cosmetic changes for consistency
This commit is contained in:
@ -297,7 +297,7 @@ the chapter on errors in the
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manual gives some additional information about error messages, if possible.
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manual gives some additional information about error messages, if possible.
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.SH COPYRIGHT
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.SH COPYRIGHT
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© 2003--2020 Sandia Corporation
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© 2003--2021 Sandia Corporation
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This package is free software; you can redistribute it and/or modify
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This package is free software; you can redistribute it and/or modify
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it under the terms of the GNU General Public License version 2 as
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it under the terms of the GNU General Public License version 2 as
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@ -98,7 +98,7 @@ msi2lmp decane -c 0 -f oplsaa
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.SH COPYRIGHT
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.SH COPYRIGHT
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© 2003--2019 Sandia Corporation
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© 2003--2021 Sandia Corporation
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This package is free software; you can redistribute it and/or modify
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This package is free software; you can redistribute it and/or modify
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it under the terms of the GNU General Public License version 2 as
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it under the terms of the GNU General Public License version 2 as
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@ -74,7 +74,7 @@ folder. The following ``make`` commands are available:
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.. code-block:: bash
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.. code-block:: bash
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make html # generate HTML in html dir using Sphinx
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make html # generate HTML in html dir using Sphinx
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make pdf # generate PDF as Manual.pdf using Sphinx and pdflatex
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make pdf # generate PDF as Manual.pdf using Sphinx and PDFLaTeX
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make fetch # fetch HTML pages and PDF files from LAMMPS website
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make fetch # fetch HTML pages and PDF files from LAMMPS website
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# and unpack into the html_www folder and Manual_www.pdf
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# and unpack into the html_www folder and Manual_www.pdf
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make epub # generate LAMMPS.epub in ePUB format using Sphinx
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make epub # generate LAMMPS.epub in ePUB format using Sphinx
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@ -714,7 +714,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
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*Cannot create/grow a vector/array of pointers for %s*
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*Cannot create/grow a vector/array of pointers for %s*
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LAMMPS code is making an illegal call to the templated memory
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LAMMPS code is making an illegal call to the templated memory
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allocaters, to create a vector or array of pointers.
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allocators, to create a vector or array of pointers.
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*Cannot create_atoms after reading restart file with per-atom info*
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*Cannot create_atoms after reading restart file with per-atom info*
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The per-atom info was stored to be used when by a fix that you may
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The per-atom info was stored to be used when by a fix that you may
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@ -2248,16 +2248,16 @@ PYTHON package
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A :doc:`python <python>` command which allow you to execute Python code
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A :doc:`python <python>` command which allow you to execute Python code
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from a LAMMPS input script. The code can be in a separate file or
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from a LAMMPS input script. The code can be in a separate file or
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embedded in the input script itself. See the :doc:`Python call <Python_call>` page for an overview of using Python from
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embedded in the input script itself. See the :doc:`Python call
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LAMMPS in this manner and all the :doc:`Python <Python_head>` manual pages
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<Python_call>` page for an overview of using Python from LAMMPS in this
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for other ways to use LAMMPS and Python together.
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manner and all the :doc:`Python <Python_head>` manual pages for other
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ways to use LAMMPS and Python together.
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.. note::
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.. note::
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Building with the PYTHON package assumes you have a Python
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Building with the PYTHON package assumes you have a Python development
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shared library available on your system, which needs to be a Python 2
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environment (headers and libraries) available on your system, which needs
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version, 2.6 or later. Python 3 is not yet supported. See the
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to be either Python version 2.7 or Python 3.5 and later.
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lib/python/README for more details.
