9 |
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#include "Integrator.hpp" |
10 |
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#include "simError.h" |
11 |
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|
12 |
+ |
#ifdef IS_MPI |
13 |
+ |
#include "mpiSimulation.hpp" |
14 |
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#endif |
15 |
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|
16 |
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|
17 |
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// Basic isotropic thermostating and barostating via the Melchionna |
18 |
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// modification of the Hoover algorithm: |
19 |
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// |
24 |
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// |
25 |
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// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499. |
26 |
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|
27 |
< |
NPTi::NPTi ( SimInfo *theInfo, ForceFields* the_ff): |
28 |
< |
Integrator( theInfo, the_ff ) |
27 |
> |
template<typename T> NPTi<T>::NPTi ( SimInfo *theInfo, ForceFields* the_ff): |
28 |
> |
T( theInfo, the_ff ) |
29 |
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{ |
30 |
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chi = 0.0; |
31 |
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eta = 0.0; |
32 |
+ |
integralOfChidt = 0.0; |
33 |
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have_tau_thermostat = 0; |
34 |
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have_tau_barostat = 0; |
35 |
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have_target_temp = 0; |
36 |
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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]; |
44 |
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#ifdef IS_MPI |
45 |
+ |
Nparticles = mpiSim->getTotAtoms(); |
46 |
+ |
#else |
47 |
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Nparticles = theInfo->n_atoms; |
48 |
+ |
#endif |
49 |
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|
50 |
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} |
51 |
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|
52 |
< |
void NPTi::moveA() { |
53 |
< |
|
54 |
< |
int i,j,k; |
55 |
< |
int atomIndex, aMatIndex; |
52 |
> |
template<typename T> NPTi<T>::~NPTi() { |
53 |
> |
delete[] oldPos; |
54 |
> |
delete[] oldVel; |
55 |
> |
delete[] oldJi; |
56 |
> |
} |
57 |
> |
|
58 |
> |
template<typename T> void NPTi<T>::moveA() { |
59 |
> |
|
60 |
> |
//new version of NPTi |
61 |
> |
int i, j, k; |
62 |
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DirectionalAtom* dAtom; |
63 |
< |
double Tb[3]; |
64 |
< |
double ji[3]; |
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 |
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double rj[3]; |
69 |
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double instaTemp, instaPress, instaVol; |
70 |
< |
double tt2, tb2; |
71 |
< |
double angle; |
70 |
> |
double tt2, tb2, scaleFactor; |
71 |
> |
double COM[3]; |
72 |
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|
73 |
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tt2 = tauThermostat * tauThermostat; |
74 |
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tb2 = tauBarostat * tauBarostat; |
76 |
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instaTemp = tStats->getTemperature(); |
77 |
