9 |
|
#include "Integrator.hpp" |
10 |
|
#include "simError.h" |
11 |
|
|
12 |
+ |
#ifdef IS_MPI |
13 |
+ |
#include "mpiSimulation.hpp" |
14 |
+ |
#endif |
15 |
|
|
16 |
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// Basic non-isotropic thermostating and barostating via the Melchionna |
17 |
|
// modification of the Hoover algorithm: |
28 |
|
{ |
29 |
|
int i, j; |
30 |
|
chi = 0.0; |
31 |
+ |
integralOfChidt = 0.0; |
32 |
|
|
33 |
|
for(i = 0; i < 3; i++) |
34 |
|
for (j = 0; j < 3; j++) |
38 |
|
have_tau_barostat = 0; |
39 |
|
have_target_temp = 0; |
40 |
|
have_target_pressure = 0; |
41 |
+ |
|
42 |
+ |
have_chi_tolerance = 0; |
43 |
+ |
have_eta_tolerance = 0; |
44 |
+ |
have_pos_iter_tolerance = 0; |
45 |
+ |
|
46 |
+ |
oldPos = new double[3*nAtoms]; |
47 |
+ |
oldVel = new double[3*nAtoms]; |
48 |
+ |
oldJi = new double[3*nAtoms]; |
49 |
+ |
#ifdef IS_MPI |
50 |
+ |
Nparticles = mpiSim->getTotAtoms(); |
51 |
+ |
#else |
52 |
+ |
Nparticles = theInfo->n_atoms; |
53 |
+ |
#endif |
54 |
+ |
|
55 |
|
} |
56 |
|
|
57 |
+ |
template<typename T> NPTf<T>::~NPTf() { |
58 |
+ |
delete[] oldPos; |
59 |
+ |
delete[] oldVel; |
60 |
+ |
delete[] oldJi; |
61 |
+ |
} |
62 |
+ |
|
63 |
|
template<typename T> void NPTf<T>::moveA() { |
64 |
< |
|
64 |
> |
|
65 |
> |
// new version of NPTf |
66 |
|
int i, j, k; |
67 |
|
DirectionalAtom* dAtom; |
68 |
|
double Tb[3], ji[3]; |
69 |
< |
double A[3][3], I[3][3]; |
70 |
< |
double angle, mass; |
69 |
> |
|
70 |
> |
double mass; |
71 |
|
double vel[3], pos[3], frc[3]; |
72 |
|
|
73 |
|
double rj[3]; |
77 |
|
double eta2ij; |
78 |
|
double press[3][3], vScale[3][3], hm[3][3], hmnew[3][3], scaleMat[3][3]; |
79 |
|
double bigScale, smallScale, offDiagMax; |
80 |
+ |
double COM[3]; |
81 |
|
|
82 |
|
tt2 = tauThermostat * tauThermostat; |
83 |
|
tb2 = tauBarostat * tauBarostat; |
85 |
|
instaTemp = tStats->getTemperature(); |
86 |
|
tStats->getPressureTensor(press); |
87 |
|
instaVol = tStats->getVolume(); |
62 |
– |
|
63 |
– |
// first evolve chi a half step |
88 |
|
|
89 |
< |
chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
89 |
> |
tStats->getCOM(COM); |
90 |
|
|
91 |
+ |
//calculate scale factor of veloity |
92 |
|
for (i = 0; i < 3; i++ ) { |
93 |
|
for (j = 0; j < 3; j++ ) { |
94 |
+ |
vScale[i][j] = eta[i][j]; |
95 |
+ |
|
96 |
|
if (i == j) { |
97 |
< |
|
98 |
< |
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 |
< |
} |
97 |
> |
vScale[i][j] += chi; |
98 |
> |
} |
99 |
|
} |
100 |
|
} |
101 |
< |
|
101 |
> |
|
102 |
> |
//evolve velocity half step |
103 |
|
for( i=0; i<nAtoms; i++ ){ |
104 |
|
|
105 |
|
atoms[i]->getVel( vel ); |
89 |
– |
atoms[i]->getPos( pos ); |
106 |
|
atoms[i]->getFrc( frc ); |
107 |
|
|
108 |
|
mass = atoms[i]->getMass(); |
109 |
|
|
94 |
– |
// velocity half step |
95 |
– |
|
110 |
|
info->matVecMul3( vScale, vel, sc ); |
111 |
< |
|
112 |
< |
for (j = 0; j < 3; j++) { |
111 |
> |
|
112 |
> |
for (j=0; j < 3; j++) { |
113 |
> |
// velocity half step |
114 |
|
