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Merge remote-tracking branch 'github/develop' into collected-small-changes

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Axel Kohlmeyer
2024-09-23 14:50:45 -04:00
parent d787ecdcb3 b95f7c2ab2
commit b9600c5a67
37 changed files with 263 additions and 40 deletions
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78
doc/src/fix_adapt.rst
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@ -322,27 +322,31 @@ all types from 1 to :math:`N`. A leading asterisk means all types from
If :doc:`bond_style hybrid <bond_hybrid>` is used, *bstyle* should be a
sub-style name. 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:`fene/nm <bond_fene>` | k,r0 | type bonds |
+-----------------------------------------------------+------------+------------+
| :doc:`gromos <bond_gromos>` | k,r0 | type bonds |
+-----------------------------------------------------+------------+------------+
| :doc:`harmonic <bond_harmonic>` | k,r0 | type bonds |
+-----------------------------------------------------+------------+------------+
| :doc:`harmonic/shift <bond_harmonic_shift>` | k,r0,r1 | type bonds |
+-----------------------------------------------------+------------+------------+
| :doc:`harmonic/shift/cut <bond_harmonic_shift_cut>` | k,r0,r1 | type bonds |
+-----------------------------------------------------+------------+------------+
| :doc:`harmonic/restrain <bond_harmonic_restrain>` | k | type bonds |
+-----------------------------------------------------+------------+------------+
| :doc:`morse <bond_morse>` | r0 | type bonds |
+-----------------------------------------------------+------------+------------+
| :doc:`nonlinear <bond_nonlinear>` | epsilon,r0 | type bonds |
+-----------------------------------------------------+------------+------------+
+-----------------------------------------------------+---------------------------+------------+
| :doc:`class2 <bond_class2>` | r0 | type bonds |
+-----------------------------------------------------+---------------------------+------------+
| :doc:`fene <bond_fene>` | k,r0 | type bonds |
+-----------------------------------------------------+---------------------------+------------+
| :doc:`fene/expand <bond_fene_expand>` | k,r0,epsilon,sigma,shift | type bonds |
+-----------------------------------------------------+---------------------------+------------+
| :doc:`fene/nm <bond_fene>` | k,r0 | type bonds |
+-----------------------------------------------------+---------------------------+------------+
| :doc:`gromos <bond_gromos>` | k,r0 | type bonds |
+-----------------------------------------------------+---------------------------+------------+
| :doc:`harmonic <bond_harmonic>` | k,r0 | type bonds |
+-----------------------------------------------------+---------------------------+------------+
| :doc:`harmonic/restrain <bond_harmonic_restrain>` | k | type bonds |
+-----------------------------------------------------+---------------------------+------------+
| :doc:`harmonic/shift <bond_harmonic_shift>` | k,r0,r1 | type bonds |
+-----------------------------------------------------+---------------------------+------------+
| :doc:`harmonic/shift/cut <bond_harmonic_shift_cut>` | k,r0,r1 | type bonds |
+-----------------------------------------------------+---------------------------+------------+
| :doc:`mm3 <bond_mm3>` | k,r0 | type bonds |
+-----------------------------------------------------+---------------------------+------------+
| :doc:`morse <bond_morse>` | r0 | type bonds |
+-----------------------------------------------------+---------------------------+------------+
| :doc:`nonlinear <bond_nonlinear>` | epsilon,r0 | type bonds |
+-----------------------------------------------------+---------------------------+------------+
----------
@ -365,13 +369,31 @@ all types from 1 to :math:`N`. A leading asterisk means all types from
If :doc:`angle_style hybrid <angle_hybrid>` is used, *astyle* should be a
sub-style name. 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 |
+-----------------------------------------------+----------+-------------+
| :doc:`cosine/squared <angle_cosine_squared>` | k,theta0 | type angles |
+-----------------------------------------------+----------+-------------+
+--------------------------------------------------------------------+-----------------+-------------+
| :doc:`harmonic <angle_harmonic>` | k,theta0 | type angles |
+--------------------------------------------------------------------+-----------------+-------------+
| :doc:`charmm <angle_charmm>` | k,theta0 | type angles |
+--------------------------------------------------------------------+-----------------+-------------+
| :doc:`class2 <angle_class2>` | k2,k3,k4,theta0 | type angles |
+--------------------------------------------------------------------+-----------------+-------------+
| :doc:`cosine <angle_cosine>` | k | type angles |
+--------------------------------------------------------------------+-----------------+-------------+
| :doc:`cosine/periodic <angle_cosine_periodic>` | k,b,n | type angles |
+--------------------------------------------------------------------+-----------------+-------------+
| :doc:`cosine/squared/restricted <angle_cosine_squared_restricted>` | k,theta0 | type angles |
+--------------------------------------------------------------------+-----------------+-------------+
| :doc:`dipole <angle_dipole>` | k,gamma0 | type angles |
+--------------------------------------------------------------------+-----------------+-------------+
| :doc:`fourier <angle_fourier>` | k,c0,c1,c2 | type angles |
+--------------------------------------------------------------------+-----------------+-------------+
| :doc:`fourier/simple <angle_fourier_simple>` | k,c,n | type angles |
+--------------------------------------------------------------------+-----------------+-------------+
| :doc:`mm3 <angle_mm3>` | k,theta0 | type angles |
+--------------------------------------------------------------------+-----------------+-------------+
| :doc:`quartic <angle_quartic>` | k2,k3,k4,theta0 | type angles |
+--------------------------------------------------------------------+-----------------+-------------+
| :doc:`spica <angle_spica>` | k,theta0 | 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.