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instaPress = tStats->getPressure(); |
78 |
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instaVol = tStats->getVolume(); |
52 |
– |
|
53 |
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// first evolve chi a half step |
79 |
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|
80 |
< |
chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
81 |
< |
eta += dt2 * ( instaVol * (instaPress - targetPressure) / (NkBT*tb2)); |
82 |
< |
|
80 |
> |
tStats->getCOM(COM); |
81 |
> |
|
82 |
> |
//evolve velocity half step |
83 |
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for( i=0; i<nAtoms; i++ ){ |
59 |
– |
atomIndex = i * 3; |
60 |
– |
aMatIndex = i * 9; |
61 |
– |
|
62 |
– |
// velocity half step |
63 |
– |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
64 |
– |
vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert |
65 |
– |
- vel[j]*(chi+eta)); |
84 |
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|
85 |
< |
// position whole step |
85 |
> |
atoms[i]->getVel( vel ); |
86 |
> |
atoms[i]->getFrc( frc ); |
87 |
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|
88 |
< |
rj[0] = pos[atomIndex]; |
70 |
< |
rj[1] = pos[atomIndex+1]; |
71 |
< |
rj[2] = pos[atomIndex+2]; |
72 |
< |
|
73 |
< |
info->wrapVector(rj); |
88 |
> |
mass = atoms[i]->getMass(); |
89 |
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|
90 |
< |
pos[atomIndex] += dt * (vel[atomIndex] + eta*rj[0]); |
91 |
< |
pos[atomIndex+1] += dt * (vel[atomIndex+1] + eta*rj[1]); |
92 |
< |
pos[atomIndex+2] += dt * (vel[atomIndex+2] + eta*rj[2]); |
90 |
> |
for (j=0; j < 3; j++) { |
91 |
> |
// velocity half step (use chi from previous step here): |
92 |
> |
vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*(chi + eta)); |
93 |
> |
|
94 |
> |
} |
95 |
> |
|
96 |
> |
atoms[i]->setVel( vel ); |
97 |
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|
98 |
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if( atoms[i]->isDirectional() ){ |
99 |
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|
100 |
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dAtom = (DirectionalAtom *)atoms[i]; |
101 |
< |
|
101 |
> |
|
102 |
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// get and convert the torque to body frame |
103 |
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|
104 |
< |
Tb[0] = dAtom->getTx(); |
86 |
< |
Tb[1] = dAtom->getTy(); |
87 |
< |
Tb[2] = dAtom->getTz(); |
88 |
< |
|
104 |
> |
dAtom->getTrq( Tb ); |
105 |
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dAtom->lab2Body( Tb ); |
106 |
|
|
107 |
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// get the angular momentum, and propagate a half step |
108 |
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|
109 |
< |
ji[0] = dAtom->getJx(); |
110 |
< |
ji[1] = dAtom->getJy(); |
111 |
< |
ji[2] = dAtom->getJz(); |
109 |
> |
dAtom->getJ( ji ); |
110 |
> |
|
111 |
> |
for (j=0; j < 3; j++) |
112 |
> |
ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
113 |
|
|
97 |
– |
ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi); |
98 |
– |
ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi); |
99 |
– |
ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi); |
100 |
– |
|
114 |
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// use the angular velocities to propagate the rotation matrix a |
115 |
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// full time step |
116 |
< |
|
116 |
> |
|
117 |
> |
dAtom->getA(A); |
118 |
> |
dAtom->getI(I); |
119 |
