mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15184 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
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commit
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@ -619,13 +619,13 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.</p>
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<table border="1" class="docutils">
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<colgroup>
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<col width="15%" />
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<col width="11%" />
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<col width="13%" />
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<col width="11%" />
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<col width="12%" />
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<col width="12%" />
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<col width="11%" />
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<col width="12%" />
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<col width="10%" />
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<col width="15%" />
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<col width="12%" />
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</colgroup>
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<tbody valign="top">
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<tr class="row-odd"><td><a class="reference internal" href="fix_adapt.html"><span class="doc">adapt</span></a></td>
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@ -696,72 +696,72 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.</p>
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<td><a class="reference internal" href="fix_nvt_sllod.html"><span class="doc">nvt/sllod (io)</span></a></td>
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<td><a class="reference internal" href="fix_nvt_sphere.html"><span class="doc">nvt/sphere (o)</span></a></td>
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<td><a class="reference internal" href="fix_oneway.html"><span class="doc">oneway</span></a></td>
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<td><a class="reference internal" href="fix_orient_fcc.html"><span class="doc">orient/fcc</span></a></td>
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<td><a class="reference internal" href="fix_orient.html"><span class="doc">orient/bcc</span></a></td>
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<td><a class="reference internal" href="fix_orient.html"><span class="doc">orient/fcc</span></a></td>
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<td><a class="reference internal" href="fix_planeforce.html"><span class="doc">planeforce</span></a></td>
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<td><a class="reference internal" href="fix_poems.html"><span class="doc">poems</span></a></td>
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</tr>
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<tr class="row-odd"><td><a class="reference internal" href="fix_pour.html"><span class="doc">pour</span></a></td>
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<tr class="row-odd"><td><a class="reference internal" href="fix_poems.html"><span class="doc">poems</span></a></td>
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<td><a class="reference internal" href="fix_pour.html"><span class="doc">pour</span></a></td>
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<td><a class="reference internal" href="fix_press_berendsen.html"><span class="doc">press/berendsen</span></a></td>
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<td><a class="reference internal" href="fix_print.html"><span class="doc">print</span></a></td>
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<td><a class="reference internal" href="fix_property_atom.html"><span class="doc">property/atom</span></a></td>
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<td><a class="reference internal" href="fix_qeq_comb.html"><span class="doc">qeq/comb (o)</span></a></td>
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<td><a class="reference internal" href="fix_qeq.html"><span class="doc">qeq/dynamic</span></a></td>
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<td><a class="reference internal" href="fix_qeq.html"><span class="doc">qeq/fire</span></a></td>
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<td><a class="reference internal" href="fix_qeq.html"><span class="doc">qeq/point</span></a></td>
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</tr>
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<tr class="row-even"><td><a class="reference internal" href="fix_qeq.html"><span class="doc">qeq/shielded</span></a></td>
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<tr class="row-even"><td><a class="reference internal" href="fix_qeq.html"><span class="doc">qeq/point</span></a></td>
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<td><a class="reference internal" href="fix_qeq.html"><span class="doc">qeq/shielded</span></a></td>
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<td><a class="reference internal" href="fix_qeq.html"><span class="doc">qeq/slater</span></a></td>
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<td><a class="reference internal" href="fix_shake.html"><span class="doc">rattle</span></a></td>
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<td><a class="reference internal" href="fix_reax_bonds.html"><span class="doc">reax/bonds</span></a></td>
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<td><a class="reference internal" href="fix_recenter.html"><span class="doc">recenter</span></a></td>
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<td><a class="reference internal" href="fix_restrain.html"><span class="doc">restrain</span></a></td>
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<td><a class="reference internal" href="fix_rigid.html"><span class="doc">rigid (o)</span></a></td>
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<td><a class="reference internal" href="fix_rigid.html"><span class="doc">rigid/nph (o)</span></a></td>
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</tr>
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<tr class="row-odd"><td><a class="reference internal" href="fix_rigid.html"><span class="doc">rigid/npt (o)</span></a></td>
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<tr class="row-odd"><td><a class="reference internal" href="fix_rigid.html"><span class="doc">rigid/nph (o)</span></a></td>
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<td><a class="reference internal" href="fix_rigid.html"><span class="doc">rigid/npt (o)</span></a></td>
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<td><a class="reference internal" href="fix_rigid.html"><span class="doc">rigid/nve (o)</span></a></td>
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<td><a class="reference internal" href="fix_rigid.html"><span class="doc">rigid/nvt (o)</span></a></td>
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<td><a class="reference internal" href="fix_rigid.html"><span class="doc">rigid/small (o)</span></a></td>
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<td><a class="reference internal" href="fix_rigid.html"><span class="doc">rigid/small/nph</span></a></td>
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<td><a class="reference internal" href="fix_rigid.html"><span class="doc">rigid/small/npt</span></a></td>
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<td><a class="reference internal" href="fix_rigid.html"><span class="doc">rigid/small/nve</span></a></td>
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<td><a class="reference internal" href="fix_rigid.html"><span class="doc">rigid/small/nvt</span></a></td>
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</tr>
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<tr class="row-even"><td><a class="reference internal" href="fix_setforce.html"><span class="doc">setforce (k)</span></a></td>
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<tr class="row-even"><td><a class="reference internal" href="fix_rigid.html"><span class="doc">rigid/small/nvt</span></a></td>
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<td><a class="reference internal" href="fix_setforce.html"><span class="doc">setforce (k)</span></a></td>
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<td><a class="reference internal" href="fix_shake.html"><span class="doc">shake</span></a></td>
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<td><a class="reference internal" href="fix_spring.html"><span class="doc">spring</span></a></td>
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<td><a class="reference internal" href="fix_spring_chunk.html"><span class="doc">spring/chunk</span></a></td>
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<td><a class="reference internal" href="fix_spring_rg.html"><span class="doc">spring/rg</span></a></td>
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<td><a class="reference internal" href="fix_spring_self.html"><span class="doc">spring/self</span></a></td>
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<td><a class="reference internal" href="fix_srd.html"><span class="doc">srd</span></a></td>
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<td><a class="reference internal" href="fix_store_force.html"><span class="doc">store/force</span></a></td>
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</tr>
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<tr class="row-odd"><td><a class="reference internal" href="fix_store_state.html"><span class="doc">store/state</span></a></td>
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<tr class="row-odd"><td><a class="reference internal" href="fix_store_force.html"><span class="doc">store/force</span></a></td>
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<td><a class="reference internal" href="fix_store_state.html"><span class="doc">store/state</span></a></td>
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<td><a class="reference internal" href="fix_temp_berendsen.html"><span class="doc">temp/berendsen</span></a></td>
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<td><a class="reference internal" href="fix_temp_csvr.html"><span class="doc">temp/csld</span></a></td>
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<td><a class="reference internal" href="fix_temp_csvr.html"><span class="doc">temp/csvr</span></a></td>
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<td><a class="reference internal" href="fix_temp_rescale.html"><span class="doc">temp/rescale</span></a></td>
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<td><a class="reference internal" href="fix_tfmc.html"><span class="doc">tfmc</span></a></td>
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<td><a class="reference internal" href="fix_thermal_conductivity.html"><span class="doc">thermal/conductivity</span></a></td>
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<td><a class="reference internal" href="fix_tmd.html"><span class="doc">tmd</span></a></td>
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</tr>
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<tr class="row-even"><td><a class="reference internal" href="fix_ttm.html"><span class="doc">ttm</span></a></td>
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<tr class="row-even"><td><a class="reference internal" href="fix_tmd.html"><span class="doc">tmd</span></a></td>
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<td><a class="reference internal" href="fix_ttm.html"><span class="doc">ttm</span></a></td>
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<td><a class="reference internal" href="fix_tune_kspace.html"><span class="doc">tune/kspace</span></a></td>
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<td><a class="reference internal" href="fix_vector.html"><span class="doc">vector</span></a></td>
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<td><a class="reference internal" href="fix_viscosity.html"><span class="doc">viscosity</span></a></td>
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<td><a class="reference internal" href="fix_viscous.html"><span class="doc">viscous</span></a></td>
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<td><a class="reference internal" href="fix_wall.html"><span class="doc">wall/colloid</span></a></td>
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<td><a class="reference internal" href="fix_wall_gran.html"><span class="doc">wall/gran</span></a></td>
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<td><a class="reference internal" href="fix_wall.html"><span class="doc">wall/harmonic</span></a></td>
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</tr>
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<tr class="row-odd"><td><a class="reference internal" href="fix_wall.html"><span class="doc">wall/lj1043</span></a></td>
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<tr class="row-odd"><td><a class="reference internal" href="fix_wall.html"><span class="doc">wall/harmonic</span></a></td>
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<td><a class="reference internal" href="fix_wall.html"><span class="doc">wall/lj1043</span></a></td>
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<td><a class="reference internal" href="fix_wall.html"><span class="doc">wall/lj126</span></a></td>
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<td><a class="reference internal" href="fix_wall.html"><span class="doc">wall/lj93</span></a></td>
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<td><a class="reference internal" href="fix_wall_piston.html"><span class="doc">wall/piston</span></a></td>
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<td><a class="reference internal" href="fix_wall_reflect.html"><span class="doc">wall/reflect (k)</span></a></td>
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<td><a class="reference internal" href="fix_wall_region.html"><span class="doc">wall/region</span></a></td>
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<td><a class="reference internal" href="fix_wall_srd.html"><span class="doc">wall/srd</span></a></td>
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<td> </td>
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</tr>
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</tbody>
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</table>
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@ -457,37 +457,37 @@ with the :doc:`appropriate accelerated package <Section_accelerate>`.
