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11
doc/Section_commands.html
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@ -586,15 +586,8 @@ in the command&#8217;s documentation.</p>
</table>
<p>These are additional commands in USER packages, which can be used if
<a class="reference internal" href="Section_start.html#start-3"><span>LAMMPS is built with the appropriate package</span></a>.</p>
<table border="1" class="docutils">
<colgroup>
<col width="100%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="group2ndx.html"><em>group2ndx</em></a></td>
</tr>
</tbody>
</table>
<p><a class="reference internal" href="group2ndx.html"><em>ndx2group</em></a> |
+&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8211;+</p>
</div>
<hr class="docutils" />
<div class="section" id="fix-styles">

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doc/Section_commands.txt
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@ -468,7 +468,8 @@ These are additional commands in USER packages, which can be used if
"LAMMPS is built with the appropriate
package"_Section_start.html#start_3.
"group2ndx"_group2ndx.html :tb(c=1,ea=c)
"group2ndx"_group2ndx.html
"ndx2group"_group2ndx.html :tb(c=2,ea=c)
:line

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doc/_sources/Section_commands.txt
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@ -437,9 +437,10 @@ in the command's documentation.
These are additional commands in USER packages, which can be used if
:ref:`LAMMPS is built with the appropriate package <start_3>`.
+------------------------------+
| :doc:`group2ndx <group2ndx>` |
+------------------------------+
+-----------------------------------------------------------+
| :doc:`group2ndx <group2ndx>`
:doc:`ndx2group <group2ndx>` |
+-----------------------------------------------------------+
----------

1
doc/_sources/compute.txt
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@ -229,6 +229,7 @@ section of :ref:`this page <cmd_5>`.
* :doc:`stress/atom <compute_stress_atom>` - stress tensor for each atom
* :doc:`temp <compute_temp>` - temperature of group of atoms
* :doc:`temp/asphere <compute_temp_asphere>` - temperature of aspherical particles
* :doc:`temp/body <compute_temp_body>` - temperature of body particles
* :doc:`temp/chunk <compute_temp_chunk>` - temperature of each chunk
* :doc:`temp/com <compute_temp_com>` - temperature after subtracting center-of-mass velocity
* :doc:`temp/deform <compute_temp_deform>` - temperature excluding box deformation velocity

3
doc/_sources/fix.txt
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@ -206,9 +206,11 @@ of :ref:`this page <cmd_5>`.
* :doc:`nph <fix_nh>` - constant NPH time integration via Nose/Hoover
* :doc:`nphug <fix_nphug>` - constant-stress Hugoniostat integration
* :doc:`nph/asphere <fix_nph_asphere>` - NPH for aspherical particles
* :doc:`nph/body <fix_nve_body>` - NPH for body particles
* :doc:`nph/sphere <fix_nph_sphere>` - NPH for spherical particles
* :doc:`npt <fix_nh>` - constant NPT time integration via Nose/Hoover
* :doc:`npt/asphere <fix_npt_asphere>` - NPT for aspherical particles
* :doc:`npt/body <fix_nve_body>` - NPT for body particles
* :doc:`npt/sphere <fix_npt_sphere>` - NPT for spherical particles
* :doc:`nve <fix_nve>` - constant NVE time integration
* :doc:`nve/asphere <fix_nve_asphere>` - NVE for aspherical particles
@ -221,6 +223,7 @@ of :ref:`this page <cmd_5>`.
* :doc:`nve/tri <fix_nve_tri>` - NVE for triangles
* :doc:`nvt <fix_nh>` - constant NVT time integration via Nose/Hoover
* :doc:`nvt/asphere <fix_nvt_asphere>` - NVT for aspherical particles
* :doc:`nvt/body <fix_nve_body>` - NVT for body particles
* :doc:`nvt/sllod <fix_nvt_sllod>` - NVT for NEMD with SLLOD equations
* :doc:`nvt/sphere <fix_nvt_sphere>` - NVT for spherical particles
* :doc:`oneway <fix_oneway>` - constrain particles on move in one direction

