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root/group/trunk/OOPSE/libmdtools/Thermo.cpp
Revision: 1127
Committed: Tue Apr 20 16:56:40 2004 UTC (20 years, 2 months ago) by tim
File size: 9563 byte(s)
Log Message:
fixed getCOMVel  and velocitize at thermo

File Contents

# Content
1 #include <math.h>
2 #include <iostream>
3 using namespace std;
4
5 #ifdef IS_MPI
6 #include <mpi.h>
7 #endif //is_mpi
8
9 #include "Thermo.hpp"
10 #include "SRI.hpp"
11 #include "Integrator.hpp"
12 #include "simError.h"
13
14 #ifdef IS_MPI
15 #define __C
16 #include "mpiSimulation.hpp"
17 #endif // is_mpi
18
19 Thermo::Thermo( SimInfo* the_info ) {
20 info = the_info;
21 int baseSeed = the_info->getSeed();
22
23 gaussStream = new gaussianSPRNG( baseSeed );
24 }
25
26 Thermo::~Thermo(){
27 delete gaussStream;
28 }
29
30 double Thermo::getKinetic(){
31
32 const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2
33 double kinetic;
34 double amass;
35 double aVel[3], aJ[3], I[3][3];
36 int i, j, k, kl;
37
38 double kinetic_global;
39 vector<StuntDouble *> integrableObjects = info->integrableObjects;
40
41 kinetic = 0.0;
42 kinetic_global = 0.0;
43
44 for (kl=0; kl<integrableObjects.size(); kl++) {
45 integrableObjects[kl]->getVel(aVel);
46 amass = integrableObjects[kl]->getMass();
47
48 for(j=0; j<3; j++)
49 kinetic += amass*aVel[j]*aVel[j];
50
51 if (integrableObjects[kl]->isDirectional()){
52
53 integrableObjects[kl]->getJ( aJ );
54 integrableObjects[kl]->getI( I );
55
56 if (integrableObjects[kl]->isLinear()) {
57 i = integrableObjects[kl]->linearAxis();
58 j = (i+1)%3;
59 k = (i+2)%3;
60 kinetic += aJ[j]*aJ[j]/I[j][j] + aJ[k]*aJ[k]/I[k][k];
61 } else {
62 for (j=0; j<3; j++)
63 kinetic += aJ[j]*aJ[j] / I[j][j];
64 }
65 }
66 }
67 #ifdef IS_MPI
68 MPI_Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,
69 MPI_SUM, MPI_COMM_WORLD);
70 kinetic = kinetic_global;
71 #endif //is_mpi
72
73 kinetic = kinetic * 0.5 / e_convert;
74
75 return kinetic;
76 }
77
78 double Thermo::getPotential(){
79
80 double potential_local;
81 double potential;
82 int el, nSRI;
83 Molecule* molecules;
84
85 molecules = info->molecules;
86 nSRI = info->n_SRI;
87
88 potential_local = 0.0;
89 potential = 0.0;
90 potential_local += info->lrPot;
91
92 for( el=0; el<info->n_mol; el++ ){
93 potential_local += molecules[el].getPotential();
94 }
95
96 // Get total potential for entire system from MPI.
