Merge pull request #1820 from ornladios/adios_read_dump (f03cfba0) · Commits · 郑智淋 / lammps

doc/src/Commands_all.rst

+6 −6

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		@@ -46,7 +46,8 @@ An alphabetic list of all general LAMMPS commands.
		* :doc:`dimension <dimension>`
		* :doc:`displace_atoms <displace_atoms>`
		* :doc:`dump <dump>`
		* :doc:`dump adios <dump_adios>`
		* :doc:`dump atom/adios <dump_adios>`
		* :doc:`dump custom/adios <dump_adios>`
		* :doc:`dump image <dump_image>`
		* :doc:`dump movie <dump_image>`
		* :doc:`dump netcdf <dump_netcdf>`
		@@ -131,11 +132,10 @@ An alphabetic list of all general LAMMPS commands.
		* :doc:`units <units>`
		* :doc:`variable <variable>`
		* :doc:`velocity <velocity>`
		* :doc:`write_coeff <write_coeff>`
		* :doc:`write_data <write_data>`
		* :doc:`write_dump <write_dump>`
		* :doc:`write_restart <write_restart>`
		*
		* :doc:`write\_coeff <write_coeff>`
		* :doc:`write\_data <write_data>`
		* :doc:`write\_dump <write_dump>`
		* :doc:`write\_restart <write_restart>`
		*
		*
		*

doc/src/Packages_details.rst

+7 −2

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		@@ -1096,8 +1096,9 @@ USER-ADIOS package
		Contents:

		ADIOS is a high-performance I/O library. This package implements the
		dump "atom/adios" and dump "custom/adios" commands to write data using
		the ADIOS library.
		:doc:`dump atom/adios <dump_adios>`, :doc:`dump custom/adios <dump_adios>` and
		:doc:`read_dump ... format adios <read_dump>`
		commands to write and read data using the ADIOS library.

		Authors: Norbert Podhorszki (ORNL) from the ADIOS developer team.

		@@ -1111,6 +1112,10 @@ This package has :ref:`specific installation instructions <user-adios>` on the :
		* src/USER-ADIOS/README
		* examples/USER/adios
		* https://github.com/ornladios/ADIOS2
		* :doc:`dump atom/adios <dump_adios>`
		* :doc:`dump custom/adios <dump_adios>`
		* :doc:`read_dump <read_dump>`



		----------

doc/src/dump.rst

+9 −5

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		@@ -21,8 +21,11 @@ dump command
		:doc:`dump movie <dump_image>` command
		======================================

		:doc:`dump adios <dump_adios>` command
		======================================
		:doc:`dump atom/adios <dump_adios>` command
		===========================================

		:doc:`dump custom/adios <dump_adios>` command
		=============================================

		Syntax
		""""""
		@@ -45,12 +48,12 @@ Syntax
		atom args = none
		atom/gz args = none
		atom/mpiio args = none
		atom/adios args = none, discussed on :doc:`dump adios <dump_adios>` doc page
		atom/adios args = none, discussed on :doc:`dump atom/adios <dump_adios>` doc page
		cfg args = same as custom args, see below
		cfg/gz args = same as custom args, see below
		cfg/mpiio args = same as custom args, see below
		custom\ , custom/gz\ , custom/mpiio args = see below
		custom/adios args = same as custom args, discussed on :doc:`dump adios <dump_adios>` doc page
		custom/adios args = same as custom args, discussed on :doc:`dump custom/adios <dump_adios>` doc page
		dcd args = none
		h5md args = discussed on :doc:`dump h5md <dump_h5md>` doc page
		image args = discussed on :doc:`dump image <dump_image>` doc page
		@@ -713,7 +716,8 @@ LAMMPS was built with that package. See the :doc:`Build package <Build_package>
		Related commands
		""""""""""""""""

		:doc:`dump adios <dump_adios>` :doc:`dump h5md <dump_h5md>`, :doc:`dump image <dump_image>`,
		:doc:`dump atom/adios <dump_adios>`, :doc:`dump custom/adios <dump_adios>`,
		:doc:`dump h5md <dump_h5md>`, :doc:`dump image <dump_image>`,
		:doc:`dump molfile <dump_molfile>`, :doc:`dump\_modify <dump_modify>`,
		:doc:`undump <undump>`

doc/src/dump_adios.rst

+4 −3

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		.. index:: dump atoms/adios
		.. index:: dump atom/adios
		.. index:: dump custom/adios

		dump atoms/adios command
		dump atom/adios command
		=========================

		dump custom/adios command
		@@ -12,7 +13,7 @@ Syntax

		.. parsed-literal::

