diff --git a/doc/html/Section_commands.html b/doc/html/Section_commands.html
index 82c88e4819..b1cf39721f 100644
--- a/doc/html/Section_commands.html
+++ b/doc/html/Section_commands.html
@@ -619,13 +619,13 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.</p>
 <table border="1" class="docutils">
 <colgroup>
 <col width="15%" />
+<col width="15%" />
 <col width="11%" />
 <col width="13%" />
+<col width="11%" />
+<col width="11%" />
 <col width="12%" />
-<col width="12%" />
-<col width="12%" />
-<col width="10%" />
-<col width="15%" />
+<col width="11%" />
 </colgroup>
 <tbody valign="top">
 <tr class="row-odd"><td><a class="reference internal" href="fix_adapt.html"><span class="doc">adapt</span></a></td>
@@ -646,122 +646,131 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.</p>
 <td><a class="reference internal" href="fix_bond_swap.html"><span class="doc">bond/swap</span></a></td>
 <td><a class="reference internal" href="fix_box_relax.html"><span class="doc">box/relax</span></a></td>
 </tr>
-<tr class="row-odd"><td><a class="reference internal" href="fix_deform.html"><span class="doc">deform (k)</span></a></td>
+<tr class="row-odd"><td><a class="reference internal" href="fix_controller.html"><span class="doc">controller</span></a></td>
+<td><a class="reference internal" href="fix_deform.html"><span class="doc">deform (k)</span></a></td>
 <td><a class="reference internal" href="fix_deposit.html"><span class="doc">deposit</span></a></td>
 <td><a class="reference internal" href="fix_drag.html"><span class="doc">drag</span></a></td>
 <td><a class="reference internal" href="fix_dt_reset.html"><span class="doc">dt/reset</span></a></td>
 <td><a class="reference internal" href="fix_efield.html"><span class="doc">efield</span></a></td>
 <td><a class="reference internal" href="fix_ehex.html"><span class="doc">ehex</span></a></td>
 <td><a class="reference internal" href="fix_enforce2d.html"><span class="doc">enforce2d</span></a></td>
-<td><a class="reference internal" href="fix_evaporate.html"><span class="doc">evaporate</span></a></td>
 </tr>
-<tr class="row-even"><td><a class="reference internal" href="fix_external.html"><span class="doc">external</span></a></td>
+<tr class="row-even"><td><a class="reference internal" href="fix_evaporate.html"><span class="doc">evaporate</span></a></td>
+<td><a class="reference internal" href="fix_external.html"><span class="doc">external</span></a></td>
 <td><a class="reference internal" href="fix_freeze.html"><span class="doc">freeze</span></a></td>
 <td><a class="reference internal" href="fix_gcmc.html"><span class="doc">gcmc</span></a></td>
 <td><a class="reference internal" href="fix_gld.html"><span class="doc">gld</span></a></td>
 <td><a class="reference internal" href="fix_gravity.html"><span class="doc">gravity (o)</span></a></td>
 <td><a class="reference internal" href="fix_heat.html"><span class="doc">heat</span></a></td>
 <td><a class="reference internal" href="fix_indent.html"><span class="doc">indent</span></a></td>
-<td><a class="reference internal" href="fix_langevin.html"><span class="doc">langevin (k)</span></a></td>
 </tr>
-<tr class="row-odd"><td><a class="reference internal" href="fix_lineforce.html"><span class="doc">lineforce</span></a></td>
+<tr class="row-odd"><td><a class="reference internal" href="fix_langevin.html"><span class="doc">langevin (k)</span></a></td>
+<td><a class="reference internal" href="fix_lineforce.html"><span class="doc">lineforce</span></a></td>
 <td><a class="reference internal" href="fix_momentum.html"><span class="doc">momentum</span></a></td>
 <td><a class="reference internal" href="fix_move.html"><span class="doc">move</span></a></td>
 <td><a class="reference internal" href="fix_msst.html"><span class="doc">msst</span></a></td>
 <td><a class="reference internal" href="fix_neb.html"><span class="doc">neb</span></a></td>
 <td><a class="reference internal" href="fix_nh.html"><span class="doc">nph (ko)</span></a></td>
 <td><a class="reference internal" href="fix_nphug.html"><span class="doc">nphug (o)</span></a></td>
-<td><a class="reference internal" href="fix_nph_asphere.html"><span class="doc">nph/asphere (o)</span></a></td>
 </tr>
-<tr class="row-even"><td><a class="reference internal" href="fix_nph_body.html"><span class="doc">nph/body</span></a></td>
+<tr class="row-even"><td><a class="reference internal" href="fix_nph_asphere.html"><span class="doc">nph/asphere (o)</span></a></td>
+<td><a class="reference internal" href="fix_nph_body.html"><span class="doc">nph/body</span></a></td>
 <td><a class="reference internal" href="fix_nph_sphere.html"><span class="doc">nph/sphere (o)</span></a></td>
 <td><a class="reference internal" href="fix_nh.html"><span class="doc">npt (kio)</span></a></td>
 <td><a class="reference internal" href="fix_npt_asphere.html"><span class="doc">npt/asphere (o)</span></a></td>
 <td><a class="reference internal" href="fix_npt_body.html"><span class="doc">npt/body</span></a></td>
 <td><a class="reference internal" href="fix_npt_sphere.html"><span class="doc">npt/sphere (o)</span></a></td>
 <td><a class="reference internal" href="fix_nve.html"><span class="doc">nve (kio)</span></a></td>
-<td><a class="reference internal" href="fix_nve_asphere.html"><span class="doc">nve/asphere (i)</span></a></td>
 </tr>
-<tr class="row-odd"><td><a class="reference internal" href="fix_nve_asphere_noforce.html"><span class="doc">nve/asphere/noforce</span></a></td>
+<tr class="row-odd"><td><a class="reference internal" href="fix_nve_asphere.html"><span class="doc">nve/asphere (i)</span></a></td>
+<td><a class="reference internal" href="fix_nve_asphere_noforce.html"><span class="doc">nve/asphere/noforce</span></a></td>
 <td><a class="reference internal" href="fix_nve_body.html"><span class="doc">nve/body</span></a></td>
 <td><a class="reference internal" href="fix_nve_limit.html"><span class="doc">nve/limit</span></a></td>
 <td><a class="reference internal" href="fix_nve_line.html"><span class="doc">nve/line</span></a></td>
 <td><a class="reference internal" href="fix_nve_noforce.html"><span class="doc">nve/noforce</span></a></td>
 <td><a class="reference internal" href="fix_nve_sphere.html"><span class="doc">nve/sphere (o)</span></a></td>
 <td><a class="reference internal" href="fix_nve_tri.html"><span class="doc">nve/tri</span></a></td>
-<td><a class="reference internal" href="fix_nh.html"><span class="doc">nvt (iko)</span></a></td>
 </tr>
-<tr class="row-even"><td><a class="reference internal" href="fix_nvt_asphere.html"><span class="doc">nvt/asphere (o)</span></a></td>
+<tr class="row-even"><td><a class="reference internal" href="fix_nh.html"><span class="doc">nvt (iko)</span></a></td>
+<td><a class="reference internal" href="fix_nvt_asphere.html"><span class="doc">nvt/asphere (o)</span></a></td>
 <td><a class="reference internal" href="fix_nvt_body.html"><span class="doc">nvt/body</span></a></td>
 <td><a class="reference internal" href="fix_nvt_sllod.html"><span class="doc">nvt/sllod (io)</span></a></td>
 <td><a class="reference internal" href="fix_nvt_sphere.html"><span class="doc">nvt/sphere (o)</span></a></td>
 <td><a class="reference internal" href="fix_oneway.html"><span class="doc">oneway</span></a></td>
 <td><a class="reference internal" href="fix_orient.html"><span class="doc">orient/bcc</span></a></td>
 <td><a class="reference internal" href="fix_orient.html"><span class="doc">orient/fcc</span></a></td>
-<td><a class="reference internal" href="fix_planeforce.html"><span class="doc">planeforce</span></a></td>
 </tr>
-<tr class="row-odd"><td><a class="reference internal" href="fix_poems.html"><span class="doc">poems</span></a></td>
+<tr class="row-odd"><td><a class="reference internal" href="fix_planeforce.html"><span class="doc">planeforce</span></a></td>
+<td><a class="reference internal" href="fix_poems.html"><span class="doc">poems</span></a></td>
 <td><a class="reference internal" href="fix_pour.html"><span class="doc">pour</span></a></td>
 <td><a class="reference internal" href="fix_press_berendsen.html"><span class="doc">press/berendsen</span></a></td>
 <td><a class="reference internal" href="fix_print.html"><span class="doc">print</span></a></td>
 <td><a class="reference internal" href="fix_property_atom.html"><span class="doc">property/atom</span></a></td>
 <td><a class="reference internal" href="fix_qeq_comb.html"><span class="doc">qeq/comb (o)</span></a></td>
 <td><a class="reference internal" href="fix_qeq.html"><span class="doc">qeq/dynamic</span></a></td>
-<td><a class="reference internal" href="fix_qeq.html"><span class="doc">qeq/fire</span></a></td>
 </tr>
-<tr class="row-even"><td><a class="reference internal" href="fix_qeq.html"><span class="doc">qeq/point</span></a></td>
+<tr class="row-even"><td><a class="reference internal" href="fix_qeq.html"><span class="doc">qeq/fire</span></a></td>
+<td><a class="reference internal" href="fix_qeq.html"><span class="doc">qeq/point</span></a></td>
 <td><a class="reference internal" href="fix_qeq.html"><span class="doc">qeq/shielded</span></a></td>
 <td><a class="reference internal" href="fix_qeq.html"><span class="doc">qeq/slater</span></a></td>
 <td><a class="reference internal" href="fix_shake.html"><span class="doc">rattle</span></a></td>
 <td><a class="reference internal" href="fix_reax_bonds.html"><span class="doc">reax/bonds</span></a></td>
 <td><a class="reference internal" href="fix_recenter.html"><span class="doc">recenter</span></a></td>
 <td><a class="reference internal" href="fix_restrain.html"><span class="doc">restrain</span></a></td>
-<td><a class="reference internal" href="fix_rigid.html"><span class="doc">rigid (o)</span></a></td>
 </tr>
-<tr class="row-odd"><td><a class="reference internal" href="fix_rigid.html"><span class="doc">rigid/nph (o)</span></a></td>
+<tr class="row-odd"><td><a class="reference internal" href="fix_rigid.html"><span class="doc">rigid (o)</span></a></td>
+<td><a class="reference internal" href="fix_rigid.html"><span class="doc">rigid/nph (o)</span></a></td>
 <td><a class="reference internal" href="fix_rigid.html"><span class="doc">rigid/npt (o)</span></a></td>
 <td><a class="reference internal" href="fix_rigid.html"><span class="doc">rigid/nve (o)</span></a></td>
 <td><a class="reference internal" href="fix_rigid.html"><span class="doc">rigid/nvt (o)</span></a></td>
 <td><a class="reference internal" href="fix_rigid.html"><span class="doc">rigid/small (o)</span></a></td>
 <td><a class="reference internal" href="fix_rigid.html"><span class="doc">rigid/small/nph</span></a></td>
 <td><a class="reference internal" href="fix_rigid.html"><span class="doc">rigid/small/npt</span></a></td>
-<td><a class="reference internal" href="fix_rigid.html"><span class="doc">rigid/small/nve</span></a></td>
 </tr>
-<tr class="row-even"><td><a class="reference internal" href="fix_rigid.html"><span class="doc">rigid/small/nvt</span></a></td>
+<tr class="row-even"><td><a class="reference internal" href="fix_rigid.html"><span class="doc">rigid/small/nve</span></a></td>
+<td><a class="reference internal" href="fix_rigid.html"><span class="doc">rigid/small/nvt</span></a></td>
 <td><a class="reference internal" href="fix_setforce.html"><span class="doc">setforce (k)</span></a></td>
 <td><a class="reference internal" href="fix_shake.html"><span class="doc">shake</span></a></td>
 <td><a class="reference internal" href="fix_spring.html"><span class="doc">spring</span></a></td>
 <td><a class="reference internal" href="fix_spring_chunk.html"><span class="doc">spring/chunk</span></a></td>
 <td><a class="reference internal" href="fix_spring_rg.html"><span class="doc">spring/rg</span></a></td>
 <td><a class="reference internal" href="fix_spring_self.html"><span class="doc">spring/self</span></a></td>
-<td><a class="reference internal" href="fix_srd.html"><span class="doc">srd</span></a></td>
 </tr>
-<tr class="row-odd"><td><a class="reference internal" href="fix_store_force.html"><span class="doc">store/force</span></a></td>
+<tr class="row-odd"><td><a class="reference internal" href="fix_srd.html"><span class="doc">srd</span></a></td>
+<td><a class="reference internal" href="fix_store_force.html"><span class="doc">store/force</span></a></td>
 <td><a class="reference internal" href="fix_store_state.html"><span class="doc">store/state</span></a></td>
 <td><a class="reference internal" href="fix_temp_berendsen.html"><span class="doc">temp/berendsen</span></a></td>
 <td><a class="reference internal" href="fix_temp_csvr.html"><span class="doc">temp/csld</span></a></td>
 <td><a class="reference internal" href="fix_temp_csvr.html"><span class="doc">temp/csvr</span></a></td>
 <td><a class="reference internal" href="fix_temp_rescale.html"><span class="doc">temp/rescale</span></a></td>
 <td><a class="reference internal" href="fix_tfmc.html"><span class="doc">tfmc</span></a></td>
-<td><a class="reference internal" href="fix_thermal_conductivity.html"><span class="doc">thermal/conductivity</span></a></td>
 </tr>
-<tr class="row-even"><td><a class="reference internal" href="fix_tmd.html"><span class="doc">tmd</span></a></td>
+<tr class="row-even"><td><a class="reference internal" href="fix_thermal_conductivity.html"><span class="doc">thermal/conductivity</span></a></td>
+<td><a class="reference internal" href="fix_tmd.html"><span class="doc">tmd</span></a></td>
 <td><a class="reference internal" href="fix_ttm.html"><span class="doc">ttm</span></a></td>
 <td><a class="reference internal" href="fix_tune_kspace.html"><span class="doc">tune/kspace</span></a></td>
 <td><a class="reference internal" href="fix_vector.html"><span class="doc">vector</span></a></td>
 <td><a class="reference internal" href="fix_viscosity.html"><span class="doc">viscosity</span></a></td>
 <td><a class="reference internal" href="fix_viscous.html"><span class="doc">viscous</span></a></td>
 <td><a class="reference internal" href="fix_wall.html"><span class="doc">wall/colloid</span></a></td>
-<td><a class="reference internal" href="fix_wall_gran.html"><span class="doc">wall/gran</span></a></td>
 </tr>
-<tr class="row-odd"><td><a class="reference internal" href="fix_wall.html"><span class="doc">wall/harmonic</span></a></td>
+<tr class="row-odd"><td><a class="reference internal" href="fix_wall_gran.html"><span class="doc">wall/gran</span></a></td>
+<td><a class="reference internal" href="fix_wall.html"><span class="doc">wall/harmonic</span></a></td>
 <td><a class="reference internal" href="fix_wall.html"><span class="doc">wall/lj1043</span></a></td>
 <td><a class="reference internal" href="fix_wall.html"><span class="doc">wall/lj126</span></a></td>
 <td><a class="reference internal" href="fix_wall.html"><span class="doc">wall/lj93</span></a></td>
 <td><a class="reference internal" href="fix_wall_piston.html"><span class="doc">wall/piston</span></a></td>
 <td><a class="reference internal" href="fix_wall_reflect.html"><span class="doc">wall/reflect (k)</span></a></td>
 <td><a class="reference internal" href="fix_wall_region.html"><span class="doc">wall/region</span></a></td>
-<td><a class="reference internal" href="fix_wall_srd.html"><span class="doc">wall/srd</span></a></td>
+</tr>
+<tr class="row-even"><td><a class="reference internal" href="fix_wall_srd.html"><span class="doc">wall/srd</span></a></td>
+<td>&nbsp;</td>
+<td>&nbsp;</td>
+<td>&nbsp;</td>
+<td>&nbsp;</td>
+<td>&nbsp;</td>
+<td>&nbsp;</td>
+<td>&nbsp;</td>
 </tr>
 </tbody>
 </table>
diff --git a/doc/html/_sources/Section_commands.txt b/doc/html/_sources/Section_commands.txt
index 94561dac94..a91b18f206 100644
--- a/doc/html/_sources/Section_commands.txt
+++ b/doc/html/_sources/Section_commands.txt
@@ -457,37 +457,39 @@ with the :doc:`appropriate accelerated package <Section_accelerate>`.
