Merge remote-tracking branch 'lammps-ro/master' into lammps-icms
# Resolved Conflicts: # doc/Manual.txt
This commit is contained in:
Axel Kohlmeyer
@ -135,7 +135,7 @@
|
||||
<H1></H1><div class="section" id="lammps-documentation">
|
||||
<h1>LAMMPS-ICMS Documentation<a class="headerlink" href="#lammps-documentation" title="Permalink to this headline">¶</a></h1>
|
||||
<div class="section" id="feb-2016-version">
|
||||
<h2>17 Feb 2016 version<a class="headerlink" href="#feb-2016-version" title="Permalink to this headline">¶</a></h2>
|
||||
<h2>22 Feb 2016 version<a class="headerlink" href="#feb-2016-version" title="Permalink to this headline">¶</a></h2>
|
||||
</div>
|
||||
<div class="section" id="version-info">
|
||||
<h2>Version info:<a class="headerlink" href="#version-info" title="Permalink to this headline">¶</a></h2>
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
<!-- HTML_ONLY -->
|
||||
<HEAD>
|
||||
<TITLE>LAMMPS-ICMS Users Manual</TITLE>
|
||||
<META NAME="docnumber" CONTENT="17 Feb 2016 version">
|
||||
<META NAME="docnumber" CONTENT="22 Feb 2016 version">
|
||||
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
|
||||
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
|
||||
</HEAD>
|
||||
@ -21,7 +21,7 @@
|
||||
<H1></H1>
|
||||
|
||||
LAMMPS-ICMS Documentation :c,h3
|
||||
17 Feb 2016 version :c,h4
|
||||
22 Feb 2016 version :c,h4
|
||||
|
||||
Version info: :h4
|
||||
|
||||
|
||||
@ -1017,150 +1017,150 @@ KOKKOS, o = USER-OMP, t = OPT.</p>
|
||||
<table border="1" class="docutils">
|
||||
<colgroup>
|
||||
<col width="24%" />
|
||||
<col width="24%" />
|
||||
<col width="25%" />
|
||||
<col width="27%" />
|
||||
<col width="24%" />
|
||||
</colgroup>
|
||||
<tbody valign="top">
|
||||
<tr class="row-odd"><td><a class="reference internal" href="pair_none.html"><em>none</em></a></td>
|
||||
<td><a class="reference internal" href="pair_zero.html"><em>zero</em></a></td>
|
||||
<td><a class="reference internal" href="pair_hybrid.html"><em>hybrid</em></a></td>
|
||||
<td><a class="reference internal" href="pair_hybrid.html"><em>hybrid/overlay</em></a></td>
|
||||
<td><a class="reference internal" href="pair_adp.html"><em>adp (o)</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-even"><td><a class="reference internal" href="pair_airebo.html"><em>airebo (o)</em></a></td>
|
||||
<tr class="row-even"><td><a class="reference internal" href="pair_adp.html"><em>adp (o)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_airebo.html"><em>airebo (o)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_beck.html"><em>beck (go)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_body.html"><em>body</em></a></td>
|
||||
<td><a class="reference internal" href="pair_bop.html"><em>bop</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="pair_born.html"><em>born (go)</em></a></td>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="pair_bop.html"><em>bop</em></a></td>
|
||||
<td><a class="reference internal" href="pair_born.html"><em>born (go)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_born.html"><em>born/coul/long (cgo)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_born.html"><em>born/coul/long/cs</em></a></td>
|
||||
<td><a class="reference internal" href="pair_born.html"><em>born/coul/msm (o)</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-even"><td><a class="reference internal" href="pair_born.html"><em>born/coul/wolf (go)</em></a></td>
|
||||
<tr class="row-even"><td><a class="reference internal" href="pair_born.html"><em>born/coul/msm (o)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_born.html"><em>born/coul/wolf (go)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_brownian.html"><em>brownian (o)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_brownian.html"><em>brownian/poly (o)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_buck.html"><em>buck (cgkio)</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="pair_buck.html"><em>buck/coul/cut (cgkio)</em></a></td>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="pair_buck.html"><em>buck (cgkio)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_buck.html"><em>buck/coul/cut (cgkio)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_buck.html"><em>buck/coul/long (cgkio)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_buck.html"><em>buck/coul/long/cs</em></a></td>
|
||||
<td><a class="reference internal" href="pair_buck.html"><em>buck/coul/msm (o)</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-even"><td><a class="reference internal" href="pair_buck_long.html"><em>buck/long/coul/long (o)</em></a></td>
|
||||
<tr class="row-even"><td><a class="reference internal" href="pair_buck.html"><em>buck/coul/msm (o)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_buck_long.html"><em>buck/long/coul/long (o)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_colloid.html"><em>colloid (go)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_comb.html"><em>comb (o)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_comb.html"><em>comb3</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="pair_coul.html"><em>coul/cut (gko)</em></a></td>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="pair_comb.html"><em>comb3</em></a></td>
|
||||
<td><a class="reference internal" href="pair_coul.html"><em>coul/cut (gko)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_coul.html"><em>coul/debye (gko)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_coul.html"><em>coul/dsf (gko)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_coul.html"><em>coul/long (gko)</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-even"><td><a class="reference internal" href="pair_coul.html"><em>coul/long/cs</em></a></td>
|
||||
<tr class="row-even"><td><a class="reference internal" href="pair_coul.html"><em>coul/long (gko)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_coul.html"><em>coul/long/cs</em></a></td>
|
||||
<td><a class="reference internal" href="pair_coul.html"><em>coul/msm</em></a></td>
|
||||
<td><a class="reference internal" href="pair_coul.html"><em>coul/streitz</em></a></td>
|
||||
<td><a class="reference internal" href="pair_coul.html"><em>coul/wolf (ko)</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="pair_dpd.html"><em>dpd (o)</em></a></td>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="pair_coul.html"><em>coul/wolf (ko)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_dpd.html"><em>dpd (o)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_dpd.html"><em>dpd/tstat (o)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_dsmc.html"><em>dsmc</em></a></td>
|
||||
<td><a class="reference internal" href="pair_eam.html"><em>eam (cgkot)</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-even"><td><a class="reference internal" href="pair_eam.html"><em>eam/alloy (cgkot)</em></a></td>
|
||||
<tr class="row-even"><td><a class="reference internal" href="pair_eam.html"><em>eam (cgkot)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_eam.html"><em>eam/alloy (cgkot)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_eam.html"><em>eam/fs (cgkot)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_eim.html"><em>eim (o)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_gauss.html"><em>gauss (go)</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="pair_gayberne.html"><em>gayberne (gio)</em></a></td>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="pair_gauss.html"><em>gauss (go)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_gayberne.html"><em>gayberne (gio)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_gran.html"><em>gran/hertz/history (o)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_gran.html"><em>gran/hooke (co)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_gran.html"><em>gran/hooke/history (o)</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-even"><td><a class="reference internal" href="pair_hbond_dreiding.html"><em>hbond/dreiding/lj (o)</em></a></td>
|
||||
<tr class="row-even"><td><a class="reference internal" href="pair_gran.html"><em>gran/hooke/history (o)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_hbond_dreiding.html"><em>hbond/dreiding/lj (o)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_hbond_dreiding.html"><em>hbond/dreiding/morse (o)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_kim.html"><em>kim</em></a></td>
|
||||
<td><a class="reference internal" href="pair_lcbop.html"><em>lcbop</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="pair_line_lj.html"><em>line/lj</em></a></td>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="pair_lcbop.html"><em>lcbop</em></a></td>
|
||||
<td><a class="reference internal" href="pair_line_lj.html"><em>line/lj</em></a></td>
|
||||
<td><a class="reference internal" href="pair_charmm.html"><em>lj/charmm/coul/charmm (cko)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_charmm.html"><em>lj/charmm/coul/charmm/implicit (cko)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_charmm.html"><em>lj/charmm/coul/long (cgiko)</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-even"><td><a class="reference internal" href="pair_charmm.html"><em>lj/charmm/coul/msm</em></a></td>
|
||||
<tr class="row-even"><td><a class="reference internal" href="pair_charmm.html"><em>lj/charmm/coul/long (cgiko)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_charmm.html"><em>lj/charmm/coul/msm</em></a></td>
|
||||
<td><a class="reference internal" href="pair_class2.html"><em>lj/class2 (cgko)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_class2.html"><em>lj/class2/coul/cut (cko)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_class2.html"><em>lj/class2/coul/long (cgko)</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="pair_lj_cubic.html"><em>lj/cubic (go)</em></a></td>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="pair_class2.html"><em>lj/class2/coul/long (cgko)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_lj_cubic.html"><em>lj/cubic (go)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_lj.html"><em>lj/cut (cgikot)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_lj.html"><em>lj/cut/coul/cut (cgko)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_lj.html"><em>lj/cut/coul/debye (cgko)</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-even"><td><a class="reference internal" href="pair_lj.html"><em>lj/cut/coul/dsf (gko)</em></a></td>
|
||||
<tr class="row-even"><td><a class="reference internal" href="pair_lj.html"><em>lj/cut/coul/debye (cgko)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_lj.html"><em>lj/cut/coul/dsf (gko)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_lj.html"><em>lj/cut/coul/long (cgikot)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_lj.html"><em>lj/cut/coul/long/cs</em></a></td>
|
||||
<td><a class="reference internal" href="pair_lj.html"><em>lj/cut/coul/msm (go)</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="pair_dipole.html"><em>lj/cut/dipole/cut (go)</em></a></td>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="pair_lj.html"><em>lj/cut/coul/msm (go)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_dipole.html"><em>lj/cut/dipole/cut (go)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_dipole.html"><em>lj/cut/dipole/long</em></a></td>
|
||||
<td><a class="reference internal" href="pair_lj.html"><em>lj/cut/tip4p/cut (o)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_lj.html"><em>lj/cut/tip4p/long (ot)</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-even"><td><a class="reference internal" href="pair_lj_expand.html"><em>lj/expand (cgko)</em></a></td>
|
||||
<tr class="row-even"><td><a class="reference internal" href="pair_lj.html"><em>lj/cut/tip4p/long (ot)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_lj_expand.html"><em>lj/expand (cgko)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_gromacs.html"><em>lj/gromacs (cgko)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_gromacs.html"><em>lj/gromacs/coul/gromacs (cko)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_lj_long.html"><em>lj/long/coul/long (o)</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="pair_dipole.html"><em>lj/long/dipole/long</em></a></td>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="pair_lj_long.html"><em>lj/long/coul/long (o)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_dipole.html"><em>lj/long/dipole/long</em></a></td>
|
||||
<td><a class="reference internal" href="pair_lj_long.html"><em>lj/long/tip4p/long</em></a></td>
|
||||
<td><a class="reference internal" href="pair_lj_smooth.html"><em>lj/smooth (co)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_lj_smooth_linear.html"><em>lj/smooth/linear (o)</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-even"><td><a class="reference internal" href="pair_lj96.html"><em>lj96/cut (cgo)</em></a></td>
|
||||
<tr class="row-even"><td><a class="reference internal" href="pair_lj_smooth_linear.html"><em>lj/smooth/linear (o)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_lj96.html"><em>lj96/cut (cgo)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_lubricate.html"><em>lubricate (o)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_lubricate.html"><em>lubricate/poly (o)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_lubricateU.html"><em>lubricateU</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="pair_lubricateU.html"><em>lubricateU/poly</em></a></td>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="pair_lubricateU.html"><em>lubricateU</em></a></td>
|
||||
<td><a class="reference internal" href="pair_lubricateU.html"><em>lubricateU/poly</em></a></td>
|
||||
<td><a class="reference internal" href="pair_meam.html"><em>meam (o)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_mie.html"><em>mie/cut (o)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_morse.html"><em>morse (cgot)</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-even"><td><a class="reference internal" href="pair_nb3b_harmonic.html"><em>nb3b/harmonic (o)</em></a></td>
|
||||
<tr class="row-even"><td><a class="reference internal" href="pair_morse.html"><em>morse (cgot)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_nb3b_harmonic.html"><em>nb3b/harmonic (o)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_nm.html"><em>nm/cut (o)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_nm.html"><em>nm/cut/coul/cut (o)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_nm.html"><em>nm/cut/coul/long (o)</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="pair_peri.html"><em>peri/eps</em></a></td>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="pair_nm.html"><em>nm/cut/coul/long (o)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_peri.html"><em>peri/eps</em></a></td>
|
||||
<td><a class="reference internal" href="pair_peri.html"><em>peri/lps (o)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_peri.html"><em>peri/pmb (o)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_peri.html"><em>peri/ves</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-even"><td><a class="reference internal" href="pair_polymorphic.html"><em>polymorphic</em></a></td>
|
||||
<tr class="row-even"><td><a class="reference internal" href="pair_peri.html"><em>peri/ves</em></a></td>
|
||||
<td><a class="reference internal" href="pair_polymorphic.html"><em>polymorphic</em></a></td>
|
||||
<td><a class="reference internal" href="pair_reax.html"><em>reax</em></a></td>
|
||||
<td><a class="reference internal" href="pair_airebo.html"><em>rebo (o)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_resquared.html"><em>resquared (go)</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="pair_snap.html"><em>snap</em></a></td>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="pair_resquared.html"><em>resquared (go)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_snap.html"><em>snap</em></a></td>
|
||||
<td><a class="reference internal" href="pair_soft.html"><em>soft (go)</em></a></td>
|
||||
<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>
|
||||
</tr>
|
||||
<tr class="row-even"><td><a class="reference internal" href="pair_tersoff.html"><em>tersoff (cgkio)</em></a></td>
|
||||
<tr class="row-even"><td><a class="reference internal" href="pair_table.html"><em>table (gko)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_tersoff.html"><em>tersoff (cgkio)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_tersoff_mod.html"><em>tersoff/mod (ko)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_tersoff_zbl.html"><em>tersoff/zbl (ko)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_coul.html"><em>tip4p/cut (o)</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="pair_coul.html"><em>tip4p/long (o)</em></a></td>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="pair_coul.html"><em>tip4p/cut (o)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_coul.html"><em>tip4p/long (o)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_tri_lj.html"><em>tri/lj</em></a></td>