29
doc/_sources/group2ndx.txt
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@ -3,14 +3,18 @@
group2ndx command
=================
ndx2group command
=================
Syntax
""""""
.. parsed-literal::
group2ndx file group-ID ...
ndx2group file group-ID ...
* file = name of index file to write out
* file = name of index file to write out or read in
* zero or more group IDs may be appended
@ -21,20 +25,31 @@ Examples
group2ndx allindex.ndx
group2ndx someindex.ndx upper lower mobile
ndx2group someindex.ndx
ndx2group someindex.ndx mobile
Description
"""""""""""
Write a Gromacs style index file in text format that associates atom IDs
with the corresponding group definitions. This index file can be used
with in combination with Gromacs analysis tools or to import group
definitions into the :doc:`fix colvars <fix_colvars>` input file.
Write or read a Gromacs style index file in text format that associates
atom IDs with the corresponding group definitions. This index file can be
used with in combination with Gromacs analysis tools or to import group
definitions into the :doc:`fix colvars <fix_colvars>` input file. It can
also be used to save and restore group definitions for static groups.
The *group2ndx* command will write group definitions to an index file.
Without specifying any group IDs, all groups will be written to the index
file. When specifying group IDs, only those groups will be written to the
index file. In order to follow the Gromacs conventions, the group *all*
will be renamed to *System* in the index file.
The *ndx2group* command will create of update group definitions from those
stored in an index file. Without specifying any group IDs, all groups except
*System* will be read from the index file and the corresponding groups
recreated. If a group of the same name already exists, it will be completely
reset. When specifying group IDs, those groups, if present, will be read
from the index file and restored.
----------
@ -46,8 +61,8 @@ Restrictions
This command requires that atoms have atom IDs, since this is the
information that is written to the index file.
This fix is part of the USER-COLVARS package. It is only enabled if
LAMMPS was built with that package. See the :ref:`Making LAMMPS <start_3>` section for more info.
These commands are part of the USER-COLVARS package. They are only
enabled if LAMMPS was built with that package. See the :ref:`Making LAMMPS <start_3>` section for more info.
Related commands
""""""""""""""""

1
doc/compute.html
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@ -330,6 +330,7 @@ section of <a class="reference internal" href="Section_commands.html#cmd-5"><spa
<li><a class="reference internal" href="compute_stress_atom.html"><em>stress/atom</em></a> - stress tensor for each atom</li>
<li><a class="reference internal" href="compute_temp.html"><em>temp</em></a> - temperature of group of atoms</li>
<li><a class="reference internal" href="compute_temp_asphere.html"><em>temp/asphere</em></a> - temperature of aspherical particles</li>
<li><a class="reference internal" href="compute_temp_body.html"><em>temp/body</em></a> - temperature of body particles</li>
<li><a class="reference internal" href="compute_temp_chunk.html"><em>temp/chunk</em></a> - temperature of each chunk</li>
<li><a class="reference internal" href="compute_temp_com.html"><em>temp/com</em></a> - temperature after subtracting center-of-mass velocity</li>
<li><a class="reference internal" href="compute_temp_deform.html"><em>temp/deform</em></a> - temperature excluding box deformation velocity</li>

1
doc/compute.txt
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@ -224,6 +224,7 @@ section of "this page"_Section_commands.html#cmd_5.
"stress/atom"_compute_stress_atom.html - stress tensor for each atom
"temp"_compute_temp.html - temperature of group of atoms
"temp/asphere"_compute_temp_asphere.html - temperature of aspherical particles
"temp/body"_compute_temp_body.html - temperature of body particles
"temp/chunk"_compute_temp_chunk.html - temperature of each chunk
"temp/com"_compute_temp_com.html - temperature after subtracting center-of-mass velocity
"temp/deform"_compute_temp_deform.html - temperature excluding box deformation velocity

