1 |
gezelter |
617 |
#include <cmath> |
2 |
gezelter |
606 |
#include "Atom.hpp" |
3 |
|
|
#include "Molecule.hpp" |
4 |
|
|
#include "SRI.hpp" |
5 |
|
|
#include "AbstractClasses.hpp" |
6 |
|
|
#include "SimInfo.hpp" |
7 |
|
|
#include "ForceFields.hpp" |
8 |
|
|
#include "Thermo.hpp" |
9 |
|
|
#include "ReadWrite.hpp" |
10 |
|
|
#include "Integrator.hpp" |
11 |
|
|
#include "simError.h" |
12 |
|
|
|
13 |
mmeineke |
746 |
|
14 |
gezelter |
606 |
// Basic non-isotropic thermostating and barostating via the Melchionna |
15 |
|
|
// modification of the Hoover algorithm: |
16 |
|
|
// |
17 |
|
|
// Melchionna, S., Ciccotti, G., and Holian, B. L., 1993, |
18 |
|
|
// Molec. Phys., 78, 533. |
19 |
|
|
// |
20 |
|
|
// and |
21 |
|
|
// |
22 |
|
|
// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499. |
23 |
|
|
|
24 |
|
|
// The NPTfm variant scales the molecular center-of-mass coordinates |
25 |
|
|
// instead of the atomic coordinates |
26 |
|
|
|
27 |
tim |
645 |
template<typename T> NPTfm<T>::NPTfm ( SimInfo *theInfo, ForceFields* the_ff): |
28 |
|
|
T( theInfo, the_ff ) |
29 |
gezelter |
606 |
{ |
30 |
|
|
int i, j; |
31 |
|
|
chi = 0.0; |
32 |
|
|
|
33 |
|
|
for(i = 0; i < 3; i++) |
34 |
|
|
for (j = 0; j < 3; j++) |
35 |
|
|
eta[i][j] = 0.0; |
36 |
|
|
|
37 |
|
|
have_tau_thermostat = 0; |
38 |
|
|
have_tau_barostat = 0; |
39 |
|
|
have_target_temp = 0; |
40 |
|
|
have_target_pressure = 0; |
41 |
|
|
} |
42 |
|
|
|
43 |
tim |
645 |
template<typename T> void NPTfm<T>::moveA() { |
44 |
gezelter |
606 |
|
45 |
|
|
int i, j, k; |
46 |
|
|
DirectionalAtom* dAtom; |
47 |
|
|
double Tb[3], ji[3]; |
48 |
|
|
double A[3][3], I[3][3]; |
49 |
|
|
double angle, mass; |
50 |
|
|
double vel[3], pos[3], frc[3]; |
51 |
|
|
|
52 |
|
|
double rj[3]; |
53 |
|
|
double instaTemp, instaPress, instaVol; |
54 |
|
|
double tt2, tb2; |
55 |
|
|
double sc[3]; |
56 |
gezelter |
617 |
double eta2ij, smallScale, bigScale, offDiagMax; |
57 |
gezelter |
606 |
double press[3][3], vScale[3][3], hm[3][3], hmnew[3][3], scaleMat[3][3]; |
58 |
|
|
|
59 |
|
|
int nInMol; |
60 |
|
|
double rc[3]; |
61 |
|
|
|
62 |
|
|
nMols = info->n_mol; |
63 |
|
|
myMolecules = info->molecules; |
64 |
|
|
|
65 |
|
|
tt2 = tauThermostat * tauThermostat; |
66 |
|
|
tb2 = tauBarostat * tauBarostat; |
67 |
|
|
|
68 |
|
|
instaTemp = tStats->getTemperature(); |
69 |
|
|
tStats->getPressureTensor(press); |
70 |
|
|
instaVol = tStats->getVolume(); |
71 |
|
|
|
72 |
|
|
// first evolve chi a half step |
73 |
|
|
|
74 |
|
|
chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
75 |
|
|
|
76 |
|
|
for (i = 0; i < 3; i++ ) { |
