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@ -1183,9 +1183,9 @@ if <a class="reference internal" href="Section_start.html#start-3"><span class="
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<table border="1" class="docutils">
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<colgroup>
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<col width="21%" />
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<col width="24%" />
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<col width="25%" />
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<col width="31%" />
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<col width="24%" />
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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="pair_awpmd.html"><span class="doc">awpmd/cut</span></a></td>
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@ -1224,29 +1224,29 @@ if <a class="reference internal" href="Section_start.html#start-3"><span class="
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<td><a class="reference internal" href="pair_mgpt.html"><span class="doc">mgpt</span></a></td>
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</tr>
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<tr class="row-even"><td><a class="reference internal" href="pair_morse.html"><span class="doc">morse/smooth/linear</span></a></td>
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<td><a class="reference internal" href="pair_morse.html"><span class="doc">morse/soft</span></a></td>
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<td><a class="reference internal" href="pair_multi_lucy.html"><span class="doc">multi/lucy</span></a></td>
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<td><a class="reference internal" href="pair_quip.html"><span class="doc">quip</span></a></td>
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<td><a class="reference internal" href="pair_reax_c.html"><span class="doc">reax/c</span></a></td>
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</tr>
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<tr class="row-odd"><td><a class="reference internal" href="pair_smd_hertz.html"><span class="doc">smd/hertz</span></a></td>
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<tr class="row-odd"><td><a class="reference internal" href="pair_reax_c.html"><span class="doc">reax/c</span></a></td>
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<td><a class="reference internal" href="pair_smd_hertz.html"><span class="doc">smd/hertz</span></a></td>
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<td><a class="reference internal" href="pair_smd_tlsph.html"><span class="doc">smd/tlsph</span></a></td>
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<td><a class="reference internal" href="pair_smd_triangulated_surface.html"><span class="doc">smd/triangulated/surface</span></a></td>
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<td><a class="reference internal" href="pair_smd_ulsph.html"><span class="doc">smd/ulsph</span></a></td>
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</tr>
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<tr class="row-even"><td><a class="reference internal" href="pair_smtbq.html"><span class="doc">smtbq</span></a></td>
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<tr class="row-even"><td><a class="reference internal" href="pair_smd_ulsph.html"><span class="doc">smd/ulsph</span></a></td>
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<td><a class="reference internal" href="pair_smtbq.html"><span class="doc">smtbq</span></a></td>
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<td><a class="reference internal" href="pair_sph_heatconduction.html"><span class="doc">sph/heatconduction</span></a></td>
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<td><a class="reference internal" href="pair_sph_idealgas.html"><span class="doc">sph/idealgas</span></a></td>
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<td><a class="reference internal" href="pair_sph_lj.html"><span class="doc">sph/lj</span></a></td>
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</tr>
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<tr class="row-odd"><td><a class="reference internal" href="pair_sph_rhosum.html"><span class="doc">sph/rhosum</span></a></td>
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<tr class="row-odd"><td><a class="reference internal" href="pair_sph_lj.html"><span class="doc">sph/lj</span></a></td>
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<td><a class="reference internal" href="pair_sph_rhosum.html"><span class="doc">sph/rhosum</span></a></td>
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<td><a class="reference internal" href="pair_sph_taitwater.html"><span class="doc">sph/taitwater</span></a></td>
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<td><a class="reference internal" href="pair_sph_taitwater_morris.html"><span class="doc">sph/taitwater/morris</span></a></td>
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<td><a class="reference internal" href="pair_srp.html"><span class="doc">srp</span></a></td>
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</tr>
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<tr class="row-even"><td><a class="reference internal" href="pair_tersoff.html"><span class="doc">tersoff/table (o)</span></a></td>
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<tr class="row-even"><td><a class="reference internal" href="pair_srp.html"><span class="doc">srp</span></a></td>
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<td><a class="reference internal" href="pair_tersoff.html"><span class="doc">tersoff/table (o)</span></a></td>
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<td><a class="reference internal" href="pair_thole.html"><span class="doc">thole</span></a></td>
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<td><a class="reference internal" href="pair_lj_soft.html"><span class="doc">tip4p/long/soft (o)</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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@ -648,31 +648,31 @@ KOKKOS, o = USER-OMP, t = OPT.
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These are additional pair styles in USER packages, which can be used
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if :ref:`LAMMPS is built with the appropriate package <start_3>`.
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+--------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+--------------------------------------------------+
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| :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>` |
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+--------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+--------------------------------------------------+
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| :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>` |
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+--------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+--------------------------------------------------+
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| :doc:`edip (o) <pair_edip>` | :doc:`eff/cut <pair_eff>` | :doc:`gauss/cut <pair_gauss>` | :doc:`lennard/mdf <pair_mdf>` |
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+--------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+--------------------------------------------------+
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| :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>` |
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+--------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+--------------------------------------------------+
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| :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>` |
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+--------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+--------------------------------------------------+
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| :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>` |
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+--------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+--------------------------------------------------+
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| :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>` |
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+--------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+--------------------------------------------------+
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| :doc:`morse/smooth/linear <pair_morse>` | :doc:`multi/lucy <pair_multi_lucy>` | :doc:`quip <pair_quip>` | :doc:`reax/c <pair_reax_c>` |
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+--------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+--------------------------------------------------+
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| :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>` |
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+--------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+--------------------------------------------------+
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| :doc:`smtbq <pair_smtbq>` | :doc:`sph/heatconduction <pair_sph_heatconduction>` | :doc:`sph/idealgas <pair_sph_idealgas>` | :doc:`sph/lj <pair_sph_lj>` |
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+--------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+--------------------------------------------------+
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| :doc:`sph/rhosum <pair_sph_rhosum>` | :doc:`sph/taitwater <pair_sph_taitwater>` | :doc:`sph/taitwater/morris <pair_sph_taitwater_morris>` | :doc:`srp <pair_srp>` |
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+--------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+--------------------------------------------------+
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| :doc:`tersoff/table (o) <pair_tersoff>` | :doc:`thole <pair_thole>` | :doc:`tip4p/long/soft (o) <pair_lj_soft>` | |
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+--------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+--------------------------------------------------+
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+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
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| :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>` |
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+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
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| :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>` |
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+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
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| :doc:`edip (o) <pair_edip>` | :doc:`eff/cut <pair_eff>` | :doc:`gauss/cut <pair_gauss>` | :doc:`lennard/mdf <pair_mdf>` |
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+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
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| :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>` |
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+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
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| :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>` |
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+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
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| :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>` |
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+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
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| :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>` |
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+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
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| :doc:`morse/smooth/linear <pair_morse>` | :doc:`morse/soft <pair_morse>` | :doc:`multi/lucy <pair_multi_lucy>` | :doc:`quip <pair_quip>` |
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+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
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| :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>` |
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+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
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| :doc:`smd/ulsph <pair_smd_ulsph>` | :doc:`smtbq <pair_smtbq>` | :doc:`sph/heatconduction <pair_sph_heatconduction>` | :doc:`sph/idealgas <pair_sph_idealgas>` |
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+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
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| :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>` |
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+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
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| :doc:`srp <pair_srp>` | :doc:`tersoff/table (o) <pair_tersoff>` | :doc:`thole <pair_thole>` | :doc:`tip4p/long/soft (o) <pair_lj_soft>` |
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+--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+
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----------
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|
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@ -61,15 +61,15 @@ thermodynamic integration (FDTI) or Bennet's acceptance ratio method
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The potential energy of the system is decomposed in three terms: a
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background term corresponding to interaction sites whose parameters
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remain constant, a reference term *U*\ <sub>0</sub> corresponding to the
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remain constant, a reference term :math:`U_0` corresponding to the
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initial interactions of the atoms that will undergo perturbation, and
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a term *U*\ <sub>1</sub> corresponding to the final interactions of
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a term :math:`U_1` corresponding to the final interactions of
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these atoms:
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.. image:: Eqs/compute_fep_u.jpg
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:align: center
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A coupling parameter λ varying from 0 to 1 connects the
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A coupling parameter :math:`\lambda` varying from 0 to 1 connects the
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reference and perturbed systems:
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.. image:: Eqs/compute_fep_lambda.jpg
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@ -79,7 +79,7 @@ It is possible but not necessary that the coupling parameter (or a
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function thereof) appears as a multiplication factor of the potential
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energy. Therefore, this compute can apply perturbations to interaction
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parameters that are not directly proportional to the potential energy
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(e.g. σ in Lennard-Jones potentials).
