Merge remote-tracking branch 'lammps-ro/master' into lammps-icms
This commit is contained in:
Axel Kohlmeyer
@ -134,7 +134,8 @@
|
||||
|
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<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>
|
||||
<h2>28 Mar20 2016 version<a class="headerlink" href="#mar20-2016-version" title="Permalink to this headline">¶</a></h2>
|
||||
<div class="section" id="apr-2016-version">
|
||||
<h2>7 Apr 2016 version<a class="headerlink" href="#apr-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 @@
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||||
<!-- HTML_ONLY -->
|
||||
<HEAD>
|
||||
<TITLE>LAMMPS-ICMS Users Manual</TITLE>
|
||||
<META NAME="docnumber" CONTENT="28 Mar20 2016 version">
|
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<META NAME="docnumber" CONTENT="7 Apr 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
|
||||
28 Mar20 2016 version :c,h4
|
||||
7 Apr 2016 version :c,h4
|
||||
|
||||
Version info: :h4
|
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|
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|
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@ -463,8 +463,8 @@ in the command’s documentation.</p>
|
||||
<table border="1" class="docutils">
|
||||
<colgroup>
|
||||
<col width="17%" />
|
||||
<col width="15%" />
|
||||
<col width="17%" />
|
||||
<col width="15%" />
|
||||
<col width="17%" />
|
||||
<col width="17%" />
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<col width="17%" />
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@ -478,109 +478,109 @@ in the command’s documentation.</p>
|
||||
<td><a class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-even"><td><a class="reference internal" href="bond_style.html"><em>bond_style</em></a></td>
|
||||
<td><a class="reference internal" href="bond_write.html"><em>bond_write</em></a></td>
|
||||
<td><a class="reference internal" href="boundary.html"><em>boundary</em></a></td>
|
||||
<td><a class="reference internal" href="box.html"><em>box</em></a></td>
|
||||
<td><a class="reference internal" href="change_box.html"><em>change_box</em></a></td>
|
||||
<td><a class="reference internal" href="clear.html"><em>clear</em></a></td>
|
||||
<td><a class="reference internal" href="comm_modify.html"><em>comm_modify</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="comm_style.html"><em>comm_style</em></a></td>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="comm_modify.html"><em>comm_modify</em></a></td>
|
||||
<td><a class="reference internal" href="comm_style.html"><em>comm_style</em></a></td>
|
||||
<td><a class="reference internal" href="compute.html"><em>compute</em></a></td>
|
||||
<td><a class="reference internal" href="compute_modify.html"><em>compute_modify</em></a></td>
|
||||
<td><a class="reference internal" href="create_atoms.html"><em>create_atoms</em></a></td>
|
||||
<td><a class="reference internal" href="create_bonds.html"><em>create_bonds</em></a></td>
|
||||
<td><a class="reference internal" href="create_box.html"><em>create_box</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-even"><td><a class="reference internal" href="delete_atoms.html"><em>delete_atoms</em></a></td>
|
||||
<tr class="row-even"><td><a class="reference internal" href="create_box.html"><em>create_box</em></a></td>
|
||||
<td><a class="reference internal" href="delete_atoms.html"><em>delete_atoms</em></a></td>
|
||||
<td><a class="reference internal" href="delete_bonds.html"><em>delete_bonds</em></a></td>
|
||||
<td><a class="reference internal" href="dielectric.html"><em>dielectric</em></a></td>
|
||||
<td><a class="reference internal" href="dihedral_coeff.html"><em>dihedral_coeff</em></a></td>
|
||||
<td><a class="reference internal" href="dihedral_style.html"><em>dihedral_style</em></a></td>
|
||||
<td><a class="reference internal" href="dimension.html"><em>dimension</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="displace_atoms.html"><em>displace_atoms</em></a></td>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="dimension.html"><em>dimension</em></a></td>
|
||||
<td><a class="reference internal" href="displace_atoms.html"><em>displace_atoms</em></a></td>
|
||||
<td><a class="reference internal" href="dump.html"><em>dump</em></a></td>
|
||||
<td><a class="reference internal" href="dump_image.html"><em>dump image</em></a></td>
|
||||
<td><a class="reference internal" href="dump_modify.html"><em>dump_modify</em></a></td>
|
||||
<td><a class="reference internal" href="dump_image.html"><em>dump movie</em></a></td>
|
||||
<td><a class="reference internal" href="echo.html"><em>echo</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-even"><td><a class="reference internal" href="fix.html"><em>fix</em></a></td>
|
||||
<tr class="row-even"><td><a class="reference internal" href="echo.html"><em>echo</em></a></td>
|
||||
<td><a class="reference internal" href="fix.html"><em>fix</em></a></td>
|
||||
<td><a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a></td>
|
||||
<td><a class="reference internal" href="group.html"><em>group</em></a></td>
|
||||
<td><a class="reference internal" href="if.html"><em>if</em></a></td>
|
||||
<td><a class="reference internal" href="info.html"><em>info</em></a></td>
|
||||
<td><a class="reference internal" href="improper_coeff.html"><em>improper_coeff</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="improper_style.html"><em>improper_style</em></a></td>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="improper_coeff.html"><em>improper_coeff</em></a></td>
|
||||
<td><a class="reference internal" href="improper_style.html"><em>improper_style</em></a></td>
|
||||
<td><a class="reference internal" href="include.html"><em>include</em></a></td>
|
||||
<td><a class="reference internal" href="jump.html"><em>jump</em></a></td>
|
||||
<td><a class="reference internal" href="kspace_modify.html"><em>kspace_modify</em></a></td>
|
||||
<td><a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a></td>
|
||||
<td><a class="reference internal" href="label.html"><em>label</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-even"><td><a class="reference internal" href="lattice.html"><em>lattice</em></a></td>
|
||||
<tr class="row-even"><td><a class="reference internal" href="label.html"><em>label</em></a></td>
|
||||
<td><a class="reference internal" href="lattice.html"><em>lattice</em></a></td>
|
||||
<td><a class="reference internal" href="log.html"><em>log</em></a></td>
|
||||
<td><a class="reference internal" href="mass.html"><em>mass</em></a></td>
|
||||
<td><a class="reference internal" href="minimize.html"><em>minimize</em></a></td>
|
||||
<td><a class="reference internal" href="min_modify.html"><em>min_modify</em></a></td>
|
||||
<td><a class="reference internal" href="min_style.html"><em>min_style</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="molecule.html"><em>molecule</em></a></td>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="min_style.html"><em>min_style</em></a></td>
|
||||
<td><a class="reference internal" href="molecule.html"><em>molecule</em></a></td>
|
||||
<td><a class="reference internal" href="neb.html"><em>neb</em></a></td>
|
||||
<td><a class="reference internal" href="neigh_modify.html"><em>neigh_modify</em></a></td>
|
||||
<td><a class="reference internal" href="neighbor.html"><em>neighbor</em></a></td>
|
||||
<td><a class="reference internal" href="newton.html"><em>newton</em></a></td>
|
||||
<td><a class="reference internal" href="next.html"><em>next</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-even"><td><a class="reference internal" href="package.html"><em>package</em></a></td>
|
||||
<tr class="row-even"><td><a class="reference internal" href="next.html"><em>next</em></a></td>
|
||||
<td><a class="reference internal" href="package.html"><em>package</em></a></td>
|
||||
<td><a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a></td>
|
||||
<td><a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a></td>
|
||||
<td><a class="reference internal" href="pair_style.html"><em>pair_style</em></a></td>
|
||||
<td><a class="reference internal" href="pair_write.html"><em>pair_write</em></a></td>
|
||||
<td><a class="reference internal" href="partition.html"><em>partition</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="prd.html"><em>prd</em></a></td>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="partition.html"><em>partition</em></a></td>
|
||||
<td><a class="reference internal" href="prd.html"><em>prd</em></a></td>
|
||||
<td><a class="reference internal" href="print.html"><em>print</em></a></td>
|
||||
<td><a class="reference internal" href="processors.html"><em>processors</em></a></td>
|
||||
<td><a class="reference internal" href="python.html"><em>python</em></a></td>
|
||||
<td><a class="reference internal" href="quit.html"><em>quit</em></a></td>
|
||||
<td><a class="reference internal" href="read_data.html"><em>read_data</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-even"><td><a class="reference internal" href="read_dump.html"><em>read_dump</em></a></td>
|
||||
<tr class="row-even"><td><a class="reference internal" href="read_data.html"><em>read_data</em></a></td>
|
||||
<td><a class="reference internal" href="read_dump.html"><em>read_dump</em></a></td>
|
||||
<td><a class="reference internal" href="read_restart.html"><em>read_restart</em></a></td>
|
||||
<td><a class="reference internal" href="region.html"><em>region</em></a></td>
|
||||
<td><a class="reference internal" href="replicate.html"><em>replicate</em></a></td>
|
||||
<td><a class="reference internal" href="rerun.html"><em>rerun</em></a></td>
|
||||
<td><a class="reference internal" href="reset_timestep.html"><em>reset_timestep</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="restart.html"><em>restart</em></a></td>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="reset_timestep.html"><em>reset_timestep</em></a></td>
|
||||
<td><a class="reference internal" href="restart.html"><em>restart</em></a></td>
|
||||
<td><a class="reference internal" href="run.html"><em>run</em></a></td>
|
||||
<td><a class="reference internal" href="run_style.html"><em>run_style</em></a></td>
|
||||
<td><a class="reference internal" href="set.html"><em>set</em></a></td>
|
||||
<td><a class="reference internal" href="shell.html"><em>shell</em></a></td>
|
||||
<td><a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-even"><td><a class="reference internal" href="suffix.html"><em>suffix</em></a></td>
|
||||
<tr class="row-even"><td><a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a></td>
|
||||
<td><a class="reference internal" href="suffix.html"><em>suffix</em></a></td>
|
||||
<td><a class="reference internal" href="tad.html"><em>tad</em></a></td>
|
||||
<td><a class="reference internal" href="temper.html"><em>temper</em></a></td>
|
||||
<td><a class="reference internal" href="thermo.html"><em>thermo</em></a></td>
|
||||
<td><a class="reference internal" href="thermo_modify.html"><em>thermo_modify</em></a></td>
|
||||
<td><a class="reference internal" href="thermo_style.html"><em>thermo_style</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="timer.html"><em>timer</em></a></td>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="thermo_style.html"><em>thermo_style</em></a></td>
|
||||
<td><a class="reference internal" href="timer.html"><em>timer</em></a></td>
|
||||
<td><a class="reference internal" href="timestep.html"><em>timestep</em></a></td>
|
||||
<td><a class="reference internal" href="uncompute.html"><em>uncompute</em></a></td>
|
||||
<td><a class="reference internal" href="undump.html"><em>undump</em></a></td>
|
||||
<td><a class="reference internal" href="unfix.html"><em>unfix</em></a></td>
|
||||
<td><a class="reference internal" href="units.html"><em>units</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-even"><td><a class="reference internal" href="variable.html"><em>variable</em></a></td>
|
||||
<tr class="row-even"><td><a class="reference internal" href="units.html"><em>units</em></a></td>
|
||||
<td><a class="reference internal" href="variable.html"><em>variable</em></a></td>
|
||||
<td><a class="reference internal" href="velocity.html"><em>velocity</em></a></td>
|
||||
<td><a class="reference internal" href="write_data.html"><em>write_data</em></a></td>
|
||||
<td><a class="reference internal" href="write_dump.html"><em>write_dump</em></a></td>
|
||||
<td><a class="reference internal" href="write_restart.html"><em>write_restart</em></a></td>
|
||||
<td> </td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@ -1157,9 +1157,9 @@ KOKKOS, o = USER-OMP, t = OPT.</p>
|
||||
<tr class="row-even"><td><a class="reference internal" href="pair_sw.html"><em>sw (cgkio)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_table.html"><em>table (gko)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_tersoff.html"><em>tersoff (cgkio)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_tersoff_mod.html"><em>tersoff/mod (ko)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_tersoff_mod.html"><em>tersoff/mod (gko)</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="pair_tersoff_zbl.html"><em>tersoff/zbl (ko)</em></a></td>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="pair_tersoff_zbl.html"><em>tersoff/zbl (gko)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_coul.html"><em>tip4p/cut (o)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_coul.html"><em>tip4p/long (o)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_tri_lj.html"><em>tri/lj</em></a></td>
|
||||
|
||||
@ -375,6 +375,7 @@ in the command's documentation.