|
||||
<td><a class="reference internal" href="pair_vashishta.html"><em>vashishta (o)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_yukawa.html"><em>yukawa (go)</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-even"><td><a class="reference internal" href="pair_yukawa_colloid.html"><em>yukawa/colloid (go)</em></a></td>
|
||||
<tr class="row-even"><td><a class="reference internal" href="pair_yukawa.html"><em>yukawa (go)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_yukawa_colloid.html"><em>yukawa/colloid (go)</em></a></td>
|
||||
<td><a class="reference internal" href="pair_zbl.html"><em>zbl (go)</em></a></td>
|
||||
<td> </td>
|
||||
<td> </td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@ -1248,26 +1248,26 @@ letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
|
||||
KOKKOS, o = USER-OMP, t = OPT.</p>
|
||||
<table border="1" class="docutils">
|
||||
<colgroup>
|
||||
<col width="25%" />
|
||||
<col width="28%" />
|
||||
<col width="25%" />
|
||||
<col width="22%" />
|
||||
<col width="25%" />
|
||||
</colgroup>
|
||||
<tbody valign="top">
|
||||
<tr class="row-odd"><td><a class="reference internal" href="bond_none.html"><em>none</em></a></td>
|
||||
<td><a class="reference internal" href="bond_zero.html"><em>zero</em></a></td>
|
||||
<td><a class="reference internal" href="bond_hybrid.html"><em>hybrid</em></a></td>
|
||||
<td><a class="reference internal" href="bond_class2.html"><em>class2 (o)</em></a></td>
|
||||
<td><a class="reference internal" href="bond_fene.html"><em>fene (ko)</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-even"><td><a class="reference internal" href="bond_fene_expand.html"><em>fene/expand (o)</em></a></td>
|
||||
<tr class="row-even"><td><a class="reference internal" href="bond_fene.html"><em>fene (ko)</em></a></td>
|
||||
<td><a class="reference internal" href="bond_fene_expand.html"><em>fene/expand (o)</em></a></td>
|
||||
<td><a class="reference internal" href="bond_harmonic.html"><em>harmonic (ko)</em></a></td>
|
||||
<td><a class="reference internal" href="bond_morse.html"><em>morse (o)</em></a></td>
|
||||
<td><a class="reference internal" href="bond_nonlinear.html"><em>nonlinear (o)</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="bond_quartic.html"><em>quartic (o)</em></a></td>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="bond_nonlinear.html"><em>nonlinear (o)</em></a></td>
|
||||
<td><a class="reference internal" href="bond_quartic.html"><em>quartic (o)</em></a></td>
|
||||
<td><a class="reference internal" href="bond_table.html"><em>table (o)</em></a></td>
|
||||
<td> </td>
|
||||
<td> </td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@ -1296,26 +1296,26 @@ letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
|
||||
KOKKOS, o = USER-OMP, t = OPT.</p>
|
||||
<table border="1" class="docutils">
|
||||
<colgroup>
|
||||
<col width="27%" />
|
||||
<col width="21%" />
|
||||
<col width="24%" />
|
||||
<col width="28%" />
|
||||
<col width="27%" />
|
||||
</colgroup>
|
||||
<tbody valign="top">
|
||||
<tr class="row-odd"><td><a class="reference internal" href="angle_none.html"><em>none</em></a></td>
|
||||
<td><a class="reference internal" href="angle_zero.html"><em>zero</em></a></td>
|
||||
<td><a class="reference internal" href="angle_hybrid.html"><em>hybrid</em></a></td>
|
||||
<td><a class="reference internal" href="angle_charmm.html"><em>charmm (ko)</em></a></td>
|
||||
<td><a class="reference internal" href="angle_class2.html"><em>class2 (o)</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-even"><td><a class="reference internal" href="angle_cosine.html"><em>cosine (o)</em></a></td>
|
||||
<tr class="row-even"><td><a class="reference internal" href="angle_class2.html"><em>class2 (o)</em></a></td>
|
||||
<td><a class="reference internal" href="angle_cosine.html"><em>cosine (o)</em></a></td>
|
||||
<td><a class="reference internal" href="angle_cosine_delta.html"><em>cosine/delta (o)</em></a></td>
|
||||
<td><a class="reference internal" href="angle_cosine_periodic.html"><em>cosine/periodic (o)</em></a></td>
|
||||
<td><a class="reference internal" href="angle_cosine_squared.html"><em>cosine/squared (o)</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="angle_harmonic.html"><em>harmonic (iko)</em></a></td>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="angle_cosine_squared.html"><em>cosine/squared (o)</em></a></td>
|
||||
<td><a class="reference internal" href="angle_harmonic.html"><em>harmonic (iko)</em></a></td>
|
||||
<td><a class="reference internal" href="angle_table.html"><em>table (o)</em></a></td>
|
||||
<td> </td>
|
||||
<td> </td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@ -1353,21 +1353,26 @@ letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
|
||||
KOKKOS, o = USER-OMP, t = OPT.</p>
|
||||
<table border="1" class="docutils">
|
||||
<colgroup>
|
||||
<col width="22%" />
|
||||
<col width="25%" />
|
||||
<col width="21%" />
|
||||
<col width="32%" />
|
||||
<col width="22%" />
|
||||
</colgroup>
|
||||
<tbody valign="top">
|
||||
<tr class="row-odd"><td><a class="reference internal" href="dihedral_none.html"><em>none</em></a></td>
|
||||
<td><a class="reference internal" href="dihedral_zero.html"><em>zero</em></a></td>
|
||||
<td><a class="reference internal" href="dihedral_hybrid.html"><em>hybrid</em></a></td>
|
||||
<td><a class="reference internal" href="dihedral_charmm.html"><em>charmm (ko)</em></a></td>
|
||||
<td><a class="reference internal" href="dihedral_class2.html"><em>class2 (o)</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-even"><td><a class="reference internal" href="dihedral_harmonic.html"><em>harmonic (io)</em></a></td>
|
||||
<tr class="row-even"><td><a class="reference internal" href="dihedral_class2.html"><em>class2 (o)</em></a></td>
|
||||
<td><a class="reference internal" href="dihedral_harmonic.html"><em>harmonic (io)</em></a></td>
|
||||
<td><a class="reference internal" href="dihedral_helix.html"><em>helix (o)</em></a></td>
|
||||
<td><a class="reference internal" href="dihedral_multi_harmonic.html"><em>multi/harmonic (o)</em></a></td>
|
||||
<td><a class="reference internal" href="dihedral_opls.html"><em>opls (iko)</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="dihedral_opls.html"><em>opls (iko)</em></a></td>
|
||||
<td> </td>
|
||||
<td> </td>
|
||||
<td> </td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@ -1405,21 +1410,21 @@ letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
|
||||
KOKKOS, o = USER-OMP, t = OPT.</p>
|
||||
<table border="1" class="docutils">
|
||||
<colgroup>
|
||||
<col width="22%" />
|
||||
<col width="27%" />
|
||||
<col width="27%" />
|
||||
<col width="24%" />
|
||||
<col width="22%" />
|
||||
</colgroup>
|
||||
<tbody valign="top">
|
||||
<tr class="row-odd"><td><a class="reference internal" href="improper_none.html"><em>none</em></a></td>
|
||||
<td><a class="reference internal" href="improper_zero.html"><em>zero</em></a></td>
|
||||
<td><a class="reference internal" href="improper_hybrid.html"><em>hybrid</em></a></td>
|
||||
<td><a class="reference internal" href="improper_class2.html"><em>class2 (o)</em></a></td>
|
||||
<td><a class="reference internal" href="improper_cvff.html"><em>cvff (io)</em></a></td>
|
||||
</tr>
|
||||
<tr class="row-even"><td><a class="reference internal" href="improper_harmonic.html"><em>harmonic (ko)</em></a></td>
|
||||
<tr class="row-even"><td><a class="reference internal" href="improper_cvff.html"><em>cvff (io)</em></a></td>
|
||||
<td><a class="reference internal" href="improper_harmonic.html"><em>harmonic (ko)</em></a></td>
|
||||
<td><a class="reference internal" href="improper_umbrella.html"><em>umbrella (o)</em></a></td>
|
||||
<td> </td>
|
||||
<td> </td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
|
||||
@ -797,6 +797,7 @@ letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
|
||||
KOKKOS, o = USER-OMP, t = OPT.
|
||||
|
||||
"none"_pair_none.html,
|
||||
"zero"_pair_zero.html,
|
||||
"hybrid"_pair_hybrid.html,
|
||||
"hybrid/overlay"_pair_hybrid.html,
|
||||
"adp (o)"_pair_adp.html,
|
||||
@ -969,6 +970,7 @@ letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
|
||||
KOKKOS, o = USER-OMP, t = OPT.
|
||||
|
||||
"none"_bond_none.html,
|
||||
"zero"_bond_zero.html,
|
||||
"hybrid"_bond_hybrid.html,
|
||||
"class2 (o)"_bond_class2.html,
|
||||
"fene (ko)"_bond_fene.html,
|
||||
@ -999,6 +1001,7 @@ letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
|
||||
KOKKOS, o = USER-OMP, t = OPT.
|
||||
|
||||
"none"_angle_none.html,
|
||||
"zero"_angle_zero.html,
|
||||
"hybrid"_angle_hybrid.html,
|
||||
"charmm (ko)"_angle_charmm.html,
|
||||
"class2 (o)"_angle_class2.html,
|
||||
@ -1034,6 +1037,7 @@ letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
|
||||
KOKKOS, o = USER-OMP, t = OPT.
|
||||
|
||||
"none"_dihedral_none.html,
|
||||
"zero"_dihedral_zero.html,
|
||||
"hybrid"_dihedral_hybrid.html,
|
||||
"charmm (ko)"_dihedral_charmm.html,
|
||||
"class2 (o)"_dihedral_class2.html,
|
||||
@ -1065,6 +1069,7 @@ letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
|
||||
KOKKOS, o = USER-OMP, t = OPT.
|
||||
|
||||
"none"_improper_none.html,
|
||||
"zero"_improper_zero.html,
|
||||
"hybrid"_improper_hybrid.html,
|
||||
"class2 (o)"_improper_class2.html,
|
||||
"cvff (io)"_improper_cvff.html,
|
||||
|
||||
@ -507,7 +507,7 @@ name links to a sub-section below with more details.</p>
|
||||
<td>python</td>
|
||||
<td>lib/python</td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="#reax"><span>REAX</span></a></td>
|
||||
<tr class="row-odd"><td><a class="reference internal" href="Section_tools.html#reax"><span>REAX</span></a></td>
|
||||
<td>ReaxFF potential</td>
|
||||
<td>Aidan Thompson (Sandia)</td>
|
||||
<td><a class="reference internal" href="pair_reax.html"><em>pair_style reax</em></a></td>
|
||||
|
||||
@ -5,7 +5,7 @@
|
||||
LAMMPS Documentation
|
||||
====================
|
||||
|
||||
17 Feb 2016 version
|
||||
22 Feb 2016 version
|
||||
-------------------
|
||||
|
||||
Version info:
|
||||
|
||||
@ -583,63 +583,63 @@ is built with the :doc:`appropriate accelerated package <Section_accelerate>`.
|
||||
letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
|
||||
KOKKOS, o = USER-OMP, t = OPT.
|
||||
|
||||
+----------------------------------------------------+-------------------------------------------------------+-----------------------------------------------------------+-----------------------------------------------------+
|
||||
| :doc:`none <pair_none>` | :doc:`hybrid <pair_hybrid>` | :doc:`hybrid/overlay <pair_hybrid>` | :doc:`adp (o) <pair_adp>` |
|
||||
+----------------------------------------------------+-------------------------------------------------------+-----------------------------------------------------------+-----------------------------------------------------+
|
||||
| :doc:`airebo (o) <pair_airebo>` | :doc:`beck (go) <pair_beck>` | :doc:`body <pair_body>` | :doc:`bop <pair_bop>` |
|
||||
+----------------------------------------------------+-------------------------------------------------------+-----------------------------------------------------------+-----------------------------------------------------+
|
||||
| :doc:`born (go) <pair_born>` | :doc:`born/coul/long (cgo) <pair_born>` | :doc:`born/coul/long/cs <pair_born>` | :doc:`born/coul/msm (o) <pair_born>` |
|
||||
+----------------------------------------------------+-------------------------------------------------------+-----------------------------------------------------------+-----------------------------------------------------+
|
||||
| :doc:`born/coul/wolf (go) <pair_born>` | :doc:`brownian (o) <pair_brownian>` | :doc:`brownian/poly (o) <pair_brownian>` | :doc:`buck (cgkio) <pair_buck>` |
|
||||
+----------------------------------------------------+-------------------------------------------------------+-----------------------------------------------------------+-----------------------------------------------------+
|
||||
| :doc:`buck/coul/cut (cgkio) <pair_buck>` | :doc:`buck/coul/long (cgkio) <pair_buck>` | :doc:`buck/coul/long/cs <pair_buck>` | :doc:`buck/coul/msm (o) <pair_buck>` |
|
||||
+----------------------------------------------------+-------------------------------------------------------+-----------------------------------------------------------+-----------------------------------------------------+
|
||||
| :doc:`buck/long/coul/long (o) <pair_buck_long>` | :doc:`colloid (go) <pair_colloid>` | :doc:`comb (o) <pair_comb>` | :doc:`comb3 <pair_comb>` |
|
||||
+----------------------------------------------------+-------------------------------------------------------+-----------------------------------------------------------+-----------------------------------------------------+
|
||||
| :doc:`coul/cut (gko) <pair_coul>` | :doc:`coul/debye (gko) <pair_coul>` | :doc:`coul/dsf (gko) <pair_coul>` | :doc:`coul/long (gko) <pair_coul>` |
|
||||
+----------------------------------------------------+-------------------------------------------------------+-----------------------------------------------------------+-----------------------------------------------------+
|
||||
| :doc:`coul/long/cs <pair_coul>` | :doc:`coul/msm <pair_coul>` | :doc:`coul/streitz <pair_coul>` | :doc:`coul/wolf (ko) <pair_coul>` |
|
||||
+----------------------------------------------------+-------------------------------------------------------+-----------------------------------------------------------+-----------------------------------------------------+
|
||||
| :doc:`dpd (o) <pair_dpd>` | :doc:`dpd/tstat (o) <pair_dpd>` | :doc:`dsmc <pair_dsmc>` | :doc:`eam (cgkot) <pair_eam>` |
|
||||
+----------------------------------------------------+-------------------------------------------------------+-----------------------------------------------------------+-----------------------------------------------------+
|
||||
| :doc:`eam/alloy (cgkot) <pair_eam>` | :doc:`eam/fs (cgkot) <pair_eam>` | :doc:`eim (o) <pair_eim>` | :doc:`gauss (go) <pair_gauss>` |
|
||||
+----------------------------------------------------+-------------------------------------------------------+-----------------------------------------------------------+-----------------------------------------------------+
|
||||
| :doc:`gayberne (gio) <pair_gayberne>` | :doc:`gran/hertz/history (o) <pair_gran>` | :doc:`gran/hooke (co) <pair_gran>` | :doc:`gran/hooke/history (o) <pair_gran>` |
|
||||
+----------------------------------------------------+-------------------------------------------------------+-----------------------------------------------------------+-----------------------------------------------------+
|
||||
| :doc:`hbond/dreiding/lj (o) <pair_hbond_dreiding>` | :doc:`hbond/dreiding/morse (o) <pair_hbond_dreiding>` | :doc:`kim <pair_kim>` | :doc:`lcbop <pair_lcbop>` |
|
||||
+----------------------------------------------------+-------------------------------------------------------+-----------------------------------------------------------+-----------------------------------------------------+
|
||||
| :doc:`line/lj <pair_line_lj>` | :doc:`lj/charmm/coul/charmm (cko) <pair_charmm>` | :doc:`lj/charmm/coul/charmm/implicit (cko) <pair_charmm>` | :doc:`lj/charmm/coul/long (cgiko) <pair_charmm>` |
|
||||
+----------------------------------------------------+-------------------------------------------------------+-----------------------------------------------------------+-----------------------------------------------------+
|
||||
| :doc:`lj/charmm/coul/msm <pair_charmm>` | :doc:`lj/class2 (cgko) <pair_class2>` | :doc:`lj/class2/coul/cut (cko) <pair_class2>` | :doc:`lj/class2/coul/long (cgko) <pair_class2>` |
|
||||
+----------------------------------------------------+-------------------------------------------------------+-----------------------------------------------------------+-----------------------------------------------------+
|
||||
| :doc:`lj/cubic (go) <pair_lj_cubic>` | :doc:`lj/cut (cgikot) <pair_lj>` | :doc:`lj/cut/coul/cut (cgko) <pair_lj>` | :doc:`lj/cut/coul/debye (cgko) <pair_lj>` |
|
||||
+----------------------------------------------------+-------------------------------------------------------+-----------------------------------------------------------+-----------------------------------------------------+
|
||||