77 |
|
|
for (j = 0; j < 3; j++ ) { |
78 |
|
|
if (i == j) { |
79 |
|
|
|
80 |
|
|
eta[i][j] += dt2 * instaVol * |
81 |
|
|
(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
82 |
|
|
|
83 |
|
|
vScale[i][j] = eta[i][j] + chi; |
84 |
|
|
|
85 |
|
|
} else { |
86 |
|
|
|
87 |
|
|
eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2); |
88 |
|
|
|
89 |
|
|
vScale[i][j] = eta[i][j]; |
90 |
|
|
|
91 |
|
|
} |
92 |
|
|
} |
93 |
|
|
} |
94 |
|
|
|
95 |
|
|
|
96 |
|
|
for (i = 0; i < nMols; i++) { |
97 |
|
|
|
98 |
|
|
myMolecules[i].getCOM(rc); |
99 |
|
|
|
100 |
|
|
nInMol = myMolecules[i].getNAtoms(); |
101 |
|
|
myAtoms = myMolecules[i].getMyAtoms(); |
102 |
|
|
|
103 |
|
|
// find the minimum image coordinates of the molecular centers of mass: |
104 |
|
|
|
105 |
|
|
info->wrapVector(rc); |
106 |
|
|
|
107 |
|
|
for( j=0; j< nInMol; j++ ){ |
108 |
|
|
|
109 |
|
|
if(myAtoms[j] != NULL) { |
110 |
|
|
|
111 |
|
|
myAtoms[j]->getVel( vel ); |
112 |
|
|
myAtoms[j]->getPos( pos ); |
113 |
|
|
myAtoms[j]->getFrc( frc ); |
114 |
|
|
|
115 |
|
|
mass = myAtoms[j]->getMass(); |
116 |
|
|
|
117 |
|
|
// velocity half step |
118 |
|
|
|
119 |
|
|
info->matVecMul3( vScale, vel, sc ); |
120 |
|
|
|
121 |
|
|
for (k = 0; k < 3; k++) |
122 |
|
|
vel[k] += dt2 * ((frc[k] / mass) * eConvert - sc[k]); |
123 |
|
|
|
124 |
|
|
myAtoms[j]->setVel( vel ); |
125 |
|
|
|
126 |
|
|
// position whole step |
127 |
|
|
|
128 |
|
|
info->matVecMul3( eta, rc, sc ); |
129 |
|
|
|
130 |
|
|
for (k = 0; k < 3; k++ ) |
131 |
|
|
pos[k] += dt * (vel[k] + sc[k]); |
132 |
gezelter |
617 |
|
133 |
|
|
myAtoms[j]->setPos( pos ); |
134 |
gezelter |
606 |
|
135 |
|
|
if( myAtoms[j]->isDirectional() ){ |
136 |
|
|
|
137 |
|
|
dAtom = (DirectionalAtom *)myAtoms[j]; |
138 |
|
|
|
139 |
|
|
// get and convert the torque to body frame |
140 |
|
|
|
141 |
|
|
dAtom->getTrq( Tb ); |
142 |
|
|
dAtom->lab2Body( Tb ); |
143 |
|
|
|
144 |
|
|
// get the angular momentum, and propagate a half step |
145 |
|
|
|
146 |
|
|
dAtom->getJ( ji ); |
147 |
|
|
|
148 |
|
|
for (k=0; k < 3; k++) |
149 |
|
|
ji[k] += dt2 * (Tb[k] * eConvert - ji[k]*chi); |
150 |
|
|
|
151 |
|
|
// use the angular velocities to propagate the rotation matrix a |
152 |
|
|
// full time step |
153 |
|
|
|
154 |
|
|
dAtom->getA(A); |
155 |
|
|
dAtom->getI(I); |
156 |
|
|
|
157 |
|
|
// rotate about the x-axis |
158 |
|
|
angle = dt2 * ji[0] / I[0][0]; |
159 |
|
|
this->rotate( 1, 2, angle, ji, A ); |
160 |
|
|
|
161 |
|
|
// rotate about the y-axis |
162 |
|
|
angle = dt2 * ji[1] / I[1][1]; |
163 |
|
|
this->rotate( 2, 0, angle, ji, A ); |