> |
|
120 |
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// rotate about the x-axis |
121 |
< |
angle = dt2 * ji[0] / dAtom->getIxx(); |
122 |
< |
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
123 |
< |
|
121 |
> |
angle = dt2 * ji[0] / I[0][0]; |
122 |
> |
this->rotate( 1, 2, angle, ji, A ); |
123 |
> |
|
124 |
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// rotate about the y-axis |
125 |
< |
angle = dt2 * ji[1] / dAtom->getIyy(); |
126 |
< |
this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
125 |
> |
angle = dt2 * ji[1] / I[1][1]; |
126 |
> |
this->rotate( 2, 0, angle, ji, A ); |
127 |
|
|
128 |
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// rotate about the z-axis |
129 |
< |
angle = dt * ji[2] / dAtom->getIzz(); |
130 |
< |
this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] ); |
129 |
> |
angle = dt * ji[2] / I[2][2]; |
130 |
> |
this->rotate( 0, 1, angle, ji, A); |
131 |
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|
132 |
|
// rotate about the y-axis |
133 |
< |
angle = dt2 * ji[1] / dAtom->getIyy(); |
134 |
< |
this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
133 |
> |
angle = dt2 * ji[1] / I[1][1]; |
134 |
> |
this->rotate( 2, 0, angle, ji, A ); |
135 |
|
|
136 |
|
// rotate about the x-axis |
137 |
< |
angle = dt2 * ji[0] / dAtom->getIxx(); |
138 |
< |
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
137 |
> |
angle = dt2 * ji[0] / I[0][0]; |
138 |
> |
this->rotate( 1, 2, angle, ji, A ); |
139 |
|
|
140 |
< |
dAtom->setJx( ji[0] ); |
141 |
< |
dAtom->setJy( ji[1] ); |
142 |
< |
dAtom->setJz( ji[2] ); |
143 |
< |
} |
140 |
> |
dAtom->setJ( ji ); |
141 |
> |
dAtom->setA( A ); |
142 |
> |
} |
143 |
> |
} |
144 |
> |
|
145 |
> |
// evolve chi and eta half step |
146 |
> |
|
147 |
> |
chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
148 |
> |
eta += dt2 * ( instaVol * (instaPress - targetPressure) / (p_convert*NkBT*tb2)); |
149 |
> |
|
150 |
> |
//calculate the integral of chidt |
151 |
> |
integralOfChidt += dt2*chi; |
152 |
> |
|
153 |
> |
//save the old positions |
154 |
> |
for(i = 0; i < nAtoms; i++){ |
155 |
> |
atoms[i]->getPos(pos); |
156 |
> |
for(j = 0; j < 3; j++) |
157 |
> |
oldPos[i*3 + j] = pos[j]; |
158 |
> |
} |
159 |
> |
|
160 |
> |
//the first estimation of r(t+dt) is equal to r(t) |
161 |
|
|
162 |
+ |
for(k = 0; k < 4; k ++){ |
163 |
+ |
|
164 |
+ |
for(i =0 ; i < nAtoms; i++){ |
165 |
+ |
|
166 |
+ |
atoms[i]->getVel(vel); |
167 |
+ |
atoms[i]->getPos(pos); |
168 |
+ |
|
169 |
+ |
for(j = 0; j < 3; j++) |
170 |
+ |
rj[j] = (oldPos[i*3 + j] + pos[j])/2 - COM[j]; |
171 |
+ |
|
172 |
+ |
for(j = 0; j < 3; j++) |
173 |
+ |
pos[j] = oldPos[i*3 + j] + dt*(vel[j] + eta*rj[j]); |
174 |
+ |
|
175 |
+ |
atoms[i]->setPos( pos ); |
176 |
+ |
|
177 |
+ |
} |
178 |
+ |
|
179 |
|
} |
180 |
+ |
|
181 |
+ |
|
182 |
|
// Scale the box after all the positions have been moved: |
183 |
+ |
|
184 |
+ |
scaleFactor = exp(dt*eta); |
185 |
|
|
186 |
< |
info->scaleBox(exp(dt*eta)); |
186 |
> |
if ((scaleFactor > 1.1) || (scaleFactor < 0.9)) { |
187 |
> |
sprintf( painCave.errMsg, |
188 |
> |
"NPTi error: Attempting a Box scaling of more than 10 percent" |
189 |
> |
" check your tauBarostat, as it is probably too small!\n" |
190 |
> |
" eta = %lf, scaleFactor = %lf\n", eta, scaleFactor |
191 |
> |
); |
192 |
> |
painCave.isFatal = 1; |
193 |
> |
simError(); |
194 |
> |
} else { |
195 |
> |
info->scaleBox(scaleFactor); |
196 |
> |
} |
197 |
|
|
198 |
|
} |
199 |
|
|
200 |
< |
