# | Line 1 | Line 1 | |
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1 | + | #include <cmath> |
2 | #include "Atom.hpp" | |
3 | #include "SRI.hpp" | |
4 | #include "AbstractClasses.hpp" | |
# | Line 9 | Line 10 | |
10 | #include "simError.h" | |
11 | ||
12 | ||
13 | < | // Basic isotropic thermostating and barostating via the Melchionna |
13 | > | // Basic non-isotropic thermostating and barostating via the Melchionna |
14 | // modification of the Hoover algorithm: | |
15 | // | |
16 | // Melchionna, S., Ciccotti, G., and Holian, B. L., 1993, | |
# | Line 22 | Line 23 | NPTf::NPTf ( SimInfo *theInfo, ForceFields* the_ff): | |
23 | NPTf::NPTf ( SimInfo *theInfo, ForceFields* the_ff): | |
24 | Integrator( theInfo, the_ff ) | |
25 | { | |
26 | < | int i; |
26 | > | int i, j; |
27 | chi = 0.0; | |
28 | < | for(i = 0; i < 9; i++) eta[i] = 0.0; |
28 | > | |
29 | > | for(i = 0; i < 3; i++) |
30 | > | for (j = 0; j < 3; j++) |
31 | > | eta[i][j] = 0.0; |
32 | > | |
33 | have_tau_thermostat = 0; | |
34 | have_tau_barostat = 0; | |
35 | have_target_temp = 0; | |
# | Line 33 | Line 38 | void NPTf::moveA() { | |
38 | ||
39 | void NPTf::moveA() { | |
40 | ||
41 | < | int i,j,k; |
37 | < | int atomIndex, aMatIndex; |
41 | > | int i, j, k; |
42 | DirectionalAtom* dAtom; | |
43 | < | double Tb[3]; |
44 | < | double ji[3]; |
43 | > | double Tb[3], ji[3]; |
44 | > | double A[3][3], I[3][3]; |
45 | > | double angle, mass; |
46 | > | double vel[3], pos[3], frc[3]; |
47 | > | |
48 | double rj[3]; | |
49 | double instaTemp, instaPress, instaVol; | |
50 | double tt2, tb2; | |
51 | < | double angle; |
52 | < | double press[9]; |
53 | < | const double p_convert = 1.63882576e8; |
51 | > | double sc[3]; |
52 | > | double eta2ij; |
53 | > | double press[3][3], vScale[3][3], hm[3][3], hmnew[3][3], scaleMat[3][3]; |
54 | > | double bigScale, smallScale, offDiagMax; |
55 | ||
56 | tt2 = tauThermostat * tauThermostat; | |
57 | tb2 = tauBarostat * tauBarostat; | |
58 | ||
59 | instaTemp = tStats->getTemperature(); | |
60 | tStats->getPressureTensor(press); | |
53 | – | |
54 | – | for (i=0; i < 9; i++) press[i] *= p_convert; |
55 | – | |
61 | instaVol = tStats->getVolume(); | |
62 | ||
63 | // first evolve chi a half step | |
64 | ||
65 | chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; | |
66 | < | |
67 | < | eta[0] += dt2 * instaVol * (press[0] - targetPressure) / (NkBT*tb2); |
68 | < | eta[1] += dt2 * instaVol * press[1] / (NkBT*tb2); |
69 | < | eta[2] += dt2 * instaVol * press[2] / (NkBT*tb2); |
70 | < | eta[3] += dt2 * instaVol * press[3] / (NkBT*tb2); |
71 | < | eta[4] += dt2 * instaVol * (press[4] - targetPressure) / (NkBT*tb2); |
72 | < | eta[5] += dt2 * instaVol * press[5] / (NkBT*tb2); |
73 | < | eta[6] += dt2 * instaVol * press[6] / (NkBT*tb2); |
74 | < | eta[7] += dt2 * instaVol * press[7] / (NkBT*tb2); |
75 | < | eta[8] += dt2 * instaVol * (press[8] - targetPressure) / (NkBT*tb2); |
76 | < | |
66 | > | |
67 | > | for (i = 0; i < 3; i++ ) { |
68 | > | for (j = 0; j < 3; j++ ) { |
69 | > | if (i == j) { |
70 | > | |
71 | > | eta[i][j] += dt2 * instaVol * |
72 | > | (press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
73 | > | |