 This is indicated by additional letters in parenthesis: g = GPU, i =
 USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
 
-+------------------------------------------------------+-----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+
-| :doc:`adapt <fix_adapt>`                             | :doc:`addforce <fix_addforce>`          | :doc:`append/atoms <fix_append_atoms>`       | :doc:`atom/swap <fix_atom_swap>`         | :doc:`aveforce <fix_aveforce>`           | :doc:`ave/atom <fix_ave_atom>`             | :doc:`ave/chunk <fix_ave_chunk>`     | :doc:`ave/correlate <fix_ave_correlate>`               |
-+------------------------------------------------------+-----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+
-| :doc:`ave/histo <fix_ave_histo>`                     | :doc:`ave/histo/weight <fix_ave_histo>` | :doc:`ave/time <fix_ave_time>`               | :doc:`balance <fix_balance>`             | :doc:`bond/break <fix_bond_break>`       | :doc:`bond/create <fix_bond_create>`       | :doc:`bond/swap <fix_bond_swap>`     | :doc:`box/relax <fix_box_relax>`                       |
-+------------------------------------------------------+-----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+
-| :doc:`deform (k) <fix_deform>`                       | :doc:`deposit <fix_deposit>`            | :doc:`drag <fix_drag>`                       | :doc:`dt/reset <fix_dt_reset>`           | :doc:`efield <fix_efield>`               | :doc:`ehex <fix_ehex>`                     | :doc:`enforce2d <fix_enforce2d>`     | :doc:`evaporate <fix_evaporate>`                       |
-+------------------------------------------------------+-----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+
-| :doc:`external <fix_external>`                       | :doc:`freeze <fix_freeze>`              | :doc:`gcmc <fix_gcmc>`                       | :doc:`gld <fix_gld>`                     | :doc:`gravity (o) <fix_gravity>`         | :doc:`heat <fix_heat>`                     | :doc:`indent <fix_indent>`           | :doc:`langevin (k) <fix_langevin>`                     |
-+------------------------------------------------------+-----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+
-| :doc:`lineforce <fix_lineforce>`                     | :doc:`momentum <fix_momentum>`          | :doc:`move <fix_move>`                       | :doc:`msst <fix_msst>`                   | :doc:`neb <fix_neb>`                     | :doc:`nph (ko) <fix_nh>`                   | :doc:`nphug (o) <fix_nphug>`         | :doc:`nph/asphere (o) <fix_nph_asphere>`               |
-+------------------------------------------------------+-----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+
-| :doc:`nph/body <fix_nph_body>`                       | :doc:`nph/sphere (o) <fix_nph_sphere>`  | :doc:`npt (kio) <fix_nh>`                    | :doc:`npt/asphere (o) <fix_npt_asphere>` | :doc:`npt/body <fix_npt_body>`           | :doc:`npt/sphere (o) <fix_npt_sphere>`     | :doc:`nve (kio) <fix_nve>`           | :doc:`nve/asphere (i) <fix_nve_asphere>`               |
-+------------------------------------------------------+-----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+
-| :doc:`nve/asphere/noforce <fix_nve_asphere_noforce>` | :doc:`nve/body <fix_nve_body>`          | :doc:`nve/limit <fix_nve_limit>`             | :doc:`nve/line <fix_nve_line>`           | :doc:`nve/noforce <fix_nve_noforce>`     | :doc:`nve/sphere (o) <fix_nve_sphere>`     | :doc:`nve/tri <fix_nve_tri>`         | :doc:`nvt (iko) <fix_nh>`                              |
-+------------------------------------------------------+-----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+
-| :doc:`nvt/asphere (o) <fix_nvt_asphere>`             | :doc:`nvt/body <fix_nvt_body>`          | :doc:`nvt/sllod (io) <fix_nvt_sllod>`        | :doc:`nvt/sphere (o) <fix_nvt_sphere>`   | :doc:`oneway <fix_oneway>`               | :doc:`orient/bcc <fix_orient>`             | :doc:`orient/fcc <fix_orient>`       | :doc:`planeforce <fix_planeforce>`                     |
-+------------------------------------------------------+-----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+
-| :doc:`poems <fix_poems>`                             | :doc:`pour <fix_pour>`                  | :doc:`press/berendsen <fix_press_berendsen>` | :doc:`print <fix_print>`                 | :doc:`property/atom <fix_property_atom>` | :doc:`qeq/comb (o) <fix_qeq_comb>`         | :doc:`qeq/dynamic <fix_qeq>`         | :doc:`qeq/fire <fix_qeq>`                              |
-+------------------------------------------------------+-----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+
-| :doc:`qeq/point <fix_qeq>`                           | :doc:`qeq/shielded <fix_qeq>`           | :doc:`qeq/slater <fix_qeq>`                  | :doc:`rattle <fix_shake>`                | :doc:`reax/bonds <fix_reax_bonds>`       | :doc:`recenter <fix_recenter>`             | :doc:`restrain <fix_restrain>`       | :doc:`rigid (o) <fix_rigid>`                           |
-+------------------------------------------------------+-----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+
-| :doc:`rigid/nph (o) <fix_rigid>`                     | :doc:`rigid/npt (o) <fix_rigid>`        | :doc:`rigid/nve (o) <fix_rigid>`             | :doc:`rigid/nvt (o) <fix_rigid>`         | :doc:`rigid/small (o) <fix_rigid>`       | :doc:`rigid/small/nph <fix_rigid>`         | :doc:`rigid/small/npt <fix_rigid>`   | :doc:`rigid/small/nve <fix_rigid>`                     |
-+------------------------------------------------------+-----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+
-| :doc:`rigid/small/nvt <fix_rigid>`                   | :doc:`setforce (k) <fix_setforce>`      | :doc:`shake <fix_shake>`                     | :doc:`spring <fix_spring>`               | :doc:`spring/chunk <fix_spring_chunk>`   | :doc:`spring/rg <fix_spring_rg>`           | :doc:`spring/self <fix_spring_self>` | :doc:`srd <fix_srd>`                                   |
-+------------------------------------------------------+-----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+
-| :doc:`store/force <fix_store_force>`                 | :doc:`store/state <fix_store_state>`    | :doc:`temp/berendsen <fix_temp_berendsen>`   | :doc:`temp/csld <fix_temp_csvr>`         | :doc:`temp/csvr <fix_temp_csvr>`         | :doc:`temp/rescale <fix_temp_rescale>`     | :doc:`tfmc <fix_tfmc>`               | :doc:`thermal/conductivity <fix_thermal_conductivity>` |
-+------------------------------------------------------+-----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+
-| :doc:`tmd <fix_tmd>`                                 | :doc:`ttm <fix_ttm>`                    | :doc:`tune/kspace <fix_tune_kspace>`         | :doc:`vector <fix_vector>`               | :doc:`viscosity <fix_viscosity>`         | :doc:`viscous <fix_viscous>`               | :doc:`wall/colloid <fix_wall>`       | :doc:`wall/gran <fix_wall_gran>`                       |
-+------------------------------------------------------+-----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+
-| :doc:`wall/harmonic <fix_wall>`                      | :doc:`wall/lj1043 <fix_wall>`           | :doc:`wall/lj126 <fix_wall>`                 | :doc:`wall/lj93 <fix_wall>`              | :doc:`wall/piston <fix_wall_piston>`     | :doc:`wall/reflect (k) <fix_wall_reflect>` | :doc:`wall/region <fix_wall_region>` | :doc:`wall/srd <fix_wall_srd>`                         |
-+------------------------------------------------------+-----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+
++--------------------------------------------------------+------------------------------------------------------+----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+------------------------------------------+
+| :doc:`adapt <fix_adapt>`                               | :doc:`addforce <fix_addforce>`                       | :doc:`append/atoms <fix_append_atoms>` | :doc:`atom/swap <fix_atom_swap>`             | :doc:`aveforce <fix_aveforce>`           | :doc:`ave/atom <fix_ave_atom>`           | :doc:`ave/chunk <fix_ave_chunk>`           | :doc:`ave/correlate <fix_ave_correlate>` |
++--------------------------------------------------------+------------------------------------------------------+----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+------------------------------------------+
+| :doc:`ave/histo <fix_ave_histo>`                       | :doc:`ave/histo/weight <fix_ave_histo>`              | :doc:`ave/time <fix_ave_time>`         | :doc:`balance <fix_balance>`                 | :doc:`bond/break <fix_bond_break>`       | :doc:`bond/create <fix_bond_create>`     | :doc:`bond/swap <fix_bond_swap>`           | :doc:`box/relax <fix_box_relax>`         |
++--------------------------------------------------------+------------------------------------------------------+----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+------------------------------------------+
+| :doc:`controller <fix_controller>`                     | :doc:`deform (k) <fix_deform>`                       | :doc:`deposit <fix_deposit>`           | :doc:`drag <fix_drag>`                       | :doc:`dt/reset <fix_dt_reset>`           | :doc:`efield <fix_efield>`               | :doc:`ehex <fix_ehex>`                     | :doc:`enforce2d <fix_enforce2d>`         |
++--------------------------------------------------------+------------------------------------------------------+----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+------------------------------------------+
+| :doc:`evaporate <fix_evaporate>`                       | :doc:`external <fix_external>`                       | :doc:`freeze <fix_freeze>`             | :doc:`gcmc <fix_gcmc>`                       | :doc:`gld <fix_gld>`                     | :doc:`gravity (o) <fix_gravity>`         | :doc:`heat <fix_heat>`                     | :doc:`indent <fix_indent>`               |
++--------------------------------------------------------+------------------------------------------------------+----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+------------------------------------------+
+| :doc:`langevin (k) <fix_langevin>`                     | :doc:`lineforce <fix_lineforce>`                     | :doc:`momentum <fix_momentum>`         | :doc:`move <fix_move>`                       | :doc:`msst <fix_msst>`                   | :doc:`neb <fix_neb>`                     | :doc:`nph (ko) <fix_nh>`                   | :doc:`nphug (o) <fix_nphug>`             |
++--------------------------------------------------------+------------------------------------------------------+----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+------------------------------------------+
+| :doc:`nph/asphere (o) <fix_nph_asphere>`               | :doc:`nph/body <fix_nph_body>`                       | :doc:`nph/sphere (o) <fix_nph_sphere>` | :doc:`npt (kio) <fix_nh>`                    | :doc:`npt/asphere (o) <fix_npt_asphere>` | :doc:`npt/body <fix_npt_body>`           | :doc:`npt/sphere (o) <fix_npt_sphere>`     | :doc:`nve (kio) <fix_nve>`               |
++--------------------------------------------------------+------------------------------------------------------+----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+------------------------------------------+
+| :doc:`nve/asphere (i) <fix_nve_asphere>`               | :doc:`nve/asphere/noforce <fix_nve_asphere_noforce>` | :doc:`nve/body <fix_nve_body>`         | :doc:`nve/limit <fix_nve_limit>`             | :doc:`nve/line <fix_nve_line>`           | :doc:`nve/noforce <fix_nve_noforce>`     | :doc:`nve/sphere (o) <fix_nve_sphere>`     | :doc:`nve/tri <fix_nve_tri>`             |
++--------------------------------------------------------+------------------------------------------------------+----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+------------------------------------------+
+| :doc:`nvt (iko) <fix_nh>`                              | :doc:`nvt/asphere (o) <fix_nvt_asphere>`             | :doc:`nvt/body <fix_nvt_body>`         | :doc:`nvt/sllod (io) <fix_nvt_sllod>`        | :doc:`nvt/sphere (o) <fix_nvt_sphere>`   | :doc:`oneway <fix_oneway>`               | :doc:`orient/bcc <fix_orient>`             | :doc:`orient/fcc <fix_orient>`           |
++--------------------------------------------------------+------------------------------------------------------+----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+------------------------------------------+
+| :doc:`planeforce <fix_planeforce>`                     | :doc:`poems <fix_poems>`                             | :doc:`pour <fix_pour>`                 | :doc:`press/berendsen <fix_press_berendsen>` | :doc:`print <fix_print>`                 | :doc:`property/atom <fix_property_atom>` | :doc:`qeq/comb (o) <fix_qeq_comb>`         | :doc:`qeq/dynamic <fix_qeq>`             |
++--------------------------------------------------------+------------------------------------------------------+----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+------------------------------------------+
+| :doc:`qeq/fire <fix_qeq>`                              | :doc:`qeq/point <fix_qeq>`                           | :doc:`qeq/shielded <fix_qeq>`          | :doc:`qeq/slater <fix_qeq>`                  | :doc:`rattle <fix_shake>`                | :doc:`reax/bonds <fix_reax_bonds>`       | :doc:`recenter <fix_recenter>`             | :doc:`restrain <fix_restrain>`           |
++--------------------------------------------------------+------------------------------------------------------+----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+------------------------------------------+
+| :doc:`rigid (o) <fix_rigid>`                           | :doc:`rigid/nph (o) <fix_rigid>`                     | :doc:`rigid/npt (o) <fix_rigid>`       | :doc:`rigid/nve (o) <fix_rigid>`             | :doc:`rigid/nvt (o) <fix_rigid>`         | :doc:`rigid/small (o) <fix_rigid>`       | :doc:`rigid/small/nph <fix_rigid>`         | :doc:`rigid/small/npt <fix_rigid>`       |
++--------------------------------------------------------+------------------------------------------------------+----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+------------------------------------------+
+| :doc:`rigid/small/nve <fix_rigid>`                     | :doc:`rigid/small/nvt <fix_rigid>`                   | :doc:`setforce (k) <fix_setforce>`     | :doc:`shake <fix_shake>`                     | :doc:`spring <fix_spring>`               | :doc:`spring/chunk <fix_spring_chunk>`   | :doc:`spring/rg <fix_spring_rg>`           | :doc:`spring/self <fix_spring_self>`     |
++--------------------------------------------------------+------------------------------------------------------+----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+------------------------------------------+
+| :doc:`srd <fix_srd>`                                   | :doc:`store/force <fix_store_force>`                 | :doc:`store/state <fix_store_state>`   | :doc:`temp/berendsen <fix_temp_berendsen>`   | :doc:`temp/csld <fix_temp_csvr>`         | :doc:`temp/csvr <fix_temp_csvr>`         | :doc:`temp/rescale <fix_temp_rescale>`     | :doc:`tfmc <fix_tfmc>`                   |
++--------------------------------------------------------+------------------------------------------------------+----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+------------------------------------------+
+| :doc:`thermal/conductivity <fix_thermal_conductivity>` | :doc:`tmd <fix_tmd>`                                 | :doc:`ttm <fix_ttm>`                   | :doc:`tune/kspace <fix_tune_kspace>`         | :doc:`vector <fix_vector>`               | :doc:`viscosity <fix_viscosity>`         | :doc:`viscous <fix_viscous>`               | :doc:`wall/colloid <fix_wall>`           |
++--------------------------------------------------------+------------------------------------------------------+----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+------------------------------------------+
+| :doc:`wall/gran <fix_wall_gran>`                       | :doc:`wall/harmonic <fix_wall>`                      | :doc:`wall/lj1043 <fix_wall>`          | :doc:`wall/lj126 <fix_wall>`                 | :doc:`wall/lj93 <fix_wall>`              | :doc:`wall/piston <fix_wall_piston>`     | :doc:`wall/reflect (k) <fix_wall_reflect>` | :doc:`wall/region <fix_wall_region>`     |
++--------------------------------------------------------+------------------------------------------------------+----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+------------------------------------------+
+| :doc:`wall/srd <fix_wall_srd>`                         |                                                      |                                        |                                              |                                          |                                          |                                            |                                          |
++--------------------------------------------------------+------------------------------------------------------+----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+------------------------------------------+
 
 These are additional fix styles in USER packages, which can be used if
 :ref:`LAMMPS is built with the appropriate package <start_3>`.
diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js
index 027eac1a3e..531aa9c6b4 100644
--- a/doc/html/searchindex.js
+++ b/doc/html/searchindex.js
@@ -1 +1 @@
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[40,43],branch:[3,161],branicio2009:157,branicio:[30,157],breakdown:[1,93],brennan:[31,64,109,139,140,152],brenner:93,brick:[19,59,162],brief:[1,2,68,93,96],briefli:[2,71,103,146,161],brilliantov:117,broadwel:4,broken:[28,29,68,96],brook:2,brown:[4,40,42],brownian:[2,37,130,131],brows:0,browser:57,bryantsev:119,btype:[104,121,125,129,152],buc:98,buck:[2,4,32,97],buckingham:[97,98,99,106,132],buckplusattr:146,buffer:57,bufi:57,bug:0,bui:57,build:[0,1,2],built:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,31,32,37,39,40,41,43,45,46,47,48,49,50,51,52,53,54,55,56,60,63,64,65,66,67,68,69,70,71,72,74,75,77,78,79,82,83,84,85,86,87,88,89,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160],bulatov:[134,135],bulk:[2,29,67,70,105,133,136,146],bundl:[57,161],button:161,bypass:2,c11:133,c_0:[79,93,150,151],c_1:[40,43,66],c_2:[40,43],c_cluster:2,c_cstherm:2,c_doubl:3,c_e:79,c_flux:35,c_foo:162,c_gauss:115,c_hb:119,c_i:65,c_id:[2,32,62,162],c_ij:2,c_ijkl:2,c_k:66,c_mychunk:[2,34],c_mytemp:162,c_n_k:66,c_p:42,c_peratom:42,c_pi:96,c_prop:2,c_sigma:96,c_size:2,c_thermo_temp:62,ca2:43,cach:4,cacul:75,calcforc:67,calclat:35,calcluat:[37,39,42,104],calcualt:35,calcul:[0,1],caldwel:[2,45],calhoun:71,call:[1,2,3,4,71,93,102,159,161,162],callabl:3,callback:3,caltech:[2,112],calucl:2,calul:[3,29],can:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],cannot:[1,2,3,4,19,28,57,59,60,61,66,68,72,79,80,81,90,91,98,99,101,110,116,118,121,125,127,129,142,144,145,152,162],canon:[68,71,78,136],cao1:71,cao2:71,cao:71,capabl:[3,4,93,101],capac:[64,79,149],capolungo:[40,43],captur:[2,93,99,112,117,125,133],carbid:104,carbon:[57,88,93,103,133],card:[4,32,119],care:[2,44,55,67,68,95],carefulli:[3,28],carlo:[2,60],caro:110,carri:[4,79,117],carrillo:4,cartesian:[2,92],cascad:79,cast:162,cat:[4,57],cate:67,categori:[0,93,162],cation:[113,146],caus:[1,2,4,44,61,68,70,74,75,80,81,90,91,119,121,127,130,131,162],caution:1,cautious:93,caveat:93,cbecker:[92,110],cc1:[2,34],ccc:[111,153,154,156,157],ccflag:4,ccflags:4,ccm6:110,ccsi:[111,153,154,156,157],ccu:96,cd2:43,cdeam:110,cdll:3,cdof:2,cdte:96,cdte_bop:96,cdtese:96,cdzn:96,cdznte:96,ce3:43,ce4:43,ceil:162,cell:[2,40,43,44,61,68,69,72,79,112,136],cella:2,cellalpha:2,cellb:2,cellbeta:2,cellc:2,cellgamma:2,center:[2,9,33,34,37,40,44,57,61,66,68,76,78,80,81,82,95,111,112,116,117,130,131,133,134,135,153,154,155,156,157,162],centr:63,central:[29,36,38,41,70,75,76,85,136,141,157],centro:2,centroid:71,centrosymmetri:29,certain:[1,2,57,60,62,162],cfg:[2,57],cg_type:145,ch2:75,ch2lmp:[0,2],ch3:75,chain:[0,2,13,28,60,68,69,71,75,78,88,107,108,152],challeng:2,champaign:130,chan:136,chandler:[92,110],chandrasekhar:[2,121],chang:[1,2,3,4,19,22,32,44,57,58,59,60,61,62,67,68,69,70,72,73,74,75,77,78,79,81,90,91,108,112,117,130,131,133,136,146,152,161,162],change_box:2,chapter:71,charact:[2,19,57,59,65,74,112,114,120,139,140,143,146,162],character:[2,29,38,41,147],characterist:77,charg:[1,2,3,32,40,43,44,97,98,103,104,106,107,110,112,113,121,125,129,142,146,156,157,159,160,162],charl:62,charmm:0,cheaper:[116,144],check:[2,3,19,35,59,73,75,78,90,91,120,162],checkout:161,chem:[2,5,6,9,20,21,22,32,38,39,42,45,46,53,63,66,67,68,71,72,77,78,80,82,88,89,91,93,97,100,101,103,104,105,107,108,109,112,115,116,118,119,121,125,126,129,133,137,139,140,142,146,152],chemic:[31,40,43,58,114,140],chemistri:[72,93,96,112],chen:79,cheng:103,chi:[70,113,116],chiral:88,chmod:3,cho:133,choic:[2,4,19,28,29,32,42,55,59,60,67,68,71,91,129],choos:[1,2,13,28,32,57,60,61,62,67,68,69],chose:[154,156],chosen:[2,41,44,50,57,61,62,66,67,68,69,71,109,112,117,120,123,145,154],chunk:0,chunkid:34,ciccotti:75,cieplak:[2,45],circular:2,circumv:[36,38],citat:[0,67],cite:146,cl1:43,clarendon:[13,107],clarifi:[154,156],clark:142,classic:[0,2,4,71,72,79,89,112],classifi:157,clean:2,clear:[2,3,62,162],clebsch:41,click:[3,44,56,57,91,161],climb:91,clockwis:45,clone:161,close:[2,3,19,42,60,61,67,68,75,81,91,93,96,104,105,133,139,140,156,161],closer:[19,59,61,77,91],closest:[70,116,144,152],cloud:146,cluster:[2,4,42,63,75],cmax:133,cmd:[3,71],cmdarg:3,cmin:133,cmm:[18,145],cna:29,co2:[43,74,75,114],coars:[13,18,28,50,65,74,114,118,140,145],coarser:162,coarsest:41,code:[0,1],coeff:[6,45,46,55,82,120,148],coeffici:0,coefficienct:108,coefficient0:110,coefficient1:110,coeffieci:[2,94],coeffincientn:110,coexist:112,cohes:[2,113,133],coincid:[81,100,130,131],cold:2,coleman:[40,43],collect:[2,34,44,102],colliex:43,collis:[67,117,160],colloid:2,color:[19,57,59,66,72],column:[2,29,34,36,38,41,42,43,72,79,93,115,119,162],colvar:0,com:[2,37,63,95,161],comand:60,combiant:105,combin:[2,3,18,32,55,57,58,63,68,71,81,82,102,104,105,109,112,113,114,128,129,147,153,154,156,157,159,162],come:[0,2,13,61,62,68,77,78,153,154,156,157,161],comit:161,comm:[0,3,30,91,108],comm_modifi:[2,96,102,108,112,117,162],comm_styl:[19,59,162],comm_world:3,command:[0,1],comment:[3,45,65,74,79,91,92,110,111,113,114,120,133,139,140,141,146,147,153,154,155,156,157,161,162],commit:161,commmand:2,common:[0,1,2,3,4,30,61,71,81,82,117,119,153,154,156],commonli:[2,9,37,38,57,89,118,123,147,154,156],commun:[1,2,3,4,19,57,59,61,67,68,79,109,162],comp:[75,91,112,144,151,155],compar:[1,2,4,40,43,56,90,91,133,146],comparison:0,compass:[6,20,46,56,82,101],compat:[3,19,49,59,62,63,80,136,162],compens:[2,112],compil:[4,57,136,162],complain:3,complement:133,complementari:[104,121],complet:[2,3,19,59,71,91,113,162],complex:[2,3,9,36,38,41,44,67,81,91,112,136,162],complic:2,compon:[2,29,30,33,34,35,36,37,38,39,41,42,57,60,61,62,63,67,68,69,71,75,81,90,91,108,112,117,130,131,146,147,162],componenet:2,composit:[2,67,110],compound:[103,112,113,157],compress:[2,57,69,72],compris:[81,114,144],compton:[40,43],comput:[0,1],computation:[2,79,96],compute_modifi:[60,61,68,69],compute_sa:40,compute_xrd:43,concav:81,concentr:[65,74,110,114,140],concept:2,conceptu:[2,61,91,104,133],concern:[2,30,32,66],concis:3,concurr:[4,162],conden:[79,154,156],condens:[2,79,93,106,110,121,157],condit:[2,39,40,42,43,57,58,67,69,70,72,75,76,79,109,112,118],conducit:2,conduct:0,confer:[4,136],configur:[1,2,4,57,61,71,90,91,93,96,111,133,136,153,154,156,157,161],conflict:161,conform:[2,60,61,73,88,91,112],confus:157,conjuct:108,conjug:112,conjunct:[2,32,44,67,91,97,98,104,108,112,119,121,142,145],connect:[2,32,60,75,91,105,117,152,156],conner:93,connor:93,consecut:[3,44,104,121,125],consequ:[1,2,79,120],conserv:[13,60,66,67,68,74,75,91,107,108,109,117,127,146],consid:[2,29,32,59,60,79,112,144,146,152,162],consider:2,consist:[2,3,39,44,50,62,66,68,69,72,73,74,91,93,96,102,104,112,116,130,131,133,136,139,140,144,146,162],consistent_fe_initi:58,constant:0,constantli:63,constitu:[2,80,81,102,144],constrain:[2,63,66,75,76,90,112],constraint:[19,39,42,59,63,75,76,80,90,131],construct:[2,28,29,30,36,38,40,41,43,61,68,73,74,81,107,136,152,153,162],constructor:3,consult:4,consum:[1,162],contact:[0,105,111,113,116,117,144],contain:[0,1,2,3,19,32,35,40,41,43,44,45,56,57,58,59,62,65,67,70,72,74,79,81,91,92,93,96,103,104,107,110,111,112,114,133,136,139,140,141,143,147,153,154,155,156,157,161,162],context:[2,4,159,162],contibut:29,contin:4,continu:[0,2,19,59,60,61,62,63,66,68,69,72,77,78,79,81,96,108,123,126,144,155,162],continuum:[2,58,79],contour_integr:58,contract:[61,68],contrain:75,contrast:[1,2,159],contrib:79,contribut:[2,29,32,33,34,35,39,41,42,61,67,75,90,91,108,110,112,130,131,136,146,161],control:[2,3,4,11,13,19,32,35,41,47,57,58,59,61],control_typ:58,convect:35,conveni:[2,13,147,161,162],convent:[13,49,54,56,73,110,112,162],converg:[2,19,57,59,60,61,69,72,73,75,90,91,103,104,121,146],convers:[41,57,104,105,106,112,121,125,129,142],convert:[2,5,6,8,12,16,17,18,35,44,46,57,82,83,87,88,91,92,110,136,154,156,160,162],convex:81,cool:63,coord:[2,3,36,38,70,80,91],coordb:146,coordbb:146,coordiat:90,coordin:[1,2,3,19,32,33,34,41,44,57,59,60,61,63,68,70,75,76,78,79,90,91,92,93,95,111,146,162],coords:146,copi:[0,3,57,79,91,161],copper:160,coprocessor:[1,4],core:[0,1],coreshel:2,coreshell:[2,98,104,106],cornel:[2,45],corner:[2,57,81,161],corpor:4,corr:103,correct:[2,3,32,45,57,63,68,72,80,81,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,110,111,112,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],correction_max_iter:58,correctli:[3,68,75,81,91,106,131,136,161],correl:[2,35,36,41,66,71,162],correpond:65,correspond:[1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,29,32,39,40,41,43,45,46,47,48,49,50,51,52,53,54,55,57,61,62,63,65,67,68,69,70,71,74,75,80,81,82,83,84,86,87,88,89,91,92,93,94,97,98,99,100,101,102,103,104,107,108,110,111,112,113,114,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,133,134,136,138,140,141,142,143,144,145,146,147,148,153,154,155,156,157,158,159,160,162],correspondingli:[130,131],cosin:2,cosineshift:11,cost:[1,2,3,19,40,42,43,57,59,68,74,79,104,121,125,136,153],costheta0:[153,154,156,157],costheta:143,costli:[3,4],coul:[2,4,18,21,22,32,45,90],could:[2,3,19,32,34,35,39,57,59,62,72,79,80,81,90,93,115,119,162],coulomb:[2,42,90,97,98,99,100,101,103,104,105,106,107,112,117,118,121,125,129,132,142,145,146,156,157,159],coulommb:2,count:[1,2,3,19,35,45,59,68,75,81,90,91,115,119,162],counteract:62,counterbal:63,counterbalanc:13,counterclockwis:45,coupl:0,couple:[2,3],cours:[4,66,73,80,130,148,162],cov:146,coval:[2,13,112,133,146],cover:[2,58,67,112],cpp:[1,2,3,32,75],cpu:[1,4,162],cpuinfo:4,cr2:43,cr3:43,creat:[0,1,2,3,19,35,39,40,44,57,58,59,60,61,65,68,69,70,71,73,79,91,93,96,103,110,111,129,138,139,140,143,146,153,154,155,156,157,161,162],create_atom:[2,19,35],create_box:[2,19,35,44,61,68,152],create_elementset:58,create_faceset:58,create_nodeset:58,createatom:0,creation:44,criteria:[57,60,90,162],criterion:[19,44,59,60,90,91,103,112,117,146],critic:[2,24,25,79,90],cross:[4,33,57,91,100,108,110,118,119,121,123,125,143,145,154,156,160],crossov:1,crozier:0,crucial:72,crystal:[2,4,29,30,38,70,78],crystallin:[2,155],crystallogr:[40,43],crystallographi:[40,43],cs1:43,cs_chunk:2,csanyi:[41,147],cscl:133,csequ:2,csh:[3,4],cshrc:3,csic:[111,153,154,156,157],csinfo:2,csisi:[111,153,154,156,157],cst:110,cstherm:2,csvr:2,ctcm:[92,110],ctype:3,cu1:43,cu2:43,cu3au:133,cube:[2,81],cubes:[19,59],cubic:[38,67,70,110],cuda:[1,162],cuh:96,cummul:[2,60,119],cumul:[2,68,69,91],currenlti:62,current:[0,1,2,3,4,19,30,32,42,57,58,59,60,61,62,63,68,73,74,75,76,79,80,90,91,96,103,107,110,112,113,117,120,130,131,133,134,135,143,148,154,156,161,162],curv:[2,44],curvatur:[116,144,160],custom:[0,2,3,33,34,35,42,57,60,61,68,69,72,90,93,115,119,162],cut:[1,2,4,19],cuthi:70,cutinn:[130,131],cutlo:70,cutmax:143,cutoff1:[101,107,121,125,129,132,142,145],cutoff2:[97,98,99,101,106,107,121,125,129,132,142,145],cutoff:[2,4,21,22,28,29,30,32,36,38,41,60,65,70,72,80,81,90,92,93,94,95,96,97,98,99,100,101,102,104,105,106,107,108,109,110,111,112,113,114,115,116,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,162],cutoffa:111,cutoffc:111,cuu3:110,cval:43,cvar:62,cvff:4,cwiggl:[80,162],cyan:57,cycl:[68,69],cyclic:45,cylind:[57,81],cylindr:2,cyrot:96,d3q15:67,d3q19:67,d_e:79,daan:78,damp:[2,68,69,72,90,91,97,98,100,104,107,112,117,121,129,142,145],dampflag:117,danger:108,darden:107,darken:57,dash:117,dat:[2,35,58],data2xmovi:0,data:1,databas:0,date:[0,2,162],datum:2,davenport:132,davi:80,david:[154,156],daw:[110,143],dcd:[2,57,71],deactiv:129,debug:[2,3,40,43,44,71,162],decai:[36,104,160],decid:[2,4,161],decod:57,decompos:[32,147],decomposit:[58,71],decoupl:2,decreas:[4,60,63],dedic:4,defect:[2,29,136],defin:[2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,64,65,67,68,69,70,71,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,93,94,95,97,98,99,100,101,102,104,105,107,108,109,111,112,114,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,131,132,136,137,138,139,140,141,142,143,144,145,147,148,149,150,151,152,153,154,155,156