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root/group/trunk/OOPSE-1.0/libmdtools/Thermo.cpp
Revision: 1334
Committed: Fri Jul 16 18:58:03 2004 UTC (20 years ago) by gezelter
File size: 9661 byte(s)
Log Message:
Initial import of OOPSE-1.0 source tree

File Contents

# User Rev Content
1 gezelter 1334 #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     #include "MatVec3.h"
14    
15     #ifdef IS_MPI
16     #define __C
17     #include "mpiSimulation.hpp"
18     #endif // is_mpi
19    
20     inline double roundMe( double x ){
21     return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
22     }
23    
24     Thermo::Thermo( SimInfo* the_info ) {
25     info = the_info;
26     int baseSeed = the_info->getSeed();
27    
28     gaussStream = new gaussianSPRNG( baseSeed );
29     }
30    
31     Thermo::~Thermo(){
32     delete gaussStream;
33     }
34    
35     double Thermo::getKinetic(){
36    
37     const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2
38     double kinetic;
39     double amass;
40     double aVel[3], aJ[3], I[3][3];
41     int i, j, k, kl;
42    
43     double kinetic_global;
44     vector<StuntDouble *> integrableObjects = info->integrableObjects;
45    
46     kinetic = 0.0;
47     kinetic_global = 0.0;
48    
49     for (kl=0; kl<integrableObjects.size(); kl++) {
50     integrableObjects[kl]->getVel(aVel);
51     amass = integrableObjects[kl]->getMass();
52    
53     for(j=0; j<3; j++)
54     kinetic += amass*aVel[j]*aVel[j];
55    
56     if (integrableObjects[kl]->isDirectional()){
57    
58     integrableObjects[kl]->getJ( aJ );
59     integrableObjects[kl]->getI( I );
60    
61     if (integrableObjects[kl]->isLinear()) {
62     i = integrableObjects[kl]->linearAxis();
63     j = (i+1)%3;
64     k = (i+2)%3;
65     kinetic += aJ[j]*aJ[j]/I[j][j] + aJ[k]*aJ[k]/I[k][k];
66     } else {
67     for (j=0; j<3; j++)
68     kinetic += aJ[j]*aJ[j] / I[j][j];
69     }
70     }
71     }
72     #ifdef IS_MPI
73     MPI_Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,
74     MPI_SUM, MPI_COMM_WORLD);
75     kinetic = kinetic_global;
76     #endif //is_mpi
77    
78     kinetic = kinetic * 0.5 / e_convert;
79    
80     return kinetic;
81     }
82    
83     double Thermo::getPotential(){
84    
85     double potential_local;
86     double potential;
87     int el, nSRI;
88     Molecule* molecules;
89    
90     molecules = info->molecules;
91     nSRI = info->n_SRI;
92    
93     potential_local = 0.0;
94     potential = 0.0;
95     potential_local += info->lrPot;
96    
97     for( el=0; el<info->n_mol; el++ ){
98     potential_local += molecules[el].getPotential();
99     }
100    
101     // Get total potential for entire system from MPI.