164 |
|
|
|
165 |
|
|
// rotate about the z-axis |
166 |
|
|
angle = dt * ji[2] / I[2][2]; |
167 |
|
|
this->rotate( 0, 1, angle, ji, A); |
168 |
|
|
|
169 |
|
|
// rotate about the y-axis |
170 |
|
|
angle = dt2 * ji[1] / I[1][1]; |
171 |
|
|
this->rotate( 2, 0, angle, ji, A ); |
172 |
|
|
|
173 |
|
|
// rotate about the x-axis |
174 |
|
|
angle = dt2 * ji[0] / I[0][0]; |
175 |
|
|
this->rotate( 1, 2, angle, ji, A ); |
176 |
|
|
|
177 |
|
|
dAtom->setJ( ji ); |
178 |
|
|
dAtom->setA( A ); |
179 |
|
|
} |
180 |
|
|
} |
181 |
|
|
} |
182 |
|
|
} |
183 |
|
|
|
184 |
|
|
// Scale the box after all the positions have been moved: |
185 |
|
|
|
186 |
|
|
// Use a taylor expansion for eta products: Hmat = Hmat . exp(dt * etaMat) |
187 |
|
|
// Hmat = Hmat . ( Ident + dt * etaMat + dt^2 * etaMat*etaMat / 2) |
188 |
|
|
|
189 |
|
|
|
190 |
gezelter |
617 |
bigScale = 1.0; |
191 |
|
|
smallScale = 1.0; |
192 |
|
|
offDiagMax = 0.0; |
193 |
|
|
|
194 |
gezelter |
606 |
for(i=0; i<3; i++){ |
195 |
|
|
for(j=0; j<3; j++){ |
196 |
|
|
|
197 |
|
|
// Calculate the matrix Product of the eta array (we only need |
198 |
|
|
// the ij element right now): |
199 |
|
|
|
200 |
|
|
eta2ij = 0.0; |
201 |
|
|
for(k=0; k<3; k++){ |
202 |
|
|
eta2ij += eta[i][k] * eta[k][j]; |
203 |
|
|
} |
204 |
|
|
|
205 |
|
|
scaleMat[i][j] = 0.0; |
206 |
|
|
// identity matrix (see above): |
207 |
|
|
if (i == j) scaleMat[i][j] = 1.0; |
208 |
|
|
// Taylor expansion for the exponential truncated at second order: |
209 |
|
|
scaleMat[i][j] += dt*eta[i][j] + 0.5*dt*dt*eta2ij; |
210 |
gezelter |
617 |
|
211 |
|
|
if (i != j) |
212 |
|
|
if (fabs(scaleMat[i][j]) > offDiagMax) |
213 |
|
|
offDiagMax = fabs(scaleMat[i][j]); |
214 |
gezelter |
606 |
} |
215 |
gezelter |
617 |
if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i]; |
216 |
|
|
if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i]; |
217 |
gezelter |
606 |
} |
218 |
|
|
|
219 |
gezelter |
617 |
if ((bigScale > 1.1) || (smallScale < 0.9)) { |
220 |
|
|
sprintf( painCave.errMsg, |
221 |
|
|
"NPTf error: Attempting a Box scaling of more than 10 percent.\n" |
222 |
|
|
" Check your tauBarostat, as it is probably too small!\n\n" |
223 |
|
|
" scaleMat = [%lf\t%lf\t%lf]\n" |
224 |
|
|
" [%lf\t%lf\t%lf]\n" |
225 |
|
|
" [%lf\t%lf\t%lf]\n", |
226 |
|
|
scaleMat[0][0],scaleMat[0][1],scaleMat[0][2], |
227 |
|
|
scaleMat[1][0],scaleMat[1][1],scaleMat[1][2], |
228 |
|
|
scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]); |
229 |
|
|
painCave.isFatal = 1; |
230 |
|
|
simError(); |
231 |
|
|
} else if (offDiagMax > 0.1) { |
232 |
|
|
