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Merge remote-tracking branch 'lammps-ro/master' into lammps-icms

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Axel Kohlmeyer
2016-04-08 06:24:09 -04:00
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doc/Manual.html
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@ -134,7 +134,8 @@
<H1></H1><div class="section" id="lammps-documentation"> <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> <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>
<div class="section" id="version-info"> <div class="section" id="version-info">
<h2>Version info:<a class="headerlink" href="#version-info" title="Permalink to this headline"></a></h2> <h2>Version info:<a class="headerlink" href="#version-info" title="Permalink to this headline"></a></h2>

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doc/Manual.txt
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@ -1,7 +1,7 @@
<!-- HTML_ONLY --> <!-- HTML_ONLY -->
<HEAD> <HEAD>
<TITLE>LAMMPS-ICMS Users Manual</TITLE> <TITLE>LAMMPS-ICMS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="28 Mar20 2016 version"> <META NAME="docnumber" CONTENT="7 Apr 2016 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories"> <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."> <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD> </HEAD>
@ -21,7 +21,7 @@
<H1></H1> <H1></H1>
LAMMPS-ICMS Documentation :c,h3 LAMMPS-ICMS Documentation :c,h3
28 Mar20 2016 version :c,h4 7 Apr 2016 version :c,h4
Version info: :h4 Version info: :h4

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doc/Section_commands.html
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@ -463,8 +463,8 @@ in the command&#8217;s documentation.</p>
<table border="1" class="docutils"> <table border="1" class="docutils">
<colgroup> <colgroup>
<col width="17%" /> <col width="17%" />
<col width="15%" />
<col width="17%" /> <col width="17%" />
<col width="15%" />
<col width="17%" /> <col width="17%" />
<col width="17%" /> <col width="17%" />
<col width="17%" /> <col width="17%" />
@ -478,109 +478,109 @@ in the command&#8217;s documentation.</p>
<td><a class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a></td> <td><a class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a></td>
</tr> </tr>
<tr class="row-even"><td><a class="reference internal" href="bond_style.html"><em>bond_style</em></a></td> <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="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="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="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="clear.html"><em>clear</em></a></td>
<td><a class="reference internal" href="comm_modify.html"><em>comm_modify</em></a></td>
</tr> </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.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="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_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_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>
<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="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="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_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="dihedral_style.html"><em>dihedral_style</em></a></td>
<td><a class="reference internal" href="dimension.html"><em>dimension</em></a></td>
</tr> </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.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_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_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="dump_image.html"><em>dump movie</em></a></td>
<td><a class="reference internal" href="echo.html"><em>echo</em></a></td>
</tr> </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="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="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="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="info.html"><em>info</em></a></td>
<td><a class="reference internal" href="improper_coeff.html"><em>improper_coeff</em></a></td>
</tr> </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="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="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_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="kspace_style.html"><em>kspace_style</em></a></td>
<td><a class="reference internal" href="label.html"><em>label</em></a></td>
</tr> </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="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="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="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_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>
<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="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="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="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="newton.html"><em>newton</em></a></td>
<td><a class="reference internal" href="next.html"><em>next</em></a></td>
</tr> </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_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_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_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="pair_write.html"><em>pair_write</em></a></td>
<td><a class="reference internal" href="partition.html"><em>partition</em></a></td>
</tr> </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="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="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="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="quit.html"><em>quit</em></a></td>
<td><a class="reference internal" href="read_data.html"><em>read_data</em></a></td>
</tr> </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="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="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="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="rerun.html"><em>rerun</em></a></td>
<td><a class="reference internal" href="reset_timestep.html"><em>reset_timestep</em></a></td>
</tr> </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.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="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="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="shell.html"><em>shell</em></a></td>
<td><a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a></td>
</tr> </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="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="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.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_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>
<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="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="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="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="unfix.html"><em>unfix</em></a></td>
<td><a class="reference internal" href="units.html"><em>units</em></a></td>
</tr> </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="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_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_dump.html"><em>write_dump</em></a></td>
<td><a class="reference internal" href="write_restart.html"><em>write_restart</em></a></td> <td><a class="reference internal" href="write_restart.html"><em>write_restart</em></a></td>
<td>&nbsp;</td>
</tr> </tr>
</tbody> </tbody>
</table> </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> <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_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.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>
<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/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_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> <td><a class="reference internal" href="pair_tri_lj.html"><em>tri/lj</em></a></td>

5
doc/Section_commands.txt
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@ -375,6 +375,7 @@ in the command's documentation.
"balance"_balance.html, "balance"_balance.html,
"bond_coeff"_bond_coeff.html, "bond_coeff"_bond_coeff.html,
"bond_style"_bond_style.html, "bond_style"_bond_style.html,
"bond_write"_bond_write.html,
"boundary"_boundary.html, "boundary"_boundary.html,
"box"_box.html, "box"_box.html,
"change_box"_change_box.html, "change_box"_change_box.html,
@ -903,8 +904,8 @@ KOKKOS, o = USER-OMP, t = OPT.
"sw (cgkio)"_pair_sw.html, "sw (cgkio)"_pair_sw.html,
"table (gko)"_pair_table.html, "table (gko)"_pair_table.html,
"tersoff (cgkio)"_pair_tersoff.html, "tersoff (cgkio)"_pair_tersoff.html,
"tersoff/mod (ko)"_pair_tersoff_mod.html, "tersoff/mod (gko)"_pair_tersoff_mod.html,
"tersoff/zbl (ko)"_pair_tersoff_zbl.html, "tersoff/zbl (gko)"_pair_tersoff_zbl.html,
"tip4p/cut (o)"_pair_coul.html, "tip4p/cut (o)"_pair_coul.html,
"tip4p/long (o)"_pair_coul.html, "tip4p/long (o)"_pair_coul.html,
"tri/lj"_pair_tri_lj.html, "tri/lj"_pair_tri_lj.html,

