Merge remote-tracking branch 'lammps-ro/master' into lammps-icms
# Resolved Conflicts: # doc/Manual.txt
This commit is contained in:
Axel Kohlmeyer
@ -135,7 +135,7 @@
|
||||
<H1></H1><div class="section" id="lammps-documentation">
|
||||
<h1>LAMMPS-ICMS Documentation<a class="headerlink" href="#lammps-documentation" title="Permalink to this headline">¶</a></h1>
|
||||
<div class="section" id="mar-2016-version">
|
||||
<h2>10 Mar 2016 version<a class="headerlink" href="#mar-2016-version" title="Permalink to this headline">¶</a></h2>
|
||||
<h2>14 Mar 2016 version<a class="headerlink" href="#mar-2016-version" title="Permalink to this headline">¶</a></h2>
|
||||
</div>
|
||||
<div class="section" id="version-info">
|
||||
<h2>Version info:<a class="headerlink" href="#version-info" title="Permalink to this headline">¶</a></h2>
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
<!-- HTML_ONLY -->
|
||||
<HEAD>
|
||||
<TITLE>LAMMPS-ICMS Users Manual</TITLE>
|
||||
<META NAME="docnumber" CONTENT="10 Mar 2016 version">
|
||||
<META NAME="docnumber" CONTENT="14 Mar 2016 version">
|
||||
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
|
||||
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
|
||||
</HEAD>
|
||||
@ -21,7 +21,7 @@
|
||||
<H1></H1>
|
||||
|
||||
LAMMPS-ICMS Documentation :c,h3
|
||||
10 Mar 2016 version :c,h4
|
||||
14 Mar 2016 version :c,h4
|
||||
|
||||
Version info: :h4
|
||||
|
||||
|
||||
@ -847,97 +847,97 @@ letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
|
||||
KOKKOS, o = USER-OMP, t = OPT.</p>
|
||||
<table border="1" class="docutils">
|
||||
<colgroup>
|
||||
<col width="17%" />
|
||||
<col width="16%" />
|
||||
<col width="19%" />
|
||||
<col width="16%" />
|
||||
<col width="15%" />
|
||||
<col width="16%" />
|
||||
<col width="17%" />
|
||||
</colgroup>
|
||||
<tbody valign="top">
|
||||
<tr class="row-odd"><td><a class="reference internal" href="compute_angle_local.html"><em>angle/local</em></a></td>
|
||||
<td><a class="reference internal" href="compute_angmom_chunk.html"><em>angmom/chunk</em></a></td>
|
||||
<td><a class="reference internal" href="compute_body_local.html"><em>body/local</em></a></td>
|
||||
<td><a class="reference internal" href="compute_bond.html"><em>bond</em></a></td>
|
||||
<td><a class="reference internal" href="compute_bond_local.html"><em>bond/local</em></a></td>
|
||||
<td><a class="reference internal" href="compute_centro_atom.html"><em>centro/atom</em></a></td>
|
||||
<td><a class="reference internal" href="compute_chunk_atom.html"><em>chunk/atom</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-even"><td><a class="reference internal" href="compute_cluster_atom.html"><em>cluster/atom</em></a></td>
|
||||
<tr class="row-even"><td><a class="reference internal" href="compute_chunk_atom.html"><em>chunk/atom</em></a></td>
|
||||
<td><a class="reference internal" href="compute_cluster_atom.html"><em>cluster/atom</em></a></td>
|
||||
<td><a class="reference internal" href="compute_cna_atom.html"><em>cna/atom</em></a></td>
|
||||
<td><a class="reference internal" href="compute_com.html"><em>com</em></a></td>
|
||||
<td><a class="reference internal" href="compute_com_chunk.html"><em>com/chunk</em></a></td>
|
||||
<td><a class="reference internal" href="compute_contact_atom.html"><em>contact/atom</em></a></td>
|
||||
<td><a class="reference internal" href="compute_coord_atom.html"><em>coord/atom</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="compute_damage_atom.html"><em>damage/atom</em></a></td>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="compute_coord_atom.html"><em>coord/atom</em></a></td>
|
||||
<td><a class="reference internal" href="compute_damage_atom.html"><em>damage/atom</em></a></td>
|
||||
<td><a class="reference internal" href="compute_dihedral_local.html"><em>dihedral/local</em></a></td>
|
||||
<td><a class="reference internal" href="compute_dilatation_atom.html"><em>dilatation/atom</em></a></td>
|
||||
<td><a class="reference internal" href="compute_displace_atom.html"><em>displace/atom</em></a></td>
|
||||
<td><a class="reference internal" href="compute_erotate_asphere.html"><em>erotate/asphere</em></a></td>
|
||||
<td><a class="reference internal" href="compute_erotate_rigid.html"><em>erotate/rigid</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-even"><td><a class="reference internal" href="compute_erotate_sphere.html"><em>erotate/sphere</em></a></td>
|
||||
<tr class="row-even"><td><a class="reference internal" href="compute_erotate_rigid.html"><em>erotate/rigid</em></a></td>
|
||||
<td><a class="reference internal" href="compute_erotate_sphere.html"><em>erotate/sphere</em></a></td>
|
||||
<td><a class="reference internal" href="compute_erotate_sphere_atom.html"><em>erotate/sphere/atom</em></a></td>
|
||||
<td><a class="reference internal" href="compute_event_displace.html"><em>event/displace</em></a></td>
|
||||
<td><a class="reference internal" href="compute_group_group.html"><em>group/group</em></a></td>
|
||||
<td><a class="reference internal" href="compute_gyration.html"><em>gyration</em></a></td>
|
||||
<td><a class="reference internal" href="compute_gyration_chunk.html"><em>gyration/chunk</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="compute_heat_flux.html"><em>heat/flux</em></a></td>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="compute_gyration_chunk.html"><em>gyration/chunk</em></a></td>
|
||||
<td><a class="reference internal" href="compute_heat_flux.html"><em>heat/flux</em></a></td>
|
||||
<td><a class="reference internal" href="compute_hexorder_atom.html"><em>hexorder/atom</em></a></td>
|
||||
<td><a class="reference internal" href="compute_improper_local.html"><em>improper/local</em></a></td>
|
||||
<td><a class="reference internal" href="compute_inertia_chunk.html"><em>inertia/chunk</em></a></td>
|
||||
<td><a class="reference internal" href="compute_ke.html"><em>ke</em></a></td>
|
||||
<td><a class="reference internal" href="compute_ke_atom.html"><em>ke/atom</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-even"><td><a class="reference internal" href="compute_ke_rigid.html"><em>ke/rigid</em></a></td>
|
||||
<tr class="row-even"><td><a class="reference internal" href="compute_ke_atom.html"><em>ke/atom</em></a></td>
|
||||
<td><a class="reference internal" href="compute_ke_rigid.html"><em>ke/rigid</em></a></td>
|
||||
<td><a class="reference internal" href="compute_msd.html"><em>msd</em></a></td>
|
||||
<td><a class="reference internal" href="compute_msd_chunk.html"><em>msd/chunk</em></a></td>
|
||||
<td><a class="reference internal" href="compute_msd_nongauss.html"><em>msd/nongauss</em></a></td>
|
||||
<td><a class="reference internal" href="compute_omega_chunk.html"><em>omega/chunk</em></a></td>
|
||||
<td><a class="reference internal" href="compute_orientorder_atom.html"><em>orientorder/atom</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="compute_pair.html"><em>pair</em></a></td>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="compute_orientorder_atom.html"><em>orientorder/atom</em></a></td>
|
||||
<td><a class="reference internal" href="compute_pair.html"><em>pair</em></a></td>
|
||||
<td><a class="reference internal" href="compute_pair_local.html"><em>pair/local</em></a></td>
|
||||
<td><a class="reference internal" href="compute_pe.html"><em>pe (c)</em></a></td>
|
||||
<td><a class="reference internal" href="compute_pe_atom.html"><em>pe/atom</em></a></td>
|
||||
<td><a class="reference internal" href="compute_plasticity_atom.html"><em>plasticity/atom</em></a></td>
|
||||
<td><a class="reference internal" href="compute_pressure.html"><em>pressure (c)</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-even"><td><a class="reference internal" href="compute_property_atom.html"><em>property/atom</em></a></td>
|
||||
<tr class="row-even"><td><a class="reference internal" href="compute_pressure.html"><em>pressure (c)</em></a></td>
|
||||
<td><a class="reference internal" href="compute_property_atom.html"><em>property/atom</em></a></td>
|
||||
<td><a class="reference internal" href="compute_property_local.html"><em>property/local</em></a></td>
|
||||
<td><a class="reference internal" href="compute_property_chunk.html"><em>property/chunk</em></a></td>
|
||||
<td><a class="reference internal" href="compute_rdf.html"><em>rdf</em></a></td>
|
||||
<td><a class="reference internal" href="compute_reduce.html"><em>reduce</em></a></td>
|
||||