74 | > | vScale[i][j] = eta[i][j] + chi; |
75 | > | |
76 | > | } else { |
77 | > | |
78 | > | eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2); |
79 | > | |
80 | > | vScale[i][j] = eta[i][j]; |
81 | > | |
82 | > | } |
83 | > | } |
84 | > | } |
85 | > | |
86 | for( i=0; i<nAtoms; i++ ){ | |
87 | < | atomIndex = i * 3; |
88 | < | aMatIndex = i * 9; |
87 | > | |
88 | > | atoms[i]->getVel( vel ); |
89 | > | atoms[i]->getPos( pos ); |
90 | > | atoms[i]->getFrc( frc ); |
91 | > | |
92 | > | mass = atoms[i]->getMass(); |
93 | ||
94 | // velocity half step | |
95 | + | |
96 | + | info->matVecMul3( vScale, vel, sc ); |
97 | ||
98 | < | vx = vel[atomIndex]; |
99 | < | vy = vel[atomIndex+1]; |
100 | < | vz = vel[atomIndex+2]; |
101 | < | |
82 | < | scx = (chi + eta[0])*vx + eta[1]*vy + eta[2]*vz; |
83 | < | scy = eta[3]*vx + (chi + eta[4])*vy + eta[5]*vz; |
84 | < | scz = eta[6]*vx + eta[7]*vy + (chi + eta[8])*vz; |
85 | < | |
86 | < | vx += dt2 * ((frc[atomIndex] /atoms[i]->getMass())*eConvert - scx); |
87 | < | vy += dt2 * ((frc[atomIndex+1]/atoms[i]->getMass())*eConvert - scy); |
88 | < | vz += dt2 * ((frc[atomIndex+2]/atoms[i]->getMass())*eConvert - scz); |
98 | > | for (j = 0; j < 3; j++) { |
99 | > | vel[j] += dt2 * ((frc[j] / mass) * eConvert - sc[j]); |
100 | > | rj[j] = pos[j]; |
101 | > | } |
102 | ||
103 | < | vel[atomIndex] = vx; |
91 | < | vel[atomIndex+1] = vy; |
92 | < | vel[atomIndex+2] = vz; |
103 | > | atoms[i]->setVel( vel ); |
104 | ||
105 | // position whole step | |
106 | ||
96 | – | rj[0] = pos[atomIndex]; |
97 | – | rj[1] = pos[atomIndex+1]; |
98 | – | rj[2] = pos[atomIndex+2]; |
99 | – | |
107 | info->wrapVector(rj); | |
108 | ||
109 | < | scx = eta[0]*rj[0] + eta[1]*rj[1] + eta[2]*rj[2]; |
103 | < | scy = eta[3]*rj[0] + eta[4]*rj[1] + eta[5]*rj[2]; |
104 | < | scz = eta[6]*rj[0] + eta[7]*rj[1] + eta[8]*rj[2]; |
109 | > | info->matVecMul3( eta, rj, sc ); |
110 | ||
111 | < | pos[atomIndex] += dt * (vel[atomIndex] + scx); |
112 | < | pos[atomIndex+1] += dt * (vel[atomIndex+1] + scy); |
113 | < | pos[atomIndex+2] += dt * (vel[atomIndex+2] + scz); |
111 | > | for (j = 0; j < 3; j++ ) |
112 | > | pos[j] += dt * (vel[j] + sc[j]); |
113 | > | |
114 | > | atoms[i]->setPos( pos ); |
115 | ||
116 | if( atoms[i]->isDirectional() ){ | |
117 | ||
# | Line 113 | Line 119 | void NPTf::moveA() { | |
119 | ||
120 | // get and convert the torque to body frame | |
121 | ||
122 | < | Tb[0] = dAtom->getTx(); |
117 | < | Tb[1] = dAtom->getTy(); |
118 | < | Tb[2] = dAtom->getTz(); |
119 | < | |
122 | > | dAtom->getTrq( Tb ); |
123 | dAtom->lab2Body( Tb ); | |
124 | ||
125 | // get the angular momentum, and propagate a half step | |
126 | ||
127 | < | ji[0] = dAtom->getJx(); |
128 | < | ji[1] = dAtom->getJy(); |
129 | < | ji[2] = dAtom->getJz(); |
127 | > | dAtom->getJ( ji ); |
128 | > | |
129 | > | for (j=0; j < 3; j++) |
130 | > | ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
131 | ||
128 | – | ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi); |
129 | – | ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi); |
130 | – | ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi); |
131 | – | |
132 | // use the angular velocities to propagate the rotation matrix a | |