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doc/_sources/Manual.txt
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@ -5,8 +5,8 @@
LAMMPS Documentation LAMMPS Documentation
==================== ====================
23 Mar 2016 version 28 Mar20 2016 version
------------------- ---------------------
Version info: Version info:
------------- -------------

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@ -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 default LAMMPS build. These dependencies are listed as Restrictions
in the command's documentation. 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:`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:`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_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:`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:`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:`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:`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:`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:`fix <fix>` | :doc:`fix_modify <fix_modify>` | :doc:`group <group>` | :doc:`if <if>` | :doc:`info <info>` | :doc:`improper_coeff <improper_coeff>` | | :doc:`echo <echo>` | :doc:`fix <fix>` | :doc:`fix_modify <fix_modify>` | :doc:`group <group>` | :doc:`if <if>` | :doc:`info <info>` |
+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+ +----------------------------------------+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
| :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:`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:`lattice <lattice>` | :doc:`log <log>` | :doc:`mass <mass>` | :doc:`minimize <minimize>` | :doc:`min_modify <min_modify>` | :doc:`min_style <min_style>` | | :doc:`label <label>` | :doc:`lattice <lattice>` | :doc:`log <log>` | :doc:`mass <mass>` | :doc:`minimize <minimize>` | :doc:`min_modify <min_modify>` |
+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+ +----------------------------------------+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
| :doc:`molecule <molecule>` | :doc:`neb <neb>` | :doc:`neigh_modify <neigh_modify>` | :doc:`neighbor <neighbor>` | :doc:`newton <newton>` | :doc:`next <next>` | | :doc:`min_style <min_style>` | :doc:`molecule <molecule>` | :doc:`neb <neb>` | :doc:`neigh_modify <neigh_modify>` | :doc:`neighbor <neighbor>` | :doc:`newton <newton>` |
+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+ +----------------------------------------+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
| :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:`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:`prd <prd>` | :doc:`print <print>` | :doc:`processors <processors>` | :doc:`python <python>` | :doc:`quit <quit>` | :doc:`read_data <read_data>` | | :doc:`partition <partition>` | :doc:`prd <prd>` | :doc:`print <print>` | :doc:`processors <processors>` | :doc:`python <python>` | :doc:`quit <quit>` |
+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+ +----------------------------------------+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
| :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:`read_data <read_data>` | :doc:`read_dump <read_dump>` | :doc:`read_restart <read_restart>` | :doc:`region <region>` | :doc:`replicate <replicate>` | :doc:`rerun <rerun>` |
+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+ +----------------------------------------+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
| :doc:`restart <restart>` | :doc:`run <run>` | :doc:`run_style <run_style>` | :doc:`set <set>` | :doc:`shell <shell>` | :doc:`special_bonds <special_bonds>` | | :doc:`reset_timestep <reset_timestep>` | :doc:`restart <restart>` | :doc:`run <run>` | :doc:`run_style <run_style>` | :doc:`set <set>` | :doc:`shell <shell>` |
+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+ +----------------------------------------+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
| :doc:`suffix <suffix>` | :doc:`tad <tad>` | :doc:`temper <temper>` | :doc:`thermo <thermo>` | :doc:`thermo_modify <thermo_modify>` | :doc:`thermo_style <thermo_style>` | | :doc:`special_bonds <special_bonds>` | :doc:`suffix <suffix>` | :doc:`tad <tad>` | :doc:`temper <temper>` | :doc:`thermo <thermo>` | :doc:`thermo_modify <thermo_modify>` |
+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+ +----------------------------------------+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
| :doc:`timer <timer>` | :doc:`timestep <timestep>` | :doc:`uncompute <uncompute>` | :doc:`undump <undump>` | :doc:`unfix <unfix>` | :doc:`units <units>` | | :doc:`thermo_style <thermo_style>` | :doc:`timer <timer>` | :doc:`timestep <timestep>` | :doc:`uncompute <uncompute>` | :doc:`undump <undump>` | :doc:`unfix <unfix>` |
+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+ +----------------------------------------+----------------------------------------+------------------------------------+----------------------------------------+----------------------------------------+----------------------------------------+
| :doc:`variable <variable>` | :doc:`velocity <velocity>` | :doc:`write_data <write_data>` | :doc:`write_dump <write_dump>` | :doc:`write_restart <write_restart>` | | | :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 These are additional commands in USER packages, which can be used if
:ref:`LAMMPS is built with the appropriate package <start_3>`. :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:`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>` | | :doc:`vashishta (o) <pair_vashishta>` | :doc:`yukawa (go) <pair_yukawa>` | :doc:`yukawa/colloid (go) <pair_yukawa_colloid>` | :doc:`zbl (go) <pair_zbl>` |
+-----------------------------------------------------------+-----------------------------------------------------+----------------------------------------------------+-------------------------------------------------------+ +-----------------------------------------------------------+-----------------------------------------------------+----------------------------------------------------+-------------------------------------------------------+

2
doc/_sources/bond_table.txt
View File

@ -110,7 +110,7 @@ values in the table.
The "EQ" parameter is also optional. If used, it is followed by a the 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 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. 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 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
View 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

8
doc/_sources/lattice.txt
View File

@ -275,7 +275,7 @@ of Aidan Thompson), with its 8 atom unit cell.
variable 1_6 equal 1.0/6.0 variable 1_6 equal 1.0/6.0
variable 5_6 equal 5.0/6.0 variable 5_6 equal 5.0/6.0
variable 1_12 equal 1.0/12.0 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:: .. parsed-literal::
@ -296,7 +296,11 @@ of Aidan Thompson), with its 8 atom unit cell.
region myreg block 0 1 0 1 0 1 region myreg block 0 1 0 1 0 1
create_box 2 myreg create_box 2 myreg
create_atoms 1 box create_atoms 1 box &
basis 5 2 &
basis 6 2 &
basis 7 2 &
basis 8 2
---------- ----------

2
doc/_sources/pair_colloid.txt
View File

@ -128,7 +128,7 @@ colloid-solvent cutoff in this case.
When using pair_style colloid for a mixture with 2 (or more) When using pair_style colloid for a mixture with 2 (or more)
widely different particles sizes (e.g. sigma=10 colloids in a 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 commands for efficiency: :doc:`neighbor multi <neighbor>` and
:doc:`comm_modify multi <comm_modify>`. :doc:`comm_modify multi <comm_modify>`.

