1 |
#include <cmath> |
2 |
#include "Atom.hpp" |
3 |
#include "SRI.hpp" |
4 |
#include "AbstractClasses.hpp" |
5 |
#include "SimInfo.hpp" |
6 |
#include "ForceFields.hpp" |
7 |
#include "Thermo.hpp" |
8 |
#include "ReadWrite.hpp" |
9 |
#include "Integrator.hpp" |
10 |
#include "simError.h" |
11 |
|
12 |
#ifdef IS_MPI |
13 |
#include "mpiSimulation.hpp" |
14 |
#endif |
15 |
|
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|
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// Basic isotropic thermostating and barostating via the Melchionna |
18 |
// modification of the Hoover algorithm: |
19 |
// |
20 |
// Melchionna, S., Ciccotti, G., and Holian, B. L., 1993, |
21 |
// Molec. Phys., 78, 533. |
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// |
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// and |
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// |
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// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499. |
26 |
|
27 |
template<typename T> NPTi<T>::NPTi ( SimInfo *theInfo, ForceFields* the_ff): |
28 |
T( theInfo, the_ff ) |
29 |
{ |
30 |
chi = 0.0; |
31 |
eta = 0.0; |
32 |
integralOfChidt = 0.0; |
33 |
have_tau_thermostat = 0; |
34 |
have_tau_barostat = 0; |
35 |
have_target_temp = 0; |
36 |
have_target_pressure = 0; |
37 |
have_chi_tolerance = 0; |
38 |
have_eta_tolerance = 0; |
39 |
have_pos_iter_tolerance = 0; |
40 |
|
41 |
oldPos = new double[3*nAtoms]; |
42 |
oldVel = new double[3*nAtoms]; |
43 |
oldJi = new double[3*nAtoms]; |
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#ifdef IS_MPI |
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Nparticles = mpiSim->getTotAtoms(); |
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#else |
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Nparticles = theInfo->n_atoms; |
48 |
#endif |
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|
50 |
} |
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|
52 |
template<typename T> NPTi<T>::~NPTi() { |
53 |
delete[] oldPos; |
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delete[] oldVel; |
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delete[] oldJi; |
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} |
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|
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template<typename T> void NPTi<T>::moveA() { |
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|
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|
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// int i, j; |
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// DirectionalAtom* dAtom; |
63 |
// double Tb[3], ji[3]; |
64 |
// double A[3][3], I[3][3]; |
65 |
// double angle, mass; |
66 |
// double vel[3], pos[3], frc[3]; |
67 |
|
68 |
// double rj[3]; |
69 |
// double instaTemp, instaPress, instaVol; |
70 |
// double tt2, tb2, scaleFactor; |
71 |
|
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// tt2 = tauThermostat * tauThermostat; |
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// tb2 = tauBarostat * tauBarostat; |
74 |
|
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// instaTemp = tStats->getTemperature(); |
76 |
// instaPress = tStats->getPressure(); |
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// instaVol = tStats->getVolume(); |
78 |
|
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// // first evolve chi a half step |
80 |
|
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// chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
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// eta += dt2 * ( instaVol * (instaPress - targetPressure) / |
83 |
// (p_convert*NkBT*tb2)); |
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|
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// integralOfChidt += dt2* chi; |
86 |
|
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// for( i=0; i<nAtoms; i++ ){ |
88 |
// atoms[i]->getVel( vel ); |