133 | // full time step | |
134 | < | |
134 | > | |
135 | > | dAtom->getA(A); |
136 | > | dAtom->getI(I); |
137 | > | |
138 | // rotate about the x-axis | |
139 | < | angle = dt2 * ji[0] / dAtom->getIxx(); |
140 | < | this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
141 | < | |
139 | > | angle = dt2 * ji[0] / I[0][0]; |
140 | > | this->rotate( 1, 2, angle, ji, A ); |
141 | > | |
142 | // rotate about the y-axis | |
143 | < | angle = dt2 * ji[1] / dAtom->getIyy(); |
144 | < | this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
143 | > | angle = dt2 * ji[1] / I[1][1]; |
144 | > | this->rotate( 2, 0, angle, ji, A ); |
145 | ||
146 | // rotate about the z-axis | |
147 | < | angle = dt * ji[2] / dAtom->getIzz(); |
148 | < | this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] ); |
147 | > | angle = dt * ji[2] / I[2][2]; |
148 | > | this->rotate( 0, 1, angle, ji, A); |
149 | ||
150 | // rotate about the y-axis | |
151 | < | angle = dt2 * ji[1] / dAtom->getIyy(); |
152 | < | this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
151 | > | angle = dt2 * ji[1] / I[1][1]; |
152 | > | this->rotate( 2, 0, angle, ji, A ); |
153 | ||
154 | // rotate about the x-axis | |
155 | < | angle = dt2 * ji[0] / dAtom->getIxx(); |
156 | < | this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
155 | > | angle = dt2 * ji[0] / I[0][0]; |
156 | > | this->rotate( 1, 2, angle, ji, A ); |
157 | ||
158 | < | dAtom->setJx( ji[0] ); |
159 | < | dAtom->setJy( ji[1] ); |
160 | < | dAtom->setJz( ji[2] ); |
158 | < | } |
159 | < | |
158 | > | dAtom->setJ( ji ); |
159 | > | dAtom->setA( A ); |
160 | > | } |
161 | } | |
162 | < | |
162 | > | |
163 | // Scale the box after all the positions have been moved: | |
164 | ||
165 | < | |
166 | < | |
166 | < | // Use a taylor expansion for eta products |
167 | < | |
168 | < | info->getBoxM(hm); |
165 | > | // Use a taylor expansion for eta products: Hmat = Hmat . exp(dt * etaMat) |
166 | > | // Hmat = Hmat . ( Ident + dt * etaMat + dt^2 * etaMat*etaMat / 2) |
167 | ||
168 | < | |
168 | > | bigScale = 1.0; |
169 | > | smallScale = 1.0; |
170 | > | offDiagMax = 0.0; |
171 | > | |
172 | > | for(i=0; i<3; i++){ |
173 | > | for(j=0; j<3; j++){ |
174 | > | |
175 | > | // Calculate the matrix Product of the eta array (we only need |
176 | > | // the ij element right now): |
177 | > | |
178 | > | eta2ij = 0.0; |
179 | > | for(k=0; k<3; k++){ |
180 | > | eta2ij += eta[i][k] * eta[k][j]; |
181 | > | } |
182 | > | |
183 | > | scaleMat[i][j] = 0.0; |
184 | > | // identity matrix (see above): |
185 | > | if (i == j) scaleMat[i][j] = 1.0; |
186 | > | // Taylor expansion for the exponential truncated at second order: |
187 | > | scaleMat[i][j] += dt*eta[i][j] + 0.5*dt*dt*eta2ij; |
188 | ||
189 | + | if (i != j) |
190 | + | if (fabs(scaleMat[i][j]) > offDiagMax) |
191 | + | offDiagMax = fabs(scaleMat[i][j]); |
192 | + | |
193 | + | } |
194 | ||
195 | < | |
196 | < | |
197 | < | info->scaleBox(exp(dt*eta)); |
198 | < | |
199 | < | |
195 | > | if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i]; |
196 | > | if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i]; |
197 | > | } |
198 | > | |