<td><a class="reference internal" href="compute_reduce.html"><em>reduce/region</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="compute_slice.html"><em>slice</em></a></td>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="compute_reduce.html"><em>reduce/region</em></a></td>
|
||||
<td><a class="reference internal" href="compute_slice.html"><em>slice</em></a></td>
|
||||
<td><a class="reference internal" href="compute_sna_atom.html"><em>sna/atom</em></a></td>
|
||||
<td><a class="reference internal" href="compute_sna_atom.html"><em>snad/atom</em></a></td>
|
||||
<td><a class="reference internal" href="compute_sna_atom.html"><em>snav/atom</em></a></td>
|
||||
<td><a class="reference internal" href="compute_stress_atom.html"><em>stress/atom</em></a></td>
|
||||
<td><a class="reference internal" href="compute_temp.html"><em>temp (ck)</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-even"><td><a class="reference internal" href="compute_temp_asphere.html"><em>temp/asphere</em></a></td>
|
||||
<tr class="row-even"><td><a class="reference internal" href="compute_temp.html"><em>temp (ck)</em></a></td>
|
||||
<td><a class="reference internal" href="compute_temp_asphere.html"><em>temp/asphere</em></a></td>
|
||||
<td><a class="reference internal" href="compute_temp_body.html"><em>temp/body</em></a></td>
|
||||
<td><a class="reference internal" href="compute_temp_chunk.html"><em>temp/chunk</em></a></td>
|
||||
<td><a class="reference internal" href="compute_temp_com.html"><em>temp/com</em></a></td>
|
||||
<td><a class="reference internal" href="compute_temp_deform.html"><em>temp/deform</em></a></td>
|
||||
<td><a class="reference internal" href="compute_temp_partial.html"><em>temp/partial (c)</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="compute_temp_profile.html"><em>temp/profile</em></a></td>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="compute_temp_partial.html"><em>temp/partial (c)</em></a></td>
|
||||
<td><a class="reference internal" href="compute_temp_profile.html"><em>temp/profile</em></a></td>
|
||||
<td><a class="reference internal" href="compute_temp_ramp.html"><em>temp/ramp</em></a></td>
|
||||
<td><a class="reference internal" href="compute_temp_region.html"><em>temp/region</em></a></td>
|
||||
<td><a class="reference internal" href="compute_temp_sphere.html"><em>temp/sphere</em></a></td>
|
||||
<td><a class="reference internal" href="compute_ti.html"><em>ti</em></a></td>
|
||||
<td><a class="reference internal" href="compute_torque_chunk.html"><em>torque/chunk</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-even"><td><a class="reference internal" href="compute_vacf.html"><em>vacf</em></a></td>
|
||||
<tr class="row-even"><td><a class="reference internal" href="compute_torque_chunk.html"><em>torque/chunk</em></a></td>
|
||||
<td><a class="reference internal" href="compute_vacf.html"><em>vacf</em></a></td>
|
||||
<td><a class="reference internal" href="compute_vcm_chunk.html"><em>vcm/chunk</em></a></td>
|
||||
<td><a class="reference internal" href="compute_voronoi_atom.html"><em>voronoi/atom</em></a></td>
|
||||
<td> </td>
|
||||
<td> </td>
|
||||
<td> </td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@ -1168,10 +1168,10 @@ KOKKOS, o = USER-OMP, t = OPT.</p>
|
||||
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="24%" />
|
||||
<col width="23%" />
|
||||
<col width="25%" />
|
||||
<col width="30%" />
|
||||
<col width="23%" />
|
||||
<col width="23%" />
|
||||
<col width="22%" />
|
||||
</colgroup>
|
||||
<tbody valign="top">
|
||||
<tr class="row-odd"><td><a class="reference internal" href="pair_awpmd.html"><em>awpmd/cut</em></a></td>
|
||||
@ -1197,42 +1197,42 @@ if <a class="reference internal" href="Section_start.html#start-3"><span>LAMMPS
|
||||
<tr class="row-odd"><td><a class="reference internal" href="pair_lj_soft.html"><em>lj/cut/coul/long/soft (o)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_dipole.html"><em>lj/cut/dipole/sf (go)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_lj_soft.html"><em>lj/cut/soft (o)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_lj_soft.html"><em>lj/cut/tip4p/long/soft (o)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_thole.html"><em>lj/cut/thole/long (o)</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-even"><td><a class="reference internal" href="pair_mdf.html"><em>lj/mdf</em></a></td>
|
||||
<tr class="row-even"><td><a class="reference internal" href="pair_lj_soft.html"><em>lj/cut/tip4p/long/soft (o)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_mdf.html"><em>lj/mdf</em></a></td>
|
||||
<td><a class="reference internal" href="pair_sdk.html"><em>lj/sdk (gko)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_sdk.html"><em>lj/sdk/coul/long (go)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_sdk.html"><em>lj/sdk/coul/msm (o)</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="pair_lj_sf.html"><em>lj/sf (o)</em></a></td>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="pair_sdk.html"><em>lj/sdk/coul/msm (o)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_lj_sf.html"><em>lj/sf (o)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_meam_spline.html"><em>meam/spline</em></a></td>
|
||||
<td><a class="reference internal" href="pair_meam_sw_spline.html"><em>meam/sw/spline</em></a></td>
|
||||
<td><a class="reference internal" href="pair_mgpt.html"><em>mgpt</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-even"><td><a class="reference internal" href="pair_morse.html"><em>morse/smooth/linear</em></a></td>
|
||||
<tr class="row-even"><td><a class="reference internal" href="pair_mgpt.html"><em>mgpt</em></a></td>
|
||||
<td><a class="reference internal" href="pair_morse.html"><em>morse/smooth/linear</em></a></td>
|
||||
<td><a class="reference internal" href="pair_quip.html"><em>quip</em></a></td>
|
||||
<td><a class="reference internal" href="pair_reax_c.html"><em>reax/c</em></a></td>
|
||||
<td><a class="reference internal" href="pair_smd_hertz.html"><em>smd/hertz</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="pair_smd_tlsph.html"><em>smd/tlsph</em></a></td>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="pair_smd_hertz.html"><em>smd/hertz</em></a></td>
|
||||
<td><a class="reference internal" href="pair_smd_tlsph.html"><em>smd/tlsph</em></a></td>
|
||||
<td><a class="reference internal" href="pair_smd_triangulated_surface.html"><em>smd/triangulated/surface</em></a></td>
|
||||
<td><a class="reference internal" href="pair_smd_ulsph.html"><em>smd/ulsph</em></a></td>
|
||||
<td><a class="reference internal" href="pair_smtbq.html"><em>smtbq</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-even"><td><a class="reference internal" href="pair_sph_heatconduction.html"><em>sph/heatconduction</em></a></td>
|
||||
<tr class="row-even"><td><a class="reference internal" href="pair_smtbq.html"><em>smtbq</em></a></td>
|
||||
<td><a class="reference internal" href="pair_sph_heatconduction.html"><em>sph/heatconduction</em></a></td>
|
||||
<td><a class="reference internal" href="pair_sph_idealgas.html"><em>sph/idealgas</em></a></td>
|
||||
<td><a class="reference internal" href="pair_sph_lj.html"><em>sph/lj</em></a></td>
|
||||
<td><a class="reference internal" href="pair_sph_rhosum.html"><em>sph/rhosum</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="pair_sph_taitwater.html"><em>sph/taitwater</em></a></td>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="pair_sph_rhosum.html"><em>sph/rhosum</em></a></td>
|
||||
<td><a class="reference internal" href="pair_sph_taitwater.html"><em>sph/taitwater</em></a></td>
|
||||
<td><a class="reference internal" href="pair_sph_taitwater_morris.html"><em>sph/taitwater/morris</em></a></td>
|
||||
<td><a class="reference internal" href="pair_srp.html"><em>srp</em></a></td>
|
||||
<td><a class="reference internal" href="pair_tersoff.html"><em>tersoff/table (o)</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-even"><td><a class="reference internal" href="pair_thole.html"><em>thole</em></a></td>
|
||||
<tr class="row-even"><td><a class="reference internal" href="pair_tersoff.html"><em>tersoff/table (o)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_thole.html"><em>thole</em></a></td>
|
||||
<td><a class="reference internal" href="pair_lj_soft.html"><em>tip4p/long/soft (o)</em></a></td>
|
||||
<td> </td>
|
||||
<td> </td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
|
||||
@ -671,6 +671,7 @@ KOKKOS, o = USER-OMP, t = OPT.