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This is indicated by additional letters in parenthesis: g = GPU, i =
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USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
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+------------------------------------------------------+----------------------------------------------+----------------------------------------+------------------------------------------+--------------------------------------------+----------------------------------------+--------------------------------------------------------+------------------------------------------+
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| :doc:`adapt <fix_adapt>` | :doc:`addforce <fix_addforce>` | :doc:`append/atoms <fix_append_atoms>` | :doc:`atom/swap <fix_atom_swap>` | :doc:`aveforce <fix_aveforce>` | :doc:`ave/atom <fix_ave_atom>` | :doc:`ave/chunk <fix_ave_chunk>` | :doc:`ave/correlate <fix_ave_correlate>` |
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+------------------------------------------------------+----------------------------------------------+----------------------------------------+------------------------------------------+--------------------------------------------+----------------------------------------+--------------------------------------------------------+------------------------------------------+
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| :doc:`ave/histo <fix_ave_histo>` | :doc:`ave/histo/weight <fix_ave_histo>` | :doc:`ave/time <fix_ave_time>` | :doc:`balance <fix_balance>` | :doc:`bond/break <fix_bond_break>` | :doc:`bond/create <fix_bond_create>` | :doc:`bond/swap <fix_bond_swap>` | :doc:`box/relax <fix_box_relax>` |
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+------------------------------------------------------+----------------------------------------------+----------------------------------------+------------------------------------------+--------------------------------------------+----------------------------------------+--------------------------------------------------------+------------------------------------------+
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| :doc:`deform (k) <fix_deform>` | :doc:`deposit <fix_deposit>` | :doc:`drag <fix_drag>` | :doc:`dt/reset <fix_dt_reset>` | :doc:`efield <fix_efield>` | :doc:`ehex <fix_ehex>` | :doc:`enforce2d <fix_enforce2d>` | :doc:`evaporate <fix_evaporate>` |
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+------------------------------------------------------+----------------------------------------------+----------------------------------------+------------------------------------------+--------------------------------------------+----------------------------------------+--------------------------------------------------------+------------------------------------------+
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| :doc:`external <fix_external>` | :doc:`freeze <fix_freeze>` | :doc:`gcmc <fix_gcmc>` | :doc:`gld <fix_gld>` | :doc:`gravity (o) <fix_gravity>` | :doc:`heat <fix_heat>` | :doc:`indent <fix_indent>` | :doc:`langevin (k) <fix_langevin>` |
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+------------------------------------------------------+----------------------------------------------+----------------------------------------+------------------------------------------+--------------------------------------------+----------------------------------------+--------------------------------------------------------+------------------------------------------+
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| :doc:`lineforce <fix_lineforce>` | :doc:`momentum <fix_momentum>` | :doc:`move <fix_move>` | :doc:`msst <fix_msst>` | :doc:`neb <fix_neb>` | :doc:`nph (ko) <fix_nh>` | :doc:`nphug (o) <fix_nphug>` | :doc:`nph/asphere (o) <fix_nph_asphere>` |
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+------------------------------------------------------+----------------------------------------------+----------------------------------------+------------------------------------------+--------------------------------------------+----------------------------------------+--------------------------------------------------------+------------------------------------------+
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| :doc:`nph/body <fix_nph_body>` | :doc:`nph/sphere (o) <fix_nph_sphere>` | :doc:`npt (kio) <fix_nh>` | :doc:`npt/asphere (o) <fix_npt_asphere>` | :doc:`npt/body <fix_npt_body>` | :doc:`npt/sphere (o) <fix_npt_sphere>` | :doc:`nve (kio) <fix_nve>` | :doc:`nve/asphere (i) <fix_nve_asphere>` |
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+------------------------------------------------------+----------------------------------------------+----------------------------------------+------------------------------------------+--------------------------------------------+----------------------------------------+--------------------------------------------------------+------------------------------------------+
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| :doc:`nve/asphere/noforce <fix_nve_asphere_noforce>` | :doc:`nve/body <fix_nve_body>` | :doc:`nve/limit <fix_nve_limit>` | :doc:`nve/line <fix_nve_line>` | :doc:`nve/noforce <fix_nve_noforce>` | :doc:`nve/sphere (o) <fix_nve_sphere>` | :doc:`nve/tri <fix_nve_tri>` | :doc:`nvt (iko) <fix_nh>` |
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+------------------------------------------------------+----------------------------------------------+----------------------------------------+------------------------------------------+--------------------------------------------+----------------------------------------+--------------------------------------------------------+------------------------------------------+
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| :doc:`nvt/asphere (o) <fix_nvt_asphere>` | :doc:`nvt/body <fix_nvt_body>` | :doc:`nvt/sllod (io) <fix_nvt_sllod>` | :doc:`nvt/sphere (o) <fix_nvt_sphere>` | :doc:`oneway <fix_oneway>` | :doc:`orient/fcc <fix_orient_fcc>` | :doc:`planeforce <fix_planeforce>` | :doc:`poems <fix_poems>` |
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+------------------------------------------------------+----------------------------------------------+----------------------------------------+------------------------------------------+--------------------------------------------+----------------------------------------+--------------------------------------------------------+------------------------------------------+
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| :doc:`pour <fix_pour>` | :doc:`press/berendsen <fix_press_berendsen>` | :doc:`print <fix_print>` | :doc:`property/atom <fix_property_atom>` | :doc:`qeq/comb (o) <fix_qeq_comb>` | :doc:`qeq/dynamic <fix_qeq>` | :doc:`qeq/fire <fix_qeq>` | :doc:`qeq/point <fix_qeq>` |
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+------------------------------------------------------+----------------------------------------------+----------------------------------------+------------------------------------------+--------------------------------------------+----------------------------------------+--------------------------------------------------------+------------------------------------------+
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| :doc:`qeq/shielded <fix_qeq>` | :doc:`qeq/slater <fix_qeq>` | :doc:`rattle <fix_shake>` | :doc:`reax/bonds <fix_reax_bonds>` | :doc:`recenter <fix_recenter>` | :doc:`restrain <fix_restrain>` | :doc:`rigid (o) <fix_rigid>` | :doc:`rigid/nph (o) <fix_rigid>` |
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+------------------------------------------------------+----------------------------------------------+----------------------------------------+------------------------------------------+--------------------------------------------+----------------------------------------+--------------------------------------------------------+------------------------------------------+
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| :doc:`rigid/npt (o) <fix_rigid>` | :doc:`rigid/nve (o) <fix_rigid>` | :doc:`rigid/nvt (o) <fix_rigid>` | :doc:`rigid/small (o) <fix_rigid>` | :doc:`rigid/small/nph <fix_rigid>` | :doc:`rigid/small/npt <fix_rigid>` | :doc:`rigid/small/nve <fix_rigid>` | :doc:`rigid/small/nvt <fix_rigid>` |
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+------------------------------------------------------+----------------------------------------------+----------------------------------------+------------------------------------------+--------------------------------------------+----------------------------------------+--------------------------------------------------------+------------------------------------------+
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| :doc:`setforce (k) <fix_setforce>` | :doc:`shake <fix_shake>` | :doc:`spring <fix_spring>` | :doc:`spring/chunk <fix_spring_chunk>` | :doc:`spring/rg <fix_spring_rg>` | :doc:`spring/self <fix_spring_self>` | :doc:`srd <fix_srd>` | :doc:`store/force <fix_store_force>` |
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+------------------------------------------------------+----------------------------------------------+----------------------------------------+------------------------------------------+--------------------------------------------+----------------------------------------+--------------------------------------------------------+------------------------------------------+