2
doc/_sources/pair_dpd.txt
View File

@ -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 :doc:`pair style <pair_style>`, and in leiu of per-particle thermostats
like :doc:`fix langevin <fix_langevin>` or ensemble thermostats like like :doc:`fix langevin <fix_langevin>` or ensemble thermostats like
Nose Hoover as implemented by :doc:`fix nvt <fix_nh>`. To use 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. 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 For style *dpd*, the force on atom I due to atom J is given as a sum

2
doc/_sources/pair_table.txt
View File

@ -279,7 +279,7 @@ Restrictions
Related commands Related commands
"""""""""""""""" """"""""""""""""
:doc:`pair_coeff <pair_coeff>` :doc:`pair_coeff <pair_coeff>`, :doc:`pair_write <pair_write>`
**Default:** none **Default:** none

3
doc/_sources/pair_tersoff_mod.txt
View File

@ -3,6 +3,9 @@
pair_style tersoff/mod command pair_style tersoff/mod command
============================== ==============================
pair_style tersoff/mod/gpu command
==================================
pair_style tersoff/mod/kk command pair_style tersoff/mod/kk command
================================= =================================

3
doc/_sources/pair_tersoff_zbl.txt
View File

@ -3,6 +3,9 @@
pair_style tersoff/zbl command pair_style tersoff/zbl command
============================== ==============================
pair_style tersoff/zbl/gpu command
==================================
pair_style tersoff/zbl/kk command pair_style tersoff/zbl/kk command
================================= =================================

1
doc/_sources/pair_write.txt
View File

@ -78,6 +78,7 @@ pairwise portion of the potential, not the embedding portion.
Related commands Related commands
"""""""""""""""" """"""""""""""""
:doc:`pair_style table <pair_table>`,
:doc:`pair_style <pair_style>`, :doc:`pair_coeff <pair_coeff>` :doc:`pair_style <pair_style>`, :doc:`pair_coeff <pair_coeff>`
**Default:** none **Default:** none

6
doc/_sources/temper.txt
View File

@ -43,9 +43,9 @@ would see with one or more physical processors per replica. See :ref:`this sect
discussion. discussion.
Each replica's temperature is controlled at a different value by a fix Each replica's temperature is controlled at a different value by a fix
with *fix-ID* that controls temperature. Possible fix styles are with *fix-ID* that controls temperature. Most thermostat fix styles
:doc:`nvt <fix_nh>`, :doc:`temp/berendsen <fix_nh>`, (with and without included time integration) are supported. The command
:doc:`langevin <fix_langevin>` and :doc:`temp/rescale <fix_temp_rescale>`. will print an error message and abort, if the chosen fix is unsupported.
The desired temperature is specified by *temp*, which is typically a The desired temperature is specified by *temp*, which is typically a
variable previously set in the input script, so that each partition is variable previously set in the input script, so that each partition is
assigned a different temperature. See the :doc:`variable <variable>` assigned a different temperature. See the :doc:`variable <variable>`

2
doc/bond_table.html
View File

@ -217,7 +217,7 @@ are estimated (less accurately) by the first two and last two force
values in the table.</p> values in the table.</p>
<p>The &#8220;EQ&#8221; parameter is also optional. If used, it is followed by a the <p>The &#8220;EQ&#8221; 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 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. <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 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 the bond length r (in distance units), the 3rd value is the energy (in

248
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@ -0,0 +1,248 @@
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<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 &gt; 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>
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8
doc/genindex.html
View File

@ -287,12 +287,12 @@
<dt><a href="bond_harmonic_shift_cut.html#index-0">bond_style harmonic/shift/cut</a> <dt><a href="bond_harmonic_shift_cut.html#index-0">bond_style harmonic/shift/cut</a>
</dt> </dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="bond_hybrid.html#index-0">bond_style hybrid</a> <dt><a href="bond_hybrid.html#index-0">bond_style hybrid</a>
</dt> </dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="bond_morse.html#index-0">bond_style morse</a> <dt><a href="bond_morse.html#index-0">bond_style morse</a>
</dt> </dt>
@ -318,6 +318,10 @@
</dt> </dt>
<dt><a href="bond_write.html#index-0">bond_write</a>
</dt>
<dt><a href="boundary.html#index-0">boundary</a> <dt><a href="boundary.html#index-0">boundary</a>
</dt> </dt>

8
doc/lattice.html
View File

@ -359,7 +359,7 @@ variable 2_3 equal 2.0/3.0
variable 1_6 equal 1.0/6.0 variable 1_6 equal 1.0/6.0
variable 5_6 equal 5.0/6.0 variable 5_6 equal 5.0/6.0
variable 1_12 equal 1.0/12.0 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> </pre></div>
</div> </div>
<div class="highlight-python"><div class="highlight"><pre>lattice custom 1.0 &amp; <div class="highlight-python"><div class="highlight"><pre>lattice custom 1.0 &amp;
@ -378,7 +378,11 @@ variable 5_12 equal 5.0/12/0
</div> </div>
<div class="highlight-python"><div class="highlight"><pre>region myreg block 0 1 0 1 0 1 <div class="highlight-python"><div class="highlight"><pre>region myreg block 0 1 0 1 0 1
create_box 2 myreg create_box 2 myreg
create_atoms 1 box create_atoms 1 box &amp;
basis 5 2 &amp;
basis 6 2 &amp;
basis 7 2 &amp;
basis 8 2
</pre></div> </pre></div>
</div> </div>
</div> </div>