vel[j] += dt2 * ((frc[j] / mass) * eConvert - sc[j]); |
100 |
– |
rj[j] = pos[j]; |
115 |
|
} |
116 |
|
|
117 |
|
atoms[i]->setVel( vel ); |
104 |
– |
|
105 |
– |
// position whole step |
106 |
– |
|
107 |
– |
info->wrapVector(rj); |
108 |
– |
|
109 |
– |
info->matVecMul3( eta, rj, sc ); |
110 |
– |
|
111 |
– |
for (j = 0; j < 3; j++ ) |
112 |
– |
pos[j] += dt * (vel[j] + sc[j]); |
113 |
– |
|
114 |
– |
atoms[i]->setPos( pos ); |
118 |
|
|
119 |
|
if( atoms[i]->isDirectional() ){ |
120 |
|
|
121 |
|
dAtom = (DirectionalAtom *)atoms[i]; |
122 |
< |
|
122 |
> |
|
123 |
|
// get and convert the torque to body frame |
124 |
|
|
125 |
|
dAtom->getTrq( Tb ); |
131 |
|
|
132 |
|
for (j=0; j < 3; j++) |
133 |
|
ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
131 |
– |
|
132 |
– |
// use the angular velocities to propagate the rotation matrix a |
133 |
– |
// full time step |
134 |
– |
|
135 |
– |
dAtom->getA(A); |
136 |
– |
dAtom->getI(I); |
137 |
– |
|
138 |
– |
// rotate about the x-axis |
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] / I[1][1]; |
144 |
– |
this->rotate( 2, 0, angle, ji, A ); |
145 |
– |
|
146 |
– |
// rotate about the z-axis |
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] / I[1][1]; |
152 |
– |
this->rotate( 2, 0, angle, ji, A ); |
153 |
– |
|
154 |
– |
// rotate about the x-axis |
155 |
– |
angle = dt2 * ji[0] / I[0][0]; |
156 |
– |
this->rotate( 1, 2, angle, ji, A ); |
134 |
|
|
135 |
+ |
this->rotationPropagation( dAtom, ji ); |
136 |
+ |
|
137 |
|
dAtom->setJ( ji ); |
138 |
< |
dAtom->setA( A ); |
160 |
< |
} |
138 |
> |
} |
139 |
|
} |
140 |
+ |
|
141 |
+ |
// advance chi half step |
142 |
+ |
chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
143 |
+ |
|
144 |
+ |
// calculate the integral of chidt |
145 |
+ |
integralOfChidt += dt2*chi; |
146 |
+ |
|
147 |
+ |
// advance eta half step |
148 |
+ |
|
149 |
+ |
for(i = 0; i < 3; i ++) |
150 |
+ |
for(j = 0; j < 3; j++){ |
151 |
+ |
if( i == j) |
152 |
+ |
eta[i][j] += dt2 * instaVol * |
153 |
+ |
(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
154 |
+ |
else |
155 |
+ |
eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2); |
156 |
+ |
} |
157 |
+ |
|
158 |
+ |
//save the old positions |
159 |
+ |
for(i = 0; i < nAtoms; i++){ |
160 |
+ |
atoms[i]->getPos(pos); |
161 |
+ |
for(j = 0; j < 3; j++) |
162 |
+ |
oldPos[i*3 + j] = pos[j]; |
163 |
+ |
} |
164 |
|
|
165 |
+ |
//the first estimation of r(t+dt) is equal to r(t) |
166 |
+ |
|
167 |
+ |
for(k = 0; k < 4; k ++){ |
168 |
+ |
|
169 |
+ |
for(i =0 ; i < nAtoms; i++){ |
170 |
+ |
|
171 |
+ |
atoms[i]->getVel(vel); |
172 |
+ |
atoms[i]->getPos(pos); |
173 |
+ |
|
174 |
+ |
for(j = 0; j < 3; j++) |
175 |
+ |
rj[j] = (oldPos[i*3 + j] + pos[j])/2 - COM[j]; |
176 |
+ |
|
177 |
+ |
info->matVecMul3( eta, rj, sc ); |
178 |
+ |
|
179 |
+ |
for(j = 0; j < 3; j++) |
180 |
+ |
pos[j] = oldPos[i*3 + j] + dt*(vel[j] + sc[j]); |
181 |
+ |
|
182 |
+ |
atoms[i]->setPos( pos ); |
183 |
+ |
|
184 |
+ |
} |
185 |
+ |
|