,157,158,159,160,162],definit:[2,41,62,64,69,80,96,102,109,112,143,147,162],deform:[2,42,61,68,130,131],deg2theta:43,degre:[2,5,6,8,12,13,16,17,18,36,38,39,43,44,45,46,48,49,54,55,57,60,68,69,71,73,75,78,82,83,87,88,89,90,107,110,119],delai:2,delet:[28,60,68,152,161,162],delete_atom:44,delete_bond:[20,21,22,23,24,25,26,27,28],delete_el:58,delimit:[74,162],dellago:[2,63],deloc:[112,146],delr:133,delta_1:96,delta_3:96,delta_7:96,delta_ij:[133,143],delta_pi:96,delta_r:143,delta_sigma:96,deltah_f:65,demo:3,demonstr:[72,133],dendrim:119,denniston:67,denot:[40,63,104,118],dens:[60,74,112],densiti:[2,19,41,44,58,59,67,79,80,92,93,96,110,133,134,135,139,140,143,144,146,149,150,151],depart:0,departur:72,depend:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,29,36,39,41,44,45,46,47,48,49,50,51,52,53,54,56,57,59,61,65,67,68,69,70,74,75,77,79,80,81,82,83,84,86,87,88,89,90,92,93,94,95,96,97,98,99,100,101,102,103,104,105,107,108,110,111,112,113,114,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,133,134,136,137,138,139,140,141,142,143,144,145,146,147,148,153,154,155,156,157,158,159,160,162],dependend:2,deposit:[68,75],depth:[26,57,79,114,116,144],der:[32,102,103,129,159],deriv:[2,32,41,61,62,63,68,69,70,77,78,79,80,81,93,96,102,107,112,113,118,123,127,128,133,136,159],derjagin:159,derlet:70,descib:57,describ:[0,1,2,3,4,19,29,30,40,41,42,43,44,50,53,59,60,61,62,65,66,67,68,69,70,71,72,74,77,78,80,90,91,93,95,97,98,100,101,102,103,104,107,110,112,113,114,116,117,118,121,122,123,124,125,126,127,128,129,130,131,132,133,136,137,139,140,143,144,145,146,147,148,152,153,154,155,156,157,158,159,160,161,162],descript:[2,3],descriptor:41,design:[0,2,3,40,43,58,60,68,70,79,94,95,100,104,106,112,129,130,131,134,135,143],desir:[2,3,4,35,39,42,44,61,62,66,68,75,90,91,108,110,119,130,131,153,154,156,162],desktop:[2,57],destabil:96,destre:88,destroi:3,detail:[1,2,3,4,19,34,35,39,41,42,44,56,57,58,59,60,61,62,63,66,67,68,69,72,75,78,79,90,92,93,95,96,99,100,101,102,103,104,107,108,112,113,116,117,118,119,121,122,123,124,125,126,127,128,129,130,131,132,133,137,139,140,144,146,147,148,158,159,161,162],detect:[36,91,103,119,120,162],determin:[1,2,4,26,32,39,40,42,43,44,57,59,61,65,68,70,71,72,73,74,80,81,93,99,103,107,110,114,115,117,125,133,136,140,144,146,152,159,162],devan:145,devanathan:156,develop:[0,2,3,4,62,69,72,93,96,112,135,136,146,157],deviat:[69,70,115],devic:1,devin:103,devis:135,dfactor:57,dft:136,dhug:72,dhugoniot:72,dia:133,diag:74,diagnost:[4,60,74],diagon:[2,41,42,61,68],diagonalstyl:147,diagram:[19,40,43,56,59,71],diallo:119,diam:57,diamet:[2,44,57,102,116,117,123,144,159],diamond:[112,133],dick:2,dicken:62,did:[90,108,110,117,154,156],dielectr:[100,104,105,106,121,125,129,142],diff:[2,4],differ:[1,2,3,4,19,28,29,32,36,41,44,56,57,59,60,61,62,63,66,67,68,70,71,72,75,76,77,78,79,80,81,82,91,92,93,96,99,100,102,103,108,109,110,112,114,116,117,118,121,122,124,125,132,133,134,135,137,138,139,140,141,143,144,145,146,147,148,153,154,156,157,159,162],differenti:[1,2,13,74,104,143,155],difficult:[61,62,71,119],difficulti:[36,38,75],diffract:[40,43],diffraction:[40,43],diffus:0,diffuse:2,digit:[136,162],dihedr:[0,4,28,36,38,39,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,60,73,83,84,85,87,90,93,96,100,162],dihedral_coeff:[45,46,47,48,49,50,51,52,53,54,55,56],dihedral_cosine_shift_exp:11,dihedral_styl:[0,2,42],dihydrid:112,dij:75,dilat:[61,68,69],dim:[44,133,162],dimdim:162,dimens:[1,2,19,35,42,44,57,59,61,67,68,69,72,80,91],dimension:[36,39,40,41,43,79,91,143],dimensionless:[37,41,62,79,147,159],dimer:[2,133],dimstr:[19,59],dintel_offload_noaffinity:4,dipol:0,dipolar:13,dipole:107,dir:[1,3,70,72,143,162],dirac:41,direc:143,direct:[2,4,13,29,38,40,41,43,44,45,57,67,69,70,72,77,78,79,80,81,90,91,108,109,117,131],directli:[2,3,32,41,44,57,62,67,74,81,92,93,97,98,99,104,107,110,112,121,125,142,145,152,162],directori:[0,1,2,3,4,62,77,78,91,92,93,96,103,104,110,111,113,129,133,134,135,136,141,143,146,147,153,154,155,156,157,162],disabl:[4,79,120,162],disadvantag:[2,59],disallow:68,discard:[19,59,81],discontinu:[90,127],discourag:133,discret:[2,57,62,67],discuss:[0,1],disk:[2,36],disloc:[29,136],disord:[29,136],disp:0,dispar:144,disperion:[107,125],dispers:[2,99,107,125,130,157],displac:[2,37,61,68,70,117,162],displai:[3,56,57],disregard:136,dissip:[2,31,64,66,77,78,108,109,117,130,131],dist:[2,35,71,73,152],distanc:[2,5,6,20,21,22,23,24,25,26,27,28,30,33,34,36,37,38,40,41,44,46,57,60,61,63,67,68,69,70,72,73,75,76,78,79,80,81,82],distinct:[2,144],distinguish:[2,41,112,162],distort:92,distrbut:92,distribut:[0,2,3,19,32,41,56,59,66,67,68,92,96,104,110,111,113,133,134,135,141,143,144,153,154,155,156,157],distro:143,ditto:160,div:4,diverg:[78,93],divid:[2,4,19,35,39,42,56,59,70,90,91,113,146,157,162],divis:[2,55,67,96,129,162],dl_poly:2,dlammps_ffmpeg:57,dlammps_gzip:57,dlammps_jpeg:57,dlammps_memalign:4,dlammps_png:57,dlm:68,dlmp_intel_offload:4,dlopen:2,dlvo:[102,159],dm_lb:67,doc:[0,1,2,3,32,34,37,39,42,44,56,57,62,68,81,90,91,92,93,95,103,104,110,111,113,119,133,134,135,141,143,147,153,154,156,157,161,162],docuement:144,doe:[0,1,2,3,19,28,29,32,35,40,43,44,45,56,57,58,59,60,61,62,63,65,66,67,68,79,80,81,83,84,85,87,88,91,92,93,94,95,96,99,100,101,102,103,104,105,107,108,110,111,112,114,115,116,117,118,120,123,124,126,127,128,130,131,133,134,135,136,139,140,143,144,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],doesn:[44,93,103,111,153,154,155,156,157],dof:39,doi:[2,70],domain:[2,19,40,43,57,59,61,67,68,71,79,80,91],domin:[1,112],don:[0,4,81,133,146,161],donald:62,done:[1,2,19,44,55,57,58,59,60,61,62,65,68,71,75,77,78,90,91,93,99,110,125,131,132,133,139,140,152,161,162],donor:119,dot:42,doti:[96,143],doubl:[1,2,3,4,32,45,81,96,113,118,136,162],dover:58,down:[2,3,61,112,146],download:3,downsid:2,dpd:2,dpdtheta:[31,109],dpdtheta_i:[64,65],dr_ewald:40,drag:[2,35,68,69,76],dragforc:67,drai:[57,72],drain:90,dramat:[60,61,68,146],drautz:96,draw:57,drawn:[57,66],drayleigh:72,dreid:2,dreiding:0,drfourth:37,drho:[92,110,139,140],drift:[2,37,63,66],drive:[3,61,68,70,91],driven:[2,50],driver:2,drop:108,drsquar:37,drude:0,dt_collis:67,dt_lb:67,dt_md:67,dtqm:72,dudarev:43,due:[1,2,4,28,29,33,34,37,40,41,42,43,44,57,60,61,66,67,68,69,70,73,77,78,79,80,81,90,91,105,108,109,110,115,116,130,131,143,144,145,152,154,156,159,160,162],duffi:79,dullweb:68,dummi:[13,155],dump:[0,1],dump_modifi:[2,57,162],dunbrack:[2,5,45,100],duplic:[19,59,70],durat:[56,79,117],dure:[2,4,19,32,45,58,59,60,61,62,63,65,66,67,68,69,70,71,72,73,75,76,77,78,79,80,81,90,91,108,129,136,138,139,140,162],dvlo:159,dvx:2,dx_lb:67,dy3:43,dyanam:2,dynam:[0,2,3,4,19,31,37,44,57,58,59,60,62,64,66,68,69,71,72,73,77,78,79,90,91,108,109,112,130,131,151],dynamo:[92,110,133],dyre:126,e28637:13,e_1:96,e_2:96,e_a:74,e_b:113,e_ee:112,e_hbond:119,e_i:[2,96,113],e_j:[2,96],e_k:96,e_ke:112,e_kl:2,e_lj:[93,107],e_n:[62,96],e_ne:112,e_nn:112,e_pr:112,e_rebo:93,e_torsion:93,e_tot:136,e_vol:136,eaa:82,eaat:46,each:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,32,33,34,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,65,66,67,68,69,70,71,74,75,76,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,156,157,158,159,160,162],eacn:[19,59],eam:[0,92,104],earli:[19,59],earlier:[91,117,133],earth:112,easi:[2,3,32,42,80],easier:[4,57],easili:[3,57,91,162],eat:46,eaxmpl:2,eba:6,ebb13:46,ebb:6,ebond:162,ebt:46,ec_ii:133,ec_ij:133,ec_jj:133,echo:[3,40,43],ecp:112,edg:[2,19,40,43,57,80,81],edge:80,edit:[4,161],edition:4,edu:[3,110,130],eebt:46,eff:0,effect:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,33,34,37,39,42,45,46,47,48,49,50,51,52,53,54,56,57,58,60,61,63,66,68,69,70,71,72,73,75,78,79,80,81,82,83,84,86,87,88,89,90,91,92,93,94,96,97,98,99,100,101,102,103,104,107,108,110,111,112,113,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,134,136,138,139,140,141,142,144,145,146,148,153,154,155,156,157,158,159,160,162],effici:[0,1,2,4,39,55,57,61,68,71,75,96,102,104,121,125,136,139,140,144],efficienc:4,efield:[75,90],eggebrecht:[104,146],ehex:2,eigenvalu:71,einstein:[2,78],either:[1,2,3,4,19,29,40,41,42,43,44,57,59,60,61,62,63,67,68,69,70,74,75,81,90,96,102,110,114,117,130,131,133,136,140,143,152,154,156,162],ejtehadi:[102,116,144],elaplong:162,elaps:[80,148,162],elast:[2,21,22,91,117,155],elastic:0,elba:13,electr:[2,58,113,160],electric:4,electrolyt:159,electron:[2,40,58,79,92,103,107,110,112,113,133,136,143,146,156,157,160],electron_integr:58,electron_temperatur:58,electron_unit:112,electroneg:[2,103,113,146],electroneg_compon:146,electrostat:[2,4,102,107,112,121,129,131,146,159],elem1:[113,133,147],elem2:[113,133,147],elem:146,element1:[92,110,146],element2:[92,110,146],element:[2,33,37,39,41,42,57,58,92,93,96,103,110,111,112,113,133,134,135,136,141,143,146,147,153,154,155,156,157,162],elementn:[92,110],elementset:58,elif:41,elig:119,elimin:[2,66,75,77,78],elj:107,ellips:2,ellipsoid:[2,44,90,116,131,144],els:[57,62,68,79,162],elsewher:[133,162],elt:133,emac:0,email:[0,3,113],emb:81,emb_lin_neg:133,embed:[3,13,79,92,110,113,129,133,134,135,143],embt:46,emphas:117,empir:[58,112],empiric:93,emploi:[63,155],empti:[120,162],enabl:[2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,31,32,37,39,40,41,43,45,46,47,48,49,50,51,52,53,54,56,60,62,63,64,65,66,67,68,69,70,71,72,73,74,75,77,78,79,80,81,82,83,84,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,133,134,135,136,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,162],enclos:[2,133,146,162],encod:57,encompass:2,encount:[38,162],encourag:[74,76],end:[1,2,3,4,19,46,57,60,63,66,68,73,74,79,91,108,110,116,132,136,144,147,148,162],endbondtors:46,energet:[60,93],energi:[0,1,2,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,31,32,35,39,42,44,45,46,47,48,49,50,51,52,53,54,55,56,58,59,60,61,62,63,64,65,66,67,68,69,70,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108],energy_compon:146,enforc:[2,57,60,68,75,121,162],enforce2d:[2,90],eng:[3,103,135],engineer:[58,77,110],enginer:134,enhanc:[58,63],enlarg:57,enough:[44,59,72,80,81,104],enpub:110,ensembl:[2,32,35,68,71,72,108,146],ensight:2,ensur:[2,41,61,66,68,96,129,153,157],enter:[113,136,157],enthalpi:[74,110,162],entir:[0,2,3,19,31,39,40,42,43,44,59,60,63,66,68,69,70,71,74,76,79,107,125],entiti:2,entri:[40,65,72,96,111,133,139,140,141,147,153,154,155,156,157,162],entry1:[139,140],enumuer:2,environ:[1,2,3,4,57,70,92,96,103,111,112,143,154,162],eos:65,epair:[93,115,119],epp:107,epq:107,eps0:159,eps14:129,epsilon0:156,epsilon:[2,18,21,22,27,28,32,45,80,81,90,95,100,101,102,104,105,106,107,114,116,118,119,120,121,122,123,124,125,126,127,128,129,132,137,142,144,145,153,158,159],epsilon_0:160,epsilon_14:100,epsilon_:144,epsilon_d:105,epsilon_i:[116,144],epsilon_i_:144,epsilon_i_a:[116,144],epsilon_i_b:[116,144],epsilon_i_c:[116,144],epsilon_j:[116,144],epsilon_j_:144,epsilon_j_a:[116,144],epsilon_j_b:[116,144],epsilon_j_c:[116,144],epsilon_lj:144,eqp:107,eqq:107,equal:[2,3,19,28,32,35,42,44,57,59,61,62,66,67,69,70,71,72,73,74,77,78,79,80,90,91,93,103,108,109,115,116,119,130,136,137,143,144,146,147,148,157,160,162],equat:[2,35,38,39,40,43,56,61,62,63,64,65,67,68,69,70,71,72,74,75,79,80,102,107,108,109,112,113,114,117,130,131,133,140,144,149,150,151,160],equation:[70,88],equilibr:[2,35,44,60,61,68,72,77,78,103,104],equilibrium:[1,2,6,8,10,11,12,13,16,17,18,20,23,24,25,26,27,46,47,61,66,67,68,69,72,73,75,78,82,83,87,88,103,133,141,146],equilibrium_start:58,equival:[2,13,61,68,73,93,108,112,146,154,156],equlibrium:2,er3:43,eradiu:112,eras:77,erat:131,erc:104,erfc:[104,121],erhart:[110,154,156],eros:133,erose_form:133,erot:2,errata:[154,156],erratum:80,error:[0,1,2,3,11,47,57,61,62,63,65,68,74,79,80,81,90,104,121,144,152,154,156,162],erta:117,especi:[4,44,59,72,73],essenti:[3,11,47,93,104,121,156],essential:69,essex:13,establish:32,estim:[1,2,19,29,35,42,58,59,74],esub:133,eta:[2,67,68,72,111,113,116,143,155,157],eta_dot:68,eta_ij:143,eta_ji:113,etap:68,etap_dot:68,etc:[1,2,3,4,28,33,34,35,42,44,57,58,66,68,79,81,90,91,110,111,129,131,136,153,154,156,157,162],etol:[90,91