sprintf( painCave.errMsg, |
233 |
|
|
"NPTf error: Attempting an off-diagonal Box scaling of more than 10 percent.\n" |
234 |
|
|
" Check your tauBarostat, as it is probably too small!\n\n" |
235 |
|
|
" scaleMat = [%lf\t%lf\t%lf]\n" |
236 |
|
|
" [%lf\t%lf\t%lf]\n" |
237 |
|
|
" [%lf\t%lf\t%lf]\n", |
238 |
|
|
scaleMat[0][0],scaleMat[0][1],scaleMat[0][2], |
239 |
|
|
scaleMat[1][0],scaleMat[1][1],scaleMat[1][2], |
240 |
|
|
scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]); |
241 |
|
|
painCave.isFatal = 1; |
242 |
|
|
simError(); |
243 |
|
|
} else { |
244 |
|
|
info->getBoxM(hm); |
245 |
|
|
info->matMul3(hm, scaleMat, hmnew); |
246 |
|
|
info->setBoxM(hmnew); |
247 |
|
|
} |
248 |
gezelter |
606 |
} |
249 |
|
|
|
250 |
tim |
645 |
template<typename T> void NPTfm<T>::moveB( void ){ |
251 |
gezelter |
606 |
|
252 |
|
|
int i, j; |
253 |
|
|
DirectionalAtom* dAtom; |
254 |
|
|
double Tb[3], ji[3]; |
255 |
|
|
double vel[3], frc[3]; |
256 |
|
|
double mass; |
257 |
|
|
|
258 |
|
|
double instaTemp, instaPress, instaVol; |
259 |
|
|
double tt2, tb2; |
260 |
|
|
double sc[3]; |
261 |
|
|
double press[3][3], vScale[3][3]; |
262 |
|
|
|
263 |
|
|
tt2 = tauThermostat * tauThermostat; |
264 |
|
|
tb2 = tauBarostat * tauBarostat; |
265 |
|
|
|
266 |
|
|
instaTemp = tStats->getTemperature(); |
267 |
|
|
tStats->getPressureTensor(press); |
268 |
|
|
instaVol = tStats->getVolume(); |
269 |
|
|
|
270 |
|
|
// first evolve chi a half step |
271 |
|
|
|
272 |
|
|
chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
273 |
|
|
|
274 |
|
|
for (i = 0; i < 3; i++ ) { |
275 |
|
|
for (j = 0; j < 3; j++ ) { |
276 |
|
|
if (i == j) { |
277 |
|
|
|
278 |
|
|
eta[i][j] += dt2 * instaVol * |
279 |
|
|
(press[i][j] - targetPressure/p_convert) / (NkBT*tb2); |
280 |
|
|
|
281 |
|
|
vScale[i][j] = eta[i][j] + chi; |
282 |
|
|
|
283 |
|
|
} else { |
284 |
|
|
|
285 |
|
|
eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2); |
286 |
|
|
|
287 |
|
|
vScale[i][j] = eta[i][j]; |
288 |
|
|
|
289 |
|
|
} |
290 |
|
|
} |
291 |
|
|
} |
292 |
|
|
|
293 |
|
|
for( i=0; i<nAtoms; i++ ){ |
294 |
|
|
|
295 |
|
|
atoms[i]->getVel( vel ); |
296 |
|
|
atoms[i]->getFrc( frc ); |
297 |
|
|
|
298 |
|
|
mass = atoms[i]->getMass(); |
299 |
|
|
|
300 |
|
|
// velocity half step |
301 |
|
|
|
302 |
|
|
info->matVecMul3( vScale, vel, sc ); |
303 |
|
|
|
304 |
|
|
for (j = 0; j < 3; j++) { |
305 |
|
|
vel[j] += dt2 * ((frc[j] / mass) * eConvert - sc[j]); |
306 |
|
|
} |
307 |
|
|
|
308 |
|
|
atoms[i]->setVel( vel ); |
309 |
|
|
|
310 |
|
|
if( atoms[i]->isDirectional() ){ |
311 |
|
|
|
312 |
|
|
