update documentation for new centroid stress for shake and rigid/small
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Donatas Surblys
@ -1123,9 +1123,12 @@ Bibliography
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**(Sun)**
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Sun, J. Phys. Chem. B, 102, 7338-7364 (1998).
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**(Surblys)**
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**(Surblys2019)**
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Surblys, Matsubara, Kikugawa, Ohara, Phys Rev E, 99, 051301(R) (2019).
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**(Surblys2021)**
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Surblys, Matsubara, Kikugawa, Ohara, J Appl Phys 130, 215104 (2021).
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**(Sutmann)**
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Sutmann, Arnold, Fahrenberger, et. al., Physical review / E 88(6), 063308 (2013)
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@ -89,13 +89,20 @@ included in the calculation.
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.. warning::
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The compute *heat/flux* has been reported to produce unphysical
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values for angle, dihedral and improper contributions
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values for angle, dihedral, improper and constraint force contributions
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when used with :doc:`compute stress/atom <compute_stress_atom>`,
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as discussed in :ref:`(Surblys) <Surblys2>` and :ref:`(Boone) <Boone>`.
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You are strongly advised to
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as discussed in :ref:`(Surblys2019) <Surblys3>`, :ref:`(Boone) <Boone>`
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and :ref:`(Surblys2021) <Surblys4>`. You are strongly advised to
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use :doc:`compute centroid/stress/atom <compute_stress_atom>`,
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which has been implemented specifically for such cases.
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.. warning::
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Due to an implementation detail, the :math:`y` and :math:`z`
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components of heat flux from :doc:`fix rigid <fix_rigid>`
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contribution when computed via :doc:`compute stress/atom <compute_stress_atom>`
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are highly unphysical and should not be used.
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The Green-Kubo formulas relate the ensemble average of the
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auto-correlation of the heat flux :math:`\mathbf{J}`
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to the thermal conductivity :math:`\kappa`:
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@ -232,10 +239,14 @@ none
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----------
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.. _Surblys2:
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.. _Surblys3:
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**(Surblys)** Surblys, Matsubara, Kikugawa, Ohara, Phys Rev E, 99, 051301(R) (2019).
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**(Surblys2019)** Surblys, Matsubara, Kikugawa, Ohara, Phys Rev E, 99, 051301(R) (2019).
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.. _Boone:
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**(Boone)** Boone, Babaei, Wilmer, J Chem Theory Comput, 15, 5579--5587 (2019).
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.. _Surblys4:
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**(Surblys2021)** Surblys, Matsubara, Kikugawa, Ohara, J Appl Phys 130, 215104 (2021).
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@ -87,6 +87,10 @@ Tersoff 3-body interaction) is assigned in equal portions to each atom
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in the set. E.g. 1/4 of the dihedral virial to each of the 4 atoms,
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or 1/3 of the fix virial due to SHAKE constraints applied to atoms in
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a water molecule via the :doc:`fix shake <fix_shake>` command.
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As an exception, the virial contribution from
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constraint forces in :doc:`fix rigid <fix_rigid>` on each atom
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is computed from the constraint force acting on the corresponding atom
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and its position, i.e. the total virial is not equally distributed.
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In case of compute *centroid/stress/atom*, the virial contribution is:
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@ -103,13 +107,25 @@ atom :math:`I` due to the interaction and the relative position
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:math:`\mathbf{r}_{I0}` of the atom :math:`I` to the geometric center
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of the interacting atoms, i.e. centroid, is used. As the geometric
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center is different for each interaction, the :math:`\mathbf{r}_{I0}`
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also differs. The sixth and seventh terms, Kspace and :doc:`fix
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<fix>` contribution respectively, are computed identical to compute
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*stress/atom*. Although the total system virial is the same as
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also differs. The sixth term, Kspace contribution,
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is computed identically to compute *stress/atom*.
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The seventh term is handed differently depending on
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if the constraint forces are due to :doc:`fix shake <fix_shake>`
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or :doc:`fix rigid <fix_rigid>`.
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In case of SHAKE constraints, each distance constraint is
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handed as a pairwise interaction.
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E.g. in case of a water molecule, two OH and one HH distance
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constraints are treated as three pairwise interactions.
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In case of :doc:`fix rigid <fix_rigid>`,
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all constraint forces in the molecule are treated
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as a single many-body interaction with a single centroid position.
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In case of water molecule, the formula expression would become
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identical to that of the three-body angle interaction.
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Although the total system virial is the same as
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compute *stress/atom*, compute *centroid/stress/atom* is know to
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result in more consistent heat flux values for angle, dihedrals and
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improper contributions when computed via :doc:`compute heat/flux
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<compute_heat_flux>`.
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result in more consistent heat flux values for angle, dihedrals,
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improper and constraint force contributions
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when computed via :doc:`compute heat/flux <compute_heat_flux>`.
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If no extra keywords are listed, the kinetic contribution all of the
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virial contribution terms are included in the per-atom stress tensor.
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@ -134,7 +150,8 @@ contribution for the cluster interaction is divided evenly among those
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atoms.
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Details of how compute *centroid/stress/atom* obtains the virial for
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individual atoms is given in :ref:`(Surblys) <Surblys1>`, where the
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individual atoms are given in :ref:`(Surblys2019) <Surblys1>` and
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:ref:`(Surblys2021) <Surblys2>`, where the
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idea is that the virial of the atom :math:`I` is the result of only
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the force :math:`\mathbf{F}_I` on the atom due to the interaction and
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its positional vector :math:`\mathbf{r}_{I0}`, relative to the
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@ -235,10 +252,10 @@ between the pair of particles. All bond styles are supported. All
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angle, dihedral, improper styles are supported with the exception of
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INTEL and KOKKOS variants of specific styles. It also does not
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support models with long-range Coulombic or dispersion forces,
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i.e. the kspace_style command in LAMMPS. It also does not support the
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following fixes which add rigid-body constraints: :doc:`fix shake
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<fix_shake>`, :doc:`fix rattle <fix_shake>`, :doc:`fix rigid
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<fix_rigid>`, :doc:`fix rigid/small <fix_rigid>`.
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i.e. the kspace_style command in LAMMPS. It also does not implement the
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following fixes which add rigid-body constraints:
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:doc:`fix rigid/* <fix_rigid>` and the OpenMP accelerated version of :doc:`fix rigid/small <fix_rigid>`,
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while all other :doc:`fix rigid/*/small <fix_rigid>` are implemented.
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LAMMPS will generate an error if one of these options is included in
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your model. Extension of centroid stress calculations to these force
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@ -270,4 +287,8 @@ none
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.. _Surblys1:
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**(Surblys)** Surblys, Matsubara, Kikugawa, Ohara, Phys Rev E, 99, 051301(R) (2019).
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**(Surblys2019)** Surblys, Matsubara, Kikugawa, Ohara, Phys Rev E, 99, 051301(R) (2019).
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.. _Surblys2:
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**(Surblys2021)** Surblys, Matsubara, Kikugawa, Ohara, J Appl Phys 130, 215104 (2021).
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