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// atoms[i]->getPos( pos ); |
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// atoms[i]->getFrc( frc ); |
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|
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// mass = atoms[i]->getMass(); |
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|
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// for (j=0; j < 3; j++) { |
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// vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*(chi+eta)); |
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// rj[j] = pos[j]; |
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// } |
98 |
|
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// atoms[i]->setVel( vel ); |
100 |
|
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// info->wrapVector(rj); |
102 |
|
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// for (j = 0; j < 3; j++) |
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// pos[j] += dt * (vel[j] + eta*rj[j]); |
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|
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// atoms[i]->setPos( pos ); |
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|
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// if( atoms[i]->isDirectional() ){ |
109 |
|
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// dAtom = (DirectionalAtom *)atoms[i]; |
111 |
|
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// // get and convert the torque to body frame |
113 |
|
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// dAtom->getTrq( Tb ); |
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// dAtom->lab2Body( Tb ); |
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|
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// // get the angular momentum, and propagate a half step |
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|
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// dAtom->getJ( ji ); |
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|
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// for (j=0; j < 3; j++) |
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// ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
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|
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// // use the angular velocities to propagate the rotation matrix a |
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// // full time step |
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|
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// dAtom->getA(A); |
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// dAtom->getI(I); |
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|
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// // rotate about the x-axis |
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// angle = dt2 * ji[0] / I[0][0]; |
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// this->rotate( 1, 2, angle, ji, A ); |
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|
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// // rotate about the y-axis |
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// angle = dt2 * ji[1] / I[1][1]; |
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// this->rotate( 2, 0, angle, ji, A ); |
137 |
|
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// // rotate about the z-axis |
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// angle = dt * ji[2] / I[2][2]; |
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// this->rotate( 0, 1, angle, ji, A); |
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|
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// // rotate about the y-axis |
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// angle = dt2 * ji[1] / I[1][1]; |
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// this->rotate( 2, 0, angle, ji, A ); |
