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sjplimp 2016-03-21 16:06:09 +00:00
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108
doc/Section_commands.html
View File

@ -1016,10 +1016,10 @@ 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="24%" />
<col width="24%" />
<col width="25%" />
<col width="27%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="pair_none.html"><em>none</em></a></td>
@ -1029,138 +1029,138 @@ KOKKOS, o = USER-OMP, t = OPT.</p>
</tr>
<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_airebo.html"><em>airebo/morse (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>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_bop.html"><em>bop</em></a></td>
<tr class="row-odd"><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>
<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>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_born.html"><em>born/coul/msm (o)</em></a></td>
<tr class="row-even"><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>
<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>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_buck.html"><em>buck (cgkio)</em></a></td>
<tr class="row-odd"><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>
<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>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_buck.html"><em>buck/coul/msm (o)</em></a></td>
<tr class="row-even"><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>
<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>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_comb.html"><em>comb3</em></a></td>
<tr class="row-odd"><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>
<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>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_coul.html"><em>coul/long (gko)</em></a></td>
<tr class="row-even"><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>
<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>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_coul.html"><em>coul/wolf (ko)</em></a></td>
<tr class="row-odd"><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>
<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>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_eam.html"><em>eam (cgkot)</em></a></td>
<tr class="row-even"><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>
<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>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_gauss.html"><em>gauss (go)</em></a></td>
<tr class="row-odd"><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>
<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>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_gran.html"><em>gran/hooke/history (o)</em></a></td>
<tr class="row-even"><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>
<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>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_lcbop.html"><em>lcbop</em></a></td>
<tr class="row-odd"><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>
<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>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_charmm.html"><em>lj/charmm/coul/long (cgiko)</em></a></td>
<tr class="row-even"><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>
<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>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_class2.html"><em>lj/class2/coul/long (cgko)</em></a></td>
<tr class="row-odd"><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>
<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>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_lj.html"><em>lj/cut/coul/debye (cgko)</em></a></td>
<tr class="row-even"><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>
<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>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_lj.html"><em>lj/cut/coul/msm (go)</em></a></td>
<tr class="row-odd"><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>
<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>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_lj.html"><em>lj/cut/tip4p/long (ot)</em></a></td>
<tr class="row-even"><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>
<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>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_lj_long.html"><em>lj/long/coul/long (o)</em></a></td>
<tr class="row-odd"><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>
<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>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_lj_smooth_linear.html"><em>lj/smooth/linear (o)</em></a></td>
<tr class="row-even"><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>
<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>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_lubricateU.html"><em>lubricateU</em></a></td>
<tr class="row-odd"><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>
<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>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_morse.html"><em>morse (cgot)</em></a></td>
<tr class="row-even"><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>
<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>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_nm.html"><em>nm/cut/coul/long (o)</em></a></td>
<tr class="row-odd"><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>
<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>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_peri.html"><em>peri/ves</em></a></td>
<tr class="row-even"><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>
<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>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_resquared.html"><em>resquared (go)</em></a></td>
<tr class="row-odd"><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>
<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>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_table.html"><em>table (gko)</em></a></td>
<tr class="row-even"><td><a class="reference internal" href="pair_sw.html"><em>sw (cgkio)</em></a></td>
<td><a class="reference internal" href="pair_table.html"><em>table (gko)</em></a></td>
<td><a class="reference internal" href="pair_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>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_coul.html"><em>tip4p/cut (o)</em></a></td>
<tr class="row-odd"><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>
<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>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_yukawa.html"><em>yukawa (go)</em></a></td>
<tr class="row-even"><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>
<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>&nbsp;</td>
</tr>
</tbody>
</table>

1
doc/Section_commands.txt
View File

@ -804,6 +804,7 @@ KOKKOS, o = USER-OMP, t = OPT.
"hybrid/overlay"_pair_hybrid.html,
"adp (o)"_pair_adp.html,
"airebo (o)"_pair_airebo.html,
"airebo/morse (o)"_pair_airebo.html,
"beck (go)"_pair_beck.html,
"body"_pair_body.html,
"bop"_pair_bop.html,

2
doc/_sources/Manual.txt
View File

@ -5,7 +5,7 @@
LAMMPS Documentation
====================
10 Mar 2016 version
14 Mar 2016 version
-------------------
Version info:

114
doc/_sources/Section_commands.txt
View File

@ -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:`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>` | |
+-----------------------------------------------------+----------------------------------------------------+-------------------------------------------------------+-----------------------------------------------------------+
+-----------------------------------------------------------+-----------------------------------------------------+----------------------------------------------------+-------------------------------------------------------+
| :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:`airebo/morse (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>`.