| :doc:`lj/cut/coul/dsf (gko) <pair_lj>` | :doc:`lj/cut/coul/long (cgikot) <pair_lj>` | :doc:`lj/cut/coul/long/cs <pair_lj>` | :doc:`lj/cut/coul/msm (go) <pair_lj>` |
|
||||
+----------------------------------------------------+-------------------------------------------------------+-----------------------------------------------------------+-----------------------------------------------------+
|
||||
| :doc:`lj/cut/dipole/cut (go) <pair_dipole>` | :doc:`lj/cut/dipole/long <pair_dipole>` | :doc:`lj/cut/tip4p/cut (o) <pair_lj>` | :doc:`lj/cut/tip4p/long (ot) <pair_lj>` |
|
||||
+----------------------------------------------------+-------------------------------------------------------+-----------------------------------------------------------+-----------------------------------------------------+
|
||||
| :doc:`lj/expand (cgko) <pair_lj_expand>` | :doc:`lj/gromacs (cgko) <pair_gromacs>` | :doc:`lj/gromacs/coul/gromacs (cko) <pair_gromacs>` | :doc:`lj/long/coul/long (o) <pair_lj_long>` |
|
||||
+----------------------------------------------------+-------------------------------------------------------+-----------------------------------------------------------+-----------------------------------------------------+
|
||||
| :doc:`lj/long/dipole/long <pair_dipole>` | :doc:`lj/long/tip4p/long <pair_lj_long>` | :doc:`lj/smooth (co) <pair_lj_smooth>` | :doc:`lj/smooth/linear (o) <pair_lj_smooth_linear>` |
|
||||
+----------------------------------------------------+-------------------------------------------------------+-----------------------------------------------------------+-----------------------------------------------------+
|
||||
| :doc:`lj96/cut (cgo) <pair_lj96>` | :doc:`lubricate (o) <pair_lubricate>` | :doc:`lubricate/poly (o) <pair_lubricate>` | :doc:`lubricateU <pair_lubricateU>` |
|
||||
+----------------------------------------------------+-------------------------------------------------------+-----------------------------------------------------------+-----------------------------------------------------+
|
||||
| :doc:`lubricateU/poly <pair_lubricateU>` | :doc:`meam (o) <pair_meam>` | :doc:`mie/cut (o) <pair_mie>` | :doc:`morse (cgot) <pair_morse>` |
|
||||
+----------------------------------------------------+-------------------------------------------------------+-----------------------------------------------------------+-----------------------------------------------------+
|
||||
| :doc:`nb3b/harmonic (o) <pair_nb3b_harmonic>` | :doc:`nm/cut (o) <pair_nm>` | :doc:`nm/cut/coul/cut (o) <pair_nm>` | :doc:`nm/cut/coul/long (o) <pair_nm>` |
|
||||
+----------------------------------------------------+-------------------------------------------------------+-----------------------------------------------------------+-----------------------------------------------------+
|
||||
| :doc:`peri/eps <pair_peri>` | :doc:`peri/lps (o) <pair_peri>` | :doc:`peri/pmb (o) <pair_peri>` | :doc:`peri/ves <pair_peri>` |
|
||||
+----------------------------------------------------+-------------------------------------------------------+-----------------------------------------------------------+-----------------------------------------------------+
|
||||
| :doc:`polymorphic <pair_polymorphic>` | :doc:`reax <pair_reax>` | :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:`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:`vashishta (o) <pair_vashishta>` | :doc:`yukawa (go) <pair_yukawa>` |
|
||||
+----------------------------------------------------+-------------------------------------------------------+-----------------------------------------------------------+-----------------------------------------------------+
|
||||
| :doc:`yukawa/colloid (go) <pair_yukawa_colloid>` | :doc:`zbl (go) <pair_zbl>` | | |
|
||||
+----------------------------------------------------+-------------------------------------------------------+-----------------------------------------------------------+-----------------------------------------------------+
|
||||
+-----------------------------------------------------+----------------------------------------------------+-------------------------------------------------------+-----------------------------------------------------------+
|
||||
| :doc:`none <pair_none>` | :doc:`zero <pair_zero>` | :doc:`hybrid <pair_hybrid>` | :doc:`hybrid/overlay <pair_hybrid>` |
|
||||
+-----------------------------------------------------+----------------------------------------------------+-------------------------------------------------------+-----------------------------------------------------------+
|
||||
| :doc:`adp (o) <pair_adp>` | :doc:`airebo (o) <pair_airebo>` | :doc:`beck (go) <pair_beck>` | :doc:`body <pair_body>` |
|
||||
+-----------------------------------------------------+----------------------------------------------------+-------------------------------------------------------+-----------------------------------------------------------+
|
||||
| :doc:`bop <pair_bop>` | :doc:`born (go) <pair_born>` | :doc:`born/coul/long (cgo) <pair_born>` | :doc:`born/coul/long/cs <pair_born>` |
|
||||
+-----------------------------------------------------+----------------------------------------------------+-------------------------------------------------------+-----------------------------------------------------------+
|
||||
| :doc:`born/coul/msm (o) <pair_born>` | :doc:`born/coul/wolf (go) <pair_born>` | :doc:`brownian (o) <pair_brownian>` | :doc:`brownian/poly (o) <pair_brownian>` |
|
||||
+-----------------------------------------------------+----------------------------------------------------+-------------------------------------------------------+-----------------------------------------------------------+
|
||||
| :doc:`buck (cgkio) <pair_buck>` | :doc:`buck/coul/cut (cgkio) <pair_buck>` | :doc:`buck/coul/long (cgkio) <pair_buck>` | :doc:`buck/coul/long/cs <pair_buck>` |
|
||||
+-----------------------------------------------------+----------------------------------------------------+-------------------------------------------------------+-----------------------------------------------------------+
|
||||
| :doc:`buck/coul/msm (o) <pair_buck>` | :doc:`buck/long/coul/long (o) <pair_buck_long>` | :doc:`colloid (go) <pair_colloid>` | :doc:`comb (o) <pair_comb>` |
|
||||
+-----------------------------------------------------+----------------------------------------------------+-------------------------------------------------------+-----------------------------------------------------------+
|
||||
| :doc:`comb3 <pair_comb>` | :doc:`coul/cut (gko) <pair_coul>` | :doc:`coul/debye (gko) <pair_coul>` | :doc:`coul/dsf (gko) <pair_coul>` |
|
||||
+-----------------------------------------------------+----------------------------------------------------+-------------------------------------------------------+-----------------------------------------------------------+
|
||||
| :doc:`coul/long (gko) <pair_coul>` | :doc:`coul/long/cs <pair_coul>` | :doc:`coul/msm <pair_coul>` | :doc:`coul/streitz <pair_coul>` |
|
||||
+-----------------------------------------------------+----------------------------------------------------+-------------------------------------------------------+-----------------------------------------------------------+
|
||||
| :doc:`coul/wolf (ko) <pair_coul>` | :doc:`dpd (o) <pair_dpd>` | :doc:`dpd/tstat (o) <pair_dpd>` | :doc:`dsmc <pair_dsmc>` |
|
||||
+-----------------------------------------------------+----------------------------------------------------+-------------------------------------------------------+-----------------------------------------------------------+
|
||||
| :doc:`eam (cgkot) <pair_eam>` | :doc:`eam/alloy (cgkot) <pair_eam>` | :doc:`eam/fs (cgkot) <pair_eam>` | :doc:`eim (o) <pair_eim>` |
|
||||
+-----------------------------------------------------+----------------------------------------------------+-------------------------------------------------------+-----------------------------------------------------------+
|
||||
| :doc:`gauss (go) <pair_gauss>` | :doc:`gayberne (gio) <pair_gayberne>` | :doc:`gran/hertz/history (o) <pair_gran>` | :doc:`gran/hooke (co) <pair_gran>` |
|
||||
+-----------------------------------------------------+----------------------------------------------------+-------------------------------------------------------+-----------------------------------------------------------+
|
||||
| :doc:`gran/hooke/history (o) <pair_gran>` | :doc:`hbond/dreiding/lj (o) <pair_hbond_dreiding>` | :doc:`hbond/dreiding/morse (o) <pair_hbond_dreiding>` | :doc:`kim <pair_kim>` |
|
||||
+-----------------------------------------------------+----------------------------------------------------+-------------------------------------------------------+-----------------------------------------------------------+
|
||||
| :doc:`lcbop <pair_lcbop>` | :doc:`line/lj <pair_line_lj>` | :doc:`lj/charmm/coul/charmm (cko) <pair_charmm>` | :doc:`lj/charmm/coul/charmm/implicit (cko) <pair_charmm>` |
|
||||
+-----------------------------------------------------+----------------------------------------------------+-------------------------------------------------------+-----------------------------------------------------------+
|
||||
| :doc:`lj/charmm/coul/long (cgiko) <pair_charmm>` | :doc:`lj/charmm/coul/msm <pair_charmm>` | :doc:`lj/class2 (cgko) <pair_class2>` | :doc:`lj/class2/coul/cut (cko) <pair_class2>` |
|
||||
+-----------------------------------------------------+----------------------------------------------------+-------------------------------------------------------+-----------------------------------------------------------+
|
||||
| :doc:`lj/class2/coul/long (cgko) <pair_class2>` | :doc:`lj/cubic (go) <pair_lj_cubic>` | :doc:`lj/cut (cgikot) <pair_lj>` | :doc:`lj/cut/coul/cut (cgko) <pair_lj>` |
|
||||
+-----------------------------------------------------+----------------------------------------------------+-------------------------------------------------------+-----------------------------------------------------------+
|
||||
| :doc:`lj/cut/coul/debye (cgko) <pair_lj>` | :doc:`lj/cut/coul/dsf (gko) <pair_lj>` | :doc:`lj/cut/coul/long (cgikot) <pair_lj>` | :doc:`lj/cut/coul/long/cs <pair_lj>` |
|
||||
+-----------------------------------------------------+----------------------------------------------------+-------------------------------------------------------+-----------------------------------------------------------+
|
||||
| :doc:`lj/cut/coul/msm (go) <pair_lj>` | :doc:`lj/cut/dipole/cut (go) <pair_dipole>` | :doc:`lj/cut/dipole/long <pair_dipole>` | :doc:`lj/cut/tip4p/cut (o) <pair_lj>` |
|
||||
+-----------------------------------------------------+----------------------------------------------------+-------------------------------------------------------+-----------------------------------------------------------+
|
||||
| :doc:`lj/cut/tip4p/long (ot) <pair_lj>` | :doc:`lj/expand (cgko) <pair_lj_expand>` | :doc:`lj/gromacs (cgko) <pair_gromacs>` | :doc:`lj/gromacs/coul/gromacs (cko) <pair_gromacs>` |
|
||||
+-----------------------------------------------------+----------------------------------------------------+-------------------------------------------------------+-----------------------------------------------------------+
|
||||
| :doc:`lj/long/coul/long (o) <pair_lj_long>` | :doc:`lj/long/dipole/long <pair_dipole>` | :doc:`lj/long/tip4p/long <pair_lj_long>` | :doc:`lj/smooth (co) <pair_lj_smooth>` |
|
||||
+-----------------------------------------------------+----------------------------------------------------+-------------------------------------------------------+-----------------------------------------------------------+
|
||||
| :doc:`lj/smooth/linear (o) <pair_lj_smooth_linear>` | :doc:`lj96/cut (cgo) <pair_lj96>` | :doc:`lubricate (o) <pair_lubricate>` | :doc:`lubricate/poly (o) <pair_lubricate>` |
|
||||
+-----------------------------------------------------+----------------------------------------------------+-------------------------------------------------------+-----------------------------------------------------------+
|
||||
| :doc:`lubricateU <pair_lubricateU>` | :doc:`lubricateU/poly <pair_lubricateU>` | :doc:`meam (o) <pair_meam>` | :doc:`mie/cut (o) <pair_mie>` |
|
||||
+-----------------------------------------------------+----------------------------------------------------+-------------------------------------------------------+-----------------------------------------------------------+
|
||||
| :doc:`morse (cgot) <pair_morse>` | :doc:`nb3b/harmonic (o) <pair_nb3b_harmonic>` | :doc:`nm/cut (o) <pair_nm>` | :doc:`nm/cut/coul/cut (o) <pair_nm>` |
|
||||
+-----------------------------------------------------+----------------------------------------------------+-------------------------------------------------------+-----------------------------------------------------------+
|
||||
| :doc:`nm/cut/coul/long (o) <pair_nm>` | :doc:`peri/eps <pair_peri>` | :doc:`peri/lps (o) <pair_peri>` | :doc:`peri/pmb (o) <pair_peri>` |
|
||||
+-----------------------------------------------------+----------------------------------------------------+-------------------------------------------------------+-----------------------------------------------------------+
|
||||
| :doc:`peri/ves <pair_peri>` | :doc:`polymorphic <pair_polymorphic>` | :doc:`reax <pair_reax>` | :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:`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:`vashishta (o) <pair_vashishta>` |
|
||||
+-----------------------------------------------------+----------------------------------------------------+-------------------------------------------------------+-----------------------------------------------------------+
|
||||
| :doc:`yukawa (go) <pair_yukawa>` | :doc:`yukawa/colloid (go) <pair_yukawa_colloid>` | :doc:`zbl (go) <pair_zbl>` | |
|
||||
+-----------------------------------------------------+----------------------------------------------------+-------------------------------------------------------+-----------------------------------------------------------+
|
||||
|
||||
These are additional pair styles in USER packages, which can be used
|
||||
if :ref:`LAMMPS is built with the appropriate package <start_3>`.
|
||||
@ -684,13 +684,13 @@ is built with the :doc:`appropriate accelerated package <Section_accelerate>`.
|
||||
letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
|
||||
KOKKOS, o = USER-OMP, t = OPT.
|
||||
|
||||
+-------------------------------------------+--------------------------------------+---------------------------------+---------------------------------------+
|
||||
| :doc:`none <bond_none>` | :doc:`hybrid <bond_hybrid>` | :doc:`class2 (o) <bond_class2>` | :doc:`fene (ko) <bond_fene>` |
|
||||
+-------------------------------------------+--------------------------------------+---------------------------------+---------------------------------------+
|
||||
| :doc:`fene/expand (o) <bond_fene_expand>` | :doc:`harmonic (ko) <bond_harmonic>` | :doc:`morse (o) <bond_morse>` | :doc:`nonlinear (o) <bond_nonlinear>` |
|
||||
+-------------------------------------------+--------------------------------------+---------------------------------+---------------------------------------+
|
||||
| :doc:`quartic (o) <bond_quartic>` | :doc:`table (o) <bond_table>` | | |
|
||||
+-------------------------------------------+--------------------------------------+---------------------------------+---------------------------------------+
|
||||
+---------------------------------------+-------------------------------------------+--------------------------------------+---------------------------------+
|
||||
| :doc:`none <bond_none>` | :doc:`zero <bond_zero>` | :doc:`hybrid <bond_hybrid>` | :doc:`class2 (o) <bond_class2>` |
|
||||
+---------------------------------------+-------------------------------------------+--------------------------------------+---------------------------------+
|
||||
| :doc:`fene (ko) <bond_fene>` | :doc:`fene/expand (o) <bond_fene_expand>` | :doc:`harmonic (ko) <bond_harmonic>` | :doc:`morse (o) <bond_morse>` |
|
||||
+---------------------------------------+-------------------------------------------+--------------------------------------+---------------------------------+
|
||||
| :doc:`nonlinear (o) <bond_nonlinear>` | :doc:`quartic (o) <bond_quartic>` | :doc:`table (o) <bond_table>` | |
|
||||
+---------------------------------------+-------------------------------------------+--------------------------------------+---------------------------------+
|
||||
|
||||
These are additional bond styles in USER packages, which can be used
|
||||
if :ref:`LAMMPS is built with the appropriate package <start_3>`.