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|
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// // rotate about the x-axis |
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// angle = dt2 * ji[0] / I[0][0]; |
148 |
// this->rotate( 1, 2, angle, ji, A ); |
149 |
|
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// dAtom->setJ( ji ); |
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// dAtom->setA( A ); |
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// } |
153 |
|
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// } |
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|
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// // Scale the box after all the positions have been moved: |
157 |
|
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// scaleFactor = exp(dt*eta); |
159 |
|
160 |
// if ((scaleFactor > 1.1) || (scaleFactor < 0.9)) { |
161 |
// sprintf( painCave.errMsg, |
162 |
// "NPTi error: Attempting a Box scaling of more than 10 percent" |
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// " check your tauBarostat, as it is probably too small!\n" |
164 |
// " eta = %lf, scaleFactor = %lf\n", eta, scaleFactor |
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// ); |
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// painCave.isFatal = 1; |
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// simError(); |
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// } else { |
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// info->scaleBox(exp(dt*eta)); |
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// } |
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|
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|
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//new version of NPTi |
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int i, j, k; |
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DirectionalAtom* dAtom; |
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double Tb[3], ji[3]; |
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double A[3][3], I[3][3]; |
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double angle, mass; |
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double vel[3], pos[3], frc[3]; |
180 |
|
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double rj[3]; |
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double instaTemp, instaPress, instaVol; |
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double tt2, tb2, scaleFactor; |
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double COM[3]; |
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|
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tt2 = tauThermostat * tauThermostat; |
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tb2 = tauBarostat * tauBarostat; |
188 |
|
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instaTemp = tStats->getTemperature(); |
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instaPress = tStats->getPressure(); |
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instaVol = tStats->getVolume(); |
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|
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tStats->getCOM(COM); |
194 |
|
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//evolve velocity half step |
196 |
for( i=0; i<nAtoms; i++ ){ |
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|
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atoms[i]->getVel( vel ); |
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atoms[i]->getFrc( frc ); |
200 |
|
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mass = atoms[i]->getMass(); |
202 |
|
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for (j=0; j < 3; j++) { |
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// velocity half step (use chi from previous step here): |
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vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*(chi + eta)); |
206 |
|
