16 |
|
#include "mpiSimulation.hpp" |
17 |
|
#endif // is_mpi |
18 |
|
|
19 |
< |
|
20 |
< |
#define BASE_SEED 123456789 |
21 |
< |
|
22 |
< |
Thermo::Thermo( SimInfo* the_entry_plug ) { |
23 |
< |
entry_plug = the_entry_plug; |
24 |
< |
int baseSeed = BASE_SEED; |
19 |
> |
Thermo::Thermo( SimInfo* the_info ) { |
20 |
> |
info = the_info; |
21 |
> |
int baseSeed = the_info->getSeed(); |
22 |
|
|
23 |
|
gaussStream = new gaussianSPRNG( baseSeed ); |
24 |
|
} |
42 |
|
Atom** atoms; |
43 |
|
|
44 |
|
|
45 |
< |
n_atoms = entry_plug->n_atoms; |
46 |
< |
atoms = entry_plug->atoms; |
45 |
> |
n_atoms = info->n_atoms; |
46 |
> |
atoms = info->atoms; |
47 |
|
|
48 |
|
kinetic = 0.0; |
49 |
|
kinetic_global = 0.0; |
85 |
|
int el, nSRI; |
86 |
|
Molecule* molecules; |
87 |
|
|
88 |
< |
molecules = entry_plug->molecules; |
89 |
< |
nSRI = entry_plug->n_SRI; |
88 |
> |
molecules = info->molecules; |
89 |
> |
nSRI = info->n_SRI; |
90 |
|
|
91 |
|
potential_local = 0.0; |
92 |
|
potential = 0.0; |
93 |
< |
potential_local += entry_plug->lrPot; |
93 |
> |
potential_local += info->lrPot; |
94 |
|
|
95 |
< |
for( el=0; el<entry_plug->n_mol; el++ ){ |
95 |
> |
for( el=0; el<info->n_mol; el++ ){ |
96 |
|
potential_local += molecules[el].getPotential(); |
97 |
|
} |
98 |
|
|
123 |
|
|
124 |
|
double Thermo::getTemperature(){ |
125 |
|
|
126 |
< |
const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K) |
126 |
> |
const double kb = 1.9872156E-3; // boltzman's constant in kcal/(mol K) |
127 |
|
double temperature; |
128 |
|
|
129 |
< |
temperature = ( 2.0 * this->getKinetic() ) / ((double)entry_plug->ndf * kb ); |
129 |
> |
temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb ); |
130 |
|
return temperature; |
131 |
|
} |
132 |
|
|
148 |
|
|
149 |
|
double Thermo::getVolume() { |
150 |
|
|
151 |
< |
return entry_plug->boxVol; |
151 |
> |
return info->boxVol; |
152 |
|
} |
153 |
|
|
154 |
|
double Thermo::getPressure() { |
166 |
|
return pressure; |
167 |
|
} |
168 |
|
|
169 |
+ |
double Thermo::getPressureX() { |
170 |
|
|
171 |
+ |
// Relies on the calculation of the full molecular pressure tensor |
172 |
+ |
|
173 |
+ |
const double p_convert = 1.63882576e8; |
174 |
+ |
double press[3][3]; |
175 |
+ |
double pressureX; |
176 |
+ |
|
177 |
+ |
this->getPressureTensor(press); |
178 |
+ |
|
179 |
+ |
pressureX = p_convert * press[0][0]; |
180 |
+ |
|
181 |
+ |
return pressureX; |
182 |
+ |
} |
183 |
+ |
|
184 |
+ |
double Thermo::getPressureY() { |
185 |
+ |
|
186 |
+ |
// Relies on the calculation of the full molecular pressure tensor |
187 |
+ |
|
188 |
+ |
const double p_convert = 1.63882576e8; |
189 |
+ |
double press[3][3]; |
190 |
+ |
double pressureY; |
191 |
+ |
|
192 |
+ |
this->getPressureTensor(press); |
193 |
+ |
|
194 |
+ |
pressureY = p_convert * press[1][1]; |
195 |
+ |
|
196 |
+ |
return pressureY; |
197 |
+ |
} |
198 |
+ |
|
199 |
+ |
double Thermo::getPressureZ() { |
200 |
+ |
|
201 |
+ |
// Relies on the calculation of the full molecular pressure tensor |
202 |
+ |
|
203 |
+ |
const double p_convert = 1.63882576e8; |
204 |
+ |
double press[3][3]; |
205 |
+ |
double pressureZ; |
206 |
+ |
|
207 |
+ |
this->getPressureTensor(press); |
208 |
+ |
|
209 |
+ |
pressureZ = p_convert * press[2][2]; |
210 |
+ |
|
211 |
+ |
return pressureZ; |
212 |
+ |
} |
213 |
+ |
|
214 |
+ |
|
215 |
|
void Thermo::getPressureTensor(double press[3][3]){ |
216 |
|
// returns pressure tensor in units amu*fs^-2*Ang^-1 |
217 |
|