|
||||
@ -713,13 +713,13 @@ LAMMPS is built with the :doc:`appropriate accelerated package <Section_accelera
|
||||
letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
|
||||
KOKKOS, o = USER-OMP, t = OPT.
|
||||
|
||||
+----------------------------------------+----------------------------------------------+----------------------------------------------------+--------------------------------------------------+
|
||||
| :doc:`none <angle_none>` | :doc:`hybrid <angle_hybrid>` | :doc:`charmm (ko) <angle_charmm>` | :doc:`class2 (o) <angle_class2>` |
|
||||
+----------------------------------------+----------------------------------------------+----------------------------------------------------+--------------------------------------------------+
|
||||
| :doc:`cosine (o) <angle_cosine>` | :doc:`cosine/delta (o) <angle_cosine_delta>` | :doc:`cosine/periodic (o) <angle_cosine_periodic>` | :doc:`cosine/squared (o) <angle_cosine_squared>` |
|
||||
+----------------------------------------+----------------------------------------------+----------------------------------------------------+--------------------------------------------------+
|
||||
| :doc:`harmonic (iko) <angle_harmonic>` | :doc:`table (o) <angle_table>` | | |
|
||||
+----------------------------------------+----------------------------------------------+----------------------------------------------------+--------------------------------------------------+
|
||||
+--------------------------------------------------+----------------------------------------+----------------------------------------------+----------------------------------------------------+
|
||||
| :doc:`none <angle_none>` | :doc:`zero <angle_zero>` | :doc:`hybrid <angle_hybrid>` | :doc:`charmm (ko) <angle_charmm>` |
|
||||
+--------------------------------------------------+----------------------------------------+----------------------------------------------+----------------------------------------------------+
|
||||
| :doc:`class2 (o) <angle_class2>` | :doc:`cosine (o) <angle_cosine>` | :doc:`cosine/delta (o) <angle_cosine_delta>` | :doc:`cosine/periodic (o) <angle_cosine_periodic>` |
|
||||
+--------------------------------------------------+----------------------------------------+----------------------------------------------+----------------------------------------------------+
|
||||
| :doc:`cosine/squared (o) <angle_cosine_squared>` | :doc:`harmonic (iko) <angle_harmonic>` | :doc:`table (o) <angle_table>` | |
|
||||
+--------------------------------------------------+----------------------------------------+----------------------------------------------+----------------------------------------------------+
|
||||
|
||||
These are additional angle styles in USER packages, which can be used
|
||||
if :ref:`LAMMPS is built with the appropriate package <start_3>`.
|
||||
@ -744,11 +744,13 @@ be used if LAMMPS is built with the :doc:`appropriate accelerated package <Secti
|
||||
letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
|
||||
KOKKOS, o = USER-OMP, t = OPT.
|
||||
|
||||
+------------------------------------------+-----------------------------------+-----------------------------------------------------+-------------------------------------+
|
||||
| :doc:`none <dihedral_none>` | :doc:`hybrid <dihedral_hybrid>` | :doc:`charmm (ko) <dihedral_charmm>` | :doc:`class2 (o) <dihedral_class2>` |
|
||||
+------------------------------------------+-----------------------------------+-----------------------------------------------------+-------------------------------------+
|
||||
| :doc:`harmonic (io) <dihedral_harmonic>` | :doc:`helix (o) <dihedral_helix>` | :doc:`multi/harmonic (o) <dihedral_multi_harmonic>` | :doc:`opls (iko) <dihedral_opls>` |
|
||||
+------------------------------------------+-----------------------------------+-----------------------------------------------------+-------------------------------------+
|
||||
+-------------------------------------+------------------------------------------+-----------------------------------+-----------------------------------------------------+
|
||||
| :doc:`none <dihedral_none>` | :doc:`zero <dihedral_zero>` | :doc:`hybrid <dihedral_hybrid>` | :doc:`charmm (ko) <dihedral_charmm>` |
|
||||
+-------------------------------------+------------------------------------------+-----------------------------------+-----------------------------------------------------+
|
||||
| :doc:`class2 (o) <dihedral_class2>` | :doc:`harmonic (io) <dihedral_harmonic>` | :doc:`helix (o) <dihedral_helix>` | :doc:`multi/harmonic (o) <dihedral_multi_harmonic>` |
|
||||
+-------------------------------------+------------------------------------------+-----------------------------------+-----------------------------------------------------+
|
||||
| :doc:`opls (iko) <dihedral_opls>` | | | |
|
||||
+-------------------------------------+------------------------------------------+-----------------------------------+-----------------------------------------------------+
|
||||
|
||||
These are additional dihedral styles in USER packages, which can be
|
||||
used if :ref:`LAMMPS is built with the appropriate package <start_3>`.
|
||||
@ -773,11 +775,11 @@ be used if LAMMPS is built with the :doc:`appropriate accelerated package <Secti
|
||||
letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k =
|
||||
KOKKOS, o = USER-OMP, t = OPT.
|
||||
|
||||
+------------------------------------------+-----------------------------------------+-------------------------------------+----------------------------------+
|
||||
| :doc:`none <improper_none>` | :doc:`hybrid <improper_hybrid>` | :doc:`class2 (o) <improper_class2>` | :doc:`cvff (io) <improper_cvff>` |
|
||||
+------------------------------------------+-----------------------------------------+-------------------------------------+----------------------------------+
|
||||
| :doc:`harmonic (ko) <improper_harmonic>` | :doc:`umbrella (o) <improper_umbrella>` | | |
|
||||
+------------------------------------------+-----------------------------------------+-------------------------------------+----------------------------------+
|
||||
+----------------------------------+------------------------------------------+-----------------------------------------+-------------------------------------+
|
||||
| :doc:`none <improper_none>` | :doc:`zero <improper_zero>` | :doc:`hybrid <improper_hybrid>` | :doc:`class2 (o) <improper_class2>` |
|
||||
+----------------------------------+------------------------------------------+-----------------------------------------+-------------------------------------+
|
||||
| :doc:`cvff (io) <improper_cvff>` | :doc:`harmonic (ko) <improper_harmonic>` | :doc:`umbrella (o) <improper_umbrella>` | |
|
||||
+----------------------------------+------------------------------------------+-----------------------------------------+-------------------------------------+
|
||||
|
||||
These are additional improper styles in USER packages, which can be
|
||||
used if :ref:`LAMMPS is built with the appropriate package <start_3>`.
|
||||
|
||||
@ -20,15 +20,21 @@ Examples
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
Using an angle style of none means angle forces are not computed, even
|
||||
if triplets of angle atoms were listed in the data file read by the
|
||||
:doc:`read_data <read_data>` command.
|
||||
Using an angle style of none means angle forces and energies are not
|
||||
computed, even if triplets of angle atoms were listed in the data file
|
||||
read by the :doc:`read_data <read_data>` command.
|
||||
|
||||
See the :doc:`angle_style zero <angle_zero>` command for a way to
|
||||
calculate angle statistics, but compute no angle interactions.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
none
|
||||
|
||||
**Related commands:** none
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`angle_style zero <angle_zero>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
@ -67,6 +67,7 @@ which are included in the LAMMPS distribution. The list of these with
|
||||
links to the individual styles are given in the angle section of :ref:`this page <cmd_5>`.
|
||||
|
||||
* :doc:`angle_style none <angle_none>` - turn off angle interactions
|
||||
* :doc:`angle_style zero <angle_zero>` - topology but no interactions
|
||||
* :doc:`angle_style hybrid <angle_hybrid>` - define multiple styles of angle interactions
|
||||
|
||||
* :doc:`angle_style charmm <angle_charmm>` - CHARMM angle
|
||||
|
||||
51
doc/_sources/angle_zero.txt
Normal file
51
doc/_sources/angle_zero.txt
Normal file
@ -0,0 +1,51 @@
|
||||
.. index:: angle_style zero
|
||||
|
||||
angle_style zero command
|
||||
========================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
angle_style zero
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
angle_style zero
|
||||
angle_coeff *
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
Using an angle style of zero means angle forces and energies are not
|
||||
computed, but the geometry of angle triplets is still accessible to
|
||||
other commands.
|
||||
|
||||
As an example, the :doc:`compute angle/local <compute_angle_local>`
|
||||
command can be used to compute the theta values for the list of
|
||||
triplets of angle atoms listed in the data file read by the
|
||||
:doc:`read_data <read_data>` command. If no angle style is defined,
|
||||
this command cannot be used.
|
||||
|
||||
Note that the :doc:`angle_coeff <angle_coeff>` command must be used for
|
||||
all angle types, though no additional values are specified.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
none
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`angle_style none <angle_none>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Section_commands.html#comm
|
||||
@ -20,9 +20,12 @@ Examples
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
Using a bond style of none means bond forces are not computed, even if
|
||||
pairs of bonded atoms were listed in the data file read by the
|
||||
:doc:`read_data <read_data>` command.
|
||||
Using a bond style of none means bond forces and energies are not
|
||||
computed, even if pairs of bonded atoms were listed in the data file
|
||||
read by the :doc:`read_data <read_data>` command.
|
||||
|
||||
See the :doc:`bond_style zero <bond_zero>` command for a way to
|
||||
calculate bond statistics, but compute no bond interactions.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
@ -30,6 +33,8 @@ Restrictions
|
||||
|
||||
**Related commands:** none
|
||||
|
||||
:doc:`bond_style zero <bond_zero>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
|
||||
@ -78,6 +78,7 @@ which are included in the LAMMPS distribution. The list of these with
|
||||
links to the individual styles are given in the bond section of :ref:`this page <cmd_5>`.
|
||||
|
||||
* :doc:`bond_style none <bond_none>` - turn off bonded interactions
|
||||
* :doc:`bond_style zero <bond_zero>` - topology but no interactions
|
||||
* :doc:`bond_style hybrid <bond_hybrid>` - define multiple styles of bond interactions
|
||||
|
||||
* :doc:`bond_style class2 <bond_class2>` - COMPASS (class 2) bond
|
||||
|
||||
50
doc/_sources/bond_zero.txt
Normal file
50
doc/_sources/bond_zero.txt
Normal file
@ -0,0 +1,50 @@
|
||||
.. index:: bond_style zero
|
||||
|
||||
bond_style zero command
|
||||
=======================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
bond_style zero
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
bond_style zero
|
||||
bond_coeff *
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
Using an bond style of zero means bond forces and energies are not
|
||||
computed, but the geometry of bond pairs is still accessible to other
|
||||
commands.
|
||||
|
||||
As an example, the :doc:`compute bond/local <compute_bond_local>`
|
||||
command can be used to compute distances for the list of pairs of bond
|
||||
atoms listed in the data file read by the :doc:`read_data <read_data>`
|
||||
command. If no bond style is defined, this command cannot be used.
|
||||
|
||||
Note that the :doc:`bond_coeff <bond_coeff>` command must be used for
|
||||
all bond types, though no additional values are specified.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
none
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`bond_style none <bond_none>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Section_commands.html#comm
|
||||
@ -20,15 +20,21 @@ Examples
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
Using an dihedral style of none means dihedral forces are not
|
||||
computed, even if quadruplets of dihedral atoms were listed in the
|
||||
Using a dihedral style of none means dihedral forces and energies are
|
||||
not computed, even if quadruplets of dihedral atoms were listed in the
|
||||
data file read by the :doc:`read_data <read_data>` command.
|
||||
|
||||
See the :doc:`dihedral_style zero <dihedral_zero>` command for a way to
|
||||
calculate dihedral statistics, but compute no dihedral interactions.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
none
|
||||
|
||||
**Related commands:** none
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`dihedral_style zero <dihedral_zero>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
@ -94,6 +94,7 @@ links to the individual styles are given in the dihedral section of
|
||||
:ref:`this page <cmd_5>`.
|
||||
|
||||
* :doc:`dihedral_style none <dihedral_none>` - turn off dihedral interactions
|
||||
* :doc:`dihedral_style zero <dihedral_zero>` - topology but no interactions
|
||||
* :doc:`dihedral_style hybrid <dihedral_hybrid>` - define multiple styles of dihedral interactions
|
||||
|
||||
* :doc:`dihedral_style charmm <dihedral_charmm>` - CHARMM dihedral
|
||||
|
||||
51
doc/_sources/dihedral_zero.txt
Normal file
51
doc/_sources/dihedral_zero.txt
Normal file
@ -0,0 +1,51 @@
|
||||
.. index:: dihedral_style zero
|
||||
|
||||
dihedral_style zero command
|
||||
===========================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
dihedral_style zero
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
dihedral_style zero
|
||||
dihedral_coeff *
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
Using a dihedral style of zero means dihedral forces and energies are
|
||||
not computed, but the geometry of dihedral quadruplets is still
|
||||
accessible to other commands.
|
||||
|
||||
As an example, the :doc:`compute dihedral/local <compute_dihedral_local>` command can be used to
|
||||
compute the theta values for the list of quadruplets of dihedral atoms
|
||||
listed in the data file read by the :doc:`read_data <read_data>`
|
||||
command. If no dihedral style is defined, this command cannot be
|
||||
used.
|
||||
|
||||
Note that the :doc:`dihedral_coeff <dihedral_coeff>` command must be
|
||||
used for all dihedral types, though no additional values are
|
||||
specified.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
none
|
||||
|
||||
**Related commands:** none
|
||||
|
||||
:doc:`dihedral_style none <dihedral_none>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Section_commands.html#comm
|
||||
@ -20,15 +20,21 @@ Examples
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
Using an improper style of none means improper forces are not
|
||||
computed, even if quadruplets of improper atoms were listed in the
|
||||
Using an improper style of none means imroper forces and energies are
|
||||
not computed, even if quadruplets of improper atoms were listed in the
|
||||
data file read by the :doc:`read_data <read_data>` command.
|
||||
|
||||
See the :doc:`improper_style zero <improper_zero>` command for a way to
|
||||
calculate improper statistics, but compute no improper interactions.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
none
|
||||
|
||||
**Related commands:** none
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`improper_style zero <improper_zero>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
@ -71,6 +71,7 @@ links to the individual styles are given in the improper section of
|
||||
:ref:`this page <cmd_5>`.
|
||||
|
||||
* :doc:`improper_style none <improper_none>` - turn off improper interactions
|
||||
* :doc:`improper_style zero <improper_zero>` - topology but no interactions
|
||||
* :doc:`improper_style hybrid <improper_hybrid>` - define multiple styles of improper interactions
|
||||
|
||||
* :doc:`improper_style class2 <improper_class2>` - COMPASS (class 2) improper
|
||||
|
||||
51
doc/_sources/improper_zero.txt
Normal file
51
doc/_sources/improper_zero.txt
Normal file
@ -0,0 +1,51 @@
|
||||
.. index:: improper_style zero
|
||||
|
||||
improper_style zero command
|
||||
===========================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
improper_style zero
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
improper_style zero
|
||||
improper_coeff *
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
Using an improper style of zero means improper forces and energies are
|
||||
not computed, but the geometry of improper quadruplets is still
|
||||
accessible to other commands.
|
||||
|
||||
As an example, the :doc:`compute improper/local <compute_improper_local>` command can be used to
|
||||
compute the chi values for the list of quadruplets of improper atoms
|
||||
listed in the data file read by the :doc:`read_data <read_data>`
|
||||
command. If no improper style is defined, this command cannot be
|
||||
used.
|
||||
|
||||
Note that the :doc:`improper_coeff <improper_coeff>` command must be
|
||||
used for all improper types, though no additional values are
|
||||
specified.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
none
|
||||
|
||||
**Related commands:** none
|
||||
|
||||
:doc:`improper_style none <improper_none>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Section_commands.html#comm
|
||||
@ -20,7 +20,8 @@ Examples
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
Using a pair style of none means pair forces are not computed.