199 | > | if ((bigScale > 1.1) || (smallScale < 0.9)) { |
200 | > | sprintf( painCave.errMsg, |
201 | > | "NPTf error: Attempting a Box scaling of more than 10 percent.\n" |
202 | > | " Check your tauBarostat, as it is probably too small!\n\n" |
203 | > | " scaleMat = [%lf\t%lf\t%lf]\n" |
204 | > | " [%lf\t%lf\t%lf]\n" |
205 | > | " [%lf\t%lf\t%lf]\n", |
206 | > | scaleMat[0][0],scaleMat[0][1],scaleMat[0][2], |
207 | > | scaleMat[1][0],scaleMat[1][1],scaleMat[1][2], |
208 | > | scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]); |
209 | > | painCave.isFatal = 1; |
210 | > | simError(); |
211 | > | } else if (offDiagMax > 0.1) { |
212 | > | sprintf( painCave.errMsg, |
213 | > | "NPTf error: Attempting an off-diagonal Box scaling of more than 10 percent.\n" |
214 | > | " Check your tauBarostat, as it is probably too small!\n\n" |
215 | > | " scaleMat = [%lf\t%lf\t%lf]\n" |
216 | > | " [%lf\t%lf\t%lf]\n" |
217 | > | " [%lf\t%lf\t%lf]\n", |
218 | > | scaleMat[0][0],scaleMat[0][1],scaleMat[0][2], |
219 | > | scaleMat[1][0],scaleMat[1][1],scaleMat[1][2], |
220 | > | scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]); |
221 | > | painCave.isFatal = 1; |
222 | > | simError(); |
223 | > | } else { |
224 | > | info->getBoxM(hm); |
225 | > | info->matMul3(hm, scaleMat, hmnew); |
226 | > | info->setBoxM(hmnew); |
227 | > | } |
228 | > | |
229 | } | |
230 | ||
231 | < | void NPTi::moveB( void ){ |
232 | < | int i,j,k; |
233 | < | int atomIndex; |
231 | > | void NPTf::moveB( void ){ |
232 | > | |
233 | > | int i, j; |
234 | DirectionalAtom* dAtom; | |
235 | < | double Tb[3]; |
236 | < | double ji[3]; |
235 | > | double Tb[3], ji[3]; |
236 | > | double vel[3], frc[3]; |
237 | > | double mass; |
238 | > | |
239 | double instaTemp, instaPress, instaVol; | |
240 | double tt2, tb2; | |
241 | + | double sc[3]; |
242 | + | double press[3][3], vScale[3][3]; |
243 | ||
244 | tt2 = tauThermostat * tauThermostat; | |
245 | tb2 = tauBarostat * tauBarostat; | |
246 | ||
247 | instaTemp = tStats->getTemperature(); | |
248 | < | instaPress = tStats->getPressure(); |
248 | > | tStats->getPressureTensor(press); |
249 | instaVol = tStats->getVolume(); | |
250 | < | |
250 | > | |
251 | > | // first evolve chi a half step |
252 | > | |
253 | chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; | |
197 | – | eta += dt2 * ( instaVol * (instaPress - targetPressure) / (NkBT*tb2)); |
254 | ||
255 | + | for (i = 0; i < 3; i++ ) { |
256 | + | for (j = 0; j < 3; j++ ) { |
257 | + | if (i == j) { |
258 | + | |
259 | + | eta[i][j] += dt2 * instaVol * |
260 | + | (press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
261 | + | |
262 | + | vScale[i][j] = eta[i][j] + chi; |
263 | + | |
264 | + | } else { |
265 | + | |
266 | + | eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2); |
267 | + | |
268 | + | vScale[i][j] = eta[i][j]; |
269 | + | |
270 | + | } |
271 | + | } |
272 | + | } |
273 | + | |
274 | for( i=0; i<nAtoms; i++ ){ | |
275 | < | atomIndex = i * 3; |
275 | > | |
276 | > | atoms[i]->getVel( vel ); |
277 | > | atoms[i]->getFrc( frc ); |
278 | > | |
279 | > | mass = atoms[i]->getMass(); |
280 | ||
281 | // velocity half step | |
282 | < | for( j=atomIndex; j<(atomIndex+3); j++ ) |