|
||||
"balance"_balance.html,
|
||||
"bond_coeff"_bond_coeff.html,
|
||||
"bond_style"_bond_style.html,
|
||||
"bond_write"_bond_write.html,
|
||||
"boundary"_boundary.html,
|
||||
"box"_box.html,
|
||||
"change_box"_change_box.html,
|
||||
@ -903,8 +904,8 @@ KOKKOS, o = USER-OMP, t = OPT.
|
||||
"sw (cgkio)"_pair_sw.html,
|
||||
"table (gko)"_pair_table.html,
|
||||
"tersoff (cgkio)"_pair_tersoff.html,
|
||||
"tersoff/mod (ko)"_pair_tersoff_mod.html,
|
||||
"tersoff/zbl (ko)"_pair_tersoff_zbl.html,
|
||||
"tersoff/mod (gko)"_pair_tersoff_mod.html,
|
||||
"tersoff/zbl (gko)"_pair_tersoff_zbl.html,
|
||||
"tip4p/cut (o)"_pair_coul.html,
|
||||
"tip4p/long (o)"_pair_coul.html,
|
||||
"tri/lj"_pair_tri_lj.html,
|
||||
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 30 KiB After Width: | Height: | Size: 67 KiB |
@ -5,8 +5,8 @@
|
||||
LAMMPS Documentation
|
||||
====================
|
||||
|
||||
23 Mar 2016 version
|
||||
-------------------
|
||||
28 Mar20 2016 version
|
||||
---------------------
|
||||
|
||||
Version info:
|
||||
-------------
|
||||
|
||||
@ -400,39 +400,39 @@ included when LAMMPS was built. Not all packages are included in a
|
||||
default LAMMPS build. These dependencies are listed as Restrictions
|
||||
in the command's documentation.
|
||||
|
||||
+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
|
||||
| :doc:`angle_coeff <angle_coeff>` | :doc:`angle_style <angle_style>` | :doc:`atom_modify <atom_modify>` | :doc:`atom_style <atom_style>` | :doc:`balance <balance>` | :doc:`bond_coeff <bond_coeff>` |
|
||||
+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
|
||||
| :doc:`bond_style <bond_style>` | :doc:`boundary <boundary>` | :doc:`box <box>` | :doc:`change_box <change_box>` | :doc:`clear <clear>` | :doc:`comm_modify <comm_modify>` |
|
||||
+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
|
||||
| :doc:`comm_style <comm_style>` | :doc:`compute <compute>` | :doc:`compute_modify <compute_modify>` | :doc:`create_atoms <create_atoms>` | :doc:`create_bonds <create_bonds>` | :doc:`create_box <create_box>` |
|
||||
+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
|
||||
| :doc:`delete_atoms <delete_atoms>` | :doc:`delete_bonds <delete_bonds>` | :doc:`dielectric <dielectric>` | :doc:`dihedral_coeff <dihedral_coeff>` | :doc:`dihedral_style <dihedral_style>` | :doc:`dimension <dimension>` |
|
||||
+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
|
||||
| :doc:`displace_atoms <displace_atoms>` | :doc:`dump <dump>` | :doc:`dump image <dump_image>` | :doc:`dump_modify <dump_modify>` | :doc:`dump movie <dump_image>` | :doc:`echo <echo>` |
|
||||
+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
|
||||
| :doc:`fix <fix>` | :doc:`fix_modify <fix_modify>` | :doc:`group <group>` | :doc:`if <if>` | :doc:`info <info>` | :doc:`improper_coeff <improper_coeff>` |
|
||||
+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
|
||||
| :doc:`improper_style <improper_style>` | :doc:`include <include>` | :doc:`jump <jump>` | :doc:`kspace_modify <kspace_modify>` | :doc:`kspace_style <kspace_style>` | :doc:`label <label>` |
|
||||
+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
|
||||
| :doc:`lattice <lattice>` | :doc:`log <log>` | :doc:`mass <mass>` | :doc:`minimize <minimize>` | :doc:`min_modify <min_modify>` | :doc:`min_style <min_style>` |
|
||||
+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
|
||||
| :doc:`molecule <molecule>` | :doc:`neb <neb>` | :doc:`neigh_modify <neigh_modify>` | :doc:`neighbor <neighbor>` | :doc:`newton <newton>` | :doc:`next <next>` |
|
||||
+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
|
||||
| :doc:`package <package>` | :doc:`pair_coeff <pair_coeff>` | :doc:`pair_modify <pair_modify>` | :doc:`pair_style <pair_style>` | :doc:`pair_write <pair_write>` | :doc:`partition <partition>` |
|
||||
+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
|
||||
| :doc:`prd <prd>` | :doc:`print <print>` | :doc:`processors <processors>` | :doc:`python <python>` | :doc:`quit <quit>` | :doc:`read_data <read_data>` |
|
||||
+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
|
||||
| :doc:`read_dump <read_dump>` | :doc:`read_restart <read_restart>` | :doc:`region <region>` | :doc:`replicate <replicate>` | :doc:`rerun <rerun>` | :doc:`reset_timestep <reset_timestep>` |
|
||||
+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
|
||||
| :doc:`restart <restart>` | :doc:`run <run>` | :doc:`run_style <run_style>` | :doc:`set <set>` | :doc:`shell <shell>` | :doc:`special_bonds <special_bonds>` |
|
||||
+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
|
||||
| :doc:`suffix <suffix>` | :doc:`tad <tad>` | :doc:`temper <temper>` | :doc:`thermo <thermo>` | :doc:`thermo_modify <thermo_modify>` | :doc:`thermo_style <thermo_style>` |
|
||||
+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
|
||||
| :doc:`timer <timer>` | :doc:`timestep <timestep>` | :doc:`uncompute <uncompute>` | :doc:`undump <undump>` | :doc:`unfix <unfix>` | :doc:`units <units>` |
|
||||
+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
|
||||
| :doc:`variable <variable>` | :doc:`velocity <velocity>` | :doc:`write_data <write_data>` | :doc:`write_dump <write_dump>` | :doc:`write_restart <write_restart>` | |
|
||||
+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
|
||||
+----------------------------------------+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
|
||||
| :doc:`angle_coeff <angle_coeff>` | :doc:`angle_style <angle_style>` | :doc:`atom_modify <atom_modify>` | :doc:`atom_style <atom_style>` | :doc:`balance <balance>` | :doc:`bond_coeff <bond_coeff>` |
|
||||
+----------------------------------------+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
|
||||
| :doc:`bond_style <bond_style>` | :doc:`bond_write <bond_write>` | :doc:`boundary <boundary>` | :doc:`box <box>` | :doc:`change_box <change_box>` | :doc:`clear <clear>` |
|
||||
+----------------------------------------+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
|
||||
| :doc:`comm_modify <comm_modify>` | :doc:`comm_style <comm_style>` | :doc:`compute <compute>` | :doc:`compute_modify <compute_modify>` | :doc:`create_atoms <create_atoms>` | :doc:`create_bonds <create_bonds>` |
|
||||
+----------------------------------------+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
|
||||
| :doc:`create_box <create_box>` | :doc:`delete_atoms <delete_atoms>` | :doc:`delete_bonds <delete_bonds>` | :doc:`dielectric <dielectric>` | :doc:`dihedral_coeff <dihedral_coeff>` | :doc:`dihedral_style <dihedral_style>` |
|
||||
+----------------------------------------+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
|
||||
| :doc:`dimension <dimension>` | :doc:`displace_atoms <displace_atoms>` | :doc:`dump <dump>` | :doc:`dump image <dump_image>` | :doc:`dump_modify <dump_modify>` | :doc:`dump movie <dump_image>` |
|
||||
+----------------------------------------+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
|
||||
| :doc:`echo <echo>` | :doc:`fix <fix>` | :doc:`fix_modify <fix_modify>` | :doc:`group <group>` | :doc:`if <if>` | :doc:`info <info>` |
|
||||
+----------------------------------------+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
|
||||
| :doc:`improper_coeff <improper_coeff>` | :doc:`improper_style <improper_style>` | :doc:`include <include>` | :doc:`jump <jump>` | :doc:`kspace_modify <kspace_modify>` | :doc:`kspace_style <kspace_style>` |
|
||||
+----------------------------------------+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
|
||||
| :doc:`label <label>` | :doc:`lattice <lattice>` | :doc:`log <log>` | :doc:`mass <mass>` | :doc:`minimize <minimize>` | :doc:`min_modify <min_modify>` |
|
||||
+----------------------------------------+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
|
||||
| :doc:`min_style <min_style>` | :doc:`molecule <molecule>` | :doc:`neb <neb>` | :doc:`neigh_modify <neigh_modify>` | :doc:`neighbor <neighbor>` | :doc:`newton <newton>` |
|
||||
+----------------------------------------+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
|
||||
| :doc:`next <next>` | :doc:`package <package>` | :doc:`pair_coeff <pair_coeff>` | :doc:`pair_modify <pair_modify>` | :doc:`pair_style <pair_style>` | :doc:`pair_write <pair_write>` |
|
||||
+----------------------------------------+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
|
||||
| :doc:`partition <partition>` | :doc:`prd <prd>` | :doc:`print <print>` | :doc:`processors <processors>` | :doc:`python <python>` | :doc:`quit <quit>` |
|
||||
+----------------------------------------+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
|
||||
| :doc:`read_data <read_data>` | :doc:`read_dump <read_dump>` | :doc:`read_restart <read_restart>` | :doc:`region <region>` | :doc:`replicate <replicate>` | :doc:`rerun <rerun>` |
|
||||
+----------------------------------------+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
|
||||
| :doc:`reset_timestep <reset_timestep>` | :doc:`restart <restart>` | :doc:`run <run>` | :doc:`run_style <run_style>` | :doc:`set <set>` | :doc:`shell <shell>` |
|
||||
+----------------------------------------+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
|
||||
| :doc:`special_bonds <special_bonds>` | :doc:`suffix <suffix>` | :doc:`tad <tad>` | :doc:`temper <temper>` | :doc:`thermo <thermo>` | :doc:`thermo_modify <thermo_modify>` |
|
||||
+----------------------------------------+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
|
||||
| :doc:`thermo_style <thermo_style>` | :doc:`timer <timer>` | :doc:`timestep <timestep>` | :doc:`uncompute <uncompute>` | :doc:`undump <undump>` | :doc:`unfix <unfix>` |
|
||||
+----------------------------------------+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
|
||||
| :doc:`units <units>` | :doc:`variable <variable>` | :doc:`velocity <velocity>` | :doc:`write_data <write_data>` | :doc:`write_dump <write_dump>` | :doc:`write_restart <write_restart>` |
|
||||
+----------------------------------------+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
|
||||
|
||||
These are additional commands in USER packages, which can be used if
|
||||
:ref:`LAMMPS is built with the appropriate package <start_3>`.
|
||||
@ -636,9 +636,9 @@ KOKKOS, o = USER-OMP, t = OPT.