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| :doc:`store/state <fix_store_state>` | :doc:`temp/berendsen <fix_temp_berendsen>` | :doc:`temp/csld <fix_temp_csvr>` | :doc:`temp/csvr <fix_temp_csvr>` | :doc:`temp/rescale <fix_temp_rescale>` | :doc:`tfmc <fix_tfmc>` | :doc:`thermal/conductivity <fix_thermal_conductivity>` | :doc:`tmd <fix_tmd>` |
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+------------------------------------------------------+----------------------------------------------+----------------------------------------+------------------------------------------+--------------------------------------------+----------------------------------------+--------------------------------------------------------+------------------------------------------+
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| :doc:`ttm <fix_ttm>` | :doc:`tune/kspace <fix_tune_kspace>` | :doc:`vector <fix_vector>` | :doc:`viscosity <fix_viscosity>` | :doc:`viscous <fix_viscous>` | :doc:`wall/colloid <fix_wall>` | :doc:`wall/gran <fix_wall_gran>` | :doc:`wall/harmonic <fix_wall>` |
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+------------------------------------------------------+----------------------------------------------+----------------------------------------+------------------------------------------+--------------------------------------------+----------------------------------------+--------------------------------------------------------+------------------------------------------+
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| :doc:`wall/lj1043 <fix_wall>` | :doc:`wall/lj126 <fix_wall>` | :doc:`wall/lj93 <fix_wall>` | :doc:`wall/piston <fix_wall_piston>` | :doc:`wall/reflect (k) <fix_wall_reflect>` | :doc:`wall/region <fix_wall_region>` | :doc:`wall/srd <fix_wall_srd>` | |
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+------------------------------------------------------+----------------------------------------------+----------------------------------------+------------------------------------------+--------------------------------------------+----------------------------------------+--------------------------------------------------------+------------------------------------------+
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+------------------------------------------------------+-----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+
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| :doc:`adapt <fix_adapt>` | :doc:`addforce <fix_addforce>` | :doc:`append/atoms <fix_append_atoms>` | :doc:`atom/swap <fix_atom_swap>` | :doc:`aveforce <fix_aveforce>` | :doc:`ave/atom <fix_ave_atom>` | :doc:`ave/chunk <fix_ave_chunk>` | :doc:`ave/correlate <fix_ave_correlate>` |
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+------------------------------------------------------+-----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+
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| :doc:`ave/histo <fix_ave_histo>` | :doc:`ave/histo/weight <fix_ave_histo>` | :doc:`ave/time <fix_ave_time>` | :doc:`balance <fix_balance>` | :doc:`bond/break <fix_bond_break>` | :doc:`bond/create <fix_bond_create>` | :doc:`bond/swap <fix_bond_swap>` | :doc:`box/relax <fix_box_relax>` |
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+------------------------------------------------------+-----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+
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| :doc:`deform (k) <fix_deform>` | :doc:`deposit <fix_deposit>` | :doc:`drag <fix_drag>` | :doc:`dt/reset <fix_dt_reset>` | :doc:`efield <fix_efield>` | :doc:`ehex <fix_ehex>` | :doc:`enforce2d <fix_enforce2d>` | :doc:`evaporate <fix_evaporate>` |
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+------------------------------------------------------+-----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+
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| :doc:`external <fix_external>` | :doc:`freeze <fix_freeze>` | :doc:`gcmc <fix_gcmc>` | :doc:`gld <fix_gld>` | :doc:`gravity (o) <fix_gravity>` | :doc:`heat <fix_heat>` | :doc:`indent <fix_indent>` | :doc:`langevin (k) <fix_langevin>` |
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+------------------------------------------------------+-----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+
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| :doc:`lineforce <fix_lineforce>` | :doc:`momentum <fix_momentum>` | :doc:`move <fix_move>` | :doc:`msst <fix_msst>` | :doc:`neb <fix_neb>` | :doc:`nph (ko) <fix_nh>` | :doc:`nphug (o) <fix_nphug>` | :doc:`nph/asphere (o) <fix_nph_asphere>` |
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+------------------------------------------------------+-----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+
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| :doc:`nph/body <fix_nph_body>` | :doc:`nph/sphere (o) <fix_nph_sphere>` | :doc:`npt (kio) <fix_nh>` | :doc:`npt/asphere (o) <fix_npt_asphere>` | :doc:`npt/body <fix_npt_body>` | :doc:`npt/sphere (o) <fix_npt_sphere>` | :doc:`nve (kio) <fix_nve>` | :doc:`nve/asphere (i) <fix_nve_asphere>` |
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+------------------------------------------------------+-----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+
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| :doc:`nve/asphere/noforce <fix_nve_asphere_noforce>` | :doc:`nve/body <fix_nve_body>` | :doc:`nve/limit <fix_nve_limit>` | :doc:`nve/line <fix_nve_line>` | :doc:`nve/noforce <fix_nve_noforce>` | :doc:`nve/sphere (o) <fix_nve_sphere>` | :doc:`nve/tri <fix_nve_tri>` | :doc:`nvt (iko) <fix_nh>` |
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+------------------------------------------------------+-----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+
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| :doc:`nvt/asphere (o) <fix_nvt_asphere>` | :doc:`nvt/body <fix_nvt_body>` | :doc:`nvt/sllod (io) <fix_nvt_sllod>` | :doc:`nvt/sphere (o) <fix_nvt_sphere>` | :doc:`oneway <fix_oneway>` | :doc:`orient/bcc <fix_orient>` | :doc:`orient/fcc <fix_orient>` | :doc:`planeforce <fix_planeforce>` |
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+------------------------------------------------------+-----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+
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| :doc:`poems <fix_poems>` | :doc:`pour <fix_pour>` | :doc:`press/berendsen <fix_press_berendsen>` | :doc:`print <fix_print>` | :doc:`property/atom <fix_property_atom>` | :doc:`qeq/comb (o) <fix_qeq_comb>` | :doc:`qeq/dynamic <fix_qeq>` | :doc:`qeq/fire <fix_qeq>` |
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+------------------------------------------------------+-----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+
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| :doc:`qeq/point <fix_qeq>` | :doc:`qeq/shielded <fix_qeq>` | :doc:`qeq/slater <fix_qeq>` | :doc:`rattle <fix_shake>` | :doc:`reax/bonds <fix_reax_bonds>` | :doc:`recenter <fix_recenter>` | :doc:`restrain <fix_restrain>` | :doc:`rigid (o) <fix_rigid>` |
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+------------------------------------------------------+-----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+
|
||||
| :doc:`rigid/nph (o) <fix_rigid>` | :doc:`rigid/npt (o) <fix_rigid>` | :doc:`rigid/nve (o) <fix_rigid>` | :doc:`rigid/nvt (o) <fix_rigid>` | :doc:`rigid/small (o) <fix_rigid>` | :doc:`rigid/small/nph <fix_rigid>` | :doc:`rigid/small/npt <fix_rigid>` | :doc:`rigid/small/nve <fix_rigid>` |
|
||||
+------------------------------------------------------+-----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+
|
||||
| :doc:`rigid/small/nvt <fix_rigid>` | :doc:`setforce (k) <fix_setforce>` | :doc:`shake <fix_shake>` | :doc:`spring <fix_spring>` | :doc:`spring/chunk <fix_spring_chunk>` | :doc:`spring/rg <fix_spring_rg>` | :doc:`spring/self <fix_spring_self>` | :doc:`srd <fix_srd>` |
|
||||
+------------------------------------------------------+-----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+
|
||||
| :doc:`store/force <fix_store_force>` | :doc:`store/state <fix_store_state>` | :doc:`temp/berendsen <fix_temp_berendsen>` | :doc:`temp/csld <fix_temp_csvr>` | :doc:`temp/csvr <fix_temp_csvr>` | :doc:`temp/rescale <fix_temp_rescale>` | :doc:`tfmc <fix_tfmc>` | :doc:`thermal/conductivity <fix_thermal_conductivity>` |
|
||||
+------------------------------------------------------+-----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+
|
||||
| :doc:`tmd <fix_tmd>` | :doc:`ttm <fix_ttm>` | :doc:`tune/kspace <fix_tune_kspace>` | :doc:`vector <fix_vector>` | :doc:`viscosity <fix_viscosity>` | :doc:`viscous <fix_viscous>` | :doc:`wall/colloid <fix_wall>` | :doc:`wall/gran <fix_wall_gran>` |
|
||||
+------------------------------------------------------+-----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+
|
||||
| :doc:`wall/harmonic <fix_wall>` | :doc:`wall/lj1043 <fix_wall>` | :doc:`wall/lj126 <fix_wall>` | :doc:`wall/lj93 <fix_wall>` | :doc:`wall/piston <fix_wall_piston>` | :doc:`wall/reflect (k) <fix_wall_reflect>` | :doc:`wall/region <fix_wall_region>` | :doc:`wall/srd <fix_wall_srd>` |
|
||||
+------------------------------------------------------+-----------------------------------------+----------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------------+--------------------------------------+--------------------------------------------------------+
|
||||
|
||||
These are additional fix styles in USER packages, which can be used if
|
||||
:ref:`LAMMPS is built with the appropriate package <start_3>`.
|
||||
|
|
|
|||
|
|
@ -226,7 +226,8 @@ of :ref:`this page <cmd_5>`.
