git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15172 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/html/Section_commands.html

@@ -622,9 +622,9 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.</p>
 <col width="13%" />
 <col width="11%" />
 <col width="12%" />
+<col width="12%" />
 <col width="11%" />
-<col width="16%" />
+<col width="15%" />
-<col width="11%" />
 <col width="12%" />
 </colgroup>
 <tbody valign="top">
@@ -730,38 +730,38 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.</p>
 <tr class="row-even"><td><a class="reference internal" href="fix_setforce.html"><span class="doc">setforce (k)</span></a></td>
 <td><a class="reference internal" href="fix_shake.html"><span class="doc">shake</span></a></td>
 <td><a class="reference internal" href="fix_spring.html"><span class="doc">spring</span></a></td>
+<td><a class="reference internal" href="fix_spring_chunk.html"><span class="doc">spring/chunk</span></a></td>
 <td><a class="reference internal" href="fix_spring_rg.html"><span class="doc">spring/rg</span></a></td>
 <td><a class="reference internal" href="fix_spring_self.html"><span class="doc">spring/self</span></a></td>
 <td><a class="reference internal" href="fix_srd.html"><span class="doc">srd</span></a></td>
 <td><a class="reference internal" href="fix_store_force.html"><span class="doc">store/force</span></a></td>
-<td><a class="reference internal" href="fix_store_state.html"><span class="doc">store/state</span></a></td>
 </tr>
-<tr class="row-odd"><td><a class="reference internal" href="fix_temp_berendsen.html"><span class="doc">temp/berendsen</span></a></td>
+<tr class="row-odd"><td><a class="reference internal" href="fix_store_state.html"><span class="doc">store/state</span></a></td>
+<td><a class="reference internal" href="fix_temp_berendsen.html"><span class="doc">temp/berendsen</span></a></td>
 <td><a class="reference internal" href="fix_temp_csvr.html"><span class="doc">temp/csld</span></a></td>
 <td><a class="reference internal" href="fix_temp_csvr.html"><span class="doc">temp/csvr</span></a></td>
 <td><a class="reference internal" href="fix_temp_rescale.html"><span class="doc">temp/rescale</span></a></td>
 <td><a class="reference internal" href="fix_tfmc.html"><span class="doc">tfmc</span></a></td>
 <td><a class="reference internal" href="fix_thermal_conductivity.html"><span class="doc">thermal/conductivity</span></a></td>
 <td><a class="reference internal" href="fix_tmd.html"><span class="doc">tmd</span></a></td>
-<td><a class="reference internal" href="fix_ttm.html"><span class="doc">ttm</span></a></td>
 </tr>
-<tr class="row-even"><td><a class="reference internal" href="fix_tune_kspace.html"><span class="doc">tune/kspace</span></a></td>
+<tr class="row-even"><td><a class="reference internal" href="fix_ttm.html"><span class="doc">ttm</span></a></td>
+<td><a class="reference internal" href="fix_tune_kspace.html"><span class="doc">tune/kspace</span></a></td>
 <td><a class="reference internal" href="fix_vector.html"><span class="doc">vector</span></a></td>
 <td><a class="reference internal" href="fix_viscosity.html"><span class="doc">viscosity</span></a></td>
 <td><a class="reference internal" href="fix_viscous.html"><span class="doc">viscous</span></a></td>
 <td><a class="reference internal" href="fix_wall.html"><span class="doc">wall/colloid</span></a></td>
 <td><a class="reference internal" href="fix_wall_gran.html"><span class="doc">wall/gran</span></a></td>
 <td><a class="reference internal" href="fix_wall.html"><span class="doc">wall/harmonic</span></a></td>
-<td><a class="reference internal" href="fix_wall.html"><span class="doc">wall/lj1043</span></a></td>
 </tr>
-<tr class="row-odd"><td><a class="reference internal" href="fix_wall.html"><span class="doc">wall/lj126</span></a></td>
+<tr class="row-odd"><td><a class="reference internal" href="fix_wall.html"><span class="doc">wall/lj1043</span></a></td>
+<td><a class="reference internal" href="fix_wall.html"><span class="doc">wall/lj126</span></a></td>
 <td><a class="reference internal" href="fix_wall.html"><span class="doc">wall/lj93</span></a></td>
 <td><a class="reference internal" href="fix_wall_piston.html"><span class="doc">wall/piston</span></a></td>
 <td><a class="reference internal" href="fix_wall_reflect.html"><span class="doc">wall/reflect (k)</span></a></td>
 <td><a class="reference internal" href="fix_wall_region.html"><span class="doc">wall/region</span></a></td>
 <td><a class="reference internal" href="fix_wall_srd.html"><span class="doc">wall/srd</span></a></td>
 <td>&nbsp;</td>
-<td>&nbsp;</td>
 </tr>
 </tbody>
 </table>

