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class Atom{ |
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public: |
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– |
Atom(int theIndex) { |
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– |
c_n_hyd = 0; |
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– |
has_dipole = 0; |
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– |
is_VDW = 0; |
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– |
is_LJ = 0; |
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|
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< |
index = theIndex; |
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< |
offset = 3 * index; |
18 |
< |
offsetX = offset; |
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< |
offsetY = offset+1; |
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< |
offsetZ = offset+2; |
11 |
> |
Atom(int theIndex); |
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> |
virtual ~Atom() {} |
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|
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< |
Axx = index*9; |
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< |
Axy = Axx+1; |
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< |
Axz = Axx+2; |
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< |
|
18 |
< |
Ayx = Axx+3; |
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< |
Ayy = Axx+4; |
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< |
Ayz = Axx+5; |
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> |
static double* pos; // the position array |
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> |
static double* vel; // the velocity array |
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> |
static double* frc; // the forc array |
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> |
static double* trq; // the torque vector ( space fixed ) |
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> |
static double* Amat; // the rotation matrix |
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> |
static double* mu; // the dipole moment array |
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> |
static double* ul; // the lab frame unit directional vector |
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> |
static int nElements; |
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|
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< |
Azx = Axx+6; |
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< |
Azy = Axx+7; |
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< |
Azz = Axx+8; |
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< |
} |
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< |
virtual ~Atom() {} |
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< |
|
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< |
static void createArrays (int nElements) { |
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< |
int i; |
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< |
|
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< |
pos = new double[nElements*3]; |
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< |
vel = new double[nElements*3]; |
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< |
frc = new double[nElements*3]; |
42 |
< |
trq = new double[nElements*3]; |
43 |
< |
Amat = new double[nElements*9]; |
44 |
< |
mu = new double[nElements]; |
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< |
ul = new double[nElements*3]; |
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< |
|
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< |
// init directional values to zero |
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< |
|
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< |
for( i=0; i<nElements; i++){ |
50 |
< |
trq[i] = 0.0; |
51 |
< |
trq[i+1] = 0.0; |
52 |
< |
trq[i+2] = 0.0; |
53 |
< |
|
54 |
< |
Amat[i] = 1.0; |
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< |
Amat[i+1] = 0.0; |
56 |
< |
Amat[i+2] = 0.0; |
57 |
< |
|
58 |
< |
Amat[i+3] = 0.0; |
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< |
Amat[i+4] = 1.0; |
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< |
Amat[i+5] = 0.0; |
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< |
|
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< |
Amat[i+6] = 0.0; |
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< |
Amat[i+7] = 0.0; |
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< |
Amat[i+8] = 1.0; |
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< |
|
66 |
< |
mu[i] = 0.0; |
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< |
|
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< |
ul[i] = 0.0; |
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< |
ul[i+1] = 0.0; |
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< |
ul[i+2] = 0.0; |
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< |
} |
72 |
< |
} |
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< |
static void destroyArrays(void) { |
74 |
< |
delete[] pos; |
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< |
delete[] vel; |
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< |
delete[] frc; |
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< |
delete[] trq; |
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< |
delete[] Amat; |
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< |
delete[] mu; |
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< |
} |
23 |
> |
static void createArrays (int nElements); |
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> |
static void destroyArrays(void); |
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> |
void addAtoms(int nAdded, double* Apos, double* Avel, double* Afrc, |
26 |
> |
double* Atrq, double* AAmat, double* Amu, |
27 |
> |
double* Aul); |
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> |
void deleteAtom(int theIndex); |
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> |
void deleteRange(int startIndex, int stopIndex); |
30 |
|
|
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static double* getPosArray( void ) { return pos; } |
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static double* getVelArray( void ) { return vel; } |
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void setCovalent(double covalent) {c_covalent = covalent;} |
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|
73 |
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int getIndex() const {return index;} |
74 |
< |
void setIndex(int theIndex) { |
126 |
< |
index = theIndex; |
127 |
< |
offset = index*3; |
128 |
< |
offsetX = offset; |
129 |
< |
offsetY = offset+1; |
130 |
< |
offsetZ = offset+2; |
131 |
< |
|
132 |
< |
Axx = index*9; |
133 |
< |
Axy = Axx+1; |
134 |
< |
Axz = Axx+2; |
135 |
< |
|
136 |
< |
Ayx = Axx+3; |
137 |
< |
Ayy = Axx+4; |
138 |
< |
Ayz = Axx+5; |
139 |
< |
|
140 |
< |
Azx = Axx+6; |
141 |
< |
Azy = Axx+7; |
142 |
< |
Azz = Axx+8; |
143 |
< |
} |
144 |
< |
|
74 |
> |
void setIndex(int theIndex); |
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char *getType() {return c_name;} |
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void setType(char * name) {strcpy(c_name,name);} |
77 |
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|
97 |
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|
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virtual int isDirectional( void ) = 0; |
99 |
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|
170 |
– |
static double* pos; // the position array |
171 |
– |
static double* vel; // the velocity array |
172 |
– |
static double* frc; // the forc array |
173 |
– |
static double* trq; // the torque vector ( space fixed ) |
174 |
– |
static double* Amat; // the rotation matrix |
175 |
– |
static double* mu; // the dipole moment array |
176 |
– |
static double* ul; // the lab frame unit directional vector |
100 |
|
|
101 |
|
protected: |
102 |
|
|
128 |
|
|
129 |
|
}; |
130 |
|
|
208 |
– |
|
209 |
– |
|
131 |
|
class GeneralAtom : public Atom{ |
132 |
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133 |
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public: |