37 |
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|
38 |
|
void NPTf::moveA() { |
39 |
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|
40 |
< |
int i,j,k; |
41 |
< |
int atomIndex, aMatIndex; |
40 |
> |
int i, j, k; |
41 |
|
DirectionalAtom* dAtom; |
42 |
< |
double Tb[3]; |
43 |
< |
double ji[3]; |
44 |
< |
double ri[3], vi[3], sc[3]; |
45 |
< |
double instaTemp, instaVol; |
46 |
< |
double tt2, tb2, eta2ij; |
47 |
< |
double angle; |
42 |
> |
double Tb[3], ji[3]; |
43 |
> |
double A[3][3], I[3][3]; |
44 |
> |
double angle, mass; |
45 |
> |
double vel[3], pos[3], frc[3]; |
46 |
> |
|
47 |
> |
double rj[3]; |
48 |
> |
double instaTemp, instaPress, instaVol; |
49 |
> |
double tt2, tb2; |
50 |
> |
double sc[3]; |
51 |
> |
double eta2ij; |
52 |
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double press[3][3], vScale[3][3], hm[3][3], hmnew[3][3], scaleMat[3][3]; |
53 |
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|
54 |
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tt2 = tauThermostat * tauThermostat; |
65 |
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for (i = 0; i < 3; i++ ) { |
66 |
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for (j = 0; j < 3; j++ ) { |
67 |
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if (i == j) { |
68 |
< |
|
68 |
> |
|
69 |
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eta[i][j] += dt2 * instaVol * |
70 |
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(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
71 |
< |
|
71 |
> |
|
72 |
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vScale[i][j] = eta[i][j] + chi; |
73 |
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|
74 |
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} else { |
82 |
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} |
83 |
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|
84 |
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for( i=0; i<nAtoms; i++ ){ |
85 |
< |
atomIndex = i * 3; |
86 |
< |
aMatIndex = i * 9; |
85 |
> |
|
86 |
> |
atoms[i]->getVel( vel ); |
87 |
> |
atoms[i]->getPos( pos ); |
88 |
> |
atoms[i]->getFrc( frc ); |
89 |
> |
|
90 |
> |
mass = atoms[i]->getMass(); |
91 |
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|
92 |
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// velocity half step |
93 |
+ |
|
94 |
+ |
info->matVecMul3( vScale, vel, sc ); |
95 |
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|
96 |
< |
vi[0] = vel[atomIndex]; |
97 |
< |
vi[1] = vel[atomIndex+1]; |
98 |
< |
vi[2] = vel[atomIndex+2]; |
99 |
< |
|
91 |
< |
info->matVecMul3( vScale, vi, sc ); |
92 |
< |
|
93 |
< |
vi[0] += dt2 * ((frc[atomIndex] /atoms[i]->getMass())*eConvert - sc[0]); |
94 |
< |
vi[1] += dt2 * ((frc[atomIndex+1]/atoms[i]->getMass())*eConvert - sc[1]); |
95 |
< |
vi[2] += dt2 * ((frc[atomIndex+2]/atoms[i]->getMass())*eConvert - sc[2]); |
96 |
> |
for (j = 0; j < 3; j++) { |
97 |
> |
vel[j] += dt2 * ((frc[j] / mass) * eConvert - sc[j]); |
98 |
> |
rj[j] = pos[j]; |
99 |
> |
} |
100 |
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|
101 |
< |
vel[atomIndex] = vi[0]; |
98 |
< |
vel[atomIndex+1] = vi[1]; |
99 |
< |
vel[atomIndex+2] = vi[2]; |
101 |
> |
atoms[i]->setVel( vel ); |
102 |
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|
103 |
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// position whole step |
104 |
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|
105 |
< |
ri[0] = pos[atomIndex]; |
104 |
< |
ri[1] = pos[atomIndex+1]; |
105 |