// routine derived via viral theorem description in: |
222 |
|
double molmass, volume; |
223 |
|
double vcom[3]; |
224 |
|
double p_local[9], p_global[9]; |
225 |
< |
int i, j, k, l, nMols; |
225 |
> |
int i, j, k, nMols; |
226 |
|
Molecule* molecules; |
227 |
|
|
228 |
< |
nMols = entry_plug->n_mol; |
229 |
< |
molecules = entry_plug->molecules; |
230 |
< |
//tau = entry_plug->tau; |
228 |
> |
nMols = info->n_mol; |
229 |
> |
molecules = info->molecules; |
230 |
> |
//tau = info->tau; |
231 |
|
|
232 |
|
// use velocities of molecular centers of mass and molecular masses: |
233 |
|
for (i=0; i < 9; i++) { |
264 |
|
for(i = 0; i < 3; i++) { |
265 |
|
for (j = 0; j < 3; j++) { |
266 |
|
k = 3*i + j; |
267 |
< |
press[i][j] = (p_global[k] + entry_plug->tau[k]*e_convert) / volume; |
267 |
> |
press[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume; |
268 |
> |
|
269 |
|
} |
270 |
|
} |
271 |
|
} |
287 |
|
int n_oriented; |
288 |
|
int n_constraints; |
289 |
|
|
290 |
< |
atoms = entry_plug->atoms; |
291 |
< |
n_atoms = entry_plug->n_atoms; |
292 |
< |
temperature = entry_plug->target_temp; |
293 |
< |
n_oriented = entry_plug->n_oriented; |
294 |
< |
n_constraints = entry_plug->n_constraints; |
290 |
> |
atoms = info->atoms; |
291 |
> |
n_atoms = info->n_atoms; |
292 |
> |
temperature = info->target_temp; |
293 |
> |
n_oriented = info->n_oriented; |
294 |
> |
n_constraints = info->n_constraints; |
295 |
|
|
296 |
< |
kebar = kb * temperature * (double)entry_plug->ndf / |
297 |
< |
( 2.0 * (double)entry_plug->ndfRaw ); |
296 |
> |
kebar = kb * temperature * (double)info->ndfRaw / |
297 |
> |
( 2.0 * (double)info->ndf ); |
298 |
|
|
299 |
|
for(vr = 0; vr < n_atoms; vr++){ |
300 |
|
|
365 |
|
// We are very careless here with the distinction between n_atoms and n_local |
366 |
|
// We should really fix this before someone pokes an eye out. |
367 |
|
|
368 |
< |
n_atoms = entry_plug->n_atoms; |
369 |
< |
atoms = entry_plug->atoms; |
368 |
> |
n_atoms = info->n_atoms; |
369 |
> |
atoms = info->atoms; |
370 |
|
|
371 |
|
mtot_local = 0.0; |
372 |
|
vdrift_local[0] = 0.0; |
400 |
|
|
401 |
|
} |
402 |
|
|
403 |
+ |
void Thermo::getCOM(double COM[3]){ |
404 |
+ |
|
405 |
+ |
double mtot, mtot_local; |
406 |
+ |
double aPos[3], amass; |
407 |
+ |
double COM_local[3]; |
408 |
+ |
int i, n_atoms, j; |
409 |
+ |
Atom** atoms; |
410 |
+ |
|
411 |
+ |
// We are very careless here with the distinction between n_atoms and n_local |
412 |
+ |
// We should really fix this before someone pokes an eye out. |
413 |
+ |
|
414 |
+ |
n_atoms = info->n_atoms; |
415 |
+ |
atoms = info->atoms; |
416 |
+ |
|
417 |
+ |
mtot_local = 0.0; |
418 |
+ |
COM_local[0] = 0.0; |
419 |
+ |
COM_local[1] = 0.0; |
420 |
+ |
COM_local[2] = 0.0; |
421 |
+ |
|
422 |
+ |
for(i = 0; i < n_atoms; i++){ |
423 |
+ |
|
424 |
+ |
amass = atoms[i]->getMass(); |
425 |
+ |
atoms[i]->getPos( aPos ); |
426 |
+ |
|
427 |
+ |
for(j = 0; j < 3; j++) |
428 |
+ |
COM_local[j] += aPos[j] * amass; |
429 |
+ |
|
430 |
+ |
mtot_local += amass; |
431 |
+ |
} |
432 |
+ |
|
433 |
+ |
#ifdef IS_MPI |
434 |
+ |
MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
435 |
+ |
MPI_Allreduce(COM_local,COM,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
436 |
+ |
#else |
437 |
+ |
mtot = mtot_local; |
438 |
+ |
for(i = 0; i < 3; i++) { |
439 |
+ |
COM[i] = COM_local[i]; |
440 |
+ |
} |
441 |
+ |
#endif |
442 |
+ |
|
443 |
+ |
for (i = 0; i < 3; i++) { |
444 |
+ |
COM[i] = COM[i] / mtot; |
445 |
+ |
} |
446 |
+ |
} |