OOPSE/libmdtools/Thermo.cpp

#include <math.h>
#include <iostream>
using namespace std;

#ifdef IS_MPI
#include <mpi.h>
#endif //is_mpi

#include "Thermo.hpp"
#include "SRI.hpp"
#include "Integrator.hpp"
#include "simError.h"

#ifdef IS_MPI
#define __C
#include "mpiSimulation.hpp"
#endif // is_mpi

Thermo::Thermo( SimInfo* the_info ) { 
  info = the_info;
  int baseSeed = the_info->getSeed();
  
  gaussStream = new gaussianSPRNG( baseSeed );
}

Thermo::~Thermo(){
  delete gaussStream;
}

double Thermo::getKinetic(){

  const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2
  double kinetic;
  double amass;
  double aVel[3], aJ[3], I[3][3];
  int j, kl;

  DirectionalAtom *dAtom;

  int n_atoms;
  double kinetic_global;
  Atom** atoms;

  
  n_atoms = info->n_atoms;
  atoms = info->atoms;

  kinetic = 0.0;
  kinetic_global = 0.0;
  for( kl=0; kl < n_atoms; kl++ ){
    
    atoms[kl]->getVel(aVel);
    amass = atoms[kl]->getMass();
    
    for (j=0; j < 3; j++) 
      kinetic += amass * aVel[j] * aVel[j];

    if( atoms[kl]->isDirectional() ){
            
      dAtom = (DirectionalAtom *)atoms[kl];

      dAtom->getJ( aJ );
      dAtom->getI( I );
      
      for (j=0; j<3; j++) 
        kinetic += aJ[j]*aJ[j] / I[j][j];
      
    }
  }
#ifdef IS_MPI
  MPI_Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,
                MPI_SUM, MPI_COMM_WORLD);
  kinetic = kinetic_global;
#endif //is_mpi

  kinetic = kinetic * 0.5 / e_convert;

  return kinetic;
}

double Thermo::getPotential(){
  
  double potential_local;
  double potential;
  int el, nSRI;
  Molecule* molecules;

  molecules = info->molecules;
  nSRI = info->n_SRI;

  potential_local = 0.0;
  potential = 0.0;
  potential_local += info->lrPot;

  for( el=0; el<info->n_mol; el++ ){    
    potential_local += molecules[el].getPotential();
  }

  // Get total potential for entire system from MPI.
#ifdef IS_MPI
  MPI_Allreduce(&potential_local,&potential,1,MPI_DOUBLE,
                MPI_SUM, MPI_COMM_WORLD);
#else
  potential = potential_local; 
#endif // is_mpi

  return potential;
}

double Thermo::getTotalE(){

  double total;

  total = this->getKinetic() + this->getPotential();
  return total;
}

double Thermo::getTemperature(){

  const double kb = 1.9872156E-3; // boltzman's constant in kcal/(mol K)
  double temperature;
  
  temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb );
  return temperature;
}

double Thermo::getVolume() {

  return info->boxVol;
}

double Thermo::getPressure() {

  // Relies on the calculation of the full molecular pressure tensor
  
  const double p_convert = 1.63882576e8;
  double press[3][3];
  double pressure;

  this->getPressureTensor(press);

  pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;

  return pressure;
}

double Thermo::getPressureX() {

  // Relies on the calculation of the full molecular pressure tensor
  
  const double p_convert = 1.63882576e8;
  double press[3][3];
  double pressureX;

  this->getPressureTensor(press);

  pressureX = p_convert * press[0][0];

  return pressureX;
}

double Thermo::getPressureY() {

  // Relies on the calculation of the full molecular pressure tensor
  
  const double p_convert = 1.63882576e8;
  double press[3][3];
  double pressureY;

  this->getPressureTensor(press);

  pressureY = p_convert * press[1][1];

  return pressureY;
}

double Thermo::getPressureZ() {

  // Relies on the calculation of the full molecular pressure tensor
  
  const double p_convert = 1.63882576e8;
  double press[3][3];
  double pressureZ;

  this->getPressureTensor(press);

  pressureZ = p_convert * press[2][2];

  return pressureZ;
}


void Thermo::getPressureTensor(double press[3][3]){
  // returns pressure tensor in units amu*fs^-2*Ang^-1
  // routine derived via viral theorem description in:
  // Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322

  const double e_convert = 4.184e-4;

  double molmass, volume;
  double vcom[3];
  double p_local[9], p_global[9];
  int i, j, k, nMols;
  Molecule* molecules;

  nMols = info->n_mol;
  molecules = info->molecules;
  //tau = info->tau;