4
doc/pair_colloid.html
View File

@ -163,7 +163,7 @@ Lennard-Jones particle of size sigma.</p>
colloidal particles, and Rc is the cutoff. This equation results from colloidal particles, and Rc is the cutoff. This equation results from
describing each colloidal particle as an integrated collection of describing each colloidal particle as an integrated collection of
Lennard-Jones particles of size sigma and is derived in 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> <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" /> <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 <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="first admonition-title">Note</p>
<p class="last">When using pair_style colloid for a mixture with 2 (or more) <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 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 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> <a class="reference internal" href="comm_modify.html"><em>comm_modify multi</em></a>.</p>
</div> </div>

2
doc/pair_dpd.html
View File

@ -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 <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 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 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> 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 <p>For style <em>dpd</em>, the force on atom I due to atom J is given as a sum
of 3 terms</p> of 3 terms</p>

2
doc/pair_table.html
View File

@ -359,7 +359,7 @@ commands do need to be specified in the restart input script.</p>
</div> </div>
<div class="section" id="related-commands"> <div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2> <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> <p><strong>Default:</strong> none</p>
<hr class="docutils" /> <hr class="docutils" />
<p id="wolff"><strong>(Wolff)</strong> Wolff and Rudd, Comp Phys Comm, 120, 200-32 (1999).</p> <p id="wolff"><strong>(Wolff)</strong> Wolff and Rudd, Comp Phys Comm, 120, 200-32 (1999).</p>

3
doc/pair_tersoff_mod.html
View File

@ -127,6 +127,9 @@
<div class="section" id="pair-style-tersoff-mod-command"> <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> <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>
<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"> <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> <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> </div>

3
doc/pair_tersoff_zbl.html
View File

@ -127,6 +127,9 @@
<div class="section" id="pair-style-tersoff-zbl-command"> <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> <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>
<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"> <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> <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> </div>

3
doc/pair_write.html
View File

@ -189,7 +189,8 @@ pairwise portion of the potential, not the embedding portion.</p>
</div> </div>
<div class="section" id="related-commands"> <div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2> <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> <p><strong>Default:</strong> none</p>
</div> </div>
</div> </div>

2
doc/searchindex.js
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6
doc/temper.html
View File

@ -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 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> discussion.</p>
<p>Each replica&#8217;s temperature is controlled at a different value by a fix <p>Each replica&#8217;s temperature is controlled at a different value by a fix
with <em>fix-ID</em> that controls temperature. Possible fix styles are with <em>fix-ID</em> that controls temperature. Most thermostat fix styles
<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>, (with and without included time integration) are supported. The command
<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>. 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 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 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> assigned a different temperature. See the <a class="reference internal" href="variable.html"><em>variable</em></a>