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(e.g. :math:`\sigma` in Lennard-Jones potentials).
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This command can be combined with :doc:`fix adapt <fix_adapt>` to
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perform multistage free-energy perturbation calculations along
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@ -91,26 +91,26 @@ stepwise alchemical transformations during a simulation run:
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This compute is suitable for the finite-difference thermodynamic
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integration (FDTI) method :ref:`(Mezei) <Mezei>`, which is based on an
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evaluation of the numerical derivative of the free energy by a
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perturbation method using a very small δ:
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perturbation method using a very small :math:`\delta`:
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.. image:: Eqs/compute_fep_fdti.jpg
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:align: center
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where *w*\ <sub>i</sub> are weights of a numerical quadrature. The :doc:`fix adapt <fix_adapt>` command can be used to define the stages of
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λ at which the derivative is calculated and averaged.
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where :math:`w_i` are weights of a numerical quadrature. The :doc:`fix adapt <fix_adapt>` command can be used to define the stages of
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:math:`\lambda` at which the derivative is calculated and averaged.
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The compute fep calculates the exponential Boltzmann term and also the
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potential energy difference *U*\ <sub>1</sub>-\ *U*\ <sub>0</sub>. By
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choosing a very small perturbation δ the thermodynamic
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potential energy difference :math:`U_1 -U_0`. By
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choosing a very small perturbation :math:`\delta` the thermodynamic
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integration method can be implemented using a numerical evaluation of
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the derivative of the potential energy with respect to λ:
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the derivative of the potential energy with respect to :math:`\lambda`:
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.. image:: Eqs/compute_fep_ti.jpg
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:align: center
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Another technique to calculate free energy differences is the
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acceptance ratio method :ref:`(Bennet) <Bennet>`, which can be implemented
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by calculating the potential energy differences with δ = 1.0 on
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by calculating the potential energy differences with :math:`\delta` = 1.0 on
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both the forward and reverse routes:
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.. image:: Eqs/compute_fep_bar.jpg
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@ -241,12 +241,12 @@ trajectories during which the volume fluctuates or changes :ref:`(Allen and Tild
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**Output info:**
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This compute calculates a global vector of length 3 which contains the
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energy difference (\ *U*\ <sub>1</sub>-\ *U*\ <sub>0</sub>) as c_ID[1], the
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Boltzmann factor exp(-(\ *U*\ <sub>1</sub>-\ *U*\ <sub>0</sub>)/\ *kT*\ ), or
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*V*\ exp(-(\ *U*\ <sub>1</sub>-\ *U*\ <sub>0</sub>)/\ *kT*\ ), as c_ID[2] and the
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volume of the simulation box *V* as c_ID[3]. *U*\ <sub>1</sub> is the
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energy difference ( :math:`U_1-U_0` ) as c_ID[1], the
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Boltzmann factor :math:`\exp(-(U_1-U_0)/kT)`, or
|
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:math:`V \exp(-(U_1-U_0)/kT)`, as c_ID[2] and the
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volume of the simulation box :math:`V` as c_ID[3]. :math:`U_1` is the
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pair potential energy obtained with the perturbed parameters and
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*U*\ <sub>0</sub> is the pair potential energy obtained with the
|
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:math:`U_0` is the pair potential energy obtained with the
|
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unperturbed parameters. The energies include kspace terms if these
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are used in the simulation.
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|
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@ -44,12 +44,8 @@ Examples
|
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compute 2 precipitate voronoi/atom surface matrix
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compute 3b precipitate voronoi/atom radius v_r
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compute 4 solute voronoi/atom only_group
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|
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.. parsed-literal::
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compute 5 defects voronoi/atom occupation
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|
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compute 6 all voronoi/atom neighbors yes
|
||||
compute 6 all voronoi/atom neighbors yes
|
||||
|
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Description
|
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"""""""""""
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|
|
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@ -89,7 +89,7 @@ Restart, fix_modify, output, run start/stop, minimize info
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No information about the *rigid* and *rigid/nve* fixes are written to
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:doc:`binary restart files <restart>`.
|
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|
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Similar to the :doc:`fix rigid <fix_rigid>` command: " The rigid
|
||||
Similar to the :doc:`fix rigid <fix_rigid>` command: The rigid
|
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fix computes a global scalar which can be accessed by various :ref:`output commands <howto_15>`. The scalar value calculated by
|
||||
these fixes is "intensive". The scalar is the current temperature of
|
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the collection of rigid bodies. This is averaged over all rigid
|
||||
|
|
@ -99,9 +99,9 @@ mass of the body and v = the velocity of its center of mass. The
|
|||
rotational energy of a rigid body is 1/2 I w^2, where I = the moment
|
||||
of inertia tensor of the body and w = its angular velocity. Degrees
|
||||
of freedom constrained by the *force* and *torque* keywords are
|
||||
removed from this calculation."
|
||||
removed from this calculation.
|
||||
|
||||
"All of these fixes compute a global array of values which can be
|
||||
All of these fixes compute a global array of values which can be
|
||||
accessed by various :ref:`output commands <howto_15>`.
|
||||
The number of rows in the array is equal to the number of rigid
|
||||
bodies. The number of columns is 15. Thus for each rigid body, 15
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||||
|
|
@ -125,7 +125,7 @@ they are independent of the number of atoms in the simulation.
