1 |
gezelter |
829 |
#include <math.h> |
2 |
mmeineke |
857 |
|
3 |
mmeineke |
778 |
#include "Atom.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 |
tim |
837 |
#include "simError.h" |
12 |
mmeineke |
778 |
|
13 |
|
|
#ifdef IS_MPI |
14 |
|
|
#include "mpiSimulation.hpp" |
15 |
|
|
#endif |
16 |
|
|
|
17 |
|
|
|
18 |
|
|
// Basic isotropic thermostating and barostating via the Melchionna |
19 |
|
|
// modification of the Hoover algorithm: |
20 |
|
|
// |
21 |
|
|
// Melchionna, S., Ciccotti, G., and Holian, B. L., 1993, |
22 |
tim |
837 |
// Molec. Phys., 78, 533. |
23 |
mmeineke |
778 |
// |
24 |
|
|
// and |
25 |
tim |
837 |
// |
26 |
mmeineke |
778 |
// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499. |
27 |
|
|
|
28 |
|
|
template<typename T> NPT<T>::NPT ( SimInfo *theInfo, ForceFields* the_ff): |
29 |
|
|
T( theInfo, the_ff ) |
30 |
|
|
{ |
31 |
tim |
837 |
GenericData* data; |
32 |
|
|
DoubleData * chiValue; |
33 |
|
|
DoubleData * integralOfChidtValue; |
34 |
|
|
|
35 |
|
|
chiValue = NULL; |
36 |
|
|
integralOfChidtValue = NULL; |
37 |
|
|
|
38 |
mmeineke |
778 |
chi = 0.0; |
39 |
|
|
integralOfChidt = 0.0; |
40 |
|
|
have_tau_thermostat = 0; |
41 |
|
|
have_tau_barostat = 0; |
42 |
|
|
have_target_temp = 0; |
43 |
|
|
have_target_pressure = 0; |
44 |
|
|
have_chi_tolerance = 0; |
45 |
|
|
have_eta_tolerance = 0; |
46 |
|
|
have_pos_iter_tolerance = 0; |
47 |
|
|
|
48 |
tim |
837 |
// retrieve chi and integralOfChidt from simInfo |
49 |
|
|
data = info->getProperty(CHIVALUE_ID); |
50 |
|
|
if(data){ |
51 |
|
|
chiValue = dynamic_cast<DoubleData*>(data); |
52 |
|
|
} |
53 |
|
|
|
54 |
|
|
data = info->getProperty(INTEGRALOFCHIDT_ID); |
55 |
|
|
if(data){ |
56 |
|
|
integralOfChidtValue = dynamic_cast<DoubleData*>(data); |
57 |
|
|
} |
58 |
|
|
|
59 |
|
|
// chi and integralOfChidt should appear by pair |
60 |
|
|
if(chiValue && integralOfChidtValue){ |
61 |
|
|
chi = chiValue->getData(); |
62 |
|
|
integralOfChidt = integralOfChidtValue->getData(); |
63 |
|
|
} |
64 |
|
|
|
65 |
mmeineke |
778 |
oldPos = new double[3*nAtoms]; |
66 |
|
|
oldVel = new double[3*nAtoms]; |
67 |
|
|
oldJi = new double[3*nAtoms]; |
68 |
|
|
#ifdef IS_MPI |
69 |
|
|
Nparticles = mpiSim->getTotAtoms(); |
70 |
|
|
#else |
71 |
|
|
Nparticles = theInfo->n_atoms; |
72 |
|
|
#endif |
73 |
|
|
|
74 |
|
|
} |
75 |
|
|
|
76 |
|
|
template<typename T> NPT<T>::~NPT() { |
77 |
|
|
delete[] oldPos; |
78 |
|
|
delete[] oldVel; |
79 |
|
|
delete[] oldJi; |
80 |
|
|
} |
81 |
|
|
|
82 |
|
|
template<typename T> void NPT<T>::moveA() { |
83 |
tim |
837 |
|
84 |
mmeineke |
778 |
//new version of NPT |
85 |
|
|
int i, j, k; |
86 |
|
|
DirectionalAtom* dAtom; |
87 |
|
|
double Tb[3], ji[3]; |
88 |
|
|
double mass; |
89 |
|
|
double vel[3], pos[3], frc[3]; |
90 |
|
|
double sc[3]; |
91 |
|
|
double COM[3]; |
92 |
|
|
|
93 |
|
|
instaTemp = tStats->getTemperature(); |
94 |
mmeineke |
780 |
tStats->getPressureTensor( press ); |
95 |
|
|
instaPress = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0; |
96 |
mmeineke |
778 |
instaVol = tStats->getVolume(); |
97 |
tim |
837 |
|
98 |
mmeineke |
778 |
tStats->getCOM(COM); |
99 |
tim |