|
||||
+-----------------------------------------------------------+-----------------------------------------------------+----------------------------------------------------+-------------------------------------------------------+
|
||||
| :doc:`rebo (o) <pair_airebo>` | :doc:`resquared (go) <pair_resquared>` | :doc:`snap <pair_snap>` | :doc:`soft (go) <pair_soft>` |
|
||||
+-----------------------------------------------------------+-----------------------------------------------------+----------------------------------------------------+-------------------------------------------------------+
|
||||
| :doc:`sw (cgkio) <pair_sw>` | :doc:`table (gko) <pair_table>` | :doc:`tersoff (cgkio) <pair_tersoff>` | :doc:`tersoff/mod (ko) <pair_tersoff_mod>` |
|
||||
| :doc:`sw (cgkio) <pair_sw>` | :doc:`table (gko) <pair_table>` | :doc:`tersoff (cgkio) <pair_tersoff>` | :doc:`tersoff/mod (gko) <pair_tersoff_mod>` |
|
||||
+-----------------------------------------------------------+-----------------------------------------------------+----------------------------------------------------+-------------------------------------------------------+
|
||||
| :doc:`tersoff/zbl (ko) <pair_tersoff_zbl>` | :doc:`tip4p/cut (o) <pair_coul>` | :doc:`tip4p/long (o) <pair_coul>` | :doc:`tri/lj <pair_tri_lj>` |
|
||||
| :doc:`tersoff/zbl (gko) <pair_tersoff_zbl>` | :doc:`tip4p/cut (o) <pair_coul>` | :doc:`tip4p/long (o) <pair_coul>` | :doc:`tri/lj <pair_tri_lj>` |
|
||||
+-----------------------------------------------------------+-----------------------------------------------------+----------------------------------------------------+-------------------------------------------------------+
|
||||
| :doc:`vashishta (o) <pair_vashishta>` | :doc:`yukawa (go) <pair_yukawa>` | :doc:`yukawa/colloid (go) <pair_yukawa_colloid>` | :doc:`zbl (go) <pair_zbl>` |
|
||||
+-----------------------------------------------------------+-----------------------------------------------------+----------------------------------------------------+-------------------------------------------------------+
|
||||
|
||||
@ -110,7 +110,7 @@ values in the table.
|
||||
|
||||
The "EQ" parameter is also optional. If used, it is followed by a the
|
||||
equilibrium bond length, which is used, for example, by the :doc:`fix shake <fix_shake>` command. If not used, the equilibrium bond
|
||||
length is set to 0.0.
|
||||
length is to the distance in the table with the lowest potential energy.
|
||||
|
||||
Following a blank line, the next N lines list the tabulated values.
|
||||
On each line, the 1st value is the index from 1 to N, the 2nd value is
|
||||
|
||||
74
doc/_sources/bond_write.txt
Normal file
74
doc/_sources/bond_write.txt
Normal file
@ -0,0 +1,74 @@
|
||||
.. index:: bond_write
|
||||
|
||||
bond_write command
|
||||
==================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
bond_write btype N inner outer file keyword itype jtype
|
||||
|
||||
* btype = bond types
|
||||
* N = # of values
|
||||
* inner,outer = inner and outer bond length (distance units)
|
||||
* file = name of file to write values to
|
||||
* keyword = section name in file for this set of tabulated values
|
||||
* itype,jtype = 2 atom types (optional)
|
||||
*
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
bond_write 1 500 0.5 3.5 table.txt Harmonic_1
|
||||
bond_write 3 1000 0.1 6.0 table.txt Morse
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
Write energy and force values to a file as a function of distance for
|
||||
the currently defined bond potential. This is useful for plotting the
|
||||
potential function or otherwise debugging its values. If the file
|
||||
already exists, the table of values is appended to the end of the file
|
||||
to allow multiple tables of energy and force to be included in one
|
||||
file.
|
||||
|
||||
The energy and force values are computed at distances from inner to
|
||||
outer for 2 interacting atoms forming a bond of type btype, using the
|
||||
appropriate :doc:`bond_coeff <bond_coeff>` coefficients. N evenly spaced
|
||||
distances are used.
|
||||
|
||||
For example, for N = 7, inner = 1.0, and outer = 4.0,
|
||||
values are computed at r = 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, 4.0.
|
||||
|
||||
The file is written in the format used as input for the
|
||||
:doc:`bond_style <bond_style>` *table* option with *keyword* as the
|
||||
section name. Each line written to the file lists an index number
|
||||
(1-N), a distance (in distance units), an energy (in energy units),
|
||||
and a force (in force units).
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
|
||||
All force field coefficients for bond and other kinds of interactions
|
||||
must be set before this command can be invoked.
|
||||
|
||||
Due to how the bond force is computed, an inner value > 0.0 must
|
||||
be specified even if the potential has a finite value at r = 0.0.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`bond_style table <bond_table>`,
|
||||
:doc:`bond_style <bond_style>`, :doc:`bond_coeff <bond_coeff>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Section_commands.html#comm
|
||||
@ -275,7 +275,7 @@ of Aidan Thompson), with its 8 atom unit cell.
|
||||
variable 1_6 equal 1.0/6.0
|
||||
variable 5_6 equal 5.0/6.0
|
||||
variable 1_12 equal 1.0/12.0
|
||||
variable 5_12 equal 5.0/12/0
|
||||
variable 5_12 equal 5.0/12.0
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
@ -296,7 +296,11 @@ of Aidan Thompson), with its 8 atom unit cell.
|
||||
|
||||
region myreg block 0 1 0 1 0 1
|
||||
create_box 2 myreg
|
||||
create_atoms 1 box
|
||||
create_atoms 1 box &
|
||||
basis 5 2 &
|
||||
basis 6 2 &
|
||||
basis 7 2 &
|
||||
basis 8 2
|
||||
|
||||
|
||||
----------
|
||||
|
||||
@ -128,7 +128,7 @@ colloid-solvent cutoff in this case.
|
||||
|
||||
When using pair_style colloid for a mixture with 2 (or more)
|
||||
widely different particles sizes (e.g. sigma=10 colloids in a
|
||||
background sigam=1 LJ fluid), you will likely want to use these
|
||||
background sigma=1 LJ fluid), you will likely want to use these
|
||||
commands for efficiency: :doc:`neighbor multi <neighbor>` and
|
||||
:doc:`comm_modify multi <comm_modify>`.
|
||||
|
||||
|
||||
@ -58,7 +58,7 @@ field. This pair-wise thermostat can be used in conjunction with any
|
||||
:doc:`pair style <pair_style>`, and in leiu of per-particle thermostats
|
||||
like :doc:`fix langevin <fix_langevin>` or ensemble thermostats like
|
||||
Nose Hoover as implemented by :doc:`fix nvt <fix_nh>`. To use
|
||||
*dpd/stat* as a thermostat for another pair style, use the :doc:`pair_style hybrid/overlay <pair_hybrid>` command to compute both the desired
|
||||
*dpd/tstat* as a thermostat for another pair style, use the :doc:`pair_style hybrid/overlay <pair_hybrid>` command to compute both the desired
|
||||
pair interaction and the thermostat for each pair of particles.
|
||||
|
||||
For style *dpd*, the force on atom I due to atom J is given as a sum
|
||||
|
||||
@ -279,7 +279,7 @@ Restrictions
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`pair_coeff <pair_coeff>`
|
||||
:doc:`pair_coeff <pair_coeff>`, :doc:`pair_write <pair_write>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
@ -3,6 +3,9 @@
|
||||
pair_style tersoff/mod command
|
||||
==============================
|
||||
|
||||
pair_style tersoff/mod/gpu command
|
||||
==================================
|
||||
|
||||
pair_style tersoff/mod/kk command
|
||||
=================================
|
||||
|
||||
|
||||
@ -3,6 +3,9 @@
|
||||
pair_style tersoff/zbl command
|
||||
==============================
|
||||
|
||||
pair_style tersoff/zbl/gpu command
|
||||
==================================
|
||||
|
||||
pair_style tersoff/zbl/kk command
|
||||
=================================
|
||||
|
||||
|
||||
@ -78,6 +78,7 @@ pairwise portion of the potential, not the embedding portion.
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`pair_style table <pair_table>`,
|
||||
:doc:`pair_style <pair_style>`, :doc:`pair_coeff <pair_coeff>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
@ -43,9 +43,9 @@ would see with one or more physical processors per replica. See :ref:`this sect
|
||||
discussion.
|
||||
|
||||
Each replica's temperature is controlled at a different value by a fix
|
||||
with *fix-ID* that controls temperature. Possible fix styles are
|
||||
:doc:`nvt <fix_nh>`, :doc:`temp/berendsen <fix_nh>`,
|
||||
:doc:`langevin <fix_langevin>` and :doc:`temp/rescale <fix_temp_rescale>`.
|
||||
with *fix-ID* that controls temperature. Most thermostat fix styles
|
||||
(with and without included time integration) are supported. The command
|
||||
will print an error message and abort, if the chosen fix is unsupported.
|
||||
The desired temperature is specified by *temp*, which is typically a
|
||||
variable previously set in the input script, so that each partition is
|
||||
assigned a different temperature. See the :doc:`variable <variable>`
|
||||
|
||||
@ -217,7 +217,7 @@ are estimated (less accurately) by the first two and last two force
|
||||
values in the table.</p>
|
||||
<p>The “EQ” parameter is also optional. If used, it is followed by a the
|
||||
equilibrium bond length, which is used, for example, by the <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> command. If not used, the equilibrium bond
|
||||
length is set to 0.0.</p>
|
||||
length is to the distance in the table with the lowest potential energy.</p>
|
||||
<p>Following a blank line, the next N lines list the tabulated values.
|
||||
On each line, the 1st value is the index from 1 to N, the 2nd value is
|
||||
the bond length r (in distance units), the 3rd value is the energy (in
|
||||
|
||||
248
doc/bond_write.html
Normal file
248
doc/bond_write.html
Normal file
@ -0,0 +1,248 @@
|
||||
|
||||
|
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|
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|
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|
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|
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|
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|
||||
|
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<ul>
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
|
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<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
|
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<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
|
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<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
|
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
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||||
|
||||
</div>
|
||||
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
|
||||
<div itemprop="articleBody">
|
||||
|
||||
<div class="section" id="bond-write-command">
|
||||
<span id="index-0"></span><h1>bond_write command<a class="headerlink" href="#bond-write-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>bond_write btype N inner outer file keyword itype jtype
|
||||
</pre></div>
|
||||
</div>
|
||||
<ul class="simple">
|
||||
<li>btype = bond types</li>
|
||||
<li>N = # of values</li>
|
||||
<li>inner,outer = inner and outer bond length (distance units)</li>
|
||||
<li>file = name of file to write values to</li>
|
||||
<li>keyword = section name in file for this set of tabulated values</li>
|
||||
<li>itype,jtype = 2 atom types (optional)</li>
|
||||
<li></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>bond_write 1 500 0.5 3.5 table.txt Harmonic_1
|
||||
bond_write 3 1000 0.1 6.0 table.txt 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>Write energy and force values to a file as a function of distance for
|
||||
the currently defined bond potential. This is useful for plotting the
|
||||
potential function or otherwise debugging its values. If the file
|
||||
already exists, the table of values is appended to the end of the file
|
||||
to allow multiple tables of energy and force to be included in one
|
||||
file.</p>
|
||||
<p>The energy and force values are computed at distances from inner to
|
||||
outer for 2 interacting atoms forming a bond of type btype, using the
|
||||
appropriate <a class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a> coefficients. N evenly spaced
|
||||
distances are used.</p>
|
||||
<p>For example, for N = 7, inner = 1.0, and outer = 4.0,
|
||||
values are computed at r = 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, 4.0.</p>
|
||||
<p>The file is written in the format used as input for the
|
||||
<a class="reference internal" href="bond_style.html"><em>bond_style</em></a> <em>table</em> option with <em>keyword</em> as the
|
||||
section name. Each line written to the file lists an index number
|
||||
(1-N), a distance (in distance units), an energy (in energy units),
|
||||
and a force (in force units).</p>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
|
||||
<p>All force field coefficients for bond and other kinds of interactions
|
||||
must be set before this command can be invoked.</p>
|
||||
<p>Due to how the bond force is computed, an inner value > 0.0 must
|
||||
be specified even if the potential has a finite value at r = 0.0.</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="bond_table.html"><em>bond_style table</em></a>,
|
||||
<a class="reference internal" href="bond_style.html"><em>bond_style</em></a>, <a class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
</div>
|
||||
<footer>
|
||||
|
||||
|
||||
<hr/>
|
||||
|
||||
<div role="contentinfo">
|
||||
<p>
|
||||
© Copyright 2013 Sandia Corporation.