|
||||
Using a pair style of none means pair forces and energies are not
|
||||
computed.
|
||||
|
||||
With this choice, the force cutoff is 0.0, which means that only atoms
|
||||
within the neighbor skin distance (see the :doc:`neighbor <neighbor>`
|
||||
@ -35,11 +36,17 @@ distance is small, then these data structures can consume a large
|
||||
amount of memory. So you should either set the neighbor style to
|
||||
*nsq* or set the skin distance to a larger value.
|
||||
|
||||
See the :doc:`pair_style zero <pair_zero>` for a way to trigger the
|
||||
building of a neighbor lists, but compute no pairwise interactions.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
none
|
||||
|
||||
**Related commands:** none
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`pair_style zero <pair_zero>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
@ -101,6 +101,7 @@ in the pair section of :ref:`this page <cmd_5>`.
|
||||
* :doc:`pair_style none <pair_none>` - turn off pairwise interactions
|
||||
* :doc:`pair_style hybrid <pair_hybrid>` - multiple styles of pairwise interactions
|
||||
* :doc:`pair_style hybrid/overlay <pair_hybrid>` - multiple styles of superposed pairwise interactions
|
||||
* :doc:`pair_style zero <pair_zero>` - neighbor list but no interactions
|
||||
|
||||
* :doc:`pair_style adp <pair_adp>` - angular dependent potential (ADP) of Mishin
|
||||
* :doc:`pair_style airebo <pair_airebo>` - AIREBO potential of Stuart
|
||||
|
||||
65
doc/_sources/pair_zero.txt
Normal file
65
doc/_sources/pair_zero.txt
Normal file
@ -0,0 +1,65 @@
|
||||
.. index:: pair_style zero
|
||||
|
||||
pair_style zero command
|
||||
=======================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
pair_style zero cutoff
|
||||
|
||||
* zero = style name of this pair style
|
||||
cutoff = global cutoff (distance units)
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
pair_style zero
|
||||
pair_coeff * *
|
||||
pair_coeff 1 2 3.0
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
Define a global cutoff length for the purpose of building a neighbor
|
||||
list and acquiring ghost atoms, but do not compute any pairwise forces
|
||||
or energies.
|
||||
|
||||
This can be useful for fixes or computes which require a neighbor list
|
||||
to enumerate pairs of atoms within some cutoff distance, but when
|
||||
pairwise forces are not otherwise needed. Examples are the :doc:`fix bond/create <fix_bond_create>`, :doc:`compute rdf <compute_rdf>`,
|
||||
:doc:`compute voronoi/atom <compute_voronoi_atom>` commands.
|
||||
|
||||
Note that the :doc:`comm_modify cutoff <comm_modify>` command can be
|
||||
used to insure communication of ghost atoms even when a pair style is
|
||||
not defined, but it will not trigger neighbor list generation.
|
||||
|
||||
The following coefficients must be defined for each pair of atoms
|
||||
types via the :doc:`pair_coeff <pair_coeff>` command as in the examples
|
||||
above, or in the data file or restart files read by the
|
||||
:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
|
||||
commands, or by mixing as described below:
|
||||
|
||||
* cutoff (distance units)
|
||||
|
||||
This coefficient is optional. If not specified, the global cutoff
|
||||
specified in the pair_style command is used.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
none
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`pair_style none <pair_none>`
|
||||
|
||||
**Default:** none
|
||||
|
||||
|
||||
.. _lws: http://lammps.sandia.gov
|
||||
.. _ld: Manual.html
|
||||
.. _lc: Section_commands.html#comm
|
||||
@ -140,15 +140,20 @@
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
|
||||
<p>Using an angle style of none means angle forces are not computed, even
|
||||
if triplets of angle atoms were listed in the data file read by the
|
||||
<a class="reference internal" href="read_data.html"><em>read_data</em></a> command.</p>
|
||||
<p>Using an angle style of none means angle forces and energies are not
|
||||
computed, even if triplets of angle atoms were listed in the data file
|
||||
read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a> command.</p>
|
||||
<p>See the <a class="reference internal" href="angle_zero.html"><em>angle_style zero</em></a> command for a way to
|
||||
calculate angle statistics, but compute no angle interactions.</p>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
|
||||
<blockquote>
|
||||
<div>none</div></blockquote>
|
||||
<p><strong>Related commands:</strong> none</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="angle_zero.html"><em>angle_style zero</em></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
@ -18,12 +18,17 @@ angle_style none :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Using an angle style of none means angle forces are not computed, even
|
||||
if triplets of angle atoms were listed in the data file read by the
|
||||
"read_data"_read_data.html command.
|
||||
Using an angle style of none means angle forces and energies are not
|
||||
computed, even if triplets of angle atoms were listed in the data file
|
||||
read by the "read_data"_read_data.html command.
|
||||
|
||||
See the "angle_style zero"_angle_zero.html command for a way to
|
||||
calculate angle statistics, but compute no angle interactions.
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
[Related commands:] none
|
||||
[Related commands:]
|
||||
|
||||
"angle_style zero"_angle_zero.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
@ -179,6 +179,7 @@ which are included in the LAMMPS distribution. The list of these with
|
||||
links to the individual styles are given in the angle section of <a class="reference internal" href="Section_commands.html#cmd-5"><span>this page</span></a>.</p>
|
||||
<ul class="simple">
|
||||
<li><a class="reference internal" href="angle_none.html"><em>angle_style none</em></a> - turn off angle interactions</li>
|
||||
<li><a class="reference internal" href="angle_zero.html"><em>angle_style zero</em></a> - topology but no interactions</li>
|
||||
<li><a class="reference internal" href="angle_hybrid.html"><em>angle_style hybrid</em></a> - define multiple styles of angle interactions</li>
|
||||
<li><a class="reference internal" href="angle_charmm.html"><em>angle_style charmm</em></a> - CHARMM angle</li>
|
||||
<li><a class="reference internal" href="angle_class2.html"><em>angle_style class2</em></a> - COMPASS (class 2) angle</li>
|
||||
|
||||
@ -63,6 +63,7 @@ links to the individual styles are given in the angle section of "this
|
||||
page"_Section_commands.html#cmd_5.
|
||||
|
||||
"angle_style none"_angle_none.html - turn off angle interactions
|
||||
"angle_style zero"_angle_zero.html - topology but no interactions
|
||||
"angle_style hybrid"_angle_hybrid.html - define multiple styles of angle interactions :ul
|
||||
|
||||
"angle_style charmm"_angle_charmm.html - CHARMM angle
|
||||
|
||||
229
doc/angle_zero.html
Normal file
229
doc/angle_zero.html
Normal file
@ -0,0 +1,229 @@
|
||||
|
||||
|
||||
<!DOCTYPE html>
|
||||
<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
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|
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|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
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<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
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|
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<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
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<div class="section" id="angle-style-zero-command">
|
||||
<span id="index-0"></span><h1>angle_style zero command<a class="headerlink" href="#angle-style-zero-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>angle_style zero
|
||||
</pre></div>
|
||||
</div>
|
||||
</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>angle_style zero
|
||||
angle_coeff *
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
|
||||
<p>Using an angle style of zero means angle forces and energies are not
|
||||
computed, but the geometry of angle triplets is still accessible to
|
||||
other commands.</p>
|
||||
<p>As an example, the <a class="reference internal" href="compute_angle_local.html"><em>compute angle/local</em></a>
|
||||
command can be used to compute the theta values for the list of
|
||||
triplets of angle atoms listed in the data file read by the
|
||||
<a class="reference internal" href="read_data.html"><em>read_data</em></a> command. If no angle style is defined,
|
||||
this command cannot be used.</p>
|
||||
<p>Note that the <a class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a> command must be used for
|
||||
all angle types, though no additional values are specified.</p>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
|
||||
<blockquote>
|
||||
<div>none</div></blockquote>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
|
||||
<p><a class="reference internal" href="angle_none.html"><em>angle_style none</em></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
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|
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<hr/>
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© Copyright 2013 Sandia Corporation.
|
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</p>
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</div>
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Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
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|
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|
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|
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|
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FILE_SUFFIX:'.html',
|
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41
doc/angle_zero.txt
Normal file
41
doc/angle_zero.txt
Normal file
@ -0,0 +1,41 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
angle_style zero command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
angle_style zero :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
angle_style zero
|
||||
angle_coeff * :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Using an angle style of zero means angle forces and energies are not
|
||||
computed, but the geometry of angle triplets is still accessible to
|
||||
other commands.
|
||||
|
||||
As an example, the "compute angle/local"_compute_angle_local.html
|
||||
command can be used to compute the theta values for the list of
|
||||
triplets of angle atoms listed in the data file read by the
|
||||
"read_data"_read_data.html command. If no angle style is defined,
|
||||
this command cannot be used.
|
||||
|
||||
Note that the "angle_coeff"_angle_coeff.html command must be used for
|
||||
all angle types, though no additional values are specified.
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"angle_style none"_angle_none.html
|
||||
|
||||
[Default:] none
|
||||
@ -140,15 +140,18 @@
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
|
||||
<p>Using a bond style of none means bond forces are not computed, even if
|
||||
pairs of bonded atoms were listed in the data file read by the
|
||||
<a class="reference internal" href="read_data.html"><em>read_data</em></a> command.</p>
|
||||
<p>Using a bond style of none means bond forces and energies are not
|
||||
computed, even if pairs of bonded atoms were listed in the data file
|
||||
read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a> command.</p>
|
||||
<p>See the <a class="reference internal" href="bond_zero.html"><em>bond_style zero</em></a> command for a way to
|
||||
calculate bond statistics, but compute no bond interactions.</p>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
|
||||
<blockquote>
|
||||
<div>none</div></blockquote>
|
||||
<p><strong>Related commands:</strong> none</p>
|
||||
<p><a class="reference internal" href="bond_zero.html"><em>bond_style zero</em></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
@ -18,12 +18,17 @@ bond_style none :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Using a bond style of none means bond forces are not computed, even if
|
||||
pairs of bonded atoms were listed in the data file read by the
|
||||
"read_data"_read_data.html command.
|
||||
Using a bond style of none means bond forces and energies are not
|
||||
computed, even if pairs of bonded atoms were listed in the data file
|
||||
read by the "read_data"_read_data.html command.
|
||||
|
||||
See the "bond_style zero"_bond_zero.html command for a way to
|
||||
calculate bond statistics, but compute no bond interactions.
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
[Related commands:] none
|
||||
|
||||
"bond_style zero"_bond_zero.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
@ -189,6 +189,7 @@ which are included in the LAMMPS distribution. The list of these with
|
||||
links to the individual styles are given in the bond section of <a class="reference internal" href="Section_commands.html#cmd-5"><span>this page</span></a>.</p>
|
||||
<ul class="simple">
|
||||
<li><a class="reference internal" href="bond_none.html"><em>bond_style none</em></a> - turn off bonded interactions</li>
|
||||
<li><a class="reference internal" href="bond_zero.html"><em>bond_style zero</em></a> - topology but no interactions</li>
|
||||
<li><a class="reference internal" href="bond_hybrid.html"><em>bond_style hybrid</em></a> - define multiple styles of bond interactions</li>
|
||||
<li><a class="reference internal" href="bond_class2.html"><em>bond_style class2</em></a> - COMPASS (class 2) bond</li>
|
||||
<li><a class="reference internal" href="bond_fene.html"><em>bond_style fene</em></a> - FENE (finite-extensible non-linear elastic) bond</li>
|
||||
|
||||
@ -71,6 +71,7 @@ links to the individual styles are given in the bond section of "this
|
||||
page"_Section_commands.html#cmd_5.
|
||||
|
||||
"bond_style none"_bond_none.html - turn off bonded interactions
|
||||
"bond_style zero"_bond_zero.html - topology but no interactions
|
||||
"bond_style hybrid"_bond_hybrid.html - define multiple styles of bond interactions :ul
|
||||
|
||||
"bond_style class2"_bond_class2.html - COMPASS (class 2) bond
|
||||
|
||||
228
doc/bond_zero.html
Normal file
228
doc/bond_zero.html
Normal file
@ -0,0 +1,228 @@
|
||||
|
||||
|
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<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
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<div class="section" id="bond-style-zero-command">
|
||||
<span id="index-0"></span><h1>bond_style zero command<a class="headerlink" href="#bond-style-zero-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_style zero
|
||||
</pre></div>
|
||||
</div>
|
||||
</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_style zero
|
||||
bond_coeff *
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
|
||||
<p>Using an bond style of zero means bond forces and energies are not
|
||||
computed, but the geometry of bond pairs is still accessible to other
|
||||
commands.</p>
|
||||
<p>As an example, the <a class="reference internal" href="compute_bond_local.html"><em>compute bond/local</em></a>
|
||||
command can be used to compute distances for the list of pairs of bond
|
||||
atoms listed in the data file read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a>
|
||||
command. If no bond style is defined, this command cannot be used.</p>
|
||||
<p>Note that the <a class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a> command must be used for
|
||||
all bond types, though no additional values are specified.</p>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
|
||||
<blockquote>
|
||||
<div>none</div></blockquote>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
|
||||
<p><a class="reference internal" href="bond_none.html"><em>bond_style none</em></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
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© Copyright 2013 Sandia Corporation.
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40
doc/bond_zero.txt
Normal file
40
doc/bond_zero.txt
Normal file
@ -0,0 +1,40 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
bond_style zero command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
bond_style zero :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
bond_style zero
|
||||
bond_coeff * :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Using an bond style of zero means bond forces and energies are not
|
||||
computed, but the geometry of bond pairs is still accessible to other
|
||||
commands.
|
||||
|
||||
As an example, the "compute bond/local"_compute_bond_local.html
|
||||
command can be used to compute distances for the list of pairs of bond
|
||||
atoms listed in the data file read by the "read_data"_read_data.html
|
||||
command. If no bond style is defined, this command cannot be used.
|
||||
|
||||
Note that the "bond_coeff"_bond_coeff.html command must be used for
|
||||
all bond types, though no additional values are specified.
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"bond_style none"_bond_none.html
|
||||
|
||||
[Default:] none
|
||||
@ -140,15 +140,20 @@
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
|
||||
<p>Using an dihedral style of none means dihedral forces are not
|
||||
computed, even if quadruplets of dihedral atoms were listed in the
|
||||
<p>Using a dihedral style of none means dihedral forces and energies are
|
||||
not computed, even if quadruplets of dihedral atoms were listed in the
|
||||
data file read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a> command.</p>
|
||||
<p>See the <a class="reference internal" href="dihedral_zero.html"><em>dihedral_style zero</em></a> command for a way to
|
||||
calculate dihedral statistics, but compute no dihedral interactions.</p>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
|
||||
<blockquote>
|
||||
<div>none</div></blockquote>
|
||||
<p><strong>Related commands:</strong> none</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="dihedral_zero.html"><em>dihedral_style zero</em></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
@ -18,12 +18,17 @@ dihedral_style none :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Using an dihedral style of none means dihedral forces are not
|
||||
computed, even if quadruplets of dihedral atoms were listed in the
|
||||
Using a dihedral style of none means dihedral forces and energies are
|
||||
not computed, even if quadruplets of dihedral atoms were listed in the
|
||||
data file read by the "read_data"_read_data.html command.
|
||||
|
||||
See the "dihedral_style zero"_dihedral_zero.html command for a way to
|
||||
calculate dihedral statistics, but compute no dihedral interactions.