void NPTi::moveB( void ){ |
201 |
< |
int i,j,k; |
202 |
< |
int atomIndex; |
200 |
> |
template<typename T> void NPTi<T>::moveB( void ){ |
201 |
> |
|
202 |
> |
//new version of NPTi |
203 |
> |
int i, j, k; |
204 |
|
DirectionalAtom* dAtom; |
205 |
< |
double Tb[3]; |
206 |
< |
double ji[3]; |
207 |
< |
double instaTemp, instaPress, instaVol; |
205 |
> |
double Tb[3], ji[3]; |
206 |
> |
double vel[3], frc[3]; |
207 |
> |
double mass; |
208 |
> |
|
209 |
> |
double instTemp, instPress, instVol; |
210 |
|
double tt2, tb2; |
211 |
+ |
double oldChi, prevChi; |
212 |
+ |
double oldEta, preEta; |
213 |
|
|
214 |
|
tt2 = tauThermostat * tauThermostat; |
215 |
|
tb2 = tauBarostat * tauBarostat; |
216 |
|
|
148 |
– |
instaTemp = tStats->getTemperature(); |
149 |
– |
instaPress = tStats->getPressure(); |
150 |
– |
instaVol = tStats->getVolume(); |
217 |
|
|
218 |
< |
chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
219 |
< |
eta += dt2 * ( instaVol * (instaPress - targetPressure) / (NkBT*tb2)); |
220 |
< |
|
218 |
> |
// Set things up for the iteration: |
219 |
> |
|
220 |
> |
oldChi = chi; |
221 |
> |
oldEta = eta; |
222 |
> |
|
223 |
|
for( i=0; i<nAtoms; i++ ){ |
224 |
< |
atomIndex = i * 3; |
225 |
< |
|
226 |
< |
// velocity half step |
227 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
228 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
229 |
< |
vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert |
162 |
< |
- vel[j]*(chi+eta)); |
163 |
< |
|
224 |
> |
|
225 |
> |
atoms[i]->getVel( vel ); |
226 |
> |
|
227 |
> |
for (j=0; j < 3; j++) |
228 |
> |
oldVel[3*i + j] = vel[j]; |
229 |
> |
|
230 |
|
if( atoms[i]->isDirectional() ){ |
231 |
< |
|
231 |
> |
|
232 |
|
dAtom = (DirectionalAtom *)atoms[i]; |
233 |
+ |
|
234 |
+ |
dAtom->getJ( ji ); |
235 |
+ |
|
236 |
+ |
for (j=0; j < 3; j++) |
237 |
+ |
oldJi[3*i + j] = ji[j]; |
238 |
+ |
|
239 |
+ |
} |
240 |
+ |
} |
241 |
+ |
|
242 |
+ |
// do the iteration: |
243 |
+ |
|
244 |
+ |
instVol = tStats->getVolume(); |
245 |
+ |
|
246 |
+ |
for (k=0; k < 4; k++) { |
247 |
+ |
|
248 |
+ |
instTemp = tStats->getTemperature(); |
249 |
+ |
instPress = tStats->getPressure(); |
250 |
+ |
|
251 |
+ |
// evolve chi another half step using the temperature at t + dt/2 |
252 |
+ |
|
253 |
+ |
prevChi = chi; |
254 |
+ |
chi = oldChi + dt2 * ( instTemp / targetTemp - 1.0) / |
255 |
+ |
(tauThermostat*tauThermostat); |
256 |
+ |
|
257 |
+ |
preEta = eta; |
258 |
+ |
eta = oldEta + dt2 * ( instVol * (instPress - targetPressure) / |
259 |
+ |
(p_convert*NkBT*tb2)); |
260 |
+ |
|
261 |
+ |
|
262 |
+ |
for( i=0; i<nAtoms; i++ ){ |
263 |
+ |
|
264 |
+ |
atoms[i]->getFrc( frc ); |
265 |
+ |
atoms[i]->getVel(vel); |
266 |
|
|
267 |
< |
// get and convert the torque to body frame |
267 |
> |
mass = atoms[i]->getMass(); |
268 |
|
|
269 |
< |
Tb[0] = dAtom->getTx(); |
270 |
< |
Tb[1] = dAtom->getTy(); |
271 |
< |
Tb[2] = dAtom->getTz(); |
269 |
> |
// velocity half step |
270 |
> |
for (j=0; j < 3; j++) |
271 |
> |
vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass ) * eConvert - oldVel[3*i + j]*(chi + eta)); |
272 |
|
|
273 |
< |
dAtom->lab2Body( Tb ); |
273 |
> |
atoms[i]->setVel( vel ); |
274 |
|
|
275 |
< |
// get the angular momentum, and complete the angular momentum |
276 |
< |
// half step |
275 |
> |
if( atoms[i]->isDirectional() ){ |
276 |
> |
|
277 |
> |
dAtom = (DirectionalAtom *)atoms[i]; |
278 |
> |
|
279 |
> |
// get and convert the torque to body frame |
280 |
> |
|
281 |
> |
dAtom->getTrq( Tb ); |