],etot0:72,etot:[2,42,72],eu2:43,eu3:43,euler:[74,90,91],eulerian:58,europhi:67,evalu:[3,32,35,41,44,45,57,58,62,66,74,80,90,136,139,140,143,146,162],evaluat:162,evanseck:[2,5,45,100],evaul:90,even:[2,4,19,29,55,59,61,63,68,79,80,81,90,91,95,112,113,117,144,157],evenli:[19,42,59,67],event:[2,68,79],eventu:2,ever:28,everaer:[102,116,144],everi:[0,1,2,3,4,19,35,57,58,59,60,61,62,63,67,68,69,70,72,74,75,79,91,108,129,146,161,162],everyth:161,everywher:123,eviri:112,evolut:[63,67,71],evolv:[67,71],ewald:[2,40,42,90,97,98,99,104,107,112,121,125,142,145],ewald_disp:107,exact:[19,59,60,66,79,162],exactli:[2,19,35,44,59,66,72,108,110,117,130,139,140,162],examin:[2,60,74],exampl:[0,1],exce:[2,4,19,59,61,68,90,162],exceed:[19,59,68],excel:112,except:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,33,34,39,42,44,45,46,47,48,49,50,51,52,53,54,56,59,61,68,69,71,75,79,82,83,84,86,87,88,89,91,92,93,94,97,98,99,100,101,102,103,104,106,107,108,110,111,112,113,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,131,134,138,141,142,144,145,148,153,154,155,156,157,158,159,160,162],excess:112,exchang:[2,58,63,79,112],excit:112,excite:112,exclud:[2,4,39,41,90,117,130,131,152],exclus:[1,4,32,45,103,136],excurs:68,execut:[1,2,3,57,162],exempl:146,exemplari:66,exemplifi:112,exert:[2,81],exhaust:[58,162],exhibit:[36,63,68,112],exist:[2,3,29,44,56,57,61,82,83,84,85,87,109,152,161,162],exit:[3,19,59,162],expans:[41,55,162],expect:[1,4,19,59,70,72,133,136,162],expens:[2,70,79],experi:[2,73,91,108],experienc:[2,4],explain:[1,2,3,19,30,57,59,61,68,70,91,95,110,146,148,161,162],explan:[2,41,70],explanatori:162,explic:137,explicit:[2,3,32,74,93,96,100,110,112,120,130,161],explicitli:[2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,44,45,46,47,48,49,50,51,52,53,54,66,68,69,72,75,79,82,83,84,86,87,88,89,92,93,94,97,98,99,100,101,102,103,104,105,107,108,110,111,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,134,136,138,139,140,141,142,144,145,148,149,150,151,153,154,155,156,157,158,159,160,161],explictli:4,exploit:71,explor:[40,43],expon:[74,110,114,116,119,129,137,145],exponenti:[32,74,114,143,153,157,160,162],expos:3,exposit:[58,108],express:[2,41,44,61,70,74,79,96,110,112,123,133,146,147,162],expressiont:96,extend:[0,2],extens:[2,4,21,22,27,32,35,62,63,68,69,70,73,77,78,79,80,81,116,133,136,144,147],extent:[1,19,21,59,93],exterior:[2,81],extern:[32,57,61,66,67,68,69,79,90,134,135],extra:[2,3,4,19,22,39,40,42,43,44,59,68,72,90,107,117,133,162],extract:[2,3,18,32,91,104,113,133,147],extract_atom:3,extract_comput:3,extract_fix:3,extract_glob:3,extract_vari:3,extrapol:1,extrem:[1,2,57,61,68,78,112,155],extrema:129,extreme:112,extrins:58,f_1:2,f_a:[154,155,156],f_c:155,f_f:156,f_fix_id:72,f_foo:162,f_harm:78,f_i:[13,143],f_id:[2,62,162],f_ij:143,f_int:77,f_j:13,f_jj:35,f_k:143,f_langevin:79,f_max:72,f_r:[154,155,156],f_sigma:96,f_solid:78,f_ss:2,face:[2,80,81,116,133,144],facil:0,facilit:2,fact:[2,4,78,117,146],factor:[1,2,8,12,16,17,18,19,22,23,32,35,40,41,43,45,53,57,59,61,63,67,68,69,71,73,74,75,80,81,87,93,96,97,98,100,104,105,106,108,109,112,117,120,121,133,136,139,140,141,142,145,148,153,162],fail:[3,61,90,91,106],failur:162,fairli:[3,161],faken:30,fall:[2,162],fals:[146,162],famili:157,familiar:[0,3,161],fan:143,far:[2,59,61,68,70,73,80,83,87,91],farrel:[154,156],fashion:[2,19,44,59,62,68,69,72,78,79,80,91,130,162],fast:[2,4,62,72,74,130,131,136],faster:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,37,39,45,46,47,48,49,50,51,52,53,54,59,68,69,75,77,79,82,83,84,86,87,88,89,92,93,94,96,97,98,99,100,101,102,103,104,107,108,110,111,113,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,134,138,141,142,144,145,148,153,154,155,156,157,158,159,160],fastest:[1,2,79],fault:29,fava:116,favor:60,fcc:[2,29,30,35,38],fcm:162,fcold:63,fdt:[64,65,74],fdti:32,fe2:43,fe3:43,fe_md_boundari:58,featur:[0,2,3,41,57,60,66,71,81,90,161],fecr:110,feedback:62,feel:[70,81,91],fehlberg:74,felling:135,felt:81,fene:[2,4],fennel:[104,121],fep:0,ferguson:[2,45],fermi:[1,156],fermion:112,fernando:132,few:[1,2,3,63,68,75,90,91,93,146,162],fewer:[1,3,4],feynman:71,ffield:[103,113,146],fflag1:57,fflag2:57,ffmpeg:57,ffplai:57,fft:[1,3,42],fhot:63,ficiti:152,fictiti:[2,71,73,104,121,125,152],field:0,fifth:[2,114,141],figshar:70,figur:[1,4,72,161],fij:107,file0:70,file1:[3,65,70],file2:[3,65],file:[0,1],filenam:[4,19,57,58,59,65,70,74,79,91,92,93,96,104,110,111,113,114,133,134,135,139,140,141,143,146,147,153,154,155,156,157,162],fill:[44,57,79,96,136,161],filter:58,finchham:[2,106],find:[0,2,3,4,30,32,60,61,62,65,70,73,90,91,104,121,125,133,139,140,146,161,162],fine:[4,78,161,162],finer:[41,44,162],finger:44,finish:[2,3,19,59,162],finit:0,finni:110,fire:[90,91],first:[0,1,2,3,4,6,19,21,22,28,29,35,37,38,39,42,43,46,57,59,60,62,65,66,67,68,70,71,72,75,76,77,78,79,82,90,91,92,93,95,96,97,98,100,103,104,110,112,113,114,117,118,120,121,125,130,131,133,135,136,139,140,141,143,146,147,152,153,154,155,156,157,160,161,162],fischer:[2,5,45,100],fit:[2,73,93,96,133,139,140,155,161,162],five:[30,72,96,134],fix:[0,1],fix_flux:58,fix_heat:63,fix_id:[61,68,69,72],fix_manifoldforc:161,fix_modifi:2,fix_nv:161,fix_rattl:75,fix_shak:75,fixedpoint:[61,68],fixid:[57,58],fji:107,flag:[3,4,33,34,40,43,57,60,93,119,120,133,136,152,161,162],flag_buck:99,flag_coul:[99,107,125],flag_lj:[107,125],flagfld:[130,131],flaghi:[130,131],flaglog:[130,131],flagvf:[130,131],flat:[2,4,79,80],fld:[80,130,131],flexibl:[2,57,112,155],flip:[2,68],floor:162,fluctuat:[2,32,61,66,67,68,69,70,78,79,88,109],fluid:[2,61],flux:2,flv:57,fly:[19,57,58,75,96,136],fmass:71,fmax:90,fmsec:68,fno:4,fnorm:90,fnve:63,focu:75,foil:[41,70,147],fold:[4,76],follow:[0,1,2,3,4,5,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,35,36,38,41,42,44,45,47,48,49,50,51,52,53,54,55,57,58,59,62,64,65,66,67,68,69,71,72,73,74,75,77,78,79,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],foo:[3,57,74,162],foo_species:74,foot:2,forc:[0,1],forcefield:[73,119],forcegroup:67,ford:107,forgiv:68,fork:161,form:[2,28,32,33,34,36,41,42,62,66,73,74,79,80,81,82,85,88,91,93,96,109,110,112,115,119,120,132,133,135,136,139,140,141,142,143,144,146,147,148,154,155,156,159,162],formal:[2,35,66,68,71,146],format:[2,19,57,59,65,74,79,91,92,93,96,110,113,114,120,133,135,139,140,145,147,157,162],formation:65,former:[2,19,59,79,96,162],formul:[1,2,42,68,73,75,93,96,110,112,116,133],formula:[2,6,28,29,30,32,33,34,35,39,40,42,43,46,56,62,70,76,80,82,84,93,95,96,100,101,102,107,108,110,111,116,117,118,119,120,121,123,124,125,127,128,130,131,133,137,138,144,145,148,153,154,155,156,157,158,159,162],forth:[1,2,3],fortran:[2,3,110,133],forward:[32,91],foster:[96,143],found:[2,30,60,63,67,104,107],four:[2,3,28,41,62,79,88,91,136],fourier:2,fourth:[2,4,37,73,100,114,141,146],fox:[2,40,45,151],fqq:107,fraction:[1,2,4,19,42,57,60,61,72,74,91,96,114,117,130,131],frame:[41,58,72,116],framer:57,framework:[92,147],frattl:63,free:[2,13,29,32,70,77,78,79,91,112,129,136,138,143,159],freedom:[2,39,60,68,69,71,75,78,90,107],freeli:[0,2,57],freez:2,frenkel:[2,63,78],frequenc:[2,4,71,72,74,108,112,146,162],frequent:[29,30,36,38,41,63],fri:72,friction:[2,72,79,117],from:[0,1],front:72,frontend:57,frozen:[2,39,66,115],fs2:[2,35],fstr:162,ftol:[90,91],fuction:104,fudg:75,fulfil:2,full:[1,2,4,35,57,63,67,70,74,96,110,112,113,116],fuller:90,fulli:[2,70,90,91,104,143,161],fulton:110,fumi:97,func:162,funcfl:110,fund:0,funrol:136,further:[2,37,57,67,71,79,90,91,92,95,103,136,146,162],furthermor:[11,47,63,74,109,112],futur:[0,2,59,66,91,134,135],g_jik:143,g_p:79,ga3:43,gaa:96,gai:116,gain:[4,62],galindo:137,gamma0:13,gamma:[2,13,67,72,108,109,111,116,133,137,149,150,151,153,154,156,157],gamma_:79,gamma_ijk:154,gamma_n:117,gamma_p:79,gamma_t:117,gammaa:137,gammafactor:67,gammar:137,gan:[143,153,154,156,157],gan_sw:143,gan_tersoff:143,gao:[2,5,45,100],gap:[130,131,147],gather:3,gather_atom:3,gathert_atom:3,gauch:50,gauss:105,gaussian:[2,35,37,66,71,73,108,112,115,162],gavhan:4,gaybern:[2,4,90],gd3:43,gdot:131,ge4:43,gec:[154,156],gen:68,gener:0,gentler:80,gentli:111,geom:2,geometr:[2,44,59,68,81,91,95,101,102,104,107,112,114,116,118,121,122,123,124,125,126,127,128,129,130,131,132,137,140,144,148,158,159,162],geometri:[2,9,19,44,59,61],gerar:162,gerber:129,germann:[69,123],germano:116,get:[0,1,2,3,4,19,35,41,44,57,59,61,81,91,104,157,161,162],get_natom:3,get_rank:3,get_siz:3,getenv:162,gewald:2,gezelt:[104,121],ghost:[2,4,30,61,68,108,109,112,117,120],gif:57,gifsicl:57,gillan:147,gingold:[149,150],git:161,give:[0,1,2,3,4,28,36,38,44,61,68,70,90,93,96,112,119,133,136,144,154,155,156],given:[2,3,4,11,38,41,42,47,56,61,63,66,67,68,69,70,71,72,73,74,75,76,79,80,81,92,93,96,97,98,99,101,102,103,104,105,108,109,110,112,113,114,116,117,119,121,122,123,125,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,160],glosli:136,glotzer:108,glue:3,gmask:162,gnu:0,gnuplot:3,goal:62,goddard:[2,9,89,112,119],goe:[28,41,44,63,90,107,111,118,123,126,148,160],gold:29,goldman:72,good:[1,2,4,19,30,40,43,59,62,68,75,91,92,102,110,136,157,161],gordan:41,gordon:2,got:161,gould:[2,45],gov:[0,92,110,113],govern: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79,91,110,113,120,133,139,140,147,161,162],tfinal:162,tfix:73,tflag:57,th4:43,thakkar:4,thakker:4,than:[1,2,3,4,11,19,36,37,38,39,42,47,59,60,61,66,67,70,72,73,74,76,79,80,81,90,91,93,95,96,97,98,99,100,110,112,116,117,130,131,133,139,140,144,146,148,152,153,156,159,160,162],thank:[154,156],thei:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,29,32,33,34,35,39,41,44,45,46,47,48,49,50,51,52,53,54,56,57,59,60,61,62,66,67,68,69,73,75,79,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,106,107,108,109,110,111,112,113,114,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,138,140,141,142,143,144,145,146,147,148,152,153,154,155,156,157,158,159,160,161,162],them:[1,2,3,19,28,35,46,57,59,60,61,62,68,69,70,73,75,79,82,91,92,96,110,113,116,144,148,161,162],themselv:[2,3,59,91,92,96,104,110,129,133,134,135,147,162],theorem:[66,96,109],theoret:[37,72,153],theori:[2,41,58,68,96,136,159],therebi:[130,131],therefor:[2,32,63,67,75,106,153],therein:[2,133],thereof:32,thermal:0,thermo:[0,1],thermo_modifi:[2,61,68,152],thermo_press:[39,61,68,69],thermo_styl:[2,31,35,39,42,44,60,61,68,69,72,80,90,93,115,119,162],thermo_temp:[39,60,61,68,69],thermoberendsen:2,thermochemistri:112,thermodyanm:60,thermodynam:0,thermost:2,thermostat:0,thermostatequ:2,thesi:130,thess:97,theta0:[5,6,8,10,11,12,16,17,18,41,47,73,88],theta0max:41,theta10:96,theta1:[46,55,82,96],theta2:[46,55,82,96],theta3:[82,96],theta4:96,theta5:96,theta6:96,theta7:96,theta8:96,theta9:96,theta:[2,10,11,36,38,41,43,44,47,57,73,79,82,88,119,143,155],theta_0:141,theta_:[88,96],theta_c:119,theta_ijk:96,theta_ijl:82,theta_jik:[134,135],theta_pi:96,theta_sigma:96,thi:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],thick:[40,57],thin:57,thing:[2,3,28,61,68,161,162],think:[2,3,62,83,87,90,162],third:[2,13,29,35,41,42,62,66,76,79,103,113,114,133,141,157],thirumalai:50,tho:111,thole:2,thompson:[0,39,41,42,147],those:[1,2,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,32,35,36,38,39,41,42,44,45,46,47,48,49,50,51,52,53,54,57,61,63,68,69,75,77,78,82,83,84,86,87,88,89,90,91,92,93,94,97,98,99,100,101,102,103,104,107,108,110,111,113,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,133,134,138,141,142,144,145,147,148,153,154,155,156,157,158,159,160,161,162],though:[2,44,61,62,91,108,110,112,113,116,117,129,130,157,162],thought:[80,117,120],thread:[1,4],three:[1,2,28,29,32,35,36,37,40,41,43,44,50,60,61,62,63,68,69,74,77,79,85,86,88,92,93,96,110,111,113,116,117,120,133,134,135,136,141,143,144,146,147,153,154,155,156,157,162],threebodi:153,thresh:[19,57,59],threshhold:[19,57,59],threshold:[19,59,70],through:[2,3,44,61,65,67,68,71,74,79,80,81,93,109,111,112,114,117,121,136,140,145,146,148,152],throughout:[2,4,40,136],thru:[2,3,33,34,37,90],thrust:1,thu:[1,2,3,19,29,30,34,35,36,38,41,42,44,45,56,57,59,60,61,63,66,68,69,70,75,76,79,80,81,82,90,91,92,93,95,96,97,98,99,100,101,102,103,104,