1 |
mmeineke |
10 |
#ifndef _ATOM_H_ |
2 |
|
|
#define _ATOM_H_ |
3 |
|
|
|
4 |
|
|
#include <cstring> |
5 |
|
|
#include <iostream> |
6 |
|
|
|
7 |
|
|
class Atom{ |
8 |
|
|
public: |
9 |
|
|
Atom() { |
10 |
|
|
c_n_hyd = 0; |
11 |
|
|
has_dipole = 0; |
12 |
|
|
is_VDW = 0; |
13 |
|
|
is_LJ = 0; |
14 |
|
|
} |
15 |
|
|
~Atom() {} |
16 |
|
|
|
17 |
|
|
double getX() const {return c_x;} |
18 |
|
|
double getY() const {return c_y;} |
19 |
|
|
double getZ() const {return c_z;} |
20 |
|
|
void setX(double x) {c_x = x;} |
21 |
|
|
void setY(double y) {c_y = y;} |
22 |
|
|
void setZ(double z) {c_z = z;} |
23 |
|
|
|
24 |
|
|
double get_vx() const {return c_vx;} |
25 |
|
|
double get_vy() const {return c_vy;} |
26 |
|
|
double get_vz() const {return c_vz;} |
27 |
|
|
void set_vx(double vx) {c_vx = vx;} |
28 |
|
|
void set_vy(double vy) {c_vy = vy;} |
29 |
|
|
void set_vz(double vz) {c_vz = vz;} |
30 |
|
|
|
31 |
|
|
double getFx() const {return c_Fx;} |
32 |
|
|
double getFy() const {return c_Fy;} |
33 |
|
|
double getFz() const {return c_Fz;} |
34 |
|
|
void addFx(double add) {c_Fx += add;} |
35 |
|
|
void addFy(double add) {c_Fy += add;} |
36 |
|
|
void addFz(double add) {c_Fz += add;} |
37 |
|
|
virtual void zeroForces() = 0; |
38 |
|
|
|
39 |
|
|
double getMass() const {return c_mass;} |
40 |
|
|
void setMass(double mass) {c_mass = mass;} |
41 |
|
|
|
42 |
|
|
double getSigma() const {return c_sigma;} |
43 |
|
|
void setSigma(double sigma) {c_sigma = sigma;} |
44 |
|
|
|
45 |
|
|
double getEpslon() const {return c_epslon;} |
46 |
|
|
void setEpslon(double epslon) {c_epslon = epslon;} |
47 |
|
|
|
48 |
|
|
double getCovalent() const {return c_covalent;} |
49 |
|
|
void setCovalent(double covalent) {c_covalent = covalent;} |
50 |
|
|
|
51 |
|
|
int getIndex() const {return c_index;} |
52 |
|
|
void setIndex(int index) {c_index = index;} |
53 |
|
|
|
54 |
|
|
char *getType() {return c_name;} |
55 |
|
|
void setType(char * name) {strcpy(c_name,name);} |
56 |
|
|
|
57 |
|
|
void set_n_hydrogens( int n_h ) {c_n_hyd = n_h;} |
58 |
|
|
int get_n_hydrogens() const {return c_n_hyd;} |
59 |
|
|
|
60 |
|
|
void setHasDipole( int value ) { has_dipole = value; } |
61 |
|
|
short int hasDipole( void ) { return has_dipole; } |
62 |
|
|
|
63 |
|
|
void setLJ( void ) { is_LJ = 1; is_VDW = 0; } |
64 |
|
|
short int isLJ( void ) { return is_LJ; } |
65 |
|
|
|
66 |
|
|
void seVDW( void ) { is_VDW = 1; is_LJ = 0; } |
67 |
|
|
short int isVDW( void ) { return is_VDW; } |
68 |
|
|
|
69 |
|
|
virtual int isDirectional( void ) = 0; |
70 |
|
|
|
71 |
|
|
protected: |
72 |
|
|
double c_x; /*the atom's position */ |