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} |
208 |
|
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atoms[i]->setVel( vel ); |
210 |
|
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if( atoms[i]->isDirectional() ){ |
212 |
|
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dAtom = (DirectionalAtom *)atoms[i]; |
214 |
|
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// get and convert the torque to body frame |
216 |
|
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dAtom->getTrq( Tb ); |
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dAtom->lab2Body( Tb ); |
219 |
|
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// get the angular momentum, and propagate a half step |
221 |
|
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dAtom->getJ( ji ); |
223 |
|
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for (j=0; j < 3; j++) |
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ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
226 |
|
227 |
// use the angular velocities to propagate the rotation matrix a |
228 |
// full time step |
229 |
|
230 |
dAtom->getA(A); |
231 |
dAtom->getI(I); |
232 |
|
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// rotate about the x-axis |
234 |
angle = dt2 * ji[0] / I[0][0]; |
235 |
this->rotate( 1, 2, angle, ji, A ); |
236 |
|
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// rotate about the y-axis |
238 |
angle = dt2 * ji[1] / I[1][1]; |
239 |
this->rotate( 2, 0, angle, ji, A ); |
240 |
|
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// rotate about the z-axis |
242 |
angle = dt * ji[2] / I[2][2]; |
243 |
this->rotate( 0, 1, angle, ji, A); |
244 |
|
245 |
// rotate about the y-axis |
246 |
angle = dt2 * ji[1] / I[1][1]; |
247 |
this->rotate( 2, 0, angle, ji, A ); |
248 |
|
249 |
// rotate about the x-axis |
250 |
angle = dt2 * ji[0] / I[0][0]; |
251 |
this->rotate( 1, 2, angle, ji, A ); |
252 |
|
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dAtom->setJ( ji ); |
254 |
dAtom->setA( A ); |
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} |
256 |
} |
257 |
|
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// evolve chi and eta half step |
259 |
|
260 |
chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
261 |
eta += dt2 * ( instaVol * (instaPress - targetPressure) / (p_convert*NkBT*tb2)); |
262 |
|
263 |
//calculate the integral of chidt |
264 |
integralOfChidt += dt2*chi; |
265 |
|
266 |
//save the old positions |
267 |
for(i = 0; i < nAtoms; i++){ |
268 |
atoms[i]->getPos(pos); |
269 |
for(j = 0; j < 3; j++) |
270 |
oldPos[i*3 + j] = pos[j]; |
271 |
} |
272 |
|
273 |
//the first estimation of r(t+dt) is equal to r(t) |
274 |
|
275 |
for(k = 0; k < 4; k ++){ |
276 |
|
277 |
for(i =0 ; i < nAtoms; i++){ |
278 |
|
279 |
atoms[i]->getVel(vel); |
280 |
atoms[i]->getPos(pos); |
281 |
|
282 |
for(j = 0; j < 3; j++) |
283 |
rj[j] = (oldPos[i*3 + j] + pos[j])/2 - COM[j]; |
284 |
|
285 |
|
286 |
//wrapVector(r(t)) = r(t)-R0 |
287 |
//info->wrapVector(rj); |
288 |
|
289 |
for(j = 0; j < 3; j++) |
290 |
pos[j] = oldPos[i*3 + j] + dt*(vel[j] + eta*rj[j]); |
291 |
|
292 |
atoms[i]->setPos( pos ); |
293 |
|
294 |
} |
295 |
|
296 |
} |
297 |
|
298 |
|
299 |
// Scale the box after all the positions have been moved: |
300 |
|
301 |
scaleFactor = exp(dt*eta); |
302 |
|
303 |
if ((scaleFactor > 1.1) || (scaleFactor < 0.9)) { |
304 |
sprintf( painCave.errMsg, |
305 |
"NPTi error: Attempting a Box scaling of more than 10 percent" |
306 |
" check your tauBarostat, as it is probably too small!\n" |
307 |
" eta = %lf, scaleFactor = %lf\n", eta, scaleFactor |
308 |
); |
309 |
painCave.isFatal = 1; |
310 |
simError(); |
311 |
} else { |
312 |
info->scaleBox(scaleFactor); |
313 |
} |
314 |
|
315 |
//advance volume; |
316 |
volume = volume * exp(dt*eta); |
317 |
} |
318 |
|
319 |
template<typename T> void NPTi<T>::moveB( void ){ |
320 |
|
321 |
/* |
322 |
int i, j; |
323 |
DirectionalAtom* dAtom; |
324 |
double Tb[3], ji[3]; |
325 |