|
||||
</p>
|
||||
</div>
|
||||
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
|
||||
|
||||
</footer>
|
||||
|
||||
</div>
|
||||
</div>
|
||||
|
||||
</section>
|
||||
|
||||
</div>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
<script type="text/javascript">
|
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var DOCUMENTATION_OPTIONS = {
|
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|
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|
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|
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|
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|
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|
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|
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|
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|
||||
|
||||
</body>
|
||||
</html>
|
||||
@ -287,12 +287,12 @@
|
||||
<dt><a href="bond_harmonic_shift_cut.html#index-0">bond_style harmonic/shift/cut</a>
|
||||
</dt>
|
||||
|
||||
</dl></td>
|
||||
<td style="width: 33%" valign="top"><dl>
|
||||
|
||||
<dt><a href="bond_hybrid.html#index-0">bond_style hybrid</a>
|
||||
</dt>
|
||||
|
||||
</dl></td>
|
||||
<td style="width: 33%" valign="top"><dl>
|
||||
|
||||
<dt><a href="bond_morse.html#index-0">bond_style morse</a>
|
||||
</dt>
|
||||
@ -318,6 +318,10 @@
|
||||
</dt>
|
||||
|
||||
|
||||
<dt><a href="bond_write.html#index-0">bond_write</a>
|
||||
</dt>
|
||||
|
||||
|
||||
<dt><a href="boundary.html#index-0">boundary</a>
|
||||
</dt>
|
||||
|
||||
|
||||
@ -359,7 +359,7 @@ variable 2_3 equal 2.0/3.0
|
||||
variable 1_6 equal 1.0/6.0
|
||||
variable 5_6 equal 5.0/6.0
|
||||
variable 1_12 equal 1.0/12.0
|
||||
variable 5_12 equal 5.0/12/0
|
||||
variable 5_12 equal 5.0/12.0
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-python"><div class="highlight"><pre>lattice custom 1.0 &
|
||||
@ -378,7 +378,11 @@ variable 5_12 equal 5.0/12/0
|
||||
</div>
|
||||
<div class="highlight-python"><div class="highlight"><pre>region myreg block 0 1 0 1 0 1
|
||||
create_box 2 myreg
|
||||
create_atoms 1 box
|
||||
create_atoms 1 box &
|
||||
basis 5 2 &
|
||||
basis 6 2 &
|
||||
basis 7 2 &
|
||||
basis 8 2
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
@ -163,7 +163,7 @@ Lennard-Jones particle of size sigma.</p>
|
||||
colloidal particles, and Rc is the cutoff. This equation results from
|
||||
describing each colloidal particle as an integrated collection of
|
||||
Lennard-Jones particles of size sigma and is derived in
|
||||
<a class="reference internal" href="pair_resquared.html#everaers"><span>(Everaers)</span></a>.</p>
|
||||
<a class="reference internal" href="#everaers"><span>(Everaers)</span></a>.</p>
|
||||
<p>The colloid-solvent interaction energy is given by</p>
|
||||
<img alt="_images/pair_colloid_cs.jpg" class="align-center" src="_images/pair_colloid_cs.jpg" />
|
||||
<p>where A_cs is the Hamaker constant, a is the radius of the colloidal
|
||||
@ -231,7 +231,7 @@ colloid-solvent cutoff in this case.</p>
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">When using pair_style colloid for a mixture with 2 (or more)
|
||||
widely different particles sizes (e.g. sigma=10 colloids in a
|
||||
background sigam=1 LJ fluid), you will likely want to use these
|
||||
background sigma=1 LJ fluid), you will likely want to use these
|
||||
commands for efficiency: <a class="reference internal" href="neighbor.html"><em>neighbor multi</em></a> and
|
||||
<a class="reference internal" href="comm_modify.html"><em>comm_modify multi</em></a>.</p>
|
||||
</div>
|
||||
|
||||
@ -177,7 +177,7 @@ field. This pair-wise thermostat can be used in conjunction with any
|
||||
<a class="reference internal" href="pair_style.html"><em>pair style</em></a>, and in leiu of per-particle thermostats
|
||||
like <a class="reference internal" href="fix_langevin.html"><em>fix langevin</em></a> or ensemble thermostats like
|
||||
Nose Hoover as implemented by <a class="reference internal" href="fix_nh.html"><em>fix nvt</em></a>. To use
|
||||
<em>dpd/stat</em> as a thermostat for another pair style, use the <a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid/overlay</em></a> command to compute both the desired
|
||||
<em>dpd/tstat</em> as a thermostat for another pair style, use the <a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid/overlay</em></a> command to compute both the desired
|
||||
pair interaction and the thermostat for each pair of particles.</p>
|
||||
<p>For style <em>dpd</em>, the force on atom I due to atom J is given as a sum
|
||||
of 3 terms</p>
|
||||
|
||||
@ -359,7 +359,7 @@ commands do need to be specified in the restart input script.</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="pair_coeff.html"><em>pair_coeff</em></a></p>
|
||||
<p><a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a>, <a class="reference internal" href="pair_write.html"><em>pair_write</em></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
<hr class="docutils" />
|
||||
<p id="wolff"><strong>(Wolff)</strong> Wolff and Rudd, Comp Phys Comm, 120, 200-32 (1999).</p>
|
||||
|
||||
@ -127,6 +127,9 @@
|
||||
<div class="section" id="pair-style-tersoff-mod-command">
|
||||
<span id="index-0"></span><h1>pair_style tersoff/mod command<a class="headerlink" href="#pair-style-tersoff-mod-command" title="Permalink to this headline">¶</a></h1>
|
||||
</div>
|
||||
<div class="section" id="pair-style-tersoff-mod-gpu-command">
|
||||
<h1>pair_style tersoff/mod/gpu command<a class="headerlink" href="#pair-style-tersoff-mod-gpu-command" title="Permalink to this headline">¶</a></h1>
|
||||
</div>
|
||||
<div class="section" id="pair-style-tersoff-mod-kk-command">
|
||||
<h1>pair_style tersoff/mod/kk command<a class="headerlink" href="#pair-style-tersoff-mod-kk-command" title="Permalink to this headline">¶</a></h1>
|
||||
</div>
|
||||
|
||||
@ -127,6 +127,9 @@
|
||||
<div class="section" id="pair-style-tersoff-zbl-command">
|
||||
<span id="index-0"></span><h1>pair_style tersoff/zbl command<a class="headerlink" href="#pair-style-tersoff-zbl-command" title="Permalink to this headline">¶</a></h1>
|
||||
</div>
|
||||
<div class="section" id="pair-style-tersoff-zbl-gpu-command">
|
||||
<h1>pair_style tersoff/zbl/gpu command<a class="headerlink" href="#pair-style-tersoff-zbl-gpu-command" title="Permalink to this headline">¶</a></h1>
|
||||
</div>
|
||||
<div class="section" id="pair-style-tersoff-zbl-kk-command">
|
||||
<h1>pair_style tersoff/zbl/kk command<a class="headerlink" href="#pair-style-tersoff-zbl-kk-command" title="Permalink to this headline">¶</a></h1>
|
||||
</div>
|
||||
|
||||
@ -189,7 +189,8 @@ pairwise portion of the potential, not the embedding portion.</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="pair_style.html"><em>pair_style</em></a>, <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a></p>
|
||||
<p><a class="reference internal" href="pair_table.html"><em>pair_style table</em></a>,
|
||||
<a class="reference internal" href="pair_style.html"><em>pair_style</em></a>, <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
File diff suppressed because one or more lines are too long
@ -162,9 +162,9 @@ two processors. You will simply not get the performance speed-up you
|
||||
would see with one or more physical processors per replica. See <a class="reference internal" href="Section_howto.html#howto-5"><span>this section</span></a> of the manual for further
|
||||
discussion.</p>
|
||||
<p>Each replica’s temperature is controlled at a different value by a fix
|
||||
with <em>fix-ID</em> that controls temperature. Possible fix styles are
|
||||
<a class="reference internal" href="fix_nh.html"><em>nvt</em></a>, <a class="reference internal" href="fix_nh.html"><em>temp/berendsen</em></a>,
|
||||
<a class="reference internal" href="fix_langevin.html"><em>langevin</em></a> and <a class="reference internal" href="fix_temp_rescale.html"><em>temp/rescale</em></a>.
|
||||
with <em>fix-ID</em> that controls temperature. Most thermostat fix styles
|
||||
(with and without included time integration) are supported. The command
|
||||
will print an error message and abort, if the chosen fix is unsupported.