doc/html/_sources/Section_commands.txt

@@ -457,37 +457,37 @@ with the :doc:`appropriate accelerated package <Section_accelerate>`.
 This is indicated by additional letters in parenthesis: g = GPU, i =
 USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
 
-+------------------------------------------------------+----------------------------------------------+----------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+--------------------------------------+------------------------------------------+
++------------------------------------------------------+----------------------------------------------+----------------------------------------+------------------------------------------+--------------------------------------------+----------------------------------------+--------------------------------------------------------+------------------------------------------+
 | :doc:`adapt <fix_adapt>`                             | :doc:`addforce <fix_addforce>`               | :doc:`append/atoms <fix_append_atoms>` | :doc:`atom/swap <fix_atom_swap>`         | :doc:`aveforce <fix_aveforce>`             | :doc:`ave/atom <fix_ave_atom>`         | :doc:`ave/chunk <fix_ave_chunk>`                       | :doc:`ave/correlate <fix_ave_correlate>` |
-+------------------------------------------------------+----------------------------------------------+----------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+--------------------------------------+------------------------------------------+
++------------------------------------------------------+----------------------------------------------+----------------------------------------+------------------------------------------+--------------------------------------------+----------------------------------------+--------------------------------------------------------+------------------------------------------+
 | :doc:`ave/histo <fix_ave_histo>`                     | :doc:`ave/histo/weight <fix_ave_histo>`      | :doc:`ave/time <fix_ave_time>`         | :doc:`balance <fix_balance>`             | :doc:`bond/break <fix_bond_break>`         | :doc:`bond/create <fix_bond_create>`   | :doc:`bond/swap <fix_bond_swap>`                       | :doc:`box/relax <fix_box_relax>`         |
-+------------------------------------------------------+----------------------------------------------+----------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+--------------------------------------+------------------------------------------+
++------------------------------------------------------+----------------------------------------------+----------------------------------------+------------------------------------------+--------------------------------------------+----------------------------------------+--------------------------------------------------------+------------------------------------------+
 | :doc:`deform (k) <fix_deform>`                       | :doc:`deposit <fix_deposit>`                 | :doc:`drag <fix_drag>`                 | :doc:`dt/reset <fix_dt_reset>`           | :doc:`efield <fix_efield>`                 | :doc:`ehex <fix_ehex>`                 | :doc:`enforce2d <fix_enforce2d>`                       | :doc:`evaporate <fix_evaporate>`         |
-+------------------------------------------------------+----------------------------------------------+----------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+--------------------------------------+------------------------------------------+
++------------------------------------------------------+----------------------------------------------+----------------------------------------+------------------------------------------+--------------------------------------------+----------------------------------------+--------------------------------------------------------+------------------------------------------+
 | :doc:`external <fix_external>`                       | :doc:`freeze <fix_freeze>`                   | :doc:`gcmc <fix_gcmc>`                 | :doc:`gld <fix_gld>`                     | :doc:`gravity (o) <fix_gravity>`           | :doc:`heat <fix_heat>`                 | :doc:`indent <fix_indent>`                             | :doc:`langevin (k) <fix_langevin>`       |
-+------------------------------------------------------+----------------------------------------------+----------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+--------------------------------------+------------------------------------------+
++------------------------------------------------------+----------------------------------------------+----------------------------------------+------------------------------------------+--------------------------------------------+----------------------------------------+--------------------------------------------------------+------------------------------------------+
 | :doc:`lineforce <fix_lineforce>`                     | :doc:`momentum <fix_momentum>`               | :doc:`move <fix_move>`                 | :doc:`msst <fix_msst>`                   | :doc:`neb <fix_neb>`                       | :doc:`nph (ko) <fix_nh>`               | :doc:`nphug (o) <fix_nphug>`                           | :doc:`nph/asphere (o) <fix_nph_asphere>` |
-+------------------------------------------------------+----------------------------------------------+----------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+--------------------------------------+------------------------------------------+
++------------------------------------------------------+----------------------------------------------+----------------------------------------+------------------------------------------+--------------------------------------------+----------------------------------------+--------------------------------------------------------+------------------------------------------+
