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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15121 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2016-06-07 15:31:35 +00:00
parent 7cb2b01ebd
commit 59497c1076
15 changed files with 1509 additions and 117 deletions
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97
doc/html/Section_commands.html
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@ -769,12 +769,12 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.</p>
<a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">LAMMPS is built with the appropriate package</span></a>.</p>
<table border="1" class="docutils">
<colgroup>
<col width="23%" />
<col width="15%" />
<col width="15%" />
<col width="15%" />
<col width="20%" />
<col width="14%" />
<col width="22%" />
<col width="15%" />
<col width="13%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="fix_adapt_fep.html"><span class="doc">adapt/fep</span></a></td>
@ -788,57 +788,57 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.</p>
<td><a class="reference internal" href="fix_drude_transform.html"><span class="doc">drude/transform/reverse</span></a></td>
<td><a class="reference internal" href="fix_eos_cv.html"><span class="doc">eos/cv</span></a></td>
<td><a class="reference internal" href="fix_eos_table.html"><span class="doc">eos/table</span></a></td>
<td><a class="reference internal" href="fix_eos_table_rx.html"><span class="doc">eos/table/rx</span></a></td>
<td><a class="reference internal" href="fix_gle.html"><span class="doc">gle</span></a></td>
<td><a class="reference internal" href="fix_imd.html"><span class="doc">imd</span></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="fix_ipi.html"><span class="doc">ipi</span></a></td>
<tr class="row-odd"><td><a class="reference internal" href="fix_imd.html"><span class="doc">imd</span></a></td>
<td><a class="reference internal" href="fix_ipi.html"><span class="doc">ipi</span></a></td>
<td><a class="reference internal" href="fix_langevin_drude.html"><span class="doc">langevin/drude</span></a></td>
<td><a class="reference internal" href="fix_langevin_eff.html"><span class="doc">langevin/eff</span></a></td>
<td><a class="reference internal" href="fix_lb_fluid.html"><span class="doc">lb/fluid</span></a></td>
<td><a class="reference internal" href="fix_lb_momentum.html"><span class="doc">lb/momentum</span></a></td>
<td><a class="reference internal" href="fix_lb_pc.html"><span class="doc">lb/pc</span></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="fix_lb_rigid_pc_sphere.html"><span class="doc">lb/rigid/pc/sphere</span></a></td>
<tr class="row-even"><td><a class="reference internal" href="fix_lb_pc.html"><span class="doc">lb/pc</span></a></td>
<td><a class="reference internal" href="fix_lb_rigid_pc_sphere.html"><span class="doc">lb/rigid/pc/sphere</span></a></td>
<td><a class="reference internal" href="fix_lb_viscous.html"><span class="doc">lb/viscous</span></a></td>
<td><a class="reference internal" href="fix_meso.html"><span class="doc">meso</span></a></td>
<td><a class="reference internal" href="fix_manifoldforce.html"><span class="doc">manifoldforce</span></a></td>
<td><a class="reference internal" href="fix_meso_stationary.html"><span class="doc">meso/stationary</span></a></td>
<td><a class="reference internal" href="fix_nve_manifold_rattle.html"><span class="doc">nve/manifold/rattle</span></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="fix_nvt_manifold_rattle.html"><span class="doc">nvt/manifold/rattle</span></a></td>
<tr class="row-odd"><td><a class="reference internal" href="fix_nve_manifold_rattle.html"><span class="doc">nve/manifold/rattle</span></a></td>
<td><a class="reference internal" href="fix_nvt_manifold_rattle.html"><span class="doc">nvt/manifold/rattle</span></a></td>
<td><a class="reference internal" href="fix_nh_eff.html"><span class="doc">nph/eff</span></a></td>
<td><a class="reference internal" href="fix_nh_eff.html"><span class="doc">npt/eff</span></a></td>
<td><a class="reference internal" href="fix_nve_eff.html"><span class="doc">nve/eff</span></a></td>
<td><a class="reference internal" href="fix_nh_eff.html"><span class="doc">nvt/eff</span></a></td>
<td><a class="reference internal" href="fix_nvt_sllod_eff.html"><span class="doc">nvt/sllod/eff</span></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="fix_phonon.html"><span class="doc">phonon</span></a></td>
<tr class="row-even"><td><a class="reference internal" href="fix_nvt_sllod_eff.html"><span class="doc">nvt/sllod/eff</span></a></td>
<td><a class="reference internal" href="fix_phonon.html"><span class="doc">phonon</span></a></td>
<td><a class="reference internal" href="fix_pimd.html"><span class="doc">pimd</span></a></td>
<td><a class="reference internal" href="fix_qbmsst.html"><span class="doc">qbmsst</span></a></td>
<td><a class="reference internal" href="fix_qeq_reax.html"><span class="doc">qeq/reax</span></a></td>
<td><a class="reference internal" href="fix_qmmm.html"><span class="doc">qmmm</span></a></td>
<td><a class="reference internal" href="fix_qtb.html"><span class="doc">qtb</span></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="fix_reax_bonds.html"><span class="doc">reax/c/bonds</span></a></td>
<tr class="row-odd"><td><a class="reference internal" href="fix_qtb.html"><span class="doc">qtb</span></a></td>
<td><a class="reference internal" href="fix_reax_bonds.html"><span class="doc">reax/c/bonds</span></a></td>
<td><a class="reference internal" href="fix_reaxc_species.html"><span class="doc">reax/c/species</span></a></td>
<td><a class="reference internal" href="fix_rx.html"><span class="doc">rx</span></a></td>
<td><a class="reference internal" href="fix_saed_vtk.html"><span class="doc">saed/vtk</span></a></td>
<td><a class="reference internal" href="fix_shardlow.html"><span class="doc">shardlow</span></a></td>
<td><a class="reference internal" href="fix_smd.html"><span class="doc">smd</span></a></td>
<td><a class="reference internal" href="fix_smd_adjust_dt.html"><span class="doc">smd/adjust/dt</span></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="fix_smd_integrate_tlsph.html"><span class="doc">smd/integrate/tlsph</span></a></td>
<tr class="row-even"><td><a class="reference internal" href="fix_smd.html"><span class="doc">smd</span></a></td>
<td><a class="reference internal" href="fix_smd_adjust_dt.html"><span class="doc">smd/adjust/dt</span></a></td>
<td><a class="reference internal" href="fix_smd_integrate_tlsph.html"><span class="doc">smd/integrate/tlsph</span></a></td>
<td><a class="reference internal" href="fix_smd_integrate_ulsph.html"><span class="doc">smd/integrate/ulsph</span></a></td>
<td><a class="reference internal" href="fix_smd_move_triangulated_surface.html"><span class="doc">smd/move/triangulated/surface</span></a></td>
<td><a class="reference internal" href="fix_smd_setvel.html"><span class="doc">smd/setvel</span></a></td>
<td><a class="reference internal" href="fix_smd_tlsph_reference_configuration.html"><span class="doc">smd/tlsph/reference/configuration</span></a></td>
<td><a class="reference internal" href="fix_smd_wall_surface.html"><span class="doc">smd/wall/surface</span></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="fix_temp_rescale_eff.html"><span class="doc">temp/rescale/eff</span></a></td>
<tr class="row-odd"><td><a class="reference internal" href="fix_smd_tlsph_reference_configuration.html"><span class="doc">smd/tlsph/reference/configuration</span></a></td>
<td><a class="reference internal" href="fix_smd_wall_surface.html"><span class="doc">smd/wall/surface</span></a></td>
<td><a class="reference internal" href="fix_temp_rescale_eff.html"><span class="doc">temp/rescale/eff</span></a></td>