< |
ri[2] = pos[atomIndex+2]; |
105 |
> |
info->wrapVector(rj); |
106 |
|
|
107 |
< |
info->wrapVector(ri); |
107 |
> |
info->matVecMul3( eta, rj, sc ); |
108 |
|
|
109 |
< |
info->matVecMul3( eta, ri, sc ); |
110 |
< |
|
111 |
< |
pos[atomIndex] += dt * (vel[atomIndex] + sc[0]); |
112 |
< |
pos[atomIndex+1] += dt * (vel[atomIndex+1] + sc[1]); |
113 |
< |
pos[atomIndex+2] += dt * (vel[atomIndex+2] + sc[2]); |
109 |
> |
for (j = 0; j < 3; j++ ) |
110 |
> |
pos[j] += dt * (vel[j] + sc[j]); |
111 |
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|
112 |
|
if( atoms[i]->isDirectional() ){ |
113 |
|
|
115 |
|
|
116 |
|
// get and convert the torque to body frame |
117 |
|
|
118 |
< |
Tb[0] = dAtom->getTx(); |
122 |
< |
Tb[1] = dAtom->getTy(); |
123 |
< |
Tb[2] = dAtom->getTz(); |
124 |
< |
|
118 |
> |
dAtom->getTrq( Tb ); |
119 |
|
dAtom->lab2Body( Tb ); |
120 |
|
|
121 |
|
// get the angular momentum, and propagate a half step |
122 |
|
|
123 |
< |
ji[0] = dAtom->getJx(); |
124 |
< |
ji[1] = dAtom->getJy(); |
125 |
< |
ji[2] = dAtom->getJz(); |
123 |
> |
dAtom->getJ( ji ); |
124 |
> |
|
125 |
> |
for (j=0; j < 3; j++) |
126 |
> |
ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
127 |
|
|
133 |
– |
ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi); |
134 |
– |
ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi); |
135 |
– |
ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi); |
136 |
– |
|
128 |
|
// use the angular velocities to propagate the rotation matrix a |
129 |
|
// full time step |
130 |
< |
|
130 |
> |
|
131 |
> |
dAtom->getA(A); |
132 |
> |
dAtom->getI(I); |
133 |
> |
|
134 |
|
// rotate about the x-axis |
135 |
< |
angle = dt2 * ji[0] / dAtom->getIxx(); |
136 |
< |
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
137 |
< |
|
135 |
> |
angle = dt2 * ji[0] / I[0][0]; |
136 |
> |
this->rotate( 1, 2, angle, ji, A ); |
137 |
> |
|
138 |
|
// rotate about the y-axis |
139 |
< |
angle = dt2 * ji[1] / dAtom->getIyy(); |
140 |
< |
this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
139 |
> |
angle = dt2 * ji[1] / I[1][1]; |
140 |
> |
this->rotate( 2, 0, angle, ji, A ); |
141 |
|
|
142 |
|
// rotate about the z-axis |
143 |
< |
angle = dt * ji[2] / dAtom->getIzz(); |
144 |
< |
this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] ); |
143 |
> |
angle = dt * ji[2] / I[2][2]; |
144 |
> |
this->rotate( 0, 1, angle, ji, A); |
145 |
|
|
146 |
|
// rotate about the y-axis |
147 |
< |
angle = dt2 * ji[1] / dAtom->getIyy(); |
148 |
< |
this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
147 |
> |
angle = dt2 * ji[1] / I[1][1]; |
148 |
> |
this->rotate( 2, 0, angle, ji, A ); |
149 |
|
|
150 |
|
// rotate about the x-axis |
151 |
< |
angle = dt2 * ji[0] / dAtom->getIxx(); |
152 |
< |
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
151 |
> |
angle = dt2 * ji[0] / I[0][0]; |
152 |
> |
this->rotate( 1, 2, angle, ji, A ); |
153 |
|
|
154 |
< |
dAtom->setJx( ji[0] ); |
155 |
< |
dAtom->setJy( ji[1] ); |
156 |
< |
dAtom->setJz( ji[2] ); |
163 |
< |
} |
164 |
< |
|
154 |
> |
dAtom->setJ( ji ); |
155 |
> |
dAtom->setA( A ); |
156 |
> |
} |
157 |
|
} |
158 |
< |
|
158 |
> |
|
159 |
|
// Scale the box after all the positions have been moved: |
160 |
< |
|
160 |
> |
|
161 |
|
// Use a taylor expansion for eta products: Hmat = Hmat . exp(dt * etaMat) |
162 |
|
// Hmat = Hmat . ( Ident + dt * etaMat + dt^2 * etaMat*etaMat / 2) |
163 |
< |
|
164 |
< |
|
163 |
> |
|
164 |
> |
|
165 |
|
for(i=0; i<3; i++){ |
166 |
|
for(j=0; j<3; j++){ |
167 |
< |
|
