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Axel Kohlmeyer
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doc/src/compute_stress_mop.rst
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Description
"""""""""""
Compute *stress/mop* and compute *stress/mop/profile* define computations that
calculate components of the local stress tensor using the method of
planes :ref:`(Todd) <mop-todd>`. Specifically in compute *stress/mop* calculates 3
components are computed in directions *dir*,\ *x*\ ; *dir*,\ *y*\ ; and
*dir*,\ *z*\ ; where *dir* is the direction normal to the plane, while
in compute *stress/mop/profile* the profile of the stress is computed.
Compute *stress/mop* and compute *stress/mop/profile* define
computations that calculate components of the local stress tensor using
the method of planes :ref:`(Todd) <mop-todd>`. Specifically in compute
*stress/mop* calculates 3 components are computed in directions *dir*,\
*x*\ ; *dir*,\ *y*\ ; and *dir*,\ *z*\ ; where *dir* is the direction
normal to the plane, while in compute *stress/mop/profile* the profile
of the stress is computed.
Contrary to methods based on histograms of atomic stress (i.e., using
:doc:`compute stress/atom <compute_stress_atom>`), the method of planes is
compatible with mechanical balance in heterogeneous systems and at
:doc:`compute stress/atom <compute_stress_atom>`), the method of planes
is compatible with mechanical balance in heterogeneous systems and at
interfaces :ref:`(Todd) <mop-todd>`.
The stress tensor is the sum of a kinetic term and a configurational
term, which are given respectively by Eq. (21) and Eq. (16) in
:ref:`(Todd) <mop-todd>`. For the kinetic part, the algorithm considers that
atoms have crossed the plane if their positions at times :math:`t-\Delta t`
and :math:`t` are one on either side of the plane, and uses the velocity at
time :math:`t-\Delta t/2` given by the velocity Verlet algorithm.
:ref:`(Todd) <mop-todd>`. For the kinetic part, the algorithm considers
that atoms have crossed the plane if their positions at times
:math:`t-\Delta t` and :math:`t` are one on either side of the plane,
and uses the velocity at time :math:`t-\Delta t/2` given by the velocity
Verlet algorithm.
Between one and six keywords can be used to indicate which
contributions to the stress must be computed: total stress (total), kinetic stress (kin),
configurational stress (conf), stress due to bond stretching (bond),
stress due to angle bending (angle) and/or due to pairwise non-bonded interactions (pair).
The angle keyword is currently available only for the stress/mop command and not the stress/mop/profile.
.. versionadded:: TBD
NOTE 1: The configurational stress is computed considering all pairs of atoms where at least one atom belongs to group group-ID.
contributions from bond and angle potentials
Between one and six keywords can be used to indicate which contributions
to the stress must be computed: total stress (total), kinetic stress
(kin), configurational stress (conf), stress due to bond stretching
(bond), stress due to angle bending (angle) and/or due to pairwise
non-bonded interactions (pair). The angle keyword is currently
available only for the *stress/mop* command and **not** the
*stress/mop/profile* command.
NOTE 1: The configurational stress is computed considering all pairs of
atoms where at least one atom belongs to group group-ID.
NOTE 2: The local stress does not include any Lennard-Jones tail
corrections to the stress added by the :doc:`pair_modify tail yes <pair_modify>`
command, since those are contributions to the global system pressure.
corrections to the stress added by the :doc:`pair_modify tail yes
<pair_modify>` command, since those are contributions to the global
system pressure.
NOTE 3: The local stress profile generated by compute *stress/mop/profile*
is similar to that obtained by compute
:doc:`stress/cartesian <compute_stress_profile>`.
A key difference is that compute *stress/mop/profile* considers particles
crossing a set of planes, while compute *stress/cartesian* computes averages
for a set of small volumes. More information
on the similarities and differences can be found in
:ref:`(Ikeshoji)<Ikeshoji2>`.