<td><a class="reference internal" href="fix_ti_rs.html"><span class="doc">ti/rs</span></a></td>
<td><a class="reference internal" href="fix_ti_spring.html"><span class="doc">ti/spring</span></a></td>
<td><a class="reference internal" href="fix_ttm.html"><span class="doc">ttm/mod</span></a></td>
<td>&nbsp;</td>
<td>&nbsp;</td>
</tr>
</tbody>
</table>
@ -1182,10 +1182,10 @@ KOKKOS, o = USER-OMP, t = OPT.</p>
if <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">LAMMPS is built with the appropriate package</span></a>.</p>
<table border="1" class="docutils">
<colgroup>
<col width="21%" />
<col width="24%" />
<col width="25%" />
<col width="31%" />
<col width="30%" />
<col width="24%" />
<col width="22%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="pair_awpmd.html"><span class="doc">awpmd/cut</span></a></td>
@ -1200,53 +1200,58 @@ if <a class="reference internal" href="Section_start.html#start-3"><span class="
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_edip.html"><span class="doc">edip (o)</span></a></td>
<td><a class="reference internal" href="pair_eff.html"><span class="doc">eff/cut</span></a></td>
<td><a class="reference internal" href="pair_exp6_rx.html"><span class="doc">exp6/rx</span></a></td>
<td><a class="reference internal" href="pair_gauss.html"><span class="doc">gauss/cut</span></a></td>
<td><a class="reference internal" href="pair_mdf.html"><span class="doc">lennard/mdf</span></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_list.html"><span class="doc">list</span></a></td>
<tr class="row-even"><td><a class="reference internal" href="pair_mdf.html"><span class="doc">lennard/mdf</span></a></td>
<td><a class="reference internal" href="pair_list.html"><span class="doc">list</span></a></td>
<td><a class="reference internal" href="pair_charmm.html"><span class="doc">lj/charmm/coul/long/soft (o)</span></a></td>
<td><a class="reference internal" href="pair_lj_soft.html"><span class="doc">lj/cut/coul/cut/soft (o)</span></a></td>
<td><a class="reference internal" href="pair_lj_soft.html"><span class="doc">lj/cut/coul/long/soft (o)</span></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_dipole.html"><span class="doc">lj/cut/dipole/sf (go)</span></a></td>
<tr class="row-odd"><td><a class="reference internal" href="pair_lj_soft.html"><span class="doc">lj/cut/coul/long/soft (o)</span></a></td>
<td><a class="reference internal" href="pair_dipole.html"><span class="doc">lj/cut/dipole/sf (go)</span></a></td>
<td><a class="reference internal" href="pair_lj_soft.html"><span class="doc">lj/cut/soft (o)</span></a></td>
<td><a class="reference internal" href="pair_thole.html"><span class="doc">lj/cut/thole/long (o)</span></a></td>
<td><a class="reference internal" href="pair_lj_soft.html"><span class="doc">lj/cut/tip4p/long/soft (o)</span></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_mdf.html"><span class="doc">lj/mdf</span></a></td>
<tr class="row-even"><td><a class="reference internal" href="pair_lj_soft.html"><span class="doc">lj/cut/tip4p/long/soft (o)</span></a></td>
<td><a class="reference internal" href="pair_mdf.html"><span class="doc">lj/mdf</span></a></td>
<td><a class="reference internal" href="pair_sdk.html"><span class="doc">lj/sdk (gko)</span></a></td>
<td><a class="reference internal" href="pair_sdk.html"><span class="doc">lj/sdk/coul/long (go)</span></a></td>
<td><a class="reference internal" href="pair_sdk.html"><span class="doc">lj/sdk/coul/msm (o)</span></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_lj_sf.html"><span class="doc">lj/sf (o)</span></a></td>
<tr class="row-odd"><td><a class="reference internal" href="pair_sdk.html"><span class="doc">lj/sdk/coul/msm (o)</span></a></td>
<td><a class="reference internal" href="pair_lj_sf.html"><span class="doc">lj/sf (o)</span></a></td>
<td><a class="reference internal" href="pair_meam_spline.html"><span class="doc">meam/spline</span></a></td>
<td><a class="reference internal" href="pair_meam_sw_spline.html"><span class="doc">meam/sw/spline</span></a></td>
<td><a class="reference internal" href="pair_mgpt.html"><span class="doc">mgpt</span></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_morse.html"><span class="doc">morse/smooth/linear</span></a></td>
<tr class="row-even"><td><a class="reference internal" href="pair_mgpt.html"><span class="doc">mgpt</span></a></td>
<td><a class="reference internal" href="pair_morse.html"><span class="doc">morse/smooth/linear</span></a></td>
<td><a class="reference internal" href="pair_morse.html"><span class="doc">morse/soft</span></a></td>
<td><a class="reference internal" href="pair_multi_lucy.html"><span class="doc">multi/lucy</span></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_multi_lucy_rx.html"><span class="doc">multi/lucy/rx</span></a></td>
<td><a class="reference internal" href="pair_quip.html"><span class="doc">quip</span></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_reax_c.html"><span class="doc">reax/c</span></a></td>
<td><a class="reference internal" href="pair_reax_c.html"><span class="doc">reax/c</span></a></td>
<td><a class="reference internal" href="pair_smd_hertz.html"><span class="doc">smd/hertz</span></a></td>
<td><a class="reference internal" href="pair_smd_tlsph.html"><span class="doc">smd/tlsph</span></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_smd_tlsph.html"><span class="doc">smd/tlsph</span></a></td>
<td><a class="reference internal" href="pair_smd_triangulated_surface.html"><span class="doc">smd/triangulated/surface</span></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_smd_ulsph.html"><span class="doc">smd/ulsph</span></a></td>
<td><a class="reference internal" href="pair_smd_ulsph.html"><span class="doc">smd/ulsph</span></a></td>
<td><a class="reference internal" href="pair_smtbq.html"><span class="doc">smtbq</span></a></td>
<td><a class="reference internal" href="pair_sph_heatconduction.html"><span class="doc">sph/heatconduction</span></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_sph_heatconduction.html"><span class="doc">sph/heatconduction</span></a></td>
<td><a class="reference internal" href="pair_sph_idealgas.html"><span class="doc">sph/idealgas</span></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_sph_lj.html"><span class="doc">sph/lj</span></a></td>
<td><a class="reference internal" href="pair_sph_lj.html"><span class="doc">sph/lj</span></a></td>
<td><a class="reference internal" href="pair_sph_rhosum.html"><span class="doc">sph/rhosum</span></a></td>
<td><a class="reference internal" href="pair_sph_taitwater.html"><span class="doc">sph/taitwater</span></a></td>
<td><a class="reference internal" href="pair_sph_taitwater_morris.html"><span class="doc">sph/taitwater/morris</span></a></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_srp.html"><span class="doc">srp</span></a></td>
<td><a class="reference internal" href="pair_tersoff.html"><span class="doc">tersoff/table (o)</span></a></td>
<tr class="row-even"><td><a class="reference internal" href="pair_sph_taitwater.html"><span class="doc">sph/taitwater</span></a></td>
<td><a class="reference internal" href="pair_sph_taitwater_morris.html"><span class="doc">sph/taitwater/morris</span></a></td>
<td><a class="reference internal" href="pair_srp.html"><span class="doc">srp</span></a></td>
<td><a class="reference internal" href="pair_table_rx.html"><span class="doc">table/rx</span></a></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_tersoff.html"><span class="doc">tersoff/table (o)</span></a></td>
<td><a class="reference internal" href="pair_thole.html"><span class="doc">thole</span></a></td>
<td><a class="reference internal" href="pair_lj_soft.html"><span class="doc">tip4p/long/soft (o)</span></a></td>
<td>&nbsp;</td>
</tr>
</tbody>
</table>