|
||||
The desired temperature is specified by <em>temp</em>, which is typically a
|
||||
variable previously set in the input script, so that each partition is
|
||||
assigned a different temperature. See the <a class="reference internal" href="variable.html"><em>variable</em></a>
|
||||
|
||||
225
src/Make.py
225
src/Make.py
@ -15,14 +15,14 @@ import sys,os,commands,re,copy,subprocess
|
||||
# setargs = makefile settings
|
||||
# actionargs = allowed actions (also lib-dir and machine)
|
||||
|
||||
abbrevs = "adhjmoprsv"
|
||||
abbrevs = "adhjmoprsvz"
|
||||
|
||||
switchclasses = ("actions","dir","help","jmake","makefile",
|
||||
"output","packages","redo","settings","verbose")
|
||||
"output","packages","redo","settings","verbose","zoutput")
|
||||
libclasses = ("atc","awpmd","colvars","cuda","gpu","h5md",
|
||||
"meam","poems","python","qmmm","voronoi")
|
||||
buildclasses = ("intel","kokkos")
|
||||
makeclasses = ("cc","mpi","fft","jpg","png")
|
||||
makeclasses = ("cc","flags","mpi","fft","jpg","png")
|
||||
|
||||
setargs = ("gzip","#gzip","ffmpeg","#ffmpeg","smallbig","bigbig","smallsmall")
|
||||
actionargs = ("lib-all","file","clean","exe")
|
||||
@ -137,27 +137,37 @@ class Actions:
|
||||
lib-all builds all auxiliary libs needed by installed packages
|
||||
lib-dir builds a specific lib whether package installed or not
|
||||
dir is any dir in lib directory (atc, cuda, meam, etc) except linalg
|
||||
(2) file = create src/MAKE/MINE/Makefile.auto
|
||||
use -m switch for Makefile.machine to start from,
|
||||
else use existing Makefile.auto
|
||||
adds settings needed for installed accelerator packages
|
||||
existing Makefile.auto is NOT changed unless "file" action is specified
|
||||
(2) file = create a new src/MAKE/MINE/Makefile.auto
|
||||
if file not specified, existing Makefile.auto is NOT changed
|
||||
except by -m switch, which will copy Makefile.machine to Makefile.auto
|
||||
note that exe action can add an -m switch, as described below
|
||||
if file is specified, new Makefile.auto is created
|
||||
if "-m machine" specified (or added by exe),
|
||||
start with existing Makefile.machine, else existing Makefile.auto
|
||||
if "-m none" specified, start Makefile.auto from scratch
|
||||
must use -cc and -mpi switches to specify compiler and MPI
|
||||
settings for these switches will alter Makefile.auto
|
||||
-s, -intel, -kokkos, -cc, -mpi, -fft, -jpg, -png
|
||||
if these accelerator packages are installed, they induce settings
|
||||
that will alter Makefile.auto: opt, user-omp, user-intel, kokkos
|
||||
use -z switch to copy final Makefile.auto to new filename
|
||||
(3) clean = invoke "make clean-auto" to insure clean build on current files
|
||||
useful if compiler flags have changed
|
||||
(4) exe or machine = build LAMMPS
|
||||
machine can be any existing Makefile.machine suffix
|
||||
machine is converted to "exe" action, as well as:
|
||||
machine is converted to "exe" action, and additionally:
|
||||
"-m machine" is added if -m switch is not specified
|
||||
"-o machine" is added if -o switch is not specified
|
||||
if either "-m" or "-o" are specified, they are not overridden
|
||||
does not invoke any lib builds, since libs could be previously built
|
||||
exe always builds using src/MAKE/MINE/Makefile.auto
|
||||
if file action also specified, it creates Makefile.auto
|
||||
exe ALWAYS builds using src/MAKE/MINE/Makefile.auto
|
||||
if file action also specified, it creates a new Makefile.auto
|
||||
else if -m switch specified,
|
||||
existing Makefile.machine is copied to create Makefile.auto
|
||||
else Makefile.auto must already exist and is not changed
|
||||
produces src/lmp_auto, or error message if unsuccessful
|
||||
build produces src/lmp_auto, or error message if unsuccessful
|
||||
use -o switch to copy src/lmp_auto to new filename
|
||||
use -z switch to copy src/MAKE/MINE/Makefile.auto to new filename
|
||||
"""
|
||||
|
||||
def check(self):
|
||||
@ -177,7 +187,7 @@ class Actions:
|
||||
cleans.append(one)
|
||||
elif one == "exe":
|
||||
exes.append(one)
|
||||
# one action can be unknown in case is a machine (checked in setup)
|
||||
# one action can be unknown, must be a machine (checked in setup)
|
||||
else:
|
||||
exes.append(one)
|
||||
if len(set(libs)) != len(libs) or \
|
||||
@ -236,9 +246,9 @@ class Actions:
|
||||
|
||||
def file(self,caller):
|
||||
|
||||
# if caller = "file", create from mpi or read from makefile.machine or auto
|
||||
# if caller = "exe" and "file" action already invoked, read from auto
|
||||
# if caller = "exe" and no "file" action, read from makefile.machine or auto
|
||||
# if caller="file", create from mpi or read from Makefile.machine or auto
|
||||
# if caller="exe" and "file" action already invoked, read from auto
|
||||
# if caller="exe" and no "file" action, read from Makefile.machine or auto
|
||||
|
||||
if caller == "file":
|
||||
if makefile and makefile.machine == "none":
|
||||
@ -279,7 +289,7 @@ class Actions:
|
||||
make.addvar("CC","-cxx=%s" % wrapper)
|
||||
make.addvar("LINK","-cxx=%s" % wrapper)
|
||||
elif "-lmpi" in txt:
|
||||
make.addvar("OMPI_CXX",wrapper,"cc")
|
||||
make.addvar("export OMPI_CXX",wrapper,"cc")
|
||||
precompiler = "env OMPI_CXX=%s " % wrapper
|
||||
else: error("Could not add MPI wrapper compiler, " +
|
||||
"did not recognize OpenMPI or MPICH")
|
||||
@ -287,8 +297,20 @@ class Actions:
|
||||
make.addvar("CCFLAGS","-O3")
|
||||
make.setvar("LINKFLAGS","-g")
|
||||
make.addvar("LINKFLAGS","-O")
|
||||
|
||||
# add CC and LINK flags
|
||||
|
||||
# add MPI settings
|
||||
if flags:
|
||||
for flag in flags.CC:
|
||||
flag = "-" + flag
|
||||
if flag[:2] == "-O": make.delvar("CCFLAGS","-O*")
|
||||
make.addvar("CCFLAGS",flag)
|
||||
for flag in flags.LINK:
|
||||
flag = "-" + flag
|
||||
if flag[:2] == "-O": make.delvar("LINKFLAGS","-O*")
|
||||
make.addvar("LINKFLAGS",flag)
|
||||
|
||||
# add MPI settings
|
||||
|
||||
if mpi:
|
||||
make.delvar("MPI_INC","*")
|
||||
@ -397,7 +419,7 @@ class Actions:
|
||||
make.addvar("KOKKOS_DEVICES","OpenMP","lmp")
|
||||
make.addvar("KOKKOS_ARCH","KNC","lmp")
|
||||
|
||||
# add LMP settings
|
||||
# add LMP_INC ifdef settings
|
||||
|
||||
if settings:
|
||||
list = settings.inlist
|
||||
@ -465,12 +487,13 @@ class Actions:
|
||||
|
||||
# set self.stubs if Makefile.auto uses STUBS lib in MPI settings
|
||||
|
||||
if "-lmpi_stubs" in make.getvar("MPI_LIB"): self.stubs = 1
|
||||
if make.getvar("MPI_LIB") and "-lmpi_stubs" in make.getvar("MPI_LIB"):
|
||||
self.stubs = 1
|
||||
else: self.stubs = 0
|
||||
|
||||
# write out Makefile.auto
|
||||
# unless caller = "exe" and "file" action already invoked
|
||||
|
||||
|
||||
if caller == "file" or "file" not in self.alist:
|
||||
make.write("%s/MAKE/MINE/Makefile.auto" % dir.src,1)
|
||||
print "Created src/MAKE/MINE/Makefile.auto"
|
||||
@ -510,13 +533,23 @@ class Actions:
|
||||
print txt
|
||||
error('Unsuccessful "make stubs"')
|
||||
print "Created src/STUBS/libmpi_stubs.a"
|
||||
if jmake: str = "cd %s; make -j %d auto" % (dir.src,jmake.n)
|
||||
else: str = "cd %s; make auto" % dir.src
|
||||
|
||||
# special hack for shannon GPU cluster
|
||||
# must use "srun make" if on it and building w/ GPU package, else just make
|
||||
# this is b/c Cuda libs are not all available on host
|
||||
|
||||
make = "make"
|
||||
if "shannon" in os.environ.get("HOST") and packages.final["gpu"]:
|
||||
make = "srun make"
|
||||
|
||||
if jmake: str = "cd %s; %s -j %d auto" % (dir.src,make,jmake.n)
|
||||
else: str = "cd %s; %s auto" % (dir.src,make)
|
||||
|
||||
# if verbose, print output as build proceeds, else only print if fails
|
||||
|
||||
if verbose: subprocess.call(str,shell=True)
|
||||
else:
|
||||
print str
|
||||
try: subprocess.check_output(str,stderr=subprocess.STDOUT,shell=True)
|
||||
except Exception as e: print e.output
|
||||
|
||||
@ -574,8 +607,8 @@ Syntax: Make.py switch args ...
|
||||
list one or more actions, in any order
|
||||
machine is a Makefile.machine suffix
|
||||
one-letter switches:
|
||||
-d (dir), -j (jmake), -m (makefile), -o (output),
|
||||
-p (packages), -r (redo), -s (settings), -v (verbose)
|
||||
-d (dir), -j (jmake), -m (makefile), -o (output), -p (packages),
|
||||
-r (redo), -s (settings), -v (verbose), -z (makefile output)
|
||||
switches for libs:
|
||||
-atc, -awpmd, -colvars, -cuda, -gpu, -h5md,
|
||||
-meam, -poems, -python, -qmmm, -voronoi
|
||||
@ -898,9 +931,13 @@ class Settings:
|
||||
def help(self):
|
||||
return """
|
||||
-s set1 set2 ...
|
||||
possible settings = gzip smallbig bigbig smallsmall
|
||||
add each setting as LAMMPS setting to created Makefile.auto
|
||||
if -s not specified, no settings are changed in Makefile.auto
|
||||
possible settings = gzip #gzip ffmpeg #ffmpeg smallbig bigbig smallsmall
|
||||
alter LAMMPS ifdef settings in Makefile.auto
|
||||
only happens if new Makefile.auto is created by use of "file" action
|
||||
gzip and #gzip turn on/off LAMMPS_GZIP setting
|
||||
ffmpeg and #ffmpeg turn on/off LAMMPS_FFMPEG setting
|
||||
smallbig, bigbig, smallsmall turn on LAMMPS_SMALLBIG, etc
|
||||
and turn off other two
|
||||
"""
|
||||
|
||||
def check(self):
|
||||
@ -924,6 +961,23 @@ class Verbose:
|
||||
def check(self):
|
||||
if len(self.inlist): error("-v args are invalid")
|
||||
|
||||
# zoutput switch for making copy of final Makefile.auto
|
||||
|
||||
class Zoutput:
|
||||
def __init__(self,list):
|
||||
self.inlist = copy.copy(list)
|
||||
|
||||
def help(self):
|
||||
return """
|
||||
-z machine
|
||||
copy created/used src/MAKE/MINE/Makefile.auto to Makefile.machine in same dir
|
||||
this can be used to preserve the machine makefile
|
||||
"""
|
||||
|
||||
def check(self):
|
||||
if len(self.inlist) != 1: error("-z args are invalid")
|
||||
self.machine = self.inlist[0]
|
||||
|
||||
# ----------------------------------------------------------------
|
||||
# lib classes, one per LAMMPS auxiliary lib
|
||||
# ----------------------------------------------------------------
|
||||
@ -1087,15 +1141,15 @@ class CUDA:
|
||||
def __init__(self,list):
|
||||
self.inlist = copy.copy(list)
|
||||
self.mode = "double"
|
||||
self.arch = "31"
|
||||
self.arch = "35"
|
||||
|
||||
def help(self):
|
||||
return """
|
||||
-cuda mode=double arch=31
|
||||
-cuda mode=double arch=35
|
||||
all args are optional and can be in any order
|
||||
mode = double or mixed or single (def = double)
|
||||
arch = M (def = 31)
|
||||
M = 31 for Kepler
|
||||