3
doc/fix.html
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@ -312,9 +312,11 @@ of <a class="reference internal" href="Section_commands.html#cmd-5"><span>this p
<li><a class="reference internal" href="fix_nh.html"><em>nph</em></a> - constant NPH time integration via Nose/Hoover</li>
<li><a class="reference internal" href="fix_nphug.html"><em>nphug</em></a> - constant-stress Hugoniostat integration</li>
<li><a class="reference internal" href="fix_nph_asphere.html"><em>nph/asphere</em></a> - NPH for aspherical particles</li>
<li><a class="reference internal" href="fix_nve_body.html"><em>nph/body</em></a> - NPH for body particles</li>
<li><a class="reference internal" href="fix_nph_sphere.html"><em>nph/sphere</em></a> - NPH for spherical particles</li>
<li><a class="reference internal" href="fix_nh.html"><em>npt</em></a> - constant NPT time integration via Nose/Hoover</li>
<li><a class="reference internal" href="fix_npt_asphere.html"><em>npt/asphere</em></a> - NPT for aspherical particles</li>
<li><a class="reference internal" href="fix_nve_body.html"><em>npt/body</em></a> - NPT for body particles</li>
<li><a class="reference internal" href="fix_npt_sphere.html"><em>npt/sphere</em></a> - NPT for spherical particles</li>
<li><a class="reference internal" href="fix_nve.html"><em>nve</em></a> - constant NVE time integration</li>
<li><a class="reference internal" href="fix_nve_asphere.html"><em>nve/asphere</em></a> - NVE for aspherical particles</li>
@ -327,6 +329,7 @@ of <a class="reference internal" href="Section_commands.html#cmd-5"><span>this p
<li><a class="reference internal" href="fix_nve_tri.html"><em>nve/tri</em></a> - NVE for triangles</li>
<li><a class="reference internal" href="fix_nh.html"><em>nvt</em></a> - constant NVT time integration via Nose/Hoover</li>
<li><a class="reference internal" href="fix_nvt_asphere.html"><em>nvt/asphere</em></a> - NVT for aspherical particles</li>
<li><a class="reference internal" href="fix_nve_body.html"><em>nvt/body</em></a> - NVT for body particles</li>
<li><a class="reference internal" href="fix_nvt_sllod.html"><em>nvt/sllod</em></a> - NVT for NEMD with SLLOD equations</li>
<li><a class="reference internal" href="fix_nvt_sphere.html"><em>nvt/sphere</em></a> - NVT for spherical particles</li>
<li><a class="reference internal" href="fix_oneway.html"><em>oneway</em></a> - constrain particles on move in one direction</li>

3
doc/fix.txt
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@ -201,9 +201,11 @@ of "this page"_Section_commands.html#cmd_5.
"nph"_fix_nh.html - constant NPH time integration via Nose/Hoover
"nphug"_fix_nphug.html - constant-stress Hugoniostat integration
"nph/asphere"_fix_nph_asphere.html - NPH for aspherical particles
"nph/body"_fix_nve_body.html - NPH for body particles
"nph/sphere"_fix_nph_sphere.html - NPH for spherical particles
"npt"_fix_nh.html - constant NPT time integration via Nose/Hoover
"npt/asphere"_fix_npt_asphere.html - NPT for aspherical particles
"npt/body"_fix_nve_body.html - NPT for body particles
"npt/sphere"_fix_npt_sphere.html - NPT for spherical particles
"nve"_fix_nve.html - constant NVE time integration
"nve/asphere"_fix_nve_asphere.html - NVE for aspherical particles
@ -216,6 +218,7 @@ of "this page"_Section_commands.html#cmd_5.
"nve/tri"_fix_nve_tri.html - NVE for triangles
"nvt"_fix_nh.html - constant NVT time integration via Nose/Hoover
"nvt/asphere"_fix_nvt_asphere.html - NVT for aspherical particles
"nvt/body"_fix_nve_body.html - NVT for body particles
"nvt/sllod"_fix_nvt_sllod.html - NVT for NEMD with SLLOD equations
"nvt/sphere"_fix_nvt_sphere.html - NVT for spherical particles
"oneway"_fix_oneway.html - constrain particles on move in one direction