|
|||
* :doc:`nvt/sllod <fix_nvt_sllod>` - NVT for NEMD with SLLOD equations
|
||||
* :doc:`nvt/sphere <fix_nvt_sphere>` - NVT for spherical particles
|
||||
* :doc:`oneway <fix_oneway>` - constrain particles on move in one direction
|
||||
* :doc:`orient/fcc <fix_orient_fcc>` - add grain boundary migration force
|
||||
* :doc:`orient/bcc <fix_orient>` - add grain boundary migration force for BCC
|
||||
* :doc:`orient/fcc <fix_orient>` - add grain boundary migration force for FCC
|
||||
* :doc:`planeforce <fix_planeforce>` - constrain atoms to move in a plane
|
||||
* :doc:`poems <fix_poems>` - constrain clusters of atoms to move as coupled rigid bodies
|
||||
* :doc:`pour <fix_pour>` - pour new atoms/molecules into a granular simulation domain
|
||||
|
|
|
|||
|
|
@ -3,14 +3,18 @@
|
|||
fix orient/fcc command
|
||||
======================
|
||||
|
||||
fix orient/bcc command
|
||||
======================
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
fix ID group-ID orient/fcc nstats dir alat dE cutlo cuthi file0 file1
|
||||
fix ID group-ID orient/bcc nstats dir alat dE cutlo cuthi file0 file1
|
||||
|
||||
* ID, group-ID are documented in :doc:`fix <fix>` command
|
||||
* nstats = print stats every this many steps, 0 = never
|
||||
* dir = 0/1 for which crystal is used as reference
|
||||
* alat = fcc cubic lattice constant (distance units)
|
||||
* alat = fcc/bcc cubic lattice constant (distance units)
|
||||
* dE = energy added to each atom (energy units)
|
||||
* cutlo,cuthi = values between 0.0 and 1.0, cutlo < cuthi
|
||||
* file0,file1 = files that specify orientation of each grain
|
||||
|
|
@ -21,6 +25,7 @@ Examples
|
|||
.. parsed-literal::
|
||||
|
||||
fix gb all orient/fcc 0 1 4.032008 0.001 0.25 0.75 xi.vec chi.vec
|
||||
fix gb all orient/bcc 0 1 2.882 0.001 0.25 0.75 ngb.left ngb.right
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
|
@ -29,8 +34,9 @@ The fix applies an orientation-dependent force to atoms near a planar
|
|||
grain boundary which can be used to induce grain boundary migration
|
||||
(in the direction perpendicular to the grain boundary plane). The
|
||||
motivation and explanation of this force and its application are
|
||||
described in :ref:`(Janssens) <Janssens>`. The force is only applied to
|
||||
atoms in the fix group.
|
||||
described in :ref:`(Janssens) <Janssens>`. The adaptiation to bcc crystals
|
||||
is described in :ref:`(Wicaksono1) <Wicaksono1>`. The computed force is only
|
||||
applied to atoms in the fix group.
|
||||
|
||||
The basic idea is that atoms in one grain (on one side of the
|
||||
boundary) have a potential energy dE added to them. Atoms in the
|
||||
|
|
@ -53,19 +59,21 @@ The potential energy added to atom I is given by these formulas
|
|||
.. image:: Eqs/fix_orient_fcc.jpg
|
||||
:align: center
|
||||
|
||||
which are fully explained in :ref:`(Janssens) <Janssens>`. The order
|
||||
parameter Xi for atom I in equation (1) is a sum over the 12 nearest
|
||||
neighbors of atom I. Rj is the vector from atom I to its neighbor J,
|
||||
and RIj is a vector in the reference (perfect) crystal. That is, if
|
||||
dir = 0/1, then RIj is a vector to an atom coord from file 0/1.
|
||||
Equation (2) gives the expected value of the order parameter XiIJ in
|
||||
the other grain. Hi and lo cutoffs are defined in equations (3) and
|
||||
(4), using the input parameters *cutlo* and *cuthi* as thresholds to
|
||||
avoid adding grain boundary energy when the deviation in the order
|
||||
parameter from 0 or 1 is small (e.g. due to thermal fluctuations in a
|
||||
perfect crystal). The added potential energy Ui for atom I is given
|
||||
in equation (6) where it is interpolated between 0 and dE using the
|
||||
two threshold Xi values and the Wi value of equation (5).
|
||||
which are fully explained in :ref:`(Janssens) <Janssens>`. For fcc crystals
|
||||
this order parameter Xi for atom I in equation (1) is a sum over the
|
||||
12 nearest neighbors of atom I. For bcc crystals it is the
|
||||
corresponding sum of the 8 nearest neighbors. Rj is the vector from
|
||||
atom I to its neighbor J, and RIj is a vector in the reference
|
||||
(perfect) crystal. That is, if dir = 0/1, then RIj is a vector to an
|
||||
atom coord from file 0/1. Equation (2) gives the expected value of
|
||||
the order parameter XiIJ in the other grain. Hi and lo cutoffs are
|
||||
defined in equations (3) and (4), using the input parameters *cutlo*
|
||||
and *cuthi* as thresholds to avoid adding grain boundary energy when
|
||||
the deviation in the order parameter from 0 or 1 is small (e.g. due to
|
||||
thermal fluctuations in a perfect crystal). The added potential
|
||||
energy Ui for atom I is given in equation (6) where it is interpolated
|
||||
between 0 and dE using the two threshold Xi values and the Wi value of
|
||||
equation (5).
|
||||
|
||||
The derivative of this energy expression gives the force on each atom
|
||||
which thus depends on the orientation of its neighbors relative to the
|
||||
|
|
@ -84,14 +92,14 @@ expense of the other. A value of 0 means the first grain will shrink;
|
|||
a value of 1 means it will grow. This assumes that *dE* is positive.
|
||||
The reverse will be true if *dE* is negative.
|
||||
|
||||
The *alat* parameter is the cubic lattice constant for the fcc
|
||||
The *alat* parameter is the cubic lattice constant for the fcc or bcc
|
||||
material and is only used to compute a cutoff distance of 1.57 * alat
|
||||
/ sqrt(2) for finding the 12 nearest neighbors of each atom (which
|
||||
should be valid for an fcc crystal). A longer/shorter cutoff can be
|
||||
imposed by adjusting *alat*\ . If a particular atom has less than 12
|
||||
neighbors within the cutoff, the order parameter of equation (1) is
|
||||
effectively multiplied by 12 divided by the actual number of neighbors
|
||||
within the cutoff.
|
||||
/ sqrt(2) for finding the 12 or 8 nearest neighbors of each atom
|
||||
(which should be valid for an fcc or bcc crystal). A longer/shorter
|
||||
cutoff can be imposed by adjusting *alat*\ . If a particular atom has
|
||||
less than 12 or 8 neighbors within the cutoff, the order parameter of
|
||||
equation (1) is effectively multiplied by 12 or 8 divided by the
|
||||
actual number of neighbors within the cutoff.
|
||||
|
||||
The *dE* parameter is the maximum amount of additional energy added to
|
||||
each atom in the grain which wants to shrink.
|
||||
|
|
@ -113,7 +121,8 @@ orientation. The vector lengths should all be identical since an fcc
|
|||
lattice has a coordination number of 12. Only 6 are listed due to
|
||||
symmetry, so the list must include one from each pair of
|
||||
equal-and-opposite neighbors. A pair of orientation files for a
|
||||
Sigma=5 tilt boundary are show below.
|
||||
Sigma=5 tilt boundary are shown below. A tutorial that can help for
|
||||
writing the orientation files is given in :ref:`(Wicaksono2) <Wicaksono2>`
|
||||
|
||||
Restart, fix_modify, output, run start/stop, minimize info
|
||||
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||
|
|
@ -145,7 +154,7 @@ Restrictions
|
|||
This fix is part of the MISC package. It is only enabled if LAMMPS
|
||||
was built with that package. See the :ref:`Making LAMMPS <start_3>` section for more info.
|
||||
|
||||
This fix should only be used with fcc lattices.
|
||||
This fix should only be used with fcc or bcc lattices.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
|
@ -165,6 +174,20 @@ Related commands
|
|||
**(Janssens)** Janssens, Olmsted, Holm, Foiles, Plimpton, Derlet, Nature
|
||||
Materials, 5, 124-127 (2006).
|
||||
|
||||
.. _Wicaksono1:
|
||||
|
||||
|
||||
|
||||
**(Wicaksono1)** Wicaksono, Sinclair, Militzer, Computational Materials
|
||||
Science, 117, 397-405 (2016).
|
||||
|
||||
.. _Wicaksono2:
|
||||
|
||||
|
||||
|
||||
**(Wicaksono2)** Wicaksono, figshare,
|
||||
https://dx.doi.org/10.6084/m9.figshare.1488628.v1 (2015).
|
||||
|
||||
|
||||
----------
|
||||
|
||||
|
|
|
|||
|
|
@ -189,6 +189,15 @@ supported by Ewald or PPPM when using a triclinic simulation cell. The
|
|||
slab correction has also been extended to point dipole interactions
|
||||
:ref:`(Klapp) <Klapp>` in :doc:`kspace_style <kspace_style>` *ewald/disp*\ .
|
||||
|
||||
.. note::
|
||||
|
||||
If you wish to apply an electric field in the Z-direction, in
|
||||
conjunction with the *slab* keyword, you should do it by adding
|
||||
explicit charged particles to the +/- Z surfaces. If you do it via
|
||||
the :doc:`fix efield <fix_efield>` command, it will not give the correct
|
||||
dielectric constant due to the Yeh/Berkowitz :ref:`(Yeh) <Yeh>` correction
|
||||
not being compatible with how :doc:`fix efield <fix_efield>` works.
|
||||
|
||||
The *compute* keyword allows Kspace computations to be turned off,
|
||||
even though a :doc:`kspace_style <kspace_style>` is defined. This is
|
||||
not useful for running a real simulation, but can be useful for
|
||||
|
|
|
|||
|
|
@ -1239,7 +1239,7 @@ script.
