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Axel Kohlmeyer
2022-04-29 17:33:37 -04:00
parent 7d9cdc7ec4
commit 514bfe77df
2 changed files with 18 additions and 17 deletions
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18
doc/src/fix_ave_time.rst
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@ -261,13 +261,15 @@ column of numbers for each input value. For *mode* = vector, an array
of numbers is written each time output is performed. The number of rows
is the length of the input vectors, and the number of columns is the
number of values. Thus the file ends up to be a series of these array
sections. If the filename ends in '.yaml' or '.yml' then the output
format is conforming to the `YAML standard <https://yaml.org/>`_ which
allows to easily import that data into tools and scripts that support
reading YAML files. The :doc:`structured data Howto
<Howto_structured_data>` contains examples for parsing and plotting such
data with very little programming effort in Python using the *pyyaml*,
*pandas*, and *matplotlib* packages.
sections.
If the filename ends in '.yaml' or '.yml' then the output format
conforms to the `YAML standard <https://yaml.org/>`_ which allows
easy import that data into tools and scripts that support reading YAML
files. The :doc:`structured data Howto <Howto_structured_data>` contains
examples for parsing and plotting such data with very little programming
effort in Python using the *pyyaml*, *pandas*, and *matplotlib*
packages.
The *overwrite* keyword will continuously overwrite the output file
with the latest output, so that it only contains one timestep worth of
@ -314,7 +316,7 @@ Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files
<restart>`. The :doc:`fix_modify colname <fix_modify>` options can be
<restart>`. The :doc:`fix_modify colname <fix_modify>` option can be
used to change the name of the column in the output file. When writing
a YAML format file this name will be in the list of keywords.

17
doc/src/fix_modify.rst
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@ -12,24 +12,23 @@ Syntax
* fix-ID = ID of the fix to modify
* one or more keyword/value pairs may be appended
* keyword = *temp* or *press* or *energy* or *virial* or *respa* or *dynamic/dof* or *bodyforces* or *colname*
* keyword = *bodyforces* or *colname* or *dynamic/dof* or *energy* or *press* or *respa* or *temp* or *virial*
.. parsed-literal::
*temp* value = compute ID that calculates a temperature
*press* value = compute ID that calculates a pressure
*energy* value = *yes* or *no*
*virial* value = *yes* or *no*
*respa* value = *1* to *max respa level* or *0* (for outermost level)
*dynamic/dof* value = *yes* or *no*
yes/no = do or do not re-compute the number of degrees of freedom (DOF) contributing to the temperature
*bodyforces* value = *early* or *late*
early/late = compute rigid-body forces/torques early or late in the timestep
*colname* values = ID string
string = new column header name
ID = integer from 1 to N, or integer from -1 to -N, where N = # of quantities being output
*or* a fix output property keyword or reference to compute, fix, property or variable.
*dynamic/dof* value = *yes* or *no*
yes/no = do or do not re-compute the number of degrees of freedom (DOF) contributing to the temperature
*energy* value = *yes* or *no*
*press* value = compute ID that calculates a pressure
*respa* value = *1* to *max respa level* or *0* (for outermost level)
*temp* value = compute ID that calculates a temperature
*virial* value = *yes* or *no*
Examples
""""""""