|
||||
"angle/local"_compute_angle_local.html,
|
||||
"angmom/chunk"_compute_angmom_chunk.html,
|
||||
"body/local"_compute_body_local.html,
|
||||
"bond"_compute_bond.html,
|
||||
"bond/local"_compute_bond_local.html,
|
||||
"centro/atom"_compute_centro_atom.html,
|
||||
"chunk/atom"_compute_chunk_atom.html,
|
||||
@ -930,6 +931,7 @@ package"_Section_start.html#start_3.
|
||||
"lj/cut/coul/long/soft (o)"_pair_lj_soft.html,
|
||||
"lj/cut/dipole/sf (go)"_pair_dipole.html,
|
||||
"lj/cut/soft (o)"_pair_lj_soft.html,
|
||||
"lj/cut/thole/long (o)"_pair_thole.html,
|
||||
"lj/cut/tip4p/long/soft (o)"_pair_lj_soft.html,
|
||||
"lj/mdf"_pair_mdf.html,
|
||||
"lj/sdk (gko)"_pair_sdk.html,
|
||||
|
||||
@ -1060,7 +1060,7 @@ then be accessed by variables) was discussed
|
||||
<p>We encourage users to submit new features to <a class="reference external" href="http://lammps.sandia.gov/authors.html">the developers</a> that they add to
|
||||
LAMMPS, especially if you think they will be of interest to other
|
||||
users. The preferred way to do this is via GitHub. Once you have
|
||||
prepared the content described below, see <code class="xref doc docutils literal"><span class="pre">this</span> <span class="pre">tutorial</span></code> for instructions on how to submit
|
||||
prepared the content described below, see <a class="reference internal" href="tutorial_github.html"><em>this tutorial</em></a> for instructions on how to submit
|
||||
your changes or new files.</p>
|
||||
<p>If the new features/files are broadly useful we may add them as core
|
||||
files to LAMMPS or as part of a <a class="reference internal" href="Section_start.html#start-3"><span>standard package</span></a>. Else we will add them as a
|
||||
|
||||
@ -626,7 +626,7 @@ developers"_http://lammps.sandia.gov/authors.html that they add to
|
||||
LAMMPS, especially if you think they will be of interest to other
|
||||
users. The preferred way to do this is via GitHub. Once you have
|
||||
prepared the content described below, see "this
|
||||
tutorial"_doc/tutorial_github.html for instructions on how to submit
|
||||
tutorial"_tutorial_github.html for instructions on how to submit
|
||||
your changes or new files.
|
||||
|
||||
If the new features/files are broadly useful we may add them as core
|
||||
|
||||
@ -494,7 +494,7 @@ name links to a sub-section below with more details.</p>
|
||||
<td>python</td>
|
||||
<td>lib/python</td>
|
||||
</tr>
|
||||
<tr class="row-even"><td><a class="reference internal" href="#reax"><span>REAX</span></a></td>
|
||||
<tr class="row-even"><td><a class="reference internal" href="Section_tools.html#reax"><span>REAX</span></a></td>
|
||||
<td>ReaxFF potential</td>
|
||||
<td>Aidan Thompson (Sandia)</td>
|
||||
<td><a class="reference internal" href="pair_reax.html"><em>pair_style reax</em></a></td>
|
||||
|
||||
@ -5,8 +5,8 @@
|
||||
LAMMPS Documentation
|
||||
====================
|
||||
|
||||
1 Mar 2016 version
|
||||
------------------
|
||||
10 Mar 2016 version
|
||||
-------------------
|
||||
|
||||
Version info:
|
||||
-------------
|
||||
|
||||
@ -524,31 +524,31 @@ is built with the :doc:`appropriate accelerated package <Section_accelerate>`.
|
||||
letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
|
||||
KOKKOS, o = USER-OMP, t = OPT.
|
||||
|
||||
+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+----------------------------------------------------+
|
||||
| :doc:`angle/local <compute_angle_local>` | :doc:`angmom/chunk <compute_angmom_chunk>` | :doc:`body/local <compute_body_local>` | :doc:`bond/local <compute_bond_local>` | :doc:`centro/atom <compute_centro_atom>` | :doc:`chunk/atom <compute_chunk_atom>` |
|
||||
+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+----------------------------------------------------+
|
||||
| :doc:`cluster/atom <compute_cluster_atom>` | :doc:`cna/atom <compute_cna_atom>` | :doc:`com <compute_com>` | :doc:`com/chunk <compute_com_chunk>` | :doc:`contact/atom <compute_contact_atom>` | :doc:`coord/atom <compute_coord_atom>` |
|
||||
+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+----------------------------------------------------+
|
||||
| :doc:`damage/atom <compute_damage_atom>` | :doc:`dihedral/local <compute_dihedral_local>` | :doc:`dilatation/atom <compute_dilatation_atom>` | :doc:`displace/atom <compute_displace_atom>` | :doc:`erotate/asphere <compute_erotate_asphere>` | :doc:`erotate/rigid <compute_erotate_rigid>` |
|
||||
+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+----------------------------------------------------+
|
||||
| :doc:`erotate/sphere <compute_erotate_sphere>` | :doc:`erotate/sphere/atom <compute_erotate_sphere_atom>` | :doc:`event/displace <compute_event_displace>` | :doc:`group/group <compute_group_group>` | :doc:`gyration <compute_gyration>` | :doc:`gyration/chunk <compute_gyration_chunk>` |
|
||||
+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+----------------------------------------------------+
|
||||
| :doc:`heat/flux <compute_heat_flux>` | :doc:`hexorder/atom <compute_hexorder_atom>` | :doc:`improper/local <compute_improper_local>` | :doc:`inertia/chunk <compute_inertia_chunk>` | :doc:`ke <compute_ke>` | :doc:`ke/atom <compute_ke_atom>` |
|
||||
+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+----------------------------------------------------+
|
||||
| :doc:`ke/rigid <compute_ke_rigid>` | :doc:`msd <compute_msd>` | :doc:`msd/chunk <compute_msd_chunk>` | :doc:`msd/nongauss <compute_msd_nongauss>` | :doc:`omega/chunk <compute_omega_chunk>` | :doc:`orientorder/atom <compute_orientorder_atom>` |
|
||||
+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+----------------------------------------------------+
|
||||
| :doc:`pair <compute_pair>` | :doc:`pair/local <compute_pair_local>` | :doc:`pe (c) <compute_pe>` | :doc:`pe/atom <compute_pe_atom>` | :doc:`plasticity/atom <compute_plasticity_atom>` | :doc:`pressure (c) <compute_pressure>` |
|
||||
+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+----------------------------------------------------+
|
||||
| :doc:`property/atom <compute_property_atom>` | :doc:`property/local <compute_property_local>` | :doc:`property/chunk <compute_property_chunk>` | :doc:`rdf <compute_rdf>` | :doc:`reduce <compute_reduce>` | :doc:`reduce/region <compute_reduce>` |
|
||||
+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+----------------------------------------------------+