186 |
+ |
if (nConstrained) { |
187 |
+ |
constrainA(); |
188 |
+ |
} |
189 |
+ |
} |
190 |
+ |
|
191 |
+ |
|
192 |
|
// Scale the box after all the positions have been moved: |
193 |
|
|
194 |
|
// Use a taylor expansion for eta products: Hmat = Hmat . exp(dt * etaMat) |
218 |
|
if (i != j) |
219 |
|
if (fabs(scaleMat[i][j]) > offDiagMax) |
220 |
|
offDiagMax = fabs(scaleMat[i][j]); |
192 |
– |
|
221 |
|
} |
222 |
|
|
223 |
|
if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i]; |
258 |
|
|
259 |
|
template<typename T> void NPTf<T>::moveB( void ){ |
260 |
|
|
261 |
< |
int i, j; |
261 |
> |
//new version of NPTf |
262 |
> |
int i, j, k; |
263 |
|
DirectionalAtom* dAtom; |
264 |
|
double Tb[3], ji[3]; |
265 |
< |
double vel[3], frc[3]; |
265 |
> |
double vel[3], myVel[3], frc[3]; |
266 |
|
double mass; |
267 |
|
|
268 |
|
double instaTemp, instaPress, instaVol; |
269 |
|
double tt2, tb2; |
270 |
|
double sc[3]; |
271 |
|
double press[3][3], vScale[3][3]; |
272 |
+ |
double oldChi, prevChi; |
273 |
+ |
double oldEta[3][3], prevEta[3][3], diffEta; |
274 |
|
|
275 |
|
tt2 = tauThermostat * tauThermostat; |
276 |
|
tb2 = tauBarostat * tauBarostat; |
277 |
|
|
278 |
< |
instaTemp = tStats->getTemperature(); |
279 |
< |
tStats->getPressureTensor(press); |
280 |
< |
instaVol = tStats->getVolume(); |
250 |
< |
|
251 |
< |
// first evolve chi a half step |
278 |
> |
// Set things up for the iteration: |
279 |
> |
|
280 |
> |
oldChi = chi; |
281 |
|
|
282 |
< |
chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
283 |
< |
|
284 |
< |
for (i = 0; i < 3; i++ ) { |
256 |
< |
for (j = 0; j < 3; j++ ) { |
257 |
< |
if (i == j) { |
282 |
> |
for(i = 0; i < 3; i++) |
283 |
> |
for(j = 0; j < 3; j++) |
284 |
> |
oldEta[i][j] = eta[i][j]; |
285 |
|
|
286 |
< |
eta[i][j] += dt2 * instaVol * |
260 |
< |
(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
286 |
> |
for( i=0; i<nAtoms; i++ ){ |
287 |
|
|
288 |
< |
vScale[i][j] = eta[i][j] + chi; |
263 |
< |
|
264 |
< |
} else { |
265 |
< |
|
266 |
< |
eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2); |
288 |
> |
atoms[i]->getVel( vel ); |
289 |
|
|
290 |
< |
vScale[i][j] = eta[i][j]; |
291 |
< |
|
292 |
< |
} |
290 |
> |
for (j=0; j < 3; j++) |
291 |
> |
oldVel[3*i + j] = vel[j]; |
292 |
> |
|
293 |
> |
if( atoms[i]->isDirectional() ){ |
294 |
> |
|
295 |
> |
dAtom = (DirectionalAtom *)atoms[i]; |
296 |
> |
|
297 |
> |
dAtom->getJ( ji ); |
298 |
> |
|
299 |
> |
for (j=0; j < 3; j++) |
300 |
> |
oldJi[3*i + j] = ji[j]; |
301 |
> |
|
302 |
|
} |
303 |
|
} |
304 |
|
|
305 |
< |
for( i=0; i<nAtoms; i++ ){ |
305 |
> |
// do the iteration: |
306 |
|
|
307 |
< |
atoms[i]->getVel( vel ); |
308 |
< |
atoms[i]->getFrc( frc ); |
307 |
> |
instaVol = tStats->getVolume(); |
308 |
> |
|
309 |
> |
for (k=0; k < 4; k++) { |
310 |
> |
|
311 |
> |
instaTemp = tStats->getTemperature(); |
312 |
> |
tStats->getPressureTensor(press); |
313 |
|
|
314 |
< |
mass = atoms[i]->getMass(); |
314 |
> |