arch = M (def = 35)
|
||||
M = 31,35,37,etc for Kepler
|
||||
M = 20 for CC2.0 (GF100/110, e.g. C2050,GTX580,GTX470)
|
||||
M = 21 for CC2.1 (GF104/114, e.g. GTX560, GTX460, GTX450)
|
||||
M = 13 for CC1.3 (GF200, e.g. C1060, GTX285)
|
||||
@ -1144,17 +1198,18 @@ class GPU:
|
||||
def __init__(self,list):
|
||||
self.inlist = copy.copy(list)
|
||||
self.make = "linux.double"
|
||||
self.lammpsflag = self.modeflag = self.archflag = 0
|
||||
self.lammpsflag = self.modeflag = self.archflag = self.homeflag = 0
|
||||
|
||||
def help(self):
|
||||
return """
|
||||
-gpu make=suffix lammps=suffix2 mode=double arch=N
|
||||
-gpu make=suffix lammps=suffix2 mode=double arch=N home=path
|
||||
all args are optional and can be in any order
|
||||
make = use Makefile.suffix (def = linux.double)
|
||||
lammps = use Makefile.lammps.suffix2 (def = EXTRAMAKE in makefile)
|
||||
mode = double or mixed or single (def = CUDA_PREC in makefile)
|
||||
arch = 31 (Kepler) or 21 (Fermi) (def = CUDA_ARCH in makefile)
|
||||
dir = home dir for CUDA include and library files (def = none)
|
||||
arch = 3x (x = digit for Kepler) or 2x (x = digit for Fermi)
|
||||
(def = CUDA_ARCH in makefile)
|
||||
home = path to Cuda, e.g. /usr/local/cuda (def = CUDA_HOME in makefile)
|
||||
"""
|
||||
|
||||
def check(self):
|
||||
@ -1173,9 +1228,9 @@ class GPU:
|
||||
elif words[0] == "arch":
|
||||
self.arch = words[1]
|
||||
self.archflag = 1
|
||||
elif words[0] == "dir":
|
||||
self.dir = words[1]
|
||||
self.dirflag = 1
|
||||
elif words[0] == "home":
|
||||
self.home = words[1]
|
||||
self.homeflag = 1
|
||||
else: error("-gpu args are invalid")
|
||||
if self.modeflag and (self.mode != "double" and
|
||||
self.mode != "mixed" and
|
||||
@ -1196,18 +1251,22 @@ class GPU:
|
||||
make.setvar("CUDA_PRECISION","-D_SINGLE_SINGLE")
|
||||
if self.archflag:
|
||||
make.setvar("CUDA_ARCH","-arch=sm_%s" % self.arch)
|
||||
if self.homeflag:
|
||||
make.setvar("CUDA_HOME",self.home)
|
||||
if self.lammpsflag:
|
||||
make.setvar("EXTRAMAKE","Makefile.lammps.%s" % self.lammps)
|
||||
if self.dirflag:
|
||||
make.setvar("CUDA_HOME","%s" % self.dir)
|
||||
lmpmake = MakeReader("%s/%s" % (libdir, make.getvar("EXTRAMAKE")[0]))
|
||||
lmpmake.setvar("gpu_SYSPATH","-L%s/lib64" % self.dir)
|
||||
lmpmake.write("%s/%s" % (libdir, make.getvar("EXTRAMAKE")[0]))
|
||||
make.write("%s/Makefile.auto" % libdir)
|
||||
|
||||
commands.getoutput("cd %s; make -f Makefile.auto clean" % libdir)
|
||||
if jmake: str = "cd %s; make -j %d -f Makefile.auto" % (libdir,jmake.n)
|
||||
else: str = "cd %s; make -f Makefile.auto" % libdir
|
||||
# special hack for shannon GPU cluster
|
||||
# must use "srun make" if on it, else just make
|
||||
# this is b/c Cuda libs are not all available on host
|
||||
|
||||
make = "make"
|
||||
if "shannon" in os.environ.get("HOST"): make = "srun make"
|
||||
|
||||
commands.getoutput("cd %s; %s -f Makefile.auto clean" % (libdir,make))
|
||||
if jmake: str = "cd %s; %s -j %d -f Makefile.auto" % (libdir,make,jmake.n)
|
||||
else: str = "cd %s; %s -f Makefile.auto" % (libdir,make)
|
||||
|
||||
# if verbose, print output as build proceeds, else only print if fails
|
||||
|
||||
@ -1532,14 +1591,16 @@ class Kokkos:
|
||||
mode is not optional, arch is optional
|
||||
mode = omp or cuda or phi (def = KOKKOS_DEVICES setting in Makefile )
|
||||
build Kokkos package for omp or cuda or phi
|
||||
set KOKKOS_DEVICES to "OpenMP" (omp, phi) or "Cuda, OpenMP" (cuda)
|
||||
arch = 31 (Kepler) or 21 (Fermi) (def = -arch setting in Makefile)
|
||||
sets KOKKOS_DEVICES to "OpenMP" (omp, phi) or "Cuda, OpenMP" (cuda)
|
||||
arch = number like 35 (Kepler) or 21 (Fermi)
|
||||
sets KOKKOS_ARCH to appropriate value
|
||||
"""
|
||||
|
||||
def check(self):
|
||||
print self.inlist
|
||||
if self.inlist != None and len(self.inlist) == 0:
|
||||
error("-kokkos args are invalid")
|
||||
|
||||
|
||||
if self.inlist == None: return
|
||||
if len(self.inlist) < 1: error("-kokkos args are invalid")
|
||||
self.mode = self.inlist[0]
|
||||
@ -1554,7 +1615,7 @@ class Kokkos:
|
||||
else: error("-kokkos args are invalid")
|
||||
|
||||
# ----------------------------------------------------------------
|
||||
# makefile classes for CC, MPI, JPG, PNG, FFT settings
|
||||
# makefile classes for CC, FLAGS, MPI, JPG, PNG, FFT settings
|
||||
# ----------------------------------------------------------------
|
||||
|
||||
# Cc class
|
||||
@ -1568,7 +1629,8 @@ class Cc:
|
||||
def help(self):
|
||||
return """
|
||||
-cc compiler wrap=wcompiler
|
||||
change CC setting in makefile
|
||||
alter CC setting in Makefile.auto
|
||||
only happens if new Makefile.auto is created by use of "file" action
|
||||
compiler is required, all other args are optional
|
||||
compiler = any string with g++ or icc or icpc
|
||||
or mpi (or mpicxx, mpiCC, mpiicpc, etc)
|
||||
@ -1602,6 +1664,41 @@ class Cc:
|
||||
self.wrap = words[1]
|
||||
else: error("-cc args are invalid")
|
||||
|
||||
# Flags class
|
||||
|
||||
class Flags:
|
||||
def __init__(self,list):
|
||||
self.inlist = copy.copy(list)
|
||||
self.CC = []
|
||||
self.LINK = []
|
||||
|
||||
def help(self):
|
||||
return """
|
||||
-flags flag f1 f2 ... flag f1 f2 ...
|
||||
alter CCFLAGS or LINKFLAGS settings in Makefile.auto
|
||||
only happens if new Makefile.auto is created by use of "file" action
|
||||
flag = CC or LINK
|
||||
one or both can be specified
|
||||
f1,f2,etc = flag to add or replace
|
||||
"-" char will be prepended to each
|
||||
for example: g, O3, xHost, "fp-model fast=2"
|
||||
will become: -g, -O3, -xHost, -fp-model fast=2
|
||||
for -O,-O2,-O3,etc: existing -O* will first be removed
|
||||
"""
|
||||
|
||||
def check(self):
|
||||
if len(self.inlist) < 1: error("-flags args are invalid")
|
||||
self.CC = [] # necessary?
|
||||
self.LINK = []
|
||||
mode = ""
|
||||
for one in self.inlist:
|
||||
if one == "CC": mode = "CC"
|
||||
elif one == "LINK": mode = "LINK"
|
||||
else:
|
||||
if not mode: error("-flags args are invalid")
|
||||
if mode == "CC": self.CC.append(one)
|
||||
elif mode == "LINK": self.LINK.append(one)
|
||||
|
||||
# Mpi class
|
||||
|
||||
class Mpi:
|
||||
@ -1612,7 +1709,8 @@ class Mpi:
|
||||
def help(self):
|
||||
return """
|
||||
-mpi style dir=path
|
||||
change MPI settings in makefile
|
||||
alter MPI settings in Makefile.auto
|
||||
only happens if new Makefile.auto is created by use of "file" action
|
||||
style is required, all other args are optional
|
||||
style = mpi or mpich or ompi or serial
|
||||
mpi = no MPI settings (assume compiler is MPI wrapper)
|
||||
@ -1645,9 +1743,10 @@ class Fft:
|
||||
def help(self):
|
||||
return """
|
||||
-fft mode lib=libname dir=homedir idir=incdir ldir=libdir
|
||||
change FFT settings in makefile
|
||||
alter FFT settings in Makefile.auto
|
||||
only happens if new Makefile.auto is created by use of "file" action
|
||||
mode is required, all other args are optional
|
||||
removes all current FFT variable settings
|
||||
first removes all current FFT variable settings
|
||||
mode = none or fftw or fftw3 or ...
|
||||
adds -DFFT_MODE setting
|
||||
lib = name of FFT library to link with (def is libname = mode)
|
||||
@ -1685,6 +1784,8 @@ class Jpg:
|
||||
def help(self):
|
||||
return """
|
||||
-jpg flag dir=homedir idir=incdir ldir=libdir
|
||||
alter JPG settings in Makefile.auto
|
||||
only happens if new Makefile.auto is created by use of "file" action
|
||||
change JPG settings in makefile
|
||||
all args are optional, flag must come first if specified
|
||||
flag = yes or no (def = yes)
|
||||
@ -1722,7 +1823,8 @@ class Png:
|
||||
def help(self):
|
||||
return """
|
||||
-png flag dir=homedir idir=incdir ldir=libdir
|
||||
change PNG settings in makefile
|
||||
alter PNG settings in Makefile.auto
|
||||
only happens if new Makefile.auto is created by use of "file" action
|
||||
all args are optional, flag must come first if specified
|
||||
flag = yes or no (def = yes)
|
||||
include or exclude PNG support
|
||||
@ -2101,13 +2203,22 @@ while 1:
|
||||
|
||||
packages.uninstall()
|
||||
|
||||
# create output file if requested and exe action performed
|
||||
# create copy of executable if requested, and exe action performed
|
||||
|
||||
if output and actions and "exe" in actions.alist:
|
||||
txt = "cp %s/lmp_auto %s/lmp_%s" % (dir.src,dir.cwd,output.machine)
|
||||
commands.getoutput(txt)
|
||||
print "Created lmp_%s in %s" % (output.machine,dir.cwd)
|
||||
|
||||
# create copy of Makefile.auto if requested, and file or exe action performed
|
||||
|
||||
if zoutput and actions and \
|
||||
("file" in actions.alist or "exe" in actions.alist):
|
||||
txt = "cp %s/MAKE/MINE/Makefile.auto %s/MAKE/MINE/Makefile.%s" % \
|
||||
(dir.src,dir.src,zoutput.machine)
|
||||
commands.getoutput(txt)
|
||||
print "Created Makefile.%s in %s/MAKE/MINE" % (zoutput.machine,dir.src)
|
||||
|
||||
# write current Make.py command to src/Make.py.last
|
||||
|
||||
fp = open("%s/Make.py.last" % dir.src,'w')
|
||||
|
||||
@ -213,8 +213,8 @@ install-python:
|
||||
tar:
|
||||
@cd STUBS; $(MAKE) clean
|
||||
@cd ..; tar cvzf src/$(ROOT)_src.tar.gz \
|
||||
src/Make* src/Package.sh src/Depend.sh \
|
||||
src/MAKE src/*.cpp src/*.h src/STUBS \
|
||||
src/Make* src/Package.sh src/Depend.sh src/Install.sh \
|
||||
src/MAKE src/DEPEND src/*.cpp src/*.h src/STUBS \
|
||||
$(patsubst %,src/%,$(PACKAGEUC)) $(patsubst %,src/%,$(PACKUSERUC)) \
|
||||
--exclude=*/.svn
|
||||
@cd STUBS; $(MAKE)
|
||||
|
||||
@ -1,67 +1,88 @@
|
||||
If you run in another directory, please edit the read_data line to point to
|
||||
the data.rhodo file. This is included in the LAMMPS distribution in the
|
||||
'bench' directory.
|
||||
#############################################################################
|
||||
# Benchmarks
|
||||
#
|
||||
# in.intel.lj - Atomic fluid (LJ Benchmark)
|
||||
# in.intel.rhodo - Protein (Rhodopsin Benchmark)
|
||||
# in.intel.lc - Liquid Crystal w/ Gay-Berne potential
|
||||
# in.intel.sw - Silicon benchmark with Stillinger-Weber
|
||||
# in.intel.tersoff - Silicon benchmark with Tersoff
|
||||
# in.intel.water - Coarse-grain water benchmark using Stillinger-Weber
|
||||
#
|
||||
#############################################################################
|
||||
|
||||
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|
||||
Expected times are the expected LOOP times based on runs using dual-socket
|
||||
Intel Xeon processor E5-2697 V2 with Intel Xeon Phi coprocessor 7120P.