|
|||
|
||||
No parameter of these fixes can be used with the *start/stop* keywords
|
||||
of the :doc:`run <run>` command. These fixes are not invoked during
|
||||
:doc:`energy minimization <minimize>`. "
|
||||
:doc:`energy minimization <minimize>`.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
|
|
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|
|
@ -118,7 +118,7 @@ Windows:
|
|||
|
||||
.. parsed-literal::
|
||||
|
||||
% set LAMMPS_POTENTIALS="C:\Path to LAMMPS\Potentials"
|
||||
% set LAMMPS_POTENTIALS="C:\\Path to LAMMPS\\Potentials"
|
||||
|
||||
|
||||
----------
|
||||
|
|
|
|||
|
|
@ -18,24 +18,43 @@ pair_style morse/smooth/linear command
|
|||
pair_style morse/smooth/linear/omp command
|
||||
==========================================
|
||||
|
||||
pair_style morse/soft command
|
||||
=============================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
pair_style morse cutoff
|
||||
pair_style style args
|
||||
|
||||
* cutoff = global cutoff for Morse interactions (distance units)
|
||||
* style = *morse* or *morse/smooth/linear* or *morse/soft*
|
||||
* args = list of arguments for a particular style
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
*morse* args = cutoff
|
||||
cutoff = global cutoff for Morse interactions (distance units)
|
||||
*morse/smooth/linear* args = cutoff
|
||||
cutoff = global cutoff for Morse interactions (distance units)
|
||||
*morse/soft* args = n lf cutoff
|
||||
n = soft-core parameter
|
||||
lf = transformation range is lf < lambda < 1
|
||||
cutoff = global cutoff for Morse interactions (distance units)
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
pair_style morse 2.5
|
||||
pair_style morse/smooth/linear 2.5
|
||||
pair_coeff * * 100.0 2.0 1.5
|
||||
pair_coeff 1 1 100.0 2.0 1.5 3.0
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
pair_style morse 2.5
|
||||
pair_style morse/smooth/linear 2.5
|
||||
pair_coeff * * 100.0 2.0 1.5
|
||||
pair_coeff 1 1 100.0 2.0 1.5 3.0
|
||||
pair_style morse/soft 4 0.9 10.0
|
||||
pair_coeff * * 100.0 2.0 1.5 1.0
|
||||
pair_coeff 1 1 100.0 2.0 1.5 1.0 3.0
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
|
@ -58,16 +77,16 @@ commands:
|
|||
* r0 (distance units)
|
||||
* cutoff (distance units)
|
||||
|
||||
* The last coefficient is optional. If not specified, the global morse
|
||||
* cutoff is used.
|
||||
The last coefficient is optional. If not specified, the global morse
|
||||
cutoff is used.
|
||||
|
||||
|
||||
----------
|
||||
|
||||
|
||||
The *smooth/linear* variant is similar to the lj/smooth/linear variant
|
||||
in that it adds to the potential a shift and a linear term to make both
|
||||
the potential energy and force go to zero at the cut-off:
|
||||
The *morse/smooth/linear* variant is similar to the lj/smooth/linear
|
||||
variant in that it adds to the potential a shift and a linear term
|
||||
so that both, potential energy and force, go to zero at the cut-off:
|
||||
|
||||
.. image:: Eqs/pair_morse_smooth_linear.jpg
|
||||
:align: center
|
||||
|
|
@ -79,6 +98,30 @@ the *morse* and *morse/smooth/linear* styles.
|
|||
----------
|
||||
|
||||
|
||||
The *morse/soft* variant is similar to the *lj/cut/soft* pair style
|
||||
in that it modifies the potential at short range to have a soft core.
|
||||
This helps to avoid singularities during free energy calculation in
|
||||
which sites are created or anihilated. The formula differs from that
|
||||
of *lj/cut/soft*\ , and is instead given by:
|
||||
|
||||
.. image:: Eqs/pair_morse_soft.jpg
|
||||
:align: center
|
||||
|
||||
The *morse/soft* style requires the following pair coefficients:
|
||||
|
||||
* D0 (energy units)
|
||||
* alpha (1/distance units)
|
||||
* r0 (distance units)
|
||||
* lamda (unitless, between 0.0 and 1.0)
|
||||
* cutoff (distance units)
|
||||
|
||||
The last coefficient is optional. If not specified, the global morse
|
||||
cutoff is used.
|
||||
|
||||
|
||||
----------
|
||||
|
||||
|
||||
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
|
|
@ -135,6 +178,9 @@ Restrictions
|
|||
The *morse/smooth/linear* pair style is only enabled if LAMMPS was
|
||||
built with the USER-MISC package. See the :ref:`Making LAMMPS <start_3>` section for more info.
|
||||
|
||||
The *morse/soft* pair style is only enabled if LAMMPS was built with
|
||||
the USER-FEP package. See the :ref:`Making LAMMPS <start_3>` section for more info.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
|
|
|
|||
|
|
@ -27,23 +27,11 @@ stiffness of the harmonic bond should be large, so that the Drude
|
|||
particle remains close ot the core. The values of Drude mass, Drude
|
||||
charge, and force constant can be chosen following different
|
||||
strategies, as in the following examples of polarizable force
|
||||
fields.
|
||||
fields:
|
||||
|
||||
* :ref:`Lamoureux and Roux <Lamoureux>` suggest adopting a global
|
||||
half-stiffness, :math:`K_D` = 500 kcal/(mol Å<sup>2</sup>) —
|
||||
which corresponds to a force constant :math:`k_D` = 4184 kJ/(mol
|
||||
Å<sup>2</sup>) — for all types of core-Drude bond, a
|
||||
global mass :math:`m_D` = 0.4 g/mol (or u) for all types of Drude
|
||||
particle, and to calculate the Drude charges for individual atom types
|
||||
from the atom polarizabilities using equation (1). This choice is
|
||||
followed in the polarizable CHARMM force field.
|
||||
* :ref:`Schroeder and Steinhauser <Schroeder>` suggest adopting a global
|
||||
charge :math:`q_D` = -1.0e and a global mass :math:`m_D` = 0.1 g/mol (or u)
|
||||
for all Drude particles, and to calculate the force constant for each
|
||||
type of core-Drude bond from equation (1). The timesteps used by these
|
||||
authors are between 0.5 and 2 fs, with the degrees of freedom of the
|
||||
Drude oscillators kept cold at 1 K. In both these force fields
|
||||
hydrogen atoms are treated as non-polarizable.
|
||||
#. :ref:`Lamoureux and Roux <Lamoureux>` suggest adopting a global half-stiffness, :math:`K_D` = 500 kcal/(mol Ang :math:`{}^2`) - which corresponds to a force constant :math:`k_D` = 4184 kJ/(mol Ang :math:`{}^2`) - for all types of core-Drude bond, a global mass :math:`m_D` = 0.4 g/mol (or u) for all types of Drude particles, and to calculate the Drude charges for individual atom types from the atom polarizabilities using equation (1). This choice is followed in the polarizable CHARMM force field.
|
||||
#. Alternately :ref:`Schroeder and Steinhauser <Schroeder>` suggest adopting a global charge :math:`q_D` = -1.0e and a global mass :math:`m_D` = 0.1 g/mol (or u) for all Drude particles, and to calculate the force constant for each type of core-Drude bond from equation (1). The timesteps used by these authors are between 0.5 and 2 fs, with the degrees of freedom of the Drude oscillators kept cold at 1 K.
|
||||
#. In both these force fields hydrogen atoms are treated as non-polarizable.
