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Minor fix for molecular DOF calculation. Update doc.

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This commit is contained in:
Zheng Gong
2020-11-16 17:23:53 +01:00
parent af785039f4
commit c3b9a30b8a
3 changed files with 14 additions and 17 deletions
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4
doc/src/fix_drude.rst
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@ -41,12 +41,12 @@ Restrictions
""""""""""""
This fix should be invoked before any other commands that implement
the Drude oscillator model, such as :doc:`fix langevin/drude <fix_langevin_drude>`, :doc:`fix drude/transform <fix_drude_transform>`, :doc:`compute temp/drude <compute_temp_drude>`, :doc:`pair_style thole <pair_thole>`.
the Drude oscillator model, such as :doc:`fix langevin/drude <fix_langevin_drude>`, :doc:`fix tgnvt/drude <fix_tgnh_drude>`, :doc:`fix drude/transform <fix_drude_transform>`, :doc:`compute temp/drude <compute_temp_drude>`, :doc:`pair_style thole <pair_thole>`.
Related commands
""""""""""""""""
:doc:`fix langevin/drude <fix_langevin_drude>`, :doc:`fix drude/transform <fix_drude_transform>`, :doc:`compute temp/drude <compute_temp_drude>`, :doc:`pair_style thole <pair_thole>`
:doc:`fix langevin/drude <fix_langevin_drude>`, :doc:`fix tgnvt/drude <fix_tgnh_drude>`, :doc:`fix drude/transform <fix_drude_transform>`, :doc:`compute temp/drude <compute_temp_drude>`, :doc:`pair_style thole <pair_thole>`
Default
"""""""

19
doc/src/fix_tgnh_drude.rst
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@ -82,25 +82,24 @@ which are defined in terms of their associated degrees of freedom (DOF):
.. math::
T_\mathrm{M}=\frac{\Sigma_{i}^{N_\mathrm{mol}} M_i V_i^2}{3 ( N_\mathrm{mol} - \frac{N_\mathrm{real} + N_\mathrm{drude}}{N_\mathrm{system}}) k_\mathrm{B}}
T_\mathrm{M}=\frac{\Sigma_{i}^{N_\mathrm{mol}} M_i V_i^2}{3 \left ( N_\mathrm{mol} - \frac{N_\mathrm{mol}}{N_\mathrm{mol,sys}} \right ) k_\mathrm{B}}
.. math::
T_\mathrm{R}=\frac{\Sigma_{i}^{N_\mathrm{real}} m_i (v_i-v_{M,i})^2}{(N_\mathrm{DOF} - 3 N_\mathrm{mol} - 3 N_\mathrm{drude}) k_\mathrm{B}}
T_\mathrm{R}=\frac{\Sigma_{i}^{N_\mathrm{real}} m_i (v_i-v_{M,i})^2}{(N_\mathrm{DOF} - 3 N_\mathrm{mol} + 3 \frac{N_\mathrm{mol}}{N_\mathrm{mol,sys}} - 3 N_\mathrm{drude}) k_\mathrm{B}}
.. math::
T_\mathrm{D}=\frac{\Sigma_{i}^{N_\mathrm{drude}} m_i^{\prime} v_i^{\prime 2}}{3 N_\mathrm{drude} k_\mathrm{B}}
Here :math:`N_\mathrm{mol}` is the number of molecules in the group,
:math:`N_\mathrm{real}` is the number of atom-Drude pairs and non-polarizable atoms in the group,
:math:`N_\mathrm{drude}` is the number of Drude particles in the group,
:math:`N_\mathrm{system}` is the number of particles (including real atoms and Drude particles) in the whole system.
Here :math:`N_\mathrm{mol}` and :math:`N_\mathrm{mol,sys}` are the numbers of molecules in the group and in the whole system, respectively.
:math:`N_\mathrm{real}` is the number of atom-Drude pairs and non-polarizable atoms in the group.
:math:`N_\mathrm{drude}` is the number of Drude particles in the group.
:math:`N_\mathrm{DOF}` is the DOF of the group.
:math:`M_i` and :math:`V_i` are the mass and the COM velocity of the i-th molecule,
:math:`m_i` is the mass of the i-th atom-Drude pair or non-polarizable atom,
:math:`v_i` is the velocity of COM of i-th atom-Drude pair or non-polarizable atom,
:math:`v_{M,i}` is the COM velocity of the molecule the i-th atom-Drude pair or non-polarizable atom belongs to,
:math:`M_i` and :math:`V_i` are the mass and the COM velocity of the i-th molecule.
:math:`m_i` is the mass of the i-th atom-Drude pair or non-polarizable atom.
:math:`v_i` is the velocity of COM of i-th atom-Drude pair or non-polarizable atom.
:math:`v_{M,i}` is the COM velocity of the molecule the i-th atom-Drude pair or non-polarizable atom belongs to.
:math:`m_i^\prime` and :math:`v_i^\prime` are the reduced mass and the relative velocity of the i-th atom-Drude pair.
.. note::