 | :doc:`nph/body <fix_nph_body>`                       | :doc:`nph/sphere (o) <fix_nph_sphere>`       | :doc:`npt (kio) <fix_nh>`              | :doc:`npt/asphere (o) <fix_npt_asphere>` | :doc:`npt/body <fix_npt_body>`             | :doc:`npt/sphere (o) <fix_npt_sphere>` | :doc:`nve (kio) <fix_nve>`                             | :doc:`nve/asphere (i) <fix_nve_asphere>` |
-+------------------------------------------------------+----------------------------------------------+----------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+--------------------------------------+------------------------------------------+
++------------------------------------------------------+----------------------------------------------+----------------------------------------+------------------------------------------+--------------------------------------------+----------------------------------------+--------------------------------------------------------+------------------------------------------+
 | :doc:`nve/asphere/noforce <fix_nve_asphere_noforce>` | :doc:`nve/body <fix_nve_body>`               | :doc:`nve/limit <fix_nve_limit>`       | :doc:`nve/line <fix_nve_line>`           | :doc:`nve/noforce <fix_nve_noforce>`       | :doc:`nve/sphere (o) <fix_nve_sphere>` | :doc:`nve/tri <fix_nve_tri>`                           | :doc:`nvt (iko) <fix_nh>`                |
-+------------------------------------------------------+----------------------------------------------+----------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+--------------------------------------+------------------------------------------+
++------------------------------------------------------+----------------------------------------------+----------------------------------------+------------------------------------------+--------------------------------------------+----------------------------------------+--------------------------------------------------------+------------------------------------------+
 | :doc:`nvt/asphere (o) <fix_nvt_asphere>`             | :doc:`nvt/body <fix_nvt_body>`               | :doc:`nvt/sllod (io) <fix_nvt_sllod>`  | :doc:`nvt/sphere (o) <fix_nvt_sphere>`   | :doc:`oneway <fix_oneway>`                 | :doc:`orient/fcc <fix_orient_fcc>`     | :doc:`planeforce <fix_planeforce>`                     | :doc:`poems <fix_poems>`                 |
-+------------------------------------------------------+----------------------------------------------+----------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+--------------------------------------+------------------------------------------+
++------------------------------------------------------+----------------------------------------------+----------------------------------------+------------------------------------------+--------------------------------------------+----------------------------------------+--------------------------------------------------------+------------------------------------------+
 | :doc:`pour <fix_pour>`                               | :doc:`press/berendsen <fix_press_berendsen>` | :doc:`print <fix_print>`               | :doc:`property/atom <fix_property_atom>` | :doc:`qeq/comb (o) <fix_qeq_comb>`         | :doc:`qeq/dynamic <fix_qeq>`           | :doc:`qeq/fire <fix_qeq>`                              | :doc:`qeq/point <fix_qeq>`               |
-+------------------------------------------------------+----------------------------------------------+----------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+--------------------------------------+------------------------------------------+
++------------------------------------------------------+----------------------------------------------+----------------------------------------+------------------------------------------+--------------------------------------------+----------------------------------------+--------------------------------------------------------+------------------------------------------+
 | :doc:`qeq/shielded <fix_qeq>`                        | :doc:`qeq/slater <fix_qeq>`                  | :doc:`rattle <fix_shake>`              | :doc:`reax/bonds <fix_reax_bonds>`       | :doc:`recenter <fix_recenter>`             | :doc:`restrain <fix_restrain>`         | :doc:`rigid (o) <fix_rigid>`                           | :doc:`rigid/nph (o) <fix_rigid>`         |
-+------------------------------------------------------+----------------------------------------------+----------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+--------------------------------------+------------------------------------------+
++------------------------------------------------------+----------------------------------------------+----------------------------------------+------------------------------------------+--------------------------------------------+----------------------------------------+--------------------------------------------------------+------------------------------------------+
 | :doc:`rigid/npt (o) <fix_rigid>`                     | :doc:`rigid/nve (o) <fix_rigid>`             | :doc:`rigid/nvt (o) <fix_rigid>`       | :doc:`rigid/small (o) <fix_rigid>`       | :doc:`rigid/small/nph <fix_rigid>`         | :doc:`rigid/small/npt <fix_rigid>`     | :doc:`rigid/small/nve <fix_rigid>`                     | :doc:`rigid/small/nvt <fix_rigid>`       |
-+------------------------------------------------------+----------------------------------------------+----------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+--------------------------------------+------------------------------------------+