|
|||
*Triangles* section:
|
||||
|
||||
* one line per triangle
|
||||
* line syntax: atom-ID x1 y1 x2 y2
|
||||
* line syntax: atom-ID x1 y1 z1 x2 y2 z2 x3 y3 z3
|
||||
.. parsed-literal::
|
||||
|
||||
atom-ID = ID of atom which is a line segment
|
||||
|
|
|
|||
|
|
@ -147,6 +147,7 @@ script that reads the restart file, though you can redefine many of
|
|||
these settings after the restart file is read.
|
||||
|
||||
* :doc:`units <units>`
|
||||
* :doc:`newton bond <newton>` (see discussion of newton command below)
|
||||
* :doc:`atom style <atom_style>` and :doc:`atom_modify <atom_modify>` settings id, map, sort
|
||||
* :doc:`comm style <comm_style>` and `comm_modify <comm_modify>`_ settings mode, cutoff, vel
|
||||
* :doc:`timestep <timestep>`
|
||||
|
|
@ -163,6 +164,7 @@ Here is a list of information not stored in a restart file, which
|
|||
means you must re-issue these commands in your input script, after
|
||||
reading the restart file.
|
||||
|
||||
* :doc:`newton pair <newton>` (see discussion of newton command below)
|
||||
* :doc:`fix <fix>` commands (see below)
|
||||
* :doc:`compute <compute>` commands (see below)
|
||||
* :doc:`variable <variable>` commands
|
||||
|
|
@ -171,6 +173,16 @@ reading the restart file.
|
|||
* :doc:`kspace_style <kspace_style>` and :doc:`kspace_modify <kspace_modify>` settings
|
||||
* info for :doc:`thermodynamic <thermo_style>`, :doc:`dump <dump>`, or :doc:`restart <restart>` output
|
||||
|
||||
The :doc:`newton <newton>` command has two settings, one for pairwise
|
||||
interactions, the other for bonded. Both settings are stored in the
|
||||
restart file. For the bond setting, the value in the file will
|
||||
overwrite the current value (at the time the read_restart command is
|
||||
issued) and warn if the two values are not the same and the current
|
||||
value is not the default. For the pair setting, the value in the file
|
||||
will not overwrite the current value (so that you can override the
|
||||
previous run's value), but a warning is issued if the two values are
|
||||
not the same and the current value is not the default.
|
||||
|
||||
Note that some force field styles (pair, bond, angle, etc) do not
|
||||
store their coefficient info in restart files. Typically these are
|
||||
many-body or tabulated potentials which read their parameters from
|
||||
|
|
|
|||
|
|
@ -332,7 +332,8 @@ of <a class="reference internal" href="Section_commands.html#cmd-5"><span class=
|
|||
<li><a class="reference internal" href="fix_nvt_sllod.html"><span class="doc">nvt/sllod</span></a> - NVT for NEMD with SLLOD equations</li>
|
||||
<li><a class="reference internal" href="fix_nvt_sphere.html"><span class="doc">nvt/sphere</span></a> - NVT for spherical particles</li>
|
||||
<li><a class="reference internal" href="fix_oneway.html"><span class="doc">oneway</span></a> - constrain particles on move in one direction</li>
|
||||
<li><a class="reference internal" href="fix_orient_fcc.html"><span class="doc">orient/fcc</span></a> - add grain boundary migration force</li>
|
||||
<li><a class="reference internal" href="fix_orient.html"><span class="doc">orient/bcc</span></a> - add grain boundary migration force for BCC</li>
|
||||
<li><a class="reference internal" href="fix_orient.html"><span class="doc">orient/fcc</span></a> - add grain boundary migration force for FCC</li>
|
||||
<li><a class="reference internal" href="fix_planeforce.html"><span class="doc">planeforce</span></a> - constrain atoms to move in a plane</li>
|
||||
<li><a class="reference internal" href="fix_poems.html"><span class="doc">poems</span></a> - constrain clusters of atoms to move as coupled rigid bodies</li>
|
||||
<li><a class="reference internal" href="fix_pour.html"><span class="doc">pour</span></a> - pour new atoms/molecules into a granular simulation domain</li>
|
||||
|
|
|
|||
|
|
@ -126,14 +126,18 @@
|
|||
|
||||
<div class="section" id="fix-orient-fcc-command">
|
||||
<span id="index-0"></span><h1>fix orient/fcc command</h1>
|
||||
</div>
|
||||
<div class="section" id="fix-orient-bcc-command">
|
||||
<h1>fix orient/bcc command</h1>
|
||||
<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">orient</span><span class="o">/</span><span class="n">fcc</span> <span class="n">nstats</span> <span class="nb">dir</span> <span class="n">alat</span> <span class="n">dE</span> <span class="n">cutlo</span> <span class="n">cuthi</span> <span class="n">file0</span> <span class="n">file1</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">orient</span><span class="o">/</span><span class="n">bcc</span> <span class="n">nstats</span> <span class="nb">dir</span> <span class="n">alat</span> <span class="n">dE</span> <span class="n">cutlo</span> <span class="n">cuthi</span> <span class="n">file0</span> <span class="n">file1</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>nstats = print stats every this many steps, 0 = never</li>
|
||||
<li>dir = 0/1 for which crystal is used as reference</li>
|
||||
<li>alat = fcc cubic lattice constant (distance units)</li>
|
||||
<li>alat = fcc/bcc cubic lattice constant (distance units)</li>
|
||||
<li>dE = energy added to each atom (energy units)</li>
|
||||
<li>cutlo,cuthi = values between 0.0 and 1.0, cutlo < cuthi</li>
|
||||
<li>file0,file1 = files that specify orientation of each grain</li>
|
||||
|
|
@ -141,6 +145,7 @@
|
|||
<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="n">gb</span> <span class="nb">all</span> <span class="n">orient</span><span class="o">/</span><span class="n">fcc</span> <span class="mi">0</span> <span class="mi">1</span> <span class="mf">4.032008</span> <span class="mf">0.001</span> <span class="mf">0.25</span> <span class="mf">0.75</span> <span class="n">xi</span><span class="o">.</span><span class="n">vec</span> <span class="n">chi</span><span class="o">.</span><span class="n">vec</span>
|
||||
<span class="n">fix</span> <span class="n">gb</span> <span class="nb">all</span> <span class="n">orient</span><span class="o">/</span><span class="n">bcc</span> <span class="mi">0</span> <span class="mi">1</span> <span class="mf">2.882</span> <span class="mf">0.001</span> <span class="mf">0.25</span> <span class="mf">0.75</span> <span class="n">ngb</span><span class="o">.</span><span class="n">left</span> <span class="n">ngb</span><span class="o">.</span><span class="n">right</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
|
|
@ -150,8 +155,9 @@
|
|||
grain boundary which can be used to induce grain boundary migration
|
||||
(in the direction perpendicular to the grain boundary plane). The
|
||||
motivation and explanation of this force and its application are
|
||||
described in <a class="reference internal" href="#janssens"><span class="std std-ref">(Janssens)</span></a>. The force is only applied to
|
||||
atoms in the fix group.</p>
|
||||
described in <a class="reference internal" href="fix_orient_fcc.html#janssens"><span class="std std-ref">(Janssens)</span></a>. The adaptiation to bcc crystals
|
||||
is described in <a class="reference internal" href="#wicaksono1"><span class="std std-ref">(Wicaksono1)</span></a>. The computed force is only
|
||||
applied to atoms in the fix group.</p>
|
||||
<p>The basic idea is that atoms in one grain (on one side of the
|
||||
boundary) have a potential energy dE added to them. Atoms in the
|
||||
other grain have 0.0 potential energy added. Atoms near the boundary
|
||||
|
|
@ -169,19 +175,21 @@ system can displace during the simulation, and such motion should be
|
|||
accounted for in measuring the grain boundary velocity.</p>
|
||||
<p>The potential energy added to atom I is given by these formulas</p>
|
||||
<img alt="_images/fix_orient_fcc.jpg" class="align-center" src="_images/fix_orient_fcc.jpg" />
|
||||
<p>which are fully explained in <a class="reference internal" href="#janssens"><span class="std std-ref">(Janssens)</span></a>. The order
|
||||
parameter Xi for atom I in equation (1) is a sum over the 12 nearest
|
||||
neighbors of atom I. Rj is the vector from atom I to its neighbor J,
|
||||
and RIj is a vector in the reference (perfect) crystal. That is, if
|
||||
dir = 0/1, then RIj is a vector to an atom coord from file 0/1.