837 |
|
100 |
mmeineke |
778 |
//evolve velocity half step |
101 |
mmeineke |
857 |
|
102 |
|
|
calcVelScale(); |
103 |
|
|
|
104 |
mmeineke |
778 |
for( i=0; i<nAtoms; i++ ){ |
105 |
|
|
|
106 |
|
|
atoms[i]->getVel( vel ); |
107 |
|
|
atoms[i]->getFrc( frc ); |
108 |
|
|
|
109 |
|
|
mass = atoms[i]->getMass(); |
110 |
|
|
|
111 |
|
|
getVelScaleA( sc, vel ); |
112 |
|
|
|
113 |
|
|
for (j=0; j < 3; j++) { |
114 |
tim |
837 |
|
115 |
mmeineke |
778 |
// velocity half step (use chi from previous step here): |
116 |
|
|
vel[j] += dt2 * ((frc[j] / mass ) * eConvert - sc[j]); |
117 |
tim |
837 |
|
118 |
mmeineke |
778 |
} |
119 |
|
|
|
120 |
|
|
atoms[i]->setVel( vel ); |
121 |
tim |
837 |
|
122 |
mmeineke |
778 |
if( atoms[i]->isDirectional() ){ |
123 |
|
|
|
124 |
|
|
dAtom = (DirectionalAtom *)atoms[i]; |
125 |
|
|
|
126 |
|
|
// get and convert the torque to body frame |
127 |
tim |
837 |
|
128 |
mmeineke |
778 |
dAtom->getTrq( Tb ); |
129 |
|
|
dAtom->lab2Body( Tb ); |
130 |
tim |
837 |
|
131 |
mmeineke |
778 |
// get the angular momentum, and propagate a half step |
132 |
|
|
|
133 |
|
|
dAtom->getJ( ji ); |
134 |
|
|
|
135 |
tim |
837 |
for (j=0; j < 3; j++) |
136 |
mmeineke |
778 |
ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
137 |
tim |
837 |
|
138 |
mmeineke |
778 |
this->rotationPropagation( dAtom, ji ); |
139 |
tim |
837 |
|
140 |
mmeineke |
778 |
dAtom->setJ( ji ); |
141 |
tim |
837 |
} |
142 |
mmeineke |
778 |
} |
143 |
|
|
|
144 |
|
|
// evolve chi and eta half step |
145 |
tim |
837 |
|
146 |
mmeineke |
778 |
evolveChiA(); |
147 |
|
|
evolveEtaA(); |
148 |
|
|
|
149 |
|
|
//calculate the integral of chidt |
150 |
|
|
integralOfChidt += dt2*chi; |
151 |
|
|
|
152 |
|
|
//save the old positions |
153 |
|
|
for(i = 0; i < nAtoms; i++){ |
154 |
|
|
atoms[i]->getPos(pos); |
155 |
|
|
for(j = 0; j < 3; j++) |
156 |
|
|
oldPos[i*3 + j] = pos[j]; |
157 |
|
|
} |
158 |
tim |
837 |
|
159 |
|
|
//the first estimation of r(t+dt) is equal to r(t) |
160 |
|
|
|
161 |
mmeineke |
778 |
for(k = 0; k < 5; k ++){ |
162 |
|
|
|
163 |
|
|
for(i =0 ; i < nAtoms; i++){ |
164 |
|
|
|
165 |
|
|
atoms[i]->getVel(vel); |
166 |
|
|
atoms[i]->getPos(pos); |
167 |
|
|
|
168 |
|
|
this->getPosScale( pos, COM, i, sc ); |
169 |
tim |
837 |
|
170 |
mmeineke |
778 |
for(j = 0; j < 3; j++) |
171 |
|
|
pos[j] = oldPos[i*3 + j] + dt*(vel[j] + sc[j]); |
172 |
|
|
|
173 |
|
|
atoms[i]->setPos( pos ); |
174 |
|
|
} |
175 |
tim |
837 |
|
176 |
mmeineke |
778 |
if (nConstrained){ |
177 |
|
|
constrainA(); |
178 |
|
|
} |
179 |
|
|
} |
180 |
|
|
|
181 |
tim |
837 |
|
182 |
mmeineke |
778 |
// Scale the box after all the positions have been moved: |
183 |
tim |
837 |
|
184 |
mmeineke |
778 |
this->scaleSimBox(); |
185 |
|
|
} |
186 |
|
|
|
187 |
|
|
template<typename T> void NPT<T>::moveB( void ){ |
188 |
tim |
837 |
|
189 |
mmeineke |
778 |
//new version of NPT |
190 |
|
|
int i, j, k; |
191 |
|
|
DirectionalAtom* dAtom; |
192 |
|
|
double Tb[3], ji[3], sc[3]; |
193 |
|
|
double vel[3], frc[3]; |
194 |
|
|
double mass; |
195 |
tim |
837 |
|
196 |
mmeineke |
778 |
// Set things up for the iteration: |
197 |
|
|
|
198 |
|
|