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
[Related commands:] none
|
||||
[Related commands:]
|
||||
|
||||
"dihedral_style zero"_dihedral_zero.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
@ -202,6 +202,7 @@ links to the individual styles are given in the dihedral section of
|
||||
<a class="reference internal" href="Section_commands.html#cmd-5"><span>this page</span></a>.</p>
|
||||
<ul class="simple">
|
||||
<li><a class="reference internal" href="dihedral_none.html"><em>dihedral_style none</em></a> - turn off dihedral interactions</li>
|
||||
<li><a class="reference internal" href="dihedral_zero.html"><em>dihedral_style zero</em></a> - topology but no interactions</li>
|
||||
<li><a class="reference internal" href="dihedral_hybrid.html"><em>dihedral_style hybrid</em></a> - define multiple styles of dihedral interactions</li>
|
||||
<li><a class="reference internal" href="dihedral_charmm.html"><em>dihedral_style charmm</em></a> - CHARMM dihedral</li>
|
||||
<li><a class="reference internal" href="dihedral_class2.html"><em>dihedral_style class2</em></a> - COMPASS (class 2) dihedral</li>
|
||||
|
||||
@ -86,6 +86,7 @@ links to the individual styles are given in the dihedral section of
|
||||
"this page"_Section_commands.html#cmd_5.
|
||||
|
||||
"dihedral_style none"_dihedral_none.html - turn off dihedral interactions
|
||||
"dihedral_style zero"_dihedral_zero.html - topology but no interactions
|
||||
"dihedral_style hybrid"_dihedral_hybrid.html - define multiple styles of dihedral interactions :ul
|
||||
|
||||
"dihedral_style charmm"_dihedral_charmm.html - CHARMM dihedral
|
||||
|
||||
228
doc/dihedral_zero.html
Normal file
228
doc/dihedral_zero.html
Normal file
@ -0,0 +1,228 @@
|
||||
|
||||
|
||||
<!DOCTYPE html>
|
||||
<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
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|
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|
||||
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||||
|
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|
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|
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|
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|
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|
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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|
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<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
|
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<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
|
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<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
|
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<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
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<div itemprop="articleBody">
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||||
<div class="section" id="dihedral-style-zero-command">
|
||||
<span id="index-0"></span><h1>dihedral_style zero command<a class="headerlink" href="#dihedral-style-zero-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>dihedral_style zero
|
||||
</pre></div>
|
||||
</div>
|
||||
</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>dihedral_style zero
|
||||
dihedral_coeff *
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
|
||||
<p>Using a dihedral style of zero means dihedral forces and energies are
|
||||
not computed, but the geometry of dihedral quadruplets is still
|
||||
accessible to other commands.</p>
|
||||
<p>As an example, the <a class="reference internal" href="compute_dihedral_local.html"><em>compute dihedral/local</em></a> command can be used to
|
||||
compute the theta values for the list of quadruplets of dihedral atoms
|
||||
listed in the data file read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a>
|
||||
command. If no dihedral style is defined, this command cannot be
|
||||
used.</p>
|
||||
<p>Note that the <a class="reference internal" href="dihedral_coeff.html"><em>dihedral_coeff</em></a> command must be
|
||||
used for all dihedral types, though no additional values are
|
||||
specified.</p>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
|
||||
<blockquote>
|
||||
<div>none</div></blockquote>
|
||||
<p><strong>Related commands:</strong> none</p>
|
||||
<p><a class="reference internal" href="dihedral_none.html"><em>dihedral_style none</em></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
</div>
|
||||
</div>
|
||||
|
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|
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</div>
|
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<hr/>
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<p>
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© Copyright 2013 Sandia Corporation.
|
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</p>
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43
doc/dihedral_zero.txt
Normal file
43
doc/dihedral_zero.txt
Normal file
@ -0,0 +1,43 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
dihedral_style zero command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
dihedral_style zero :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
dihedral_style zero
|
||||
dihedral_coeff * :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Using a dihedral style of zero means dihedral forces and energies are
|
||||
not computed, but the geometry of dihedral quadruplets is still
|
||||
accessible to other commands.
|
||||
|
||||
As an example, the "compute
|
||||
dihedral/local"_compute_dihedral_local.html command can be used to
|
||||
compute the theta values for the list of quadruplets of dihedral atoms
|
||||
listed in the data file read by the "read_data"_read_data.html
|
||||
command. If no dihedral style is defined, this command cannot be
|
||||
used.
|
||||
|
||||
Note that the "dihedral_coeff"_dihedral_coeff.html command must be
|
||||
used for all dihedral types, though no additional values are
|
||||
specified.
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
[Related commands:] none
|
||||
|
||||
"dihedral_style none"_dihedral_none.html
|
||||
|
||||
[Default:] none
|
||||
@ -175,7 +175,7 @@ fix 1 all langevin 1.0 1.1 100.0 48279 angmom 3.333
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
|
||||
<p>Apply a Langevin thermostat as described in <a class="reference internal" href="#schneider"><span>(Schneider)</span></a>
|
||||
<p>Apply a Langevin thermostat as described in <a class="reference internal" href="fix_langevin_eff.html#schneider"><span>(Schneider)</span></a>
|
||||
to a group of atoms which models an interaction with a background
|
||||
implicit solvent. Used with <a class="reference internal" href="fix_nve.html"><em>fix nve</em></a>, this command
|
||||
performs Brownian dynamics (BD), since the total force on each atom
|
||||
@ -203,7 +203,7 @@ dt damp), where Kb is the Boltzmann constant, T is the desired
|
||||
temperature, m is the mass of the particle, dt is the timestep size,
|
||||
and damp is the damping factor. Random numbers are used to randomize
|
||||
the direction and magnitude of this force as described in
|
||||
<a class="reference internal" href="#dunweg"><span>(Dunweg)</span></a>, where a uniform random number is used (instead of
|
||||
<a class="reference internal" href="fix_langevin_eff.html#dunweg"><span>(Dunweg)</span></a>, where a uniform random number is used (instead of
|
||||
a Gaussian random number) for speed.</p>
|
||||
<p>Note that unless you use the <em>omega</em> or <em>angmom</em> keywords, the
|
||||
thermostat effect of this fix is applied to only the translational
|
||||
|
||||
@ -234,6 +234,10 @@
|
||||
</dt>
|
||||
|
||||
|
||||
<dt><a href="angle_zero.html#index-0">angle_style zero</a>
|
||||
</dt>
|
||||
|
||||
|
||||
<dt><a href="atom_modify.html#index-0">atom_modify</a>
|
||||
</dt>
|
||||
|
||||
@ -310,6 +314,10 @@
|
||||
</dt>
|
||||
|
||||
|
||||
<dt><a href="bond_zero.html#index-0">bond_style zero</a>
|
||||
</dt>
|
||||
|
||||
|
||||
<dt><a href="boundary.html#index-0">boundary</a>
|
||||
</dt>
|
||||
|
||||
@ -835,12 +843,12 @@
|
||||
<dt><a href="dihedral_multi_harmonic.html#index-0">dihedral_style multi/harmonic</a>
|
||||
</dt>
|
||||
|
||||
</dl></td>
|
||||
<td style="width: 33%" valign="top"><dl>
|
||||
|
||||
<dt><a href="dihedral_nharmonic.html#index-0">dihedral_style nharmonic</a>
|
||||
</dt>
|
||||
|
||||
</dl></td>
|
||||
<td style="width: 33%" valign="top"><dl>
|
||||
|
||||
<dt><a href="dihedral_none.html#index-0">dihedral_style none</a>
|
||||
</dt>
|
||||
@ -858,6 +866,10 @@
|
||||
</dt>
|
||||
|
||||
|
||||
<dt><a href="dihedral_zero.html#index-0">dihedral_style zero</a>
|
||||
</dt>
|
||||
|
||||
|
||||
<dt><a href="dimension.html#index-0">dimension</a>
|
||||
</dt>
|
||||
|
||||
@ -1548,6 +1560,10 @@
|
||||
</dt>
|
||||
|
||||
|
||||
<dt><a href="improper_zero.html#index-0">improper_style zero</a>
|
||||
</dt>
|
||||
|
||||
|
||||
<dt><a href="include.html#index-0">include</a>
|
||||
</dt>
|
||||
|
||||
@ -2030,6 +2046,10 @@
|
||||
</dt>
|
||||
|
||||
|
||||
<dt><a href="pair_zero.html#index-0">pair_style zero</a>
|
||||
</dt>
|
||||
|
||||
|
||||
<dt><a href="pair_write.html#index-0">pair_write</a>
|
||||
</dt>
|
||||
|
||||
|
||||
@ -140,15 +140,20 @@
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
|
||||
<p>Using an improper style of none means improper forces are not
|
||||
computed, even if quadruplets of improper atoms were listed in the
|
||||
<p>Using an improper style of none means imroper forces and energies are
|
||||
not computed, even if quadruplets of improper atoms were listed in the
|
||||
data file read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a> command.</p>
|
||||
<p>See the <a class="reference internal" href="improper_zero.html"><em>improper_style zero</em></a> command for a way to
|
||||
calculate improper statistics, but compute no improper interactions.</p>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
|
||||
<blockquote>
|
||||
<div>none</div></blockquote>
|
||||
<p><strong>Related commands:</strong> none</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="improper_zero.html"><em>improper_style zero</em></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
@ -18,12 +18,17 @@ improper_style none :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Using an improper style of none means improper forces are not
|
||||
computed, even if quadruplets of improper atoms were listed in the
|
||||
Using an improper style of none means imroper forces and energies are
|
||||
not computed, even if quadruplets of improper atoms were listed in the
|
||||
data file read by the "read_data"_read_data.html command.
|
||||
|
||||
See the "improper_style zero"_improper_zero.html command for a way to
|
||||
calculate improper statistics, but compute no improper interactions.
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
[Related commands:] none
|
||||
[Related commands:]
|
||||
|
||||
"improper_style zero"_improper_zero.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
@ -184,6 +184,7 @@ links to the individual styles are given in the improper section of
|
||||
<a class="reference internal" href="Section_commands.html#cmd-5"><span>this page</span></a>.</p>
|
||||
<ul class="simple">
|
||||
<li><a class="reference internal" href="improper_none.html"><em>improper_style none</em></a> - turn off improper interactions</li>
|
||||
<li><a class="reference internal" href="improper_zero.html"><em>improper_style zero</em></a> - topology but no interactions</li>
|
||||
<li><a class="reference internal" href="improper_hybrid.html"><em>improper_style hybrid</em></a> - define multiple styles of improper interactions</li>
|
||||
<li><a class="reference internal" href="improper_class2.html"><em>improper_style class2</em></a> - COMPASS (class 2) improper</li>
|
||||
<li><a class="reference internal" href="improper_cvff.html"><em>improper_style cvff</em></a> - CVFF improper</li>
|
||||
|
||||
@ -65,6 +65,7 @@ links to the individual styles are given in the improper section of
|
||||
"this page"_Section_commands.html#cmd_5.
|
||||
|
||||
"improper_style none"_improper_none.html - turn off improper interactions
|
||||
"improper_style zero"_improper_zero.html - topology but no interactions
|
||||
"improper_style hybrid"_improper_hybrid.html - define multiple styles of improper interactions :ul
|
||||
|
||||
"improper_style class2"_improper_class2.html - COMPASS (class 2) improper
|
||||
|
||||
228
doc/improper_zero.html
Normal file
228
doc/improper_zero.html
Normal file
@ -0,0 +1,228 @@
|
||||
|
||||
|
||||
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|
||||
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|
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|
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|
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|
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|
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|
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|
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|
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<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
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<div class="section" id="improper-style-zero-command">
|
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<span id="index-0"></span><h1>improper_style zero command<a class="headerlink" href="#improper-style-zero-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>improper_style zero
|
||||
</pre></div>
|
||||
</div>
|
||||
</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>improper_style zero
|
||||
improper_coeff *
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
|
||||
<p>Using an improper style of zero means improper forces and energies are
|
||||
not computed, but the geometry of improper quadruplets is still
|
||||
accessible to other commands.</p>
|
||||
<p>As an example, the <a class="reference internal" href="compute_improper_local.html"><em>compute improper/local</em></a> command can be used to
|
||||
compute the chi values for the list of quadruplets of improper atoms
|
||||
listed in the data file read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a>
|
||||
command. If no improper style is defined, this command cannot be
|
||||
used.</p>
|
||||
<p>Note that the <a class="reference internal" href="improper_coeff.html"><em>improper_coeff</em></a> command must be
|
||||
used for all improper types, though no additional values are
|
||||
specified.</p>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
|
||||
<blockquote>
|
||||
<div>none</div></blockquote>
|
||||
<p><strong>Related commands:</strong> none</p>
|
||||
<p><a class="reference internal" href="improper_none.html"><em>improper_style none</em></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
</div>
|
||||
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|
||||
|
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|
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© Copyright 2013 Sandia Corporation.
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43
doc/improper_zero.txt
Normal file
43
doc/improper_zero.txt
Normal file
@ -0,0 +1,43 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
improper_style zero command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
improper_style zero :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
improper_style zero
|
||||
improper_coeff * :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Using an improper style of zero means improper forces and energies are
|
||||
not computed, but the geometry of improper quadruplets is still
|
||||
accessible to other commands.
|
||||
|
||||
As an example, the "compute
|
||||
improper/local"_compute_improper_local.html command can be used to
|
||||
compute the chi values for the list of quadruplets of improper atoms
|
||||
listed in the data file read by the "read_data"_read_data.html
|
||||
command. If no improper style is defined, this command cannot be
|
||||
used.
|
||||
|
||||
Note that the "improper_coeff"_improper_coeff.html command must be
|
||||
used for all improper types, though no additional values are
|
||||
specified.