|
||||
| :doc:`slice <compute_slice>` | :doc:`sna/atom <compute_sna_atom>` | :doc:`snad/atom <compute_sna_atom>` | :doc:`snav/atom <compute_sna_atom>` | :doc:`stress/atom <compute_stress_atom>` | :doc:`temp (ck) <compute_temp>` |
|
||||
+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+----------------------------------------------------+
|
||||
| :doc:`temp/asphere <compute_temp_asphere>` | :doc:`temp/body <compute_temp_body>` | :doc:`temp/chunk <compute_temp_chunk>` | :doc:`temp/com <compute_temp_com>` | :doc:`temp/deform <compute_temp_deform>` | :doc:`temp/partial (c) <compute_temp_partial>` |
|
||||
+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+----------------------------------------------------+
|
||||
| :doc:`temp/profile <compute_temp_profile>` | :doc:`temp/ramp <compute_temp_ramp>` | :doc:`temp/region <compute_temp_region>` | :doc:`temp/sphere <compute_temp_sphere>` | :doc:`ti <compute_ti>` | :doc:`torque/chunk <compute_torque_chunk>` |
|
||||
+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+----------------------------------------------------+
|
||||
| :doc:`vacf <compute_vacf>` | :doc:`vcm/chunk <compute_vcm_chunk>` | :doc:`voronoi/atom <compute_voronoi_atom>` | | | |
|
||||
+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+----------------------------------------------------+
|
||||
+----------------------------------------------------+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+
|
||||
| :doc:`angle/local <compute_angle_local>` | :doc:`angmom/chunk <compute_angmom_chunk>` | :doc:`body/local <compute_body_local>` | :doc:`bond <compute_bond>` | :doc:`bond/local <compute_bond_local>` | :doc:`centro/atom <compute_centro_atom>` |
|
||||
+----------------------------------------------------+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+
|
||||
| :doc:`chunk/atom <compute_chunk_atom>` | :doc:`cluster/atom <compute_cluster_atom>` | :doc:`cna/atom <compute_cna_atom>` | :doc:`com <compute_com>` | :doc:`com/chunk <compute_com_chunk>` | :doc:`contact/atom <compute_contact_atom>` |
|
||||
+----------------------------------------------------+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+
|
||||
| :doc:`coord/atom <compute_coord_atom>` | :doc:`damage/atom <compute_damage_atom>` | :doc:`dihedral/local <compute_dihedral_local>` | :doc:`dilatation/atom <compute_dilatation_atom>` | :doc:`displace/atom <compute_displace_atom>` | :doc:`erotate/asphere <compute_erotate_asphere>` |
|
||||
+----------------------------------------------------+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+
|
||||
| :doc:`erotate/rigid <compute_erotate_rigid>` | :doc:`erotate/sphere <compute_erotate_sphere>` | :doc:`erotate/sphere/atom <compute_erotate_sphere_atom>` | :doc:`event/displace <compute_event_displace>` | :doc:`group/group <compute_group_group>` | :doc:`gyration <compute_gyration>` |
|
||||
+----------------------------------------------------+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+
|
||||
| :doc:`gyration/chunk <compute_gyration_chunk>` | :doc:`heat/flux <compute_heat_flux>` | :doc:`hexorder/atom <compute_hexorder_atom>` | :doc:`improper/local <compute_improper_local>` | :doc:`inertia/chunk <compute_inertia_chunk>` | :doc:`ke <compute_ke>` |
|
||||
+----------------------------------------------------+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+
|
||||
| :doc:`ke/atom <compute_ke_atom>` | :doc:`ke/rigid <compute_ke_rigid>` | :doc:`msd <compute_msd>` | :doc:`msd/chunk <compute_msd_chunk>` | :doc:`msd/nongauss <compute_msd_nongauss>` | :doc:`omega/chunk <compute_omega_chunk>` |
|
||||
+----------------------------------------------------+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+
|
||||
| :doc:`orientorder/atom <compute_orientorder_atom>` | :doc:`pair <compute_pair>` | :doc:`pair/local <compute_pair_local>` | :doc:`pe (c) <compute_pe>` | :doc:`pe/atom <compute_pe_atom>` | :doc:`plasticity/atom <compute_plasticity_atom>` |
|
||||
+----------------------------------------------------+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+
|
||||
| :doc:`pressure (c) <compute_pressure>` | :doc:`property/atom <compute_property_atom>` | :doc:`property/local <compute_property_local>` | :doc:`property/chunk <compute_property_chunk>` | :doc:`rdf <compute_rdf>` | :doc:`reduce <compute_reduce>` |
|
||||
+----------------------------------------------------+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+
|
||||
| :doc:`reduce/region <compute_reduce>` | :doc:`slice <compute_slice>` | :doc:`sna/atom <compute_sna_atom>` | :doc:`snad/atom <compute_sna_atom>` | :doc:`snav/atom <compute_sna_atom>` | :doc:`stress/atom <compute_stress_atom>` |
|
||||
+----------------------------------------------------+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+
|
||||
| :doc:`temp (ck) <compute_temp>` | :doc:`temp/asphere <compute_temp_asphere>` | :doc:`temp/body <compute_temp_body>` | :doc:`temp/chunk <compute_temp_chunk>` | :doc:`temp/com <compute_temp_com>` | :doc:`temp/deform <compute_temp_deform>` |
|
||||
+----------------------------------------------------+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+
|
||||
| :doc:`temp/partial (c) <compute_temp_partial>` | :doc:`temp/profile <compute_temp_profile>` | :doc:`temp/ramp <compute_temp_ramp>` | :doc:`temp/region <compute_temp_region>` | :doc:`temp/sphere <compute_temp_sphere>` | :doc:`ti <compute_ti>` |
|
||||
+----------------------------------------------------+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+
|
||||
| :doc:`torque/chunk <compute_torque_chunk>` | :doc:`vacf <compute_vacf>` | :doc:`vcm/chunk <compute_vcm_chunk>` | :doc:`voronoi/atom <compute_voronoi_atom>` | | |
|
||||
+----------------------------------------------------+------------------------------------------------+----------------------------------------------------------+--------------------------------------------------+----------------------------------------------+--------------------------------------------------+
|
||||
|
||||
These are additional compute styles in USER packages, which can be
|
||||
used if :ref:`LAMMPS is built with the appropriate package <start_3>`.
|
||||
@ -644,31 +644,31 @@ KOKKOS, o = USER-OMP, t = OPT.
|
||||
These are additional pair styles in USER packages, which can be used
|
||||
if :ref:`LAMMPS is built with the appropriate package <start_3>`.