|
||||
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|
||||
#############################################################################
|
||||
# Expected Timesteps/second on E5-2697v3 with turbo on and HT enabled
|
||||
#
|
||||
# in.intel.lj - 131.943
|
||||
# in.intel.rhodo - 8.661
|
||||
# in.intel.lc - 14.015
|
||||
# in.intel.sw - 103.53
|
||||
# in.intel.tersoff - 55.525
|
||||
# in.intel.water - 44.079
|
||||
#
|
||||
#############################################################################
|
||||
|
||||
#############################################################################
|
||||
# For Haswell and Broadwell architectures, depending on the compiler version,
|
||||
# it may give better performance to compile for an AVX target (with -xAVX
|
||||
# compiler option) instead of -xHost or -xCORE-AVX2 for some of the
|
||||
# workloads due to inefficient code generation for gathers. Aside from
|
||||
# Tersoff, this will not significantly impact performance because FMA
|
||||
# sensitive routines will still use AVX2 (MKL and SVML detect the processor
|
||||
# at runtime)
|
||||
#############################################################################
|
||||
|
||||
#############################################################################
|
||||
# The default benchmark timesteps will run between 30s and 1 minute with
|
||||
# the Intel package. You can specify a multiplier for all of the benchmarks
|
||||
# to increase or decrease the runtime. Example commandline arguments:
|
||||
#
|
||||
# -v m 2 # Run for twice as long
|
||||
# -v m 0.5 # Run for half as long
|
||||
#############################################################################
|
||||
|
||||
# Example for running benchmarks:
|
||||
|
||||
# Number of physical cores per node not including hyperthreads
|
||||
export LMP_CORES=28
|
||||
|
||||
# If hyperthreading is enabled, number of hyperthreads to use per core
|
||||
# (2 for Xeon; 2 or 4 for Xeon Phi)
|
||||
export OMP_NUM_THREADS=2
|
||||
|
||||
# Name of the LAMMPS binary
|
||||
export LMP_BIN=../../lmp_intel_cpu
|
||||
|
||||
# LAMMPS root directory
|
||||
export LMP_ROOT=../../../
|
||||
|
||||
source /opt/intel/parallel_studio_xe_2016.2.062/psxevars.sh
|
||||
export I_MPI_PIN_DOMAIN=core
|
||||
export I_MPI_FABRICS=shm # For single node
|
||||
|
||||
# Generate the restart file for use with liquid crystal benchmark
|
||||
mpirun -np $LMP_CORES $LMP_BIN -in in.lc_generate_restart -log none
|
||||
|
||||
# Benchmark to run
|
||||
export bench=in.intel.lj
|
||||
|
||||
|
||||
TO RUN WITHOUT A PACKAGE:
|
||||
-----------------------------------------------------------------------------
|
||||
mpirun -np 48 ../../../src/lmp_YOUR_MACHINE -in in.intel.rhodo -log none -v b 0 -v s off
|
||||
mpirun -np 48 ../../../src/lmp_YOUR_MACHINE -in in.intel.lc -log none -v b 0 -v s off
|
||||
#############################################################################
|
||||
# To run without a optimization package
|
||||
#############################################################################
|
||||
mpirun -np $LMP_CORES $LMP_BIN -in $bench -log none
|
||||
|
||||
#############################################################################
|
||||
# To run with USER-OMP package
|
||||
#############################################################################
|
||||
mpirun -np $LMP_CORES $LMP_BIN -in $bench -log none -pk omp 0
|
||||
|
||||
TO RUN WITH OMP PACKAGE
|
||||
-----------------------------------------------------------------------------
|
||||
env OMP_NUM_THREADS=2 mpirun -np 24 ../../../src/lmp_YOUR_MACHINE -in in.intel.rhodo -log none -v b 0 -v s omp
|
||||
+++++++++++++++++++++++
|
||||
+ EXPECTED TIME: 20.33s
|
||||
+++++++++++++++++++++++
|
||||
|
||||
env OMP_NUM_THREADS=1 mpirun -np 48 ../../../src/lmp_YOUR_MACHINE -in in.intel.lc -log none -v b 0 -v s omp
|
||||
+++++++++++++++++++++++
|
||||
+ EXPECTED TIME: 19.92s
|
||||
+++++++++++++++++++++++
|
||||
|
||||
|
||||
TO RUN WITH INTEL+OMP PACKAGE WITHOUT OFFLOAD:
|
||||
-----------------------------------------------------------------------------
|
||||
env OMP_NUM_THREADS=2 mpirun -np 24 ../../../src/lmp_YOUR_MACHINE -in in.intel.rhodo -log none -v b 0 -v s intel
|
||||
+++++++++++++++++++++++
|
||||
+ EXPECTED TIME: 16.94s
|
||||
+++++++++++++++++++++++
|
||||
|
||||
env OMP_NUM_THREADS=2 mpirun -np 24 ../../../src/lmp_YOUR_MACHINE -in in.intel.lc -log none -v b 0 -v s intel
|
||||
+++++++++++++++++++++++
|
||||
+ EXPECTED TIME: 5.80s
|
||||
+++++++++++++++++++++++
|
||||
|
||||
|
||||
TO RUN WITH INTEL+OMP PACKAGE WITH OFFLOAD TO XEON PHI (AUTO-BALANCED):
|
||||
-----------------------------------------------------------------------------
|
||||
env OMP_NUM_THREADS=1 mpirun -np 24 ../../../src/lmp_YOUR_MACHINE -in in.intel.rhodo -log none -v b -1 -v s intel
|
||||
+++++++++++++++++++++++
|
||||
+ EXPECTED TIME: 12.31s
|
||||
+++++++++++++++++++++++
|
||||
|
||||
env OMP_NUM_THREADS=1 mpirun -np 24 ../../../src/lmp_YOUR_MACHINE -in in.intel.lc -log none -v b -1 -v s intel
|
||||
+++++++++++++++++++++++
|
||||
+ EXPECTED TIME: 4.00s
|
||||
+++++++++++++++++++++++
|
||||
|
||||
|
||||
TO RUN WITH INTEL+OMP PACKAGE WITH OFFLOAD TO XEON PHI (FIXED BALANCE):
|
||||
-----------------------------------------------------------------------------
|
||||
env OMP_NUM_THREADS=1 mpirun -np 24 ../../../src/lmp_YOUR_MACHINE -in in.intel.rhodo -log none -v b 0.68 -v s intel
|
||||
+++++++++++++++++++++++
|
||||
+ EXPECTED TIME: 11.40s
|
||||
+++++++++++++++++++++++
|
||||
|
||||
env OMP_NUM_THREADS=1 mpirun -np 24 ../../../src/lmp_YOUR_MACHINE -in in.intel.lc -log none -v b 0.53 -v s intel
|
||||
+++++++++++++++++++++++
|
||||
+ EXPECTED TIME: 3.93s
|
||||
+++++++++++++++++++++++
|
||||
#############################################################################
|
||||
# To run with USER-INTEL package and no coprocessor
|
||||
#############################################################################
|
||||
mpirun -np $LMP_CORES $LMP_BIN -in $bench -log none -pk intel 0
|
||||
|
||||
#############################################################################
|
||||
# To run with USER-INTEL and automatic load balancing to 1 coprocessor
|
||||
#############################################################################
|
||||
mpirun -np $LMP_CORES $LMP_BIN -in $bench -log none -pk intel 1
|
||||
|
||||
@ -2,60 +2,44 @@
|
||||
# biaxial ellipsoid mesogens in isotropic phase
|
||||
# shape: 2 1.5 1
|
||||
# cutoff 4.0 with skin 0.8
|
||||
# NPT, T=2.4, P=8.0
|
||||
|
||||
package intel 1 mode mixed balance $b
|
||||
package omp 0
|
||||
suffix $s
|
||||
# processors * * * grid numa
|
||||
variable w index 10 # Warmup Timesteps
|
||||
variable t index 840 # Main Run Timesteps
|
||||
variable m index 1 # Main Run Timestep Multiplier
|
||||
variable n index 0 # Use NUMA Mapping for Multi-Node
|
||||
variable p index 0 # Use Power Measurement
|
||||
|
||||
variable x index 4
|
||||
variable y index 2
|
||||
variable z index 2
|
||||
|
||||
variable i equal $x*32
|
||||
variable j equal $y*32
|
||||
variable k equal $z*32
|
||||
variable rr equal floor($t*$m)
|
||||
|
||||
units lj
|
||||
atom_style ellipsoid
|
||||
if "$n > 0" then "processors * * * grid numa"
|
||||
|
||||
# creation
|
||||
lattice sc 0.22
|
||||
region box block 0 $i 0 $j 0 $k
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
units lj
|
||||
atom_style ellipsoid
|
||||
pair_style gayberne 1.0 3.0 1.0 4.0
|
||||
read_restart restart.lc
|
||||
replicate $x $y $z
|
||||
|
||||
# read_data data.gb
|
||||
compute rot all temp/asphere
|
||||
group spheroid type 1
|
||||
variable dof equal count(spheroid)+3
|
||||
compute_modify rot extra ${dof}
|
||||
|
||||
set type 1 mass 1.5
|
||||
set type 1 shape 1 1.5 2
|
||||
set group all quat/random 982381
|
||||
pair_style gayberne 1.0 3.0 1.0 4.0
|
||||
pair_coeff 1 1 1.0 1.0 1.0 0.5 0.2 1.0 0.5 0.2
|
||||
|
||||
compute rot all temp/asphere
|
||||
group spheroid type 1
|
||||
variable dof equal count(spheroid)+3
|
||||
compute_modify rot extra ${dof}
|
||||
neighbor 0.8 bin
|
||||
|
||||
velocity all create 2.4 41787 loop geom
|
||||
timestep 0.002
|
||||
|
||||
pair_style gayberne 1.0 3.0 1.0 4.0
|
||||
pair_coeff 1 1 1.0 1.0 1.0 0.5 0.2 1.0 0.5 0.2
|
||||
thermo 100
|
||||
|
||||
neighbor 0.8 bin
|
||||
fix 1 all nve/asphere
|
||||
|
||||
timestep 0.002
|
||||
thermo 300
|
||||
|
||||
# equilibration run
|
||||
fix 1 all npt/asphere temp 2.4 2.4 0.1 iso 5.0 8.0 0.1
|
||||
compute_modify 1_temp extra ${dof}
|
||||
run 210
|
||||
thermo 100
|
||||
|
||||
reset_timestep 0
|
||||
unfix 1
|
||||
fix 1 all nve/asphere
|
||||
run 10
|
||||
run 50
|
||||
if "$p > 0" then "run_style verlet/power"
|
||||
|
||||
if "$w > 0" then "run $w"
|
||||
run ${rr}
|
||||
|
||||
43
src/USER-INTEL/TEST/in.intel.lj
Normal file
43
src/USER-INTEL/TEST/in.intel.lj
Normal file
@ -0,0 +1,43 @@
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
variable w index 10 # Warmup Timesteps
|
||||
variable t index 7900 # Main Run Timesteps
|
||||
variable m index 1 # Main Run Timestep Multiplier
|
||||
variable n index 0 # Use NUMA Mapping for Multi-Node
|
||||
variable p index 0 # Use Power Measurement
|
||||
|
||||
variable x index 4
|
||||
variable y index 2
|
||||
variable z index 2
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable yy equal 20*$y