  // use velocities of molecular centers of mass and molecular masses:
  for (i=0; i < 9; i++) {    
    p_local[i] = 0.0;
    p_global[i] = 0.0;
  }

  for (i=0; i < nMols; i++) {
    molmass = molecules[i].getCOMvel(vcom);

    p_local[0] += molmass * (vcom[0] * vcom[0]); 
    p_local[1] += molmass * (vcom[0] * vcom[1]); 
    p_local[2] += molmass * (vcom[0] * vcom[2]); 
    p_local[3] += molmass * (vcom[1] * vcom[0]); 
    p_local[4] += molmass * (vcom[1] * vcom[1]); 
    p_local[5] += molmass * (vcom[1] * vcom[2]); 
    p_local[6] += molmass * (vcom[2] * vcom[0]); 
    p_local[7] += molmass * (vcom[2] * vcom[1]); 
    p_local[8] += molmass * (vcom[2] * vcom[2]); 
  }

  // Get total for entire system from MPI.

#ifdef IS_MPI
  MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
#else
  for (i=0; i<9; i++) {
    p_global[i] = p_local[i]; 
  }
#endif // is_mpi

  volume = this->getVolume();

  for(i = 0; i < 3; i++) {
    for (j = 0; j < 3; j++) {
      k = 3*i + j;
      press[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume;

    }
  }
}

void Thermo::velocitize() {
  
  double aVel[3], aJ[3], I[3][3];
  int i, j, vr, vd; // velocity randomizer loop counters
  double vdrift[3];
  double vbar;
  const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
  double av2;
  double kebar;
  int n_atoms;
  Atom** atoms;
  DirectionalAtom* dAtom;
  double temperature;
  int n_oriented;
  int n_constraints;

  atoms         = info->atoms;
  n_atoms       = info->n_atoms;
  temperature   = info->target_temp;
  n_oriented    = info->n_oriented;
  n_constraints = info->n_constraints;
  
  kebar = kb * temperature * (double)info->ndfRaw / 
    ( 2.0 * (double)info->ndf );
  
  for(vr = 0; vr < n_atoms; vr++){
    
    // uses equipartition theory to solve for vbar in angstrom/fs

    av2 = 2.0 * kebar / atoms[vr]->getMass();
    vbar = sqrt( av2 );

    // picks random velocities from a gaussian distribution
    // centered on vbar

    for (j=0; j<3; j++) 
      aVel[j] = vbar * gaussStream->getGaussian();
    
    atoms[vr]->setVel( aVel );

  }

  // Get the Center of Mass drift velocity.

  getCOMVel(vdrift);
  
  //  Corrects for the center of mass drift.
  // sums all the momentum and divides by total mass.

  for(vd = 0; vd < n_atoms; vd++){
    
    atoms[vd]->getVel(aVel);
    
    for (j=0; j < 3; j++) 
      aVel[j] -= vdrift[j];
        
    atoms[vd]->setVel( aVel );
  }
  if( n_oriented ){
  
    for( i=0; i<n_atoms; i++ ){
      
      if( atoms[i]->isDirectional() ){
        
        dAtom = (DirectionalAtom *)atoms[i];
        dAtom->getI( I );
        
        for (j = 0 ; j < 3; j++) {

          vbar = sqrt( 2.0 * kebar * I[j][j] );
          aJ[j] = vbar * gaussStream->getGaussian();

        }       

        dAtom->setJ( aJ );

