ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

add option to read_dump that prevents resetting the timestep

Browse Source
This commit is contained in:
Axel Kohlmeyer
2022-07-10 05:00:03 -04:00
parent be25a83210
commit bf6ad1bb45
4 changed files with 32 additions and 18 deletions
Download Patch File Download Diff File Expand all files Collapse all files

5
doc/src/dump.rst
View File

@ -783,6 +783,11 @@ To write gzipped dump files, you must either compile LAMMPS with the
-DLAMMPS_GZIP option or use the styles from the COMPRESS package.
See the :doc:`Build settings <Build_settings>` page for details.
While a dump command is active (i.e. has not been stopped by using
the undump command), no commands may be used that will change the
timestep (e.g. :doc:`reset_timestep <reset_timestep>`). LAMMPS
will terminate with an error otherwise.
The *atom/gz*, *cfg/gz*, *custom/gz*, and *xyz/gz* styles are part of
the COMPRESS package. They are only enabled if LAMMPS was built with
that package. See the :doc:`Build package <Build_package>` page for

35
doc/src/read_dump.rst
View File

@ -24,12 +24,13 @@ Syntax
*fx*,\ *fy*,\ *fz* = force components
* zero or more keyword/value pairs may be appended
* keyword = *nfile* or *box* or *replace* or *purge* or *trim* or *add* or *label* or *scaled* or *wrapped* or *format*
* keyword = *nfile* or *box* or *timestep* or *replace* or *purge* or *trim* or *add* or *label* or *scaled* or *wrapped* or *format*
.. parsed-literal::
*nfile* value = Nfiles = how many parallel dump files exist
*box* value = *yes* or *no* = replace simulation box with dump box
*timestep* value = *yes* or *no* = reset simulation timestep with dump timestep
*replace* value = *yes* or *no* = overwrite atoms with dump atoms
*purge* value = *yes* or *no* = delete all atoms before adding dump atoms
*trim* value = *yes* or *no* = trim atoms not in dump snapshot
@ -60,6 +61,7 @@ Examples
read_dump dump.dcd 0 x y z box yes format molfile dcd
read_dump dump.file 1000 x y z vx vy vz box yes format molfile lammpstrj /usr/local/lib/vmd/plugins/LINUXAMD64/plugins/molfile
read_dump dump.file 5000 x y vx vy trim yes
read_dump dump.file 5000 x y vx vy add yes box no timestep no
read_dump ../run7/dump.file.gz 10000 x y z box yes
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
@ -71,9 +73,9 @@ Description
"""""""""""
Read atom information from a dump file to overwrite the current atom
coordinates, and optionally the atom velocities and image flags and
the simulation box dimensions. This is useful for restarting a run
from a particular snapshot in a dump file. See the
coordinates, and optionally the atom velocities and image flags, the
simulation timestep, and the simulation box dimensions. This is useful
for restarting a run from a particular snapshot in a dump file. See the
:doc:`read_restart <read_restart>` and :doc:`read_data <read_data>`
commands for alternative methods to do this. Also see the
:doc:`rerun <rerun>` command for a means of reading multiple snapshots
@ -89,9 +91,9 @@ Also note that reading per-atom information from a dump snapshot is
limited to the atom coordinates, velocities and image flags, as
explained below. Other atom properties, which may be necessary to run
a valid simulation, such as atom charge, or bond topology information
for a molecular system, are not read from (or even contained in) dump
files. Thus this auxiliary information should be defined in the usual
way, e.g. in a data file read in by a :doc:`read_data <read_data>`
for a molecular system, are not read from (or may not even be contained
in) dump files. Thus this auxiliary information should be defined in
the usual way, e.g. in a data file read in by a :doc:`read_data <read_data>`
command, before using the read_dump command, or by the :doc:`set <set>`
command, after the dump snapshot is read.
@ -165,11 +167,10 @@ variable *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*
formatted dump file, use *Nstep* = 9.
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* formatted dump file, use *Nstep* = 9.
The dimensions of the simulation box for the selected snapshot are
also read; see the *box* keyword discussion below. For the *native*
@ -266,8 +267,10 @@ for how this is done, determined by the specified fields and optional
keywords.
The timestep of the snapshot becomes the current timestep for the
simulation. See the :doc:`reset_timestep <reset_timestep>` command if
you wish to change this after the dump snapshot is read.
simulation unless the *timestep* keyword is specified with a *no* value
(default setting is *yes*). See the :doc:`reset_timestep <reset_timestep>`
command if you wish to change this to a different value after the dump
snapshot is read.
If the *box* keyword is specified with a *yes* value, then the current
simulation box dimensions are replaced by the dump snapshot box
@ -391,7 +394,7 @@ Related commands
Default
"""""""
The option defaults are box = yes, replace = yes, purge = no, trim =
no, add = no, scaled = no, wrapped = yes, and format = native.
The option defaults are box = yes, timestep = yes, replace = yes, purge = no,
trim = no, add = no, scaled = no, wrapped = yes, and format = native.
.. _vmd: http://www.ks.uiuc.edu/Research/vmd