13
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@ -9,6 +9,9 @@ compute heat/flux/tally command
compute pe/tally command
========================
compute pe/mol/tally command
============================
compute stress/tally command
============================
@ -20,7 +23,7 @@ Syntax
compute ID group-ID style group2-ID
* ID, group-ID are documented in :doc:`compute <compute>` command
* style = *force/tally* or *pe/tally* or *stress/tally*
* style = *force/tally* or *pe/tally* or *pe/mol/tally* or *stress/tally*
* group2-ID = group ID of second (or same) group
Examples
@ -63,7 +66,13 @@ pairwise property computations.
Compute *pe/tally* calculates a global scalar (the energy) and a per
atom scalar (the contributions of the single atom to the global
scalar). Compute *force/tally* calculates a global scalar (the force
scalar). Compute *pe/mol/tally* calculates a global 4-element vector
containing (in this order): *evdwl* and *ecoul* for intramolecular pairs
and *evdwl* and *ecoul* for intermolecular pairs. Since molecules are
identified my their molecule IDs, the partitioning does not have to be
related to molecules, but the energies are tallied into the respective
slots depending on whether the molecule IDs of a pair are the same or
different. Compute *force/tally* calculates a global scalar (the force
magnitude) and a per atom 3-element vector (force contribution from
each atom). Compute *stress/tally* calculates a global scalar
(average of the diagonal elements of the stress tensor) and a per atom

2
doc/_sources/compute_voronoi_atom.txt
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@ -164,7 +164,7 @@ which must be installed on your system when building LAMMPS for use
with this compute. See instructions on obtaining and installing the
Voro++ software in the src/VORONOI/README file.
.. _voronoi: http://math.lbl.gov/voro++
.. _voronoi: http://math.lbl.gov/voro++/