double vel[3], frc[3]; |
326 |
double mass; |
327 |
|
328 |
double instaTemp, instaPress, instaVol; |
329 |
double tt2, tb2; |
330 |
|
331 |
tt2 = tauThermostat * tauThermostat; |
332 |
tb2 = tauBarostat * tauBarostat; |
333 |
|
334 |
instaTemp = tStats->getTemperature(); |
335 |
instaPress = tStats->getPressure(); |
336 |
instaVol = tStats->getVolume(); |
337 |
|
338 |
chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
339 |
eta += dt2 * ( instaVol * (instaPress - targetPressure) / |
340 |
(p_convert*NkBT*tb2)); |
341 |
integralOfChidt += dt2*chi; |
342 |
|
343 |
for( i=0; i<nAtoms; i++ ){ |
344 |
|
345 |
atoms[i]->getVel( vel ); |
346 |
atoms[i]->getFrc( frc ); |
347 |
|
348 |
mass = atoms[i]->getMass(); |
349 |
|
350 |
// velocity half step |
351 |
for (j=0; j < 3; j++) |
352 |
vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*(chi+eta)); |
353 |
|
354 |
atoms[i]->setVel( vel ); |
355 |
|
356 |
if( atoms[i]->isDirectional() ){ |
357 |
|
358 |
dAtom = (DirectionalAtom *)atoms[i]; |
359 |
|
360 |
// get and convert the torque to body frame |
361 |
|
362 |
dAtom->getTrq( Tb ); |
363 |
dAtom->lab2Body( Tb ); |
364 |
|
365 |
// get the angular momentum, and propagate a half step |
366 |
|
367 |
dAtom->getJ( ji ); |
368 |
|
369 |
for (j=0; j < 3; j++) |
370 |
ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
371 |
|
372 |
dAtom->setJ( ji ); |
373 |
} |
374 |
} |
375 |
|
376 |
*/ |
377 |
|
378 |
//new version of NPTi |
379 |
int i, j, k; |
380 |
DirectionalAtom* dAtom; |
381 |
double Tb[3], ji[3]; |
382 |
double vel[3], frc[3]; |
383 |
double mass; |
384 |
|
385 |
double instTemp, instPress, instVol; |
386 |
double tt2, tb2; |
387 |
double oldChi, prevChi; |
388 |
double oldEta, preEta; |
389 |
|
390 |
tt2 = tauThermostat * tauThermostat; |
391 |
tb2 = tauBarostat * tauBarostat; |
392 |
|
393 |
|
394 |
// Set things up for the iteration: |
395 |
|
396 |
oldChi = chi; |
397 |
oldEta = eta; |
398 |
|
399 |
for( i=0; i<nAtoms; i++ ){ |
400 |
|
401 |
atoms[i]->getVel( vel ); |
402 |
|
403 |
for (j=0; j < 3; j++) |
404 |
oldVel[3*i + j] = vel[j]; |
405 |
|
406 |
if( atoms[i]->isDirectional() ){ |
407 |
|
408 |
dAtom = (DirectionalAtom *)atoms[i]; |
409 |
|
410 |
dAtom->getJ( ji ); |
411 |
|
412 |
for (j=0; j < 3; j++) |
413 |
oldJi[3*i + j] = ji[j]; |
414 |
|
415 |
} |
416 |
} |
417 |
|
418 |
// do the iteration: |
419 |
|
420 |
instVol = tStats->getVolume(); |
421 |
|
422 |
for (k=0; k < 4; k++) { |
423 |
|
424 |
instTemp = tStats->getTemperature(); |
425 |
instPress = tStats->getPressure(); |
426 |
|
427 |
// evolve chi another half step using the temperature at t + dt/2 |
428 |
|
429 |
prevChi = chi; |
430 |
chi = oldChi + dt2 * ( instTemp / targetTemp - 1.0) / |
431 |
(tauThermostat*tauThermostat); |
432 |
|
433 |
preEta = eta; |
434 |
eta = oldEta + dt2 * ( instVol * (instPress - targetPressure) / |
435 |
(p_convert*NkBT*tb2)); |
436 |
|
437 |
|
438 |
for( i=0; i<nAtoms; i++ ){ |
439 |
|
440 |
atoms[i]->getFrc( frc ); |
441 |
atoms[i]->getVel(vel); |
442 |
|
443 |
mass = atoms[i]->getMass(); |
444 |
|
445 |
// velocity half step |
446 |
for (j=0; j < 3; j++) |
447 |
vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass ) * eConvert - oldVel[3*i + j]*(chi + eta)); |
448 |
|
449 |
atoms[i]->setVel( vel ); |
450 |
|
451 |
if( atoms[i]->isDirectional() ){ |
452 |
|
453 |
dAtom = (DirectionalAtom *)atoms[i]; |
454 |
|
455 |
// get and convert the torque to body frame |
456 |
|
457 |
dAtom->getTrq( Tb ); |
458 |
dAtom->lab2Body( Tb ); |
459 |
|
460 |
for (j=0; j < 3; j++) |
461 |
ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi); |
462 |
|
463 |
dAtom->setJ( ji ); |
464 |
} |
465 |
} |
466 |
|
467 |
if (fabs(prevChi - chi) <= chiTolerance && fabs(preEta -eta) <= etaTolerance) |
468 |
break; |
469 |
} |
470 |
|
471 |
//calculate integral of chida |
472 |
integralOfChidt += dt2*chi; |
473 |
|
474 |
|
475 |
} |
476 |
|
477 |
template<typename T> void NPTi<T>::resetIntegrator() { |
478 |
chi = 0.0; |
479 |
eta = 0.0; |