++------------------------------------------------------+----------------------------------------------+----------------------------------------+------------------------------------------+--------------------------------------------+----------------------------------------+--------------------------------------------------------+------------------------------------------+
-| :doc:`setforce (k) <fix_setforce>`                   | :doc:`shake <fix_shake>`                     | :doc:`spring <fix_spring>`             | :doc:`spring/rg <fix_spring_rg>`           | :doc:`spring/self <fix_spring_self>` | :doc:`srd <fix_srd>`                                   | :doc:`store/force <fix_store_force>` | :doc:`store/state <fix_store_state>`     |
+| :doc:`setforce (k) <fix_setforce>`                   | :doc:`shake <fix_shake>`                     | :doc:`spring <fix_spring>`             | :doc:`spring/chunk <fix_spring_chunk>`   | :doc:`spring/rg <fix_spring_rg>`           | :doc:`spring/self <fix_spring_self>`   | :doc:`srd <fix_srd>`                                   | :doc:`store/force <fix_store_force>`     |
-+------------------------------------------------------+----------------------------------------------+----------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+--------------------------------------+------------------------------------------+
++------------------------------------------------------+----------------------------------------------+----------------------------------------+------------------------------------------+--------------------------------------------+----------------------------------------+--------------------------------------------------------+------------------------------------------+
-| :doc:`temp/berendsen <fix_temp_berendsen>`           | :doc:`temp/csld <fix_temp_csvr>`             | :doc:`temp/csvr <fix_temp_csvr>`       | :doc:`temp/rescale <fix_temp_rescale>`     | :doc:`tfmc <fix_tfmc>`               | :doc:`thermal/conductivity <fix_thermal_conductivity>` | :doc:`tmd <fix_tmd>`                 | :doc:`ttm <fix_ttm>`                     |
+| :doc:`store/state <fix_store_state>`                 | :doc:`temp/berendsen <fix_temp_berendsen>`   | :doc:`temp/csld <fix_temp_csvr>`       | :doc:`temp/csvr <fix_temp_csvr>`         | :doc:`temp/rescale <fix_temp_rescale>`     | :doc:`tfmc <fix_tfmc>`                 | :doc:`thermal/conductivity <fix_thermal_conductivity>` | :doc:`tmd <fix_tmd>`                     |
-+------------------------------------------------------+----------------------------------------------+----------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+--------------------------------------+------------------------------------------+
++------------------------------------------------------+----------------------------------------------+----------------------------------------+------------------------------------------+--------------------------------------------+----------------------------------------+--------------------------------------------------------+------------------------------------------+
-| :doc:`tune/kspace <fix_tune_kspace>`                 | :doc:`vector <fix_vector>`                   | :doc:`viscosity <fix_viscosity>`       | :doc:`viscous <fix_viscous>`               | :doc:`wall/colloid <fix_wall>`       | :doc:`wall/gran <fix_wall_gran>`                       | :doc:`wall/harmonic <fix_wall>`      | :doc:`wall/lj1043 <fix_wall>`            |
+| :doc:`ttm <fix_ttm>`                                 | :doc:`tune/kspace <fix_tune_kspace>`         | :doc:`vector <fix_vector>`             | :doc:`viscosity <fix_viscosity>`         | :doc:`viscous <fix_viscous>`               | :doc:`wall/colloid <fix_wall>`         | :doc:`wall/gran <fix_wall_gran>`                       | :doc:`wall/harmonic <fix_wall>`          |
-+------------------------------------------------------+----------------------------------------------+----------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+--------------------------------------+------------------------------------------+
++------------------------------------------------------+----------------------------------------------+----------------------------------------+------------------------------------------+--------------------------------------------+----------------------------------------+--------------------------------------------------------+------------------------------------------+
-| :doc:`wall/lj126 <fix_wall>`                         | :doc:`wall/lj93 <fix_wall>`                  | :doc:`wall/piston <fix_wall_piston>`   | :doc:`wall/reflect (k) <fix_wall_reflect>` | :doc:`wall/region <fix_wall_region>` | :doc:`wall/srd <fix_wall_srd>`                         |                                      |                                          |
+| :doc:`wall/lj1043 <fix_wall>`                        | :doc:`wall/lj126 <fix_wall>`                 | :doc:`wall/lj93 <fix_wall>`            | :doc:`wall/piston <fix_wall_piston>`     | :doc:`wall/reflect (k) <fix_wall_reflect>` | :doc:`wall/region <fix_wall_region>`   | :doc:`wall/srd <fix_wall_srd>`                         |                                          |
-+------------------------------------------------------+----------------------------------------------+----------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+--------------------------------------+------------------------------------------+
++------------------------------------------------------+----------------------------------------------+----------------------------------------+------------------------------------------+--------------------------------------------+----------------------------------------+--------------------------------------------------------+------------------------------------------+
 