|
||||
|
||||
+-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+--------------------------------------------------+
|
||||
| :doc:`awpmd/cut <pair_awpmd>` | :doc:`buck/mdf <pair_mdf>` | :doc:`coul/cut/soft (o) <pair_lj_soft>` | :doc:`coul/diel (o) <pair_coul_diel>` |
|
||||
+-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+--------------------------------------------------+
|
||||
| :doc:`coul/long/soft (o) <pair_lj_soft>` | :doc:`dpd/conservative <pair_dpd_conservative>` | :doc:`dpd/fdt <pair_dpd_fdt>` | :doc:`dpd/fdt/energy <pair_dpd_fdt>` |
|
||||
+-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+--------------------------------------------------+
|
||||
| :doc:`eam/cd (o) <pair_eam>` | :doc:`edip (o) <pair_edip>` | :doc:`eff/cut <pair_eff>` | :doc:`gauss/cut <pair_gauss>` |
|
||||
+-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+--------------------------------------------------+
|
||||
| :doc:`lennard/mdf <pair_mdf>` | :doc:`list <pair_list>` | :doc:`lj/charmm/coul/long/soft (o) <pair_charmm>` | :doc:`lj/cut/coul/cut/soft (o) <pair_lj_soft>` |
|
||||
+-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+--------------------------------------------------+
|
||||
| :doc:`lj/cut/coul/long/soft (o) <pair_lj_soft>` | :doc:`lj/cut/dipole/sf (go) <pair_dipole>` | :doc:`lj/cut/soft (o) <pair_lj_soft>` | :doc:`lj/cut/tip4p/long/soft (o) <pair_lj_soft>` |
|
||||
+-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+--------------------------------------------------+
|
||||
| :doc:`lj/mdf <pair_mdf>` | :doc:`lj/sdk (gko) <pair_sdk>` | :doc:`lj/sdk/coul/long (go) <pair_sdk>` | :doc:`lj/sdk/coul/msm (o) <pair_sdk>` |
|
||||
+-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+--------------------------------------------------+
|
||||
| :doc:`lj/sf (o) <pair_lj_sf>` | :doc:`meam/spline <pair_meam_spline>` | :doc:`meam/sw/spline <pair_meam_sw_spline>` | :doc:`mgpt <pair_mgpt>` |
|
||||
+-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+--------------------------------------------------+
|
||||
| :doc:`morse/smooth/linear <pair_morse>` | :doc:`quip <pair_quip>` | :doc:`reax/c <pair_reax_c>` | :doc:`smd/hertz <pair_smd_hertz>` |
|
||||
+-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+--------------------------------------------------+
|
||||
| :doc:`smd/tlsph <pair_smd_tlsph>` | :doc:`smd/triangulated/surface <pair_smd_triangulated_surface>` | :doc:`smd/ulsph <pair_smd_ulsph>` | :doc:`smtbq <pair_smtbq>` |
|
||||
+-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+--------------------------------------------------+
|
||||
| :doc:`sph/heatconduction <pair_sph_heatconduction>` | :doc:`sph/idealgas <pair_sph_idealgas>` | :doc:`sph/lj <pair_sph_lj>` | :doc:`sph/rhosum <pair_sph_rhosum>` |
|
||||
+-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+--------------------------------------------------+
|
||||
| :doc:`sph/taitwater <pair_sph_taitwater>` | :doc:`sph/taitwater/morris <pair_sph_taitwater_morris>` | :doc:`srp <pair_srp>` | :doc:`tersoff/table (o) <pair_tersoff>` |
|
||||
+-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+--------------------------------------------------+
|
||||
| :doc:`thole <pair_thole>` | :doc:`tip4p/long/soft (o) <pair_lj_soft>` | | |
|
||||
+-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+--------------------------------------------------+
|
||||
+--------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+------------------------------------------------+
|
||||
| :doc:`awpmd/cut <pair_awpmd>` | :doc:`buck/mdf <pair_mdf>` | :doc:`coul/cut/soft (o) <pair_lj_soft>` | :doc:`coul/diel (o) <pair_coul_diel>` |
|
||||
+--------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+------------------------------------------------+
|
||||
| :doc:`coul/long/soft (o) <pair_lj_soft>` | :doc:`dpd/conservative <pair_dpd_conservative>` | :doc:`dpd/fdt <pair_dpd_fdt>` | :doc:`dpd/fdt/energy <pair_dpd_fdt>` |
|
||||
+--------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+------------------------------------------------+
|
||||
| :doc:`eam/cd (o) <pair_eam>` | :doc:`edip (o) <pair_edip>` | :doc:`eff/cut <pair_eff>` | :doc:`gauss/cut <pair_gauss>` |
|
||||
+--------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+------------------------------------------------+
|
||||
| :doc:`lennard/mdf <pair_mdf>` | :doc:`list <pair_list>` | :doc:`lj/charmm/coul/long/soft (o) <pair_charmm>` | :doc:`lj/cut/coul/cut/soft (o) <pair_lj_soft>` |
|
||||
+--------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+------------------------------------------------+
|
||||
| :doc:`lj/cut/coul/long/soft (o) <pair_lj_soft>` | :doc:`lj/cut/dipole/sf (go) <pair_dipole>` | :doc:`lj/cut/soft (o) <pair_lj_soft>` | :doc:`lj/cut/thole/long (o) <pair_thole>` |
|
||||
+--------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+------------------------------------------------+
|
||||
| :doc:`lj/cut/tip4p/long/soft (o) <pair_lj_soft>` | :doc:`lj/mdf <pair_mdf>` | :doc:`lj/sdk (gko) <pair_sdk>` | :doc:`lj/sdk/coul/long (go) <pair_sdk>` |
|
||||
+--------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+------------------------------------------------+
|
||||
| :doc:`lj/sdk/coul/msm (o) <pair_sdk>` | :doc:`lj/sf (o) <pair_lj_sf>` | :doc:`meam/spline <pair_meam_spline>` | :doc:`meam/sw/spline <pair_meam_sw_spline>` |
|
||||
+--------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+------------------------------------------------+
|
||||
| :doc:`mgpt <pair_mgpt>` | :doc:`morse/smooth/linear <pair_morse>` | :doc:`quip <pair_quip>` | :doc:`reax/c <pair_reax_c>` |
|
||||
+--------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+------------------------------------------------+
|
||||
| :doc:`smd/hertz <pair_smd_hertz>` | :doc:`smd/tlsph <pair_smd_tlsph>` | :doc:`smd/triangulated/surface <pair_smd_triangulated_surface>` | :doc:`smd/ulsph <pair_smd_ulsph>` |
|
||||
+--------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+------------------------------------------------+
|
||||
| :doc:`smtbq <pair_smtbq>` | :doc:`sph/heatconduction <pair_sph_heatconduction>` | :doc:`sph/idealgas <pair_sph_idealgas>` | :doc:`sph/lj <pair_sph_lj>` |
|
||||
+--------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+------------------------------------------------+
|
||||
| :doc:`sph/rhosum <pair_sph_rhosum>` | :doc:`sph/taitwater <pair_sph_taitwater>` | :doc:`sph/taitwater/morris <pair_sph_taitwater_morris>` | :doc:`srp <pair_srp>` |
|
||||
+--------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+------------------------------------------------+
|
||||
| :doc:`tersoff/table (o) <pair_tersoff>` | :doc:`thole <pair_thole>` | :doc:`tip4p/long/soft (o) <pair_lj_soft>` | |
|
||||
+--------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+------------------------------------------------+
|
||||
|
||||
|
||||
----------
|
||||
|
||||
@ -845,7 +845,7 @@ Submitting new features for inclusion in LAMMPS
|
||||
We encourage users to submit new features to `the developers <http://lammps.sandia.gov/authors.html>`_ that they add to
|
||||
LAMMPS, especially if you think they will be of interest to other
|
||||
users. The preferred way to do this is via GitHub. Once you have
|
||||
prepared the content described below, see :doc:`this tutorial <doc/tutorial_github>` for instructions on how to submit
|
||||
prepared the content described below, see :doc:`this tutorial <tutorial_github>` for instructions on how to submit
|
||||
your changes or new files.
|
||||
|
||||
If the new features/files are broadly useful we may add them as core
|
||||
|
||||
@ -177,6 +177,7 @@ section of :ref:`this page <cmd_5>`.
|
||||
* :doc:`angle/local <compute_bond_local>` - theta and energy of each angle
|
||||
* :doc:`angmom/chunk <compute_angmom_chunk>` - angular momentum for each chunk
|
||||
* :doc:`body/local <compute_body_local>` - attributes of body sub-particles
|
||||
* :doc:`bond <compute_bond>` - values computed by a bond style
|
||||
* :doc:`bond/local <compute_bond_local>` - distance and energy of each bond
|
||||
* :doc:`centro/atom <compute_centro_atom>` - centro-symmetry parameter for each atom
|
||||
* :doc:`chunk/atom <compute_chunk_atom>` - assign chunk IDs to each atom
|
||||
|
||||
66
doc/_sources/compute_bond.txt
Normal file
66
doc/_sources/compute_bond.txt
Normal file
@ -0,0 +1,66 @@
|
||||
.. index:: compute bond
|
||||
|
||||
compute bond command
|
||||
====================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
compute ID group-ID bond bstyle
|
||||
|
||||
* ID, group-ID are documented in :doc:`compute <compute>` command
|
||||
* bond = style name of this compute command
|
||||
* bstyle = style name of a bond style that calculates additional values
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
compute 1 all bond harmonic
|
||||
compute 2 all bond morse
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
Define a computation that extracts additional values calculated by a
|
||||
bond style, sums them across processors, and makes them accessible for
|
||||
output or further processing by other commands. The group specified
|
||||
for this command is ignored.
|
||||
|
||||
The specified *bstyle* must be a bond style used in your simulation
|
||||
either by itself or as a sub-style in a :doc:`bond_style hybrid <bond_hybrid>`
|
||||
command.
|
||||
|
||||
This compute is useful when using :doc:`bond_style hybrid <bond_hybrid>`
|
||||
if you want to know the portion of the total energy contributed by one
|
||||
sub-style.
|
||||
|
||||
**Output info:**
|
||||
|
||||
This compute calculates a global scalar which is the contribution of
|
||||
the named bond style to the bond energy *ebond*.
|
||||
|
||||
The scalar value calculated by this compute is "extensive" and will be
|
||||
in energy :doc:`units <units>`.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
none
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`compute pe <compute_pe>`, :doc:`compute pair <compute_pair>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
The default for *evalue* is *ebond*.
