| Bsoft 2.0.5 Bernard's software package

model_mechanics.h
Go to the documentation of this file.
1
9 #include "rwmodel.h"
10 #include "rwmodel_param.h"
11 #include "rwimg.h"
12
13 // Function prototypes
14 double model_mechanics(Bmodel* model, Bmodparam* mp, int mm_type, int max_iter,
15 double max_shift, double velocitylimit);
16 int model_minimize(Bmodel* model, double max_shift);
17 double model_verlet(Bmodel* model, double timestep, double Kfriction, double velocitylimit);
18 double model_distance_energy(Bmodel* model, Bmodparam* mp);
19 double model_neighbor_distance_energy(Bmodel* model, Bmodparam* mp);
20 double model_soft_sphere_energy(Bmodel* model, double Kdistance, double dist_ref);
21 double model_lennard_jones_energy(Bmodel* model, double Kdistance, double distance);
22 double model_morse_energy(Bmodel* model, double Kdistance, double distance);
23 double model_link_energy(Bmodel* model, Bmodparam* mp);
24 double model_link_energy(Bmodel* model, double Klink);
25 double model_angle_energy(Bmodel* model, Bmodparam* mp);
26 double model_polygon_angle_energy(Bmodel* model, double Kangle);
27 double model_polygon_energy(Bmodel* model, double Kpoly);
28 double model_polygon_plane_energy(Bmodel* model, double Kpolyplane);
29 double model_neighbor_plane_energy(Bmodel* model, double Kplane);
30 double model_point_force(Bmodel* model, Vector3<double> point, double Kpoint, double decay);
31 double model_radial_energy(Bmodel* model, Vector3<double> point, double d0, double Kd);
32 double model_polyhedron_guide_energy(Bmodel* model, Bmodel* gmod, double Kguide);
33 double model_map_energy(Bmodel* model, Bimage* map, double Kmap);
34 double model_map_energy(Bmodel* model, Bimage* map, double Kmap, double sigma);
35 int model_zero_forces(Bmodel* model);
36 int model_calculate_deviations(Bmodel* model);
37 int model_calculate_deviations(Bmodel* model, Bmodparam* mp);
38 int model_regularize(Bmodel* model, int reg_iter, double distance,
39 double Kdistance, double Klink, double Kangle, double Kpoly,
40 double Kpolyplane, double Kpoint, double decay);
41
distance
double distance(vector< T1 > &v1, vector< T2 > &v2)
Definition: Vector3.h:536
model_neighbor_plane_energy
double model_neighbor_plane_energy(Bmodel *model, double Kplane)
Calculates the planarity energy and forces with respect to neighbors.
Definition: model_mechanics.cpp:937
model_polyhedron_guide_energy
double model_polyhedron_guide_energy(Bmodel *model, Bmodel *gmod, double Kguide)
Calculates the potential with respect to a guide polyhedron.
Definition: model_mechanics.cpp:1041
model_map_energy
double model_map_energy(Bmodel *model, Bimage *map, double Kmap)
Energy calculation of a model into a map.
Definition: model_mechanics.cpp:1091
model_morse_energy
double model_morse_energy(Bmodel *model, double Kdistance, double distance)
Calculates the Morse potential between components.
Definition: model_mechanics.cpp:673
model_regularize
int model_regularize(Bmodel *model, int reg_iter, double distance, double Kdistance, double Klink, double Kangle, double Kpoly, double Kpolyplane, double Kpoint, double decay)
Regularizes a model.
Definition: model_mechanics.cpp:1411
model_angle_energy
double model_angle_energy(Bmodel *model, Bmodparam *mp)
Calculates the model angular energy.
Definition: model_mechanics.cpp:751
model_point_force
double model_point_force(Bmodel *model, Vector3< double > point, double Kpoint, double decay)
Calculates the forces and energy resulting from a single point force.
Definition: model_mechanics.cpp:984
model_soft_sphere_energy
double model_soft_sphere_energy(Bmodel *model, double Kdistance, double dist_ref)
Calculates the soft sphere potential between components.
Definition: model_mechanics.cpp:616
model_distance_energy
double model_distance_energy(Bmodel *model, Bmodparam *mp)
Calculates the distance-related potentials between components.
Definition: model_mechanics.cpp:501
model_polygon_energy
double model_polygon_energy(Bmodel *model, double Kpoly)
Calculates the polygon regularity energy and forces.
Definition: model_mechanics.cpp:882
Bmodparam
Definition: rwmodel_param.h:35
model_link_energy
double model_link_energy(Bmodel *model, Bmodparam *mp)
Calculates the model link energy.
Definition: model_mechanics.cpp:699
Bimage
General image parameter class.
Definition: Bimage.h:163
model_neighbor_distance_energy
double model_neighbor_distance_energy(Bmodel *model, Bmodparam *mp)
Calculates the distance-related potentials between components and their neighbors.
Definition: model_mechanics.cpp:556
model_polygon_angle_energy
double model_polygon_angle_energy(Bmodel *model, double Kangle)
Calculates the link angular forces and energy.
Definition: model_mechanics.cpp:794
model_verlet
double model_verlet(Bmodel *model, double timestep, double Kfriction, double velocitylimit)
Model dynamics using the velocity verlet integrator.
Definition: model_mechanics.cpp:254
model_calculate_deviations
int model_calculate_deviations(Bmodel *model)
Calculates the deviations from regularity in a polyhedral model.
Definition: model_mechanics.cpp:1247
model_mechanics
double model_mechanics(Bmodel *model, Bmodparam *mp, int mm_type, int max_iter, double max_shift, double velocitylimit)
Minimizes the energy of a model.
Definition: model_mechanics.cpp:40
model_radial_energy
double model_radial_energy(Bmodel *model, Vector3< double > point, double d0, double Kd)
Calculates the potential between a components and a point.
Definition: model_mechanics.cpp:1019
model
Bmodel * model
Definition: bshow.cpp:32
model_lennard_jones_energy
double model_lennard_jones_energy(Bmodel *model, double Kdistance, double distance)
Calculates the Lennard-Jones potential between components.
Definition: model_mechanics.cpp:644
rwmodel_param.h
Header to read and write model dynamics parameters in STAR format.
rwmodel.h
Header file for reading and writing atomic model files.
Vector3< double >
model_minimize
int model_minimize(Bmodel *model, double max_shift)
Move components random distances down the energy gradient.
Definition: model_mechanics.cpp:215
Bmodel
Definition: rwmodel.h:119
model_zero_forces
int model_zero_forces(Bmodel *model)
Zeroes the component forces.
Definition: model_mechanics.cpp:1221
rwimg.h
Header file for 2D and 3D image I/O.
model_polygon_plane_energy
double model_polygon_plane_energy(Bmodel *model, double Kpolyplane)
Calculates the polygon planarity energy and forces.
Definition: model_mechanics.cpp:900