// evolve chi another half step using the temperature at t + dt/2 |
315 |
> |
|
316 |
> |
prevChi = chi; |
317 |
> |
chi = oldChi + dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
318 |
|
|
319 |
< |
// velocity half step |
320 |
< |
|
321 |
< |
info->matVecMul3( vScale, vel, sc ); |
284 |
< |
|
285 |
< |
for (j = 0; j < 3; j++) { |
286 |
< |
vel[j] += dt2 * ((frc[j] / mass) * eConvert - sc[j]); |
287 |
< |
} |
319 |
> |
for(i = 0; i < 3; i++) |
320 |
> |
for(j = 0; j < 3; j++) |
321 |
> |
prevEta[i][j] = eta[i][j]; |
322 |
|
|
323 |
< |
atoms[i]->setVel( vel ); |
323 |
> |
//advance eta half step and calculate scale factor for velocity |
324 |
> |
|
325 |
> |
for(i = 0; i < 3; i ++) |
326 |
> |
for(j = 0; j < 3; j++){ |
327 |
> |
if( i == j) { |
328 |
> |
eta[i][j] = oldEta[i][j] + dt2 * instaVol * |
329 |
> |
(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
330 |
> |
vScale[i][j] = eta[i][j] + chi; |
331 |
> |
} else { |
332 |
> |
eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2); |
333 |
> |
vScale[i][j] = eta[i][j]; |
334 |
> |
} |
335 |
> |
} |
336 |
|
|
337 |
< |
if( atoms[i]->isDirectional() ){ |
337 |
> |
for( i=0; i<nAtoms; i++ ){ |
338 |
|
|
339 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
340 |
< |
|
295 |
< |
// get and convert the torque to body frame |
339 |
> |
atoms[i]->getFrc( frc ); |
340 |
> |
atoms[i]->getVel(vel); |
341 |
|
|
342 |
< |
dAtom->getTrq( Tb ); |
343 |
< |
dAtom->lab2Body( Tb ); |
342 |
> |
mass = atoms[i]->getMass(); |
343 |
> |
|
344 |
> |
for (j = 0; j < 3; j++) |
345 |
> |
myVel[j] = oldVel[3*i + j]; |
346 |
|
|
347 |
< |
// get the angular momentum, and propagate a half step |
347 |
> |
info->matVecMul3( vScale, myVel, sc ); |
348 |
|
|
349 |
< |
dAtom->getJ( ji ); |
349 |
> |
// velocity half step |
350 |
> |
for (j=0; j < 3; j++) { |
351 |
> |
// velocity half step (use chi from previous step here): |
352 |
> |
vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass) * eConvert - sc[j]); |
353 |
> |
} |
354 |
|
|
355 |
< |
for (j=0; j < 3; j++) |
305 |
< |
ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
355 |
> |
atoms[i]->setVel( vel ); |
356 |
|
|
357 |
< |
dAtom->setJ( ji ); |
357 |
> |
if( atoms[i]->isDirectional() ){ |
358 |
|
|
359 |
< |
} |
359 |
> |
dAtom = (DirectionalAtom *)atoms[i]; |
360 |
> |
|
361 |
> |
// get and convert the torque to body frame |
362 |
> |
|
363 |
> |
dAtom->getTrq( Tb ); |
364 |
> |
dAtom->lab2Body( Tb ); |
365 |
> |
|
366 |
> |
for (j=0; j < 3; j++) |
367 |
> |
ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi); |
368 |
> |
|
369 |
> |
dAtom->setJ( ji ); |
370 |
> |
} |
371 |
> |
} |
372 |
> |
|
373 |
> |
if (nConstrained) { |
374 |
> |
constrainB(); |
375 |
> |
} |
376 |
> |
|
377 |
> |
diffEta = 0; |
378 |
> |
for(i = 0; i < 3; i++) |
379 |
> |
diffEta += pow(prevEta[i][i] - eta[i][i], 2); |
380 |
> |
|
381 |
> |
if (fabs(prevChi - chi) <= chiTolerance && sqrt(diffEta / 3) <= etaTolerance) |
382 |
> |
break; |
383 |
|
} |
384 |
+ |
|
385 |
+ |
//calculate integral of chidt |