97 #ifdef IS_MPI
98 MPI_Allreduce(&potential_local,&potential,1,MPI_DOUBLE,
99 MPI_SUM, MPI_COMM_WORLD);
100 #else
101 potential = potential_local;
102 #endif // is_mpi
103
104 return potential;
105 }
106
107 double Thermo::getTotalE(){
108
109 double total;
110
111 total = this->getKinetic() + this->getPotential();
112 return total;
113 }
114
115 double Thermo::getTemperature(){
116
117 const double kb = 1.9872156E-3; // boltzman's constant in kcal/(mol K)
118 double temperature;
119
120 temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb );
121 return temperature;
122 }
123
124 double Thermo::getVolume() {
125
126 return info->boxVol;
127 }
128
129 double Thermo::getPressure() {
130
131 // Relies on the calculation of the full molecular pressure tensor
132
133 const double p_convert = 1.63882576e8;
134 double press[3][3];
135 double pressure;
136
137 this->getPressureTensor(press);
138
139 pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
140
141 return pressure;
142 }
143
144 double Thermo::getPressureX() {
145
146 // Relies on the calculation of the full molecular pressure tensor
147
148 const double p_convert = 1.63882576e8;
149 double press[3][3];
150 double pressureX;
151
152 this->getPressureTensor(press);
153
154 pressureX = p_convert * press[0][0];
155
156 return pressureX;
157 }
158
159 double Thermo::getPressureY() {
160
161 // Relies on the calculation of the full molecular pressure tensor
162
163 const double p_convert = 1.63882576e8;
164 double press[3][3];
165 double pressureY;
166
167 this->getPressureTensor(press);
168
169 pressureY = p_convert * press[1][1];
170
171 return pressureY;
172 }
173
174 double Thermo::getPressureZ() {
175
176 // Relies on the calculation of the full molecular pressure tensor
177
178 const double p_convert = 1.63882576e8;
179 double press[3][3];
180 double pressureZ;
181
182 this->getPressureTensor(press);
183
184 pressureZ = p_convert * press[2][2];
185
186 return pressureZ;
187 }
188
189
190 void Thermo::getPressureTensor(double press[3][3]){
191 // returns pressure tensor in units amu*fs^-2*Ang^-1
192 // routine derived via viral theorem description in:
193 // Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
194
195 const double e_convert = 4.184e-4;
196
197 double molmass, volume;
198 double vcom[3];
199 double p_local[9], p_global[9];
200 int i, j, k, nMols;
201 Molecule* molecules;
202
203 nMols = info->n_mol;
204 molecules = info->molecules;
205 //tau = info->tau;
206
207 // use velocities of molecular centers of mass and molecular masses:
208 for (i=0; i < 9; i++) {
209 p_local[i] = 0.0;
210 p_global[i] = 0.0;
211 }
212
213 for (i=0; i < nMols; i++) {
214 molmass = molecules[i].getCOMvel(vcom);
215
216 p_local[0] += molmass * (vcom[0] * vcom[0]);
217 p_local[1] += molmass * (vcom[0] * vcom[1]);
218 p_local[2] += molmass * (vcom[0] * vcom[2]);
219 p_local[3] += molmass * (vcom[1] * vcom[0]);
220 p_local[4] += molmass * (vcom[1] * vcom[1]);
221 p_local[5] += molmass * (vcom[1] * vcom[2]);
222 p_local[6] += molmass * (vcom[2] * vcom[0]);
223 p_local[7] += molmass * (vcom[2] * vcom[1]);
224 p_local[8] += molmass * (vcom[2] * vcom[2]);
225 }
226
227 // Get total for entire system from MPI.
228
229 #ifdef IS_MPI
230 MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
231 #else
232 for (i=0; i<9; i++) {
233 p_global[i] = p_local[i];
234 }
235 #endif // is_mpi
236
237 volume = this->getVolume();
238
239 for(i = 0; i < 3; i++) {
240 for (j = 0; j < 3; j++) {
241 k = 3*i + j;
242 press[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume;
243
244 }
245 }
246 }
247
248 void Thermo::velocitize() {
249
250 double aVel[3], aJ[3], I[3][3];
251 int i, j, l, m, n, vr, vd; // velocity randomizer loop counters
252 double vdrift[3];
253 double vbar;
254 const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
255 double av2;
256 double kebar;
257 double temperature;
258 int nobj;
259
260 nobj = info->integrableObjects.size();
261
262 temperature = info->target_temp;
263
264 kebar = kb * temperature * (double)info->ndfRaw /
265 ( 2.0 * (double)info->ndf );
266
267 for(vr = 0; vr < nobj; vr++){
268
269 // uses equipartition theory to solve for vbar in angstrom/fs
270
271 av2 = 2.0 * kebar / info->integrableObjects[vr]->getMass();
272 vbar = sqrt( av2 );
273
274 // picks random velocities from a gaussian distribution
275 // centered on vbar
276
277 for (j=0; j<3; j++)
278 aVel[j] = vbar * gaussStream->getGaussian();
279
280 info->integrableObjects[vr]->setVel( aVel );
281
282 if(info->integrableObjects[vr]->isDirectional()){
283
284 info->integrableObjects[vr]->getI( I );
285
286 if (info->integrableObjects[vr]->isLinear()) {
287
288 l= info->integrableObjects[vr]->linearAxis();
289 m = (l+1)%3;
290 n = (l+2)%3;
291
292 aJ[l] = 0.0;
293 vbar = sqrt( 2.0 * kebar * I[m][m] );
294 aJ[m] = vbar * gaussStream->getGaussian();
295 vbar = sqrt( 2.0 * kebar * I[n][n] );
296 aJ[n] = vbar * gaussStream->getGaussian();
297
298 } else {
299 for (j = 0 ; j < 3; j++) {
300 vbar = sqrt( 2.0 * kebar * I[j][j] );
301 aJ[j] = vbar * gaussStream->getGaussian();
302 }
303 } // else isLinear
304
305 info->integrableObjects[vr]->setJ( aJ );
306
307 }//isDirectional
308
309 }
310
311 // Get the Center of Mass drift velocity.