217
src/Make.py
View File

@ -15,14 +15,14 @@ import sys,os,commands,re,copy,subprocess
# setargs = makefile settings # setargs = makefile settings
# actionargs = allowed actions (also lib-dir and machine) # actionargs = allowed actions (also lib-dir and machine)
abbrevs = "adhjmoprsv" abbrevs = "adhjmoprsvz"
switchclasses = ("actions","dir","help","jmake","makefile", switchclasses = ("actions","dir","help","jmake","makefile",
"output","packages","redo","settings","verbose") "output","packages","redo","settings","verbose","zoutput")
libclasses = ("atc","awpmd","colvars","cuda","gpu","h5md", libclasses = ("atc","awpmd","colvars","cuda","gpu","h5md",
"meam","poems","python","qmmm","voronoi") "meam","poems","python","qmmm","voronoi")
buildclasses = ("intel","kokkos") buildclasses = ("intel","kokkos")
makeclasses = ("cc","mpi","fft","jpg","png") makeclasses = ("cc","flags","mpi","fft","jpg","png")
setargs = ("gzip","#gzip","ffmpeg","#ffmpeg","smallbig","bigbig","smallsmall") setargs = ("gzip","#gzip","ffmpeg","#ffmpeg","smallbig","bigbig","smallsmall")
actionargs = ("lib-all","file","clean","exe") actionargs = ("lib-all","file","clean","exe")
@ -137,27 +137,37 @@ class Actions:
lib-all builds all auxiliary libs needed by installed packages lib-all builds all auxiliary libs needed by installed packages
lib-dir builds a specific lib whether package installed or not lib-dir builds a specific lib whether package installed or not
dir is any dir in lib directory (atc, cuda, meam, etc) except linalg dir is any dir in lib directory (atc, cuda, meam, etc) except linalg
(2) file = create src/MAKE/MINE/Makefile.auto (2) file = create a new src/MAKE/MINE/Makefile.auto
use -m switch for Makefile.machine to start from, if file not specified, existing Makefile.auto is NOT changed
else use existing Makefile.auto except by -m switch, which will copy Makefile.machine to Makefile.auto
adds settings needed for installed accelerator packages note that exe action can add an -m switch, as described below
existing Makefile.auto is NOT changed unless "file" action is specified 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 (3) clean = invoke "make clean-auto" to insure clean build on current files
useful if compiler flags have changed useful if compiler flags have changed
(4) exe or machine = build LAMMPS (4) exe or machine = build LAMMPS
machine can be any existing Makefile.machine suffix 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 "-m machine" is added if -m switch is not specified
"-o machine" is added if -o 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 if either "-m" or "-o" are specified, they are not overridden
does not invoke any lib builds, since libs could be previously built does not invoke any lib builds, since libs could be previously built
exe always builds using src/MAKE/MINE/Makefile.auto exe ALWAYS builds using src/MAKE/MINE/Makefile.auto
if file action also specified, it creates Makefile.auto if file action also specified, it creates a new Makefile.auto
else if -m switch specified, else if -m switch specified,
existing Makefile.machine is copied to create Makefile.auto existing Makefile.machine is copied to create Makefile.auto
else Makefile.auto must already exist and is not changed 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 -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): def check(self):
@ -177,7 +187,7 @@ class Actions:
cleans.append(one) cleans.append(one)
elif one == "exe": elif one == "exe":
exes.append(one) 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: else:
exes.append(one) exes.append(one)
if len(set(libs)) != len(libs) or \ if len(set(libs)) != len(libs) or \
@ -236,9 +246,9 @@ class Actions:
def file(self,caller): def file(self,caller):
# if caller = "file", create from mpi or 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 "file" action already invoked, read from auto
# if caller = "exe" and no "file" action, read from makefile.machine or auto # if caller="exe" and no "file" action, read from Makefile.machine or auto
if caller == "file": if caller == "file":
if makefile and makefile.machine == "none": if makefile and makefile.machine == "none":
@ -279,7 +289,7 @@ class Actions:
make.addvar("CC","-cxx=%s" % wrapper) make.addvar("CC","-cxx=%s" % wrapper)
make.addvar("LINK","-cxx=%s" % wrapper) make.addvar("LINK","-cxx=%s" % wrapper)
elif "-lmpi" in txt: elif "-lmpi" in txt:
make.addvar("OMPI_CXX",wrapper,"cc") make.addvar("export OMPI_CXX",wrapper,"cc")
precompiler = "env OMPI_CXX=%s " % wrapper precompiler = "env OMPI_CXX=%s " % wrapper
else: error("Could not add MPI wrapper compiler, " + else: error("Could not add MPI wrapper compiler, " +
"did not recognize OpenMPI or MPICH") "did not recognize OpenMPI or MPICH")
@ -288,6 +298,18 @@ class Actions:
make.setvar("LINKFLAGS","-g") make.setvar("LINKFLAGS","-g")
make.addvar("LINKFLAGS","-O") make.addvar("LINKFLAGS","-O")
# add CC and LINK flags
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 # add MPI settings
if mpi: if mpi:
@ -397,7 +419,7 @@ class Actions:
make.addvar("KOKKOS_DEVICES","OpenMP","lmp") make.addvar("KOKKOS_DEVICES","OpenMP","lmp")
make.addvar("KOKKOS_ARCH","KNC","lmp") make.addvar("KOKKOS_ARCH","KNC","lmp")
# add LMP settings # add LMP_INC ifdef settings
if settings: if settings:
list = settings.inlist list = settings.inlist
@ -465,7 +487,8 @@ class Actions:
# set self.stubs if Makefile.auto uses STUBS lib in MPI settings # 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 else: self.stubs = 0
# write out Makefile.auto # write out Makefile.auto
@ -510,13 +533,23 @@ class Actions:
print txt print txt
error('Unsuccessful "make stubs"') error('Unsuccessful "make stubs"')
print "Created src/STUBS/libmpi_stubs.a" 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, print output as build proceeds, else only print if fails
if verbose: subprocess.call(str,shell=True) if verbose: subprocess.call(str,shell=True)
else: else:
print str
try: subprocess.check_output(str,stderr=subprocess.STDOUT,shell=True) try: subprocess.check_output(str,stderr=subprocess.STDOUT,shell=True)
except Exception as e: print e.output except Exception as e: print e.output
@ -574,8 +607,8 @@ Syntax: Make.py switch args ...
list one or more actions, in any order list one or more actions, in any order
machine is a Makefile.machine suffix machine is a Makefile.machine suffix
one-letter switches: one-letter switches:
-d (dir), -j (jmake), -m (makefile), -o (output), -d (dir), -j (jmake), -m (makefile), -o (output), -p (packages),
-p (packages), -r (redo), -s (settings), -v (verbose) -r (redo), -s (settings), -v (verbose), -z (makefile output)
switches for libs: switches for libs:
-atc, -awpmd, -colvars, -cuda, -gpu, -h5md, -atc, -awpmd, -colvars, -cuda, -gpu, -h5md,
-meam, -poems, -python, -qmmm, -voronoi -meam, -poems, -python, -qmmm, -voronoi
@ -898,9 +931,13 @@ class Settings:
def help(self): def help(self):
return """ return """
-s set1 set2 ... -s set1 set2 ...
possible settings = gzip smallbig bigbig smallsmall possible settings = gzip #gzip ffmpeg #ffmpeg smallbig bigbig smallsmall
add each setting as LAMMPS setting to created Makefile.auto alter LAMMPS ifdef settings in Makefile.auto
if -s not specified, no settings are changed 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): def check(self):
@ -924,6 +961,23 @@ class Verbose:
def check(self): def check(self):
