| Bsoft 2.0.5 Bernard's software package

rwmodel_param.h
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1
9 #include "rwmodel.h"
10
11 #ifndef _Bmodparam_
12 #define _Bmodparam_
13 #define DISTMAT_COMPTYPE1 "distance_matrix.component_type1"
14 #define DISTMAT_COMPTYPE2 "distance_matrix.component_type2"
15 #define DISTMAT_LLEN "distance_matrix.link_length"
16 #define DISTMAT_DIST "distance_matrix.distance"
17 #define DISTMAT_KL "distance_matrix.link_constant"
18 #define DISTMAT_KD "distance_matrix.distance_constant"
19 #define DISTMAT_POTTYPE "distance_matrix.potential_type"
20
21 #define ANGLEMAT_COMPTYPE1 "angle_matrix.component_type1"
22 #define ANGLEMAT_COMPTYPE2 "angle_matrix.component_type2"
23 #define ANGLEMAT_COMPTYPE3 "angle_matrix.component_type3"
24 #define ANGLEMAT_ANGLE "angle_matrix.angle"
25 #define ANGLEMAT_KA "angle_matrix.angle_constant"
26
27 /************************************************************************
28 @Object: struct Bmodparam
29 @Description:
30 A structure used for model mechanics.
31 @Features:
32 This defines variables and constants for doing model dynamics or
33 other model mechanics.
34 *************************************************************************/
35 struct Bmodparam {
36 Bstring comment;
37 double timestep; // Integration time step for MD
38 double Kfriction; // Friction coefficient
39 double Kdistance; // Distance force constant
40 double Klink; // Link force constant
41 double Kangle; // Angular force constant
42 double Kpolyangle; // Angular force constant for polygons
43 double Kpolygon; // Polygon regularity force constant
44 double Kpolyplane; // Polygon planarity force constant
45 double Kpoint; // Point force constant
46 double Kradial; // Radial force constant
47 double Kplane; // Neighbor plane force constant
48 double Kguide; // Polyhedron guide force constant
49 double Kmap; // Density map force constant
50 double sepdist; // Separation distance grid sampling
51 double cutoff; // Distance cutoff for non-bonded calculations
52 double pointdecay; // Decay constant for the point force
53 double radius; // Radius for radial force
54 Vector3<float> point; // Center of point or radial force
55 Bmodel* guide; // Polyhedron guide model
56 int linksteps; // Number of sampling intervals along a link
57 int wrap; // Flag to turn periodic boundaries on
58 double sigma; // Gaussian decay for density fitting
59 double Edistance; // Non-linked distance energy
60 double Elink; // Link energy
61 double Eangle; // Angle energy
62 double Epolyangle; // Angle energy for polygons
63 double Epolygon; // Polygon regularity energy
64 double Epolyplane; // Polygon planarity energy
65 double Epoint; // Point force energy
66 double Eradial; // Radial force energy
67 double Eplane; // Neighbor plane force energy
68 double Eguide; // Polyhedron guide force energy
69 double Emap; // Density map associated energy
70 double Ekin; // Kinetic energy
71 double Epot; // Potential energy
72 int ntype; // Number of component types
73 Bstring* type; // List of component types
74 float* llen; // Reference link lengths (0=no link)
75 float* dist; // Reference distance lengths (0=no interaction)
76 float* Kl; // Link interaction strength constant
77 float* Kd; // Non-linked interaction strength constant
78 int* pot; // 0=no interaction, 1=harmonic, 2=soft sphere, 3=Lennard-Jones, 4=Morse
79 float* angle; // Reference angles in radians (0=not to be used)
80 float* Ka; // Angular interaction strength constant
81 } ;
82 #endif
83
84 // Function prototypes
85 Bmodparam* model_param_init(int num);
86 int model_param_kill(Bmodparam* mp);
87 Bmodparam* model_param_read(Bstring& filename);
88 int model_param_write(Bstring& filename, Bmodparam* mp);
89 int model_param_display(Bmodparam* mp);
90 Bmodparam* model_param_generate(Bmodel* model);
91 int model_param_set_type_indices(Bmodel* model, Bmodparam* mp);
92
Bmodparam::Elink
double Elink
Definition: rwmodel_param.h:60
Bmodparam::Kpolyplane
double Kpolyplane
Definition: rwmodel_param.h:44
model_param_read
Bmodparam * model_param_read(Bstring &filename)
Reads a model parameter file.