for( i=0; i<nAtoms; i++ ){ |
199 |
|
|
|
200 |
|
|
atoms[i]->getVel( vel ); |
201 |
|
|
|
202 |
|
|
for (j=0; j < 3; j++) |
203 |
|
|
oldVel[3*i + j] = vel[j]; |
204 |
|
|
|
205 |
|
|
if( atoms[i]->isDirectional() ){ |
206 |
|
|
|
207 |
|
|
dAtom = (DirectionalAtom *)atoms[i]; |
208 |
|
|
|
209 |
|
|
dAtom->getJ( ji ); |
210 |
|
|
|
211 |
|
|
for (j=0; j < 3; j++) |
212 |
|
|
oldJi[3*i + j] = ji[j]; |
213 |
|
|
|
214 |
|
|
} |
215 |
|
|
} |
216 |
|
|
|
217 |
|
|
// do the iteration: |
218 |
|
|
|
219 |
|
|
instaVol = tStats->getVolume(); |
220 |
tim |
837 |
|
221 |
mmeineke |
778 |
for (k=0; k < 4; k++) { |
222 |
tim |
837 |
|
223 |
mmeineke |
778 |
instaTemp = tStats->getTemperature(); |
224 |
|
|
instaPress = tStats->getPressure(); |
225 |
|
|
|
226 |
|
|
// evolve chi another half step using the temperature at t + dt/2 |
227 |
|
|
|
228 |
|
|
this->evolveChiB(); |
229 |
|
|
this->evolveEtaB(); |
230 |
mmeineke |
857 |
this->calcVelScale(); |
231 |
tim |
837 |
|
232 |
mmeineke |
778 |
for( i=0; i<nAtoms; i++ ){ |
233 |
|
|
|
234 |
|
|
atoms[i]->getFrc( frc ); |
235 |
|
|
atoms[i]->getVel(vel); |
236 |
tim |
837 |
|
237 |
mmeineke |
778 |
mass = atoms[i]->getMass(); |
238 |
tim |
837 |
|
239 |
mmeineke |
778 |
getVelScaleB( sc, i ); |
240 |
|
|
|
241 |
|
|
// velocity half step |
242 |
tim |
837 |
for (j=0; j < 3; j++) |
243 |
mmeineke |
778 |
vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass ) * eConvert - sc[j]); |
244 |
tim |
837 |
|
245 |
mmeineke |
778 |
atoms[i]->setVel( vel ); |
246 |
tim |
837 |
|
247 |
mmeineke |
778 |
if( atoms[i]->isDirectional() ){ |
248 |
|
|
|
249 |
|
|
dAtom = (DirectionalAtom *)atoms[i]; |
250 |
tim |
837 |
|
251 |
|
|
// get and convert the torque to body frame |
252 |
|
|
|
253 |
mmeineke |
778 |
dAtom->getTrq( Tb ); |
254 |
tim |
837 |
dAtom->lab2Body( Tb ); |
255 |
|
|
|
256 |
|
|
for (j=0; j < 3; j++) |
257 |
mmeineke |
778 |
ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi); |
258 |
tim |
837 |
|
259 |
mmeineke |
778 |
dAtom->setJ( ji ); |
260 |
|
|
} |
261 |
|
|
} |
262 |
tim |
837 |
|
263 |
mmeineke |
778 |
if (nConstrained){ |
264 |
|
|
constrainB(); |
265 |
tim |
837 |
} |
266 |
|
|
|
267 |
mmeineke |
778 |
if ( this->chiConverged() && this->etaConverged() ) break; |
268 |
|
|
} |
269 |
|
|
|
270 |
|
|
//calculate integral of chida |
271 |
|
|
integralOfChidt += dt2*chi; |
272 |
|
|
|
273 |
|
|
|
274 |
|
|
} |
275 |
|
|
|
276 |
|
|
template<typename T> void NPT<T>::resetIntegrator() { |
277 |
|
|
chi = 0.0; |
278 |
|
|
T::resetIntegrator(); |
279 |
|
|
} |
280 |
|
|
|
281 |
|
|
template<typename T> void NPT<T>::evolveChiA() { |
282 |
|
|
chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
283 |
|
|
oldChi = chi; |
284 |
|
|
} |
285 |
|
|
|
286 |
|
|
template<typename T> void NPT<T>::evolveChiB() { |
287 |
tim |
837 |
|
288 |
mmeineke |
778 |
prevChi = chi; |
289 |
|
|
chi = oldChi + dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
290 |
|
|
} |
291 |
|
|
|
292 |
|
|
template<typename T> bool NPT<T>::chiConverged() { |
293 |
tim |
837 |
|
294 |
|
|
return ( fabs( prevChi - chi ) <= chiTolerance ); |
295 |
mmeineke |
778 |
} |
296 |
|
|
|
297 |
|
|