|
||||
Equation (2) gives the expected value of the order parameter XiIJ in
|
||||
the other grain. Hi and lo cutoffs are defined in equations (3) and
|
||||
(4), using the input parameters <em>cutlo</em> and <em>cuthi</em> as thresholds to
|
||||
avoid adding grain boundary energy when the deviation in the order
|
||||
parameter from 0 or 1 is small (e.g. due to thermal fluctuations in a
|
||||
perfect crystal). The added potential energy Ui for atom I is given
|
||||
in equation (6) where it is interpolated between 0 and dE using the
|
||||
two threshold Xi values and the Wi value of equation (5).</p>
|
||||
<p>which are fully explained in <a class="reference internal" href="fix_orient_fcc.html#janssens"><span class="std std-ref">(Janssens)</span></a>. For fcc crystals
|
||||
this order parameter Xi for atom I in equation (1) is a sum over the
|
||||
12 nearest neighbors of atom I. For bcc crystals it is the
|
||||
corresponding sum of the 8 nearest neighbors. Rj is the vector from
|
||||
atom I to its neighbor J, and RIj is a vector in the reference
|
||||
(perfect) crystal. That is, if dir = 0/1, then RIj is a vector to an
|
||||
atom coord from file 0/1. Equation (2) gives the expected value of
|
||||
the order parameter XiIJ in the other grain. Hi and lo cutoffs are
|
||||
defined in equations (3) and (4), using the input parameters <em>cutlo</em>
|
||||
and <em>cuthi</em> as thresholds to avoid adding grain boundary energy when
|
||||
the deviation in the order parameter from 0 or 1 is small (e.g. due to
|
||||
thermal fluctuations in a perfect crystal). The added potential
|
||||
energy Ui for atom I is given in equation (6) where it is interpolated
|
||||
between 0 and dE using the two threshold Xi values and the Wi value of
|
||||
equation (5).</p>
|
||||
<p>The derivative of this energy expression gives the force on each atom
|
||||
which thus depends on the orientation of its neighbors relative to the
|
||||
2 grain orientations. Only atoms near the grain boundary feel a net
|
||||
|
|
@ -196,14 +204,14 @@ effect of duplicate reference vector usage is small.</p>
|
|||
expense of the other. A value of 0 means the first grain will shrink;
|
||||
a value of 1 means it will grow. This assumes that <em>dE</em> is positive.
|
||||
The reverse will be true if <em>dE</em> is negative.</p>
|
||||
<p>The <em>alat</em> parameter is the cubic lattice constant for the fcc
|
||||
<p>The <em>alat</em> parameter is the cubic lattice constant for the fcc or bcc
|
||||
material and is only used to compute a cutoff distance of 1.57 * alat
|
||||
/ sqrt(2) for finding the 12 nearest neighbors of each atom (which
|
||||
should be valid for an fcc crystal). A longer/shorter cutoff can be
|
||||
imposed by adjusting <em>alat</em>. If a particular atom has less than 12
|
||||
neighbors within the cutoff, the order parameter of equation (1) is
|
||||
effectively multiplied by 12 divided by the actual number of neighbors
|
||||
within the cutoff.</p>
|
||||
/ sqrt(2) for finding the 12 or 8 nearest neighbors of each atom
|
||||
(which should be valid for an fcc or bcc crystal). A longer/shorter
|
||||
cutoff can be imposed by adjusting <em>alat</em>. If a particular atom has
|
||||
less than 12 or 8 neighbors within the cutoff, the order parameter of
|
||||
equation (1) is effectively multiplied by 12 or 8 divided by the
|
||||
actual number of neighbors within the cutoff.</p>
|
||||
<p>The <em>dE</em> parameter is the maximum amount of additional energy added to
|
||||
each atom in the grain which wants to shrink.</p>
|
||||
<p>The <em>cutlo</em> and <em>cuthi</em> parameters are used to reduce the force added
|
||||
|
|
@ -222,7 +230,8 @@ orientation. The vector lengths should all be identical since an fcc
|
|||
lattice has a coordination number of 12. Only 6 are listed due to
|
||||
symmetry, so the list must include one from each pair of
|
||||
equal-and-opposite neighbors. A pair of orientation files for a
|
||||
Sigma=5 tilt boundary are show below.</p>
|
||||
Sigma=5 tilt boundary are shown below. A tutorial that can help for
|
||||
writing the orientation files is given in <a class="reference internal" href="#wicaksono2"><span class="std std-ref">(Wicaksono2)</span></a></p>
|
||||
</div>
|
||||
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
|
||||
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
|
||||
|
|
@ -246,7 +255,7 @@ the <a class="reference internal" href="run.html"><span class="doc">run</span></
|
|||
<h2>Restrictions</h2>
|
||||
<p>This fix is part of the MISC package. It is only enabled if LAMMPS
|
||||
was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
|
||||
<p>This fix should only be used with fcc lattices.</p>
|
||||
<p>This fix should only be used with fcc or bcc lattices.</p>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
|
|
@ -255,6 +264,10 @@ was built with that package. See the <a class="reference internal" href="Sectio
|
|||
<hr class="docutils" />
|
||||
<p id="janssens"><strong>(Janssens)</strong> Janssens, Olmsted, Holm, Foiles, Plimpton, Derlet, Nature
|
||||
Materials, 5, 124-127 (2006).</p>
|
||||
<p id="wicaksono1"><strong>(Wicaksono1)</strong> Wicaksono, Sinclair, Militzer, Computational Materials
|
||||
Science, 117, 397-405 (2016).</p>
|
||||
<p id="wicaksono2"><strong>(Wicaksono2)</strong> Wicaksono, figshare,
|
||||
<a class="reference external" href="https://dx.doi.org/10.6084/m9.figshare.1488628.v1">https://dx.doi.org/10.6084/m9.figshare.1488628.v1</a> (2015).</p>
|
||||
<hr class="docutils" />
|
||||
<p>For illustration purposes, here are example files that specify a
|
||||
Sigma=5 <100> tilt boundary. This is for a lattice constant of 3.5706
|
||||
|
|
|
|||
|
|
@ -1292,7 +1292,7 @@
|
|||
</dt>
|
||||
|
||||
|
||||
<dt><a href="fix_orient_fcc.html#index-0">fix orient/fcc</a>
|
||||
<dt><a href="fix_orient.html#index-0">fix orient/fcc</a>, <a href="fix_orient_fcc.html#index-0">[1]</a>
|
||||
</dt>
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -295,6 +295,15 @@ approximation in not needed). The <em>slab</em> keyword is not currently
|
|||
supported by Ewald or PPPM when using a triclinic simulation cell. The
|
||||
slab correction has also been extended to point dipole interactions
|
||||
<a class="reference internal" href="#klapp"><span class="std std-ref">(Klapp)</span></a> in <a class="reference internal" href="kspace_style.html"><span class="doc">kspace_style</span></a> <em>ewald/disp</em>.</p>
|
||||
<div class="admonition note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">If you wish to apply an electric field in the Z-direction, in
|
||||
conjunction with the <em>slab</em> keyword, you should do it by adding
|
||||
explicit charged particles to the +/- Z surfaces. If you do it via
|
||||
the <a class="reference internal" href="fix_efield.html"><span class="doc">fix efield</span></a> command, it will not give the correct
|
||||
dielectric constant due to the Yeh/Berkowitz <a class="reference internal" href="#yeh"><span class="std std-ref">(Yeh)</span></a> correction
|
||||
not being compatible with how <a class="reference internal" href="fix_efield.html"><span class="doc">fix efield</span></a> works.</p>
|
||||
</div>
|
||||
<p>The <em>compute</em> keyword allows Kspace computations to be turned off,
|
||||
even though a <a class="reference internal" href="kspace_style.html"><span class="doc">kspace_style</span></a> is defined. This is
|
||||
not useful for running a real simulation, but can be useful for
|
||||
|
|
@ -309,7 +318,7 @@ beginning of the run to give the desired estimated error. Other
|
|||
cutoffs such as LJ will not be affected. If the grid is not set using
|
||||
the <em>mesh</em> command, this command will also attempt to use the optimal
|
||||
grid that minimizes cost using an estimate given by
|
||||
<a class="reference internal" href="kspace_style.html#hardy"><span class="std std-ref">(Hardy)</span></a>. Note that this cost estimate is not exact, somewhat
|
||||
<a class="reference internal" href="#hardy"><span class="std std-ref">(Hardy)</span></a>. Note that this cost estimate is not exact, somewhat
|
||||
experimental, and still may not yield the optimal parameters.</p>
|
||||
<p>The <em>pressure/scalar</em> keyword applies only to MSM. If this option is
|
||||
turned on, only the scalar pressure (i.e. (Pxx + Pyy + Pzz)/3.0) will
|
||||
|
|
@ -334,7 +343,7 @@ collective operations and adequate hardware.</p>
|
|||
<p>The <em>diff</em> keyword specifies the differentiation scheme used by the
|
||||
PPPM method to compute forces on particles given electrostatic
|
||||
potentials on the PPPM mesh. The <em>ik</em> approach is the default for
|
||||
PPPM and is the original formulation used in <a class="reference internal" href="kspace_style.html#hockney"><span class="std std-ref">(Hockney)</span></a>. It
|
||||
PPPM and is the original formulation used in <a class="reference internal" href="#hockney"><span class="std std-ref">(Hockney)</span></a>. It
|
||||
performs differentiation in Kspace, and uses 3 FFTs to transfer each