Definition: rwmodel_param.cpp:79
Bmodparam::Kpoint
double Kpoint
Definition: rwmodel_param.h:45
Bmodparam::sepdist
double sepdist
Definition: rwmodel_param.h:50
Bmodparam::Kradial
double Kradial
Definition: rwmodel_param.h:46
Bmodparam::linksteps
int linksteps
Definition: rwmodel_param.h:56
Bmodparam::cutoff
double cutoff
Definition: rwmodel_param.h:51
Bmodparam::Epoint
double Epoint
Definition: rwmodel_param.h:65
Bmodparam::Kplane
double Kplane
Definition: rwmodel_param.h:47
Bmodparam::Kfriction
double Kfriction
Definition: rwmodel_param.h:38
Bmodparam::radius
double radius
Definition: rwmodel_param.h:53
Bmodparam::Kdistance
double Kdistance
Definition: rwmodel_param.h:39
Bmodparam::Eguide
double Eguide
Definition: rwmodel_param.h:68
Bmodparam::pot
int * pot
Definition: rwmodel_param.h:78
Bmodparam
Definition: rwmodel_param.h:35
model_param_display
int model_param_display(Bmodparam *mp)
Displays a model parameter in the shell.
Definition: rwmodel_param.cpp:303
Bmodparam::Kangle
double Kangle
Definition: rwmodel_param.h:41
Bmodparam::Kl
float * Kl
Definition: rwmodel_param.h:76
Bmodparam::dist
float * dist
Definition: rwmodel_param.h:75
model_param_generate
Bmodparam * model_param_generate(Bmodel *model)
Generates a model parameter file from a model.
Definition: rwmodel_param.cpp:374
Bmodparam::Epolyangle
double Epolyangle
Definition: rwmodel_param.h:62
Bmodparam::wrap
int wrap
Definition: rwmodel_param.h:57
Bmodparam::sigma
double sigma
Definition: rwmodel_param.h:58
Bmodparam::Edistance
double Edistance
Definition: rwmodel_param.h:59
Bmodparam::Eplane
double Eplane
Definition: rwmodel_param.h:67
Bmodparam::llen
float * llen
Definition: rwmodel_param.h:74
Bmodparam::Ka
float * Ka
Definition: rwmodel_param.h:80
Bmodparam::Eangle
double Eangle
Definition: rwmodel_param.h:61
Bmodparam::ntype
int ntype
Definition: rwmodel_param.h:72
model
Bmodel * model
Definition: bshow.cpp:32
Bmodparam::Ekin
double Ekin
Definition: rwmodel_param.h:70
Bmodparam::Epolygon
double Epolygon
Definition: rwmodel_param.h:63
Bmodparam::Eradial
double Eradial
Definition: rwmodel_param.h:66
Bmodparam::timestep
double timestep
Definition: rwmodel_param.h:37
Bmodparam::comment
Bstring comment
Definition: rwmodel_param.h:36
Bmodparam::Kpolygon
double Kpolygon
Definition: rwmodel_param.h:43
Bstring
Definition: Bstring.h:29
Bmodparam::Kmap
double Kmap
Definition: rwmodel_param.h:49
rwmodel.h
Header file for reading and writing atomic model files.
Bmodparam::angle
float * angle
Definition: rwmodel_param.h:79
Bmodparam::Kpolyangle
double Kpolyangle
Definition: rwmodel_param.h:42
Vector3< float >
model_param_write
int model_param_write(Bstring &filename, Bmodparam *mp)
Writes a model parameter file.
Definition: rwmodel_param.cpp:233
model_param_init
Bmodparam * model_param_init(int num)
Initializes a model parameter structure and allocates memory.
Definition: rwmodel_param.cpp:23
Bmodel
Definition: rwmodel.h:119
Bmodparam::pointdecay
double pointdecay
Definition: rwmodel_param.h:52
Bmodparam::Emap
double Emap
Definition: rwmodel_param.h:69
Bmodparam::Kd
float * Kd
Definition: rwmodel_param.h:77
Bmodparam::guide
Bmodel * guide
Definition: rwmodel_param.h:55
Bmodparam::Epolyplane
double Epolyplane
Definition: rwmodel_param.h:64
Bmodparam::Klink
double Klink
Definition: rwmodel_param.h:40
Bmodparam::type
Bstring * type
Definition: rwmodel_param.h:73
model_param_set_type_indices
int model_param_set_type_indices(Bmodel *model, Bmodparam *mp)
Sets the component type indices from the model parameters.
Definition: rwmodel_param.cpp:491
model_param_kill
int model_param_kill(Bmodparam *mp)
Deallocates memory for a model parameter structure.
Definition: rwmodel_param.cpp:50
Bmodparam::Epot
double Epot
Definition: rwmodel_param.h:71
Bmodparam::point
Vector3< float > point
Definition: rwmodel_param.h:54
Bmodparam::Kguide
double Kguide
Definition: rwmodel_param.h:48