108,109,110,111,112,113,114,115,116,117,121,125,129,130,131,133,134,135,136,138,139,140,142,143,144,146,147,149,150,151,152,153,154,155,156,157,160,162],thumb:[44,102],ti2:43,ti3:43,ti4:43,tidi:161,tight:[96,146],tij:107,tildeslei:[13,32,107],tile:[2,19,44,59,162],tilt:[2,61,68,70,72,157],time:[0,1],time_integr:58,timer:1,timescal:[72,112],timespan:68,timestep:[1,2,3,19,35,42,57,59,60,61,62,63,66,67,68,69,70,73,74,75,77,78,79,80,90,91,96,108,112,119,130,131,148,162],timesteppnig:75,tin:[103,104],tini:[44,90,96],tio2:146,tio:146,tip3p:0,tip4:2,tip4p:0,tip:0,tirrel:80,titl:161,tji:107,tl1:43,tl3:43,tlbr_msw:143,tloop:[68,69],tm3:43,tmp:[2,19,34,57,59,162],tobia:68,togeth:[2,3,4,19,42,44,59,61,68,115],tol:[75,153],toler:[61,74,75,90,91,153],tolernac:74,too:[1,2,19,29,30,36,38,41,57,59,61,63,68,75,79,91,108,162],took:148,tool:[0,1,2,3,19,57,59,91],toolkit:2,top:[0,3,4,67,91,147,161],topic:162,topolog:[2,32,56],torqu:[2,13,67,90,95,107,116,117,131,162],torsion:[2,46,56,93],torsion_flag:93,tosi:97,tot:146,total:[2,3,4,19,31,33,34,35,37,41,42,59,66,67,68,69,71,72,73,74,77,78,79,80,81,90,91,92,93,95,96,103,110,112,117,133,134,135,136,143,146,147,162],toukmaji:107,toward:[13,57,67,69,70,88,91],toxvaerd:126,tptask:4,trace:112,track:[67,79,162],track_displac:58,tractabl:74,trade:[2,104,121,125],tradit:[2,55],trail:[32,91,113,133,147],trajectori:[2,32,68,71,75,108],tran:[49,50],transfer:[1,2,4,58,79,96,136],transform:[2,32,116,138],transit:[2,4,91,105,129,135,136,156],translat:[2,63,68,71,112],transmit:2,transport:[58,79],trap:[2,35,162],trapezoid:162,treat:[2,42,79,81,90,95,106,112,113,116,119,134,135,136,144,162],treatment:106,tree:129,tri:[2,3,57,61,68,69,90,162],triangl:[2,57],triangul:2,triangular:[2,61],triclin:[0,1],triflag:2,trigger:[3,59,60,90],trigon:9,trilinear:67,tringl:57,tripl:[41,96],triplet:[111,141,143,153,154,155,156,157],trivial:3,trott:[41,147],troubl:3,trump:62,truncat:[2,63,74,80,81,94,104,112,117,121,123,126,146],tscale:72,tsige:99,tstart:[66,68,108],tstat:[2,66],tstop:[66,68,108],tsuzuki:[30,157],ttm_mod:79,tucker:[41,147],tuckerman:[68,71],tune:[2,4],tunnel:71,turkand:38,turn:[2,28,41,43,56,57,60,61,68,90,91,93,106,119,133,152],tutein:93,tutori:[2,70],tweak:44,twice:[2,4,45,61,68],twist:[130,131],two:[1,2,3,4,19,28,29,32,36,40,41,43,44,55,57,59,60,61,66,67,68,69,70,71,72,78,79,81,89,90,91,92,93,95,96,97,98,99,102,103,104,106,107,108,110,111,112,113,114,116,117,120,121,125,129,130,131,133,136,140,142,143,144,146,147,148,152,153,154,155,156,157,159,160,162],two_temperatur:58,twobodi:[154,156,157],twojmax:[41,147],txt:[79,120,146,161,162],typcial:[19,59],type1:[40,43],type2:[40,43],type:[2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,32,35,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,57,58,67,75,81,82,83,84,85,86,87,88,89,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,107,108,109,110,111,112,113,114,115,116,117,118,119,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],typen:[40,43],typic:[1,2,3,4,13,19,21,22,29,32,44,55,57,58,59,60,61,62,68,73,75,90,91,100,102,104,115,116,119,120,121,125,130,131,133,144,156,161,162],tzou:79,u_chem:31,u_cond:[31,64],u_f:67,u_i:[64,65],u_ij:143,u_j:65,u_mech:[31,64],u_prom:96,uberuaga:91,ubiquit:[3,96],uchem:[114,140],uloop:[71,91,162],umbrella:2,umin:[10,11,24,25,47],unabl:[3,19,59],unaffect:[61,68],unalt:62,unambigu:157,unari:162,unbias:112,unchang:[61,68],uncom:1,uncompress:57,uncorrel:66,uncoupl:71,under:[0,2,4,6,41,46,57,62,68,72,82,109,112,129,147],underflow:57,undergo:[2,32,66,68],undergon:60,underli:[2,29,57,68,79],underpredict:2,underscor:[60,61,68,69,162],understand:[1,2,136],understood:96,undesir:[61,68],undisturb:[130,131],undump:57,unfix:[2,35,58,73,77],unfix_flux:58,unfold:76,uniaxi:69,uniform:[4,19,58,59,67,116,144,162],uniformli:[67,79,139,140,143],uninterrupt:[68,69,72,78,79],union:[2,81],uniqu:[2,66,69,91,110,112,162],unit:[2,5,6,16,17,18,29,30,31,32,33,34,35,36,37,39,40,41,42,43,44,46,57,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,76,78,79,80,81,82,83,87,88,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160],uniti:111,unitless:[29,62,68,72,74,90,117,138,142,153,154,155,156,157],univers:[2,32,91,130,135,156,162],unknown:30,unless:[3,4,40,43,44,61,68,90,102,162],unlik:[33,44,92,96,110,113,133,134,135,147],unlike:[68,69,110,119,120,134,135,162],unlimit:143,unnecessari:4,unoccupi:79,unoptim:57,unpack:[0,3],unperturb:32,unphys:[2,68],unpublish:136,unrel:[45,161],unrestrain:73,unset:112,unshift:107,unsmooth:127,unsolv:100,unstabl:67,unstag:161,until:[2,19,57,59,61,62,65,77,96,117,139,140,162],unus:96,unwant:44,unwrap:[33,34,42,60],up_intern:57,updat:[0,2,4,62,66,67,68,72,79,96,107,136],upenn:3,upon:[2,74,96],upper:[19,37,59,61,67,68,72,80,90,117,146],uppercas:0,upsid:2,upsilon:116,upstream:161,urbana:130,urey_bradlei:5,url:161,usabl:110,usag:[2,70,129],use:[2,57,79,116,133,144,146,161],useful:136,user:[0,1,2,3],user_manifold:161,user_misc:[14,15,17,48,52,54,55,86],usernam:161,using:[0,1],usr:3,usual:[2,8,12,16,17,18,23,32,53,55,57,60,61,69,72,73,79,80,81,87,91,100,102,105,107,116,120,129,130,131,141,147,152,153,162],util:116,v11:2,v22:2,v33:2,v_0:79,v_2:136,v_3:136,v_4:136,v_abc:162,v_area:162,v_avp:62,v_delta:32,v_dhug:72,v_drai:72,v_e_hbond:119,v_foo:162,v_ij:143,v_jx:35,v_jy:35,v_jz:35,v_k11:35,v_k22:35,v_k33:35,v_lgr_po:72,v_lgr_vel:72,v_linear:80,v_lj:93,v_mu:130,v_myindex:162,v_myvec:162,v_n:[67,136],v_name:[2,32,57,62,80,162],v_occ:115,v_prefactor:148,v_press:42,v_pxxwall:62,v_pxy:2,v_pxz:2,v_pyz:2,v_ramp:80,v_rebo:93,v_t_qm:72,v_torsion:93,v_v0:162,v_v11:2,v_v22:2,v_v33:2,v_v:162,v_valu:57,v_wiggl:80,v_x:[44,80,162],v_xave:2,v_xmax:2,v_xx:44,v_y:44,v_yi:44,vacanc:[77,136],vacf:2,vacuum:[79,105,156,160],valanc:96,valenc:[96,112],valent:96,valid:[2,3,40,43,61,70,110,112,116,136,143,162],valon:133,value0:162,value1:69,value2:69,van:[27,32,102,103,129,133,159],vanadium:136,vanilla:2,vanish:75,vapor:[19,59],vare:79,vari:[1,19,32,40,43,58,59,61,68,73,79,80,100,108,109,118,127,130,148],variabl:0,varianc:[108,162],variant:[1,2,68,69,117,134,135,138,154,156],variat:[19,59,162],varieti:[1,2,57,133,157,162],variou:0,varshalovich:41,vashishta1990:157,vashishta2007:157,vbia:2,vcm:[2,162],vdisplac:[80,162],vdw:103,vec:7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Documentation","5. Accelerating LAMMPS performance","6. How-to discussions","11. Python interface to LAMMPS","5.USER-INTEL package","angle_style charmm command","angle_style class2 command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style quartic command","angle_style sdk command","balance command","bond_style class2 command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style morse command","bond_style nonlinear command","bond_style quartic command","compute centro/atom command","compute cna/atom command","compute dpd command","compute fep command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute msd/nongauss command","compute orientorder/atom command","compute pressure command","compute saed command","compute sna/atom command","compute stress/atom command","compute xrd command","create_atoms command","dihedral_style charmm command","dihedral_style class2 command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style spherical command","dihedral_style command","dump image command","fix atc command","fix balance command","fix bond/swap command","fix box/relax command","fix controller command","fix ehex command","fix eos/cv command","fix eos/table/rx command","fix gld command","fix lb/fluid command","fix nvt command","fix nphug command","fix orient/fcc command","fix pimd command","fix qbmsst command","fix restrain command","fix rx command","fix shake command","fix spring/rg command","fix ti/rs command","fix ti/spring command","fix ttm command","fix wall/lj93 command","fix wall/region command","improper_style class2 command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style ring command","improper_style umbrella command","minimize command","neb command","pair_style adp command","pair_style airebo command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dpd/fdt command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style exp6/rx command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_style morse command","pair_style multi/lucy command","pair_style multi/lucy/rx command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style polymorphic command","pair_style resquared command","pair_style lj/sdk command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/idealgas command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style sw command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style vashishta command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","LAMMPS GitHub tutorial","variable 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80,94,116,120],colvar:[0,2],com:[2,3,38,64,96,162],comand:61,comb3:2,comb:2,combiant:106,combin:[3,4,19,33,56,58,59,64,69,72,82,83,103,105,106,110,113,114,115,129,130,148,154,155,157,158,160],come:[0,2,3,14,62,63,69,78,79,154,155,157,158,162],comit:162,comm:[0,4,31,92,109],comm_modifi:[2,3,97,103,109,113,118],comm_styl:[2,20,60],comm_world:4,command:[0,1],comment:[2,4,46,66,75,80,92,93,111,112,114,115,121,134,140,141,142,147,148,154,155,156,157,158,162],commit:162,commmand:3,common:[0,1,3,4,5,31,62,72,82,83,118,120,154,155,157],commonli:[3,10,38,39,58,90,119,124,148,155,157],commun:[1,3,4,5,20,58,60,62,68,69,80,110],comp:[76,92,113,145,152,156],compar:[1,3,5,41,44,57,91,92,134,147],comparison:0,compass:[7,21,47,57,83,102],compat:[4,20,50,60,63,64,81,137],compens:[3,113],compil:[5,58,137],complain:4,complement:134,complementari:[105,122],complet:[3,4,20,60,72,92,114],complex:[3,4,10,37,39,42,45,68,82,92,113,137],complic:3,compon:[3,30,31,34,35,36,37,38,39,40,42,43,58,61,62,63,64,68,69,70,72,76,82,91,92,109,113,118,131,132,147,148],componenet:3,composit:[3,68,111],compound:[104,113,114,158],compress:[3,58,70,73],compris:[82,115,145],compton:[41,44],comput:[0,1],computation:[3,80,97],compute_modifi:[2,61,62,69,70],compute_sa:41,compute_xrd:44,concaten:2,concav:82,concentr:[66,75,111,115,141],concept:3,conceptu:[3,62,92,105,134],concern:[3,31,33,67],concis:4,concurr:5,conden:[80,155,157],condens:[3,80,94,107,111,122,158],condit:[2,3,40,41,43,44,58,59,68,70,71,73,76,77,80,110,113,119],conducit:3,conduct:[0,2],confer:[5,137],configur:[1,2,3,5,58,62,72,91,92,94,97,112,134,137,154,155,157,158,162],conflict:162,conform:[3,61,62,74,89,92,113],confus:158,conjuct:109,conjug:113,conjunct:[3,33,45,68,92,98,99,105,109,113,120,122,143,146],connect:[3,33,61,76,92,106,118,153,157],conner:94,connor:94,consecut:[4,45,105,122,126],consequ:[1,3,80,121],conserv:[14,61,67,68,69,75,76,92,108,109,110,118,128,147],consid:[3,30,33,60,61,80,113,145,147,153],consider:3,consist:[3,4,40,45,51,63,67,69,70,73,74,75,92,94,97,103,105,113,117,131,132,134,137,140,141,145,147],consistent_fe_initi:59,constant:0,constantli:64,constitu:[3,81,82,103,145],constrain:[3,64,67,76,77,91,113],constraint:[20,40,43,60,64,76,77,81,91,132],construct:[3,29,30,31,37,39,41,42,44,62,69,74,75,82,108,137,153,154],constructor:4,consult:5,consum:1,contact:[0,2,106,112,114,117,118,145],contain:[0,1,2,3,4,20,33,36,41,42,44,45,46,57,58,59,60,63,66,68,71,73,75,80,82,92,93,94,97,104,105,108,111,112,113,115,134,137,140,141,142,144,148,154,155,156,157,158,162],context:[3,5,160],contibut:30,contin:5,continu:[0,2,3,20,60,61,62,63,64,67,69,70,73,78,79,80,82,97,109,124,127,145,156],continuum:[3,59,80],contour_integr:59,contract:[62,69],contrain:76,contrast:[1,3,160],contrib:80,contribut:[3,30,33,34,35,36,40,42,43,62,68,76,91,92,109,111,113,131,132,137,147,162],control:[2,3,4,5,12,14,20,33,36,42,48,58,59,60,62],control_typ:59,convect:36,conveni:[3,14,148,162],convent:[14,50,55,57,74,111,113],converg:[3,20,58,60,61,62,70,73,74,76,91,92,104,105,122,147],convers:[42,58,105,106,107,113,122,126,130,143],convert:[2,3,6,7,9,13,17,18,19,36,45,47,58,83,84,88,89,92,93,111,137,155,157,161],convex:82,cool:64,coord:[2,3,4,37,39,71,81,92],coordb:147,coordbb:147,coordiat:91,coordin:[1,3,4,20,33,34,35,42,45,58,60,61,62,64,69,71,76,77,79,80,91,92,93,94,96,112,147],coords:147,copi:[0,4,58,80,92,162],copper:161,coprocessor:[1,5],core:[0,1],coreshel:3,coreshell:[3,99,105,107],cornel:[3,46],corner:[3,58,82,162],corpor:5,corr:104,correct:[3,4,33,46,58,64,69,73,81,82,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,111,112,113,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],correction_max_iter:59,correctli:[4,69,76,82,92,107,132,137,162],correl:[2,3,36,37,42,67,72],correpond:66,correspond:[1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,23,24,25,26,27,28,29,30,33,40,41,42,44,46,47,48,49,50,51,52,53,54,55,56,58,62,63,64,66,68,69,70,71,72,75,76,81,82,83,84,85,87,88,89,90,92,93,94,95,98,99,100,101,102,103,104,105,108,109,111,112,113,114,115,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,134,135,137,139,141,142,143,144,145,146,147,148,149,154,155,156,157,158,159,160,161],correspondingli:[131,132],cosin:[2,3],cosineshift:12,cossq:2,cost:[1,3,4,20,41,43,44,58,60,69,75,80,105,122,126,137,154],costheta0:[154,155,157,158],costheta:144,costli:[4,5],coul:[2,3,5,19,22,23,33,46,91],could:[2,3,4,20,33,35,36,40,58,60,63,73,80,81,82,91,94,116,120],coulomb:[3,43,91,98,99,100,101,102,104,105,106,107,108,113,118,119,122,126,130,133,143,146,147,157,158,160],coulommb:3,count:[1,3,4,20,36,46,60,69,76,82,91,92,116,120],counteract:63,counterbal:64,counterbalanc:14,counterclockwis:46,coupl:0,couple:[3,4],cours:[5,67,74,81,131,149],cov:147,coval:[3,14,113,134,147],cover:[3,59,68,113],cpp:[1,3,4,33,76],cpu:[1,5],cpuinfo:5,cr2:44,cr3:44,creat:[0,1,2,3,4,20,36,40,41,45,58,59,60,61,62,66,69,70,71,72,74,80,92,94,97,104,111,112,130,139,140,141,144,147,154,155,156,157,158,162],create_atom:[2,3,20,36],create_bond:2,create_box:[2,3,20,36,45,62,69,153],create_elementset:59,create_faceset:59,create_nodeset:59,createatom:0,creation:45,criteria:[58,61,91],criterion:[20,45,60,61,91,92,104,113,118,147],critic:[3,25,26,80,91],cross:[5,34,58,92,101,109,111,119,120,122,124,126,144,146,155,157,161],crossov:1,crozier:0,crucial:73,crystal:[3,5,30,31,39,71,79],crystallin:[3,156],crystallogr:[41,44],crystallographi:[41,44],cs1:44,cs_chunk:3,csanyi:[42,148],cscl:134,csequ:3,csh:[4,5],cshrc:4,csic:[112,154,155,157,158],csinfo:3,csisi:[112,154,155,157,158],csld:2,cst:111,cstherm:3,csvr:[2,3],ctcm:[93,111],ctype:4,cu1:44,cu2:44,cu3au:134,cube:[3,82],cubes:[20,60],cubic:[2,39,68,71,111],cuda:1,cuh:97,cummul:[3,61,120],cumul:[3,69,70,92],curli:2,currenlti:63,current:[0,1,3,4,5,20,31,33,43,58,59,60,61,62,63,64,69,74,75,76,77,80,81,91,92,97,104,108,111,113,114,118,121,131,132,134,135,136,144,149,155,157,162],curv:[3,45],curvatur:[117,145,161],custom:[0,2,3,4,34,35,36,43,58,61,62,69,70,73,91,94,116,120],cut:[1,2,3,5,20],cuthi:71,cutinn:[131,132],cutlo:71,cutmax:144,cutoff1:[102,108,122,126,130,133,143,146],cutoff2:[98,99,100,102,107,108,122,126,130,133,143,146],cutoff:[3,5,22,23,29,30,31,33,37,39,42,61,66,71,73,81,82,91,93,94,95,96,97,98,99,100,101,102,103,105,106,107,108,109,110,111,112,113,114,115,116,117,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],cutoffa:112,cutoffc:112,cuu3:111,cval:44,cvar:63,cvff:[2,5],cwiggl:81,cyan:[2,58],cycl:[69,70],cyclic:46,cylind:[58,82],cylindr:3,cyrot:97,d3q15:68,d3q19:68,d_e:80,daan:79,damag:2,damp:[3,69,70,73,91,92,98,99,101,105,108,113,118,122,130,143,146],dampflag:118,danger:109,darden:108,darken:58,dash:118,dat:[3,36,59],data2xmovi:0,data:[1,2],databas:0,date:[0,3],datum:3,davenport:133,davi:81,david:[155,157],daw:[111,144],dcd:[3,58,72],deactiv:130,debug:[3,4,41,44,45,72],deby:2,decai:[37,105,161],decid:[3,5,162],decod:58,decompos:[33,148],decomposit:[59,72],decoupl:3,decreas:[5,61,64],dedic:5,defect:[3,30,137],defgrad:2,defin:[2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,65,66,68,69,70,71,72,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,94,95,96,98,99,100,101,102,103,105,106,108,109,110,112,113,115,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,132,133,137,138,139,140,141,142,143,144,145,146,148,149,150,151,152,153,154,155,156,157,158,159,160,161],definit:[2,3,42,63,65,70,81,97,103,110,113,144,148],deform:[2,3,43,62,69,131,132],deg2theta:44,degre:[3,6,7,9,13,14,17,18,19,37,39,40,44,45,46,47,49,50,55,56,58,61,69,70,72,74,76,79,83,84,88,89,90,91,108,111,120],delai:3,delet:[2,29,61,69,153,162],delete_atom:[2,45],delete_bond:[2,21,22,23,24,25,26,27,28,29],delete_el:59,delimit:75,dellago:[3,64],deloc:[113,147],delr:134,delta:2,delta_1:97,delta_3:97,delta_7:97,delta_ij:[134,144],delta_pi:97,delta_r:144,delta_sigma:97,deltah_f:66,demo:4,demonstr:[73,134],dendrim:120,denniston:68,denot:[41,64,105,119],dens:[61,75,113],densiti:[3,20,42,45,59,60,68,80,81,93,94,97,111,134,135,136,140,141,144,145,147,150,151,152],depart:0,departur:73,depend:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,29,30,37,40,42,45,46,47,48,49,50,51,52,53,54,55,57,58,60,62,66,68,69,70,71,75,76,78,80,81,82,83,84,85,87,88,89,90,91,93,94,95,96,97,98,99,100,101,102,103,104,105,106,108,109,111,112,113,114,115,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,134,135,137,138,139,140,141,142,143,144,145,146,147,148,149,154,155,156,157,158,159,160,161],dependend:3,deposit:[2,69,76],depth:[27,58,80,115,117,145],der:[33,103,104,130,160],deriv:[3,33,42,62,63,64,69,70,71,78,79,80,81,82,94,97,103,108,113,114,119,124,128,129,134,137,160],derjagin:160,derlet:71,descib:58,describ:[0,1,2,3,4,5,20,30,31,41,42,43,44,45,51,54,60,61,62,63,66,67,68,69,70,71,72,73,75,78,79,81,91,92,94,96,98,99,101,102,103,104,105,108,111,113,114,115,117,118,119,122,123,124,125,126,127,128,129,130,131,132,133,134,137,138,140,141,144,145,146,147,148,149,153,154,155,156,157,158,159,160,161,162],descript:[2,3,4],descriptor:42,design:[0,3,4,41,44,59,61,69,71,80,95,96,101,105,107,113,130,131,132,135,136,144],desir:[2,3,4,5,36,40,43,45,62,63,67,69,76,91,92,109,111,120,131,132,154,155,157],desktop:[3,58],destabil:97,destre:89,destroi:4,detail:[1,2,3,4,5,20,35,36,40,42,43,45,57,58,59,60,61,62,63,64,67,68,69,70,73,76,79,80,91,93,94,96,97,100,101,102,103,104,105,108,109,113,114,117,118,119,120,122,123,124,125,126,127,128,129,130,131,132,133,134,138,140,141,145,147,148,149,159,160,162],detect:[2,37,92,104,120,121],determin:[1,3,5,27,33,40,41,43,44,45,58,60,62,66,69,71,72,73,74,75,81,82,94,100,104,108,111,115,116,118,126,134,137,141,145,147,153,160],devan:146,devanathan:157,develop:[0,3,4,5,63,70,73,94,97,113,136,137,147,158],deviat:[70,71,116],devic:1,devin:104,devis:136,dfactor:58,dft:137,dhug:73,dhugoniot:73,dia:134,diag:75,diagnost:[2,5,61,75],diagon:[3,42,43,62,69],diagonalstyl:148,diagram:[20,41,44,57,60,72],diallo:120,diam:58,diamet:[3,45,58,103,117,118,124,145,160],diamond:[113,134],dick:3,dicken:63,did:[91,109,111,118,155,157],diel:2,dielectr:[2,101,105,106,107,122,126,130,143],diff:[3,5],differ:[1,2,3,4,5,20,29,30,33,37,42,45,57,58,60,61,62,63,64,67,68,69,71,72,73,76,77,78,79,80,81,82,83,92,93,94,97,100,101,103,104,109,110,111,113,115,117,118,119,122,123,125,126,133,134,135,136,138,139,140,141,142,144,145,146,147,148,149,154,155,157,158,160],differenti:[1,3,14,75,105,144,156],difficult:[62,63,72,120],difficulti:[37,39,76],diffract:[41,44],diffraction:[41,44],diffus:0,diffuse:3,digit:[2,137],dihedr:[0,2,5,29,37,39,40,42,43,45,46,47,48,49,50,51,52,53,54,55,56,57,61,74,84,85,86,88,91,94,97,101],dihedral_coeff:[2,46,47,48,49,50,51,52,53,54,55,56,57],dihedral_cosine_shift_exp:12,dihedral_styl:0,dihydrid:113,dij:76,dilat:[2,62,69,70],dim:[45,134],dimens:[1,2,3,20,36,43,45,58,60,62,68,69,70,73,81,92],dimension:[37,40,41,42,44,80,92,144],dimensionless:[38,42,63,80,148,160],dimer:[3,134],dimstr:[20,60],dintel_offload_noaffinity:5,dipol:[0,2],dipolar:14,dipole:108,dir:[1,4,71,73,144],dirac:42,direc:144,direct:[2,3,5,14,30,39,41,42,44,45,46,58,68,70,71,73,78,79,80,81,82,91,92,109,110,118,132],directli:[3,4,33,42,45,58,63,68,75,82,93,94,98,99,100,105,108,111,113,122,126,143,146,153],directori:[0,1,2,3,4,5,63,78,79,92,93,94,97,104,105,111,112,114,130,134,135,136,137,142,144,147,148,154,155,156,157,158],disabl:[5,80,121],disadvantag:[3,60],disallow:69,discard:[2,20,60,82],discontinu:[91,128],discourag:134,discret:[3,58,63,68],discuss:[0,1,2],disk:[3,37],disloc:[30,137],disord:[30,137],disp:[0,2],dispar:145,disperion:[108,126],dispers:[3,100,108,126,131,158],displac:[2,3,38,62,69,71,118],displace_atom:2,displai:[4,57,58],disregard:137,dissip:[3,32,65,67,78,79,109,110,118,131,132],dist:[3,36,72,74,153],distanc:[2,3,6,7,21,22,23,24,25,26,27,28,29,31,34,35,37,38,39,41,42,45,47,58,61,62,64,68,69,70,71,73,74,76,77,79,80,81,82,83],distinct:[3,145],distinguish:[3,42,113],distort:93,distrbut:93,distribut:[0,2,3,4,20,33,42,57,60,67,68,69,93,97,105,111,112,114,134,135,136,142,144,145,154,155,156,157,158],distro:144,ditto:161,div:5,diverg:[79,94],divid:[3,5,20,36,40,43,57,60,71,91,92,114,147,158],divis:[3,56,68,97,130],dl_poly:3,dlammps_ffmpeg:58,dlammps_gzip:58,dlammps_jpeg:58,dlammps_memalign:5,dlammps_png:58,dlm:69,dlmp_intel_offload:5,dlopen:3,dlvo:[103,160],dm_lb:68,doc:[0,1,2,3,4,33,35,38,40,43,45,57,58,63,69,82,91,92,93,94,96,104,105,111,112,114,120,134,135,136,142,144,148,154,155,157,158,162],docuement:145,doe:[0,1,2,3,4,20,29,30,33,36,41,44,45,46,57,58,59,60,61,62,63,64,66,67,68,69,80,81,82,84,85,86,88,89,92,93,94,95,96,97,100,101,102,103,104,105,106,108,109,111,112,113,115,116,117,118,119,121,124,125,127,128,129,131,132,134,135,136,137,140,141,144,145,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],doesn:[45,94,104,112,154,155,156,157,158],dof:40,doi:[3,71],domain:[3,20,41,44,58,60,62,68,69,72,80,81,92],domin:[1,113],don:[0,5,82,134,147,162],donald:63,done:[1,3,20,45,56,58,59,60,61,62,63,66,69,72,76,78,79,91,92,94,100,111,126,132,133,134,140,141,153,162],donor:120,dot:43,doti:[97,144],doubl:[1,2,3,4,5,33,46,82,97,114,119,137],dover:59,down:[3,4,62,113,147],download:4,downsid:3,dpd:[2,3],dpdtheta:[32,110],dpdtheta_i:[65,66],dr_ewald:41,drag:[2,3,36,69,70,77],dragforc:68,drai:[58,73],drain:91,dramat:[61,62,69,147],drautz:97,draw:58,drawn:[58,67],drayleigh:73,dreid:[2,3],dreiding:0,drfourth:38,drho:[93,111,140,141],drift:[3,38,64,67],drive:[4,62,69,71,92],driven:[3,51],driver:3,drop:109,drsquar:38,drude:[0,2],dsf:2,dsmc:2,dt_collis:68,dt_lb:68,dt_md:68,dtqm:73,dudarev:44,due:[1,3,5,29,30,34,35,38,41,42,43,44,45,58,61,62,67,68,69,70,71,74,78,79,80,81,82,91,92,106,109,110,111,116,117,131,132,144,145,146,153,155,157,160,161],duffi:80,dullweb:69,dummi:[14,156],dump:[0,1,2],dump_modifi:[2,3,58],dunbrack:[3,6,46,101],duplic:[2,20,60,71],durat:[57,80,118],dure:[2,3,5,20,33,46,59,60,61,62,63,64,66,67,68,69,70,71,72,73,74,76,77,78,79,80,81,82,91,92,109,130,137,139,140,141],dvlo:160,dvx:3,dx_lb:68,dy3:44,dyanam:3,dynam:[0,2,3,4,5,20,32,38,45,58,59,60,61,63,65,67,69,70,72,73,74,78,79,80,91,92,109,110,113,131,132,152],dynamo:[93,111,134],dyre:127,e28637:14,e_1:97,e_2:97,e_a:75,e_b:114,e_ee:113,e_hbond:120,e_i:[3,97,114],e_j:[3,97],e_k:97,e_ke:113,e_kl:3,e_lj:[94,108],e_n:[63,97],e_ne:113,e_nn:113,e_pr:113,e_rebo:94,e_torsion:94,e_tot:137,e_vol:137,eaa:83,eaat:47,each:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,33,34,35,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,66,67,68,69,70,71,72,75,76,77,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,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22,157],essential:70,essex:14,establish:33,estim:[1,3,20,30,36,43,59,60,75],esub:134,eta:[3,68,69,73,112,114,117,144,156,158],eta_dot:69,eta_ij:144,eta_ji:114,etap:69,etap_dot:69,etc:[1,2,3,4,5,29,34,35,36,43,45,58,59,67,69,80,82,91,92,111,112,130,132,137,154,155,157,158],etol:[91,92],etot0:73,etot:[3,43,73],eu2:44,eu3:44,euler:[75,91,92],eulerian:59,europhi:68,evalu:[2,4,33,36,42,45,46,58,59,63,67,75,81,91,137,140,141,144,147],evanseck:[3,6,46,101],evapor:2,evaul:91,even:[3,5,20,30,56,60,62,64,69,80,81,82,91,92,96,113,114,118,145,158],evenli:[20,43,60,68],event:[2,3,69,80],eventu:3,ever:29,everaer:[103,117,145],everi:[0,1,2,3,4,5,20,36,58,59,60,61,62,63,64,68,69,70,71,73,75,76,80,92,109,130,147,162],everyth:162