if len(self.inlist): error("-v args are invalid") 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 # lib classes, one per LAMMPS auxiliary lib
# ---------------------------------------------------------------- # ----------------------------------------------------------------
@ -1087,15 +1141,15 @@ class CUDA:
def __init__(self,list): def __init__(self,list):
self.inlist = copy.copy(list) self.inlist = copy.copy(list)
self.mode = "double" self.mode = "double"
self.arch = "31" self.arch = "35"
def help(self): def help(self):
return """ return """
-cuda mode=double arch=31 -cuda mode=double arch=35
all args are optional and can be in any order all args are optional and can be in any order
mode = double or mixed or single (def = double) mode = double or mixed or single (def = double)
arch = M (def = 31) arch = M (def = 35)
M = 31 for Kepler M = 31,35,37,etc for Kepler
M = 20 for CC2.0 (GF100/110, e.g. C2050,GTX580,GTX470) 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 = 21 for CC2.1 (GF104/114, e.g. GTX560, GTX460, GTX450)
M = 13 for CC1.3 (GF200, e.g. C1060, GTX285) M = 13 for CC1.3 (GF200, e.g. C1060, GTX285)
@ -1144,17 +1198,18 @@ class GPU:
def __init__(self,list): def __init__(self,list):
self.inlist = copy.copy(list) self.inlist = copy.copy(list)
self.make = "linux.double" self.make = "linux.double"
self.lammpsflag = self.modeflag = self.archflag = 0 self.lammpsflag = self.modeflag = self.archflag = self.homeflag = 0
def help(self): def help(self):
return """ 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 all args are optional and can be in any order
make = use Makefile.suffix (def = linux.double) make = use Makefile.suffix (def = linux.double)
lammps = use Makefile.lammps.suffix2 (def = EXTRAMAKE in makefile) lammps = use Makefile.lammps.suffix2 (def = EXTRAMAKE in makefile)
mode = double or mixed or single (def = CUDA_PREC in makefile) mode = double or mixed or single (def = CUDA_PREC in makefile)
arch = 31 (Kepler) or 21 (Fermi) (def = CUDA_ARCH in makefile) arch = 3x (x = digit for Kepler) or 2x (x = digit for Fermi)
dir = home dir for CUDA include and library files (def = none) (def = CUDA_ARCH in makefile)
home = path to Cuda, e.g. /usr/local/cuda (def = CUDA_HOME in makefile)
""" """
def check(self): def check(self):
@ -1173,9 +1228,9 @@ class GPU:
elif words[0] == "arch": elif words[0] == "arch":
self.arch = words[1] self.arch = words[1]
self.archflag = 1 self.archflag = 1
elif words[0] == "dir": elif words[0] == "home":
self.dir = words[1] self.home = words[1]
self.dirflag = 1 self.homeflag = 1
else: error("-gpu args are invalid") else: error("-gpu args are invalid")
if self.modeflag and (self.mode != "double" and if self.modeflag and (self.mode != "double" and
self.mode != "mixed" and self.mode != "mixed" and
@ -1196,18 +1251,22 @@ class GPU:
make.setvar("CUDA_PRECISION","-D_SINGLE_SINGLE") make.setvar("CUDA_PRECISION","-D_SINGLE_SINGLE")
if self.archflag: if self.archflag:
make.setvar("CUDA_ARCH","-arch=sm_%s" % self.arch) make.setvar("CUDA_ARCH","-arch=sm_%s" % self.arch)
if self.homeflag:
make.setvar("CUDA_HOME",self.home)
if self.lammpsflag: if self.lammpsflag:
make.setvar("EXTRAMAKE","Makefile.lammps.%s" % self.lammps) 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) make.write("%s/Makefile.auto" % libdir)
commands.getoutput("cd %s; make -f Makefile.auto clean" % libdir) # special hack for shannon GPU cluster
if jmake: str = "cd %s; make -j %d -f Makefile.auto" % (libdir,jmake.n) # must use "srun make" if on it, else just make
else: str = "cd %s; make -f Makefile.auto" % libdir # 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 # if verbose, print output as build proceeds, else only print if fails
@ -1532,11 +1591,13 @@ class Kokkos:
mode is not optional, arch is optional mode is not optional, arch is optional
mode = omp or cuda or phi (def = KOKKOS_DEVICES setting in Makefile ) mode = omp or cuda or phi (def = KOKKOS_DEVICES setting in Makefile )
build Kokkos package for omp or cuda or phi build Kokkos package for omp or cuda or phi
set KOKKOS_DEVICES to "OpenMP" (omp, phi) or "Cuda, OpenMP" (cuda) sets KOKKOS_DEVICES to "OpenMP" (omp, phi) or "Cuda, OpenMP" (cuda)
arch = 31 (Kepler) or 21 (Fermi) (def = -arch setting in Makefile) arch = number like 35 (Kepler) or 21 (Fermi)
sets KOKKOS_ARCH to appropriate value
""" """
def check(self): def check(self):
print self.inlist
if self.inlist != None and len(self.inlist) == 0: if self.inlist != None and len(self.inlist) == 0:
error("-kokkos args are invalid") error("-kokkos args are invalid")
@ -1554,7 +1615,7 @@ class Kokkos:
else: error("-kokkos args are invalid") 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 # Cc class
@ -1568,7 +1629,8 @@ class Cc:
def help(self): def help(self):
return """ return """
-cc compiler wrap=wcompiler -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 is required, all other args are optional
compiler = any string with g++ or icc or icpc compiler = any string with g++ or icc or icpc
or mpi (or mpicxx, mpiCC, mpiicpc, etc) or mpi (or mpicxx, mpiCC, mpiicpc, etc)
@ -1602,6 +1664,41 @@ class Cc:
self.wrap = words[1] self.wrap = words[1]
else: error("-cc args are invalid") 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 # Mpi class
class Mpi: class Mpi:
@ -1612,7 +1709,8 @@ class Mpi:
def help(self): def help(self):
return """ return """
-mpi style dir=path -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 is required, all other args are optional
style = mpi or mpich or ompi or serial style = mpi or mpich or ompi or serial
mpi = no MPI settings (assume compiler is MPI wrapper) mpi = no MPI settings (assume compiler is MPI wrapper)
@ -1645,9 +1743,10 @@ class Fft:
def help(self): def help(self):
return """ return """
-fft mode lib=libname dir=homedir idir=incdir ldir=libdir -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 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 ... mode = none or fftw or fftw3 or ...
adds -DFFT_MODE setting adds -DFFT_MODE setting
lib = name of FFT library to link with (def is libname = mode) lib = name of FFT library to link with (def is libname = mode)
@ -1685,6 +1784,8 @@ class Jpg:
def help(self): def help(self):
return """ return """
-jpg flag dir=homedir idir=incdir ldir=libdir -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 change JPG settings in makefile
all args are optional, flag must come first if specified all args are optional, flag must come first if specified
flag = yes or no (def = yes) flag = yes or no (def = yes)
@ -1722,7 +1823,8 @@ class Png:
def help(self): def help(self):
return """ return """
-png flag dir=homedir idir=incdir ldir=libdir -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 all args are optional, flag must come first if specified
flag = yes or no (def = yes) flag = yes or no (def = yes)
include or exclude PNG support include or exclude PNG support
@ -2101,13 +2203,22 @@ while 1:
packages.uninstall() 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: if output and actions and "exe" in actions.alist:
txt = "cp %s/lmp_auto %s/lmp_%s" % (dir.src,dir.cwd,output.machine) txt = "cp %s/lmp_auto %s/lmp_%s" % (dir.src,dir.cwd,output.machine)
commands.getoutput(txt) commands.getoutput(txt)
print "Created lmp_%s in %s" % (output.machine,dir.cwd) 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 # write current Make.py command to src/Make.py.last
fp = open("%s/Make.py.last" % dir.src,'w') fp = open("%s/Make.py.last" % dir.src,'w')