90
doc/html/_sources/Section_commands.txt
View File

@ -492,25 +492,25 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
These are additional fix styles in USER packages, which can be used if
:ref:`LAMMPS is built with the appropriate package <start_3>`.
+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+------------------------------------------------------+
| :doc:`adapt/fep <fix_adapt_fep>` | :doc:`addtorque <fix_addtorque>` | :doc:`atc <fix_atc>` | :doc:`ave/correlate/long <fix_ave_correlate_long>` | :doc:`colvars <fix_colvars>` | :doc:`drude <fix_drude>` |
+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+------------------------------------------------------+
| :doc:`drude/transform/direct <fix_drude_transform>` | :doc:`drude/transform/reverse <fix_drude_transform>` | :doc:`eos/cv <fix_eos_cv>` | :doc:`eos/table <fix_eos_table>` | :doc:`gle <fix_gle>` | :doc:`imd <fix_imd>` |
+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+------------------------------------------------------+
| :doc:`ipi <fix_ipi>` | :doc:`langevin/drude <fix_langevin_drude>` | :doc:`langevin/eff <fix_langevin_eff>` | :doc:`lb/fluid <fix_lb_fluid>` | :doc:`lb/momentum <fix_lb_momentum>` | :doc:`lb/pc <fix_lb_pc>` |
+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+------------------------------------------------------+
| :doc:`lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>` | :doc:`lb/viscous <fix_lb_viscous>` | :doc:`meso <fix_meso>` | :doc:`manifoldforce <fix_manifoldforce>` | :doc:`meso/stationary <fix_meso_stationary>` | :doc:`nve/manifold/rattle <fix_nve_manifold_rattle>` |
+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+------------------------------------------------------+
| :doc:`nvt/manifold/rattle <fix_nvt_manifold_rattle>` | :doc:`nph/eff <fix_nh_eff>` | :doc:`npt/eff <fix_nh_eff>` | :doc:`nve/eff <fix_nve_eff>` | :doc:`nvt/eff <fix_nh_eff>` | :doc:`nvt/sllod/eff <fix_nvt_sllod_eff>` |
+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+------------------------------------------------------+
| :doc:`phonon <fix_phonon>` | :doc:`pimd <fix_pimd>` | :doc:`qbmsst <fix_qbmsst>` | :doc:`qeq/reax <fix_qeq_reax>` | :doc:`qmmm <fix_qmmm>` | :doc:`qtb <fix_qtb>` |
+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+------------------------------------------------------+
| :doc:`reax/c/bonds <fix_reax_bonds>` | :doc:`reax/c/species <fix_reaxc_species>` | :doc:`saed/vtk <fix_saed_vtk>` | :doc:`shardlow <fix_shardlow>` | :doc:`smd <fix_smd>` | :doc:`smd/adjust/dt <fix_smd_adjust_dt>` |
+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+------------------------------------------------------+
| :doc:`smd/integrate/tlsph <fix_smd_integrate_tlsph>` | :doc:`smd/integrate/ulsph <fix_smd_integrate_ulsph>` | :doc:`smd/move/triangulated/surface <fix_smd_move_triangulated_surface>` | :doc:`smd/setvel <fix_smd_setvel>` | :doc:`smd/tlsph/reference/configuration <fix_smd_tlsph_reference_configuration>` | :doc:`smd/wall/surface <fix_smd_wall_surface>` |
+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+------------------------------------------------------+
| :doc:`temp/rescale/eff <fix_temp_rescale_eff>` | :doc:`ti/rs <fix_ti_rs>` | :doc:`ti/spring <fix_ti_spring>` | :doc:`ttm/mod <fix_ttm>` | | |
+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------------+----------------------------------------------------------------------------------+------------------------------------------------------+
+----------------------------------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------+
| :doc:`adapt/fep <fix_adapt_fep>` | :doc:`addtorque <fix_addtorque>` | :doc:`atc <fix_atc>` | :doc:`ave/correlate/long <fix_ave_correlate_long>` | :doc:`colvars <fix_colvars>` | :doc:`drude <fix_drude>` |
+----------------------------------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------+
| :doc:`drude/transform/direct <fix_drude_transform>` | :doc:`drude/transform/reverse <fix_drude_transform>` | :doc:`eos/cv <fix_eos_cv>` | :doc:`eos/table <fix_eos_table>` | :doc:`eos/table/rx <fix_eos_table_rx>` | :doc:`gle <fix_gle>` |
+----------------------------------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------+
| :doc:`imd <fix_imd>` | :doc:`ipi <fix_ipi>` | :doc:`langevin/drude <fix_langevin_drude>` | :doc:`langevin/eff <fix_langevin_eff>` | :doc:`lb/fluid <fix_lb_fluid>` | :doc:`lb/momentum <fix_lb_momentum>` |
+----------------------------------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------+
| :doc:`lb/pc <fix_lb_pc>` | :doc:`lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>` | :doc:`lb/viscous <fix_lb_viscous>` | :doc:`meso <fix_meso>` | :doc:`manifoldforce <fix_manifoldforce>` | :doc:`meso/stationary <fix_meso_stationary>` |
+----------------------------------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------+
| :doc:`nve/manifold/rattle <fix_nve_manifold_rattle>` | :doc:`nvt/manifold/rattle <fix_nvt_manifold_rattle>` | :doc:`nph/eff <fix_nh_eff>` | :doc:`npt/eff <fix_nh_eff>` | :doc:`nve/eff <fix_nve_eff>` | :doc:`nvt/eff <fix_nh_eff>` |
+----------------------------------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------+
| :doc:`nvt/sllod/eff <fix_nvt_sllod_eff>` | :doc:`phonon <fix_phonon>` | :doc:`pimd <fix_pimd>` | :doc:`qbmsst <fix_qbmsst>` | :doc:`qeq/reax <fix_qeq_reax>` | :doc:`qmmm <fix_qmmm>` |
+----------------------------------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------+
| :doc:`qtb <fix_qtb>` | :doc:`reax/c/bonds <fix_reax_bonds>` | :doc:`reax/c/species <fix_reaxc_species>` | :doc:`rx <fix_rx>` | :doc:`saed/vtk <fix_saed_vtk>` | :doc:`shardlow <fix_shardlow>` |
+----------------------------------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------+
| :doc:`smd <fix_smd>` | :doc:`smd/adjust/dt <fix_smd_adjust_dt>` | :doc:`smd/integrate/tlsph <fix_smd_integrate_tlsph>` | :doc:`smd/integrate/ulsph <fix_smd_integrate_ulsph>` | :doc:`smd/move/triangulated/surface <fix_smd_move_triangulated_surface>` | :doc:`smd/setvel <fix_smd_setvel>` |
+----------------------------------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------+
| :doc:`smd/tlsph/reference/configuration <fix_smd_tlsph_reference_configuration>` | :doc:`smd/wall/surface <fix_smd_wall_surface>` | :doc:`temp/rescale/eff <fix_temp_rescale_eff>` | :doc:`ti/rs <fix_ti_rs>` | :doc:`ti/spring <fix_ti_spring>` | :doc:`ttm/mod <fix_ttm>` |
+----------------------------------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+------------------------------------------------------+--------------------------------------------------------------------------+----------------------------------------------+
----------
@ -648,31 +648,33 @@ KOKKOS, o = USER-OMP, t = OPT.
These are additional pair styles in USER packages, which can be used
if :ref:`LAMMPS is built with the appropriate package <start_3>`.
+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`awpmd/cut <pair_awpmd>` | :doc:`buck/mdf <pair_mdf>` | :doc:`coul/cut/soft (o) <pair_lj_soft>` | :doc:`coul/diel (o) <pair_coul_diel>` |
+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`coul/long/soft (o) <pair_lj_soft>` | :doc:`dpd/fdt <pair_dpd_fdt>` | :doc:`dpd/fdt/energy <pair_dpd_fdt>` | :doc:`eam/cd (o) <pair_eam>` |
+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`edip (o) <pair_edip>` | :doc:`eff/cut <pair_eff>` | :doc:`gauss/cut <pair_gauss>` | :doc:`lennard/mdf <pair_mdf>` |
+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`list <pair_list>` | :doc:`lj/charmm/coul/long/soft (o) <pair_charmm>` | :doc:`lj/cut/coul/cut/soft (o) <pair_lj_soft>` | :doc:`lj/cut/coul/long/soft (o) <pair_lj_soft>` |
+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`lj/cut/dipole/sf (go) <pair_dipole>` | :doc:`lj/cut/soft (o) <pair_lj_soft>` | :doc:`lj/cut/thole/long (o) <pair_thole>` | :doc:`lj/cut/tip4p/long/soft (o) <pair_lj_soft>` |
+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`lj/mdf <pair_mdf>` | :doc:`lj/sdk (gko) <pair_sdk>` | :doc:`lj/sdk/coul/long (go) <pair_sdk>` | :doc:`lj/sdk/coul/msm (o) <pair_sdk>` |
+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`lj/sf (o) <pair_lj_sf>` | :doc:`meam/spline <pair_meam_spline>` | :doc:`meam/sw/spline <pair_meam_sw_spline>` | :doc:`mgpt <pair_mgpt>` |
+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`morse/smooth/linear <pair_morse>` | :doc:`morse/soft <pair_morse>` | :doc:`multi/lucy <pair_multi_lucy>` | :doc:`quip <pair_quip>` |
+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`reax/c <pair_reax_c>` | :doc:`smd/hertz <pair_smd_hertz>` | :doc:`smd/tlsph <pair_smd_tlsph>` | :doc:`smd/triangulated/surface <pair_smd_triangulated_surface>` |
+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`smd/ulsph <pair_smd_ulsph>` | :doc:`smtbq <pair_smtbq>` | :doc:`sph/heatconduction <pair_sph_heatconduction>` | :doc:`sph/idealgas <pair_sph_idealgas>` |
+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`sph/lj <pair_sph_lj>` | :doc:`sph/rhosum <pair_sph_rhosum>` | :doc:`sph/taitwater <pair_sph_taitwater>` | :doc:`sph/taitwater/morris <pair_sph_taitwater_morris>` |
+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
| :doc:`srp <pair_srp>` | :doc:`tersoff/table (o) <pair_tersoff>` | :doc:`thole <pair_thole>` | :doc:`tip4p/long/soft (o) <pair_lj_soft>` |
+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
+-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+------------------------------------------------+
| :doc:`awpmd/cut <pair_awpmd>` | :doc:`buck/mdf <pair_mdf>` | :doc:`coul/cut/soft (o) <pair_lj_soft>` | :doc:`coul/diel (o) <pair_coul_diel>` |
+-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+------------------------------------------------+
| :doc:`coul/long/soft (o) <pair_lj_soft>` | :doc:`dpd/fdt <pair_dpd_fdt>` | :doc:`dpd/fdt/energy <pair_dpd_fdt>` | :doc:`eam/cd (o) <pair_eam>` |
+-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+------------------------------------------------+
| :doc:`edip (o) <pair_edip>` | :doc:`eff/cut <pair_eff>` | :doc:`exp6/rx <pair_exp6_rx>` | :doc:`gauss/cut <pair_gauss>` |
+-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+------------------------------------------------+
| :doc:`lennard/mdf <pair_mdf>` | :doc:`list <pair_list>` | :doc:`lj/charmm/coul/long/soft (o) <pair_charmm>` | :doc:`lj/cut/coul/cut/soft (o) <pair_lj_soft>` |
+-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+------------------------------------------------+
| :doc:`lj/cut/coul/long/soft (o) <pair_lj_soft>` | :doc:`lj/cut/dipole/sf (go) <pair_dipole>` | :doc:`lj/cut/soft (o) <pair_lj_soft>` | :doc:`lj/cut/thole/long (o) <pair_thole>` |
+-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+------------------------------------------------+
| :doc:`lj/cut/tip4p/long/soft (o) <pair_lj_soft>` | :doc:`lj/mdf <pair_mdf>` | :doc:`lj/sdk (gko) <pair_sdk>` | :doc:`lj/sdk/coul/long (go) <pair_sdk>` |
+-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+------------------------------------------------+
| :doc:`lj/sdk/coul/msm (o) <pair_sdk>` | :doc:`lj/sf (o) <pair_lj_sf>` | :doc:`meam/spline <pair_meam_spline>` | :doc:`meam/sw/spline <pair_meam_sw_spline>` |
+-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+------------------------------------------------+
| :doc:`mgpt <pair_mgpt>` | :doc:`morse/smooth/linear <pair_morse>` | :doc:`morse/soft <pair_morse>` | :doc:`multi/lucy <pair_multi_lucy>` |
+-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+------------------------------------------------+
| :doc:`multi/lucy/rx <pair_multi_lucy_rx>` | :doc:`quip <pair_quip>` | :doc:`reax/c <pair_reax_c>` | :doc:`smd/hertz <pair_smd_hertz>` |
+-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+------------------------------------------------+
| :doc:`smd/tlsph <pair_smd_tlsph>` | :doc:`smd/triangulated/surface <pair_smd_triangulated_surface>` | :doc:`smd/ulsph <pair_smd_ulsph>` | :doc:`smtbq <pair_smtbq>` |
+-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+------------------------------------------------+
| :doc:`sph/heatconduction <pair_sph_heatconduction>` | :doc:`sph/idealgas <pair_sph_idealgas>` | :doc:`sph/lj <pair_sph_lj>` | :doc:`sph/rhosum <pair_sph_rhosum>` |
+-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+------------------------------------------------+
| :doc:`sph/taitwater <pair_sph_taitwater>` | :doc:`sph/taitwater/morris <pair_sph_taitwater_morris>` | :doc:`srp <pair_srp>` | :doc:`table/rx <pair_table_rx>` |
+-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+------------------------------------------------+
| :doc:`tersoff/table (o) <pair_tersoff>` | :doc:`thole <pair_thole>` | :doc:`tip4p/long/soft (o) <pair_lj_soft>` | |
+-----------------------------------------------------+-----------------------------------------------------------------+---------------------------------------------------+------------------------------------------------+
----------