|
||||
component of the computed fields back to real space for total of 4
|
||||
FFTs per timestep.</p>
|
||||
|
|
@ -369,7 +378,7 @@ speed-up the simulations but introduces some error in the force
|
|||
computations, as shown in <a class="reference internal" href="#wennberg"><span class="std std-ref">(Wennberg)</span></a>. With <em>none</em>, it is
|
||||
assumed that no mixing rule is applicable. Splitting of the dispersion
|
||||
coefficients will be performed as described in
|
||||
<a class="reference internal" href="kspace_style.html#isele-holder"><span class="std std-ref">(Isele-Holder)</span></a>. This splitting can be influenced with
|
||||
<a class="reference internal" href="#isele-holder"><span class="std std-ref">(Isele-Holder)</span></a>. This splitting can be influenced with
|
||||
the <em>splittol</em> keywords. Only the eigenvalues that are larger than tol
|
||||
compared to the largest eigenvalues are included. Using this keywords
|
||||
the original matrix of dispersion coefficients is approximated. This
|
||||
|
|
@ -377,7 +386,7 @@ leads to faster computations, but the accuracy in the reciprocal space
|
|||
computations of the dispersion part is decreased.</p>
|
||||
<p>The <em>force/disp/real</em> and <em>force/disp/kspace</em> keywords set the force
|
||||
accuracy for the real and space computations for the dispersion part
|
||||
of pppm/disp. As shown in <a class="reference internal" href="kspace_style.html#isele-holder"><span class="std std-ref">(Isele-Holder)</span></a>, optimal
|
||||
of pppm/disp. As shown in <a class="reference internal" href="#isele-holder"><span class="std std-ref">(Isele-Holder)</span></a>, optimal
|
||||
performance and accuracy in the results is obtained when these values
|
||||
are different.</p>
|
||||
<p>The <em>disp/auto</em> option controlls whether the pppm/disp is allowed to
|
||||
|
|
|
|||
|
|
@ -1188,7 +1188,7 @@ script.</p>
|
|||
<p><em>Triangles</em> section:</p>
|
||||
<ul class="simple">
|
||||
<li>one line per triangle</li>
|
||||
<li>line syntax: atom-ID x1 y1 x2 y2</li>
|
||||
<li>line syntax: atom-ID x1 y1 z1 x2 y2 z2 x3 y3 z3</li>
|
||||
</ul>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">atom</span><span class="o">-</span><span class="n">ID</span> <span class="o">=</span> <span class="n">ID</span> <span class="n">of</span> <span class="n">atom</span> <span class="n">which</span> <span class="ow">is</span> <span class="n">a</span> <span class="n">line</span> <span class="n">segment</span>
|
||||
<span class="n">x1</span><span class="p">,</span><span class="n">y1</span><span class="p">,</span><span class="n">z1</span> <span class="o">=</span> <span class="mi">1</span><span class="n">st</span> <span class="n">corner</span> <span class="n">point</span>
|
||||
|
|
|
|||
|
|
@ -249,6 +249,7 @@ script that reads the restart file, though you can redefine many of
|
|||
these settings after the restart file is read.</p>
|
||||
<ul class="simple">
|
||||
<li><a class="reference internal" href="units.html"><span class="doc">units</span></a></li>
|
||||
<li><a class="reference internal" href="newton.html"><span class="doc">newton bond</span></a> (see discussion of newton command below)</li>
|
||||
<li><a class="reference internal" href="atom_style.html"><span class="doc">atom style</span></a> and <a class="reference internal" href="atom_modify.html"><span class="doc">atom_modify</span></a> settings id, map, sort</li>
|
||||
<li><a class="reference internal" href="comm_style.html"><span class="doc">comm style</span></a> and <a class="reference external" href="comm_modify">comm_modify</a> settings mode, cutoff, vel</li>
|
||||
<li><a class="reference internal" href="timestep.html"><span class="doc">timestep</span></a></li>
|
||||
|
|
@ -265,6 +266,7 @@ these settings after the restart file is read.</p>
|
|||
means you must re-issue these commands in your input script, after
|
||||
reading the restart file.</p>
|
||||
<ul class="simple">
|
||||
<li><a class="reference internal" href="newton.html"><span class="doc">newton pair</span></a> (see discussion of newton command below)</li>
|
||||
<li><a class="reference internal" href="fix.html"><span class="doc">fix</span></a> commands (see below)</li>
|
||||
<li><a class="reference internal" href="compute.html"><span class="doc">compute</span></a> commands (see below)</li>
|
||||
<li><a class="reference internal" href="variable.html"><span class="doc">variable</span></a> commands</li>
|
||||
|
|
@ -273,6 +275,15 @@ reading the restart file.</p>
|
|||
<li><a class="reference internal" href="kspace_style.html"><span class="doc">kspace_style</span></a> and <a class="reference internal" href="kspace_modify.html"><span class="doc">kspace_modify</span></a> settings</li>
|
||||
<li>info for <a class="reference internal" href="thermo_style.html"><span class="doc">thermodynamic</span></a>, <a class="reference internal" href="dump.html"><span class="doc">dump</span></a>, or <a class="reference internal" href="restart.html"><span class="doc">restart</span></a> output</li>
|
||||
</ul>
|
||||
<p>The <a class="reference internal" href="newton.html"><span class="doc">newton</span></a> command has two settings, one for pairwise
|
||||
interactions, the other for bonded. Both settings are stored in the
|
||||
restart file. For the bond setting, the value in the file will
|
||||
overwrite the current value (at the time the read_restart command is
|
||||
issued) and warn if the two values are not the same and the current
|
||||
value is not the default. For the pair setting, the value in the file
|
||||
will not overwrite the current value (so that you can override the
|
||||
previous run’s value), but a warning is issued if the two values are
|
||||
not the same and the current value is not the default.</p>
|
||||
<p>Note that some force field styles (pair, bond, angle, etc) do not
|
||||
store their coefficient info in restart files. Typically these are
|
||||
many-body or tabulated potentials which read their parameters from
|
||||
|
|
|
|||
File diff suppressed because one or more lines are too long
|
|
@ -546,7 +546,8 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
|
|||
"nvt/sllod (io)"_fix_nvt_sllod.html,
|
||||
"nvt/sphere (o)"_fix_nvt_sphere.html,
|
||||
"oneway"_fix_oneway.html,
|
||||
"orient/fcc"_fix_orient_fcc.html,
|
||||
"orient/bcc"_fix_orient.html,
|
||||
"orient/fcc"_fix_orient.html,
|
||||
"planeforce"_fix_planeforce.html,
|
||||
"poems"_fix_poems.html,
|
||||
"pour"_fix_pour.html,
|
||||
|
|
|
|||
|
|
@ -221,7 +221,8 @@ of "this page"_Section_commands.html#cmd_5.
|
|||
"nvt/sllod"_fix_nvt_sllod.html - NVT for NEMD with SLLOD equations
|
||||
"nvt/sphere"_fix_nvt_sphere.html - NVT for spherical particles
|
||||
"oneway"_fix_oneway.html - constrain particles on move in one direction
|
||||
"orient/fcc"_fix_orient_fcc.html - add grain boundary migration force
|
||||
"orient/bcc"_fix_orient.html - add grain boundary migration force for BCC
|
||||
"orient/fcc"_fix_orient.html - add grain boundary migration force for FCC
|
||||
"planeforce"_fix_planeforce.html - constrain atoms to move in a plane
|
||||
"poems"_fix_poems.html - constrain clusters of atoms to move \
|
||||
as coupled rigid bodies
|
||||
|
|
|
|||
|
|
@ -7,20 +7,23 @@
|
|||
:line
|
||||
|
||||
fix orient/fcc command :h3
|
||||
fix orient/bcc command :h3
|
||||
|
||||
fix ID group-ID orient/fcc nstats dir alat dE cutlo cuthi file0 file1 :pre
|
||||
fix ID group-ID orient/fcc nstats dir alat dE cutlo cuthi file0 file1
|
||||
fix ID group-ID orient/bcc nstats dir alat dE cutlo cuthi file0 file1 :pre
|
||||
|
||||
ID, group-ID are documented in "fix"_fix.html command
|
||||
nstats = print stats every this many steps, 0 = never
|
||||
dir = 0/1 for which crystal is used as reference
|
||||
alat = fcc cubic lattice constant (distance units)
|
||||
alat = fcc/bcc cubic lattice constant (distance units)
|
||||
dE = energy added to each atom (energy units)
|
||||
cutlo,cuthi = values between 0.0 and 1.0, cutlo < cuthi
|
||||
file0,file1 = files that specify orientation of each grain :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix gb all orient/fcc 0 1 4.032008 0.001 0.25 0.75 xi.vec chi.vec :pre
|
||||
fix gb all orient/fcc 0 1 4.032008 0.001 0.25 0.75 xi.vec chi.vec
|
||||
fix gb all orient/bcc 0 1 2.882 0.001 0.25 0.75 ngb.left ngb.right :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
|
|
@ -28,8 +31,9 @@ The fix applies an orientation-dependent force to atoms near a planar
|
|||
grain boundary which can be used to induce grain boundary migration
|
||||
(in the direction perpendicular to the grain boundary plane). The
|
||||
motivation and explanation of this force and its application are
|
||||
described in "(Janssens)"_#Janssens. The force is only applied to
|
||||
atoms in the fix group.
|
||||
described in "(Janssens)"_#Janssens. The adaptiation to bcc crystals
|
||||
is described in "(Wicaksono1)"_#Wicaksono1. The computed force is only
|
||||
applied to atoms in the fix group.