      }
    }   
  }
}

void Thermo::getCOMVel(double vdrift[3]){

  double mtot, mtot_local;
  double aVel[3], amass;
  double vdrift_local[3];
  int vd, n_atoms, j;
  Atom** atoms;

  // We are very careless here with the distinction between n_atoms and n_local
  // We should really fix this before someone pokes an eye out.

  n_atoms = info->n_atoms;  
  atoms   = info->atoms;

  mtot_local = 0.0;
  vdrift_local[0] = 0.0;
  vdrift_local[1] = 0.0;
  vdrift_local[2] = 0.0;
  
  for(vd = 0; vd < n_atoms; vd++){
    
    amass = atoms[vd]->getMass();
    atoms[vd]->getVel( aVel );

    for(j = 0; j < 3; j++) 
      vdrift_local[j] += aVel[j] * amass;
    
    mtot_local += amass;
  }

#ifdef IS_MPI
  MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
  MPI_Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
#else
  mtot = mtot_local;
  for(vd = 0; vd < 3; vd++) {
    vdrift[vd] = vdrift_local[vd];
  }
#endif
    
  for (vd = 0; vd < 3; vd++) {
    vdrift[vd] = vdrift[vd] / mtot;
  }
  
}

void Thermo::getCOM(double COM[3]){

  double mtot, mtot_local;
  double aPos[3], amass;
  double COM_local[3];
  int i, n_atoms, j;
  Atom** atoms;

  // We are very careless here with the distinction between n_atoms and n_local
  // We should really fix this before someone pokes an eye out.

  n_atoms = info->n_atoms;  
  atoms   = info->atoms;

  mtot_local = 0.0;
  COM_local[0] = 0.0;
  COM_local[1] = 0.0;
  COM_local[2] = 0.0;
  
  for(i = 0; i < n_atoms; i++){
    
    amass = atoms[i]->getMass();
    atoms[i]->getPos( aPos );

    for(j = 0; j < 3; j++) 
      COM_local[j] += aPos[j] * amass;
    
    mtot_local += amass;
  }

#ifdef IS_MPI
  MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
  MPI_Allreduce(COM_local,COM,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
#else
  mtot = mtot_local;
  for(i = 0; i < 3; i++) {
    COM[i] = COM_local[i];
  }
#endif
    