10
doc/html/_sources/atom_style.txt
View File

@ -154,9 +154,13 @@ position, which is represented by the eradius = electron size.
For the *peri* style, the particles are spherical and each stores a
per-particle mass and volume.
The *dpd* style is for dissipative particle dynamics (DPD) particles
which store the particle internal temperature (dpdTheta), internal
conductive energy (uCond) and internal mechanical energy (uMech).
The *dpd* style is for dissipative particle dynamics (DPD) particles.
Note that it is part of the USER-DPD package, and is not for use with
the :doc:`pair_style dpd or dpd/stat <pair_dpd>` commands, which can
simply use atom_style atomic. Atom_style dpd extends DPD particle
properties with internal temperature (dpdTheta), internal conductive
energy (uCond), internal mechanical energy (uMech), and internal
chemical energy (uChem).
The *meso* style is for smoothed particle hydrodynamics (SPH)
particles which store a density (rho), energy (e), and heat capacity

4
doc/html/_sources/compute_dpd.txt
View File

@ -25,7 +25,7 @@ Description
Define a computation that accumulates the total internal conductive
energy (U_cond), the total internal mechanical energy (U_mech), the
total internal energy (U) and the *harmonic* average of the internal
total chemical energy (U_chem) and the *harmonic* average of the internal
temperature (dpdTheta) for the entire system of particles. See the
:doc:`compute dpd/atom <compute_dpd_atom>` command if you want
per-particle internal energies and internal temperatures.
@ -45,7 +45,7 @@ where N is the number of particles in the system
**Output info:**
This compute calculates a global vector of length 5 (U_cond, U_mech,
U, dpdTheta, N_particles), which can be accessed by indices 1-5. See
U_chem, dpdTheta, N_particles), which can be accessed by indices 1-5. See
:ref:`this section <howto_15>` for an overview of LAMMPS
output options.

14
doc/html/_sources/compute_dpd_atom.txt
View File

@ -22,23 +22,25 @@ Description
"""""""""""
Define a computation that accesses the per-particle internal
conductive energy (u_cond), internal mechanical energy (u_mech) and
conductive energy (u_cond), internal mechanical energy (u_mech),
internal chemical energy (u_chem) and
internal temperatures (dpdTheta) for each particle in a group. See
the :doc:`compute dpd <compute_dpd>` command if you want the total
internal conductive energy, the total internal mechanical energy, and
internal conductive energy, the total internal mechanical energy, the
total chemical energy and
average internal temperature of the entire system or group of dpd
particles.
**Output info:**
This compute calculates a per-particle array with 3 columns (u_cond,
u_mech, dpdTheta), which can be accessed by indices 1-3 by any command
This compute calculates a per-particle array with 4 columns (u_cond,
u_mech, u_chem, dpdTheta), which can be accessed by indices 1-4 by any command
that uses per-particle values from a compute as input. See
:ref:`Section_howto15 <howto_15>` for an overview of
LAMMPS output options.
The per-particle array values will be in energy (u_cond, u_mech) and
temperature (dpdTheta) :doc:`units <units>`.
The per-particle array values will be in energy (u_cond, u_mech, u_chem)
and temperature (dpdTheta) :doc:`units <units>`.
Restrictions
""""""""""""

10
doc/html/atom_style.html
View File

@ -309,9 +309,13 @@ Gaussians with a specified position and bandwidth or uncertainty in
position, which is represented by the eradius = electron size.</p>
<p>For the <em>peri</em> style, the particles are spherical and each stores a
per-particle mass and volume.</p>
<p>The <em>dpd</em> style is for dissipative particle dynamics (DPD) particles
which store the particle internal temperature (dpdTheta), internal
conductive energy (uCond) and internal mechanical energy (uMech).</p>
<p>The <em>dpd</em> style is for dissipative particle dynamics (DPD) particles.
Note that it is part of the USER-DPD package, and is not for use with
the <a class="reference internal" href="pair_dpd.html"><span class="doc">pair_style dpd or dpd/stat</span></a> commands, which can
simply use atom_style atomic. Atom_style dpd extends DPD particle
properties with internal temperature (dpdTheta), internal conductive
energy (uCond), internal mechanical energy (uMech), and internal
chemical energy (uChem).</p>
<p>The <em>meso</em> style is for smoothed particle hydrodynamics (SPH)
particles which store a density (rho), energy (e), and heat capacity
(cv).</p>

4
doc/html/compute_dpd.html
View File

@ -146,7 +146,7 @@
<h2>Description</h2>
<p>Define a computation that accumulates the total internal conductive
energy (U_cond), the total internal mechanical energy (U_mech), the
total internal energy (U) and the <em>harmonic</em> average of the internal
total chemical energy (U_chem) and the <em>harmonic</em> average of the internal
temperature (dpdTheta) for the entire system of particles. See the
<a class="reference internal" href="compute_dpd_atom.html"><span class="doc">compute dpd/atom</span></a> command if you want
per-particle internal energies and internal temperatures.</p>
@ -157,7 +157,7 @@ relations:</p>
<hr class="docutils" />
<p><strong>Output info:</strong></p>
<p>This compute calculates a global vector of length 5 (U_cond, U_mech,
U, dpdTheta, N_particles), which can be accessed by indices 1-5. See
U_chem, dpdTheta, N_particles), which can be accessed by indices 1-5. See
<a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">this section</span></a> for an overview of LAMMPS
output options.</p>
<p>The vector values will be in energy and temperature <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>

14
doc/html/compute_dpd_atom.html
View File

@ -143,20 +143,22 @@
<div class="section" id="description">
<h2>Description</h2>
<p>Define a computation that accesses the per-particle internal
conductive energy (u_cond), internal mechanical energy (u_mech) and
conductive energy (u_cond), internal mechanical energy (u_mech),
internal chemical energy (u_chem) and
internal temperatures (dpdTheta) for each particle in a group. See
the <a class="reference internal" href="compute_dpd.html"><span class="doc">compute dpd</span></a> command if you want the total
internal conductive energy, the total internal mechanical energy, and
internal conductive energy, the total internal mechanical energy, the
total chemical energy and
average internal temperature of the entire system or group of dpd
particles.</p>
<p><strong>Output info:</strong></p>
<p>This compute calculates a per-particle array with 3 columns (u_cond,
u_mech, dpdTheta), which can be accessed by indices 1-3 by any command
<p>This compute calculates a per-particle array with 4 columns (u_cond,
u_mech, u_chem, dpdTheta), which can be accessed by indices 1-4 by any command
that uses per-particle values from a compute as input. See
<a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">Section_howto15</span></a> for an overview of
LAMMPS output options.</p>
<p>The per-particle array values will be in energy (u_cond, u_mech) and
temperature (dpdTheta) <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
<p>The per-particle array values will be in energy (u_cond, u_mech, u_chem)
and temperature (dpdTheta) <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions</h2>