4
src/Makefile
View File

@ -213,8 +213,8 @@ install-python:
tar: tar:
@cd STUBS; $(MAKE) clean @cd STUBS; $(MAKE) clean
@cd ..; tar cvzf src/$(ROOT)_src.tar.gz \ @cd ..; tar cvzf src/$(ROOT)_src.tar.gz \
src/Make* src/Package.sh src/Depend.sh \ src/Make* src/Package.sh src/Depend.sh src/Install.sh \
src/MAKE src/*.cpp src/*.h src/STUBS \ src/MAKE src/DEPEND src/*.cpp src/*.h src/STUBS \
$(patsubst %,src/%,$(PACKAGEUC)) $(patsubst %,src/%,$(PACKUSERUC)) \ $(patsubst %,src/%,$(PACKAGEUC)) $(patsubst %,src/%,$(PACKUSERUC)) \
--exclude=*/.svn --exclude=*/.svn
@cd STUBS; $(MAKE) @cd STUBS; $(MAKE)

143
src/USER-INTEL/TEST/README
View File

@ -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 # Benchmarks
'bench' directory. #
# 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 # Expected Timesteps/second on E5-2697v3 with turbo on and HT enabled
Intel Xeon processor E5-2697 V2 with Intel Xeon Phi coprocessor 7120P. #
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ # 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: #############################################################################
----------------------------------------------------------------------------- # To run without a optimization 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 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 #############################################################################
----------------------------------------------------------------------------- # To run with USER-INTEL package and no coprocessor
env OMP_NUM_THREADS=2 mpirun -np 24 ../../../src/lmp_YOUR_MACHINE -in in.intel.rhodo -log none -v b 0 -v s omp #############################################################################
+++++++++++++++++++++++ mpirun -np $LMP_CORES $LMP_BIN -in $bench -log none -pk intel 0
+ 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 and automatic load balancing to 1 coprocessor
#############################################################################
mpirun -np $LMP_CORES $LMP_BIN -in $bench -log none -pk intel 1

46
src/USER-INTEL/TEST/in.intel.lc
View File

@ -2,60 +2,44 @@
# biaxial ellipsoid mesogens in isotropic phase # biaxial ellipsoid mesogens in isotropic phase
# shape: 2 1.5 1 # shape: 2 1.5 1
# cutoff 4.0 with skin 0.8 # cutoff 4.0 with skin 0.8
# NPT, T=2.4, P=8.0
package intel 1 mode mixed balance $b variable w index 10 # Warmup Timesteps
package omp 0 variable t index 840 # Main Run Timesteps
suffix $s variable m index 1 # Main Run Timestep Multiplier
# processors * * * grid numa variable n index 0 # Use NUMA Mapping for Multi-Node
variable p index 0 # Use Power Measurement
variable x index 4 variable x index 4
variable y index 2 variable y index 2
variable z index 2 variable z index 2
variable i equal $x*32 variable rr equal floor($t*$m)
variable j equal $y*32
variable k equal $z*32 if "$n > 0" then "processors * * * grid numa"
units lj units lj
atom_style ellipsoid atom_style ellipsoid
pair_style gayberne 1.0 3.0 1.0 4.0
# creation read_restart restart.lc
lattice sc 0.22 replicate $x $y $z
region box block 0 $i 0 $j 0 $k
create_box 1 box
create_atoms 1 box
# read_data data.gb
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 compute rot all temp/asphere
group spheroid type 1 group spheroid type 1
variable dof equal count(spheroid)+3 variable dof equal count(spheroid)+3
compute_modify rot extra ${dof} 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_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 pair_coeff 1 1 1.0 1.0 1.0 0.5 0.2 1.0 0.5 0.2
neighbor 0.8 bin neighbor 0.8 bin
timestep 0.002 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 ${dof}
run 210
thermo 100 thermo 100
reset_timestep 0
unfix 1
fix 1 all nve/asphere fix 1 all nve/asphere
run 10
run 50
if "$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
View 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}

32
src/USER-INTEL/TEST/in.intel.rhodo
View File

@ -1,18 +1,27 @@
# Rhodopsin model # Rhodopsin model
package intel 1 mode mixed balance $b variable w index 10 # Warmup Timesteps
package omp 0 variable t index 520 # Main Run Timesteps
suffix $s variable m index 1 # Main Run Timestep Multiplier
variable n index 0 # Use NUMA Mapping for Multi-Node
variable b index 3 # Neighbor binsize
variable p index 0 # Use Power Measurement
variable c index 0 # 1 to use collectives for PPPM
variable d index 0 # 1 to use 'diff ad' for PPPM
variable x index 4 variable x index 4
variable y index 2 variable y index 2
variable z index 2 variable z index 2
variable rr equal floor($t*$m)
variable root getenv LMP_ROOT
if "$n > 0" then "processors * * * grid numa"
units real units real
neigh_modify delay 5 every 1 neigh_modify delay 5 every 1 binsize $b
atom_style full atom_style full
atom_modify map hash
bond_style harmonic bond_style harmonic
angle_style charmm angle_style charmm
dihedral_style charmm dihedral_style charmm
@ -21,7 +30,10 @@ pair_style lj/charmm/coul/long 8.0 10.0
pair_modify mix arithmetic pair_modify mix arithmetic
kspace_style pppm 1e-4 kspace_style pppm 1e-4
read_data ../../../bench/data.rhodo if "$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 replicate $x $y $z
@ -31,9 +43,11 @@ fix 2 all npt temp 300.0 300.0 100.0 &
special_bonds charmm special_bonds charmm
thermo 50 thermo 100
thermo_style multi thermo_style multi
timestep 2.0 timestep 2.0
run 10 if "$p > 0" then "run_style verlet/power"
run 100
if "$w > 0" then "run $w"
run ${rr}