 These are additional fix styles in USER packages, which can be used if
 :ref:`LAMMPS is built with the appropriate package <start_3>`.

doc/html/_sources/fix.txt

@@ -249,6 +249,7 @@ of :ref:`this page <cmd_5>`.
 * :doc:`setforce <fix_setforce>` - set the force on each atom
 * :doc:`shake <fix_shake>` - SHAKE constraints on bonds and/or angles
 * :doc:`spring <fix_spring>` - apply harmonic spring force to group of atoms
+* :doc:`spring/chunk <fix_spring_chunk>` - apply harmonic spring force to each chunk of atoms
 * :doc:`spring/rg <fix_spring_rg>` - spring on radius of gyration of      group of atoms
 * :doc:`spring/self <fix_spring_self>` - spring from each atom to its origin
 * :doc:`srd <fix_srd>` - stochastic rotation dynamics (SRD)

doc/html/_sources/fix_rigid.txt

@@ -223,10 +223,11 @@ via several options.
 
 .. note::
 
-   With fix rigid/small, which requires bodystyle *molecule*\ , you
+   With fix rigid/small, which requires that *bodystyle* be
-   can define a system that has no rigid bodies initially.  This is
+   specified as *molecule*\ , you can define a system that has no rigid
-   useful when you are using the *mol* keyword in conjunction with
+   bodies initially.  This is useful when you are using the *mol* keyword
-   another fix that is adding rigid bodies on-the-fly, such as :doc:`fix deposit <fix_deposit>` or :doc:`fix pour <fix_pour>`.
+   in conjunction with another fix that is adding rigid bodies on-the-fly
+   as molecules, such as :doc:`fix deposit <fix_deposit>` or :doc:`fix pour <fix_pour>`.
 
 For bodystyle *single* the entire fix group of atoms is treated as one
 rigid body.  This option is only allowed for fix rigid and its

doc/html/_sources/fix_spring_chunk.txt

@@ -0,0 +1,94 @@
+.. index:: fix spring/chunk
+
+fix spring/chunk command
+========================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix ID group-ID spring/chunk K chunkID comID
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* spring/chunk = style name of this fix command
+* K = spring constant for each chunk (force/distance units)
+* chunkID = ID of :doc:`compute chunk/atom <compute_chunk_atom>` command
+* comID = ID of :doc:`compute com/chunk <compute_com_chunk>` command
+
+Examples
+""""""""
+
+.. parsed-literal::
+
+   fix restrain all spring/chunk 100 chunkID comID
+
+Description
+"""""""""""
+
+Apply a spring force to the center-of-mass (COM) of chunks of atoms as
+defined by the :doc:`compute chunk/atom <compute_chunk_atom>` command.
+Chunks can be molecules or spatial bins or other groupings of atoms.
+This is a way of tethering each chunk to its initial COM coordinates.
+
+The *chunkID* is the ID of a compute chunk/atom command defined in the
+input script.  It is used to define the chunks.  The *comID* is the ID
+of a compute com/chunk command defined in the input script.  It is
+used to compute the COMs of each chunk.
+
+At the beginning of the first :doc:`run <run>` or
+:doc:`minimize <miminize>` command after this fix is defined, the
+initial COM of each chunk is calculated and stored as R0c, where C is
+the chunk number.  Thereafter, at every timestep (or minimization
+iteration), the current COM of each chunk is calculated as Rc.  A
+restoring force of magnitude K (Rc - R0c) Mi / Mc is applied to each
+atom in each chunk where *K* is the specified spring constant, Mi is
+the mass of the atom, and Mc is the total mass of all atoms in the
+chunk.  Note that *K* thus represents the spring constant for the
+total force on each chunk of atoms, not for a spring applied to each
+atom.
+
+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 <fix_modify>` *energy* option is supported by this
+fix to add the energy stored in all the springs to the system's potential
+energy as part of :doc:`thermodynamic output <thermo_style>`.
+
+This fix computes a global scalar which can be accessed by various
+:ref:`output commands <howto_15>`.  The scalar is the
+energy of all the springs, i.e. 0.5 * K * r^2 per-spring.
+
+The scalar value calculated by this fix is "extensive".
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.
+
+The forces due to this fix are imposed during an energy minimization,
+invoked by the :doc:`minimize <minimize>` command.
+
+.. note::
+
+   If you want the spring energies to be included in the total
+   potential energy of the system (the quantity being minimized), you
+   MUST enable the :doc:`fix_modify <fix_modify>` *energy* option for this
+   fix.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`fix spring <fix_spring>`, :doc:`fix spring/self <fix_spring_self>`,
+:doc:`fix spring/rg <fix_spring_rg>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Section_commands.html#comm

