Merge pull request #216 from akohlmey/user-nc-dump

   dump_image

   dump_modify

   dump_molfile

   dump_nc

   echo

   fix

   fix_modify

"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

# 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.

netcdf_SYSINC =

netcdf_SYSLIB =

netcdf_SYSPATH =

ifneq ($(shell which nc-config 2>> /dev/null),)

netcdf_SYSINC += -DLMP_HAS_NETCDF $(shell nc-config --cflags)

netcdf_SYSLIB += $(shell nc-config --libs)

endif

ifneq ($(shell which ncmpidump 2>> /dev/null),)

PNETCDF_PATH = $(shell which ncmpidump | sed -e 's,bin/ncmpidump,,')

netcdf_SYSINC += -DLMP_HAS_PNETCDF -I$(PNETCDF_PATH)/include

netcdf_SYSLIB += -lpnetcdf

netcdf_SYSPATH += -L$(PNETCDF_PATH)/lib

endif

The Makefile.lammps file in this directory is used when building

LAMMPS with packages that make use of the NetCDF library or its

parallel version.  The file has several settings needed to compile

and link LAMMPS with the NetCDF and parallel NetCDF support.

For any regular NetCDF installation, all required flags should be

autodetected. Please note that parallel NetCDF support is

beneficial only when you run on a machine with very many processors

like an IBM BlueGene or Cray. For most people regular NetCDF

support should be sufficient and not cause any performance

penalties.

If you have problems compiling or linking, you may have to set

the flags manually. There are three makefile variables

1) netcdf_SYSINC

This is for setting preprocessor options and include file paths.

Set -DLMP_HAS_NETCDF, if you have NetCDF installed.

Set -DLMP_HAS_PNETCDF, if you have parallel NetCDF installed.

You can have either or both defines set. If none of these are

set, LAMMPS will compile, but the NetCDF enabled functionality

will not be available.

In addition you may have to point to the folder with the include

with -I/path/to/netcdf/include

Example for a Fedora 24 machine with serial NetCDF installed as

netcdf-devel-4.4.0-3.fc24.x86_64 RPM package:

netcdf_SYSINC = -DLMP_HAS_NETCDF -I/usr/include -I/usr/include/hdf

2) netcdf_SYSLIB

This is the setting for all required libraries that need to be linked to.

Example for a Fedora 24 machine with serial NetCDF installed as

netcdf-devel-4.4.0-3.fc24.x86_64 RPM package:

netcdf_SYSLIB = -lnetcdf

3) netcdf_SYSPATH

This is the setting for the path of directories with the NetCDF libraries.

Typically, this will be of the form -L/path/to/netcdf/lib

In the example from above, it can be left empty, because the Linux

distribution provided libraries are installed in a system library location.

/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