79
doc/_sources/pair_airebo.txt
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@ -6,6 +6,12 @@ pair_style airebo command
pair_style airebo/omp command
=============================
pair_style airebo/morse command
===============================
pair_style airebo/morse/omp command
===================================
pair_style rebo command
=======================
@ -19,10 +25,10 @@ Syntax
pair_style style cutoff LJ_flag TORSION_flag
* style = *airebo* or *rebo*
* cutoff = LJ cutoff (sigma scale factor) (AIREBO only)
* LJ_flag = 0/1 to turn off/on the LJ term (AIREBO only, optional)
* TORSION_flag = 0/1 to turn off/on the torsion term (AIREBO only, optional)
* style = *airebo* or *airebo/morse* or *rebo*
* cutoff = LJ or Morse cutoff (sigma scale factor) (AIREBO and AIREBO-M only)
* LJ_flag = 0/1 to turn off/on the LJ or Morse term (AIREBO and AIREBO-M only, optional)
* TORSION_flag = 0/1 to turn off/on the torsion term (AIREBO and AIREBO-M only, optional)
Examples
""""""""
@ -33,6 +39,11 @@ Examples
pair_style airebo 2.5 1 0
pair_coeff * * ../potentials/CH.airebo H C
.. parsed-literal::
pair_style airebo/morse 3.0
pair_coeff * * ../potentials/CH.airebo-m H C
.. parsed-literal::
pair_style rebo
@ -44,12 +55,21 @@ Description
The *airebo* pair style computes the Adaptive Intermolecular Reactive
Empirical Bond Order (AIREBO) Potential of :ref:`(Stuart) <Stuart>` for a
system of carbon and/or hydrogen atoms. Note that this is the initial
formulation of AIREBO from 2000, not the later formulation. The
*rebo* pair style computes the Reactive Empirical Bond Order (REBO)
Potential of :ref:`(Brenner) <Brenner>`. Note that this is the so-called
2nd generation REBO from 2002, not the original REBO from 1990. As
discussed below, 2nd generation REBO is closely related to the intial
AIREBO; it is just a subset of the potential energy terms.
formulation of AIREBO from 2000, not the later formulation.
The *airebo/morse* pair style computes the AIREBO-M potential, which
is equivalent to AIREBO, but replaces the LJ term with a Morse potential.
The Morse potentials are parameterized by high-quality quantum chemistry
(MP2) calculations and do not diverge as quickly as particle density
increases. This allows AIREBO-M to retain accuracy to much higher pressures
than AIREBO (up to 40 GPa for Polyethylene). Details for this potential
and its parameterization are given in :ref:`(O'Conner) <OConnor>`.
The *rebo* pair style computes the Reactive Empirical Bond Order (REBO)
Potential of :ref:`(Brenner) <Brenner>`. Note that this is the so-called
2nd generation REBO from 2002, not the original REBO from 1990.
As discussed below, 2nd generation REBO is closely related to the
intial AIREBO; it is just a subset of the potential energy terms.
The AIREBO potential consists of three terms:
@ -62,7 +82,7 @@ included, the LJ and torsional terms can be turned off. Note that
both or neither of the flags must be included. If both of the LJ an
torsional terms are turned off, it becomes the 2nd-generation REBO
potential, with a small caveat on the spline fitting procedure
mentioned below. This can be specified directly as pair_style rebo
mentioned below. This can be specified directly as pair_style *rebo*
with no additional arguments.
The detailed formulas for this potential are given in
@ -101,12 +121,13 @@ various dihedral angle preferences in hydrocarbon configurations.
----------
Only a single pair_coeff command is used with the *airebo* or *rebo*
style which specifies an AIREBO potential file with parameters for C
and H. Note that the *rebo* style in LAMMPS uses the same
AIREBO-formatted potential file. These are mapped to LAMMPS atom
types by specifying N additional arguments after the filename in the
pair_coeff command, where N is the number of LAMMPS atom types:
Only a single pair_coeff command is used with the *airebo*, *airebo*
or *rebo* style which specifies an AIREBO or AIREBO-M potential file
with parameters for C and H. Note that the *rebo* style in LAMMPS
uses the same AIREBO-formatted potential file. These are mapped to
LAMMPS atom types by specifying N additional arguments after the
filename in the pair_coeff command, where N is the number of LAMMPS
atom types:
* filename
* N element names = mapping of AIREBO elements to atom types
@ -136,6 +157,13 @@ the CH.airebo file to agree with the original :ref:`(Stuart) <Stuart>`
paper. Thus the parameters are specific to this potential and the way
it was fit, so modifying the file should be done cautiously.
Similarly the parameters/coefficients for the AIREBO-M potentials are
listed in the CH.airebo-m file to agree with the :ref:`(O'Connor) <OConnor>`
paper. Thus the parameters are specific to this potential and the way
it was fit, so modifying the file should be done cautiously. The
AIREBO-M Morse potentials were parameterized using a cutoff of
3.0 (sigma). Modifying this cutoff may impact simulation accuracy.
----------
@ -188,11 +216,12 @@ for more info.
These pair potentials require the :doc:`newton <newton>` setting to be
"on" for pair interactions.
The CH.airebo potential file provided with LAMMPS (see the potentials
directory) is parameterized for metal :doc:`units <units>`. You can use
the AIREBO or REBO potential with any LAMMPS units, but you would need
to create your own AIREBO potential file with coefficients listed in
the appropriate units if your simulation doesn't use "metal" units.
The CH.airebo and CH.airebo-m potential files provided with LAMMPS
(see the potentials directory) are parameterized for metal :doc:`units <units>`.
You can use the AIREBO, AIREBO-M or REBO potential with any LAMMPS units,
but you would need to create your own AIREBO or AIREBO-M potential file
with coefficients listed in the appropriate units, if your simulation
doesn't use "metal" units.
Related commands
""""""""""""""""
@ -219,6 +248,12 @@ Related commands
**(Brenner)** Brenner, Shenderova, Harrison, Stuart, Ni, Sinnott, J
Physics: Condensed Matter, 14, 783-802 (2002).
.. _OConnor:
**(O'Connor)** O'Connor et al., J. Chem. Phys. 142, 024903 (2015).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html

1
doc/_sources/pair_style.txt
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@ -105,6 +105,7 @@ in the pair section of :ref:`this page <cmd_5>`.
* :doc:`pair_style adp <pair_adp>` - angular dependent potential (ADP) of Mishin
* :doc:`pair_style airebo <pair_airebo>` - AIREBO potential of Stuart
* :doc:`pair_style airebo/morse <pair_airebo>` - AIREBO with Morse instead of LJ
* :doc:`pair_style beck <pair_beck>` - Beck potential
* :doc:`pair_style body <pair_body>` - interactions between body particles
* :doc:`pair_style bop <pair_bop>` - BOP potential of Pettifor