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Section_commands.html#comm
|
||||
@ -83,7 +83,7 @@ Restrictions
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`compute pe <compute_pe>`
|
||||
:doc:`compute pe <compute_pe>`, :doc:`compute bond <compute_bond>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
@ -18,6 +18,9 @@ pair_style morse/opt command
|
||||
pair_style morse/smooth/linear command
|
||||
======================================
|
||||
|
||||
pair_style morse/smooth/linear/omp command
|
||||
==========================================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
@ -75,8 +78,6 @@ the potential energy and force go to zero at the cut-off:
|
||||
The syntax of the pair_style and pair_coeff commands are the same for
|
||||
the *morse* and *morse/smooth/linear* styles.
|
||||
|
||||
same
|
||||
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -3,16 +3,31 @@
|
||||
pair_style thole command
|
||||
========================
|
||||
|
||||
pair_style lj/cut/thole/long command
|
||||
====================================
|
||||
|
||||
pair_style lj/cut/thole/long/omp command
|
||||
========================================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
pair_style thole damp cutoff
|
||||
pair_style style args
|
||||
|
||||
* thole = style name
|
||||
* damp = global damping parameter
|
||||
* cutoff = global cutoff
|
||||
* style = *thole* or *lj/cut/thole/long* or *lj/cut/thole/long/omp*
|
||||
* args = list of arguments for a particular style
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
*thole* args = damp cutoff
|
||||
damp = global damping parameter
|
||||
cutoff = global cutoff (distance units)
|
||||
*lj/cut/thole/long* or *lj/cut/thole/long/omp* args = damp cutoff (cutoff2)
|
||||
damp = global damping parameter
|
||||
cutoff = global cutoff for LJ (and Thole if only 1 arg) (distance units)
|
||||
cutoff2 = global cutoff for Thole (optional) (distance units)
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
@ -24,10 +39,14 @@ Examples
|
||||
pair_coeff 1 2 thole 1.0 2.6 10.0
|
||||
pair_coeff * 2 thole 1.0 2.6
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
pair_style lj/cut/thole/long 2.6 12.0
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
The *thole* pair style is meant to be used with force fields that
|
||||
The *thole* pair styles are meant to be used with force fields that
|
||||
include explicit polarization through Drude dipoles. This link
|
||||
describes how to use the :doc:`thermalized Drude oscillator model <tutorial_drude>` in LAMMPS and polarizable models in LAMMPS
|
||||
are discussed in :ref:`this Section <howto_25>`.
|
||||
@ -37,7 +56,17 @@ The *thole* pair style should be used as a sub-style within in the
|
||||
main pair style including Coulomb interactions, i.e. any pair style
|
||||
containing *coul/cut* or *coul/long* in its style name.
|
||||
|
||||
The *thole* pair style computes the Coulomb interaction damped at
|
||||
The *lj/cut/thole/long* pair style is equivalent to, but more convenient that
|
||||
the frequent combination *hybrid/overlay lj/cut/coul/long cutoff thole damp
|
||||
cutoff2*. It is not only a shorthand for this pair_style combination, but
|
||||
it also allows for mixing pair coefficients instead of listing them all.
|
||||
The *lj/cut/thole/long* pair style is also a bit faster because it avoids an
|
||||
overlay and can benefit from OMP acceleration. Moreover, it uses a more
|
||||
precise approximation of the direct Coulomb interaction at short range similar
|
||||
to :doc:`coul/long/cs <pair_coul_long_cs>`, which stabilizes the temperature of
|
||||
Drude particles.
|
||||
|
||||
The *thole* pair styles compute the Coulomb interaction damped at
|
||||
short distances by a function
|
||||
|
||||
|
||||
@ -79,9 +108,9 @@ non-polarizable atoms are also subject to these weighting factors. The
|
||||
Drude particles inherit the 1-2, 1-3 and 1-4 neighbor relations from
|
||||
their respective cores.
|
||||
|
||||
The following coefficients must be defined for each pair of atoms
|
||||
types via the :doc:`pair_coeff <pair_coeff>` command as in the example
|
||||
above.
|
||||
For pair_style *thole*, the following coefficients must be defined for
|
||||
each pair of atoms types via the :doc:`pair_coeff <pair_coeff>` command
|
||||
as in the example above.
|
||||
|
||||
* alpha (distance units^3)
|
||||
* damp
|
||||
@ -92,11 +121,60 @@ Thole damping parameter or global cutoff specified in the pair_style
|
||||
command are used. In order to specify a cutoff (third argument) a damp
|
||||
parameter (second argument) must also be specified.
|
||||
|
||||
For pair style *lj/cut/thole/long*, the following coefficients must be
|
||||
defined for each pair of atoms types via the :doc:`pair_coeff <pair_coeff>`
|
||||
command.
|
||||
|
||||
* epsilon (energy units)
|
||||
* sigma (length units)
|
||||
* alpha (distance units^3)
|
||||
* damps
|
||||
* LJ cutoff (distance units)
|
||||
|
||||
The last two coefficients are optional and default to the global values from
|
||||
the *pair_style* command line.
|
||||
|
||||
|
||||
----------
|
||||
|
||||
|
||||
Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed in :doc:`Section_accelerate <Section_accelerate>`
|
||||
of the manual. The accelerated styles take the same arguments and
|
||||
should produce the same results, except for round-off and precision
|
||||
issues.
|
||||
|
||||
These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
|
||||
KOKKOS, USER-OMP and OPT packages, respectively. They are only
|
||||
enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS <start_3>` section for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :ref:`-suffix command-line switch <start_7>` when you invoke LAMMPS, or you can
|
||||
use the :doc:`suffix <suffix>` command in your input script.
|
||||
|
||||
See :doc:`Section_accelerate <Section_accelerate>` of the manual for
|
||||
more instructions on how to use the accelerated styles effectively.
|
||||
|
||||
**Mixing**:
|
||||
|
||||
The *thole* pair style does not support mixing. Thus, coefficients
|
||||
for all I,J pairs must be specified explicitly.
|
||||
|
||||
The *lj/cut/thole/long* pair style does support mixing. Mixed coefficients
|
||||
are defined using
|
||||
|
||||
|
||||
.. math::
|
||||
|
||||
\begin{equation} \alpha_{ij} = \sqrt{\alpha_i\alpha_j}\end{equation}
|
||||
|
||||
|
||||
.. math::
|
||||
|
||||
\begin{equation} a_{ij} = \frac 1 2 (a_i + a_j)\end{equation}
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
@ -108,10 +186,15 @@ This pair_style should currently not be used with the :doc:`charmm dihedral styl
|
||||
factors. This is because the *thole* pair style does not know which
|
||||
pairs are 1-4 partners of which dihedrals.
|
||||
|
||||
The *lj/cut/thole/long* pair style should be used with a :doc:`Kspace solver <kspace_style>`
|
||||
like PPPM or Ewald, which is only enabled if LAMMPS was built with the kspace
|
||||
package.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`fix drude <fix_drude>`, :doc:`fix langevin/drude <fix_langevin_drude>`, :doc:`fix drude/transform <fix_drude_transform>`, :doc:`compute temp/drude <compute_temp_drude>`
|
||||
`pair_style lj/cut/coul/long <pair_lj_cut_coul_long>`_
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
@ -278,6 +278,7 @@ section of <a class="reference internal" href="Section_commands.html#cmd-5"><spa
|
||||
<li><a class="reference internal" href="compute_bond_local.html"><em>angle/local</em></a> - theta and energy of each angle</li>
|
||||
<li><a class="reference internal" href="compute_angmom_chunk.html"><em>angmom/chunk</em></a> - angular momentum for each chunk</li>
|
||||
<li><a class="reference internal" href="compute_body_local.html"><em>body/local</em></a> - attributes of body sub-particles</li>
|
||||
<li><a class="reference internal" href="compute_bond.html"><em>bond</em></a> - values computed by a bond style</li>
|
||||
<li><a class="reference internal" href="compute_bond_local.html"><em>bond/local</em></a> - distance and energy of each bond</li>
|
||||
<li><a class="reference internal" href="compute_centro_atom.html"><em>centro/atom</em></a> - centro-symmetry parameter for each atom</li>
|
||||
<li><a class="reference internal" href="compute_chunk_atom.html"><em>chunk/atom</em></a> - assign chunk IDs to each atom</li>
|
||||
|
||||
@ -172,6 +172,7 @@ section of "this page"_Section_commands.html#cmd_5.