386 |
+ |
integralOfChidt += dt2*chi; |
387 |
+ |
|
388 |
|
} |
389 |
|
|
390 |
+ |
template<typename T> void NPTf<T>::resetIntegrator() { |
391 |
+ |
int i,j; |
392 |
+ |
|
393 |
+ |
chi = 0.0; |
394 |
+ |
|
395 |
+ |
for(i = 0; i < 3; i++) |
396 |
+ |
for (j = 0; j < 3; j++) |
397 |
+ |
eta[i][j] = 0.0; |
398 |
+ |
|
399 |
+ |
} |
400 |
+ |
|
401 |
|
template<typename T> int NPTf<T>::readyCheck() { |
402 |
+ |
|
403 |
+ |
//check parent's readyCheck() first |
404 |
+ |
if (T::readyCheck() == -1) |
405 |
+ |
return -1; |
406 |
|
|
407 |
|
// First check to see if we have a target temperature. |
408 |
|
// Not having one is fatal. |
449 |
|
return -1; |
450 |
|
} |
451 |
|
|
452 |
< |
// We need NkBT a lot, so just set it here: |
452 |
> |
|
453 |
> |
// We need NkBT a lot, so just set it here: This is the RAW number |
454 |
> |
// of particles, so no subtraction or addition of constraints or |
455 |
> |
// orientational degrees of freedom: |
456 |
> |
|
457 |
> |
NkBT = (double)Nparticles * kB * targetTemp; |
458 |
> |
|
459 |
> |
// fkBT is used because the thermostat operates on more degrees of freedom |
460 |
> |
// than the barostat (when there are particles with orientational degrees |
461 |
> |
// of freedom). ndf = 3 * (n_atoms + n_oriented -1) - n_constraint - nZcons |
462 |
> |
|
463 |
> |
fkBT = (double)info->ndf * kB * targetTemp; |
464 |
|
|
362 |
– |
NkBT = (double)info->ndf * kB * targetTemp; |
363 |
– |
|
465 |
|
return 1; |
466 |
|
} |
467 |
+ |
|
468 |
+ |
template<typename T> double NPTf<T>::getConservedQuantity(void){ |
469 |
+ |
|
470 |
+ |
double conservedQuantity; |
471 |
+ |
double Energy; |
472 |
+ |
double thermostat_kinetic; |
473 |
+ |
double thermostat_potential; |
474 |
+ |
double barostat_kinetic; |
475 |
+ |
double barostat_potential; |
476 |
+ |
double trEta; |
477 |
+ |
double a[3][3], b[3][3]; |
478 |
+ |
|
479 |
+ |
Energy = tStats->getTotalE(); |
480 |
+ |
|
481 |
+ |
thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi / |
482 |
+ |
(2.0 * eConvert); |
483 |
+ |
|
484 |
+ |
thermostat_potential = fkBT* integralOfChidt / eConvert; |
485 |
+ |
|
486 |
+ |
info->transposeMat3(eta, a); |
487 |
+ |
info->matMul3(a, eta, b); |
488 |
+ |
trEta = info->matTrace3(b); |
489 |
+ |
|
490 |
+ |
barostat_kinetic = NkBT * tauBarostat * tauBarostat * trEta / |
491 |
+ |
(2.0 * eConvert); |
492 |
+ |
|
493 |
+ |
barostat_potential = (targetPressure * tStats->getVolume() / p_convert) / |
494 |
+ |
eConvert; |
495 |
+ |
|
496 |
+ |
conservedQuantity = Energy + thermostat_kinetic + thermostat_potential + |
497 |
+ |
barostat_kinetic + barostat_potential; |
498 |
+ |
|
499 |
+ |
cout.width(8); |
500 |
+ |
cout.precision(8); |
501 |
+ |
|
502 |
+ |
cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic << |
503 |
+ |
"\t" << thermostat_potential << "\t" << barostat_kinetic << |
504 |
+ |
"\t" << barostat_potential << "\t" << conservedQuantity << endl; |
505 |
+ |
|
506 |
+ |
return conservedQuantity; |
507 |
+ |
} |