|
||||
The motion of of the Drude particles can be calculated by minimizing
|
||||
the energy of the induced dipoles at each timestep, by an interative,
|
||||
self-consistent procedure. The Drude particles can be massless and
|
||||
|
|
@ -67,17 +55,8 @@ are such that the core-shell model is sufficiently stable. But to be
|
|||
applicable to molecular/covalent systems the Drude model includes two
|
||||
important features:
|
||||
|
||||
#. The possibility to thermostat the additional degrees of freedom
|
||||
associated with the induced dipoles at very low temperature, in terms
|
||||
of the reduced coordinates of the Drude particles with respect to
|
||||
their cores. This makes the trajectory close to that of relaxed
|
||||
induced dipoles.
|
||||
#. The Drude dipoles on covalently bonded atoms interact too strongly
|
||||
due to the short distances, so an atom may capture the Drude particle
|
||||
(shell) of a neighbor, or the induced dipoles within the same molecule
|
||||
may align too much. To avoid this, damping at short of the
|
||||
interactions between the point charges composing the induced dipole
|
||||
can be done by :ref:`Thole <Thole>` functions.
|
||||
#. The possibility to thermostat the additional degrees of freedom associated with the induced dipoles at very low temperature, in terms of the reduced coordinates of the Drude particles with respect to their cores. This makes the trajectory close to that of relaxed induced dipoles.
|
||||
#. The Drude dipoles on covalently bonded atoms interact too strongly due to the short distances, so an atom may capture the Drude particle (shell) of a neighbor, or the induced dipoles within the same molecule may align too much. To avoid this, damping at short of the interactions between the point charges composing the induced dipole can be done by :ref:`Thole <Thole>` functions.
|
||||
|
||||
----------
|
||||
|
||||
|
|
@ -483,7 +462,7 @@ NPT ensemble using Nose-Hoover thermostat:
|
|||
|
||||
|
||||
|
||||
**(Schroeder)** Schröder and Steinhauser, J Chem Phys, 133,
|
||||
**(Schroeder)** Schroeder and Steinhauser, J Chem Phys, 133,
|
||||
154511 (2010).
|
||||
|
||||
.. _Jiang:
|
||||
|
|
|
|||
|
|
@ -1,5 +1,5 @@
|
|||
LAMMPS GitHub tutorial
|
||||
######################
|
||||
**********************
|
||||
|
||||
written by Stefan Paquay
|
||||
========================
|
||||
|
|
|
|||
|
|
@ -46,7 +46,7 @@ Syntax
|
|||
constants = PI, version, on, off, true, false, yes, no
|
||||
thermo keywords = vol, ke, press, etc from :doc:`thermo_style <thermo_style>`
|
||||
math operators = (), -x, x+y, x-y, x*y, x/y, x^y, x%y,
|
||||
x == y, x != y, x < y, x <= y, x > y, x >= y, x && y, x || y, !x
|
||||
x == y, x != y, x < y, x <= y, x > y, x >= y, x && y, x || y, !x
|
||||
math functions = sqrt(x), exp(x), ln(x), log(x), abs(x),
|
||||
sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x),
|
||||
random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x)
|
||||
|
|
@ -456,9 +456,7 @@ references, and references to other variables.
|
|||
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
|
||||
| Thermo keywords | vol, pe, ebond, etc |
|
||||
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
|
||||
| Math operators | (), -x, x+y, x-y, x*y, x/y, x^y, x%y, |
|
||||
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
|
||||
| Math operators | (), -x, x+y, x-y, x*y, x/y, x^y, x%y, x == y, x != y, x < y, x <= y, x > y, x >= y, x && y, x || y, !x |
|
||||
| Math operators | (), -x, x+y, x-y, x*y, x/y, x^y, x%y, x == y, x != y, x < y, x <= y, x > y, x >= y, x && y, x || y, !x |
|
||||
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
|
||||
| Math functions | sqrt(x), exp(x), ln(x), log(x), abs(x), sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x), random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x), ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(x,y,z), stride(x,y,z), stride2(x,y,z,a,b,c), vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z) |
|
||||
+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
|
||||
|
|
|
|||
|
|
@ -180,19 +180,19 @@ thermodynamic integration (FDTI) or Bennet’s acceptance ratio method
|
|||
(BAR).</p>
|
||||
<p>The potential energy of the system is decomposed in three terms: a
|
||||
background term corresponding to interaction sites whose parameters
|
||||
remain constant, a reference term <em>U</em><sub>0</sub> corresponding to the
|
||||
remain constant, a reference term <span class="math">\(U_0\)</span> corresponding to the
|
||||
initial interactions of the atoms that will undergo perturbation, and
|
||||
a term <em>U</em><sub>1</sub> corresponding to the final interactions of
|
||||
a term <span class="math">\(U_1\)</span> corresponding to the final interactions of
|
||||
these atoms:</p>
|
||||
<img alt="_images/compute_fep_u.jpg" class="align-center" src="_images/compute_fep_u.jpg" />
|
||||
<p>A coupling parameter &lambda; varying from 0 to 1 connects the
|
||||
<p>A coupling parameter <span class="math">\(\lambda\)</span> varying from 0 to 1 connects the
|
||||
reference and perturbed systems:</p>
|
||||
<img alt="_images/compute_fep_lambda.jpg" class="align-center" src="_images/compute_fep_lambda.jpg" />
|
||||
<p>It is possible but not necessary that the coupling parameter (or a
|
||||
function thereof) appears as a multiplication factor of the potential
|
||||
energy. Therefore, this compute can apply perturbations to interaction
|
||||
parameters that are not directly proportional to the potential energy
|
||||
(e.g. &sigma; in Lennard-Jones potentials).</p>
|
||||
(e.g. <span class="math">\(\sigma\)</span> in Lennard-Jones potentials).</p>
|
||||
<p>This command can be combined with <a class="reference internal" href="fix_adapt.html"><span class="doc">fix adapt</span></a> to
|
||||
perform multistage free-energy perturbation calculations along
|
||||
stepwise alchemical transformations during a simulation run:</p>
|
||||
|
|
@ -200,19 +200,19 @@ stepwise alchemical transformations during a simulation run:</p>
|
|||
<p>This compute is suitable for the finite-difference thermodynamic
|
||||
integration (FDTI) method <a class="reference internal" href="#mezei"><span class="std std-ref">(Mezei)</span></a>, which is based on an
|
||||
evaluation of the numerical derivative of the free energy by a
|
||||
perturbation method using a very small &delta;:</p>
|
||||
perturbation method using a very small <span class="math">\(\delta\)</span>:</p>
|
||||
<img alt="_images/compute_fep_fdti.jpg" class="align-center" src="_images/compute_fep_fdti.jpg" />
|
||||
<p>where <em>w</em><sub>i</sub> are weights of a numerical quadrature. The <a class="reference internal" href="fix_adapt.html"><span class="doc">fix adapt</span></a> command can be used to define the stages of
|
||||
&lambda; at which the derivative is calculated and averaged.</p>
|
||||
<p>where <span class="math">\(w_i\)</span> are weights of a numerical quadrature. The <a class="reference internal" href="fix_adapt.html"><span class="doc">fix adapt</span></a> command can be used to define the stages of
