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sjplimp 2016-06-14 22:33:59 +00:00
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18
doc/html/Section_commands.html
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@ -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="11%" />
<col width="15%" />
<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>

62
doc/html/_sources/Section_commands.txt
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@ -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:`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:`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:`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:`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/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:`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:`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/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>`.

1
doc/html/_sources/fix.txt
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@ -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)

9
doc/html/_sources/fix_rigid.txt
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@ -223,10 +223,11 @@ via several options.
.. note::
With fix rigid/small, which requires bodystyle *molecule*\ , you
can define a system that has no rigid bodies initially. This is
useful when you are using the *mol* keyword in conjunction with
another fix that is adding rigid bodies on-the-fly, such as :doc:`fix deposit <fix_deposit>` or :doc:`fix pour <fix_pour>`.
With fix rigid/small, which requires that *bodystyle* be
specified as *molecule*\ , you can define a system that has no rigid
bodies initially. This is useful when you are using the *mol* keyword
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

94
doc/html/_sources/fix_spring_chunk.txt Normal file
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@ -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

1
doc/html/fix.html
View File

@ -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>

9
doc/html/fix_rigid.html
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@ -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
can define a system that has no rigid bodies initially. This is
useful when you are using the <em>mol</em> keyword in conjunction with
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>
<p class="last">With fix rigid/small, which requires that <em>bodystyle</em> be
specified as <em>molecule</em>, you can define a system that has no rigid
bodies initially. This is useful when you are using the <em>mol</em> keyword
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

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<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>
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</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>

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