311
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View File

@ -0,0 +1,311 @@
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<div class="section" id="fix-eos-table-rx-command">
<span id="index-0"></span><h1>fix eos/table/rx command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">eos</span><span class="o">/</span><span class="n">table</span><span class="o">/</span><span class="n">rx</span> <span class="n">style</span> <span class="n">file1</span> <span class="n">N</span> <span class="n">keyword</span> <span class="n">file2</span>
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
<li>eos/table/rx = style name of this fix command</li>
<li>style = <em>linear</em> = method of interpolation</li>
<li>file1 = filename containing the tabulated equation of state</li>
<li>N = use N values in <em>linear</em> tables</li>
<li>keyword = name of table keyword correponding to table file</li>
<li>file2 = filename containing the heats of formation of each species</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">eos</span><span class="o">/</span><span class="n">table</span><span class="o">/</span><span class="n">rx</span> <span class="n">linear</span> <span class="n">eos</span><span class="o">.</span><span class="n">table</span> <span class="mi">10000</span> <span class="n">KEYWORD</span> <span class="n">thermo</span><span class="o">.</span><span class="n">table</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>Fix <em>eos/table/rx</em> applies a tabulated mesoparticle equation
of state to relate the concentration-dependent particle internal
energy (u_i) to the particle internal temperature (dpdTheta_i).</p>
<p>The concentration-dependent particle internal energy (u_i) is
computed according to the following relation:</p>
<img alt="Eqs/fix_eos_table_rx.jpg" class="align-center" src="Eqs/fix_eos_table_rx.jpg" />
<p>where <em>m</em> is the number of species, <em>c_i,j</em> is the concentration of
species <em>j</em> in particle <em>i</em>, <em>u_j</em> is the internal energy of species j,
<em>DeltaH_f,j</em> is the heat of formation of species <em>j</em>, N is the number of
molecules represented by the coarse-grained particle, kb is the
Boltzmann constant, and T is the temperature of the system.</p>
<p>Fix <em>eos/table/rx</em> creates interpolation tables of length <em>N</em> from <em>m</em>
internal energy values of each species <em>u_j</em> listed in a file as a
function of internal temperature. During a simulation, these tables
are used to interpolate internal energy or temperature values as needed.
The interpolation is done with the <em>linear</em> style. For the <em>linear</em> style,
the internal temperature is used to find 2 surrounding table values from
which an internal energy is computed by linear interpolation. A secant
solver is used to determine the internal temperature from the internal energy.</p>
<p>The first filename specifies a file containing tabulated internal
temperature and <em>m</em> internal energy values for each species <em>u_j</em>.
The keyword specifies a section of the file. The format of this
file is described below.</p>
<p>The second filename specifies a file containing heat of formation
<em>DeltaH_f,j</em> for each species.</p>
<hr class="docutils" />
<p>The format of a tabulated file is as follows (without the
parenthesized comments):</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># EOS TABLE (one or more comment or blank lines)</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">KEYWORD</span> <span class="p">(</span><span class="n">keyword</span> <span class="ow">is</span> <span class="n">first</span> <span class="n">text</span> <span class="n">on</span> <span class="n">line</span><span class="p">)</span>
<span class="n">N</span> <span class="mi">500</span> <span class="n">h2</span> <span class="n">no2</span> <span class="n">n2</span> <span class="o">...</span> <span class="n">no</span> <span class="p">(</span><span class="n">N</span> <span class="n">parameter</span> <span class="n">species1</span> <span class="n">species2</span> <span class="o">...</span> <span class="n">speciesN</span><span class="p">)</span>
<span class="p">(</span><span class="n">blank</span><span class="p">)</span>
<span class="mi">1</span> <span class="mf">1.00</span> <span class="mf">0.000</span> <span class="o">...</span> <span class="mf">0.0000</span> <span class="p">(</span><span class="n">index</span><span class="p">,</span> <span class="n">internal</span> <span class="n">temperature</span><span class="p">,</span> <span class="n">internal</span> <span class="n">energy</span> <span class="n">of</span> <span class="n">species</span> <span class="mi">1</span><span class="p">,</span> <span class="o">...</span><span class="p">,</span> <span class="n">internal</span> <span class="n">energy</span> <span class="n">of</span> <span class="n">species</span> <span class="n">m</span><span class="p">)</span>
<span class="mi">2</span> <span class="mf">1.02</span> <span class="mf">0.001</span> <span class="o">...</span> <span class="mf">0.0002</span>
<span class="o">...</span>
<span class="mi">500</span> <span class="mf">10.0</span> <span class="mf">0.500</span> <span class="o">...</span> <span class="mf">1.0000</span>
</pre></div>
</div>
<p>A section begins with a non-blank line whose 1st character is not a
&#8220;#&#8221;; blank lines or lines starting with &#8220;#&#8221; can be used as comments
between sections. The first line begins with a keyword which
identifies the section. The line can contain additional text, but the
initial text must match the argument specified in the fix command.</p>
<p>The next line lists the number of table entries and the species names
that correspond with all the species listed in the reaction equations
through the <em>fix rx</em> command.
The parameter &#8220;N&#8221; is required and its value is the number of table
entries that follow. Let Nfile = &#8220;N&#8221; in the tabulated file.
What LAMMPS does is a preliminary interpolation by creating splines
using the Nfile tabulated values as nodal points.</p>
<p>Following a blank line, the next N lines list the tabulated values.
On each line, the 1st value is the index from 1 to N, the 2nd value is
the internal temperature (in temperature units), the 3rd value until
the <em>m+3</em> value are the internal energies of the m species (in energy units).</p>
<p>Note that all internal temperature and internal energy values must
increase from one line to the next.</p>
<p>Note that one file can contain many sections, each with a tabulated
potential. LAMMPS reads the file section by section until it finds
one that matches the specified keyword.</p>
<hr class="docutils" />
<p>The format of a heat of formation file is as follows (without the
parenthesized comments):</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># HEAT OF FORMATION TABLE (one or more comment or blank lines)</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span> <span class="p">(</span><span class="n">blank</span><span class="p">)</span>
<span class="n">h2</span> <span class="mf">0.00</span> <span class="p">(</span><span class="n">species</span> <span class="n">name</span><span class="p">,</span> <span class="n">heat</span> <span class="n">of</span> <span class="n">formation</span><span class="p">)</span>
<span class="n">no2</span> <span class="mf">0.34</span>
<span class="n">n2</span> <span class="mf">0.00</span>
<span class="o">...</span>
<span class="n">no</span> <span class="mf">0.93</span>
</pre></div>
</div>
<p>Note that the species can be listed in any order. The tag that is
used as the species name must correspond with the tags used to define
the reactions with the <a class="reference internal" href="fix_rx.html"><span class="doc">fix rx</span></a> command.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>The fix <em>eos/table/rx</em> is only available if LAMMPS is built with the
USER-DPD package.</p>
<p>The equation of state must be a monotonically increasing function.</p>
<p>An exit error will occur if the internal temperature or internal
energies are not within the table cutoffs.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="fix_rx.html"><span class="doc">fix rx</span></a>,
<span class="xref doc">pair dpd/fdt</span></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
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24
doc/html/genindex.html
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@ -1070,6 +1070,10 @@
</dt>
<dt><a href="fix_eos_table_rx.html#index-0">fix eos/table/rx</a>
</dt>
<dt><a href="fix_evaporate.html#index-0">fix evaporate</a>
</dt>
@ -1364,6 +1368,10 @@
</dt>
<dt><a href="fix_rx.html#index-0">fix rx</a>
</dt>
<dt><a href="fix_saed_vtk.html#index-0">fix saed/vtk</a>
</dt>
@ -1816,6 +1824,10 @@
</dt>
<dt><a href="pair_exp6_rx.html#index-0">pair_style exp6/rx</a>
</dt>
<dt><a href="pair_gauss.html#index-0">pair_style gauss</a>
</dt>
@ -1907,12 +1919,12 @@
<dt><a href="pair_lj_smooth_linear.html#index-0">pair_style lj/smooth/linear</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="pair_lj96.html#index-0">pair_style lj96/cut</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
<dt><a href="pair_lubricate.html#index-0">pair_style lubricate</a>
</dt>
@ -1942,6 +1954,10 @@
</dt>
<dt><a href="pair_multi_lucy_rx.html#index-0">pair_style multi/lucy/rx</a>
</dt>
<dt><a href="pair_nb3b_harmonic.html#index-0">pair_style nb3b/harmonic</a>
</dt>
@ -2042,6 +2058,10 @@
</dt>
<dt><a href="pair_table_rx.html#index-0">pair_style table/rx</a>
</dt>
<dt><a href="pair_tersoff.html#index-0">pair_style tersoff</a>
</dt>