		dump ID group-ID atoms/adios N file.bp
		dump ID group-ID atom/adios N file.bp

		dump ID group-ID custom/adios N file.bp args

doc/src/read_dump.rst

+47 −2

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		@@ -43,6 +43,9 @@ Syntax
		format values = format of dump file, must be last keyword if used
		native = native LAMMPS dump file
		xyz = XYZ file
		adios [timeout value] = dump file written by the :doc:`dump adios <dump_adios>` command
		timeout = specify waiting time for the arrival of the timestep when running concurrently.
		The value is a float number and is interpreted in seconds.
		molfile style path = VMD molfile plugin interface
		style = dcd or xyz or others supported by molfile plugins
		path = optional path for location of molfile plugins
		@@ -65,6 +68,8 @@ Examples
		read_dump dump.xyz 10 x y z box no format molfile xyz ../plugins
		read_dump dump.dcd 0 x y z format molfile dcd
		read_dump dump.file 1000 x y z vx vy vz format molfile lammpstrj /usr/local/lib/vmd/plugins/LINUXAMD64/plugins/molfile
		read_dump dump.bp 5000 x y z vx vy vz format adios
		read_dump dump.bp 5000 x y z vx vy vz format adios timeout 60.0

		Description
		"""""""""""
		@@ -136,6 +141,17 @@ contain multiple directories separated by a colon (or semi-colon on
		windows). The path keyword is optional and defaults to ".",
		i.e. the current directory.

		The adios format supports reading data that was written by the
		:doc:`dump adios <dump_adios>` command. The
		entire dump is read in parallel across all the processes, dividing
		the atoms evenly amongs the processes. The number of writers that
		has written the dump file does not matter. Using the adios style for
		dump and read_dump is a convenient way to dump all atoms from N
		writers and read it back by M readers. If one is running two
		LAMMPS instances concurrently where one dumps data and the other is
		reading it with the rerun command, the timeout option can be specified
		to wait on the reader side for the arrival of the requested step.

		Support for other dump format readers may be added in the future.


		@@ -147,7 +163,19 @@ and box information.

		The dump file is scanned for a snapshot with a timestamp that matches
		the specified Nstep\ . This means the LAMMPS timestep the dump file
		snapshot was written on for the native format. Note that the xyz
		snapshot was written on for the native or adios formats.

		The list of timestamps available in an adios .bp file is stored in the
		variable ntimestep:

		.. parsed-literal::

		$ bpls dump.bp -d ntimestep
		uint64_t ntimestep 5*scalar
		(0) 0 50 100 150 200


		Note that the xyz
		and molfile formats do not store the timestep. For these formats,
		timesteps are numbered logically, in a sequential manner, starting
		from 0. Thus to access the 10th snapshot in an xyz or mofile
		@@ -160,7 +188,8 @@ and the current simulation box is orthogonal or vice versa. A warning
		will be generated if the snapshot box boundary conditions (periodic,
		shrink-wrapped, etc) do not match the current simulation boundary
		conditions, but the boundary condition information in the snapshot is
		otherwise ignored. See the "boundary" command for more details.
		otherwise ignored. See the "boundary" command for more details. The
		adios reader does the same as the native format reader.

		For the xyz format, no information about the box is available, so
		you must set the box flag to no\ . See details below.
		@@ -231,6 +260,18 @@ consistent from snapshot to snapshot in the molfile dump file.
		See the :doc:`dump\_modify sort <dump_modify>` command if the dump file
		was written by LAMMPS.

		The adios format supports all fields that the native format supports
		except for the q charge field.
		The list of fields stored in an adios .bp file is recorded in the attributes
		columns (array of short strings) and columnstr (space-separated single string).

		.. parsed-literal::

		$ bpls -la dump.bp column*
		string columns attr = {"id", "type", "x", "y", "z", "vx", "vy", "vz"}
		string columnstr attr = "id type x y z vx vy vz "



		----------

		@@ -357,10 +398,14 @@ The molfile dump file formats are part of the USER-MOLFILE package.
		They are only enabled if LAMMPS was built with that packages. See the
		:doc:`Build package <Build_package>` doc page for more info.

		To write and read adios .bp files, you must compile LAMMPS with the
		:ref:`USER-ADIOS <PKG-USER-ADIOS>` package.

		Related commands
		""""""""""""""""

		:doc:`dump <dump>`, :doc:`dump molfile <dump_molfile>`,
		:doc:`dump adios <dump_adios>`,
		:doc:`read\_data <read_data>`, :doc:`read\_restart <read_restart>`,
		:doc:`rerun <rerun>`

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