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
[Related commands:] none
|
||||
|
||||
"improper_style none"_improper_none.html
|
||||
|
||||
[Default:] none
|
||||
@ -310,7 +310,7 @@ beginning of the run to give the desired estimated error. Other
|
||||
cutoffs such as LJ will not be affected. If the grid is not set using
|
||||
the <em>mesh</em> command, this command will also attempt to use the optimal
|
||||
grid that minimizes cost using an estimate given by
|
||||
<a class="reference internal" href="#hardy"><span>(Hardy)</span></a>. Note that this cost estimate is not exact, somewhat
|
||||
<a class="reference internal" href="kspace_style.html#hardy"><span>(Hardy)</span></a>. Note that this cost estimate is not exact, somewhat
|
||||
experimental, and still may not yield the optimal parameters.</p>
|
||||
<p>The <em>pressure/scalar</em> keyword applies only to MSM. If this option is
|
||||
turned on, only the scalar pressure (i.e. (Pxx + Pyy + Pzz)/3.0) will
|
||||
@ -335,7 +335,7 @@ collective operations and adequate hardware.</p>
|
||||
<p>The <em>diff</em> keyword specifies the differentiation scheme used by the
|
||||
PPPM method to compute forces on particles given electrostatic
|
||||
potentials on the PPPM mesh. The <em>ik</em> approach is the default for
|
||||
PPPM and is the original formulation used in <a class="reference internal" href="#hockney"><span>(Hockney)</span></a>. It
|
||||
PPPM and is the original formulation used in <a class="reference internal" href="kspace_style.html#hockney"><span>(Hockney)</span></a>. It
|
||||
performs differentiation in Kspace, and uses 3 FFTs to transfer each
|
||||
component of the computed fields back to real space for total of 4
|
||||
FFTs per timestep.</p>
|
||||
@ -370,7 +370,7 @@ speed-up the simulations but introduces some error in the force
|
||||
computations, as shown in <a class="reference internal" href="#wennberg"><span>(Wennberg)</span></a>. With <em>none</em>, it is
|
||||
assumed that no mixing rule is applicable. Splitting of the dispersion
|
||||
coefficients will be performed as described in
|
||||
<a class="reference internal" href="#isele-holder"><span>(Isele-Holder)</span></a>. This splitting can be influenced with
|
||||
<a class="reference internal" href="kspace_style.html#isele-holder"><span>(Isele-Holder)</span></a>. This splitting can be influenced with
|
||||
the <em>splittol</em> keywords. Only the eigenvalues that are larger than tol
|
||||
compared to the largest eigenvalues are included. Using this keywords
|
||||
the original matrix of dispersion coefficients is approximated. This
|
||||
@ -378,7 +378,7 @@ leads to faster computations, but the accuracy in the reciprocal space
|
||||
computations of the dispersion part is decreased.</p>
|
||||
<p>The <em>force/disp/real</em> and <em>force/disp/kspace</em> keywords set the force
|
||||
accuracy for the real and space computations for the dispersion part
|
||||
of pppm/disp. As shown in <a class="reference internal" href="#isele-holder"><span>(Isele-Holder)</span></a>, optimal
|
||||
of pppm/disp. As shown in <a class="reference internal" href="kspace_style.html#isele-holder"><span>(Isele-Holder)</span></a>, optimal
|
||||
performance and accuracy in the results is obtained when these values
|
||||
are different.</p>
|
||||
<p>The <em>disp/auto</em> option controlls whether the pppm/disp is allowed to
|
||||
|
||||
@ -228,7 +228,7 @@ see the doc page for individual styles to see which potentials support
|
||||
these options. If N is non-zero, a table of length 2^N is
|
||||
pre-computed for forces and energies, which can shrink their
|
||||
computational cost by up to a factor of 2. The table is indexed via a
|
||||
bit-mapping technique <a class="reference internal" href="#wolff"><span>(Wolff)</span></a> and a linear interpolation is
|
||||
bit-mapping technique <a class="reference internal" href="pair_table.html#wolff"><span>(Wolff)</span></a> and a linear interpolation is
|
||||
performed between adjacent table values. In our experiments with
|
||||
different table styles (lookup, linear, spline), this method typically
|
||||
gave the best performance in terms of speed and accuracy.</p>
|
||||
|
||||
@ -140,7 +140,8 @@
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
|
||||
<p>Using a pair style of none means pair forces are not computed.</p>
|
||||
<p>Using a pair style of none means pair forces and energies are not
|
||||
computed.</p>
|
||||
<p>With this choice, the force cutoff is 0.0, which means that only atoms
|
||||
within the neighbor skin distance (see the <a class="reference internal" href="neighbor.html"><em>neighbor</em></a>
|
||||
command) are communicated between processors. You must insure the
|
||||
@ -152,12 +153,17 @@ data structures for binning are still allocated. If the neighbor skin
|
||||
distance is small, then these data structures can consume a large
|
||||
amount of memory. So you should either set the neighbor style to
|
||||
<em>nsq</em> or set the skin distance to a larger value.</p>
|
||||
<p>See the <a class="reference internal" href="pair_zero.html"><em>pair_style zero</em></a> for a way to trigger the
|
||||
building of a neighbor lists, but compute no pairwise interactions.</p>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
|
||||
<blockquote>
|
||||
<div>none</div></blockquote>
|
||||
<p><strong>Related commands:</strong> none</p>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
|
||||
<p><a class="reference internal" href="pair_zero.html"><em>pair_style zero</em></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
@ -18,7 +18,8 @@ pair_style none :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Using a pair style of none means pair forces are not computed.
|
||||
Using a pair style of none means pair forces and energies are not
|
||||
computed.
|
||||
|
||||
With this choice, the force cutoff is 0.0, which means that only atoms
|
||||
within the neighbor skin distance (see the "neighbor"_neighbor.html
|
||||
@ -33,8 +34,13 @@ distance is small, then these data structures can consume a large
|
||||
amount of memory. So you should either set the neighbor style to
|
||||
{nsq} or set the skin distance to a larger value.
|
||||
|
||||
See the "pair_style zero"_pair_zero.html for a way to trigger the
|
||||
building of a neighbor lists, but compute no pairwise interactions.
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
[Related commands:] none
|
||||
[Related commands:]
|
||||
|
||||
"pair_style zero"_pair_zero.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
@ -208,6 +208,7 @@ in the pair section of <a class="reference internal" href="Section_commands.html
|
||||
<li><a class="reference internal" href="pair_none.html"><em>pair_style none</em></a> - turn off pairwise interactions</li>
|
||||
<li><a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid</em></a> - multiple styles of pairwise interactions</li>
|
||||
<li><a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid/overlay</em></a> - multiple styles of superposed pairwise interactions</li>
|
||||
<li><a class="reference internal" href="pair_zero.html"><em>pair_style zero</em></a> - neighbor list but no interactions</li>
|
||||
<li><a class="reference internal" href="pair_adp.html"><em>pair_style adp</em></a> - angular dependent potential (ADP) of Mishin</li>
|
||||
<li><a class="reference internal" href="pair_airebo.html"><em>pair_style airebo</em></a> - AIREBO potential of Stuart</li>
|
||||
<li><a class="reference internal" href="pair_beck.html"><em>pair_style beck</em></a> - Beck potential</li>
|
||||
|
||||
@ -97,7 +97,8 @@ in the pair section of "this page"_Section_commands.html#cmd_5.
|
||||
|
||||
"pair_style none"_pair_none.html - turn off pairwise interactions
|
||||
"pair_style hybrid"_pair_hybrid.html - multiple styles of pairwise interactions
|
||||
"pair_style hybrid/overlay"_pair_hybrid.html - multiple styles of superposed pairwise interactions :ul
|
||||
"pair_style hybrid/overlay"_pair_hybrid.html - multiple styles of superposed pairwise interactions
|
||||
"pair_style zero"_pair_zero.html - neighbor list but no interactions :ul
|
||||
|
||||
"pair_style adp"_pair_adp.html - angular dependent potential (ADP) of Mishin
|
||||
"pair_style airebo"_pair_airebo.html - AIREBO potential of Stuart
|
||||
|
||||
244
doc/pair_zero.html
Normal file
244
doc/pair_zero.html
Normal file
@ -0,0 +1,244 @@
|
||||
|
||||
|
||||
<!DOCTYPE html>
|
||||
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|
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|
||||
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|
||||
|
||||
|
||||
|
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|
||||
|
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|
||||
|
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|
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
|
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|
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<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
|
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<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
|
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
|
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<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
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||||
<div class="section" id="pair-style-zero-command">
|
||||
<span id="index-0"></span><h1>pair_style zero command<a class="headerlink" href="#pair-style-zero-command" title="Permalink to this headline">¶</a></h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
|
||||
<div class="highlight-python"><div class="highlight"><pre>pair_style zero cutoff
|
||||
</pre></div>
|
||||
</div>
|
||||
<ul class="simple">
|
||||
<li>zero = style name of this pair style
|
||||
cutoff = global cutoff (distance units)</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>pair_style zero
|
||||
pair_coeff * *
|
||||
pair_coeff 1 2 3.0
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
|
||||
<p>Define a global cutoff length for the purpose of building a neighbor
|
||||
list and acquiring ghost atoms, but do not compute any pairwise forces
|
||||
or energies.</p>
|
||||
<p>This can be useful for fixes or computes which require a neighbor list
|
||||
to enumerate pairs of atoms within some cutoff distance, but when
|
||||
pairwise forces are not otherwise needed. Examples are the <a class="reference internal" href="fix_bond_create.html"><em>fix bond/create</em></a>, <a class="reference internal" href="compute_rdf.html"><em>compute rdf</em></a>,
|
||||
<a class="reference internal" href="compute_voronoi_atom.html"><em>compute voronoi/atom</em></a> commands.</p>
|
||||
<p>Note that the <a class="reference internal" href="comm_modify.html"><em>comm_modify cutoff</em></a> command can be
|
||||
used to insure communication of ghost atoms even when a pair style is
|
||||
not defined, but it will not trigger neighbor list generation.</p>
|
||||
<p>The following coefficients must be defined for each pair of atoms
|
||||
types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples
|
||||
above, or in the data file or restart files read by the
|
||||
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
|
||||
commands, or by mixing as described below:</p>
|
||||
<ul class="simple">
|
||||
<li>cutoff (distance units)</li>
|
||||
</ul>
|
||||
<p>This coefficient is optional. If not specified, the global cutoff
|
||||
specified in the pair_style command is used.</p>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
|
||||
<blockquote>
|
||||
<div>none</div></blockquote>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
|
||||
<p><a class="reference internal" href="pair_none.html"><em>pair_style none</em></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
</div>
|
||||
</div>
|
||||
|
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|
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© Copyright 2013 Sandia Corporation.
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58
doc/pair_zero.txt
Normal file
58
doc/pair_zero.txt
Normal file
@ -0,0 +1,58 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
pair_style zero command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
pair_style zero cutoff :pre
|
||||
|
||||
zero = style name of this pair style
|
||||
cutoff = global cutoff (distance units) :l
|
||||
|
||||
[Examples:]
|
||||
|
||||
pair_style zero
|
||||
pair_coeff * *
|
||||
pair_coeff 1 2 3.0 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Define a global cutoff length for the purpose of building a neighbor
|
||||
list and acquiring ghost atoms, but do not compute any pairwise forces
|
||||
or energies.
|
||||
|
||||
This can be useful for fixes or computes which require a neighbor list
|
||||
to enumerate pairs of atoms within some cutoff distance, but when
|
||||
pairwise forces are not otherwise needed. Examples are the "fix
|
||||
bond/create"_fix_bond_create.html, "compute rdf"_compute_rdf.html,
|
||||
"compute voronoi/atom"_compute_voronoi_atom.html commands.
|
||||
|
||||
Note that the "comm_modify cutoff"_comm_modify.html command can be
|
||||
used to insure communication of ghost atoms even when a pair style is
|
||||
not defined, but it will not trigger neighbor list generation.
|
||||
|
||||
The following coefficients must be defined for each pair of atoms
|
||||
types via the "pair_coeff"_pair_coeff.html command as in the examples
|
||||
above, or in the data file or restart files read by the
|
||||
"read_data"_read_data.html or "read_restart"_read_restart.html
|
||||
commands, or by mixing as described below:
|
||||
|
||||
cutoff (distance units) :ul
|
||||
|
||||
This coefficient is optional. If not specified, the global cutoff
|
||||
specified in the pair_style command is used.
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"pair_style none"_pair_none.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
File diff suppressed because one or more lines are too long
@ -51,8 +51,8 @@ MPI_LIB =
|
||||
# PATH = path for FFT library
|
||||
# LIB = name of FFT library
|
||||
|
||||
FFT_INC = -DFFT_FFTW -I/home/sjplimp/fftw/fftw
|
||||
FFT_PATH = -L/home/sjplimp/fftw/fftw/.libs
|
||||
FFT_INC = -DFFT_FFTW
|
||||
FFT_PATH =
|
||||
FFT_LIB = -lfftw
|
||||
|
||||
# JPEG and/or PNG library
|
||||
|
||||
109
src/angle_zero.cpp
Normal file
109
src/angle_zero.cpp
Normal file
@ -0,0 +1,109 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Carsten Svaneborg (SDU)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include <math.h>
|
||||
#include <stdlib.h>
|
||||
#include "angle_zero.h"
|
||||
#include "atom.h"
|
||||
#include "force.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
AngleZero::AngleZero(LAMMPS *lmp) : Angle(lmp) {}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
AngleZero::~AngleZero()
|
||||
{
|
||||
if (allocated && !copymode) {
|
||||
memory->destroy(setflag);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void AngleZero::compute(int eflag, int vflag)
|
||||
{
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = 0;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void AngleZero::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int n = atom->nangletypes;
|
||||
|
||||
memory->create(setflag,n+1,"angle:setflag");
|
||||
for (int i = 1; i <= n; i++) setflag[i] = 0;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set coeffs for one or more types
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void AngleZero::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg != 1) error->all(FLERR,"Incorrect args for angle coefficients");
|
||||
if (!allocated) allocate();
|
||||
|
||||
int ilo,ihi;
|
||||
force->bounds(arg[0],atom->nangletypes,ilo,ihi);
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
setflag[i] = 1;
|
||||
count++;
|
||||
}
|
||||
|
||||
if (count == 0) error->all(FLERR,"Incorrect args for angle coefficients");
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double AngleZero::equilibrium_angle(int i)
|
||||
{
|
||||
return 0.0;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes out coeffs to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void AngleZero::write_restart(FILE *fp) {}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads coeffs from restart file, bcasts them
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void AngleZero::read_restart(FILE *fp)
|
||||
{
|
||||
allocate();
|
||||
for (int i = 1; i <= atom->nangletypes; i++) setflag[i] = 1;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double AngleZero::single(int type, int i1, int i2, int i3)
|
||||
{
|
||||
return 0.0;
|
||||
}
|
||||
54
src/angle_zero.h
Normal file
54
src/angle_zero.h
Normal file
@ -0,0 +1,54 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef ANGLE_CLASS
|
||||
|
||||
AngleStyle(zero,AngleZero)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_ANGLE_ZERO_H
|
||||
#define LMP_ANGLE_ZERO_H
|
||||
|
||||
#include <stdio.h>
|
||||
#include "angle.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class AngleZero : public Angle {
|
||||
public:
|
||||
AngleZero(class LAMMPS *);
|
||||
virtual ~AngleZero();
|
||||
virtual void compute(int, int);
|
||||
virtual void coeff(int, char **);
|
||||
double equilibrium_angle(int);
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
double single(int, int, int, int);
|
||||
|
||||
protected:
|
||||
void allocate();
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Incorrect args for angle coefficients
|
||||
|
||||
Self-explanatory. Check the input script or data file.
|
||||
|
||||
*/
|
||||
112
src/bond_zero.cpp
Normal file
112
src/bond_zero.cpp
Normal file
@ -0,0 +1,112 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Carsten Svaneborg (SDU)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include <math.h>
|
||||
#include <stdlib.h>
|
||||
#include "bond_zero.h"
|
||||
#include "atom.h"
|
||||
#include "force.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
BondZero::BondZero(LAMMPS *lmp) : Bond(lmp) {}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
BondZero::~BondZero()
|
||||
{
|
||||
if (allocated && !copymode) {
|
||||
memory->destroy(setflag);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void BondZero::compute(int eflag, int vflag)
|
||||
{
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = 0;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void BondZero::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int n = atom->nbondtypes;
|
||||
|
||||
memory->create(setflag,n+1,"bond:setflag");
|
||||
for (int i = 1; i <= n; i++) setflag[i] = 0;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set coeffs for one or more types
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void BondZero::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg != 1) error->all(FLERR,"Incorrect args for bond coefficients");
|
||||
if (!allocated) allocate();
|
||||
|
||||
int ilo,ihi;
|
||||
force->bounds(arg[0],atom->nbondtypes,ilo,ihi);
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
setflag[i] = 1;
|
||||
count++;
|
||||
}
|
||||
|
||||
if (count == 0) error->all(FLERR,"Incorrect args for bond coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
return an equilbrium bond length
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double BondZero::equilibrium_distance(int i)
|
||||
{
|
||||
return 0.0;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes out coeffs to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void BondZero::write_restart(FILE *fp) {}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads coeffs from restart file, bcasts them
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void BondZero::read_restart(FILE *fp)
|
||||
{
|
||||
allocate();
|
||||
for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double BondZero::single(int type, double rsq, int i, int j,
|
||||
double &fforce)
|
||||
{
|
||||
return 0.0;
|
||||
}
|
||||
54
src/bond_zero.h
Normal file
54
src/bond_zero.h
Normal file
@ -0,0 +1,54 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef BOND_CLASS
|
||||
|
||||
BondStyle(zero,BondZero)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_BOND_ZERO_H
|
||||
#define LMP_BOND_ZERO_H
|
||||
|
||||
#include <stdio.h>
|
||||
#include "bond.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class BondZero : public Bond {
|
||||
public:
|
||||
BondZero(class LAMMPS *);
|
||||
virtual ~BondZero();
|
||||
virtual void compute(int, int);
|
||||
void coeff(int, char **);
|
||||
double equilibrium_distance(int);
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
double single(int, double, int, int, double &);
|
||||
|
||||
protected:
|
||||
virtual void allocate();
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Incorrect args for bond coefficients
|
||||
|
||||
Self-explanatory. Check the input script or data file.