13
doc/compute_tally.html
View File

@ -133,6 +133,9 @@
<div class="section" id="compute-pe-tally-command">
<h1>compute pe/tally command<a class="headerlink" href="#compute-pe-tally-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="compute-pe-mol-tally-command">
<h1>compute pe/mol/tally command<a class="headerlink" href="#compute-pe-mol-tally-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="compute-stress-tally-command">
<h1>compute stress/tally command<a class="headerlink" href="#compute-stress-tally-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">
@ -142,7 +145,7 @@
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><em>compute</em></a> command</li>
<li>style = <em>force/tally</em> or <em>pe/tally</em> or <em>stress/tally</em></li>
<li>style = <em>force/tally</em> or <em>pe/tally</em> or <em>pe/mol/tally</em> or <em>stress/tally</em></li>
<li>group2-ID = group ID of second (or same) group</li>
</ul>
</div>
@ -175,7 +178,13 @@ pairwise property computations.</p>
<p><strong>Output info:</strong></p>
<p>Compute <em>pe/tally</em> calculates a global scalar (the energy) and a per
atom scalar (the contributions of the single atom to the global
scalar). Compute <em>force/tally</em> calculates a global scalar (the force
scalar). Compute <em>pe/mol/tally</em> calculates a global 4-element vector
containing (in this order): <em>evdwl</em> and <em>ecoul</em> for intramolecular pairs
and <em>evdwl</em> and <em>ecoul</em> for intermolecular pairs. Since molecules are
identified my their molecule IDs, the partitioning does not have to be
related to molecules, but the energies are tallied into the respective
slots depending on whether the molecule IDs of a pair are the same or
different. Compute <em>force/tally</em> calculates a global scalar (the force
magnitude) and a per atom 3-element vector (force contribution from
each atom). Compute <em>stress/tally</em> calculates a global scalar
(average of the diagonal elements of the stress tensor) and a per atom

11
doc/compute_tally.txt
View File

@ -9,6 +9,7 @@
compute force/tally command :h3
compute heat/flux/tally command :h3
compute pe/tally command :h3
compute pe/mol/tally command :h3
compute stress/tally command :h3
[Syntax:]
@ -16,7 +17,7 @@ compute stress/tally command :h3
compute ID group-ID style group2-ID :pre
ID, group-ID are documented in "compute"_compute.html command
style = {force/tally} or {pe/tally} or {stress/tally}
style = {force/tally} or {pe/tally} or {pe/mol/tally} or {stress/tally}
group2-ID = group ID of second (or same) group :ul
[Examples:]
@ -52,7 +53,13 @@ pairwise property computations.
Compute {pe/tally} calculates a global scalar (the energy) and a per
atom scalar (the contributions of the single atom to the global
scalar). Compute {force/tally} calculates a global scalar (the force
scalar). Compute {pe/mol/tally} calculates a global 4-element vector
containing (in this order): {evdwl} and {ecoul} for intramolecular pairs
and {evdwl} and {ecoul} for intermolecular pairs. Since molecules are
identified my their molecule IDs, the partitioning does not have to be
related to molecules, but the energies are tallied into the respective
slots depending on whether the molecule IDs of a pair are the same or
different. Compute {force/tally} calculates a global scalar (the force
magnitude) and a per atom 3-element vector (force contribution from
each atom). Compute {stress/tally} calculates a global scalar
(average of the diagonal elements of the stress tensor) and a per atom

2
doc/compute_voronoi_atom.html
View File

@ -256,7 +256,7 @@ dump d2 all local 1 dump.neighbors index c_6[1] c_6[2] c_6[3]
<p>If the <em>face_threshold</em> keyword is used, then only faces
with areas greater than the threshold are stored.</p>
<hr class="docutils" />
<p>The Voronoi calculation is performed by the freely available <a class="reference external" href="http://math.lbl.gov/voro++">Voro++ package</a>, written by Chris Rycroft at UC Berkeley and LBL,
<p>The Voronoi calculation is performed by the freely available <a class="reference external" href="http://math.lbl.gov/voro++/">Voro++ package</a>, written by Chris Rycroft at UC Berkeley and LBL,
which must be installed on your system when building LAMMPS for use
with this compute. See instructions on obtaining and installing the
Voro++ software in the src/VORONOI/README file.</p>