73 |
|
|
double c_y; |
74 |
|
|
double c_z; |
75 |
|
|
|
76 |
|
|
double c_vx; /*the atom's velocity */ |
77 |
|
|
double c_vy; |
78 |
|
|
double c_vz; |
79 |
|
|
|
80 |
|
|
double c_Fx; /* the atom's forces */ |
81 |
|
|
double c_Fy; |
82 |
|
|
double c_Fz; |
83 |
|
|
|
84 |
|
|
double c_mass; /* the mass of the atom in amu */ |
85 |
|
|
double c_sigma; /* the sigma parameter for van der walls interactions */ |
86 |
|
|
double c_epslon; /* the esplon parameter for VDW interactions */ |
87 |
|
|
double c_covalent; // The covalent radius of the atom. |
88 |
|
|
|
89 |
|
|
int c_index; /* set the atom's index */ |
90 |
|
|
|
91 |
|
|
char c_name[100]; /* it's name */ |
92 |
|
|
|
93 |
|
|
int c_n_hyd; // the number of hydrogens bonded to the atom |
94 |
|
|
|
95 |
|
|
short int has_dipole; // dipole boolean |
96 |
|
|
short int is_VDW; // VDW boolean |
97 |
|
|
short int is_LJ; // LJ boolean |
98 |
|
|
|
99 |
|
|
}; |
100 |
|
|
|
101 |
|
|
class GeneralAtom : public Atom{ |
102 |
|
|
|
103 |
|
|
public: |
104 |
|
|
GeneralAtom(){} |
105 |
|
|
~GeneralAtom(){} |
106 |
|
|
|
107 |
|
|
int isDirectional( void ){ return 0; } |
108 |
|
|
void zeroForces() { |
109 |
|
|
c_Fx = 0.0; c_Fy = 0.0; c_Fz = 0.0; |
110 |
|
|
} |
111 |
|
|
}; |
112 |
|
|
|
113 |
|
|
class DirectionalAtom : public Atom { |
114 |
|
|
|
115 |
|
|
public: |
116 |
|
|
DirectionalAtom() { ssdIdentity = 0; } |
117 |
|
|
~DirectionalAtom() {} |
118 |
|
|
|
119 |
|
|
int isDirectional(void) { return 1; } |
120 |
|
|
|
121 |
|
|
void setSSD( int value) { ssdIdentity = value; } |
122 |
|
|
int isSSD(void) {return ssdIdentity; } |
123 |
|
|
|
124 |
|
|
void setA( double the_A[3][3] ); |
125 |
|
|
|
126 |
|
|
void setI( double the_I[3][3] ); |
127 |
|
|
|
128 |
|
|
void setQ( double the_q[4] ); |
129 |
|
|
|
130 |
|
|
void setEuler( double phi, double theta, double psi ); |
131 |
|
|
|
132 |
|
|
void setSUx( double the_sux ) { sux = the_sux; } |
133 |
|
|
void setSUy( double the_suy ) { suy = the_suy; } |
134 |
|
|
void setSUz( double the_suz ) { suz = the_suz; } |
135 |
|
|
|
136 |
|
|
void setJx( double the_jx ) { jx = the_jx; } |
137 |
|
|
void setJy( double the_jy ) { jy = the_jy; } |
138 |
|
|
void setJz( double the_jz ) { jz = the_jz; } |
139 |
|
|
|
140 |
|
|
void addTx( double the_tx ) { tx += the_tx;} |
141 |
|
|
void addTy( double the_ty ) { ty += the_ty;} |
142 |
|
|
void addTz( double the_tz ) { tz += the_tz;} |
143 |
|
|
|
144 |
|
|
void setMu( double the_mu ) { mu = the_mu; } |
145 |
|
|
|
146 |
|
|
void zeroForces() { |
147 |
|
|
c_Fx = 0.0; c_Fy = 0.0; c_Fz = 0.0; |
148 |
|
|
tx = 0.0; ty = 0.0; tz = 0.0; |
149 |
|
|