  for (i = 0; i < 3; i++) {
    COM[i] = COM[i] / mtot;
  }
}
Revision:	853
Committed:	Thu Nov 6 19:11:38 2003 UTC (20 years, 8 months ago) by mmeineke
File size:	8882 byte(s)
Log Message:	did a merge by hand from the new-templateless branch to the main trunk. bug Fixes include: * fixed the switching function from ortho to non-ortho box. !!!!! THis was responsible for all of the sudden deaths we saw. * some formating in the string when we write out the extended system state. * added NPT.cpp to the makefile.in
#	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 j, kl;
37
38	DirectionalAtom *dAtom;
39
40	int n_atoms;
41	double kinetic_global;
42	Atom** atoms;
43
44
45	n_atoms = info->n_atoms;
46	atoms = info->atoms;
47
48	kinetic = 0.0;
49	kinetic_global = 0.0;
50	for( kl=0; kl < n_atoms; kl++ ){
51
52	atoms[kl]->getVel(aVel);
53	amass = atoms[kl]->getMass();
54
55	for (j=0; j < 3; j++)
56	kinetic += amass * aVel[j] * aVel[j];
57
58	if( atoms[kl]->isDirectional() ){
59
60	dAtom = (DirectionalAtom *)atoms[kl];
61
62	dAtom->getJ( aJ );
63	dAtom->getI( I );
64
65	for (j=0; j<3; j++)
66	kinetic += aJ[j]*aJ[j] / I[j][j];
67
68	}
69	}
70	#ifdef IS_MPI
71	MPI_Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,
72	MPI_SUM, MPI_COMM_WORLD);
73	kinetic = kinetic_global;
74	#endif //is_mpi
75
76	kinetic = kinetic * 0.5 / e_convert;
77
78	return kinetic;
79	}
80
81	double Thermo::getPotential(){
82
83	double potential_local;
84	double potential;
85	int el, nSRI;
86	Molecule* molecules;
87
88	molecules = info->molecules;
89	nSRI = info->n_SRI;
90
91	potential_local = 0.0;
92	potential = 0.0;
93	potential_local += info->lrPot;
94
95	for( el=0; el<info->n_mol; el++ ){
96	potential_local += molecules[el].getPotential();
97	}
98
99	// Get total potential for entire system from MPI.
100	#ifdef IS_MPI
101	MPI_Allreduce(&potential_local,&potential,1,MPI_DOUBLE,
102	MPI_SUM, MPI_COMM_WORLD);
103	#else
104	potential = potential_local;
105	#endif // is_mpi
106
107	return potential;
108	}
109
110	double Thermo::getTotalE(){
111
112	double total;
113
114	total = this->getKinetic() + this->getPotential();
115	return total;
116	}
117
118	double Thermo::getTemperature(){
119
120	const double kb = 1.9872156E-3; // boltzman's constant in kcal/(mol K)
121	double temperature;
122
123	temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb );
124	return temperature;
125	}
126
127	double Thermo::getVolume() {
128
129	return info->boxVol;
130	}
131
132	double Thermo::getPressure() {
133
134	// Relies on the calculation of the full molecular pressure tensor
135
136	const double p_convert = 1.63882576e8;
137	double press[3][3];
138	double pressure;
139
140	this->getPressureTensor(press);
141
142	pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
143
144	return pressure;
145	}
146
147	double Thermo::getPressureX() {
148
149	// Relies on the calculation of the full molecular pressure tensor
150
151	const double p_convert = 1.63882576e8;
152	double press[3][3];
153	double pressureX;
154
155	this->getPressureTensor(press);
156
157	pressureX = p_convert * press[0][0];
158
159	return pressureX;
160	}
161
162	double Thermo::getPressureY() {
163
164	// Relies on the calculation of the full molecular pressure tensor
165
166	const double p_convert = 1.63882576e8;
167	double press[3][3];
168	double pressureY;
169
170	this->getPressureTensor(press);
171
172	pressureY = p_convert * press[1][1];
173
174	return pressureY;
175	}
176
177	double Thermo::getPressureZ() {
178
179	// Relies on the calculation of the full molecular pressure tensor
180
181	const double p_convert = 1.63882576e8;
182	double press[3][3];
183	double pressureZ;
184
185	this->getPressureTensor(press);
186
187	pressureZ = p_convert * press[2][2];
188
189	return pressureZ;
190	}
191
192
193	void Thermo::getPressureTensor(double press[3][3]){
194	// returns pressure tensor in units amufs^-2Ang^-1
195	// routine derived via viral theorem description in:
196	// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
197
198	const double e_convert = 4.184e-4;
199
200	double molmass, volume;
201	double vcom[3];
202	double p_local[9], p_global[9];
203	int i, j, k, nMols;
204	Molecule* molecules;
