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Added documentation for 'read_dump ... format adios' command and fixed links and names for 'dump atom/adios' and 'dump custom/adios' commands.

This commit is contained in:
Podhorszki Norbert 2020-01-03 14:52:54 -05:00
parent 125a82f572
commit 95b4613e16
5 changed files with 68 additions and 17 deletions
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12
doc/src/Commands_all.rst
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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>`
@ -131,10 +132,11 @@ 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>`
*
*
*
*

9
doc/src/Packages_details.rst
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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>`
----------

14
doc/src/dump.rst
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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>`

7
doc/src/dump_adios.rst
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@ -1,6 +1,7 @@
.. 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

43
doc/src/read_dump.rst
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@ -43,6 +43,7 @@ Syntax
*format* values = format of dump file, must be last keyword if used
*native* = native LAMMPS dump file
*xyz* = XYZ file
*adios* = dump file written by the :doc:`dump adios <dump_adios>` command
*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 +66,7 @@ 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
Description
"""""""""""
@ -136,6 +138,14 @@ 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.
Support for other dump format readers may be added in the future.
@ -147,7 +157,19 @@ 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 +182,8 @@ 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 +254,18 @@ 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 +392,14 @@ 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>`