|
||||
"angle/local"_compute_bond_local.html - theta and energy of each angle
|
||||
"angmom/chunk"_compute_angmom_chunk.html - angular momentum for each chunk
|
||||
"body/local"_compute_body_local.html - attributes of body sub-particles
|
||||
"bond"_compute_bond.html - values computed by a bond style
|
||||
"bond/local"_compute_bond_local.html - distance and energy of each bond
|
||||
"centro/atom"_compute_centro_atom.html - centro-symmetry parameter for each atom
|
||||
"chunk/atom"_compute_chunk_atom.html - assign chunk IDs to each atom
|
||||
|
||||
242
doc/compute_bond.html
Normal file
242
doc/compute_bond.html
Normal file
@ -0,0 +1,242 @@
|
||||
|
||||
|
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||||
|
||||
<div class="section" id="compute-bond-command">
|
||||
<span id="index-0"></span><h1>compute bond command<a class="headerlink" href="#compute-bond-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>compute ID group-ID bond bstyle
|
||||
</pre></div>
|
||||
</div>
|
||||
<ul class="simple">
|
||||
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><em>compute</em></a> command</li>
|
||||
<li>bond = style name of this compute command</li>
|
||||
<li>bstyle = style name of a bond style that calculates additional values</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
|
||||
<div class="highlight-python"><div class="highlight"><pre>compute 1 all bond harmonic
|
||||
compute 2 all bond morse
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
|
||||
<p>Define a computation that extracts additional values calculated by a
|
||||
bond style, sums them across processors, and makes them accessible for
|
||||
output or further processing by other commands. The group specified
|
||||
for this command is ignored.</p>
|
||||
<p>The specified <em>bstyle</em> must be a bond style used in your simulation
|
||||
either by itself or as a sub-style in a <a class="reference internal" href="bond_hybrid.html"><em>bond_style hybrid</em></a>
|
||||
command.</p>
|
||||
<p>This compute is useful when using <a class="reference internal" href="bond_hybrid.html"><em>bond_style hybrid</em></a>
|
||||
if you want to know the portion of the total energy contributed by one
|
||||
sub-style.</p>
|
||||
<p><strong>Output info:</strong></p>
|
||||
<p>This compute calculates a global scalar which is the contribution of
|
||||
the named bond style to the bond energy <em>ebond</em>.</p>
|
||||
<p>The scalar value calculated by this compute is “extensive” and will be
|
||||
in energy <a class="reference internal" href="units.html"><em>units</em></a>.</p>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
|
||||
<blockquote>
|
||||
<div>none</div></blockquote>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
|
||||
<p><a class="reference internal" href="compute_pe.html"><em>compute pe</em></a>, <a class="reference internal" href="compute_pair.html"><em>compute pair</em></a></p>
|
||||
</div>
|
||||
<div class="section" id="default">
|
||||
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline">¶</a></h2>
|
||||
<p>The default for <em>evalue</em> is <em>ebond</em>.</p>
|
||||
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|
||||
@ -197,7 +197,7 @@ see the doc page for the pair style for details.</p>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
|
||||
<p><a class="reference internal" href="compute_pe.html"><em>compute pe</em></a></p>
|
||||
<p><a class="reference internal" href="compute_pe.html"><em>compute pe</em></a>, <a class="reference internal" href="compute_bond.html"><em>compute bond</em></a></p>
|
||||
</div>
|
||||
<div class="section" id="default">
|
||||
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline">¶</a></h2>
|
||||
|
||||
@ -372,6 +372,10 @@
|
||||
</dt>
|
||||
|
||||
|
||||
<dt><a href="compute_bond.html#index-0">compute bond</a>
|
||||
</dt>
|
||||
|
||||
|
||||
<dt><a href="compute_bond_local.html#index-0">compute bond/local</a>
|
||||
</dt>
|
||||
|
||||
@ -555,12 +559,12 @@
|
||||
<dt><a href="compute_pe_atom.html#index-0">compute pe/atom</a>
|
||||
</dt>
|
||||
|
||||
</dl></td>
|
||||
<td style="width: 33%" valign="top"><dl>
|
||||
|
||||
<dt><a href="compute_plasticity_atom.html#index-0">compute plasticity/atom</a>
|
||||
</dt>
|
||||
|
||||
</dl></td>
|
||||
<td style="width: 33%" valign="top"><dl>
|
||||
|
||||
<dt><a href="compute_pressure.html#index-0">compute pressure</a>
|
||||
</dt>
|
||||
|
||||
@ -141,6 +141,9 @@
|
||||
</div>
|
||||
<div class="section" id="pair-style-morse-smooth-linear-command">
|
||||
<h1>pair_style morse/smooth/linear command<a class="headerlink" href="#pair-style-morse-smooth-linear-command" title="Permalink to this headline">¶</a></h1>
|
||||
</div>
|
||||
<div class="section" id="pair-style-morse-smooth-linear-omp-command">
|
||||
<h1>pair_style morse/smooth/linear/omp command<a class="headerlink" href="#pair-style-morse-smooth-linear-omp-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>pair_style morse cutoff
|
||||
@ -184,7 +187,6 @@ the potential energy and force go to zero at the cut-off:</p>
|
||||
<img alt="_images/pair_morse_smooth_linear.jpg" class="align-center" src="_images/pair_morse_smooth_linear.jpg" />
|
||||
<p>The syntax of the pair_style and pair_coeff commands are the same for
|
||||
the <em>morse</em> and <em>morse/smooth/linear</em> styles.</p>
|
||||
<p>same</p>
|
||||
<hr class="docutils" />
|
||||
<p>Styles with a <em>cuda</em>, <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
|
||||
@ -126,16 +126,30 @@
|
||||
|
||||
<div class="section" id="pair-style-thole-command">
|
||||
<span id="index-0"></span><h1>pair_style thole command<a class="headerlink" href="#pair-style-thole-command" title="Permalink to this headline">¶</a></h1>
|
||||
</div>
|
||||
<div class="section" id="pair-style-lj-cut-thole-long-command">
|
||||
<h1>pair_style lj/cut/thole/long command<a class="headerlink" href="#pair-style-lj-cut-thole-long-command" title="Permalink to this headline">¶</a></h1>
|
||||
</div>
|
||||
<div class="section" id="pair-style-lj-cut-thole-long-omp-command">
|
||||
<h1>pair_style lj/cut/thole/long/omp command<a class="headerlink" href="#pair-style-lj-cut-thole-long-omp-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>pair_style thole damp cutoff
|
||||
<div class="highlight-python"><div class="highlight"><pre>pair_style style args
|
||||
</pre></div>
|
||||
</div>
|
||||
<ul class="simple">
|
||||
<li>thole = style name</li>
|
||||
<li>damp = global damping parameter</li>
|
||||
<li>cutoff = global cutoff</li>
|
||||
<li>style = <em>thole</em> or <em>lj/cut/thole/long</em> or <em>lj/cut/thole/long/omp</em></li>
|
||||
<li>args = list of arguments for a particular style</li>
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>thole</em> args = damp cutoff
|
||||
damp = global damping parameter
|
||||
cutoff = global cutoff (distance units)
|
||||
<em>lj/cut/thole/long</em> or <em>lj/cut/thole/long/omp</em> args = damp cutoff (cutoff2)
|
||||
damp = global damping parameter
|
||||
cutoff = global cutoff for LJ (and Thole if only 1 arg) (distance units)
|
||||
cutoff2 = global cutoff for Thole (optional) (distance units)
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
|
||||
@ -145,10 +159,13 @@ pair_coeff 1 2 thole 1.0 2.6 10.0
|
||||
pair_coeff * 2 thole 1.0 2.6
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-python"><div class="highlight"><pre>pair_style lj/cut/thole/long 2.6 12.0
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
|
||||
<p>The <em>thole</em> pair style is meant to be used with force fields that
|
||||
<p>The <em>thole</em> pair styles are meant to be used with force fields that
|
||||
include explicit polarization through Drude dipoles. This link
|
||||
describes how to use the <a class="reference internal" href="tutorial_drude.html"><em>thermalized Drude oscillator model</em></a> in LAMMPS and polarizable models in LAMMPS
|
||||
are discussed in <a class="reference internal" href="Section_howto.html#howto-25"><span>this Section</span></a>.</p>
|
||||
@ -156,15 +173,24 @@ are discussed in <a class="reference internal" href="Section_howto.html#howto-25
|
||||
<a class="reference internal" href="pair_hybrid.html"><em>pair_hybrid/overlay</em></a> command, in conjunction with a
|
||||
main pair style including Coulomb interactions, i.e. any pair style
|
||||
containing <em>coul/cut</em> or <em>coul/long</em> in its style name.</p>
|
||||
<p>The <em>thole</em> pair style computes the Coulomb interaction damped at
|
||||
<p>The <em>lj/cut/thole/long</em> pair style is equivalent to, but more convenient that
|
||||
the frequent combination <em>hybrid/overlay lj/cut/coul/long cutoff thole damp
|
||||
cutoff2</em>. It is not only a shorthand for this pair_style combination, but
|
||||
it also allows for mixing pair coefficients instead of listing them all.