167 |
> |
|
168 |
|
// Calculate the matrix Product of the eta array (we only need |
169 |
|
// the ij element right now): |
170 |
< |
|
170 |
> |
|
171 |
|
eta2ij = 0.0; |
172 |
|
for(k=0; k<3; k++){ |
173 |
|
eta2ij += eta[i][k] * eta[k][j]; |
178 |
|
if (i == j) scaleMat[i][j] = 1.0; |
179 |
|
// Taylor expansion for the exponential truncated at second order: |
180 |
|
scaleMat[i][j] += dt*eta[i][j] + 0.5*dt*dt*eta2ij; |
181 |
< |
|
181 |
> |
|
182 |
|
} |
183 |
|
} |
184 |
< |
|
184 |
> |
|
185 |
|
info->getBoxM(hm); |
186 |
|
info->matMul3(hm, scaleMat, hmnew); |
187 |
|
info->setBoxM(hmnew); |
189 |
|
} |
190 |
|
|
191 |
|
void NPTf::moveB( void ){ |
192 |
< |
int i,j, k; |
193 |
< |
int atomIndex; |
192 |
> |
|
193 |
> |
int i, j; |
194 |
|
DirectionalAtom* dAtom; |
195 |
< |
double Tb[3]; |
196 |
< |
double ji[3]; |
197 |
< |
double vi[3], sc[3]; |
198 |
< |
double instaTemp, instaVol; |
195 |
> |
double Tb[3], ji[3]; |
196 |
> |
double vel[3], frc[3]; |
197 |
> |
double mass; |
198 |
> |
|
199 |
> |
double instaTemp, instaPress, instaVol; |
200 |
|
double tt2, tb2; |
201 |
+ |
double sc[3]; |
202 |
|
double press[3][3], vScale[3][3]; |
203 |
|
|
204 |
|
tt2 = tauThermostat * tauThermostat; |
232 |
|
} |
233 |
|
|
234 |
|
for( i=0; i<nAtoms; i++ ){ |
241 |
– |
atomIndex = i * 3; |
235 |
|
|
236 |
+ |
atoms[i]->getVel( vel ); |
237 |
+ |
atoms[i]->getFrc( frc ); |
238 |
+ |
|
239 |
+ |
mass = atoms[i]->getMass(); |
240 |
+ |
|
241 |
|
// velocity half step |
242 |
+ |
|
243 |
+ |
info->matVecMul3( vScale, vel, sc ); |
244 |
|
|
245 |
< |
vi[0] = vel[atomIndex]; |
246 |
< |
vi[1] = vel[atomIndex+1]; |
247 |
< |
vi[2] = vel[atomIndex+2]; |
248 |
< |
|
249 |
< |
info->matVecMul3( vScale, vi, sc ); |
250 |
< |
|
251 |
< |
vi[0] += dt2 * ((frc[atomIndex] /atoms[i]->getMass())*eConvert - sc[0]); |
252 |
< |
vi[1] += dt2 * ((frc[atomIndex+1]/atoms[i]->getMass())*eConvert - sc[1]); |
253 |
< |
vi[2] += dt2 * ((frc[atomIndex+2]/atoms[i]->getMass())*eConvert - sc[2]); |
245 |
> |
for (j = 0; j < 3; j++) { |
246 |
> |
vel[j] += dt2 * ((frc[j] / mass) * eConvert - sc[j]); |
247 |
> |
} |
248 |
|
|
249 |
< |
vel[atomIndex] = vi[0]; |
256 |
< |
vel[atomIndex+1] = vi[1]; |
257 |
< |
vel[atomIndex+2] = vi[2]; |
249 |
> |
atoms[i]->setVel( vel ); |
250 |
|
|
251 |
|
if( atoms[i]->isDirectional() ){ |
252 |
< |
|
252 |
> |
|
253 |
|
dAtom = (DirectionalAtom *)atoms[i]; |
254 |
< |
|
254 |
> |
|
255 |
|
// get and convert the torque to body frame |
256 |
|
|
257 |
< |
Tb[0] = dAtom->getTx(); |
266 |
< |
Tb[1] = dAtom->getTy(); |
267 |
< |
Tb[2] = dAtom->getTz(); |
268 |
< |
|
257 |
> |
dAtom->getTrq( Tb ); |
258 |
|
dAtom->lab2Body( Tb ); |
259 |
|
|
260 |
< |
// get the angular momentum, and complete the angular momentum |
272 |
< |
// half step |
260 |
> |
// get the angular momentum, and propagate a half step |
261 |
|
|
262 |
< |
ji[0] = dAtom->getJx(); |
275 |
< |
ji[1] = dAtom->getJy(); |
276 |
< |
ji[2] = dAtom->getJz(); |
262 |
> |
dAtom->getJ( ji ); |
263 |
|
|
264 |
< |
ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi); |
265 |
< |
ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi); |
280 |
< |
ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi); |
264 |
> |
for (j=0; j < 3; j++) |
265 |
> |
ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
266 |
|
|
267 |
< |
dAtom->setJx( ji[0] ); |
268 |
< |
dAtom->setJy( ji[1] ); |
269 |
< |
dAtom->setJz( ji[2] ); |
285 |
< |
} |
267 |
> |
dAtom->setJ( ji ); |
268 |
> |
|
269 |
> |
} |
270 |
|
} |
271 |
|
} |
272 |
|
|