NOTE 3: The local stress profile generated by compute
*stress/mop/profile* is similar to that obtained by compute
:doc:`stress/cartesian <compute_stress_profile>`. A key difference is
that compute *stress/mop/profile* considers particles crossing a set of
planes, while compute *stress/cartesian* computes averages for a set of
small volumes. More information on the similarities and differences can
be found in :ref:`(Ikeshoji)<Ikeshoji2>`.
Output info
"""""""""""
Compute *stress/mop* calculates a global vector (indices starting at 1), with 3
values for each declared keyword (in the order the keywords have been
declared). For each keyword, the stress tensor components are ordered as
follows: stress_dir,x, stress_dir,y, and stress_dir,z.
Compute *stress/mop* calculates a global vector (indices starting at 1),
with 3 values for each declared keyword (in the order the keywords have
been declared). For each keyword, the stress tensor components are
ordered as follows: stress_dir,x, stress_dir,y, and stress_dir,z.
Compute *stress/mop/profile* instead calculates a global array, with 1 column
giving the position of the planes where the stress tensor was computed,
and with 3 columns of values for each declared keyword (in the order the
keywords have been declared). For each keyword, the profiles of stress
tensor components are ordered as follows: stress_dir,x; stress_dir,y;
and stress_dir,z.
Compute *stress/mop/profile* instead calculates a global array, with 1
column giving the position of the planes where the stress tensor was
computed, and with 3 columns of values for each declared keyword (in the
order the keywords have been declared). For each keyword, the profiles
of stress tensor components are ordered as follows: stress_dir,x;
stress_dir,y; and stress_dir,z.
The values are in pressure :doc:`units <units>`.
The values produced by this compute can be accessed by various :doc:`output commands <Howto_output>`.
For instance, the results can be written to a file using the
:doc:`fix ave/time <fix_ave_time>` command. Please see the example
in the examples/PACKAGES/mop folder.
The values produced by this compute can be accessed by various
:doc:`output commands <Howto_output>`. For instance, the results can be
written to a file using the :doc:`fix ave/time <fix_ave_time>`
command. Please see the example in the examples/PACKAGES/mop folder.
Restrictions
""""""""""""
These styles are part of the EXTRA-COMPUTE package. They are only enabled if
LAMMPS is built with that package. See the :doc:`Build package <Build_package>`
doc page on for more info.
These styles are part of the EXTRA-COMPUTE package. They are only
enabled if LAMMPS is built with that package. See the :doc:`Build
package <Build_package>` doc page on for more info.
The method is only implemented for 3d orthogonal simulation boxes whose
size does not change in time, and axis-aligned planes.
The method only works with two-body pair interactions, because it
requires the class method pair->single() to be implemented. In
particular, compute *stress/mop/profile* does not work with more than
two-body pair interactions, long range (kspace) interactions and angle/dihedral/improper
intramolecular interactions. Similarly, compute *stress/mop* does not work with more than
two-body pair interactions, long range (kspace) interactions and dihedral/improper
intramolecular interactions but works with all bond interactions with the class method
single() implemented and all angle interactions with the class method born_matrix()
implemented.
requires the class method ``Pair::single()`` to be implemented, which is
not possible for manybody potentials. In particular, compute
*stress/mop/profile* does not work with more than two-body pair
interactions, long range (kspace) interactions and
angle/dihedral/improper intramolecular interactions. Similarly, compute
*stress/mop* does not work with more than two-body pair interactions,
long range (kspace) interactions and dihedral/improper intramolecular
interactions but works with all bond interactions with the class method
single() implemented and all angle interactions with the class method
born_matrix() implemented.
Related commands
""""""""""""""""
:doc:`compute stress/atom <compute_stress_atom>`, :doc:`compute pressure <compute_pressure>`, :doc:`compute stress/cartesian <compute_stress_profile>`, :doc:`compute stress/cylinder <compute_stress_profile>`, :doc:`compute stress/spherical <compute_stress_profile>`
:doc:`compute stress/atom <compute_stress_atom>`,
:doc:`compute pressure <compute_pressure>`,
:doc:`compute stress/cartesian <compute_stress_profile>`,
:doc:`compute stress/cylinder <compute_stress_profile>`,
:doc:`compute stress/spherical <compute_stress_profile>`
Default
"""""""