480 |
} |
481 |
|
482 |
template<typename T> int NPTi<T>::readyCheck() { |
483 |
|
484 |
//check parent's readyCheck() first |
485 |
if (T::readyCheck() == -1) |
486 |
return -1; |
487 |
|
488 |
// First check to see if we have a target temperature. |
489 |
// Not having one is fatal. |
490 |
|
491 |
if (!have_target_temp) { |
492 |
sprintf( painCave.errMsg, |
493 |
"NPTi error: You can't use the NPTi integrator\n" |
494 |
" without a targetTemp!\n" |
495 |
); |
496 |
painCave.isFatal = 1; |
497 |
simError(); |
498 |
return -1; |
499 |
} |
500 |
|
501 |
if (!have_target_pressure) { |
502 |
sprintf( painCave.errMsg, |
503 |
"NPTi error: You can't use the NPTi integrator\n" |
504 |
" without a targetPressure!\n" |
505 |
); |
506 |
painCave.isFatal = 1; |
507 |
simError(); |
508 |
return -1; |
509 |
} |
510 |
|
511 |
// We must set tauThermostat. |
512 |
|
513 |
if (!have_tau_thermostat) { |
514 |
sprintf( painCave.errMsg, |
515 |
"NPTi error: If you use the NPTi\n" |
516 |
" integrator, you must set tauThermostat.\n"); |
517 |
painCave.isFatal = 1; |
518 |
simError(); |
519 |
return -1; |
520 |
} |
521 |
|
522 |
// We must set tauBarostat. |
523 |
|
524 |
if (!have_tau_barostat) { |
525 |
sprintf( painCave.errMsg, |
526 |
"NPTi error: If you use the NPTi\n" |
527 |
" integrator, you must set tauBarostat.\n"); |
528 |
painCave.isFatal = 1; |
529 |
simError(); |
530 |
return -1; |
531 |
} |
532 |
|
533 |
if (!have_chi_tolerance) { |
534 |
sprintf( painCave.errMsg, |
535 |
"NPTi warning: setting chi tolerance to 1e-6\n"); |
536 |
chiTolerance = 1e-6; |
537 |
have_chi_tolerance = 1; |
538 |
painCave.isFatal = 0; |
539 |
simError(); |
540 |
} |
541 |
|
542 |
if (!have_eta_tolerance) { |
543 |
sprintf( painCave.errMsg, |
544 |
"NPTi warning: setting eta tolerance to 1e-6\n"); |
545 |
etaTolerance = 1e-6; |
546 |
have_eta_tolerance = 1; |
547 |
painCave.isFatal = 0; |
548 |
simError(); |
549 |
} |
550 |
// We need NkBT a lot, so just set it here: |
551 |
|
552 |
NkBT = (double)Nparticles * kB * targetTemp; |
553 |
fkBT = (double)info->ndf * kB * targetTemp; |
554 |
|
555 |
return 1; |
556 |
} |
557 |
|
558 |
template<typename T> double NPTi<T>::getConservedQuantity(void){ |
559 |
|
560 |
double conservedQuantity; |
561 |
double tb2; |
562 |
double eta2; |
563 |
double E_NPT; |
564 |
double U; |
565 |
double TS; |
566 |
double PV; |
567 |
double extra; |
568 |
|
569 |
static double pre_U; |
570 |
static double pre_TS; |
571 |
static double pre_PV; |
572 |
static double pre_extra; |
573 |
static int hackCount = 0; |
574 |
|
575 |
double delta_U; |
576 |
double delta_TS; |
577 |
double delta_PV; |
578 |
double delta_extra; |
579 |
|
580 |
U = tStats->getTotalE(); |
581 |
|
582 |
TS = fkBT * |
583 |
(integralOfChidt + tauThermostat * tauThermostat * chi * chi / 2.0) / eConvert; |
584 |
|
585 |
PV = (targetPressure * tStats->getVolume() / p_convert) / eConvert; |
586 |
|
587 |
tb2 = tauBarostat * tauBarostat; |
588 |
eta2 = eta * eta; |
589 |
|
590 |
extra = (fkBT * tb2 * eta2 / 2.0 ) / eConvert; |
591 |
/* |
592 |
if(hackCount == 0){ |
593 |
pre_U = U; |
594 |
pre_TS =TS; |
595 |
pre_PV = PV; |
596 |
pre_extra =extra; |
597 |
hackCount ++; |
598 |
} |
599 |
|
600 |
delta_U = U - pre_U; |
601 |
delta_TS = TS - pre_TS; |
602 |
delta_PV = PV - pre_PV; |
603 |
delta_extra = extra - pre_extra; |
604 |
*/ |
605 |
cout.width(8); |
606 |
cout.precision(8); |
607 |
|
608 |
|
609 |
cout << info->getTime() << "\t" |
610 |
<< chi << "\t" |
611 |
<< eta << "\t" |
612 |
<< U << "\t" |
613 |
<< TS << "\t" |
614 |
<< PV << "\t" |
615 |
<< extra << "\t" |
616 |
<< U+TS+PV+extra << endl; |
617 |
|
618 |
/* |
619 |
pre_U = U; |
620 |
pre_TS =TS; |
621 |
pre_PV = PV; |
622 |
pre_extra =extra; |
623 |
|
624 |
|
625 |
cout << info->getTime() << "\t" |
626 |
<< U << "\t" |
627 |
<< U+TS << "\t" |
628 |
<< U+TS+PV << "\t" |
629 |
<< U+TS+PV+extra << endl; |
630 |
*/ |
631 |
conservedQuantity = U+TS+PV+extra; |
632 |
return conservedQuantity; |
633 |
} |