|
||||
variable zz equal 20*$z
|
||||
variable rr equal floor($t*$m)
|
||||
|
||||
if "$n > 0" then "processors * * * grid numa"
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 20 check no
|
||||
|
||||
fix 1 all nve
|
||||
thermo 1000
|
||||
|
||||
if "$p > 0" then "run_style verlet/power"
|
||||
|
||||
if "$w > 0" then "run $w"
|
||||
run ${rr}
|
||||
@ -1,27 +1,39 @@
|
||||
# Rhodopsin model
|
||||
|
||||
package intel 1 mode mixed balance $b
|
||||
package omp 0
|
||||
suffix $s
|
||||
variable w index 10 # Warmup Timesteps
|
||||
variable t index 520 # Main Run Timesteps
|
||||
variable m index 1 # Main Run Timestep Multiplier
|
||||
variable n index 0 # Use NUMA Mapping for Multi-Node
|
||||
variable b index 3 # Neighbor binsize
|
||||
variable p index 0 # Use Power Measurement
|
||||
variable c index 0 # 1 to use collectives for PPPM
|
||||
variable d index 0 # 1 to use 'diff ad' for PPPM
|
||||
|
||||
variable x index 4
|
||||
variable y index 2
|
||||
variable z index 2
|
||||
|
||||
variable rr equal floor($t*$m)
|
||||
variable root getenv LMP_ROOT
|
||||
|
||||
if "$n > 0" then "processors * * * grid numa"
|
||||
|
||||
units real
|
||||
neigh_modify delay 5 every 1
|
||||
neigh_modify delay 5 every 1 binsize $b
|
||||
|
||||
atom_style full
|
||||
atom_modify map hash
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
pair_style lj/charmm/coul/long 8.0 10.0
|
||||
pair_modify mix arithmetic
|
||||
kspace_style pppm 1e-4
|
||||
kspace_style pppm 1e-4
|
||||
|
||||
read_data ../../../bench/data.rhodo
|
||||
if "$c > 0" then "kspace_modify collective yes"
|
||||
if "$d > 0" then "kspace_modify diff ad"
|
||||
|
||||
read_data ${root}/bench/data.rhodo
|
||||
|
||||
replicate $x $y $z
|
||||
|
||||
@ -31,9 +43,11 @@ fix 2 all npt temp 300.0 300.0 100.0 &
|
||||
|
||||
special_bonds charmm
|
||||
|
||||
thermo 50
|
||||
thermo 100
|
||||
thermo_style multi
|
||||
timestep 2.0
|
||||
|
||||
run 10
|
||||
run 100
|
||||
if "$p > 0" then "run_style verlet/power"
|
||||
|
||||
if "$w > 0" then "run $w"
|
||||
run ${rr}
|
||||
|
||||
@ -1,7 +1,10 @@
|
||||
# bulk Si via Stillinger-Weber
|
||||
package intel 1 mode mixed balance $b
|
||||
package omp 0
|
||||
suffix $s
|
||||
|
||||
variable w index 10 # Warmup Timesteps
|
||||
variable t index 6200 # Main Run Timesteps
|
||||
variable m index 1 # Main Run Timestep Multiplier
|
||||
variable n index 0 # Use NUMA Mapping for Multi-Node
|
||||
variable p index 0 # Use Power Measurement
|
||||
|
||||
variable x index 2
|
||||
variable y index 2
|
||||
@ -10,6 +13,10 @@ variable z index 4
|
||||
variable xx equal 20*$x
|
||||
variable yy equal 20*$y
|
||||
variable zz equal 10*$z
|
||||
variable rr equal floor($t*$m)
|
||||
variable root getenv LMP_ROOT
|
||||
|
||||
if "$n > 0" then "processors * * * grid numa"
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
@ -20,7 +27,7 @@ create_box 1 box
|
||||
create_atoms 1 box
|
||||
|
||||
pair_style sw
|
||||
pair_coeff * * ../../../bench/POTENTIALS/Si.sw Si
|
||||
pair_coeff * * ${root}/bench/POTENTIALS/Si.sw Si
|
||||
mass 1 28.06
|
||||
|
||||
velocity all create 1000.0 376847 loop geom
|
||||
@ -29,8 +36,10 @@ neighbor 1.0 bin
|
||||
neigh_modify delay 5 every 1
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 1000
|
||||
timestep 0.001
|
||||
|
||||
run 10
|
||||
run 100
|
||||
if "$p > 0" then "run_style verlet/power"
|
||||
|
||||
if "$w > 0" then "run $w"
|
||||
run ${rr}
|
||||
|
||||
@ -1,7 +1,10 @@
|
||||
# bulk Si via Tersoff
|
||||
package intel 1 mode mixed balance $b
|
||||
package omp 0
|
||||
suffix $s
|
||||
|
||||
variable w index 10 # Warmup Timesteps
|
||||
variable t index 2420 # Main Run Timesteps
|
||||
variable m index 1 # Main Run Timestep Multiplier
|
||||
variable n index 0 # Use NUMA Mapping for Multi-Node
|
||||
variable p index 0 # Use Power Measurement
|
||||
|
||||
variable x index 2
|
||||
variable y index 2
|
||||
@ -10,6 +13,10 @@ variable z index 4
|
||||
variable xx equal 20*$x
|
||||
variable yy equal 20*$y
|
||||
variable zz equal 10*$z
|
||||
variable rr equal floor($t*$m)
|
||||
variable root getenv LMP_ROOT
|
||||
|
||||
if "$n > 0" then "processors * * * grid numa"
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
@ -20,7 +27,7 @@ create_box 1 box
|
||||
create_atoms 1 box
|
||||
|
||||
pair_style tersoff
|
||||
pair_coeff * * ../../../bench/POTENTIALS/Si.tersoff Si
|
||||
pair_coeff * * ${root}/bench/POTENTIALS/Si.tersoff Si
|
||||
mass 1 28.06
|
||||
|
||||
velocity all create 1000.0 376847 loop geom
|
||||
@ -29,8 +36,10 @@ neighbor 1.0 bin
|
||||
neigh_modify delay 5 every 1
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 1000
|
||||
timestep 0.001
|
||||
|
||||
run 10
|
||||
run 100
|
||||
if "$p > 0" then "run_style verlet/power"
|
||||
|
||||
if "$w > 0" then "run $w"
|
||||
run ${rr}
|
||||
|
||||
@ -1,48 +1,45 @@
|
||||
package intel 1 mode mixed balance $b
|
||||
package omp 0
|
||||
suffix $s
|
||||
# Coarse-grain water simulation using Stillinger-Weber
|
||||
|
||||
# processors * * * grid numa
|
||||
variable w index 10 # Warmup Timesteps
|
||||
variable t index 2600 # Main Run Timesteps
|
||||
variable m index 1 # Main Run Timestep Multiplier
|
||||
variable n index 0 # Use NUMA Mapping for Multi-Node
|
||||
variable p index 0 # Use Power Measurement
|
||||
|
||||
variable x index 4
|
||||
variable y index 2
|
||||
variable z index 2
|
||||
variable rr equal floor($t*$m)
|
||||
|
||||
units real
|
||||
atom_style atomic
|
||||
if "$n > 0" then "processors * * * grid numa"
|
||||
|
||||
boundary p p p
|
||||
lattice fcc 4.8
|
||||
#region waterbox block -10 10 -10 10 -10 10
|
||||
#create_box 1 waterbox
|
||||
#create_atoms 1 region waterbox
|
||||
units real
|
||||
atom_style atomic
|
||||
|
||||
read_data mW_32k_cube.data
|
||||
reset_timestep 0
|
||||
replicate $x $y $z
|
||||
read_data mW_32k_cube.data
|
||||
reset_timestep 0
|
||||
replicate $x $y $z
|
||||
|
||||
pair_style sw
|
||||
pair_coeff * * mW.sw mW
|
||||
pair_style sw
|
||||
pair_coeff * * mW.sw mW
|
||||
|
||||
mass 1 18.015 #g/mol
|
||||
group mW type 1
|
||||
mass 1 18.015 #g/mol
|
||||
group mW type 1
|
||||
|
||||
neighbor 1 bin #Angstroms
|
||||
neigh_modify every 2 delay 2 check yes
|
||||
neighbor 2 bin #Angstroms
|
||||
neigh_modify every 1 delay 4
|
||||
|
||||
fix 1 all nvt temp 300.0 300.0 1000.0
|
||||
fix 1 all nvt temp 300.0 300.0 1000.0
|
||||
|
||||
#velocity all create 300.0 2323 dist gaussian #Kelvin
|
||||
velocity all zero linear
|
||||
velocity all zero linear
|
||||
|
||||
timestep 10 #femtoseconds
|
||||
timestep 10 #femtoseconds
|
||||
|
||||
#variable Density equal "mass(mW)/vol/0.602214179"
|
||||
#thermo_style custom step temp press pe spcpu
|
||||
thermo_modify norm yes
|
||||
thermo_modify norm yes
|
||||
|
||||
#restart 100 mW_32k_cube.res mW_32k_cube.res
|
||||
thermo 100
|
||||
thermo 1000
|
||||
|
||||
run 10 #actual runs
|
||||
run 100
|
||||
if "$p > 0" then "run_style verlet/power"
|
||||
|
||||
if "$w > 0" then "run $w"
|
||||
run ${rr}
|
||||
|
||||
57
src/USER-INTEL/TEST/in.lc_generate_restart
Normal file
57
src/USER-INTEL/TEST/in.lc_generate_restart
Normal file
@ -0,0 +1,57 @@
|
||||
# Gay-Berne benchmark
|
||||
# biaxial ellipsoid mesogens in isotropic phase
|
||||
# shape: 2 1.5 1
|
||||
# cutoff 4.0 with skin 0.8
|
||||
# NPT, T=2.4, P=8.0
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable i equal $x*32
|
||||
variable j equal $y*32
|
||||
variable k equal $z*32
|
||||
|
||||
units lj
|
||||
atom_style ellipsoid
|
||||
|
||||
lattice sc 0.22
|
||||
region box block 0 $i 0 $j 0 $k
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
|
||||
set type 1 mass 1.5
|
||||
set type 1 shape 1 1.5 2
|
||||
set group all quat/random 982381
|
||||
|
||||
compute rot all temp/asphere
|
||||
group spheroid type 1
|
||||
variable dof equal count(spheroid)+3
|
||||
compute_modify rot extra ${dof}
|
||||
|
||||
velocity all create 2.4 41787 loop geom
|
||||
|
||||
pair_style gayberne 1.0 3.0 1.0 4.0
|
||||
pair_coeff 1 1 1.0 1.0 1.0 0.5 0.2 1.0 0.5 0.2
|
||||
|
||||
neighbor 0.8 bin
|
||||
|
||||
timestep 0.002
|
||||
thermo 300
|
||||
|
||||
# equilibration run
|
||||
fix 1 all npt/asphere temp 2.4 2.4 0.1 iso 5.0 8.0 0.1
|
||||
compute_modify 1_temp extra ${dof}
|
||||
run 2000
|
||||
|
||||
unfix 1
|
||||
fix 1 all npt/asphere temp 2.4 2.4 0.1 iso 8.0 8.0 0.1
|
||||
compute_modify 1_temp extra ${dof}
|
||||
run 2000
|
||||
|
||||
unfix 1
|
||||
fix 1 all nve/asphere
|
||||
run 2000
|
||||
reset_timestep 0
|
||||
run 0
|
||||
write_restart restart.lc
|
||||
@ -342,7 +342,7 @@ void Neighbor::hbnni(const int offload, NeighList *list, void *buffers_in,
|
||||
in(ilist:length(0) alloc_if(0) free_if(0)) \
|
||||
in(atombin:length(aend) alloc_if(0) free_if(0)) \
|
||||
in(stencil:length(nstencil) alloc_if(0) free_if(0)) \
|
||||
in(maxnbors,nthreads,maxspecial,nstencil,pad_width,offload) \
|
||||
in(maxnbors,nthreads,maxspecial,nstencil,pad_width,offload,nall) \
|
||||
in(separate_buffers, astart, aend, nlocal, molecular, ntypes) \
|
||||
in(xperiodic, yperiodic, zperiodic, xprd_half, yprd_half, zprd_half) \
|
||||
out(overflow:length(5) alloc_if(0) free_if(0)) \
|
||||
|
||||
@ -1 +1 @@
|
||||
#define LAMMPS_VERSION "28 Mar20 2016"
|
||||
#define LAMMPS_VERSION "7 Apr 2016"
|
||||
|
||||
Reference in New Issue
Block a user