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**Install:**
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**Install:**
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@ -242,10 +242,11 @@ links with from the lib/message directory. See the
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**-cite style** or **file name**
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**-cite style** or **file name**
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Select how and where to output a reminder about citing contributions
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Select how and where to output a reminder about citing contributions
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to the LAMMPS code that were used during the run. Available styles are
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to the LAMMPS code that were used during the run. Available keywords
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"both", "none", "screen", or "log". Any flag will be considered a file
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for styles are "both", "none", "screen", or "log". Any other keyword
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name to write the detailed citation info to. Default is the "log" style
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will be considered a file name to write the detailed citation info to
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where there is a short summary in the screen output and detailed citations
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instead of logfile or screen. Default is the "log" style where there
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is a short summary in the screen output and detailed citations
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in BibTeX format in the logfile. The option "both" selects the detailed
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in BibTeX format in the logfile. The option "both" selects the detailed
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output for both, "none", the short output for both, and "screen" will
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output for both, "none", the short output for both, and "screen" will
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write the detailed info to the screen and the short version to the log
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write the detailed info to the screen and the short version to the log
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@ -537,13 +538,14 @@ partition screen files file.N.
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**-skiprun**
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**-skiprun**
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Insert the command :doc:`timer timerout 0 every 1 <timer>` at the
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Insert the command :doc:`timer timeout 0 every 1 <timer>` at the
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beginning of an input file or after a :doc:`clear <clear>` command.
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beginning of an input file or after a :doc:`clear <clear>` command.
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This has the effect that the entire LAMMPS input script is processed
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This has the effect that the entire LAMMPS input script is processed
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without executing actual runs or minimizations (their main loops are
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without executing actual :doc:`run <run>` or :doc:`minimize <minimize>`
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skipped). This can be helpful and convenient to test input scripts for
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and similar commands (their main loops are skipped). This can be
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long running calculations to avoid having them crash after a long time
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helpful and convenient to test input scripts of long running
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due to a typo or syntax error.
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calculations for correctness to avoid having them crash after a
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long time due to a typo or syntax error in the middle or at the end.
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----------
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----------
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@ -23,22 +23,23 @@ Examples
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Description
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Description
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"""""""""""
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"""""""""""
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Define a computation that extracts the angle energy calculated by each
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Define a computation that extracts the angle energy calculated by each of the
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of the angle sub-styles used in the doc:`angle_style hybrid <angle_hybrid>`
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angle sub-styles used in the :doc:`angle_style hybrid <angle_hybrid>` command.
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command. These values are made accessible
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These values are made accessible for output or further processing by other
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for output or further processing by other commands. The group
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commands. The group specified for this command is ignored.
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specified for this command is ignored.
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This compute is useful when using :doc:`angle_style hybrid <angle_hybrid>` if you want to know the portion of the total
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This compute is useful when using :doc:`angle_style hybrid <angle_hybrid>` if
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energy contributed by one or more of the hybrid sub-styles.
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you want to know the portion of the total energy contributed by one or more of
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the hybrid sub-styles.
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Output info
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Output info
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"""""""""""
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"""""""""""
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This compute calculates a global vector of length N where N is the
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This compute calculates a global vector of length N where N is the number of
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number of sub_styles defined by the :doc:`angle_style hybrid <angle_style>` command, which can be accessed by indices
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sub_styles defined by the :doc:`angle_style hybrid <angle_style>` command,
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1-N. These values can be used by any command that uses global scalar
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which can be accessed by indices 1-N. These values can be used by any command
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or vector values from a compute as input. See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
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that uses global scalar or vector values from a compute as input. See the
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:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
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options.
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options.
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The vector values are "extensive" and will be in energy
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The vector values are "extensive" and will be in energy
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@ -46,6 +47,7 @@ The vector values are "extensive" and will be in energy
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Restrictions
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Restrictions
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""""""""""""
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""""""""""""
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none
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none
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Related commands
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Related commands
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@ -738,6 +738,6 @@ smaller simulation or on more processors.
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E: Cannot create/grow a vector/array of pointers for %s
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E: Cannot create/grow a vector/array of pointers for %s
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LAMMPS code is making an illegal call to the templated memory
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LAMMPS code is making an illegal call to the templated memory
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allocaters, to create a vector or array of pointers.
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allocators, to create a vector or array of pointers.
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*/
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*/
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