21 |
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|
22 |
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void NVT::moveA() { |
23 |
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|
24 |
< |
int i,j,k; |
25 |
< |
int atomIndex, aMatIndex; |
24 |
> |
int i, j; |
25 |
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DirectionalAtom* dAtom; |
26 |
< |
double Tb[3]; |
27 |
< |
double ji[3]; |
26 |
> |
double Tb[3], ji[3]; |
27 |
> |
double A[3][3], I[3][3]; |
28 |
> |
double angle, mass; |
29 |
> |
double vel[3], pos[3], frc[3]; |
30 |
> |
|
31 |
|
double instTemp; |
30 |
– |
double angle; |
32 |
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|
33 |
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instTemp = tStats->getTemperature(); |
34 |
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|
37 |
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chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat); |
38 |
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|
39 |
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for( i=0; i<nAtoms; i++ ){ |
39 |
– |
atomIndex = i * 3; |
40 |
– |
aMatIndex = i * 9; |
41 |
– |
|
42 |
– |
// velocity half step |
43 |
– |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
44 |
– |
vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert - vel[j]*chi); |
40 |
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|
41 |
< |
// position whole step |
42 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
41 |
> |
atoms[i]->getVel( vel ); |
42 |
> |
atoms[i]->getPos( pos ); |
43 |
> |
atoms[i]->getFrc( frc ); |
44 |
> |
|
45 |
> |
mass = atoms[i]->getMass(); |
46 |
> |
|
47 |
> |
for (j=0; j < 3; j++) { |
48 |
> |
// velocity half step |
49 |
> |
vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*chi); |
50 |
> |
// position whole step |
51 |
|
pos[j] += dt * vel[j]; |
52 |
+ |
} |
53 |
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|
54 |
+ |
atoms[i]->setVel( vel ); |
55 |
+ |
atoms[i]->setPos( pos ); |
56 |
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|
57 |
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if( atoms[i]->isDirectional() ){ |
58 |
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|
60 |
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|
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// get and convert the torque to body frame |
62 |
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|
63 |
< |
Tb[0] = dAtom->getTx(); |
58 |
< |
Tb[1] = dAtom->getTy(); |
59 |
< |
Tb[2] = dAtom->getTz(); |
60 |
< |
|
63 |
> |
dAtom->getTrq( Tb ); |
64 |
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dAtom->lab2Body( Tb ); |
65 |
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|
66 |
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// get the angular momentum, and propagate a half step |
67 |
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|
68 |
< |
ji[0] = dAtom->getJx(); |
69 |
< |
ji[1] = dAtom->getJy(); |
70 |
< |
ji[2] = dAtom->getJz(); |
68 |
> |
dAtom->getJ( ji ); |
69 |
> |
|
70 |
> |
for (j=0; j < 3; j++) |
71 |
> |
ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
72 |
|
|
69 |
– |
ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi); |
70 |
– |
ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi); |
71 |
– |
ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi); |
72 |
– |
|
73 |
|
// use the angular velocities to propagate the rotation matrix a |
74 |
|
// full time step |
75 |
< |
|
75 |
> |
|
76 |
> |
dAtom->getA(A); |
77 |
> |
dAtom->getI(I); |
78 |
> |
|
79 |
|
// rotate about the x-axis |
80 |
< |
angle = dt2 * ji[0] / dAtom->getIxx(); |
81 |
< |
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