doc/html/fix.html

@@ -355,6 +355,7 @@ of <a class="reference internal" href="Section_commands.html#cmd-5"><span class=
 <li><a class="reference internal" href="fix_setforce.html"><span class="doc">setforce</span></a> - set the force on each atom</li>
 <li><a class="reference internal" href="fix_shake.html"><span class="doc">shake</span></a> - SHAKE constraints on bonds and/or angles</li>
 <li><a class="reference internal" href="fix_spring.html"><span class="doc">spring</span></a> - apply harmonic spring force to group of atoms</li>
+<li><a class="reference internal" href="fix_spring_chunk.html"><span class="doc">spring/chunk</span></a> - apply harmonic spring force to each chunk of atoms</li>
 <li><a class="reference internal" href="fix_spring_rg.html"><span class="doc">spring/rg</span></a> - spring on radius of gyration of      group of atoms</li>
 <li><a class="reference internal" href="fix_spring_self.html"><span class="doc">spring/self</span></a> - spring from each atom to its origin</li>
 <li><a class="reference internal" href="fix_srd.html"><span class="doc">srd</span></a> - stochastic rotation dynamics (SRD)</li>

doc/html/fix_rigid.html

@@ -331,10 +331,11 @@ most one rigid body.  Which atoms are in which bodies can be defined
 via several options.</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
-<p class="last">With fix rigid/small, which requires bodystyle <em>molecule</em>, you
+<p class="last">With fix rigid/small, which requires that <em>bodystyle</em> be
-can define a system that has no rigid bodies initially.  This is
+specified as <em>molecule</em>, you can define a system that has no rigid
-useful when you are using the <em>mol</em> keyword in conjunction with
+bodies initially.  This is useful when you are using the <em>mol</em> keyword
-another fix that is adding rigid bodies on-the-fly, such as <a class="reference internal" href="fix_deposit.html"><span class="doc">fix deposit</span></a> or <a class="reference internal" href="fix_pour.html"><span class="doc">fix pour</span></a>.</p>
+in conjunction with another fix that is adding rigid bodies on-the-fly
+as molecules, such as <a class="reference internal" href="fix_deposit.html"><span class="doc">fix deposit</span></a> or <a class="reference internal" href="fix_pour.html"><span class="doc">fix pour</span></a>.</p>
 </div>
 <p>For bodystyle <em>single</em> the entire fix group of atoms is treated as one
 rigid body.  This option is only allowed for fix rigid and its