2
doc/compute_voronoi_atom.txt
View File

@ -149,7 +149,7 @@ which must be installed on your system when building LAMMPS for use
with this compute. See instructions on obtaining and installing the
Voro++ software in the src/VORONOI/README file.
:link(voronoi,http://math.lbl.gov/voro++)
:link(voronoi,http://math.lbl.gov/voro++/)
NOTE: The calculation of Voronoi volumes is performed by each
processor for the atoms it owns, and includes the effect of ghost

70
doc/pair_airebo.html
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@ -130,6 +130,12 @@
<div class="section" id="pair-style-airebo-omp-command">
<h1>pair_style airebo/omp command<a class="headerlink" href="#pair-style-airebo-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-airebo-morse-command">
<h1>pair_style airebo/morse command<a class="headerlink" href="#pair-style-airebo-morse-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-airebo-morse-omp-command">
<h1>pair_style airebo/morse/omp command<a class="headerlink" href="#pair-style-airebo-morse-omp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-rebo-command">
<h1>pair_style rebo command<a class="headerlink" href="#pair-style-rebo-command" title="Permalink to this headline"></a></h1>
</div>
@ -141,10 +147,10 @@
</pre></div>
</div>
<ul class="simple">
<li>style = <em>airebo</em> or <em>rebo</em></li>
<li>cutoff = LJ cutoff (sigma scale factor) (AIREBO only)</li>
<li>LJ_flag = 0/1 to turn off/on the LJ term (AIREBO only, optional)</li>
<li>TORSION_flag = 0/1 to turn off/on the torsion term (AIREBO only, optional)</li>
<li>style = <em>airebo</em> or <em>airebo/morse</em> or <em>rebo</em></li>
<li>cutoff = LJ or Morse cutoff (sigma scale factor) (AIREBO and AIREBO-M only)</li>
<li>LJ_flag = 0/1 to turn off/on the LJ or Morse term (AIREBO and AIREBO-M only, optional)</li>
<li>TORSION_flag = 0/1 to turn off/on the torsion term (AIREBO and AIREBO-M only, optional)</li>
</ul>
</div>
<div class="section" id="examples">
@ -154,6 +160,10 @@ pair_style airebo 2.5 1 0
pair_coeff * * ../potentials/CH.airebo H C
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style airebo/morse 3.0
pair_coeff * * ../potentials/CH.airebo-m H C
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style rebo
pair_coeff * * ../potentials/CH.airebo H C
</pre></div>
@ -164,12 +174,19 @@ pair_coeff * * ../potentials/CH.airebo H C
<p>The <em>airebo</em> pair style computes the Adaptive Intermolecular Reactive
Empirical Bond Order (AIREBO) Potential of <a class="reference internal" href="#stuart"><span>(Stuart)</span></a> for a
system of carbon and/or hydrogen atoms. Note that this is the initial
formulation of AIREBO from 2000, not the later formulation. The
<em>rebo</em> pair style computes the Reactive Empirical Bond Order (REBO)
Potential of <a class="reference internal" href="#brenner"><span>(Brenner)</span></a>. Note that this is the so-called
2nd generation REBO from 2002, not the original REBO from 1990. As
discussed below, 2nd generation REBO is closely related to the intial
AIREBO; it is just a subset of the potential energy terms.</p>
formulation of AIREBO from 2000, not the later formulation.</p>
<p>The <em>airebo/morse</em> pair style computes the AIREBO-M potential, which
is equivalent to AIREBO, but replaces the LJ term with a Morse potential.
The Morse potentials are parameterized by high-quality quantum chemistry
(MP2) calculations and do not diverge as quickly as particle density
increases. This allows AIREBO-M to retain accuracy to much higher pressures
than AIREBO (up to 40 GPa for Polyethylene). Details for this potential
and its parameterization are given in <a class="reference internal" href="#oconnor"><span>(O&#8217;Conner)</span></a>.</p>
<p>The <em>rebo</em> pair style computes the Reactive Empirical Bond Order (REBO)
Potential of <a class="reference internal" href="#brenner"><span>(Brenner)</span></a>. Note that this is the so-called
2nd generation REBO from 2002, not the original REBO from 1990.
As discussed below, 2nd generation REBO is closely related to the
intial AIREBO; it is just a subset of the potential energy terms.</p>
<p>The AIREBO potential consists of three terms:</p>
<img alt="_images/pair_airebo.jpg" class="align-center" src="_images/pair_airebo.jpg" />
<p>By default, all three terms are included. For the <em>airebo</em> style, if