23
src/USER-INTEL/TEST/in.intel.sw
View File

@ -1,7 +1,10 @@
# bulk Si via Stillinger-Weber # bulk Si via Stillinger-Weber
package intel 1 mode mixed balance $b
package omp 0 variable w index 10 # Warmup Timesteps
suffix $s variable t index 6200 # Main Run Timesteps
variable m index 1 # Main Run Timestep Multiplier
variable n index 0 # Use NUMA Mapping for Multi-Node
variable p index 0 # Use Power Measurement
variable x index 2 variable x index 2
variable y index 2 variable y index 2
@ -10,6 +13,10 @@ variable z index 4
variable xx equal 20*$x variable xx equal 20*$x
variable yy equal 20*$y variable yy equal 20*$y
variable zz equal 10*$z 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 units metal
atom_style atomic atom_style atomic
@ -20,7 +27,7 @@ create_box 1 box
create_atoms 1 box create_atoms 1 box
pair_style sw pair_style sw
pair_coeff * * ../../../bench/POTENTIALS/Si.sw Si pair_coeff * * ${root}/bench/POTENTIALS/Si.sw Si
mass 1 28.06 mass 1 28.06
velocity all create 1000.0 376847 loop geom velocity all create 1000.0 376847 loop geom
@ -29,8 +36,10 @@ neighbor 1.0 bin
neigh_modify delay 5 every 1 neigh_modify delay 5 every 1
fix 1 all nve fix 1 all nve
thermo 1000
timestep 0.001 timestep 0.001
run 10 if "$p > 0" then "run_style verlet/power"
run 100
if "$w > 0" then "run $w"
run ${rr}

23
src/USER-INTEL/TEST/in.intel.tersoff
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@ -1,7 +1,10 @@
# bulk Si via Tersoff # bulk Si via Tersoff
package intel 1 mode mixed balance $b
package omp 0 variable w index 10 # Warmup Timesteps
suffix $s variable t index 2420 # Main Run Timesteps
variable m index 1 # Main Run Timestep Multiplier
variable n index 0 # Use NUMA Mapping for Multi-Node
variable p index 0 # Use Power Measurement
variable x index 2 variable x index 2
variable y index 2 variable y index 2
@ -10,6 +13,10 @@ variable z index 4
variable xx equal 20*$x variable xx equal 20*$x
variable yy equal 20*$y variable yy equal 20*$y
variable zz equal 10*$z 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 units metal
atom_style atomic atom_style atomic
@ -20,7 +27,7 @@ create_box 1 box
create_atoms 1 box create_atoms 1 box
pair_style tersoff pair_style tersoff
pair_coeff * * ../../../bench/POTENTIALS/Si.tersoff Si pair_coeff * * ${root}/bench/POTENTIALS/Si.tersoff Si
mass 1 28.06 mass 1 28.06
velocity all create 1000.0 376847 loop geom velocity all create 1000.0 376847 loop geom
@ -29,8 +36,10 @@ neighbor 1.0 bin
neigh_modify delay 5 every 1 neigh_modify delay 5 every 1
fix 1 all nve fix 1 all nve
thermo 1000
timestep 0.001 timestep 0.001
run 10 if "$p > 0" then "run_style verlet/power"
run 100
if "$w > 0" then "run $w"
run ${rr}

35
src/USER-INTEL/TEST/in.intel.water
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@ -1,22 +1,21 @@
package intel 1 mode mixed balance $b # Coarse-grain water simulation using Stillinger-Weber
package omp 0
suffix $s
# processors * * * grid numa variable w index 10 # Warmup Timesteps
variable t index 2600 # Main Run Timesteps
variable m index 1 # Main Run Timestep Multiplier
variable n index 0 # Use NUMA Mapping for Multi-Node
variable p index 0 # Use Power Measurement
variable x index 4 variable x index 4
variable y index 2 variable y index 2
variable z index 2 variable z index 2
variable rr equal floor($t*$m)
if "$n > 0" then "processors * * * grid numa"
units real units real
atom_style atomic atom_style atomic
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
read_data mW_32k_cube.data read_data mW_32k_cube.data
reset_timestep 0 reset_timestep 0
replicate $x $y $z replicate $x $y $z
@ -27,22 +26,20 @@ pair_coeff * * mW.sw mW
mass 1 18.015 #g/mol mass 1 18.015 #g/mol
group mW type 1 group mW type 1
neighbor 1 bin #Angstroms neighbor 2 bin #Angstroms
neigh_modify every 2 delay 2 check yes neigh_modify every 1 delay 4
fix 1 all nvt temp 300.0 300.0 1000.0 fix 1 all nvt temp 300.0 300.0 1000.0
#velocity all create 300.0 2323 dist gaussian #Kelvin
velocity all zero linear velocity all zero linear
timestep 10 #femtoseconds timestep 10 #femtoseconds
#variable Density equal "mass(mW)/vol/0.602214179"
#thermo_style custom step temp press pe spcpu
thermo_modify norm yes thermo_modify norm yes
#restart 100 mW_32k_cube.res mW_32k_cube.res thermo 1000
thermo 100
run 10 #actual runs if "$p > 0" then "run_style verlet/power"
run 100
if "$w > 0" then "run $w"
run ${rr}

57
src/USER-INTEL/TEST/in.lc_generate_restart Normal file
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@ -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

2
src/USER-INTEL/neigh_half_bin_intel.cpp
View File

@ -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(ilist:length(0) alloc_if(0) free_if(0)) \
in(atombin:length(aend) 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(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(separate_buffers, astart, aend, nlocal, molecular, ntypes) \
in(xperiodic, yperiodic, zperiodic, xprd_half, yprd_half, zprd_half) \ in(xperiodic, yperiodic, zperiodic, xprd_half, yprd_half, zprd_half) \
out(overflow:length(5) alloc_if(0) free_if(0)) \ out(overflow:length(5) alloc_if(0) free_if(0)) \

2
src/version.h
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@ -1 +1 @@
#define LAMMPS_VERSION "28 Mar20 2016" #define LAMMPS_VERSION "7 Apr 2016"