286
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@ -0,0 +1,286 @@
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<div class="section" id="pair-style-exp6-rx-command">
<span id="index-0"></span><h1>pair_style exp6/rx command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">exp6</span><span class="o">/</span><span class="n">rx</span> <span class="n">cutoff</span>
</pre></div>
</div>
<ul class="simple">
<li>cutoff = global cutoff for DPD interactions (distance units)</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">exp6</span><span class="o">/</span><span class="n">rx</span> <span class="mf">10.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">exp6</span><span class="o">.</span><span class="n">params</span> <span class="n">h2o</span> <span class="n">h2o</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">10.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">exp6</span><span class="o">.</span><span class="n">params</span> <span class="n">h2o</span> <span class="mi">1</span><span class="n">fluid</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">10.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">exp6</span><span class="o">.</span><span class="n">params</span> <span class="mi">1</span><span class="n">fluid</span> <span class="mi">1</span><span class="n">fluid</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">10.0</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>Style <em>exp6/rx</em> is used in reaction DPD simulations, where the coarse-grained (CG)
particles are composed of <em>m</em> species whose reaction rate kinetics are determined
from a set of <em>n</em> reaction rate equations through the <a class="reference internal" href="fix_rx.html"><span class="doc">fix rx</span></a> command.
The species of one CG particle can interact with a species in a neighboring CG
particle through a site-site interaction potential model. The <em>exp6/rx</em> style
computes an exponential-6 potential given by</p>
<img alt="Eqs/pair_exp6_rx.jpg" class="align-center" src="Eqs/pair_exp6_rx.jpg" />
<p>where the <em>epsilon</em> parameter determines the depth of the potential
minimum located at <em>Rm</em>, and <em>alpha</em> determines the softness of the repulsion.</p>
<p>The coefficients must be defined for each species in a given particle type
via the <a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> command as in the examples above, where
the first argument is the filename that includes the exponential-6 parameters
for each species. The file includes the species tag followed by the <em>alpha</em>,
<em>epsilon</em> and <em>Rm</em> parameters. The format of the file is described below.</p>
<p>The second and third arguments specify the site-site interaction
potential between two species contained within two different particles.
The species tags must either correspond to the species defined in the reaction
kinetics files specified with the <a class="reference internal" href="fix_rx.html"><span class="doc">fix rx</span></a> command
or they must correspond to the tag &#8220;1fluid&#8221;, signifying interaction
with a product species mixture determined through a one-fluid approximation.
The interaction potential is weighted by the geometric average of the
concentrations of the two species. The coarse-grained potential is
stored before and after the reaction kinetics solver is applied, where the
difference is defined to be the internal chemical energy (uChem).</p>
<p>The fourth and fifth arguments specify the <em>Rm</em> and <em>epsilon</em> scaling exponents.</p>
<p>The final argument specifies the interaction cutoff.</p>
<hr class="docutils" />
<p>The format of a tabulated file is as follows (without the parenthesized comments):</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># exponential-6 parameters for various species (one or more comment or blank lines)</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">h2o</span> <span class="n">exp6</span> <span class="mf">11.00</span> <span class="mf">0.02</span> <span class="mf">3.50</span> <span class="p">(</span><span class="n">species</span><span class="p">,</span> <span class="n">exp6</span><span class="p">,</span> <span class="n">alpha</span><span class="p">,</span> <span class="n">Rm</span><span class="p">,</span> <span class="n">epsilon</span><span class="p">)</span>
<span class="n">no2</span> <span class="n">exp6</span> <span class="mf">13.60</span> <span class="mf">0.01</span> <span class="mf">3.70</span>
<span class="o">...</span>
<span class="n">co2</span> <span class="n">exp6</span> <span class="mf">13.00</span> <span class="mf">0.03</span> <span class="mf">3.20</span>
</pre></div>
</div>
<p>A section begins with a non-blank line whose 1st character is not a
&#8220;#&#8221;; blank lines or lines starting with &#8220;#&#8221; can be used as comments
between sections.</p>
<p>Following a blank line, the next N lines list the species and their
corresponding parameters. The first argument is the species tag,
the second argument is the exp6 tag, the 3rd argument is the <em>alpha</em>
parameter (energy units), the 4th argument is the <em>epsilon</em> parameter
(energy-distance^6 units), and the 5th argument is the <em>Rm</em>
parameter (distance units). If a species tag of &#8220;1fluid&#8221; is listed as a
pair coefficient, a one-fluid approximation is specified where a
concentration-dependent combination of the parameters is computed
through the following equations:</p>
<img alt="Eqs/pair_exp6_rx_oneFluid.jpg" class="align-center" src="Eqs/pair_exp6_rx_oneFluid.jpg" />
<p>where</p>
<img alt="Eqs/pair_exp6_rx_oneFluid2.jpg" class="align-center" src="Eqs/pair_exp6_rx_oneFluid2.jpg" />
<p>and xa and xb are the mole fractions of a and b, respectively, which
comprise the gas mixture.</p>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>This pair style does not support mixing. Thus, coefficients for all
I,J pairs must be specified explicitly.</p>
<p>This style does not support the <a class="reference internal" href="pair_modify.html"><span class="doc">pair_modify</span></a> shift option
for the energy of the exp() and 1/r^6 portion of the pair interaction.</p>
<p>This style does not support the pair_modify tail option for adding long-range
tail corrections to energy and pressure for the A,C terms in the
pair interaction.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>None</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a></p>
<p><strong>Default:</strong> none</p>
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View File

@ -146,7 +146,7 @@
<div class="section" id="description">
<h2>Description</h2>
<p>Style <em>multi/lucy</em> computes a density-dependent force following from the many-body
form described in <a class="reference internal" href="#moore"><span class="std std-ref">(Moore)</span></a> and <a class="reference internal" href="#warren"><span class="std std-ref">(Warren)</span></a> as</p>
form described in <a class="reference internal" href="pair_multi_lucy_rx.html#moore"><span class="std std-ref">(Moore)</span></a> and <a class="reference internal" href="pair_multi_lucy_rx.html#warren"><span class="std std-ref">(Warren)</span></a> as</p>
<img alt="_images/pair_multi_lucy.jpg" class="align-center" src="_images/pair_multi_lucy.jpg" />
<p>which consists of a density-dependent function, A(rho), and a radial-dependent weight
function, omegaDD(rij). The radial-dependent weight function, omegaDD(rij), is taken
@ -154,7 +154,7 @@ as the Lucy function:</p>
<img alt="_images/pair_multi_lucy2.jpg" class="align-center" src="_images/pair_multi_lucy2.jpg" />
<p>The density-dependent energy for a given particle is given by:</p>
<img alt="_images/pair_multi_lucy_energy.jpg" class="align-center" src="_images/pair_multi_lucy_energy.jpg" />
<p>See the supporting information of <a class="reference internal" href="#brennan"><span class="std std-ref">(Brennan)</span></a> or the publication by <a class="reference internal" href="#moore"><span class="std std-ref">(Moore)</span></a>
<p>See the supporting information of <a class="reference internal" href="pair_multi_lucy_rx.html#brennan"><span class="std std-ref">(Brennan)</span></a> or the publication by <a class="reference internal" href="pair_multi_lucy_rx.html#moore"><span class="std std-ref">(Moore)</span></a>
for more details on the functional form.</p>
<p>An interpolation table is used to evaluate the density-dependent energy (Integral(A(rho)drho) and force (A(rho)).
Note that the pre-factor to the energy is computed after the interpolation, thus the Integral(A(rho)drho will