|
||||
<span class="math">\(\lambda\)</span> at which the derivative is calculated and averaged.</p>
|
||||
<p>The compute fep calculates the exponential Boltzmann term and also the
|
||||
potential energy difference <em>U</em><sub>1</sub>-<em>U</em><sub>0</sub>. By
|
||||
choosing a very small perturbation &delta; the thermodynamic
|
||||
potential energy difference <span class="math">\(U_1 -U_0\)</span>. By
|
||||
choosing a very small perturbation <span class="math">\(\delta\)</span> the thermodynamic
|
||||
integration method can be implemented using a numerical evaluation of
|
||||
the derivative of the potential energy with respect to &lambda;:</p>
|
||||
the derivative of the potential energy with respect to <span class="math">\(\lambda\)</span>:</p>
|
||||
<img alt="_images/compute_fep_ti.jpg" class="align-center" src="_images/compute_fep_ti.jpg" />
|
||||
<p>Another technique to calculate free energy differences is the
|
||||
acceptance ratio method <a class="reference internal" href="#bennet"><span class="std std-ref">(Bennet)</span></a>, which can be implemented
|
||||
by calculating the potential energy differences with &delta; = 1.0 on
|
||||
by calculating the potential energy differences with <span class="math">\(\delta\)</span> = 1.0 on
|
||||
both the forward and reverse routes:</p>
|
||||
<img alt="_images/compute_fep_bar.jpg" class="align-center" src="_images/compute_fep_bar.jpg" />
|
||||
<p>The value of the free energy difference is determined by numerical
|
||||
|
|
@ -346,12 +346,12 @@ trajectories during which the volume fluctuates or changes <a class="reference i
|
|||
<hr class="docutils" />
|
||||
<p><strong>Output info:</strong></p>
|
||||
<p>This compute calculates a global vector of length 3 which contains the
|
||||
energy difference (<em>U</em><sub>1</sub>-<em>U</em><sub>0</sub>) as c_ID[1], the
|
||||
Boltzmann factor exp(-(<em>U</em><sub>1</sub>-<em>U</em><sub>0</sub>)/<em>kT</em>), or
|
||||
<em>V</em>exp(-(<em>U</em><sub>1</sub>-<em>U</em><sub>0</sub>)/<em>kT</em>), as c_ID[2] and the
|
||||
volume of the simulation box <em>V</em> as c_ID[3]. <em>U</em><sub>1</sub> is the
|
||||
energy difference ( <span class="math">\(U_1-U_0\)</span> ) as c_ID[1], the
|
||||
Boltzmann factor <span class="math">\(\exp(-(U_1-U_0)/kT)\)</span>, or
|
||||
<span class="math">\(V \exp(-(U_1-U_0)/kT)\)</span>, as c_ID[2] and the
|
||||
volume of the simulation box <span class="math">\(V\)</span> as c_ID[3]. <span class="math">\(U_1\)</span> is the
|
||||
pair potential energy obtained with the perturbed parameters and
|
||||
<em>U</em><sub>0</sub> is the pair potential energy obtained with the
|
||||
<span class="math">\(U_0\)</span> is the pair potential energy obtained with the
|
||||
unperturbed parameters. The energies include kspace terms if these
|
||||
are used in the simulation.</p>
|
||||
<p>These output results can be used by any command that uses a global
|
||||
|
|
|
|||
|
|
@ -162,12 +162,10 @@ or <em>face_threshold</em> or <em>neighbors</em> or <em>peratom</em></li>
|
|||
<span class="n">compute</span> <span class="mi">2</span> <span class="n">precipitate</span> <span class="n">voronoi</span><span class="o">/</span><span class="n">atom</span> <span class="n">surface</span> <span class="n">matrix</span>
|
||||
<span class="n">compute</span> <span class="mi">3</span><span class="n">b</span> <span class="n">precipitate</span> <span class="n">voronoi</span><span class="o">/</span><span class="n">atom</span> <span class="n">radius</span> <span class="n">v_r</span>
|
||||
<span class="n">compute</span> <span class="mi">4</span> <span class="n">solute</span> <span class="n">voronoi</span><span class="o">/</span><span class="n">atom</span> <span class="n">only_group</span>
|
||||
<span class="n">compute</span> <span class="mi">5</span> <span class="n">defects</span> <span class="n">voronoi</span><span class="o">/</span><span class="n">atom</span> <span class="n">occupation</span>
|
||||
<span class="n">compute</span> <span class="mi">6</span> <span class="nb">all</span> <span class="n">voronoi</span><span class="o">/</span><span class="n">atom</span> <span class="n">neighbors</span> <span class="n">yes</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">5</span> <span class="n">defects</span> <span class="n">voronoi</span><span class="o">/</span><span class="n">atom</span> <span class="n">occupation</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>compute 6 all voronoi/atom neighbors yes</p>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
|
|||
|
|
@ -176,7 +176,7 @@
|
|||
created to be used in place of that fix, to integrate the equations of
|
||||
motion of spherical rigid bodies when a lattice-Boltzmann fluid is
|
||||
present with a user-specified value of the force-coupling constant.
|
||||
The fix uses the integration algorithm described in <a class="reference internal" href="fix_lb_viscous.html#mackay"><span class="std std-ref">Mackay et al.</span></a> to update the positions, velocities, and orientations of
|
||||
The fix uses the integration algorithm described in <a class="reference internal" href="#mackay"><span class="std std-ref">Mackay et al.</span></a> to update the positions, velocities, and orientations of
|
||||
a set of spherical rigid bodies experiencing velocity dependent
|
||||
hydrodynamic forces. The spherical bodies are assumed to rotate as
|
||||
solid, uniform density spheres, with moments of inertia calculated
|
||||
|
|
@ -207,7 +207,7 @@ assumes the constituent atoms are point particles); see
|
|||
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
|
||||
<p>No information about the <em>rigid</em> and <em>rigid/nve</em> fixes are written to
|
||||
<a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
|
||||
<p>Similar to the <a class="reference internal" href="fix_rigid.html"><span class="doc">fix rigid</span></a> command: &quot; The rigid
|
||||
<p>Similar to the <a class="reference internal" href="fix_rigid.html"><span class="doc">fix rigid</span></a> command: The rigid
|
||||
fix computes a global scalar which can be accessed by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. The scalar value calculated by
|
||||
these fixes is “intensive”. The scalar is the current temperature of
|
||||
the collection of rigid bodies. This is averaged over all rigid
|
||||
|
|
@ -217,8 +217,8 @@ mass of the body and v = the velocity of its center of mass. The
|
|||
rotational energy of a rigid body is 1/2 I w^2, where I = the moment
|
||||
of inertia tensor of the body and w = its angular velocity. Degrees
|
||||
of freedom constrained by the <em>force</em> and <em>torque</em> keywords are
|
||||
removed from this calculation.&quot;</p>
|
||||
<p>&quot;All of these fixes compute a global array of values which can be
|
||||
removed from this calculation.</p>
|
||||
<p>All of these fixes compute a global array of values which can be
|
||||
accessed by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>.