283 | < | for( j=atomIndex; j<(atomIndex+3); j++ ) |
205 | < | vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert |
206 | < | - vel[j]*(chi+eta)); |
282 | > | |
283 | > | info->matVecMul3( vScale, vel, sc ); |
284 | ||
285 | + | for (j = 0; j < 3; j++) { |
286 | + | vel[j] += dt2 * ((frc[j] / mass) * eConvert - sc[j]); |
287 | + | } |
288 | + | |
289 | + | atoms[i]->setVel( vel ); |
290 | + | |
291 | if( atoms[i]->isDirectional() ){ | |
292 | < | |
292 | > | |
293 | dAtom = (DirectionalAtom *)atoms[i]; | |
294 | < | |
294 | > | |
295 | // get and convert the torque to body frame | |
296 | ||
297 | < | Tb[0] = dAtom->getTx(); |
215 | < | Tb[1] = dAtom->getTy(); |
216 | < | Tb[2] = dAtom->getTz(); |
217 | < | |
297 | > | dAtom->getTrq( Tb ); |
298 | dAtom->lab2Body( Tb ); | |
299 | ||
300 | < | // get the angular momentum, and complete the angular momentum |
221 | < | // half step |
300 | > | // get the angular momentum, and propagate a half step |
301 | ||
302 | < | ji[0] = dAtom->getJx(); |
224 | < | ji[1] = dAtom->getJy(); |
225 | < | ji[2] = dAtom->getJz(); |
302 | > | dAtom->getJ( ji ); |
303 | ||
304 | < | ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi); |
305 | < | ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi); |
229 | < | ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi); |
304 | > | for (j=0; j < 3; j++) |
305 | > | ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
306 | ||
307 | < | dAtom->setJx( ji[0] ); |
308 | < | dAtom->setJy( ji[1] ); |
309 | < | dAtom->setJz( ji[2] ); |
234 | < | } |
307 | > | dAtom->setJ( ji ); |
308 | > | |
309 | > | } |
310 | } | |
311 | } | |
312 | ||
313 | < | int NPTi::readyCheck() { |
313 | > | int NPTf::readyCheck() { |
314 | ||
315 | // First check to see if we have a target temperature. | |
316 | // Not having one is fatal. | |
317 | ||
318 | if (!have_target_temp) { | |
319 | sprintf( painCave.errMsg, | |
320 | < | "NPTi error: You can't use the NPTi integrator\n" |
320 | > | "NPTf error: You can't use the NPTf integrator\n" |
321 | " without a targetTemp!\n" | |
322 | ); | |
323 | painCave.isFatal = 1; | |
# | Line 252 | Line 327 | int NPTi::readyCheck() { | |
327 | ||
328 | if (!have_target_pressure) { | |
329 | sprintf( painCave.errMsg, | |
330 | < | "NPTi error: You can't use the NPTi integrator\n" |
330 | > | "NPTf error: You can't use the NPTf integrator\n" |
331 | " without a targetPressure!\n" | |
332 | ); | |
333 | painCave.isFatal = 1; | |
# | Line 264 | Line 339 | int NPTi::readyCheck() { | |
339 | ||
340 | if (!have_tau_thermostat) { | |
341 | sprintf( painCave.errMsg, | |
342 | < | "NPTi error: If you use the NPTi\n" |
342 | > | "NPTf error: If you use the NPTf\n" |
343 | " integrator, you must set tauThermostat.\n"); | |
344 | painCave.isFatal = 1; | |
345 | simError(); | |
# | Line 275 | Line 350 | int NPTi::readyCheck() { | |
350 | ||
351 | if (!have_tau_barostat) { | |
352 | sprintf( painCave.errMsg, | |
353 | < | "NPTi error: If you use the NPTi\n" |
353 | > | "NPTf error: If you use the NPTf\n" |
354 | " integrator, you must set tauBarostat.\n"); | |
355 | painCave.isFatal = 1; | |
356 | simError(); |
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