@ -178,7 +195,7 @@ included, the LJ and torsional terms can be turned off. Note that
both or neither of the flags must be included. If both of the LJ an
torsional terms are turned off, it becomes the 2nd-generation REBO
potential, with a small caveat on the spline fitting procedure
mentioned below. This can be specified directly as pair_style rebo
mentioned below. This can be specified directly as pair_style <em>rebo</em>
with no additional arguments.</p>
<p>The detailed formulas for this potential are given in
<a class="reference internal" href="#stuart"><span>(Stuart)</span></a>; here we provide only a brief description.</p>
@ -209,12 +226,13 @@ would be 10.2 Angstroms.</p>
<p>The E_TORSION term is an explicit 4-body potential that describes
various dihedral angle preferences in hydrocarbon configurations.</p>
<hr class="docutils" />
<p>Only a single pair_coeff command is used with the <em>airebo</em> or <em>rebo</em>
style which specifies an AIREBO potential file with parameters for C
and H. Note that the <em>rebo</em> style in LAMMPS uses the same
AIREBO-formatted potential file. These are mapped to LAMMPS atom
types by specifying N additional arguments after the filename in the
pair_coeff command, where N is the number of LAMMPS atom types:</p>
<p>Only a single pair_coeff command is used with the <em>airebo</em>, <em>airebo</em>
or <em>rebo</em> style which specifies an AIREBO or AIREBO-M potential file
with parameters for C and H. Note that the <em>rebo</em> style in LAMMPS
uses the same AIREBO-formatted potential file. These are mapped to
LAMMPS atom types by specifying N additional arguments after the
filename in the pair_coeff command, where N is the number of LAMMPS
atom types:</p>
<ul class="simple">
<li>filename</li>
<li>N element names = mapping of AIREBO elements to atom types</li>
@ -239,6 +257,12 @@ other potentials.</p>
the CH.airebo file to agree with the original <a class="reference internal" href="#stuart"><span>(Stuart)</span></a>
paper. Thus the parameters are specific to this potential and the way
it was fit, so modifying the file should be done cautiously.</p>
<p>Similarly the parameters/coefficients for the AIREBO-M potentials are
listed in the CH.airebo-m file to agree with the <a class="reference internal" href="#oconnor"><span>(O&#8217;Connor)</span></a>
paper. Thus the parameters are specific to this potential and the way
it was fit, so modifying the file should be done cautiously. The
AIREBO-M Morse potentials were parameterized using a cutoff of
3.0 (sigma). Modifying this cutoff may impact simulation accuracy.</p>
<hr class="docutils" />
<p>Styles with a <em>cuda</em>, <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
functionally the same as the corresponding style without the suffix.
@ -274,11 +298,12 @@ default). See the <a class="reference internal" href="Section_start.html#start-
for more info.</p>
<p>These pair potentials require the <a class="reference internal" href="newton.html"><em>newton</em></a> setting to be
&#8220;on&#8221; for pair interactions.</p>
<p>The CH.airebo potential file provided with LAMMPS (see the potentials
directory) is parameterized for metal <a class="reference internal" href="units.html"><em>units</em></a>. You can use
the AIREBO or REBO potential with any LAMMPS units, but you would need
to create your own AIREBO potential file with coefficients listed in
the appropriate units if your simulation doesn&#8217;t use &#8220;metal&#8221; units.</p>
<p>The CH.airebo and CH.airebo-m potential files provided with LAMMPS
(see the potentials directory) are parameterized for metal <a class="reference internal" href="units.html"><em>units</em></a>.
You can use the AIREBO, AIREBO-M or REBO potential with any LAMMPS units,
but you would need to create your own AIREBO or AIREBO-M potential file
with coefficients listed in the appropriate units, if your simulation
doesn&#8217;t use &#8220;metal&#8221; units.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
@ -289,6 +314,7 @@ the appropriate units if your simulation doesn&#8217;t use &#8220;metal&#8221; u
(2000).</p>
<p id="brenner"><strong>(Brenner)</strong> Brenner, Shenderova, Harrison, Stuart, Ni, Sinnott, J
Physics: Condensed Matter, 14, 783-802 (2002).</p>
<p id="oconnor"><strong>(O&#8217;Connor)</strong> O&#8217;Connor et al., J. Chem. Phys. 142, 024903 (2015).</p>
</div>
</div>