} |
150 |
|
|
|
151 |
|
|
double getAxx( void ) { return Axx; } |
152 |
|
|
double getAxy( void ) { return Axy; } |
153 |
|
|
double getAxz( void ) { return Axz; } |
154 |
|
|
|
155 |
|
|
double getAyx( void ) { return Ayx; } |
156 |
|
|
double getAyy( void ) { return Ayy; } |
157 |
|
|
double getAyz( void ) { return Ayz; } |
158 |
|
|
|
159 |
|
|
double getAzx( void ) { return Azx; } |
160 |
|
|
double getAzy( void ) { return Azy; } |
161 |
|
|
double getAzz( void ) { return Azz; } |
162 |
|
|
|
163 |
mmeineke |
30 |
void getA( double the_A[3][3] ); // get the full rotation matrix |
164 |
|
|
|
165 |
mmeineke |
10 |
double getSUx( void ) { return sux; } |
166 |
|
|
double getSUy( void ) { return suy; } |
167 |
|
|
double getSUz( void ) { return suz; } |
168 |
|
|
|
169 |
|
|
void getU( double the_u[3] ); // get the unit vector |
170 |
|
|
void getQ( double the_q[4] ); // get the quanternions |
171 |
|
|
|
172 |
|
|
double getJx( void ) { return jx; } |
173 |
|
|
double getJy( void ) { return jy; } |
174 |
|
|
double getJz( void ) { return jz; } |
175 |
|
|
|
176 |
|
|
double getTx( void ) { return tx; } |
177 |
|
|
double getTy( void ) { return ty; } |
178 |
|
|
double getTz( void ) { return tz; } |
179 |
|
|
|
180 |
|
|
double getIxx( void ) { return Ixx; } |
181 |
|
|
double getIxy( void ) { return Ixy; } |
182 |
|
|
double getIxz( void ) { return Ixz; } |
183 |
|
|
|
184 |
|
|
double getIyx( void ) { return Iyx; } |
185 |
|
|
double getIyy( void ) { return Iyy; } |
186 |
|
|
double getIyz( void ) { return Iyz; } |
187 |
|
|
|
188 |
|
|
double getIzx( void ) { return Izx; } |
189 |
|
|
double getIzy( void ) { return Izy; } |
190 |
|
|
double getIzz( void ) { return Izz; } |
191 |
|
|
|
192 |
|
|
double getMu( void ) { return mu; } |
193 |
|
|
|
194 |
|
|
void lab2Body( double r[3] ); |
195 |
|
|
void body2Lab( double r[3] ); |
196 |
|
|
|
197 |
|
|
private: |
198 |
|
|
|
199 |
|
|
double Axx, Axy, Axz;; // the rotational matrix |
200 |
|
|
double Ayx, Ayy, Ayz; |
201 |
|
|
double Azx, Azy, Azz; |
202 |
|
|
|
203 |
|
|
double sux, suy, suz; // the standard unit vector ( body fixed ) |
204 |
|
|
double jx, jy, jz; // the angular momentum vector ( body fixed ) |
205 |
|
|
double tx, ty, tz; // the torque vector ( space fixed ) |
206 |
|
|
|
207 |
|
|
double Ixx, Ixy, Ixz; // the inertial tensor matrix ( body fixed ) |
208 |
|
|
double Iyx, Iyy, Iyz; |
209 |
|
|
double Izx, Izy, Izz; |
210 |
|
|
|
211 |
|
|
double mu; // the magnitude of the dipole moment |
212 |
|
|
|
213 |
|
|
int ssdIdentity; // boolean of whether atom is ssd |
214 |
|
|
|
215 |
|
|
}; |
216 |
|
|
|
217 |
|
|
#endif |