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<div class="section" id="pair-style-multi-lucy-rx-command">
<span id="index-0"></span><h1>pair_style multi/lucy/rx command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">multi</span><span class="o">/</span><span class="n">lucy</span><span class="o">/</span><span class="n">rx</span> <span class="n">style</span> <span class="n">N</span> <span class="n">keyword</span> <span class="o">...</span>
</pre></div>
</div>
<ul class="simple">
<li>style = <em>lookup</em> or <em>linear</em> = method of interpolation</li>
<li>N = use N values in <em>lookup</em>, <em>linear</em> tables</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">multi</span><span class="o">/</span><span class="n">lucy</span><span class="o">/</span><span class="n">rx</span> <span class="n">linear</span> <span class="mi">1000</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">multibody</span><span class="o">.</span><span class="n">table</span> <span class="n">ENTRY1</span> <span class="n">h2o</span> <span class="n">h2o</span> <span class="mf">7.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">multibody</span><span class="o">.</span><span class="n">table</span> <span class="n">ENTRY1</span> <span class="n">h2o</span> <span class="mi">1</span><span class="n">fluid</span> <span class="mf">7.0</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>Style <em>multi/lucy/rx</em> is used in reaction DPD simulations, where the coarse-grained
(CG) particles are composed of <em>m</em> species whose reaction rate kinetics are determined
from a set of <em>n</em> reaction rate equations through the <a class="reference internal" href="fix_rx.html"><span class="doc">fix rx</span></a> command.
The species of one CG particle can interact with a species in a neighboring CG particle
through a site-site interaction potential model. Style <em>multi/lucy/rx</em> computes the
site-site density-dependent force following from the many-body form described in
<a class="reference internal" href="#moore"><span class="std std-ref">(Moore)</span></a> and <a class="reference internal" href="#warren"><span class="std std-ref">(Warren)</span></a> as</p>
<img alt="_images/pair_multi_lucy.jpg" class="align-center" src="_images/pair_multi_lucy.jpg" />
<p>which consists of a density-dependent function, A(rho), and a radial-dependent weight
function, omegaDD(rij). The radial-dependent weight function, omegaDD(rij), is taken
as the Lucy function:</p>
<img alt="_images/pair_multi_lucy2.jpg" class="align-center" src="_images/pair_multi_lucy2.jpg" />
<p>The density-dependent energy for a given particle is given by:</p>
<img alt="_images/pair_multi_lucy_energy.jpg" class="align-center" src="_images/pair_multi_lucy_energy.jpg" />
<p>See the supporting information of <a class="reference internal" href="#brennan"><span class="std std-ref">(Brennan)</span></a> or the publication by <a class="reference internal" href="#moore"><span class="std std-ref">(Moore)</span></a>
for more details on the functional form.</p>
<p>An interpolation table is used to evaluate the density-dependent energy (Integral(A(rho)drho) and force (A(rho)).
Note that the pre-factor to the energy is computed after the interpolation, thus the Integral(A(rho)drho will
have units of energy / length^4.</p>
<p>The interpolation table is created as a pre-computation by fitting cubic splines to
the file values and interpolating the density-dependent energy and force at each of <em>N</em> densities.
During a simulation, the tables are used to interpolate the density-dependent energy and force as
needed for each pair of particles separated by a distance <em>R</em>. The interpolation is done in
one of 2 styles: <em>lookup</em> and <em>linear</em>.</p>
<p>For the <em>lookup</em> style, the density is used to find the nearest table entry, which is the
density-dependent energy and force.</p>
<p>For the <em>linear</em> style, the density is used to find the 2 surrounding table values from
which the density-dependent energy and force are computed by linear interpolation.</p>
<p>The following coefficients must be defined for each pair of atoms
types via the <a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> command as in the examples
above.</p>
<ul class="simple">
<li>filename</li>
<li>keyword</li>
<li>species1</li>
<li>species2</li>
<li>cutoff (distance units)</li>
</ul>
<p>The filename specifies a file containing the tabulated density-dependent
energy and force. The keyword specifies a section of the file.
The cutoff is an optional coefficient. If not specified, the outer cutoff in the
table itself (see below) will be used to build an interpolation table
that extend to the largest tabulated distance. If specified, only
file values up to the cutoff are used to create the interpolation
table. The format of this file is described below.</p>
<p>The species tags define the site-site interaction potential between two
species contained within two different particles.
The species tags must either correspond to the species defined in the reaction
kinetics files specified with the <a class="reference internal" href="fix_rx.html"><span class="doc">fix rx</span></a> command
or they must correspond to the tag &#8220;1fluid&#8221;, signifying interaction
with a product species mixture determined through a one-fluid approximation.
The interaction potential is weighted by the geometric average of the
concentrations of the two species. The coarse-grained potential
is stored before and after the reaction kinetics solver is applied, where
the difference is defined to be the internal chemical energy (uChem).</p>
<hr class="docutils" />
<p>The format of a tabulated file is a series of one or more sections,
defined as follows (without the parenthesized comments):</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># Density-dependent function (one or more comment or blank lines)</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">DD</span><span class="o">-</span><span class="n">FUNCTION</span> <span class="p">(</span><span class="n">keyword</span> <span class="ow">is</span> <span class="n">first</span> <span class="n">text</span> <span class="n">on</span> <span class="n">line</span><span class="p">)</span>
<span class="n">N</span> <span class="mi">500</span> <span class="n">R</span> <span class="mf">1.0</span> <span class="mf">10.0</span> <span class="p">(</span><span class="n">N</span><span class="p">,</span> <span class="n">R</span><span class="p">,</span> <span class="n">RSQ</span> <span class="n">parameters</span><span class="p">)</span>
<span class="p">(</span><span class="n">blank</span><span class="p">)</span>
<span class="mi">1</span> <span class="mf">1.0</span> <span class="mf">25.5</span> <span class="mf">102.34</span> <span class="p">(</span><span class="n">index</span><span class="p">,</span> <span class="n">density</span><span class="p">,</span> <span class="n">energy</span><span class="o">/</span><span class="n">r</span><span class="o">^</span><span class="mi">4</span><span class="p">,</span> <span class="n">force</span><span class="p">)</span>
<span class="mi">2</span> <span class="mf">1.02</span> <span class="mf">23.4</span> <span class="mf">98.5</span>
<span class="o">...</span>
<span class="mi">500</span> <span class="mf">10.0</span> <span class="mf">0.001</span> <span class="mf">0.003</span>
</pre></div>
</div>
<p>A section begins with a non-blank line whose 1st character is not a
&#8220;#&#8221;; blank lines or lines starting with &#8220;#&#8221; can be used as comments
between sections. The first line begins with a keyword which
identifies the section. The line can contain additional text, but the
initial text must match the argument specified in the pair_coeff
command. The next line lists (in any order) one or more parameters
for the table. Each parameter is a keyword followed by one or more
numeric values.</p>
<p>The parameter &#8220;N&#8221; is required and its value is the number of table
entries that follow. Note that this may be different than the <em>N</em>
specified in the <a class="reference internal" href="#"><span class="doc">pair_style multi/lucy/rx</span></a> command. Let
Ntable = <em>N</em> in the pair_style command, and Nfile = &#8220;N&#8221; in the
tabulated file. What LAMMPS does is a preliminary interpolation by
creating splines using the Nfile tabulated values as nodal points. It
uses these to interpolate the density-dependent energy and force at Ntable different
points. The resulting tables of length Ntable are then used as
described above, when computing the density-dependent energy and force.
This means that if you want the interpolation tables of
length Ntable to match exactly what is in the tabulated file (with
effectively no preliminary interpolation), you should set Ntable =
Nfile, and use the &#8220;RSQ&#8221; parameter. This is because the
internal table abscissa is always RSQ (separation distance squared),
for efficient lookup.</p>
<p>All other parameters are optional. If &#8220;R&#8221; or &#8220;RSQ&#8221; does
not appear, then the distances in each line of the table are used
as-is to perform spline interpolation. In this case, the table values
can be spaced in <em>density</em> uniformly or however you wish to position table
values in regions of large gradients.</p>
<p>If used, the parameters &#8220;R&#8221; or &#8220;RSQ&#8221; are followed by 2 values <em>rlo</em>
and <em>rhi</em>. If specified, the density associated with each density-dependent
energy and force value is computed from these 2 values (at high accuracy), rather
than using the (low-accuracy) value listed in each line of the table.
The density values in the table file are ignored in this case.
For &#8220;R&#8221;, distances uniformly spaced between <em>rlo</em> and <em>rhi</em> are
computed; for &#8220;RSQ&#8221;, squared distances uniformly spaced between
<em>rlo*rlo</em> and <em>rhi*rhi</em> are computed.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">If you use &#8220;R&#8221; or &#8220;RSQ&#8221;, the tabulated distance values in the
file are effectively ignored, and replaced by new values as described
in the previous paragraph. If the density value in the table is not
very close to the new value (i.e. round-off difference), then you will
be assigning density-dependent energy and force values to a different density,
which is probably not what you want. LAMMPS will warn if this is occurring.</p>
</div>
<p>Following a blank line, the next N lines list the tabulated values.
On each line, the 1st value is the index from 1 to N, the 2nd value is
r (in density units), the 3rd value is the density-dependent function value
(in energy units / length^4), and the 4th is the force (in force units). The
density values must increase from one line to the next.</p>
<p>Note that one file can contain many sections, each with a tabulated
potential. LAMMPS reads the file section by section until it finds
one that matches the specified keyword.</p>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>This pair style does not support mixing. Thus, coefficients for all
I,J pairs must be specified explicitly.</p>
<p>The <a class="reference internal" href="pair_modify.html"><span class="doc">pair_modify</span></a> shift, table, and tail options are
not relevant for this pair style.</p>
<p>This pair style writes the settings for the &#8220;pair_style multi/lucy/rx&#8221; command
to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>, so a pair_style command does
not need to specified in an input script that reads a restart file.
However, the coefficient information is not stored in the restart
file, since it is tabulated in the potential files. Thus, pair_coeff
commands do need to be specified in the restart input script.</p>
<p>This pair style can only be used via the <em>pair</em> keyword of the
<a class="reference internal" href="run_style.html"><span class="doc">run_style respa</span></a> command. It does not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<blockquote>
<div>none</div></blockquote>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="warren"><strong>(Warren)</strong> Warren, Phys Rev E, 68, 066702 (2003).</p>
<p id="brennan"><strong>(Brennan)</strong> Brennan, J Chem Phys Lett, 5, 2144-2149 (2014).</p>
<p id="moore"><strong>(Moore)</strong> Moore, J Chem Phys, 144, 104501 (2016).</p>
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<div class="section" id="pair-style-table-rx-command">
<span id="index-0"></span><h1>pair_style table/rx command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">table</span> <span class="n">style</span> <span class="n">N</span>
</pre></div>
</div>
<p>style = <em>lookup</em> or <em>linear</em> or <em>spline</em> or <em>bitmap</em> = method of interpolation
N = use N values in <em>lookup</em>, <em>linear</em>, <em>spline</em> tables
N = use 2^N values in <em>bitmap</em> tables</p>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">table</span><span class="o">/</span><span class="n">rx</span> <span class="n">linear</span> <span class="mi">1000</span>