70
doc/pair_airebo.txt
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@ -8,6 +8,8 @@
pair_style airebo command :h3
pair_style airebo/omp command :h3
pair_style airebo/morse command :h3
pair_style airebo/morse/omp command :h3
pair_style rebo command :h3
pair_style rebo/omp command :h3
@ -15,10 +17,10 @@ pair_style rebo/omp command :h3
pair_style style cutoff LJ_flag TORSION_flag :pre
style = {airebo} or {rebo}
cutoff = LJ cutoff (sigma scale factor) (AIREBO only)
LJ_flag = 0/1 to turn off/on the LJ term (AIREBO only, optional)
TORSION_flag = 0/1 to turn off/on the torsion term (AIREBO only, optional) :ul
style = {airebo} or {airebo/morse} or {rebo}
cutoff = LJ or Morse cutoff (sigma scale factor) (AIREBO and AIREBO-M only)
LJ_flag = 0/1 to turn off/on the LJ or Morse term (AIREBO and AIREBO-M only, optional)
TORSION_flag = 0/1 to turn off/on the torsion term (AIREBO and AIREBO-M only, optional) :ul
[Examples:]
@ -26,6 +28,9 @@ pair_style airebo 3.0
pair_style airebo 2.5 1 0
pair_coeff * * ../potentials/CH.airebo H C :pre
pair_style airebo/morse 3.0
pair_coeff * * ../potentials/CH.airebo-m H C :pre
pair_style rebo
pair_coeff * * ../potentials/CH.airebo H C :pre
@ -34,12 +39,21 @@ pair_coeff * * ../potentials/CH.airebo H C :pre
The {airebo} pair style computes the Adaptive Intermolecular Reactive
Empirical Bond Order (AIREBO) Potential of "(Stuart)"_#Stuart for a
system of carbon and/or hydrogen atoms. Note that this is the initial
formulation of AIREBO from 2000, not the later formulation. The
{rebo} pair style computes the Reactive Empirical Bond Order (REBO)
Potential of "(Brenner)"_#Brenner. Note that this is the so-called
2nd generation REBO from 2002, not the original REBO from 1990. As
discussed below, 2nd generation REBO is closely related to the intial
AIREBO; it is just a subset of the potential energy terms.
formulation of AIREBO from 2000, not the later formulation.
The {airebo/morse} pair style computes the AIREBO-M potential, which
is equivalent to AIREBO, but replaces the LJ term with a Morse potential.
The Morse potentials are parameterized by high-quality quantum chemistry
(MP2) calculations and do not diverge as quickly as particle density
increases. This allows AIREBO-M to retain accuracy to much higher pressures
than AIREBO (up to 40 GPa for Polyethylene). Details for this potential
and its parameterization are given in "(O'Conner)"_#OConnor.
The {rebo} pair style computes the Reactive Empirical Bond Order (REBO)
Potential of "(Brenner)"_#Brenner. Note that this is the so-called
2nd generation REBO from 2002, not the original REBO from 1990.
As discussed below, 2nd generation REBO is closely related to the
intial AIREBO; it is just a subset of the potential energy terms.
The AIREBO potential consists of three terms:
@ -51,7 +65,7 @@ included, the LJ and torsional terms can be turned off. Note that
both or neither of the flags must be included. If both of the LJ an
torsional terms are turned off, it becomes the 2nd-generation REBO
potential, with a small caveat on the spline fitting procedure
mentioned below. This can be specified directly as pair_style rebo
mentioned below. This can be specified directly as pair_style {rebo}
with no additional arguments.
The detailed formulas for this potential are given in
@ -88,12 +102,13 @@ various dihedral angle preferences in hydrocarbon configurations.
:line
Only a single pair_coeff command is used with the {airebo} or {rebo}
style which specifies an AIREBO potential file with parameters for C
and H. Note that the {rebo} style in LAMMPS uses the same
AIREBO-formatted potential file. These are mapped to LAMMPS atom
types by specifying N additional arguments after the filename in the
pair_coeff command, where N is the number of LAMMPS atom types:
Only a single pair_coeff command is used with the {airebo}, {airebo}
or {rebo} style which specifies an AIREBO or AIREBO-M potential file
with parameters for C and H. Note that the {rebo} style in LAMMPS
uses the same AIREBO-formatted potential file. These are mapped to
LAMMPS atom types by specifying N additional arguments after the
filename in the pair_coeff command, where N is the number of LAMMPS
atom types:
filename
N element names = mapping of AIREBO elements to atom types :ul
@ -121,6 +136,13 @@ the CH.airebo file to agree with the original "(Stuart)"_#Stuart
paper. Thus the parameters are specific to this potential and the way
it was fit, so modifying the file should be done cautiously.
Similarly the parameters/coefficients for the AIREBO-M potentials are
listed in the CH.airebo-m file to agree with the "(O'Connor)"_#OConnor
paper. Thus the parameters are specific to this potential and the way
it was fit, so modifying the file should be done cautiously. The
AIREBO-M Morse potentials were parameterized using a cutoff of
3.0 (sigma). Modifying this cutoff may impact simulation accuracy.
:line
Styles with a {cuda}, {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
@ -170,11 +192,12 @@ for more info.
These pair potentials require the "newton"_newton.html setting to be
"on" for pair interactions.
The CH.airebo potential file provided with LAMMPS (see the potentials
directory) is parameterized for metal "units"_units.html. You can use
the AIREBO or REBO potential with any LAMMPS units, but you would need
to create your own AIREBO potential file with coefficients listed in
the appropriate units if your simulation doesn't use "metal" units.
The CH.airebo and CH.airebo-m potential files provided with LAMMPS
(see the potentials directory) are parameterized for metal "units"_units.html.
You can use the AIREBO, AIREBO-M or REBO potential with any LAMMPS units,
but you would need to create your own AIREBO or AIREBO-M potential file
with coefficients listed in the appropriate units, if your simulation
doesn't use "metal" units.
[Related commands:]
@ -191,3 +214,6 @@ the appropriate units if your simulation doesn't use "metal" units.
:link(Brenner)
[(Brenner)] Brenner, Shenderova, Harrison, Stuart, Ni, Sinnott, J
Physics: Condensed Matter, 14, 783-802 (2002).
:link(OConnor)
[(O'Connor)] O'Connor et al., J. Chem. Phys. 142, 024903 (2015).

