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Merge pull request #3833 from evoyiatzis/master

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Implementation of analytical expressions for Born matrix of some potentials & inclusion of angle contribution to stress/mop/profile
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Axel Kohlmeyer
2023-12-14 20:08:12 -05:00
committed by GitHub
parent 00c3f14a63 d84ee0c4f1
commit 01ab951ff3
22 changed files with 1420 additions and 91 deletions
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21
doc/src/compute_stress_mop.rst
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@ -18,7 +18,7 @@ Syntax
* style = *stress/mop* or *stress/mop/profile*
* dir = *x* or *y* or *z* is the direction normal to the plane
* args = argument specific to the compute style
* keywords = *kin* or *conf* or *total* or *pair* or *bond* or *angle* (one or more can be specified)
* keywords = *kin* or *conf* or *total* or *pair* or *bond* or *angle* or *dihedral* (one or more can be specified)
.. parsed-literal::
@ -68,15 +68,13 @@ Verlet algorithm.
.. versionadded:: 15Jun2023
contributions from bond and angle potentials
contributions from bond, angle and dihedral potentials
Between one and six keywords can be used to indicate which contributions
Between one and seven 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.
(bond), stress due to angle bending (angle), stress due to dihedral terms (dihedral)
and/or due to pairwise non-bonded interactions (pair).
NOTE 1: The configurational stress is computed considering all pairs of
atoms where at least one atom belongs to group group-ID.
@ -134,14 +132,9 @@ 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, which is
not possible for manybody potentials. In particular, compute
*stress/mop/profile* does not work with more than two-body pair
*stress/mop/profile* and *stress/mop* do 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.
improper intramolecular interactions.
Related commands
""""""""""""""""