30
doc/group2ndx.html
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@ -126,13 +126,17 @@
<div class="section" id="group2ndx-command">
<span id="index-0"></span><h1>group2ndx command<a class="headerlink" href="#group2ndx-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="ndx2group-command">
<h1>ndx2group command<a class="headerlink" href="#ndx2group-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>group2ndx file group-ID ...
ndx2group file group-ID ...
</pre></div>
</div>
<ul class="simple">
<li>file = name of index file to write out</li>
<li>file = name of index file to write out or read in</li>
<li>zero or more group IDs may be appended</li>
</ul>
</div>
@ -140,27 +144,37 @@
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>group2ndx allindex.ndx
group2ndx someindex.ndx upper lower mobile
ndx2group someindex.ndx
ndx2group someindex.ndx mobile
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Write a Gromacs style index file in text format that associates atom IDs
with the corresponding group definitions. This index file can be used
with in combination with Gromacs analysis tools or to import group
definitions into the <a class="reference internal" href="fix_colvars.html"><em>fix colvars</em></a> input file.</p>
<p>Without specifying any group IDs, all groups will be written to the index
<p>Write or read a Gromacs style index file in text format that associates
atom IDs with the corresponding group definitions. This index file can be
used with in combination with Gromacs analysis tools or to import group
definitions into the <a class="reference internal" href="fix_colvars.html"><em>fix colvars</em></a> input file. It can
also be used to save and restore group definitions for static groups.</p>
<p>The <em>group2ndx</em> command will write group definitions to an index file.
Without specifying any group IDs, all groups will be written to the index
file. When specifying group IDs, only those groups will be written to the
index file. In order to follow the Gromacs conventions, the group <em>all</em>
will be renamed to <em>System</em> in the index file.</p>
<p>The <em>ndx2group</em> command will create of update group definitions from those
stored in an index file. Without specifying any group IDs, all groups except
<em>System</em> will be read from the index file and the corresponding groups
recreated. If a group of the same name already exists, it will be completely
reset. When specifying group IDs, those groups, if present, will be read
from the index file and restored.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This command requires that atoms have atom IDs, since this is the
information that is written to the index file.</p>
<p>This fix is part of the USER-COLVARS package. It is only enabled if
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>These commands are part of the USER-COLVARS package. They are only
enabled if LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>

31
doc/group2ndx.txt
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@ -7,32 +7,45 @@
:line
group2ndx command :h3
ndx2group command :h3
[Syntax:]
group2ndx file group-ID ... :pre
group2ndx file group-ID ...
ndx2group file group-ID ... :pre
file = name of index file to write out :ulb,l
file = name of index file to write out or read in :ulb,l
zero or more group IDs may be appended :l
:ule
[Examples:]
group2ndx allindex.ndx
group2ndx someindex.ndx upper lower mobile :pre
group2ndx someindex.ndx upper lower mobile
ndx2group someindex.ndx
ndx2group someindex.ndx mobile :pre
[Description:]
Write a Gromacs style index file in text format that associates atom IDs
with the corresponding group definitions. This index file can be used
with in combination with Gromacs analysis tools or to import group
definitions into the "fix colvars"_fix_colvars.html input file.
Write or read a Gromacs style index file in text format that associates
atom IDs with the corresponding group definitions. This index file can be
used with in combination with Gromacs analysis tools or to import group
definitions into the "fix colvars"_fix_colvars.html input file. It can
also be used to save and restore group definitions for static groups.
The {group2ndx} command will write group definitions to an index file.
Without specifying any group IDs, all groups will be written to the index
file. When specifying group IDs, only those groups will be written to the
index file. In order to follow the Gromacs conventions, the group {all}
will be renamed to {System} in the index file.
The {ndx2group} command will create of update group definitions from those
stored in an index file. Without specifying any group IDs, all groups except
{System} will be read from the index file and the corresponding groups
recreated. If a group of the same name already exists, it will be completely
reset. When specifying group IDs, those groups, if present, will be read
from the index file and restored.
:line
[Restrictions:]
@ -40,8 +53,8 @@ will be renamed to {System} in the index file.
This command requires that atoms have atom IDs, since this is the
information that is written to the index file.
This fix is part of the USER-COLVARS package. It is only enabled if
LAMMPS was built with that package. See the "Making
These commands are part of the USER-COLVARS package. They are only
enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]

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