forked from lijiext/lammps
78 lines
2.1 KiB
Plaintext
78 lines
2.1 KiB
Plaintext
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.. index:: group2ndx
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group2ndx command
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=================
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ndx2group command
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=================
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Syntax
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""""""
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.. parsed-literal::
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group2ndx file group-ID ...
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ndx2group file group-ID ...
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* file = name of index file to write out or read in
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* zero or more group IDs may be appended
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Examples
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""""""""
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.. parsed-literal::
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group2ndx allindex.ndx
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group2ndx someindex.ndx upper lower mobile
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ndx2group someindex.ndx
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ndx2group someindex.ndx mobile
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Description
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"""""""""""
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Write or read a Gromacs style index file in text format that associates
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atom IDs with the corresponding group definitions. This index file can be
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used with in combination with Gromacs analysis tools or to import group
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definitions into the :doc:`fix colvars <fix_colvars>` input file. It can
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also be used to save and restore group definitions for static groups.
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The *group2ndx* command will write group definitions to an index file.
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Without specifying any group IDs, all groups will be written to the index
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file. When specifying group IDs, only those groups will be written to the
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index file. In order to follow the Gromacs conventions, the group *all*
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will be renamed to *System* in the index file.
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The *ndx2group* command will create of update group definitions from those
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stored in an index file. Without specifying any group IDs, all groups except
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*System* will be read from the index file and the corresponding groups
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recreated. If a group of the same name already exists, it will be completely
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reset. When specifying group IDs, those groups, if present, will be read
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from the index file and restored.
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----------
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Restrictions
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""""""""""""
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This command requires that atoms have atom IDs, since this is the
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information that is written to the index file.
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These commands are part of the USER-COLVARS package. They are only
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enabled if LAMMPS was built with that package. See the :ref:`Making LAMMPS <start_3>` section for more info.
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Related commands
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""""""""""""""""
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:doc:`group <group>`, :doc:`dump <dump>`, :doc:`fix colvars <fix_colvars>`
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**Default:** none
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.. _lws: http://lammps.sandia.gov
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.. _ld: Manual.html
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.. _lc: Section_commands.html#comm
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