|
||||
|
||||
*/
|
||||
97
src/dihedral_zero.cpp
Normal file
97
src/dihedral_zero.cpp
Normal file
@ -0,0 +1,97 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Carsten Svaneborg (SDU)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include <mpi.h>
|
||||
#include <math.h>
|
||||
#include <stdlib.h>
|
||||
#include "dihedral_zero.h"
|
||||
#include "atom.h"
|
||||
#include "force.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
DihedralZero::DihedralZero(LAMMPS *lmp) : Dihedral(lmp) {}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
DihedralZero::~DihedralZero()
|
||||
{
|
||||
if (allocated) {
|
||||
memory->destroy(setflag);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void DihedralZero::compute(int eflag, int vflag)
|
||||
{
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = 0;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void DihedralZero::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int n = atom->ndihedraltypes;
|
||||
|
||||
memory->create(setflag,n+1,"dihedral:setflag");
|
||||
for (int i = 1; i <= n; i++) setflag[i] = 0;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set coeffs for one type
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void DihedralZero::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg != 1) error->all(FLERR,"Incorrect args for dihedral coefficients");
|
||||
if (!allocated) allocate();
|
||||
|
||||
int ilo,ihi;
|
||||
force->bounds(arg[0],atom->ndihedraltypes,ilo,ihi);
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
setflag[i] = 1;
|
||||
count++;
|
||||
}
|
||||
|
||||
if (count == 0) error->all(FLERR,"Incorrect args for dihedral coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes out coeffs to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void DihedralZero::write_restart(FILE *fp) {}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads coeffs from restart file, bcasts them
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void DihedralZero::read_restart(FILE *fp)
|
||||
{
|
||||
allocate();
|
||||
for (int i = 1; i <= atom->ndihedraltypes; i++) setflag[i] = 1;
|
||||
}
|
||||
|
||||
50
src/dihedral_zero.h
Normal file
50
src/dihedral_zero.h
Normal file
@ -0,0 +1,50 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
|
||||
Identical to dihedral harmonic, except if all k's are zero the
|
||||
force loop is skipped.
|
||||
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef DIHEDRAL_CLASS
|
||||
|
||||
DihedralStyle(zero,DihedralZero)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_DIHEDRAL_ZERO_H
|
||||
#define LMP_DIHEDRAL_ZERO_H
|
||||
|
||||
#include "stdio.h"
|
||||
#include "dihedral.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class DihedralZero : public Dihedral {
|
||||
public:
|
||||
DihedralZero(class LAMMPS *);
|
||||
virtual ~DihedralZero();
|
||||
virtual void compute(int, int);
|
||||
void coeff(int, char **);
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
|
||||
protected:
|
||||
|
||||
void allocate();
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
96
src/improper_zero.cpp
Normal file
96
src/improper_zero.cpp
Normal file
@ -0,0 +1,96 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Carsten Svaneborg (SDU)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include <mpi.h>
|
||||
#include <math.h>
|
||||
#include <stdlib.h>
|
||||
#include "improper_zero.h"
|
||||
#include "atom.h"
|
||||
#include "force.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
ImproperZero::ImproperZero(LAMMPS *lmp) : Improper(lmp) {}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
ImproperZero::~ImproperZero()
|
||||
{
|
||||
if (allocated && !copymode) {
|
||||
memory->destroy(setflag);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void ImproperZero::compute(int eflag, int vflag)
|
||||
{
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = 0;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void ImproperZero::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int n = atom->nimpropertypes;
|
||||
|
||||
memory->create(setflag,n+1,"improper:setflag");
|
||||
for (int i = 1; i <= n; i++) setflag[i] = 0;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set coeffs for one type
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void ImproperZero::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg != 1) error->all(FLERR,"Incorrect args for improper coefficients");
|
||||
if (!allocated) allocate();
|
||||
|
||||
int ilo,ihi;
|
||||
force->bounds(arg[0],atom->nimpropertypes,ilo,ihi);
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
setflag[i] = 1;
|
||||
count++;
|
||||
}
|
||||
|
||||
if (count == 0) error->all(FLERR,"Incorrect args for improper coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes out coeffs to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void ImproperZero::write_restart(FILE *fp) {}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads coeffs from restart file, bcasts them
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void ImproperZero::read_restart(FILE *fp)
|
||||
{
|
||||
allocate();
|
||||
for (int i = 1; i <= atom->nimpropertypes; i++) setflag[i] = 1;
|
||||
}
|
||||
57
src/improper_zero.h
Normal file
57
src/improper_zero.h
Normal file
@ -0,0 +1,57 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef IMPROPER_CLASS
|
||||
|
||||
ImproperStyle(zero,ImproperZero)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_IMPROPER_ZERO_H
|
||||
#define LMP_IMPROPER_ZERO_H
|
||||
|
||||
#include <stdio.h>
|
||||
#include "improper.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class ImproperZero : public Improper {
|
||||
public:
|
||||
ImproperZero(class LAMMPS *);
|
||||
virtual ~ImproperZero();
|
||||
virtual void compute(int, int);
|
||||
virtual void coeff(int, char **);
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
|
||||
protected:
|
||||
virtual void allocate();
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
W: Improper problem: %d %ld %d %d %d %d
|
||||
|
||||
Conformation of the 4 listed improper atoms is extreme; you may want
|
||||
to check your simulation geometry.
|
||||
|
||||
E: Incorrect args for improper coefficients
|
||||
|
||||
Self-explanatory. Check the input script or data file.
|
||||
|
||||
*/
|
||||
@ -452,8 +452,8 @@ void PairTable::read_table(Table *tb, char *file, char *keyword)
|
||||
|
||||
if (ferror) {
|
||||
char str[128];
|
||||
sprintf(str,"%d force values in table are inconsistent with -dE/dr;"
|
||||
"should only happen at inflection points",ferror);
|
||||
sprintf(str,"%d force values in table are inconsistent with -dE/dr; "
|
||||
"should only be mistakenly flagged at inflection points",ferror);
|
||||
error->warning(FLERR,str);
|
||||
}
|
||||
|
||||
|
||||
197
src/pair_zero.cpp
Normal file
197
src/pair_zero.cpp
Normal file
@ -0,0 +1,197 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Carsten Svaneborg (SDU)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include <math.h>
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
#include <string.h>
|
||||
#include "pair_zero.h"
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairZero::PairZero(LAMMPS *lmp) : Pair(lmp) {}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairZero::~PairZero()
|
||||
{
|
||||
if (allocated) {
|
||||
memory->destroy(setflag);
|
||||
memory->destroy(cutsq);
|
||||
memory->destroy(cut);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairZero::compute(int eflag, int vflag)
|
||||
{
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
|
||||
if (vflag_fdotr) virial_fdotr_compute();
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
allocate all arrays
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairZero::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int n = atom->ntypes;
|
||||
|
||||
memory->create(setflag,n+1,n+1,"pair:setflag");
|
||||
for (int i = 1; i <= n; i++)
|
||||
for (int j = i; j <= n; j++)
|
||||
setflag[i][j] = 1;
|
||||
|
||||
memory->create(cutsq,n+1,n+1,"pair:cutsq");
|
||||
memory->create(cut,n+1,n+1,"pair:cut");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
global settings
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairZero::settings(int narg, char **arg)
|
||||
{
|
||||
if (narg != 1) error->all(FLERR,"Illegal pair_style command");
|
||||
|
||||
cut_global = force->numeric(FLERR,arg[0]);
|
||||
|
||||
// reset cutoffs that have been explicitly set
|
||||
|
||||
allocate();
|
||||
int i,j;
|
||||
for (i = 1; i <= atom->ntypes; i++)
|
||||
for (j = i+1; j <= atom->ntypes; j++)
|
||||
cut[i][j] = cut_global;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set coeffs for one or more type pairs
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairZero::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg < 2 || narg > 3)
|
||||
error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
if (!allocated) allocate();
|
||||
|
||||
int ilo,ihi,jlo,jhi;
|
||||
force->bounds(arg[0],atom->ntypes,ilo,ihi);
|
||||
force->bounds(arg[1],atom->ntypes,jlo,jhi);
|
||||
|
||||
double cut_one = cut_global;
|
||||
if (narg == 3) cut_one = force->numeric(FLERR,arg[2]);
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
for (int j = MAX(jlo,i); j <= jhi; j++) {
|
||||
cut[i][j] = cut_one;
|
||||
count++;
|
||||
}
|
||||
}
|
||||
|
||||
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init for one type pair i,j and corresponding j,i
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double PairZero::init_one(int i, int j)
|
||||
{
|
||||
if (setflag[i][j] == 0) {
|
||||
cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
|
||||
}
|
||||
|
||||
return cut[i][j];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairZero::write_restart(FILE *fp)
|
||||
{
|
||||
write_restart_settings(fp);
|
||||
|
||||
int i,j;
|
||||
for (i = 1; i <= atom->ntypes; i++)
|
||||
for (j = i; j <= atom->ntypes; j++) {
|
||||
fwrite(&setflag[i][j],sizeof(int),1,fp);
|
||||
if (setflag[i][j]) {
|
||||
fwrite(&cut[i][j],sizeof(double),1,fp);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairZero::read_restart(FILE *fp)
|
||||
{
|
||||
read_restart_settings(fp);
|
||||
allocate();
|
||||
|
||||
int i,j;
|
||||
int me = comm->me;
|
||||
for (i = 1; i <= atom->ntypes; i++)
|
||||
for (j = i; j <= atom->ntypes; j++) {
|
||||
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
|
||||
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
|
||||
if (setflag[i][j]) {
|
||||
if (me == 0) {
|
||||
fread(&cut[i][j],sizeof(double),1,fp);
|
||||
}
|
||||
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairZero::write_restart_settings(FILE *fp)
|
||||
{
|
||||
fwrite(&cut_global,sizeof(double),1,fp);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairZero::read_restart_settings(FILE *fp)
|
||||
{
|
||||
int me = comm->me;
|
||||
if (me == 0) {
|
||||
fread(&cut_global,sizeof(double),1,fp);
|
||||
}
|
||||
MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
|
||||
}
|
||||
|
||||
79
src/pair_zero.h
Normal file
79
src/pair_zero.h
Normal file
@ -0,0 +1,79 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
|
||||
Pair zero is a dummy pair interaction useful for requiring a
|
||||
force cutoff distance in the absense of pair-interactions or
|
||||
with hybrid/overlay if a larger force cutoff distance is required.
|
||||
|
||||
This can be used in conjunction with bond/create to create bonds
|
||||
that are longer than the cutoff of a given force field, or to
|
||||
calculate radial distribution functions for models without
|
||||
pair interactions.
|
||||
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(zero,PairZero)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_ZERO_H
|
||||
#define LMP_PAIR_ZERO_H
|
||||
|
||||
#include "pair.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairZero : public Pair {
|
||||
public:
|
||||
PairZero(class LAMMPS *);
|
||||
virtual ~PairZero();
|
||||
virtual void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
double init_one(int, int);
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
void write_restart_settings(FILE *);
|
||||
void read_restart_settings(FILE *);
|
||||
|
||||
protected:
|
||||
double cut_global;
|
||||
double **cut;
|
||||
|
||||
virtual void allocate();
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Illegal ... command
|
||||
|
||||
Self-explanatory. Check the input script syntax and compare to the
|
||||
documentation for the command. You can use -echo screen as a
|
||||
command-line option when running LAMMPS to see the offending line.
|
||||
|
||||
E: Incorrect args for pair coefficients
|
||||
|
||||
Self-explanatory. Check the input script or data file.
|
||||
|
||||
E: Pair cutoff < Respa interior cutoff
|
||||
|
||||
One or more pairwise cutoffs are too short to use with the specified
|
||||
rRESPA cutoffs.
|
||||
|
||||
*/
|
||||
@ -1010,9 +1010,13 @@ int Thermo::evaluate_keyword(char *word, double *answer)
|
||||
// if keyword requires a compute, error if thermo doesn't use the compute
|
||||
// if inbetween runs and needed compute is not current, error
|
||||
// if in middle of run and needed compute is not current, invoke it
|
||||
// for keywords that use pe indirectly (evdwl, ebond, etc):
|
||||
// for keywords that use energy (evdwl, ebond, etc):
|
||||
// check if energy was tallied on this timestep and set pe->invoked_flag
|
||||
// this will trigger next timestep for energy tallying via addstep()
|
||||
// this means keywords that use pe (pe, etotal, enthalpy)
|
||||
// need to always invoke it even if invoked_flag is set,
|
||||
// because evdwl/etc may have set invoked_flag w/out
|
||||
// actually invoking pe->compute_scalar()
|
||||
|
||||
if (strcmp(word,"step") == 0) {
|
||||
compute_step();
|
||||
@ -1106,7 +1110,7 @@ int Thermo::evaluate_keyword(char *word, double *answer)
|
||||
if (pe->invoked_scalar != update->ntimestep)
|
||||
error->all(FLERR,"Compute used in variable thermo keyword between runs "
|
||||
"is not current");
|
||||
} else if (!(pe->invoked_flag & INVOKED_SCALAR)) {
|
||||
} else {
|
||||
pe->compute_scalar();
|
||||
pe->invoked_flag |= INVOKED_SCALAR;
|
||||
}
|
||||
@ -1134,7 +1138,7 @@ int Thermo::evaluate_keyword(char *word, double *answer)
|
||||
if (pe->invoked_scalar != update->ntimestep)
|
||||
error->all(FLERR,"Compute used in variable thermo keyword between runs "
|
||||
"is not current");
|
||||
} else if (!(pe->invoked_flag & INVOKED_SCALAR)) {
|
||||
} else {
|
||||
pe->compute_scalar();
|
||||
pe->invoked_flag |= INVOKED_SCALAR;
|
||||
}
|
||||
@ -1159,7 +1163,7 @@ int Thermo::evaluate_keyword(char *word, double *answer)
|
||||
if (pe->invoked_scalar != update->ntimestep)
|
||||
error->all(FLERR,"Compute used in variable thermo keyword between runs "
|
||||
"is not current");
|
||||
} else if (!(pe->invoked_flag & INVOKED_SCALAR)) {
|
||||
} else {
|
||||
pe->compute_scalar();
|
||||
pe->invoked_flag |= INVOKED_SCALAR;
|
||||
}
|
||||
@ -1271,10 +1275,6 @@ int Thermo::evaluate_keyword(char *word, double *answer)
|
||||
} else if (strcmp(word,"etail") == 0) {
|
||||
if (update->eflag_global != update->ntimestep)
|
||||
error->all(FLERR,"Energy was not tallied on needed timestep");
|
||||
if (!pe)
|
||||
error->all(FLERR,
|
||||
"Thermo keyword in variable requires thermo to use/init pe");
|
||||
pe->invoked_flag |= INVOKED_SCALAR;
|
||||
compute_etail();
|
||||
|
||||
} else if (strcmp(word,"vol") == 0) compute_vol();
|
||||
|
||||
@ -1 +1 @@
|
||||
#define LAMMPS_VERSION "17 Feb 2016"
|
||||
#define LAMMPS_VERSION "22 Feb 2016"
|
||||
|
||||
Reference in New Issue
Block a user