dAtom = (DirectionalAtom *)atoms[i]; |
313 |
|
|
|
314 |
|
|
// get and convert the torque to body frame |
315 |
|
|
|
316 |
|
|
dAtom->getTrq( Tb ); |
317 |
|
|
dAtom->lab2Body( Tb ); |
318 |
|
|
|
319 |
|
|
// get the angular momentum, and propagate a half step |
320 |
|
|
|
321 |
|
|
dAtom->getJ( ji ); |
322 |
|
|
|
323 |
|
|
for (j=0; j < 3; j++) |
324 |
|
|
ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
325 |
|
|
|
326 |
|
|
dAtom->setJ( ji ); |
327 |
|
|
|
328 |
|
|
} |
329 |
|
|
} |
330 |
|
|
} |
331 |
|
|
|
332 |
mmeineke |
746 |
template<typename T> void NPTfm<T>::resetIntegrator() { |
333 |
|
|
int i,j; |
334 |
|
|
|
335 |
|
|
chi = 0.0; |
336 |
|
|
|
337 |
|
|
for(i = 0; i < 3; i++) |
338 |
|
|
for (j = 0; j < 3; j++) |
339 |
|
|
eta[i][j] = 0.0; |
340 |
|
|
} |
341 |
|
|
|
342 |
tim |
645 |
template<typename T> int NPTfm<T>::readyCheck() { |
343 |
tim |
658 |
|
344 |
|
|
//check parent's readyCheck() first |
345 |
|
|
if (T::readyCheck() == -1) |
346 |
|
|
return -1; |
347 |
|
|
|
348 |
gezelter |
606 |
// First check to see if we have a target temperature. |
349 |
|
|
// Not having one is fatal. |
350 |
|
|
|
351 |
|
|
if (!have_target_temp) { |
352 |
|
|
sprintf( painCave.errMsg, |
353 |
|
|
"NPTfm error: You can't use the NPTfm integrator\n" |
354 |
|
|
" without a targetTemp!\n" |
355 |
|
|
); |
356 |
|
|
painCave.isFatal = 1; |
357 |
|
|
simError(); |
358 |
|
|
return -1; |
359 |
|
|
} |
360 |
|
|
|
361 |
|
|
if (!have_target_pressure) { |
362 |
|
|
sprintf( painCave.errMsg, |
363 |
|
|
"NPTfm error: You can't use the NPTfm integrator\n" |
364 |
|
|
" without a targetPressure!\n" |
365 |
|
|
); |
366 |
|
|
painCave.isFatal = 1; |
367 |
|
|
simError(); |
368 |
|
|
return -1; |
369 |
|
|
} |
370 |
|
|
|
371 |
|
|
// We must set tauThermostat. |
372 |
|
|
|
373 |
|
|
if (!have_tau_thermostat) { |
374 |
|
|
sprintf( painCave.errMsg, |
375 |
|
|
"NPTfm error: If you use the NPTfm\n" |
376 |
|
|
" integrator, you must set tauThermostat.\n"); |
377 |
|
|
painCave.isFatal = 1; |
378 |
|
|
simError(); |
379 |
|
|
return -1; |
380 |
|
|
} |
381 |
|
|
|
382 |
|
|
// We must set tauBarostat. |
383 |
|
|
|
384 |
|
|
if (!have_tau_barostat) { |
385 |
|
|
sprintf( painCave.errMsg, |
386 |
|
|
"NPTfm error: If you use the NPTfm\n" |
387 |
|
|
" integrator, you must set tauBarostat.\n"); |
388 |
|
|
painCave.isFatal = 1; |
389 |
|
|
simError(); |
390 |
|
|
return -1; |
391 |
|
|
} |
392 |
|
|
|
393 |
|
|
// We need NkBT a lot, so just set it here: |
394 |
|
|
|
395 |
|
|
NkBT = (double)info->ndf * kB * targetTemp; |
396 |
|
|
|
397 |
|
|
return 1; |
398 |
|
|
} |