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extract() implementation for dihedral cosine squared restricted

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This commit is contained in:
Evangelos Voyiatzis
2025-04-07 09:11:42 +02:00
committed by GitHub
parent 27ac8c0ea1
commit 55964c1233
4 changed files with 23 additions and 6 deletions
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12
doc/src/fix_adapt.rst
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@ -457,11 +457,13 @@ all types from 1 to :math:`N`. A leading asterisk means all types from
If :doc:`dihedral_style hybrid <dihedral_hybrid>` is used, *dstyle* should be a
sub-style name. The dihedral styles that currently work with fix adapt are:
+---------------------------------------------------------+----------------+----------------+
| :doc:`opls <dihedral_opls>` | k1,k2,k3,k4 | type dihedrals |
+---------------------------------------------------------+----------------+----------------+
| :doc:`quadratic <dihedral_quadratic>` | k,phi0 | type dihedrals |
+---------------------------------------------------------+----------------+----------------+
+------------------------------------------------------------------------+----------------+----------------+
| :doc:`cosine/squared/restricted <dihedral_cosine_squared_restricted>` | k,phi0 | type dihedrals |
+------------------------------------------------------------------------+----------------+----------------+
| :doc:`opls <dihedral_opls>` | k1,k2,k3,k4 | type dihedrals |
+------------------------------------------------------------------------+----------------+----------------+
| :doc:`quadratic <dihedral_quadratic>` | k,phi0 | type dihedrals |
+------------------------------------------------------------------------+----------------+----------------+
Note that internally, phi0 is stored in radians, so the variable
this fix use to reset phi0 needs to generate values in radians.

12
src/EXTRA-MOLECULE/dihedral_cosine_squared_restricted.cpp
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@ -393,3 +393,15 @@ void DihedralCosineSquaredRestricted::born_matrix(int nd, int i1, int i2, int i3
du2 = 2 * k[type] * numerator / denominator;
}
/* ----------------------------------------------------------------------
return ptr to internal members upon request
------------------------------------------------------------------------ */
void *DihedralCosineSquaredRestricted::extract(const char *str, int &dim)
{
dim = 1;
if (strcmp(str, "k") == 0) return (void *) k;
if (strcmp(str, "phi0") == 0) return (void *) phi0;
return nullptr;
}

1
src/EXTRA-MOLECULE/dihedral_cosine_squared_restricted.h
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@ -34,6 +34,7 @@ class DihedralCosineSquaredRestricted : public Dihedral {
void read_restart(FILE *) override;
void write_data(FILE *) override;
void born_matrix(int, int, int, int, int, double &, double &) override;
void *extract(const char *, int &) override;
protected:
double *k, *phi0;

4
unittest/force-styles/tests/dihedral-cosine_squared_restricted.yaml
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@ -16,7 +16,9 @@ dihedral_coeff: ! |
3 15.0 -10.0
4 12.0 0.0
5 11.0 45.0
extract: ! ""
extract: ! |
k 1
phi0 1
natoms: 29
init_energy: 10643.96352037142
init_stress: ! |2-