102     #ifdef IS_MPI
103     MPI_Allreduce(&potential_local,&potential,1,MPI_DOUBLE,
104     MPI_SUM, MPI_COMM_WORLD);
105     #else
106     potential = potential_local;
107     #endif // is_mpi
108    
109     return potential;
110     }
111    
112     double Thermo::getTotalE(){
113    
114     double total;
115    
116     total = this->getKinetic() + this->getPotential();
117     return total;
118     }
119    
120     double Thermo::getTemperature(){
121    
122     const double kb = 1.9872156E-3; // boltzman's constant in kcal/(mol K)
123     double temperature;
124    
125     temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb );
126     return temperature;
127     }
128    
129     double Thermo::getVolume() {
130    
131     return info->boxVol;
132     }
133    
134     double Thermo::getPressure() {
135    
136     // Relies on the calculation of the full molecular pressure tensor
137    
138     const double p_convert = 1.63882576e8;
139     double press[3][3];
140     double pressure;
141    
142     this->getPressureTensor(press);
143    
144     pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
145    
146     return pressure;
147     }
148    
149     double Thermo::getPressureX() {
150    
151     // Relies on the calculation of the full molecular pressure tensor
152    
153     const double p_convert = 1.63882576e8;
154     double press[3][3];
155     double pressureX;
156    
157     this->getPressureTensor(press);
158    
159     pressureX = p_convert * press[0][0];
160    
161     return pressureX;
162     }
163    
164     double Thermo::getPressureY() {
165    
166     // Relies on the calculation of the full molecular pressure tensor
167    
168     const double p_convert = 1.63882576e8;
169     double press[3][3];
170     double pressureY;
171    
172     this->getPressureTensor(press);
173    
174     pressureY = p_convert * press[1][1];
175    
176     return pressureY;
177     }
178    
179     double Thermo::getPressureZ() {
180    
181     // Relies on the calculation of the full molecular pressure tensor
182    
183     const double p_convert = 1.63882576e8;
184     double press[3][3];
185     double pressureZ;
186    
187     this->getPressureTensor(press);
188    
189     pressureZ = p_convert * press[2][2];
190    
191     return pressureZ;
192     }
193    
194    
195     void Thermo::getPressureTensor(double press[3][3]){
196     // returns pressure tensor in units amu*fs^-2*Ang^-1
197     // routine derived via viral theorem description in:
198     // Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
199    
200     const double e_convert = 4.184e-4;
201    
202     double molmass, volume;
203     double vcom[3];
204     double p_local[9], p_global[9];
205     int i, j, k;
206    
207     for (i=0; i < 9; i++) {
208     p_local[i] = 0.0;
209     p_global[i] = 0.0;
210     }
211    
212     // use velocities of integrableObjects and their masses:
213    
214     for (i=0; i < info->integrableObjects.size(); i++) {
215    
216     molmass = info->integrableObjects[i]->getMass();
217    
218     info->integrableObjects[i]->getVel(vcom);
219    
220     p_local[0] += molmass * (vcom[0] * vcom[0]);
221     p_local[1] += molmass * (vcom[0] * vcom[1]);
222     p_local[2] += molmass * (vcom[0] * vcom[2]);
223     p_local[3] += molmass * (vcom[1] * vcom[0]);
224     p_local[4] += molmass * (vcom[1] * vcom[1]);
225     p_local[5] += molmass * (vcom[1] * vcom[2]);
226     p_local[6] += molmass * (vcom[2] * vcom[0]);
227     p_local[7] += molmass * (vcom[2] * vcom[1]);
228     p_local[8] += molmass * (vcom[2] * vcom[2]);
229    
230     }
231    
232     // Get total for entire system from MPI.
233    
234     #ifdef IS_MPI
235     MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
236     #else
237     for (i=0; i<9; i++) {
238     p_global[i] = p_local[i];
239     }
240     #endif // is_mpi
241    
242     volume = this->getVolume();
243    
244    
245    
246     for(i = 0; i < 3; i++) {
247     for (j = 0; j < 3; j++) {
248     k = 3*i + j;
249     press[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume;
250     }
251     }
252     }
253    
254     void Thermo::velocitize() {
255    
256     double aVel[3], aJ[3], I[3][3];
257     int i, j, l, m, n, vr, vd; // velocity randomizer loop counters
258     double vdrift[3];
259     double vbar;
260     const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
261     double av2;
262     double kebar;
263     double temperature;
264     int nobj;
265    
266     nobj = info->integrableObjects.size();
267    
268     temperature = info->target_temp;
269    
270     kebar = kb * temperature * (double)info->ndfRaw /
271     ( 2.0 * (double)info->ndf );
272    
273     for(vr = 0; vr < nobj; vr++){
274    
275     // uses equipartition theory to solve for vbar in angstrom/fs
276    
277     av2 = 2.0 * kebar / info->integrableObjects[vr]->getMass();
278     vbar = sqrt( av2 );
279    
280     // picks random velocities from a gaussian distribution
281     // centered on vbar
282    
283     for (j=0; j<3; j++)
284     aVel[j] = vbar * gaussStream->getGaussian();
285    
286     info->integrableObjects[vr]->setVel( aVel );
287    
288     if(info->integrableObjects[vr]->isDirectional()){
289    
290     info->integrableObjects[vr]->getI( I );
291    
292     if (info->integrableObjects[vr]->isLinear()) {
293    
294     l= info->integrableObjects[vr]->linearAxis();
295     m = (l+1)%3;
296     n = (l+2)%3;
297    
298     aJ[l] = 0.0;
299     vbar = sqrt( 2.0 * kebar * I[m][m] );
300     aJ[m] = vbar * gaussStream->getGaussian();
301     vbar = sqrt( 2.0 * kebar * I[n][n] );
302     aJ[n] = vbar * gaussStream->getGaussian();
303    
304     } else {
305     for (j = 0 ; j < 3; j++) {
306     vbar = sqrt( 2.0 * kebar * I[j][j] );
307     aJ[j] = vbar * gaussStream->getGaussian();
308     }
309     } // else isLinear
310    
311     info->integrableObjects[vr]->setJ( aJ );
312    
313     }//isDirectional
314    
315     }
316    
317     // Get the Center of Mass drift velocity.