,everywher:124,eviri:113,evolut:[64,68,72],evolv:[68,72],ewald:[2,3,41,43,91,98,99,100,105,108,113,122,126,143,146],ewald_disp:108,exact:[20,60,61,67,80],exactli:[3,20,36,45,60,67,73,109,111,118,131,140,141],examin:[3,61,75],exampl:[0,1,2],exce:[3,5,20,60,62,69,91],exceed:[20,60,69],excel:113,except:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,29,34,35,40,43,45,46,47,48,49,50,51,52,53,54,55,57,60,62,69,70,72,76,80,83,84,85,87,88,89,90,92,93,94,95,98,99,100,101,102,103,104,105,107,108,109,111,112,113,114,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,132,135,139,142,143,145,146,149,154,155,156,157,158,159,160,161],excess:113,exchang:[2,3,59,64,80,113],excit:113,excite:113,exclud:[3,5,40,42,91,118,131,132,153],exclus:[1,5,33,46,104,137],excurs:69,execut:[1,2,3,4,58],exempl:147,exemplari:67,exemplifi:113,exert:[3,82],exhaust:59,exhibit:[37,64,69,113],exist:[3,4,30,45,57,58,62,83,84,85,86,88,110,153,162],exit:[2,4,20,60],exp6:2,exp:2,expand:2,expans:[42,56],expect:[1,5,20,60,71,73,134,137],expens:[3,71,80],experi:[3,74,92,109],experienc:[3,5],explain:[1,3,4,20,31,58,60,62,69,71,92,96,111,147,149,162],explan:[3,42,71],explic:138,explicit:[3,4,33,75,94,97,101,111,113,121,131,162],explicitli:[3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,23,24,25,26,27,28,29,40,45,46,47,48,49,50,51,52,53,54,55,67,69,70,73,76,80,83,84,85,87,88,89,90,93,94,95,98,99,100,101,102,103,104,105,106,108,109,111,112,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,135,137,139,140,141,142,143,145,146,149,150,151,152,154,155,156,157,158,159,160,161,162],explictli:5,exploit:72,explor:[41,44],expon:[75,111,115,117,120,130,138,146],exponenti:[33,75,115,144,154,158,161],expos:4,exposit:[59,109],express:[3,42,45,62,71,75,80,97,111,113,124,134,147,148],expressiont:97,extend:[0,3],extens:[3,5,22,23,28,33,36,63,64,69,70,71,74,78,79,80,81,82,117,134,137,145,148],extent:[1,20,22,60,94],exterior:[3,82],extern:[2,33,58,62,67,68,69,70,80,91,135,136],extra:[3,4,5,20,23,40,41,43,44,45,60,69,73,91,108,118,134],extract:[3,4,19,33,92,105,114,134,148],extract_atom:4,extract_comput:4,extract_fix:4,extract_glob:4,extract_vari:4,extrapol:1,extrem:[1,3,58,62,69,79,113,156],extrema:130,extreme:113,extrins:59,f_1:3,f_a:[155,156,157],f_c:156,f_f:157,f_fix_id:73,f_harm:79,f_i:[14,144],f_id:[3,63],f_ij:144,f_int:78,f_j:14,f_jj:36,f_k:144,f_langevin:80,f_max:73,f_r:[155,156,157],f_sigma:97,f_solid:79,f_ss:3,face:[3,81,82,117,134,145],facil:0,facilit:3,fact:[3,5,79,118,147],factor:[1,3,9,13,17,18,19,20,23,24,33,36,41,42,44,46,54,58,60,62,64,68,69,70,72,74,75,76,81,82,88,94,97,98,99,101,105,106,107,109,110,113,118,121,122,134,137,140,141,142,143,146,149,154],fail:[4,62,91,92,107],fairli:[4,162],faken:31,fall:3,fals:147,famili:158,familiar:[0,4,162],fan:144,far:[3,60,62,69,71,74,81,84,88,92],farrel:[155,157],fashion:[3,20,45,60,63,69,70,73,79,80,81,92,131],fast:[3,5,63,73,75,131,132,137],faster:[1,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,29,38,40,46,47,48,49,50,51,52,53,54,55,60,69,70,76,78,80,83,84,85,87,88,89,90,93,94,95,97,98,99,100,101,102,103,104,105,108,109,111,112,114,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,135,139,142,143,145,146,149,154,155,156,157,158,159,160,161],fastest:[1,3,80],fault:30,fava:117,favor:61,fcc:[2,3,30,31,36,39],fcold:64,fdt:[2,65,66,75],fdti:33,fe2:44,fe3:44,fe_md_boundari:59,featur:[0,3,4,42,58,61,67,72,82,91,162],fecr:111,feedback:63,feel:[71,82,92],fehlberg:75,felling:136,felt:82,fene:[2,3,5],fennel:[105,122],fep:[0,2],ferguson:[3,46],fermi:[1,157],fermion:113,fernando:133,few:[1,3,4,64,69,76,91,92,94,147],fewer:[1,4,5],feynman:72,ffield:[104,114,147],fflag1:58,fflag2:58,ffmpeg:58,ffplai:58,fft:[1,4,43],fhot:64,ficiti:153,fictiti:[3,72,74,105,122,126,153],field:[0,2],fifth:[3,115,142],figshar:71,figur:[1,5,73,162],fij:108,file0:71,file1:[4,66,71],file2:[4,66],file:[0,1,2],filenam:[5,20,58,59,60,66,71,75,80,92,93,94,97,105,111,112,114,115,134,135,136,140,141,142,144,147,148,154,155,156,157,158],fill:[45,58,80,97,137,162],filter:59,finchham:[3,107],find:[0,3,4,5,31,33,61,62,63,66,71,74,91,92,105,122,126,134,140,141,147,162],fine:[5,79,162],finer:[42,45],finger:45,finish:[3,4,20,60],finit:0,finni:111,fire:[2,91,92],first:[0,1,2,3,4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Documentation","5. Accelerating LAMMPS performance","3. Commands","6. How-to discussions","11. Python interface to LAMMPS","5.USER-INTEL package","angle_style charmm command","angle_style class2 command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style quartic command","angle_style sdk command","balance command","bond_style class2 command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style morse command","bond_style nonlinear command","bond_style quartic command","compute centro/atom command","compute cna/atom command","compute dpd command","compute fep command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute msd/nongauss command","compute orientorder/atom command","compute pressure command","compute saed command","compute sna/atom command","compute stress/atom command","compute xrd command","create_atoms command","dihedral_style charmm command","dihedral_style class2 command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style spherical command","dihedral_style command","dump image command","fix atc command","fix balance command","fix bond/swap command","fix box/relax command","fix controller command","fix ehex command","fix eos/cv command","fix eos/table/rx command","fix gld command","fix lb/fluid command","fix nvt command","fix nphug command","fix orient/fcc command","fix pimd command","fix qbmsst command","fix restrain command","fix rx command","fix shake command","fix spring/rg command","fix ti/rs command","fix ti/spring command","fix ttm command","fix wall/lj93 command","fix wall/region command","improper_style class2 command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style ring command","improper_style umbrella command","minimize command","neb command","pair_style adp command","pair_style airebo command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dpd/fdt command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style exp6/rx command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_style morse command","pair_style multi/lucy command","pair_style multi/lucy/rx command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style polymorphic command","pair_style resquared command","pair_style lj/sdk command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/idealgas command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style sw command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style vashishta command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","LAMMPS GitHub tutorial"],titleterms:{"default":[30,33,37,38,39,41,42,44,45,57,58,59,62,67,68,69,70,72,73,78,79,81,97,113,131,132,137,153],"long":[98,99,100,101,102,105,107,108,122,126,130,143,146],acceler:1,adiabat:3,adp:93,airebo:94,alloi:111,amber:3,angle_styl:[2,6,7,8,9,10,11,12,13,14,15,16,17,18,19],arrai:3,aspher:3,atc:59,atom:[3,30,31,37,39,42,43],aug:0,balanc:[20,60],barostat:3,bcc:71,beck:95,between:3,bodi:[3,96],bond:61,bond_styl:[2,21,22,23,24,25,26,27,28,29],bop:97,born:[98,107],box:[3,62],buck:[99,100,107,133],build:4,calcul:3,categori:2,centro:30,charmm:[3,6,46,101,130],chunk:[3,35],class2:[7,21,47,83,102],cna:31,code:3,coeffici:3,colloid:[81,103,160],comb3:104,comb:104,command:[2,3,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],comparison:1,compos:3,comput:[2,3,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44],conduct:3,constant:3,control:63,core:3,cosin:[8,9,10,11,12,13,48],cossq:84,coul:[98,99,100,101,102,105,106,107,119,122,126,130,143,146],coupl:3,create_atom:45,cubic:124,cut:[26,99,102,105,108,113,116,122,123,130,138,143],cvff:85,data:3,deby:[105,122],delta:9,descript:[6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],diel:106,diffus:3,dihedral_styl:[2,46,47,48,49,50,51,52,53,54,55,56,57],dipol:[3,14,108],discuss:3,disp:3,distanc:86,document:0,dpd:[32,109,110],dreid:120,dreiding:3,drude:3,dsf:[105,122],dump:[3,58],eam:111,edip:112,eff:113,ehex:64,eim:114,elastic:3,energi:110,exampl:[3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],exp6:115,exp:[12,48],expand:[23,125],extend:4,fcc:71,fdt:110,fene:[22,23],fep:33,field:3,file:3,finit:3,fix:[2,3,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82],fix_modifi:[59,60,62,63,64,68,69,70,71,73,74,76,77,78,79,80,81,82],flow:3,fluid:68,flux:36,forc:3,fourier:[15,16,49,87],from:[3,4],gauss:116,gaybern:117,gener:[1,3],github:162,gld:67,global:3,gpu:[95,98,99,101,102,103,105,108,109,111,116,117,119,122,123,124,125,138,139,145,146,149,154,155,156,157,159,160,161],gran:118,granular:3,gromac:119,gyrat:[34,35],harmon:[17,24,25,26,50,52,81,88,142],hbond:120,heat:36,helix:51,hertz:118,hexord:37,histori:118,hook:118,how:3,idealga:150,imag:58,implicit:101,improper_styl:[2,83,84,85,86,87,88,89,90],indice:0,individu:2,induc:3,info:[0,59,60,62,63,64,68,69,70,71,73,74,76,77,78,79,80,81,82],input:[2,3],install:4,integr:3,intel:[5,6,17,22,24,46,50,54,69,85,88,99,101,117,122,154,155],interfac:[3,4],kspace:2,kspace_styl:3,lammps:[0,1,2,3,4,162],lennard:133,librari:[3,4],linear:[129,139],list:[2,121],lj1043:81,lj126:81,lj93:81,lj96:123,local:3,lubric:131,lubricateu:132,luci:[140,141],mdf:133,meam:[134,135,136],measur:1,mgpt:137,mie:138,minim:[59,60,62,63,64,68,69,70,71,73,74,76,77,78,79,80,81,82,91],mod:[80,156],model:3,morri:152,mors:[27,94,120,139],movi:58,mpi:4,msd:38,msm:[98,99,101,105,122],multi:[3,52,140,141],multipl:3,nb3b:142,neb:92,nemd:3,nharmon:53,non:3,nongauss:38,nonlinear:28,nph:69,nphug:70,npt:69,nvt:69,omp:[6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,23,24,25,26,27,28,29,46,47,48,49,50,51,52,53,54,55,69,70,83,84,85,87,88,89,90,93,94,95,98,99,100,101,102,103,104,105,106,108,109,111,114,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,135,136,139,142,143,145,146,149,154,155,156,157,158,159,160,161],opl:54,opt:[101,111,122,126,139],optim:1,option:3,orient:71,orientord:39,orthogon:3,other:3,output:[3,59,60,62,63,64,68,69,70,71,73,74,76,77,78,79,80,81,82],overview:4,packag:[1,5],pair:3,pair_styl:[2,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],parallel:4,paramet:3,pars:2,particl:3,per:3,perform:1,period:10,pimd:72,polariz:3,poli:[131,132],polymorph:144,potenti:[2,3],pppm:3,pressur:40,process:3,properti:3,python:4,qbmsst:73,quadrat:55,quantiti:3,quartic:[18,29],rattl:76,rebo:94,region:82,relat:[6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,73,75,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,148,149,150,151,152,153,154,155,156,157,158,159,160,161],relax:62,replica:3,resquar:145,restart:[3,59,60,62,63,64,68,69,70,71,73,74,76,77,78,79,80,81,82],restrain:74,restrict:[5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,148,149,150,151,152,153,154,155,156,157,158,159,160,161],rigid:3,ring:89,rule:2,run:[3,4,59,60,62,63,64,68,69,70,71,73,74,76,77,78,79,80,81,82],scalar:3,script:[2,3,4],sdk:[19,146],serial:4,set:3,shake:76,share:4,shell:3,shift:[11,12,25,26,48],simpl:16,simul:3,size:3,smooth:[128,129,139],smtbq:147,sna:42,snad:42,snap:148,snapshot:3,snav:42,soft:[130,139,149],solver:2,spc:3,sph:[150,151,152],spheric:[3,56],spline:[135,136],spring:[77,79],squar:13,srp:153,start:[59,60,62,63,64,68,69,70,71,73,74,76,77,78,79,80,81,82],stop:[59,60,62,63,64,68,69,70,71,73,74,76,77,78,79,80,81,82],strategi:1,streitz:105,stress:43,structur:2,style:[1,2,3],summari:3,swap:61,syntax:[6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],system:3,tabl:[0,3,66,155],taitwat:[151,152],temperatur:3,tersoff:[155,156,157],test:4,thermal:3,thermo:3,thermodynam:3,thermostat:3,time:3,tip3p:3,tip4p:[3,105,122,126,130],triclin:3,tstat:109,ttm:80,tutori:162,umbrella:90,user:5,using:[3,4],valu:3,variabl:3,variou:1,vashishta:158,vector:3,version:0,viscos:3,visual:3,wall:[3,81,82],water:3,wolf:[98,105],wrapper:4,write:3,xrd:44,yukawa:[159,160],zbl:[157,161]}})
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