|
||||
The number of rows in the array is equal to the number of rigid
|
||||
bodies. The number of columns is 15. Thus for each rigid body, 15
|
||||
|
|
@ -239,7 +239,7 @@ of bodies.</p>
|
|||
they are independent of the number of atoms in the simulation.</p>
|
||||
<p>No parameter of these fixes can be used with the <em>start/stop</em> keywords
|
||||
of the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command. These fixes are not invoked during
|
||||
<a class="reference internal" href="minimize.html"><span class="doc">energy minimization</span></a>. &quot;</p>
|
||||
<a class="reference internal" href="minimize.html"><span class="doc">energy minimization</span></a>.</p>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions</h2>
|
||||
|
|
|
|||
|
|
@ -223,7 +223,7 @@ for</p>
|
|||
</div>
|
||||
<p>Windows:</p>
|
||||
<pre class="literal-block">
|
||||
% set LAMMPS_POTENTIALS="C:Path to LAMMPSPotentials"
|
||||
% set LAMMPS_POTENTIALS="C:\Path to LAMMPS\Potentials"
|
||||
</pre>
|
||||
<hr class="docutils" />
|
||||
<p>The alphabetic list of pair styles defined in LAMMPS is given on the
|
||||
|
|
|
|||
|
|
@ -141,21 +141,38 @@
|
|||
</div>
|
||||
<div class="section" id="pair-style-morse-smooth-linear-omp-command">
|
||||
<h1>pair_style morse/smooth/linear/omp command</h1>
|
||||
</div>
|
||||
<div class="section" id="pair-style-morse-soft-command">
|
||||
<h1>pair_style morse/soft 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">morse</span> <span class="n">cutoff</span>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">style</span> <span class="n">args</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<ul class="simple">
|
||||
<li>cutoff = global cutoff for Morse interactions (distance units)</li>
|
||||
<li>style = <em>morse</em> or <em>morse/smooth/linear</em> or <em>morse/soft</em></li>
|
||||
<li>args = list of arguments for a particular style</li>
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>morse</em> args = cutoff
|
||||
cutoff = global cutoff for Morse interactions (distance units)
|
||||
<em>morse/smooth/linear</em> args = cutoff
|
||||
cutoff = global cutoff for Morse interactions (distance units)
|
||||
<em>morse/soft</em> args = n lf cutoff
|
||||
n = soft-core parameter
|
||||
lf = transformation range is lf < lambda < 1
|
||||
cutoff = global cutoff for Morse interactions (distance units)
|
||||
</pre>
|
||||
</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">morse</span> <span class="mf">2.5</span>
|
||||
<span class="n">pair_style</span> <span class="n">morse</span><span class="o">/</span><span class="n">smooth</span><span class="o">/</span><span class="n">linear</span> <span class="mf">2.5</span>
|
||||
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">100.0</span> <span class="mf">2.0</span> <span class="mf">1.5</span>
|
||||
<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">100.0</span> <span class="mf">2.0</span> <span class="mf">1.5</span> <span class="mf">3.0</span>
|
||||
<p>pair_style morse 2.5
|
||||
pair_style morse/smooth/linear 2.5
|
||||
pair_coeff * * 100.0 2.0 1.5
|
||||
pair_coeff 1 1 100.0 2.0 1.5 3.0</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">morse</span><span class="o">/</span><span class="n">soft</span> <span class="mi">4</span> <span class="mf">0.9</span> <span class="mf">10.0</span>
|
||||
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">100.0</span> <span class="mf">2.0</span> <span class="mf">1.5</span> <span class="mf">1.0</span>
|
||||
<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">100.0</span> <span class="mf">2.0</span> <span class="mf">1.5</span> <span class="mf">1.0</span> <span class="mf">3.0</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
|
|
@ -174,17 +191,34 @@ commands:</p>
|
|||
<li>alpha (1/distance units)</li>
|
||||
<li>r0 (distance units)</li>
|
||||
<li>cutoff (distance units)</li>
|
||||
<li>The last coefficient is optional. If not specified, the global morse</li>
|
||||
<li>cutoff is used.</li>
|
||||
</ul>
|
||||
<p>The last coefficient is optional. If not specified, the global morse
|
||||
cutoff is used.</p>
|
||||
<hr class="docutils" />
|
||||
<p>The <em>smooth/linear</em> variant is similar to the lj/smooth/linear variant
|
||||
in that it adds to the potential a shift and a linear term to make both
|
||||
the potential energy and force go to zero at the cut-off:</p>
|
||||
<p>The <em>morse/smooth/linear</em> variant is similar to the lj/smooth/linear
|
||||
variant in that it adds to the potential a shift and a linear term
|
||||
so that both, potential energy and force, go to zero at the cut-off:</p>
|
||||
<img alt="_images/pair_morse_smooth_linear.jpg" class="align-center" src="_images/pair_morse_smooth_linear.jpg" />
|
||||
<p>The syntax of the pair_style and pair_coeff commands are the same for
|
||||
the <em>morse</em> and <em>morse/smooth/linear</em> styles.</p>
|
||||
<hr class="docutils" />
|
||||
<p>The <em>morse/soft</em> variant is similar to the <em>lj/cut/soft</em> pair style
|
||||
in that it modifies the potential at short range to have a soft core.