doc/html/fix_spring_chunk.html

@@ -0,0 +1,267 @@
+
+
+<!DOCTYPE html>
+<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
+<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
+<head>
+  <meta charset="utf-8">
+  
+  <meta name="viewport" content="width=device-width, initial-scale=1.0">
+  
+  <title>fix spring/chunk command &mdash; LAMMPS documentation</title>
+  
+
+  
+  
+
+  
+
+  
+  
+    
+
+  
+
+  
+  
+    <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
+  
+
+  
+    <link rel="stylesheet" href="_static/sphinxcontrib-images/LightBox2/lightbox2/css/lightbox.css" type="text/css" />
+  
+
+  
+    <link rel="top" title="LAMMPS documentation" href="index.html"/> 
+
+  
+  <script src="_static/js/modernizr.min.js"></script>
+
+</head>
+
+<body class="wy-body-for-nav" role="document">
+
+  <div class="wy-grid-for-nav">
+
+    
+    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
+      <div class="wy-side-nav-search">
+        
+
+        
+          <a href="Manual.html" class="icon icon-home"> LAMMPS
+        
+
+        
+        </a>
+
+        
+<div role="search">
+  <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
+    <input type="text" name="q" placeholder="Search docs" />
+    <input type="hidden" name="check_keywords" value="yes" />
+    <input type="hidden" name="area" value="default" />
+  </form>
+</div>
+
+        
+      </div>
+
+      <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
+        
+          
+          
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
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+    <li>fix spring/chunk command</li>
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+            <a href="Section_commands.html#comm">Commands</a>
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+           <div itemprop="articleBody">
+            
+  <div class="section" id="fix-spring-chunk-command">
+<span id="index-0"></span><h1>fix spring/chunk command</h1>
+<div class="section" id="syntax">
+<h2>Syntax</h2>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">spring</span><span class="o">/</span><span class="n">chunk</span> <span class="n">K</span> <span class="n">chunkID</span> <span class="n">comID</span>
+</pre></div>
+</div>
+<ul class="simple">
+<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
+<li>spring/chunk = style name of this fix command</li>
+<li>K = spring constant for each chunk (force/distance units)</li>
+<li>chunkID = ID of <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command</li>
+<li>comID = ID of <a class="reference internal" href="compute_com_chunk.html"><span class="doc">compute com/chunk</span></a> command</li>
+</ul>
+</div>
+<div class="section" id="examples">
+<h2>Examples</h2>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">restrain</span> <span class="nb">all</span> <span class="n">spring</span><span class="o">/</span><span class="n">chunk</span> <span class="mi">100</span> <span class="n">chunkID</span> <span class="n">comID</span>
+</pre></div>
+</div>
+</div>
+<div class="section" id="description">
+<h2>Description</h2>
+<p>Apply a spring force to the center-of-mass (COM) of chunks of atoms as
+defined by the <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command.