1
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@ -211,6 +211,7 @@ in the pair section of <a class="reference internal" href="Section_commands.html
<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_airebo.html"><em>pair_style airebo/morse</em></a> - AIREBO with Morse instead of LJ</li>
<li><a class="reference internal" href="pair_beck.html"><em>pair_style beck</em></a> - Beck potential</li>
<li><a class="reference internal" href="pair_body.html"><em>pair_style body</em></a> - interactions between body particles</li>
<li><a class="reference internal" href="pair_bop.html"><em>pair_style bop</em></a> - BOP potential of Pettifor</li>

1
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@ -102,6 +102,7 @@ in the pair section of "this page"_Section_commands.html#cmd_5.
"pair_style adp"_pair_adp.html - angular dependent potential (ADP) of Mishin
"pair_style airebo"_pair_airebo.html - AIREBO potential of Stuart
"pair_style airebo/morse"_pair_airebo.html - AIREBO with Morse instead of LJ
"pair_style beck"_pair_beck.html - Beck potential
"pair_style body"_pair_body.html - interactions between body particles
"pair_style bop"_pair_bop.html - BOP potential of Pettifor

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@ -189,8 +189,8 @@ short distances by a function</p>
\frac{s_{ij} r_{ij} }{2} \right)
\exp \left( - s_{ij} r_{ij} \right) \end{equation}\]</div>
<p>This function results from an adaptation to point charges
<a class="reference internal" href="#noskov"><span>(Noskov)</span></a> of the dipole screening scheme originally proposed
by <a class="reference internal" href="#thole"><span>Thole</span></a>. The scaling coefficient <span class="math">\(s_{ij}\)</span> is determined
<a class="reference internal" href="tutorial_drude.html#noskov"><span>(Noskov)</span></a> of the dipole screening scheme originally proposed
by <a class="reference internal" href="tutorial_drude.html#thole"><span>Thole</span></a>. The scaling coefficient <span class="math">\(s_{ij}\)</span> is determined
by the polarizability of the atoms, <span class="math">\(\alpha_i\)</span>, and by a Thole
damping parameter <span class="math">\(a\)</span>. This Thole damping parameter usually takes
a value of 2.6, but in certain force fields the value can depend upon

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