template<typename T> int NPT<T>::readyCheck() { |
298 |
|
|
|
299 |
|
|
//check parent's readyCheck() first |
300 |
|
|
if (T::readyCheck() == -1) |
301 |
|
|
return -1; |
302 |
tim |
837 |
|
303 |
|
|
// First check to see if we have a target temperature. |
304 |
|
|
// Not having one is fatal. |
305 |
|
|
|
306 |
mmeineke |
778 |
if (!have_target_temp) { |
307 |
|
|
sprintf( painCave.errMsg, |
308 |
|
|
"NPT error: You can't use the NPT integrator\n" |
309 |
|
|
" without a targetTemp!\n" |
310 |
|
|
); |
311 |
|
|
painCave.isFatal = 1; |
312 |
|
|
simError(); |
313 |
|
|
return -1; |
314 |
|
|
} |
315 |
|
|
|
316 |
|
|
if (!have_target_pressure) { |
317 |
|
|
sprintf( painCave.errMsg, |
318 |
|
|
"NPT error: You can't use the NPT integrator\n" |
319 |
|
|
" without a targetPressure!\n" |
320 |
|
|
); |
321 |
|
|
painCave.isFatal = 1; |
322 |
|
|
simError(); |
323 |
|
|
return -1; |
324 |
|
|
} |
325 |
tim |
837 |
|
326 |
mmeineke |
778 |
// We must set tauThermostat. |
327 |
tim |
837 |
|
328 |
mmeineke |
778 |
if (!have_tau_thermostat) { |
329 |
|
|
sprintf( painCave.errMsg, |
330 |
|
|
"NPT error: If you use the NPT\n" |
331 |
|
|
" integrator, you must set tauThermostat.\n"); |
332 |
|
|
painCave.isFatal = 1; |
333 |
|
|
simError(); |
334 |
|
|
return -1; |
335 |
tim |
837 |
} |
336 |
mmeineke |
778 |
|
337 |
|
|
// We must set tauBarostat. |
338 |
tim |
837 |
|
339 |
mmeineke |
778 |
if (!have_tau_barostat) { |
340 |
|
|
sprintf( painCave.errMsg, |
341 |
|
|
"NPT error: If you use the NPT\n" |
342 |
|
|
" integrator, you must set tauBarostat.\n"); |
343 |
|
|
painCave.isFatal = 1; |
344 |
|
|
simError(); |
345 |
|
|
return -1; |
346 |
tim |
837 |
} |
347 |
mmeineke |
778 |
|
348 |
|
|
if (!have_chi_tolerance) { |
349 |
|
|
sprintf( painCave.errMsg, |
350 |
|
|
"NPT warning: setting chi tolerance to 1e-6\n"); |
351 |
|
|
chiTolerance = 1e-6; |
352 |
|
|
have_chi_tolerance = 1; |
353 |
|
|
painCave.isFatal = 0; |
354 |
|
|
simError(); |
355 |
tim |
837 |
} |
356 |
mmeineke |
778 |
|
357 |
|
|
if (!have_eta_tolerance) { |
358 |
|
|
sprintf( painCave.errMsg, |
359 |
|
|
"NPT warning: setting eta tolerance to 1e-6\n"); |
360 |
|
|
etaTolerance = 1e-6; |
361 |
|
|
have_eta_tolerance = 1; |
362 |
|
|
painCave.isFatal = 0; |
363 |
|
|
simError(); |
364 |
tim |
837 |
} |
365 |
|
|
|
366 |
mmeineke |
778 |
// We need NkBT a lot, so just set it here: This is the RAW number |
367 |
|
|
// of particles, so no subtraction or addition of constraints or |
368 |
|
|
// orientational degrees of freedom: |
369 |
tim |
837 |
|
370 |
mmeineke |
778 |
NkBT = (double)Nparticles * kB * targetTemp; |
371 |
tim |
837 |
|
372 |
mmeineke |
778 |
// fkBT is used because the thermostat operates on more degrees of freedom |
373 |
|
|
// than the barostat (when there are particles with orientational degrees |
374 |
|
|
// of freedom). ndf = 3 * (n_atoms + n_oriented -1) - n_constraint - nZcons |
375 |
tim |
837 |
|
376 |
mmeineke |
778 |
fkBT = (double)info->ndf * kB * targetTemp; |
377 |
|
|
|
378 |
|
|
tt2 = tauThermostat * tauThermostat; |
379 |
|
|
tb2 = tauBarostat * tauBarostat; |
380 |
|
|
|
381 |
|
|
return 1; |
382 |
|
|
} |