+Chunks can be molecules or spatial bins or other groupings of atoms.
+This is a way of tethering each chunk to its initial COM coordinates.</p>
+<p>The <em>chunkID</em> is the ID of a compute chunk/atom command defined in the
+input script.  It is used to define the chunks.  The <em>comID</em> is the ID
+of a compute com/chunk command defined in the input script.  It is
+used to compute the COMs of each chunk.</p>
+<p>At the beginning of the first <a class="reference internal" href="run.html"><span class="doc">run</span></a> or
+<span class="xref doc">minimize</span> command after this fix is defined, the
+initial COM of each chunk is calculated and stored as R0c, where C is
+the chunk number.  Thereafter, at every timestep (or minimization
+iteration), the current COM of each chunk is calculated as Rc.  A
+restoring force of magnitude K (Rc - R0c) Mi / Mc is applied to each
+atom in each chunk where <em>K</em> is the specified spring constant, Mi is
+the mass of the atom, and Mc is the total mass of all atoms in the
+chunk.  Note that <em>K</em> thus represents the spring constant for the
+total force on each chunk of atoms, not for a spring applied to each
+atom.</p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
+<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option is supported by this
+fix to add the energy stored in all the springs to the system&#8217;s potential
+energy as part of <a class="reference internal" href="thermo_style.html"><span class="doc">thermodynamic output</span></a>.</p>
+<p>This fix computes a global scalar which can be accessed by various
+<a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>.  The scalar is the
+energy of all the springs, i.e. 0.5 * K * r^2 per-spring.</p>
+<p>The scalar value calculated by this fix is &#8220;extensive&#8221;.</p>
+<p>No parameter of this fix can be used with the <em>start/stop</em> keywords of
+the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command.</p>
+<p>The forces due to this fix are imposed during an energy minimization,
+invoked by the <a class="reference internal" href="minimize.html"><span class="doc">minimize</span></a> command.</p>
+<div class="admonition note">
+<p class="first admonition-title">Note</p>
+<p class="last">If you want the spring energies to be included in the total
+potential energy of the system (the quantity being minimized), you
+MUST enable the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option for this
+fix.</p>
+</div>
+</div>
+<div class="section" id="restrictions">
+<h2>Restrictions</h2>
+<blockquote>
+<div>none</div></blockquote>
+</div>
+<div class="section" id="related-commands">
+<h2>Related commands</h2>
+<p><a class="reference internal" href="fix_spring.html"><span class="doc">fix spring</span></a>, <a class="reference internal" href="fix_spring_self.html"><span class="doc">fix spring/self</span></a>,
+<a class="reference internal" href="fix_spring_rg.html"><span class="doc">fix spring/rg</span></a></p>
+<p><strong>Default:</strong> none</p>
+</div>
+</div>
+
+
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doc/html/genindex.html

@@ -1420,6 +1420,10 @@
   </dt>
 
       
+  <dt><a href="fix_spring_chunk.html#index-0">fix spring/chunk</a>
+  </dt>
+
+      
   <dt><a href="fix_spring_rg.html#index-0">fix spring/rg</a>
   </dt>