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Merge branch 'develop' into region-lookup-refactor

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Axel Kohlmeyer
2022-04-22 22:53:02 -04:00
parent 47564ab6bc 9be8ef09a2
commit 9f9a5ca76f
29 changed files with 249 additions and 87 deletions
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doc/src/fix_adapt.rst
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@ -14,7 +14,7 @@ Syntax
* adapt = style name of this fix command
* N = adapt simulation settings every this many timesteps
* one or more attribute/arg pairs may be appended
* attribute = *pair* or *bond* or *kspace* or *atom*
* attribute = *pair* or *bond* or *angle* or *kspace* or *atom*
.. parsed-literal::
@ -28,11 +28,16 @@ Syntax
bparam = parameter to adapt over time
I = type bond to set parameter for
v_name = variable with name that calculates value of bparam
*angle* args = astyle aparam I v_name
astyle = angle style name, e.g. harmonic
aparam = parameter to adapt over time
I = type angle to set parameter for
v_name = variable with name that calculates value of aparam
*kspace* arg = v_name
v_name = variable with name that calculates scale factor on K-space terms
*atom* args = aparam v_name
aparam = parameter to adapt over time
v_name = variable with name that calculates value of aparam
*atom* args = atomparam v_name
atomparam = parameter to adapt over time
v_name = variable with name that calculates value of atomparam
* zero or more keyword/value pairs may be appended
* keyword = *scale* or *reset* or *mass*
@ -283,30 +288,62 @@ operates. The only difference is that now a bond coefficient for a
given bond type is adapted.
A wild-card asterisk can be used in place of or in conjunction with
the bond type argument to set the coefficients for multiple bond types.
This takes the form "\*" or "\*n" or "n\*" or "m\*n". If N = the number of
atom types, then an asterisk with no numeric values means all types
from 1 to N. A leading asterisk means all types from 1 to n (inclusive).
A trailing asterisk means all types from n to N (inclusive). A middle
asterisk means all types from m to n (inclusive).
the bond type argument to set the coefficients for multiple bond
types. This takes the form "\*" or "\*n" or "n\*" or "m\*n". If N =
the number of bond types, then an asterisk with no numeric values
means all types from 1 to N. A leading asterisk means all types from
1 to n (inclusive). A trailing asterisk means all types from n to N
(inclusive). A middle asterisk means all types from m to n
(inclusive).
Currently *bond* does not support bond_style hybrid nor bond_style
hybrid/overlay as bond styles. The only bonds that currently are
working with fix_adapt are
hybrid/overlay as bond styles. The bond styles that currently work
with fix_adapt are
+------------------------------------+-------+------------+
| :doc:`class2 <bond_class2>` | r0 | type bonds |
+------------------------------------+-------+------------+
| :doc:`fene <bond_fene>` | k, r0 | type bonds |
+------------------------------------+-------+------------+
| :doc:`gromos <bond_gromos>` | k, r0 | type bonds |
+------------------------------------+-------+------------+
| :doc:`harmonic <bond_harmonic>` | k,r0 | type bonds |
+------------------------------------+-------+------------+
| :doc:`morse <bond_morse>` | r0 | type bonds |
+------------------------------------+-------+------------+
| :doc:`nonlinear <bond_nonlinear>` | r0 | type bonds |
+------------------------------------+-------+------------+
+------------------------------------+-------+-----------------+
| :doc:`class2 <bond_class2>` | r0 | type bonds |
+------------------------------------+-------+-----------------+
| :doc:`fene <bond_fene>` | k,r0 | type bonds |
+------------------------------------+-------+-----------------+
| :doc:`fene/nm <bond_fene_nm>` | k,r0 | type bonds |
+------------------------------------+-------+-----------------+
| :doc:`gromos <bond_gromos>` | k,r0 | type bonds |
+------------------------------------+-------+-----------------+
| :doc:`harmonic <bond_harmonic>` | k,r0 | type bonds |
+------------------------------------+-------+-----------------+
| :doc:`morse <bond_morse>` | r0 | type bonds |
+------------------------------------+-------+-----------------+
| :doc:`nonlinear <bond_nonlinear>` | epsilon,r0 | type bonds |
+------------------------------------+-------+-----------------+
----------
The *angle* keyword uses the specified variable to change the value of
an angle coefficient over time, very similar to how the *pair* keyword
operates. The only difference is that now an angle coefficient for a
given angle type is adapted.
A wild-card asterisk can be used in place of or in conjunction with
the angle type argument to set the coefficients for multiple angle
types. This takes the form "\*" or "\*n" or "n\*" or "m\*n". If N =
the number of angle types, then an asterisk with no numeric values
means all types from 1 to N. A leading asterisk means all types from
1 to n (inclusive). A trailing asterisk means all types from n to N
(inclusive). A middle asterisk means all types from m to n
(inclusive).
Currently *angle* does not support angle_style hybrid nor angle_style
hybrid/overlay as angle styles. The angle styles that currently work
with fix_adapt are
+------------------------------------+-------+-----------------+
| :doc:`harmonic <angle_harmonic>` | k,theta0 | type angles |
+------------------------------------+-------+-----------------+
| :doc:`cosine <angle_cosine>` | k | type angles |
+------------------------------------+-------+-----------------+
Note that internally, theta0 is stored in radians, so the variable
this fix uses to reset theta0 needs to generate values in radians.
----------