|
||||
This helps to avoid singularities during free energy calculation in
|
||||
which sites are created or anihilated. The formula differs from that
|
||||
of <em>lj/cut/soft</em>, and is instead given by:</p>
|
||||
<img alt="_images/pair_morse_soft.jpg" class="align-center" src="_images/pair_morse_soft.jpg" />
|
||||
<p>The <em>morse/soft</em> style requires the following pair coefficients:</p>
|
||||
<ul class="simple">
|
||||
<li>D0 (energy units)</li>
|
||||
<li>alpha (1/distance units)</li>
|
||||
<li>r0 (distance units)</li>
|
||||
<li>lamda (unitless, between 0.0 and 1.0)</li>
|
||||
<li>cutoff (distance units)</li>
|
||||
</ul>
|
||||
<p>The last coefficient is optional. If not specified, the global morse
|
||||
cutoff is used.</p>
|
||||
<hr class="docutils" />
|
||||
<p>Styles with a <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
|
|
@ -222,6 +256,8 @@ to be specified in an input script that reads a restart file.</p>
|
|||
<h2>Restrictions</h2>
|
||||
<p>The <em>morse/smooth/linear</em> pair style is only enabled if LAMMPS was
|
||||
built with the USER-MISC 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>The <em>morse/soft</em> pair style is only enabled if LAMMPS was built with
|
||||
the USER-FEP 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>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands</h2>
|
||||
|
|
|
|||
File diff suppressed because one or more lines are too long
|
|
@ -147,25 +147,13 @@ stiffness of the harmonic bond should be large, so that the Drude
|
|||
particle remains close ot the core. The values of Drude mass, Drude
|
||||
charge, and force constant can be chosen following different
|
||||
strategies, as in the following examples of polarizable force
|
||||
fields.</p>
|
||||
<ul class="simple">
|
||||
<li><a class="reference internal" href="#lamoureux"><span class="std std-ref">Lamoureux and Roux</span></a> suggest adopting a global
|
||||
half-stiffness, <span class="math">\(K_D\)</span> = 500 kcal/(mol &Aring;<sup>2</sup>) &mdash;
|
||||
which corresponds to a force constant <span class="math">\(k_D\)</span> = 4184 kJ/(mol
|
||||
&Aring;<sup>2</sup>) &mdash; for all types of core-Drude bond, a
|
||||
global mass <span class="math">\(m_D\)</span> = 0.4 g/mol (or u) for all types of Drude
|
||||
particle, and to calculate the Drude charges for individual atom types
|
||||
from the atom polarizabilities using equation (1). This choice is
|
||||
followed in the polarizable CHARMM force field.</li>
|
||||
<li><a class="reference internal" href="#schroeder"><span class="std std-ref">Schroeder and Steinhauser</span></a> suggest adopting a global
|
||||
charge <span class="math">\(q_D\)</span> = -1.0e and a global mass <span class="math">\(m_D\)</span> = 0.1 g/mol (or u)
|
||||
for all Drude particles, and to calculate the force constant for each
|
||||
type of core-Drude bond from equation (1). The timesteps used by these
|
||||
authors are between 0.5 and 2 fs, with the degrees of freedom of the
|
||||
Drude oscillators kept cold at 1 K. In both these force fields
|
||||
hydrogen atoms are treated as non-polarizable.</li>
|
||||
</ul>
|
||||
<p>The motion of of the Drude particles can be calculated by minimizing
|
||||
fields:</p>
|
||||
<ol class="arabic simple">
|
||||
<li><a class="reference internal" href="#lamoureux"><span class="std std-ref">Lamoureux and Roux</span></a> suggest adopting a global half-stiffness, <span class="math">\(K_D\)</span> = 500 kcal/(mol Ang <span class="math">\({}^2\)</span>) - which corresponds to a force constant <span class="math">\(k_D\)</span> = 4184 kJ/(mol Ang <span class="math">\({}^2\)</span>) - for all types of core-Drude bond, a global mass <span class="math">\(m_D\)</span> = 0.4 g/mol (or u) for all types of Drude particles, and to calculate the Drude charges for individual atom types from the atom polarizabilities using equation (1). This choice is followed in the polarizable CHARMM force field.</li>
|
||||
<li>Alternately <a class="reference internal" href="#schroeder"><span class="std std-ref">Schroeder and Steinhauser</span></a> suggest adopting a global charge <span class="math">\(q_D\)</span> = -1.0e and a global mass <span class="math">\(m_D\)</span> = 0.1 g/mol (or u) for all Drude particles, and to calculate the force constant for each type of core-Drude bond from equation (1). The timesteps used by these authors are between 0.5 and 2 fs, with the degrees of freedom of the Drude oscillators kept cold at 1 K.</li>
|
||||
</ol>
|
||||
<p>#. In both these force fields hydrogen atoms are treated as non-polarizable.
|
||||
The motion of of the Drude particles can be calculated by minimizing
|
||||
the energy of the induced dipoles at each timestep, by an interative,
|
||||
self-consistent procedure. The Drude particles can be massless and
|
||||
therefore do not contribute to the kinetic energy. However, the
|
||||
|
|
@ -187,20 +175,8 @@ are such that the core-shell model is sufficiently stable. But to be
|
|||
applicable to molecular/covalent systems the Drude model includes two
|
||||
important features:</p>
|
||||
<ol class="arabic simple">
|
||||
<li>The possibility to thermostat the additional degrees of freedom</li>
|
||||
</ol>
|
||||
<blockquote>
|
||||
<div>associated with the induced dipoles at very low temperature, in terms
|
||||
of the reduced coordinates of the Drude particles with respect to
|
||||
their cores. This makes the trajectory close to that of relaxed
|
||||
induced dipoles.</div></blockquote>
|
||||
<ol class="arabic simple">
|
||||
<li>The Drude dipoles on covalently bonded atoms interact too strongly
|
||||
due to the short distances, so an atom may capture the Drude particle
|
||||
(shell) of a neighbor, or the induced dipoles within the same molecule
|
||||
may align too much. To avoid this, damping at short of the
|
||||
interactions between the point charges composing the induced dipole
|
||||
can be done by <a class="reference internal" href="#thole"><span class="std std-ref">Thole</span></a> functions.</li>
|
||||
<li>The possibility to thermostat the additional degrees of freedom associated with the induced dipoles at very low temperature, in terms of the reduced coordinates of the Drude particles with respect to their cores. This makes the trajectory close to that of relaxed induced dipoles.</li>
|
||||
<li>The Drude dipoles on covalently bonded atoms interact too strongly due to the short distances, so an atom may capture the Drude particle (shell) of a neighbor, or the induced dipoles within the same molecule may align too much. To avoid this, damping at short of the interactions between the point charges composing the induced dipole can be done by <a class="reference internal" href="#thole"><span class="std std-ref">Thole</span></a> functions.</li>
|
||||
</ol>
|
||||
<hr class="docutils" />
|
||||
<p><strong>Preparation of the data file</strong></p>
|
||||
|
|
@ -519,7 +495,7 @@ review the different thermostats and ensemble combinations.</p>
|
|||
</div>
|
||||
<hr class="docutils" />
|
||||
<p id="lamoureux"><strong>(Lamoureux)</strong> Lamoureux and Roux, J Chem Phys, 119, 3025-3039 (2003)</p>
|
||||
<p id="schroeder"><strong>(Schroeder)</strong> Schr&ouml;der and Steinhauser, J Chem Phys, 133,
|
||||
<p id="schroeder"><strong>(Schroeder)</strong> Schroeder and Steinhauser, J Chem Phys, 133,
|
||||
154511 (2010).</p>
|
||||
<dl class="docutils" id="jiang">
|
||||