|
||||
|
||||
The basic idea is that atoms in one grain (on one side of the
|
||||
boundary) have a potential energy dE added to them. Atoms in the
|
||||
|
|
@ -51,19 +55,21 @@ The potential energy added to atom I is given by these formulas
|
|||
|
||||
:c,image(Eqs/fix_orient_fcc.jpg)
|
||||
|
||||
which are fully explained in "(Janssens)"_#Janssens. The order
|
||||
parameter Xi for atom I in equation (1) is a sum over the 12 nearest
|
||||
neighbors of atom I. Rj is the vector from atom I to its neighbor J,
|
||||
and RIj is a vector in the reference (perfect) crystal. That is, if
|
||||
dir = 0/1, then RIj is a vector to an atom coord from file 0/1.
|
||||
Equation (2) gives the expected value of the order parameter XiIJ in
|
||||
the other grain. Hi and lo cutoffs are defined in equations (3) and
|
||||
(4), using the input parameters {cutlo} and {cuthi} as thresholds to
|
||||
avoid adding grain boundary energy when the deviation in the order
|
||||
parameter from 0 or 1 is small (e.g. due to thermal fluctuations in a
|
||||
perfect crystal). The added potential energy Ui for atom I is given
|
||||
in equation (6) where it is interpolated between 0 and dE using the
|
||||
two threshold Xi values and the Wi value of equation (5).
|
||||
which are fully explained in "(Janssens)"_#Janssens. For fcc crystals
|
||||
this order parameter Xi for atom I in equation (1) is a sum over the
|
||||
12 nearest neighbors of atom I. For bcc crystals it is the
|
||||
corresponding sum of the 8 nearest neighbors. Rj is the vector from
|
||||
atom I to its neighbor J, and RIj is a vector in the reference
|
||||
(perfect) crystal. That is, if dir = 0/1, then RIj is a vector to an
|
||||
atom coord from file 0/1. Equation (2) gives the expected value of
|
||||
the order parameter XiIJ in the other grain. Hi and lo cutoffs are
|
||||
defined in equations (3) and (4), using the input parameters {cutlo}
|
||||
and {cuthi} as thresholds to avoid adding grain boundary energy when
|
||||
the deviation in the order parameter from 0 or 1 is small (e.g. due to
|
||||
thermal fluctuations in a perfect crystal). The added potential
|
||||
energy Ui for atom I is given in equation (6) where it is interpolated
|
||||
between 0 and dE using the two threshold Xi values and the Wi value of
|
||||
equation (5).
|
||||
|
||||
The derivative of this energy expression gives the force on each atom
|
||||
which thus depends on the orientation of its neighbors relative to the
|
||||
|
|
@ -82,14 +88,14 @@ expense of the other. A value of 0 means the first grain will shrink;
|
|||
a value of 1 means it will grow. This assumes that {dE} is positive.
|
||||
The reverse will be true if {dE} is negative.
|
||||
|
||||
The {alat} parameter is the cubic lattice constant for the fcc
|
||||
The {alat} parameter is the cubic lattice constant for the fcc or bcc
|
||||
material and is only used to compute a cutoff distance of 1.57 * alat
|
||||
/ sqrt(2) for finding the 12 nearest neighbors of each atom (which
|
||||
should be valid for an fcc crystal). A longer/shorter cutoff can be
|
||||
imposed by adjusting {alat}. If a particular atom has less than 12
|
||||
neighbors within the cutoff, the order parameter of equation (1) is
|
||||
effectively multiplied by 12 divided by the actual number of neighbors
|
||||
within the cutoff.
|
||||
/ sqrt(2) for finding the 12 or 8 nearest neighbors of each atom
|
||||
(which should be valid for an fcc or bcc crystal). A longer/shorter
|
||||
cutoff can be imposed by adjusting {alat}. If a particular atom has
|
||||
less than 12 or 8 neighbors within the cutoff, the order parameter of
|
||||
equation (1) is effectively multiplied by 12 or 8 divided by the
|
||||
actual number of neighbors within the cutoff.
|
||||
|
||||
The {dE} parameter is the maximum amount of additional energy added to
|
||||
each atom in the grain which wants to shrink.
|
||||
|
|
@ -111,7 +117,8 @@ orientation. The vector lengths should all be identical since an fcc
|
|||
lattice has a coordination number of 12. Only 6 are listed due to
|
||||
symmetry, so the list must include one from each pair of
|
||||
equal-and-opposite neighbors. A pair of orientation files for a
|
||||
Sigma=5 tilt boundary are show below.
|
||||
Sigma=5 tilt boundary are shown below. A tutorial that can help for
|
||||
writing the orientation files is given in "(Wicaksono2)"_#Wicaksono2
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
|
|
@ -143,7 +150,7 @@ This fix is part of the MISC package. It is only enabled if LAMMPS
|
|||
was built with that package. See the "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
This fix should only be used with fcc lattices.
|
||||
This fix should only be used with fcc or bcc lattices.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
|
|
@ -157,6 +164,14 @@ This fix should only be used with fcc lattices.
|
|||
[(Janssens)] Janssens, Olmsted, Holm, Foiles, Plimpton, Derlet, Nature
|
||||
Materials, 5, 124-127 (2006).
|
||||
|
||||
:link(Wicaksono1)
|
||||
[(Wicaksono1)] Wicaksono, Sinclair, Militzer, Computational Materials
|
||||
Science, 117, 397-405 (2016).
|
||||
|
||||
:link(Wicaksono2)
|
||||
[(Wicaksono2)] Wicaksono, figshare,
|
||||
https://dx.doi.org/10.6084/m9.figshare.1488628.v1 (2015).
|
||||
|
||||
:line
|
||||
|
||||
For illustration purposes, here are example files that specify a
|
||||
|
|
@ -184,6 +184,13 @@ supported by Ewald or PPPM when using a triclinic simulation cell. The
|
|||
slab correction has also been extended to point dipole interactions
|
||||
"(Klapp)"_#Klapp in "kspace_style"_kspace_style.html {ewald/disp}.
|
||||
|
||||
NOTE: If you wish to apply an electric field in the Z-direction, in
|
||||
conjunction with the {slab} keyword, you should do it by adding
|
||||
explicit charged particles to the +/- Z surfaces. If you do it via
|
||||
the "fix efield"_fix_efield.html command, it will not give the correct
|
||||
dielectric constant due to the Yeh/Berkowitz "(Yeh)"_#Yeh correction
|
||||
not being compatible with how "fix efield"_fix_efield.html works.
|
||||
|
||||
The {compute} keyword allows Kspace computations to be turned off,
|
||||
even though a "kspace_style"_kspace_style.html is defined. This is
|
||||
not useful for running a real simulation, but can be useful for
|
||||
|
|
|
|||
|
|
@ -1044,7 +1044,7 @@ script.
|
|||
{Triangles} section:
|
||||
|
||||
one line per triangle :ulb,l
|
||||
line syntax: atom-ID x1 y1 x2 y2 :l
|
||||
line syntax: atom-ID x1 y1 z1 x2 y2 z2 x3 y3 z3 :l
|
||||
atom-ID = ID of atom which is a line segment
|
||||
x1,y1,z1 = 1st corner point
|
||||
x2,y2,z2 = 2nd corner point
|
||||
|
|
|
|||
|
|
@ -141,6 +141,7 @@ script that reads the restart file, though you can redefine many of
|
|||
these settings after the restart file is read.
|
||||
|
||||
"units"_units.html
|
||||
"newton bond"_newton.html (see discussion of newton command below)
|
||||
"atom style"_atom_style.html and "atom_modify"_atom_modify.html settings id, map, sort
|
||||
"comm style"_comm_style.html and "comm_modify"_comm_modify settings mode, cutoff, vel
|
||||
"timestep"_timestep.html
|
||||
|
|
@ -157,6 +158,7 @@ Here is a list of information not stored in a restart file, which
|
|||
means you must re-issue these commands in your input script, after
|
||||
reading the restart file.
|
||||
|
||||
"newton pair"_newton.html (see discussion of newton command below)
|
||||
"fix"_fix.html commands (see below)
|
||||
"compute"_compute.html commands (see below)
|
||||
"variable"_variable.html commands
|
||||
|
|
@ -165,6 +167,16 @@ reading the restart file.
|
|||
"kspace_style"_kspace_style.html and "kspace_modify"_kspace_modify.html settings
|
||||
info for "thermodynamic"_thermo_style.html, "dump"_dump.html, or "restart"_restart.html output :ul
|
||||
|
||||
The "newton"_newton.html command has two settings, one for pairwise
|
||||
interactions, the other for bonded. Both settings are stored in the
|
||||
restart file. For the bond setting, the value in the file will
|
||||
overwrite the current value (at the time the read_restart command is
|
||||
issued) and warn if the two values are not the same and the current
|
||||
value is not the default. For the pair setting, the value in the file
|
||||
will not overwrite the current value (so that you can override the
|
||||
previous run's value), but a warning is issued if the two values are
|
||||
not the same and the current value is not the default.
|
||||
|
||||
Note that some force field styles (pair, bond, angle, etc) do not
|
||||
store their coefficient info in restart files. Typically these are
|
||||
many-body or tabulated potentials which read their parameters from
|
||||
|
|
|
|||
Loading…
Reference in New Issue