82 |
< |
|
80 |
> |
angle = dt2 * ji[0] / I[0][0]; |
81 |
> |
this->rotate( 1, 2, angle, ji, A ); |
82 |
> |
|
83 |
|
// rotate about the y-axis |
84 |
< |
angle = dt2 * ji[1] / dAtom->getIyy(); |
85 |
< |
this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
84 |
> |
angle = dt2 * ji[1] / I[1][1]; |
85 |
> |
this->rotate( 2, 0, angle, ji, A ); |
86 |
|
|
87 |
|
// rotate about the z-axis |
88 |
< |
angle = dt * ji[2] / dAtom->getIzz(); |
89 |
< |
this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] ); |
88 |
> |
angle = dt * ji[2] / I[2][2]; |
89 |
> |
this->rotate( 0, 1, angle, ji, A); |
90 |
|
|
91 |
|
// rotate about the y-axis |
92 |
< |
angle = dt2 * ji[1] / dAtom->getIyy(); |
93 |
< |
this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
92 |
> |
angle = dt2 * ji[1] / I[1][1]; |
93 |
> |
this->rotate( 2, 0, angle, ji, A ); |
94 |
|
|
95 |
|
// rotate about the x-axis |
96 |
< |
angle = dt2 * ji[0] / dAtom->getIxx(); |
97 |
< |
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
96 |
> |
angle = dt2 * ji[0] / I[0][0]; |
97 |
> |
this->rotate( 1, 2, angle, ji, A ); |
98 |
|
|
99 |
< |
dAtom->setJx( ji[0] ); |
100 |
< |
dAtom->setJy( ji[1] ); |
101 |
< |
dAtom->setJz( ji[2] ); |
99 |
< |
} |
100 |
< |
|
99 |
> |
dAtom->setJ( ji ); |
100 |
> |
dAtom->setA( A ); |
101 |
> |
} |
102 |
|
} |
103 |
|
} |
104 |
|
|
105 |
|
void NVT::moveB( void ){ |
106 |
< |
int i,j,k; |
106 |
< |
int atomIndex; |
106 |
> |
int i, j; |
107 |
|
DirectionalAtom* dAtom; |
108 |
< |
double Tb[3]; |
109 |
< |
double ji[3]; |
108 |
> |
double Tb[3], ji[3]; |
109 |
> |
double vel[3], frc[3]; |
110 |
> |
double mass; |
111 |
> |
|
112 |
|
double instTemp; |
113 |
|
|
114 |
|
instTemp = tStats->getTemperature(); |
115 |
|
chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat); |
116 |
|
|
117 |
|
for( i=0; i<nAtoms; i++ ){ |
118 |
< |
atomIndex = i * 3; |
119 |
< |
|
118 |
> |
|
119 |
> |
atoms[i]->getVel( vel ); |
120 |
> |
atoms[i]->getFrc( frc ); |
121 |
> |
|
122 |
> |
mass = atoms[i]->getMass(); |
123 |
> |
|
124 |
|
// velocity half step |
125 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
126 |
< |
vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert - vel[j]*chi); |
125 |
> |
for (j=0; j < 3; j++) |
126 |
> |
vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*chi); |
127 |
|
|
128 |
+ |
atoms[i]->setVel( vel ); |
129 |
+ |
|
130 |
|
if( atoms[i]->isDirectional() ){ |
131 |
< |
|
131 |
> |
|
132 |
|
dAtom = (DirectionalAtom *)atoms[i]; |
133 |
< |
|
134 |
< |
// get and convert the torque to body frame |
135 |
< |
|
136 |
< |
Tb[0] = dAtom->getTx(); |
129 |
< |
Tb[1] = dAtom->getTy(); |
130 |
< |
Tb[2] = dAtom->getTz(); |
131 |
< |
|
133 |
> |
|
134 |
> |
// get and convert the torque to body frame |
135 |
> |
|
136 |
> |
dAtom->getTrq( Tb ); |
137 |
|
dAtom->lab2Body( Tb ); |
138 |
+ |
|
139 |
+ |
// get the angular momentum, and propagate a half step |
140 |
+ |
|
141 |
+ |
dAtom->getJ( ji ); |
142 |
+ |
|
143 |
+ |
for (j=0; j < 3; j++) |
144 |
+ |
ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
145 |
|
|
146 |
< |
// get the angular momentum, and complete the angular momentum |
147 |
< |
// half step |
136 |
< |
|
137 |
< |
ji[0] = dAtom->getJx(); |
138 |
< |
ji[1] = dAtom->getJy(); |
139 |
< |
ji[2] = dAtom->getJz(); |
140 |
< |
|
141 |
< |
ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi); |
142 |
< |
ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi); |
143 |
< |
ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi); |
144 |
< |
|
145 |
< |
dAtom->setJx( ji[0] ); |
146 |
< |
dAtom->setJy( ji[1] ); |
147 |
< |
dAtom->setJz( ji[2] ); |
146 |
> |
|
147 |
> |
dAtom->setJ( ji ); |
148 |
|
} |
149 |
|
} |
150 |
|
} |