<dt><strong>(Jiang)</strong> Jiang, Hardy, Phillips, MacKerell, Schulten, and Roux,</dt>
|
||||
|
|
|
|||
|
|
@ -132,9 +132,11 @@
|
|||
<p>This document briefly describes how to use GitHub to merge changes
|
||||
into LAMMPS using GitHub. It assumes that you are familiar with
|
||||
git. You may want to have a look at the <a class="reference external" href="http://git-scm.com/book/">Git book</a> to reacquaint yourself.</p>
|
||||
</div>
|
||||
</div>
|
||||
<hr class="docutils" />
|
||||
<div class="section" id="making-an-account">
|
||||
<h3>Making an account</h3>
|
||||
<h1>Making an account</h1>
|
||||
<p>First of all, you need a GitHub account. This is fairly simple, just
|
||||
go to <a class="reference external" href="https://github.com">GitHub</a> and create an account by clicking
|
||||
the <a href="#id1"><span class="problematic" id="id2">``</span></a>Sign up for GitHub’’ button. Once your account is created, you
|
||||
|
|
@ -143,7 +145,7 @@ username or e-mail address and password.</p>
|
|||
</div>
|
||||
<hr class="docutils" />
|
||||
<div class="section" id="forking-the-repository">
|
||||
<h3>Forking the repository</h3>
|
||||
<h1>Forking the repository</h1>
|
||||
<p>To get changes into LAMMPS, you need to first fork the repository. At
|
||||
the time of writing, LAMMPS-ICMS is the preferred fork. Go to <a class="reference external" href="https://github.com/lammps/lammps">LAMMPS on GitHub</a> and make sure branch is
|
||||
set to <a href="#id3"><span class="problematic" id="id4">``</span></a>lammps-icms’‘, see the figure below.</p>
|
||||
|
|
@ -158,11 +160,9 @@ can include changes from upstream into your repository.</p>
|
|||
</div>
|
||||
<hr class="docutils" />
|
||||
<div class="section" id="adding-changes-to-your-own-fork">
|
||||
<h3>Adding changes to your own fork</h3>
|
||||
<h1>Adding changes to your own fork</h1>
|
||||
<p>Before adding changes, it is better to first create a new branch that
|
||||
will contain these changes, a so-called feature branch.</p>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="feature-branches">
|
||||
<h2>Feature branches</h2>
|
||||
<p>Since LAMMPS is such a big project and most user contributions come in
|
||||
|
|
@ -210,6 +210,8 @@ $ git add doc/fix_manifoldforce.txt doc/user_manifolds.txt
|
|||
</div>
|
||||
<p>The “-m” switch is used to add a message to the commit. Use this to
|
||||
indicate what type of change was commited.</p>
|
||||
<div class="section" id="wisdom-by-axel">
|
||||
<h3>Wisdom by Axel:</h3>
|
||||
<p><em>“Do not use “git commit -a”. the -a flag will automatically include
|
||||
*all</em> modified or new files. mercurial does that and it find it
|
||||
hugely annoying and often leading to accidental commits of files you
|
||||
|
|
@ -260,16 +262,19 @@ is now up to the maintainer(s) of the upstream repository to
|
|||
incorporate the changes into the repository and to close the pull
|
||||
request.</p>
|
||||
<img alt="_images/tutorial_pull_request4.png" class="align-center" src="_images/tutorial_pull_request4.png" />
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<hr class="docutils" />
|
||||
<div class="section" id="additional-changes">
|
||||
<h3>Additional changes</h3>
|
||||
<h1>Additional changes</h1>
|
||||
<p>Before the pull request is accepted, any additional changes you push
|
||||
into your repository will automatically become part of the pull
|
||||
request.</p>
|
||||
</div>
|
||||
<hr class="docutils" />
|
||||
<div class="section" id="after-a-merge">
|
||||
<h3>After a merge</h3>
|
||||
<h1>After a merge</h1>
|
||||
<p>When everything is fine the feature branch is merged into the LAMMPS
|
||||
repositories:</p>
|
||||
<img alt="_images/tutorial_merged.png" class="align-center" src="_images/tutorial_merged.png" />
|
||||
|
|
@ -293,8 +298,6 @@ to your remote(s) as well:</p>
|
|||
<div class="highlight-default"><div class="highlight"><pre><span></span>$ git push origin :add-user-manifold
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -168,7 +168,7 @@
|
|||
constants = PI, version, on, off, true, false, yes, no
|
||||
thermo keywords = vol, ke, press, etc from <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a>
|
||||
math operators = (), -x, x+y, x-y, x*y, x/y, x^y, x%y,
|
||||
x == y, x != y, x &lt y, x &lt= y, x &gt y, x &gt= y, x && y, x || y, !x
|
||||
x == y, x != y, x < y, x <= y, x > y, x >= y, x && y, x || y, !x
|
||||
math functions = sqrt(x), exp(x), ln(x), log(x), abs(x),
|
||||
sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x),
|
||||
random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x)
|
||||
|
|
@ -536,36 +536,33 @@ references, and references to other variables.</p>
|
|||
<td>vol, pe, ebond, etc</td>
|
||||
</tr>
|
||||
<tr class="row-even"><td>Math operators</td>
|
||||
<td>(), -x, x+y, x-y, x*y, x/y, x^y, x%y,</td>
|
||||
<td>(), -x, x+y, x-y, x*y, x/y, x^y, x%y, x == y, x != y, x < y, x <= y, x > y, x >= y, x && y, x || y, !x</td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td>Math operators</td>
|
||||
<td>(), -x, x+y, x-y, x*y, x/y, x^y, x%y, x == y, x != y, x &lt y, x &lt= y, x &gt y, x &gt= y, x && y, x || y, !x</td>
|
||||
</tr>
|
||||
<tr class="row-even"><td>Math functions</td>
|
||||
<tr class="row-odd"><td>Math functions</td>
|
||||
<td>sqrt(x), exp(x), ln(x), log(x), abs(x), sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x), random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x), ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(x,y,z), stride(x,y,z), stride2(x,y,z,a,b,c), vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z)</td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td>Group functions</td>
|
||||
<tr class="row-even"><td>Group functions</td>
|
||||
<td>count(ID), mass(ID), charge(ID), xcm(ID,dim), vcm(ID,dim), fcm(ID,dim), bound(ID,dir), gyration(ID), ke(ID), angmom(ID,dim), torque(ID,dim), inertia(ID,dimdim), omega(ID,dim)</td>
|
||||
</tr>
|
||||
<tr class="row-even"><td>Region functions</td>
|
||||
<tr class="row-odd"><td>Region functions</td>
|
||||
<td>count(ID,IDR), mass(ID,IDR), charge(ID,IDR), xcm(ID,dim,IDR), vcm(ID,dim,IDR), fcm(ID,dim,IDR), bound(ID,dir,IDR), gyration(ID,IDR), ke(ID,IDR), angmom(ID,dim,IDR), torque(ID,dim,IDR), inertia(ID,dimdim,IDR), omega(ID,dim,IDR)</td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td>Special functions</td>
|
||||
<tr class="row-even"><td>Special functions</td>
|
||||
<td>sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x)</td>
|
||||
</tr>
|
||||
<tr class="row-even"><td>Atom values</td>
|
||||
<tr class="row-odd"><td>Atom values</td>
|
||||
<td>id[i], mass[i], type[i], mol[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i], q[i]</td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td>Atom vectors</td>
|
||||
<tr class="row-even"><td>Atom vectors</td>
|
||||
<td>id, mass, type, mol, x, y, z, vx, vy, vz, fx, fy, fz, q</td>
|
||||
</tr>
|
||||
<tr class="row-even"><td>Compute references</td>
|
||||
<tr class="row-odd"><td>Compute references</td>
|
||||
<td>c_ID, c_ID[i], c_ID[i][j], C_ID, C_ID[i]</td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td>Fix references</td>
|
||||
<tr class="row-even"><td>Fix references</td>
|
||||
<td>f_ID, f_ID[i], f_ID[i][j], F_ID, F_ID[i]</td>
|
||||
</tr>
|
||||
<tr class="row-even"><td>Other variables</td>
|
||||
<tr class="row-odd"><td>Other variables</td>
|
||||
<td>v_name, v_name[i]</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
|
|
|
|||
Loading…
Reference in New Issue