318    
319     getCOMVel(vdrift);
320    
321     // Corrects for the center of mass drift.
322     // sums all the momentum and divides by total mass.
323    
324     for(vd = 0; vd < nobj; vd++){
325    
326     info->integrableObjects[vd]->getVel(aVel);
327    
328     for (j=0; j < 3; j++)
329     aVel[j] -= vdrift[j];
330    
331     info->integrableObjects[vd]->setVel( aVel );
332     }
333    
334     }
335    
336     void Thermo::getCOMVel(double vdrift[3]){
337    
338     double mtot, mtot_local;
339     double aVel[3], amass;
340     double vdrift_local[3];
341     int vd, j;
342     int nobj;
343    
344     nobj = info->integrableObjects.size();
345    
346     mtot_local = 0.0;
347     vdrift_local[0] = 0.0;
348     vdrift_local[1] = 0.0;
349     vdrift_local[2] = 0.0;
350    
351     for(vd = 0; vd < nobj; vd++){
352    
353     amass = info->integrableObjects[vd]->getMass();
354     info->integrableObjects[vd]->getVel( aVel );
355    
356     for(j = 0; j < 3; j++)
357     vdrift_local[j] += aVel[j] * amass;
358    
359     mtot_local += amass;
360     }
361    
362     #ifdef IS_MPI
363     MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
364     MPI_Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
365     #else
366     mtot = mtot_local;
367     for(vd = 0; vd < 3; vd++) {
368     vdrift[vd] = vdrift_local[vd];
369     }
370     #endif
371    
372     for (vd = 0; vd < 3; vd++) {
373     vdrift[vd] = vdrift[vd] / mtot;
374     }
375    
376     }
377    
378     void Thermo::getCOM(double COM[3]){
379    
380     double mtot, mtot_local;
381     double aPos[3], amass;
382     double COM_local[3];
383     int i, j;
384     int nobj;
385    
386     mtot_local = 0.0;
387     COM_local[0] = 0.0;
388     COM_local[1] = 0.0;
389     COM_local[2] = 0.0;
390    
391     nobj = info->integrableObjects.size();
392     for(i = 0; i < nobj; i++){
393    
394     amass = info->integrableObjects[i]->getMass();
395     info->integrableObjects[i]->getPos( aPos );
396    
397     for(j = 0; j < 3; j++)
398     COM_local[j] += aPos[j] * amass;
399    
400     mtot_local += amass;
401     }
402    
403     #ifdef IS_MPI
404     MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
405     MPI_Allreduce(COM_local,COM,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
406     #else
407     mtot = mtot_local;
408     for(i = 0; i < 3; i++) {
409     COM[i] = COM_local[i];
410     }
411     #endif
412    
413     for (i = 0; i < 3; i++) {
414     COM[i] = COM[i] / mtot;
415     }
416     }
417    
418     void Thermo::removeCOMdrift() {
419     double vdrift[3], aVel[3];
420     int vd, j, nobj;
421    
422     nobj = info->integrableObjects.size();
423    
424     // Get the Center of Mass drift velocity.
425    
426     getCOMVel(vdrift);
427    
428     // Corrects for the center of mass drift.
429     // sums all the momentum and divides by total mass.
430    
431     for(vd = 0; vd < nobj; vd++){
432    
433     info->integrableObjects[vd]->getVel(aVel);
434    
435     for (j=0; j < 3; j++)
436     aVel[j] -= vdrift[j];
437    
438     info->integrableObjects[vd]->setVel( aVel );
439     }
440     }