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extract() implementation for dihedral class2

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This commit is contained in:
Evangelos Voyiatzis
2025-04-07 11:35:20 +02:00
committed by GitHub
parent e93709d34e
commit 2b38b6d1c0
4 changed files with 40 additions and 16 deletions
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32
doc/src/fix_adapt.rst
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@ -457,21 +457,23 @@ 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:`charmm <dihedral_charmm>` | k,n,d | type dihedrals |
+------------------------------------------------------------------------+----------------+----------------+
| :doc:`charmmfsw <dihedral_charmm>` | k,n,d | type dihedrals |
+------------------------------------------------------------------------+----------------+----------------+
| :doc:`cosine/squared/restricted <dihedral_cosine_squared_restricted>` | k,phi0 | type dihedrals |
+------------------------------------------------------------------------+----------------+----------------+
| :doc:`helix <dihedral_helix>` | a,b,c | type dihedrals |
+------------------------------------------------------------------------+----------------+----------------+
| :doc:`multi/harmonic <dihedral_multi_harmonic>` | a1,a2,a3,a4,a5 | type dihedrals |
+------------------------------------------------------------------------+----------------+----------------+
| :doc:`opls <dihedral_opls>` | k1,k2,k3,k4 | type dihedrals |
+------------------------------------------------------------------------+----------------+----------------+
| :doc:`quadratic <dihedral_quadratic>` | k,phi0 | type dihedrals |
+------------------------------------------------------------------------+----------------+----------------+
+------------------------------------------------------------------------+-------------------------+----------------+
| :doc:`charmm <dihedral_charmm>` | k,n,d | type dihedrals |
+------------------------------------------------------------------------+-------------------------+----------------+
| :doc:`charmmfsw <dihedral_charmm>` | k,n,d | type dihedrals |
+------------------------------------------------------------------------+-------------------------+----------------+
| :doc:`class2 <dihedral_class2>` | k1,k2,k3,phi1,phi2,phi3 | type dihedrals |
+------------------------------------------------------------------------+-------------------------+----------------+
| :doc:`cosine/squared/restricted <dihedral_cosine_squared_restricted>` | k,phi0 | type dihedrals |
+------------------------------------------------------------------------+-------------------------+----------------+
| :doc:`helix <dihedral_helix>` | a,b,c | type dihedrals |
+------------------------------------------------------------------------+-------------------------+----------------+
| :doc:`multi/harmonic <dihedral_multi_harmonic>` | a1,a2,a3,a4,a5 | 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.

15
src/CLASS2/dihedral_class2.cpp
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@ -946,3 +946,18 @@ void DihedralClass2::write_data(FILE *fp)
at_theta0_1[i]*180.0/MY_PI,at_theta0_2[i]*180.0/MY_PI);
}
/* ----------------------------------------------------------------------
return ptr to internal members upon request
------------------------------------------------------------------------ */
void *DihedralClass2::extract(const char *str, int &dim)
{
dim = 1;
if (strcmp(str, "k1") == 0) return (void *) k1;
if (strcmp(str, "k2") == 0) return (void *) k2;
if (strcmp(str, "k3") == 0) return (void *) k3;
if (strcmp(str, "phi1") == 0) return (void *) phi1;
if (strcmp(str, "phi2") == 0) return (void *) phi2;
if (strcmp(str, "phi3") == 0) return (void *) phi3;
return nullptr;
}

1
src/CLASS2/dihedral_class2.h
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@ -33,6 +33,7 @@ class DihedralClass2 : public Dihedral {
void write_restart(FILE *) override;
void read_restart(FILE *) override;
void write_data(FILE *) override;
void *extract(const char *, int &) override;
protected:
double *k1, *k2, *k3;

8
unittest/force-styles/tests/dihedral-class2.yaml
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@ -17,7 +17,13 @@ dihedral_coeff: ! |
* at 75 42 31 75 42 31 120 50
* aat 75 120 160
* bb13 75 1.4 1.4
extract: ! ""
extract: ! |
k1 1
k2 1
k3 1
phi1 1
phi2 1
phi3 1
natoms: 29
init_energy: 3355.0074717375933
init_stress: ! |2-