<span class="n">pair_style</span> <span class="n">table</span><span class="o">/</span><span class="n">rx</span> <span class="n">bitmap</span> <span class="mi">12</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">rxn</span><span class="o">.</span><span class="n">table</span> <span class="n">ENTRY1</span> <span class="n">h2o</span> <span class="n">h2o</span> <span class="mf">10.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">rxn</span><span class="o">.</span><span class="n">table</span> <span class="n">ENTRY1</span> <span class="mi">1</span><span class="n">fluid</span> <span class="mi">1</span><span class="n">fluid</span> <span class="mf">10.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="mi">3</span> <span class="n">rxn</span><span class="o">.</span><span class="n">table</span> <span class="n">ENTRY1</span> <span class="n">h2o</span> <span class="n">no2</span> <span class="mf">10.0</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>Style <em>table/rx</em> is used in reaction DPD simulations,where the coarse-grained (CG)
particles are composed of <em>m</em> species whose reaction rate kinetics are determined
from a set of <em>n</em> reaction rate equations through the <a class="reference internal" href="fix_rx.html"><span class="doc">fix rx</span></a> command.
The species of one CG particle can interact with a species in a neighboring CG
particle through a site-site interaction potential model. Style <em>table/rx</em> creates
interpolation tables of length <em>N</em> from pair potential and force values listed in a
file(s) as a function of distance. The files are read by the
<a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> command.</p>
<p>The interpolation tables are created by fitting cubic splines to the
file values and interpolating energy and force values at each of <em>N</em>
distances. During a simulation, these tables are used to interpolate
energy and force values as needed. The interpolation is done in one
of 4 styles: <em>lookup</em>, <em>linear</em>, <em>spline</em>, or <em>bitmap</em>.</p>
<p>For the <em>lookup</em> style, the distance between 2 atoms is used to find
the nearest table entry, which is the energy or force.</p>
<p>For the <em>linear</em> style, the pair distance is used to find 2
surrounding table values from which an energy or force is computed by
linear interpolation.</p>
<p>For the <em>spline</em> style, a cubic spline coefficients are computed and
stored at each of the <em>N</em> values in the table. The pair distance is
used to find the appropriate set of coefficients which are used to
evaluate a cubic polynomial which computes the energy or force.</p>
<p>For the <em>bitmap</em> style, the N means to create interpolation tables
that are 2^N in length. &lt;The pair distance is used to index into the
table via a fast bit-mapping technique <a class="reference internal" href="#wolff"><span class="std std-ref">(Wolff)</span></a> and a linear
interpolation is performed between adjacent table values.</p>
<p>The following coefficients must be defined for each pair of atoms
types via the <a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> command as in the examples
above.</p>
<ul class="simple">
<li>filename</li>
<li>keyword</li>
<li>species1</li>
<li>species2</li>
<li>cutoff (distance units)</li>
</ul>
<p>The filename specifies a file containing tabulated energy and force
values. The keyword specifies a section of the file. The cutoff is
an optional coefficient. If not specified, the outer cutoff in the
table itself (see below) will be used to build an interpolation table
that extend to the largest tabulated distance. If specified, only
file values up to the cutoff are used to create the interpolation
table. The format of this file is described below.</p>
<p>The species tags define the site-site interaction potential between two
species contained within two different particles.
The species tags must either correspond to the species defined in the reaction
kinetics files specified with the <a class="reference internal" href="fix_rx.html"><span class="doc">fix rx</span></a> command
or they must correspond to the tag &#8220;1fluid&#8221;, signifying interaction
with a product species mixture determined through a one-fluid approximation.
The interaction potential is weighted by the geometric average of the
concentrations of the two species. The coarse-grained potential
is stored before and after the reaction kinetics solver is applied, where
the difference is defined to be the internal chemical energy (uChem).</p>
<hr class="docutils" />
<p>Here are some guidelines for using the pair_style table/rx command to
best effect:</p>
<ul class="simple">
<li>Vary the number of table points; you may need to use more than you think
to get good resolution.</li>
<li>Always use the <a class="reference internal" href="pair_write.html"><span class="doc">pair_write</span></a> command to produce a plot
of what the final interpolated potential looks like. This can show up
interpolation &#8220;features&#8221; you may not like.</li>
<li>Start with the linear style; it&#8217;s the style least likely to have problems.</li>
<li>Use <em>N</em> in the pair_style command equal to the &#8220;N&#8221; in the tabulation
file, and use the &#8220;RSQ&#8221; or &#8220;BITMAP&#8221; parameter, so additional interpolation
is not needed. See discussion below.</li>
<li>Make sure that your tabulated forces and tabulated energies are consistent
(dE/dr = -F) along the entire range of r values.</li>
<li>Use as large an inner cutoff as possible. This avoids fitting splines
to very steep parts of the potential.</li>
</ul>
<hr class="docutils" />
<p>The format of a tabulated file is a series of one or more sections,
defined as follows (without the parenthesized comments):</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># Morse potential for Fe (one or more comment or blank lines)</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">MORSE_FE</span> <span class="p">(</span><span class="n">keyword</span> <span class="ow">is</span> <span class="n">first</span> <span class="n">text</span> <span class="n">on</span> <span class="n">line</span><span class="p">)</span>
<span class="n">N</span> <span class="mi">500</span> <span class="n">R</span> <span class="mf">1.0</span> <span class="mf">10.0</span> <span class="p">(</span><span class="n">N</span><span class="p">,</span> <span class="n">R</span><span class="p">,</span> <span class="n">RSQ</span><span class="p">,</span> <span class="n">BITMAP</span><span class="p">,</span> <span class="n">FPRIME</span> <span class="n">parameters</span><span class="p">)</span>
<span class="p">(</span><span class="n">blank</span><span class="p">)</span>
<span class="mi">1</span> <span class="mf">1.0</span> <span class="mf">25.5</span> <span class="mf">102.34</span> <span class="p">(</span><span class="n">index</span><span class="p">,</span> <span class="n">r</span><span class="p">,</span> <span class="n">energy</span><span class="p">,</span> <span class="n">force</span><span class="p">)</span>
<span class="mi">2</span> <span class="mf">1.02</span> <span class="mf">23.4</span> <span class="mf">98.5</span>
<span class="o">...</span>
<span class="mi">500</span> <span class="mf">10.0</span> <span class="mf">0.001</span> <span class="mf">0.003</span>
</pre></div>
</div>
<p>A section begins with a non-blank line whose 1st character is not a
&#8220;#&#8221;; blank lines or lines starting with &#8220;#&#8221; can be used as comments
between sections. The first line begins with a keyword which
identifies the section. The line can contain additional text, but the
initial text must match the argument specified in the pair_coeff
command. The next line lists (in any order) one or more parameters
for the table. Each parameter is a keyword followed by one or more
numeric values.</p>
<p>The parameter &#8220;N&#8221; is required and its value is the number of table
entries that follow. Note that this may be different than the <em>N</em>
specified in the <a class="reference internal" href="pair_style.html"><span class="doc">pair_style table/rx</span></a> command. Let
Ntable = <em>N</em> in the pair_style command, and Nfile = &#8220;N&#8221; in the
tabulated file. What LAMMPS does is a preliminary interpolation by
creating splines using the Nfile tabulated values as nodal points. It
uses these to interpolate as needed to generate energy and force
values at Ntable different points. The resulting tables of length
Ntable are then used as described above, when computing energy and
force for individual pair distances. This means that if you want the
interpolation tables of length Ntable to match exactly what is in the
tabulated file (with effectively no preliminary interpolation), you
should set Ntable = Nfile, and use the &#8220;RSQ&#8221; or &#8220;BITMAP&#8221; parameter.
The internal table abscissa is RSQ (separation distance squared).</p>
<p>All other parameters are optional. If &#8220;R&#8221; or &#8220;RSQ&#8221; or &#8220;BITMAP&#8221; does
not appear, then the distances in each line of the table are used
as-is to perform spline interpolation. In this case, the table values
can be spaced in <em>r</em> uniformly or however you wish to position table
values in regions of large gradients.</p>
<p>If used, the parameters &#8220;R&#8221; or &#8220;RSQ&#8221; are followed by 2 values <em>rlo</em>
and <em>rhi</em>. If specified, the distance associated with each energy and
force value is computed from these 2 values (at high accuracy), rather
than using the (low-accuracy) value listed in each line of the table.
The distance values in the table file are ignored in this case.
For &#8220;R&#8221;, distances uniformly spaced between <em>rlo</em> and <em>rhi</em> are
computed; for &#8220;RSQ&#8221;, squared distances uniformly spaced between
<em>rlo*rlo</em> and <em>rhi*rhi</em> are computed.</p>
<p>If used, the parameter &#8220;BITMAP&#8221; is also followed by 2 values <em>rlo</em> and
<em>rhi</em>. These values, along with the &#8220;N&#8221; value determine the ordering
of the N lines that follow and what distance is associated with each.
This ordering is complex, so it is not documented here, since this
file is typically produced by the <a class="reference internal" href="pair_write.html"><span class="doc">pair_write</span></a> command
with its <em>bitmap</em> option. When the table is in BITMAP format, the &#8220;N&#8221;
parameter in the file must be equal to 2^M where M is the value
specified in the pair_style command. Also, a cutoff parameter cannot
be used as an optional 3rd argument in the pair_coeff command; the
entire table extent as specified in the file must be used.</p>
<p>If used, the parameter &#8220;FPRIME&#8221; is followed by 2 values <em>fplo</em> and
<em>fphi</em> which are the derivative of the force at the innermost and
outermost distances listed in the table. These values are needed by
the spline construction routines. If not specified by the &#8220;FPRIME&#8221;
parameter, they are estimated (less accurately) by the first 2 and
last 2 force values in the table. This parameter is not used by
BITMAP tables.</p>
<p>Following a blank line, the next N lines list the tabulated values.
On each line, the 1st value is the index from 1 to N, the 2nd value is
r (in distance units), the 3rd value is the energy (in energy units),
and the 4th is the force (in force units). The r values must increase
from one line to the next (unless the BITMAP parameter is specified).</p>
<p>Note that one file can contain many sections, each with a tabulated
potential. LAMMPS reads the file section by section until it finds
one that matches the specified keyword.</p>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>This pair style does not support mixing. Thus, coefficients for all
I,J pairs must be specified explicitly.</p>
<p>The <a class="reference internal" href="pair_modify.html"><span class="doc">pair_modify</span></a> shift, table, and tail options are
not relevant for this pair style.</p>
<p>This pair style writes the settings for the &#8220;pair_style table/rx&#8221; command
to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>, so a pair_style command does
not need to specified in an input script that reads a restart file.
However, the coefficient information is not stored in the restart
file, since it is tabulated in the potential files. Thus, pair_coeff
commands do need to be specified in the restart input script.</p>
<p>This pair style can only be used via the <em>pair</em> keyword of the
<a class="reference internal" href="run_style.html"><span class="doc">run_style respa</span></a> command. It does not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<blockquote>
<div>none</div></blockquote>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="wolff"><strong>(Wolff)</strong> Wolff and Rudd, Comp Phys Comm, 120, 200-32 (1999).</p>
</div>
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