312
313 getCOMVel(vdrift);
314
315 // Corrects for the center of mass drift.
316 // sums all the momentum and divides by total mass.
317
318 for(vd = 0; vd < nobj; vd++){
319
320 info->integrableObjects[vd]->getVel(aVel);
321
322 for (j=0; j < 3; j++)
323 aVel[j] -= vdrift[j];
324
325 info->integrableObjects[vd]->setVel( aVel );
326 }
327
328 }
329
330 void Thermo::getCOMVel(double vdrift[3]){
331
332 double mtot, mtot_local;
333 double aVel[3], amass;
334 double vdrift_local[3];
335 int vd, j;
336 int nobj;
337
338 nobj = info->integrableObjects.size();
339
340 mtot_local = 0.0;
341 vdrift_local[0] = 0.0;
342 vdrift_local[1] = 0.0;
343 vdrift_local[2] = 0.0;
344
345 for(vd = 0; vd < nobj; vd++){
346
347 amass = info->integrableObjects[vd]->getMass();
348 info->integrableObjects[vd]->getVel( aVel );
349
350 for(j = 0; j < 3; j++)
351 vdrift_local[j] += aVel[j] * amass;
352
353 mtot_local += amass;
354 }
355
356 #ifdef IS_MPI
357 MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
358 MPI_Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
359 #else
360 mtot = mtot_local;
361 for(vd = 0; vd < 3; vd++) {
362 vdrift[vd] = vdrift_local[vd];
363 }
364 #endif
365
366 for (vd = 0; vd < 3; vd++) {
367 vdrift[vd] = vdrift[vd] / mtot;
368 }
369
370 }
371
372 void Thermo::getCOM(double COM[3]){
373
374 double mtot, mtot_local;
375 double aPos[3], amass;
376 double COM_local[3];
377 int i, j;
378 int nobj;
379
380 mtot_local = 0.0;
381 COM_local[0] = 0.0;
382 COM_local[1] = 0.0;
383 COM_local[2] = 0.0;
384
385 nobj = info->integrableObjects.size();
386 for(i = 0; i < nobj; i++){
387
388 amass = info->integrableObjects[i]->getMass();
389 info->integrableObjects[i]->getPos( aPos );
390
391 for(j = 0; j < 3; j++)
392 COM_local[j] += aPos[j] * amass;
393
394 mtot_local += amass;
395 }
396
397 #ifdef IS_MPI
398 MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
399 MPI_Allreduce(COM_local,COM,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
400 #else
401 mtot = mtot_local;
402 for(i = 0; i < 3; i++) {
403 COM[i] = COM_local[i];
404 }
405 #endif
406
407 for (i = 0; i < 3; i++) {
408 COM[i] = COM[i] / mtot;
409 }
410 }
411
412 void Thermo::removeCOMdrift() {
413 double vdrift[3], aVel[3];
414 int vd, j, nobj;
415
416 nobj = info->integrableObjects.size();
417
418 // Get the Center of Mass drift velocity.
419
420 getCOMVel(vdrift);
421
422 // Corrects for the center of mass drift.
423 // sums all the momentum and divides by total mass.
424
425 for(vd = 0; vd < nobj; vd++){
426
427 info->integrableObjects[vd]->getVel(aVel);
428
429 for (j=0; j < 3; j++)
430 aVel[j] -= vdrift[j];
431
432 info->integrableObjects[vd]->setVel( aVel );
433 }
434 }