282 |
> |
dAtom->lab2Body( Tb ); |
283 |
> |
|
284 |
> |
for (j=0; j < 3; j++) |
285 |
> |
ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi); |
286 |
|
|
287 |
< |
ji[0] = dAtom->getJx(); |
288 |
< |
ji[1] = dAtom->getJy(); |
181 |
< |
ji[2] = dAtom->getJz(); |
182 |
< |
|
183 |
< |
ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi); |
184 |
< |
ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi); |
185 |
< |
ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi); |
186 |
< |
|
187 |
< |
dAtom->setJx( ji[0] ); |
188 |
< |
dAtom->setJy( ji[1] ); |
189 |
< |
dAtom->setJz( ji[2] ); |
287 |
> |
dAtom->setJ( ji ); |
288 |
> |
} |
289 |
|
} |
290 |
+ |
|
291 |
+ |
if (fabs(prevChi - chi) <= chiTolerance && fabs(preEta -eta) <= etaTolerance) |
292 |
+ |
break; |
293 |
|
} |
294 |
+ |
|
295 |
+ |
//calculate integral of chida |
296 |
+ |
integralOfChidt += dt2*chi; |
297 |
+ |
|
298 |
+ |
|
299 |
|
} |
300 |
|
|
301 |
< |
int NPTi::readyCheck() { |
301 |
> |
template<typename T> void NPTi<T>::resetIntegrator() { |
302 |
> |
chi = 0.0; |
303 |
> |
eta = 0.0; |
304 |
> |
} |
305 |
> |
|
306 |
> |
template<typename T> int NPTi<T>::readyCheck() { |
307 |
> |
|
308 |
> |
//check parent's readyCheck() first |
309 |
> |
if (T::readyCheck() == -1) |
310 |
> |
return -1; |
311 |
|
|
312 |
|
// First check to see if we have a target temperature. |
313 |
|
// Not having one is fatal. |
354 |
|
return -1; |
355 |
|
} |
356 |
|
|
357 |
+ |
if (!have_chi_tolerance) { |
358 |
+ |
sprintf( painCave.errMsg, |
359 |
+ |
"NPTi warning: setting chi tolerance to 1e-6\n"); |
360 |
+ |
chiTolerance = 1e-6; |
361 |
+ |
have_chi_tolerance = 1; |
362 |
+ |
painCave.isFatal = 0; |
363 |
+ |
simError(); |
364 |
+ |
} |
365 |
+ |
|
366 |
+ |
if (!have_eta_tolerance) { |
367 |
+ |
sprintf( painCave.errMsg, |
368 |
+ |
"NPTi warning: setting eta tolerance to 1e-6\n"); |
369 |
+ |
etaTolerance = 1e-6; |
370 |
+ |
have_eta_tolerance = 1; |
371 |
+ |
painCave.isFatal = 0; |
372 |
+ |
simError(); |
373 |
+ |
} |
374 |
|
// We need NkBT a lot, so just set it here: |
375 |
|
|
376 |
< |
NkBT = (double)info->ndf * kB * targetTemp; |
376 |
> |
NkBT = (double)Nparticles * kB * targetTemp; |
377 |
> |
fkBT = (double)info->ndf * kB * targetTemp; |
378 |
|
|
379 |
|
return 1; |
380 |
|
} |
381 |
+ |
|
382 |
+ |
template<typename T> double NPTi<T>::getConservedQuantity(void){ |
383 |
+ |
|
384 |
+ |
double conservedQuantity; |
385 |
+ |
double tb2; |
386 |
+ |
double eta2; |
387 |
+ |
double E_NPT; |
388 |
+ |
double U; |
389 |
+ |
double TS; |
390 |
+ |
double PV; |
391 |
+ |
double extra; |
392 |
+ |
|
393 |
+ |
U = tStats->getTotalE(); |
394 |
+ |
|
395 |
+ |
TS = fkBT * |
396 |
+ |
(integralOfChidt + tauThermostat * tauThermostat * chi * chi / 2.0) / eConvert; |
397 |
+ |
|
398 |
+ |
PV = (targetPressure * tStats->getVolume() / p_convert) / eConvert; |
399 |
+ |
|
400 |
+ |
tb2 = tauBarostat * tauBarostat; |
401 |
+ |
eta2 = eta * eta; |
402 |
+ |
|
403 |
+ |
|
404 |
+ |
extra = ((double)info->ndfTrans * kB * targetTemp * tb2 * eta2 / 2.0) / eConvert; |
405 |
+ |
|
406 |
+ |
cout.width(8); |
407 |
+ |
cout.precision(8); |
408 |
+ |
|
409 |
+ |
|
410 |
+ |
cout << info->getTime() << "\t" |
411 |
+ |
<< chi << "\t" |
412 |
+ |
<< eta << "\t" |
413 |
+ |
<< U << "\t" |
414 |
+ |
<< TS << "\t" |
415 |
+ |
<< PV << "\t" |
416 |
+ |
<< extra << "\t" |
417 |
+ |
<< U+TS+PV+extra << endl; |
418 |
+ |
|
419 |
+ |
conservedQuantity = U+TS+PV+extra; |
420 |
+ |
return conservedQuantity; |
421 |
+ |
} |