describing.
		This dump style will write only one file on the root node. The dump
		style {nc} uses the "standard NetCDF library"_netcdf-home all data is
		collected on one processor and then written to the dump file. Dump style
		{nc/mpiio} used the "parallel NetCDF library"_pnetcdf-home and MPI-IO;
		it has better performance on a larger number of processors. Note that
		'nc' outputs all atoms sorted by atom tag while 'nc/mpiio' outputs in
		order of the MPI rank.

		In addition to per-atom data, also global (i.e. not per atom, but per frame)
		quantities can be included in the dump file. This can be variables, output
		from computes or fixes data prefixed with v_, c_ and f_, respectively.
		These properties are included via "dump_modify"_dump_modify.html {global}.

		:line

		[Restrictions:]

		The {nc} and {nc/mpiio} dump styles are part of the USER-NC-DUMP package.
		It is only enabled if LAMMPS was built with that package. See the "Making
		LAMMPS"_Section_start.html#start_3 section for more info.

		:link(netcdf-home,http://www.unidata.ucar.edu/software/netcdf/)
		:link(pnetcdf-home,http://trac.mcs.anl.gov/projects/parallel-netcdf/)

		:line

		[Related commands:]

		"dump"_dump.html, "dump_modify"_dump_modify.html, "undump"_undump.html

src/.gitignore

+4 −0

Original line number	Diff line number	Diff line
		@@ -271,6 +271,10 @@
		/dump_custom_vtk.h
		/dump_h5md.cpp
		/dump_h5md.h
		/dump_nc.cpp
		/dump_nc.h
		/dump_nc_mpiio.cpp
		/dump_nc_mpiio.h
		/dump_xtc.cpp
		/dump_xtc.h
		/dump_xyz_mpiio.cpp

src/USER-NC-DUMP/README

+7 −4

Original line number	Diff line number	Diff line
		@@ -2,6 +2,9 @@ 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
		-------------------
		@@ -32,6 +35,6 @@ Contact him directly if you have questions.
		Lars Pastewka
		Institute for Applied Materials (IAM)
		Karlsruhe Institute of Technology (KIT)
		Kaiserstraße 12, 76131 Karlsruhe
		Kaiserstrasse 12, 76131 Karlsruhe
		e-mail: lars.pastewka@kit.edu