|
||||
The <em>lj/cut/thole/long</em> pair style is also a bit faster because it avoids an
|
||||
overlay and can benefit from OMP acceleration. Moreover, it uses a more
|
||||
precise approximation of the direct Coulomb interaction at short range similar
|
||||
to <code class="xref doc docutils literal"><span class="pre">coul/long/cs</span></code>, which stabilizes the temperature of
|
||||
Drude particles.</p>
|
||||
<p>The <em>thole</em> pair styles compute the Coulomb interaction damped at
|
||||
short distances by a function</p>
|
||||
<div class="math">
|
||||
\[\begin{equation} T_{ij}(r_{ij}) = 1 - \left( 1 +
|
||||
\frac{s_{ij} r_{ij} }{2} \right)
|
||||
\exp \left( - s_{ij} r_{ij} \right) \end{equation}\]</div>
|
||||
<p>This function results from an adaptation to point charges
|
||||
<a class="reference internal" href="tutorial_drude.html#noskov"><span>(Noskov)</span></a> of the dipole screening scheme originally proposed
|
||||
by <a class="reference internal" href="tutorial_drude.html#thole"><span>Thole</span></a>. The scaling coefficient <span class="math">\(s_{ij}\)</span> is determined
|
||||
<a class="reference internal" href="#noskov"><span>(Noskov)</span></a> of the dipole screening scheme originally proposed
|
||||
by <a class="reference internal" href="#thole"><span>Thole</span></a>. The scaling coefficient <span class="math">\(s_{ij}\)</span> is determined
|
||||
by the polarizability of the atoms, <span class="math">\(\alpha_i\)</span>, and by a Thole
|
||||
damping parameter <span class="math">\(a\)</span>. This Thole damping parameter usually takes
|
||||
a value of 2.6, but in certain force fields the value can depend upon
|
||||
@ -188,9 +214,9 @@ interactions between Drude particles and core charges or
|
||||
non-polarizable atoms are also subject to these weighting factors. The
|
||||
Drude particles inherit the 1-2, 1-3 and 1-4 neighbor relations from
|
||||
their respective cores.</p>
|
||||
<p>The following coefficients must be defined for each pair of atoms
|
||||
types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the example
|
||||
above.</p>
|
||||
<p>For pair_style <em>thole</em>, the following coefficients must be defined for
|
||||
each pair of atoms types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command
|
||||
as in the example above.</p>
|
||||
<ul class="simple">
|
||||
<li>alpha (distance units^3)</li>
|
||||
<li>damp</li>
|
||||
@ -200,9 +226,43 @@ above.</p>
|
||||
Thole damping parameter or global cutoff specified in the pair_style
|
||||
command are used. In order to specify a cutoff (third argument) a damp
|
||||
parameter (second argument) must also be specified.</p>
|
||||
<p>For pair style <em>lj/cut/thole/long</em>, the following coefficients must be
|
||||
defined for each pair of atoms types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a>
|
||||
command.</p>
|
||||
<ul class="simple">
|
||||
<li>epsilon (energy units)</li>
|
||||
<li>sigma (length units)</li>
|
||||
<li>alpha (distance units^3)</li>
|
||||
<li>damps</li>
|
||||
<li>LJ cutoff (distance units)</li>
|
||||
</ul>
|
||||
<p>The last two coefficients are optional and default to the global values from
|
||||
the <em>pair_style</em> command line.</p>
|
||||
<hr class="docutils" />
|
||||
<p>Styles with a <em>cuda</em>, <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed in <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a>
|
||||
of the manual. The accelerated styles take the same arguments and
|
||||
should produce the same results, except for round-off and precision
|
||||
issues.</p>
|
||||
<p>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
|
||||
KOKKOS, USER-OMP and OPT packages, respectively. They are only
|
||||
enabled if LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
|
||||
<p>You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span>-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
|
||||
use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>
|
||||
<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual for
|
||||
more instructions on how to use the accelerated styles effectively.</p>
|
||||
<p><strong>Mixing</strong>:</p>
|
||||
<p>The <em>thole</em> pair style does not support mixing. Thus, coefficients
|
||||
for all I,J pairs must be specified explicitly.</p>
|
||||
<p>The <em>lj/cut/thole/long</em> pair style does support mixing. Mixed coefficients
|
||||
are defined using</p>
|
||||
<div class="math">
|
||||
\[\begin{equation} \alpha_{ij} = \sqrt{\alpha_i\alpha_j}\end{equation}\]</div>
|
||||
<div class="math">
|
||||
\[\begin{equation} a_{ij} = \frac 1 2 (a_i + a_j)\end{equation}\]</div>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
|
||||
@ -211,10 +271,14 @@ enabled if LAMMPS was built with that package. See the <a class="reference inter
|
||||
<p>This pair_style should currently not be used with the <a class="reference internal" href="dihedral_charmm.html"><em>charmm dihedral style</em></a> if the latter has non-zero 1-4 weighting
|
||||
factors. This is because the <em>thole</em> pair style does not know which
|
||||
pairs are 1-4 partners of which dihedrals.</p>
|
||||
<p>The <em>lj/cut/thole/long</em> pair style should be used with a <a class="reference internal" href="kspace_style.html"><em>Kspace solver</em></a>
|
||||
like PPPM or Ewald, which is only enabled if LAMMPS was built with the kspace
|
||||
package.</p>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
|
||||
<p><a class="reference internal" href="fix_drude.html"><em>fix drude</em></a>, <a class="reference internal" href="fix_langevin_drude.html"><em>fix langevin/drude</em></a>, <a class="reference internal" href="fix_drude_transform.html"><em>fix drude/transform</em></a>, <a class="reference internal" href="compute_temp_drude.html"><em>compute temp/drude</em></a></p>
|
||||
<p><a class="reference internal" href="fix_drude.html"><em>fix drude</em></a>, <a class="reference internal" href="fix_langevin_drude.html"><em>fix langevin/drude</em></a>, <a class="reference internal" href="fix_drude_transform.html"><em>fix drude/transform</em></a>, <a class="reference internal" href="compute_temp_drude.html"><em>compute temp/drude</em></a>
|
||||
<a class="reference external" href="pair_lj_cut_coul_long">pair_style lj/cut/coul/long</a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
<hr class="docutils" />
|
||||
<p id="noskov"><strong>(Noskov)</strong> Noskov, Lamoureux and Roux, J Phys Chem B, 109, 6705 (2005).</p>
|
||||
|
||||
File diff suppressed because one or more lines are too long
@ -1 +1 @@
|
||||
#define LAMMPS_VERSION "10 Mar 2016"
|
||||
#define LAMMPS_VERSION "14 Mar 2016"
|
||||
|
||||
Reference in New Issue
Block a user