205
206	nMols = info->n_mol;
207	molecules = info->molecules;
208	//tau = info->tau;
209
210	// use velocities of molecular centers of mass and molecular masses:
211	for (i=0; i < 9; i++) {
212	p_local[i] = 0.0;
213	p_global[i] = 0.0;
214	}
215
216	for (i=0; i < nMols; i++) {
217	molmass = molecules[i].getCOMvel(vcom);
218
219	p_local[0] += molmass * (vcom[0] * vcom[0]);
220	p_local[1] += molmass * (vcom[0] * vcom[1]);
221	p_local[2] += molmass * (vcom[0] * vcom[2]);
222	p_local[3] += molmass * (vcom[1] * vcom[0]);
223	p_local[4] += molmass * (vcom[1] * vcom[1]);
224	p_local[5] += molmass * (vcom[1] * vcom[2]);
225	p_local[6] += molmass * (vcom[2] * vcom[0]);
226	p_local[7] += molmass * (vcom[2] * vcom[1]);
227	p_local[8] += molmass * (vcom[2] * vcom[2]);
228	}
229
230	// Get total for entire system from MPI.
231
232	#ifdef IS_MPI
233	MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
234	#else
235	for (i=0; i<9; i++) {
236	p_global[i] = p_local[i];
237	}
238	#endif // is_mpi
239
240	volume = this->getVolume();
241
242	for(i = 0; i < 3; i++) {
243	for (j = 0; j < 3; j++) {
244	k = 3*i + j;
245	press[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume;
246
247	}
248	}
249	}
250
251	void Thermo::velocitize() {
252
253	double aVel[3], aJ[3], I[3][3];
254	int i, j, vr, vd; // velocity randomizer loop counters
255	double vdrift[3];
256	double vbar;
257	const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
258	double av2;
259	double kebar;
260	int n_atoms;
261	Atom** atoms;
262	DirectionalAtom* dAtom;
263	double temperature;
264	int n_oriented;
265	int n_constraints;
266
267	atoms = info->atoms;
268	n_atoms = info->n_atoms;
269	temperature = info->target_temp;
270	n_oriented = info->n_oriented;
271	n_constraints = info->n_constraints;
272
273	kebar = kb * temperature * (double)info->ndfRaw /
274	( 2.0 * (double)info->ndf );
275
276	for(vr = 0; vr < n_atoms; vr++){
277
278	// uses equipartition theory to solve for vbar in angstrom/fs
279
280	av2 = 2.0 * kebar / atoms[vr]->getMass();
281	vbar = sqrt( av2 );
282
283	// picks random velocities from a gaussian distribution
284	// centered on vbar
285
286	for (j=0; j<3; j++)
287	aVel[j] = vbar * gaussStream->getGaussian();
288
289	atoms[vr]->setVel( aVel );
290
291	}
292
293	// Get the Center of Mass drift velocity.
294
295	getCOMVel(vdrift);
296
297	// Corrects for the center of mass drift.
298	// sums all the momentum and divides by total mass.
299
300	for(vd = 0; vd < n_atoms; vd++){
301
302	atoms[vd]->getVel(aVel);
303
304	for (j=0; j < 3; j++)
305	aVel[j] -= vdrift[j];
306
307	atoms[vd]->setVel( aVel );
308	}
309	if( n_oriented ){
310
311	for( i=0; i<n_atoms; i++ ){
312
313	if( atoms[i]->isDirectional() ){
314
315	dAtom = (DirectionalAtom *)atoms[i];
316	dAtom->getI( I );
317
318	for (j = 0 ; j < 3; j++) {
319
320	vbar = sqrt( 2.0 * kebar * I[j][j] );
321	aJ[j] = vbar * gaussStream->getGaussian();
322
323	}
324
325	dAtom->setJ( aJ );
326
327	}
328	}
329	}
330	}
331
332	void Thermo::getCOMVel(double vdrift[3]){
333
334	double mtot, mtot_local;
335	double aVel[3], amass;
336	double vdrift_local[3];
337	int vd, n_atoms, j;
338	Atom** atoms;
339
340	// We are very careless here with the distinction between n_atoms and n_local
341	// We should really fix this before someone pokes an eye out.
342
343	n_atoms = info->n_atoms;
344	atoms = info->atoms;
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 < n_atoms; vd++){
352
353	amass = atoms[vd]->getMass();
354	atoms[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, n_atoms, j;
384	Atom** atoms;
385
386	// We are very careless here with the distinction between n_atoms and n_local
387	// We should really fix this before someone pokes an eye out.
388
389	n_atoms = info->n_atoms;
390	atoms = info->atoms;
391
392	mtot_local = 0.0;
393	COM_local[0] = 0.0;
394	COM_local[1] = 0.0;
395	COM_local[2] = 0.0;
396
397	for(i = 0; i < n_atoms; i++){
398
399	amass = atoms[i]->getMass();
400	atoms[i]->getPos( aPos );
401
402	for(j = 0; j < 3; j++)
403	COM_local[j] += aPos[j] * amass;
404
405	mtot_local += amass;
406	}
407
408	#ifdef IS_MPI
409	MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
410	MPI_Allreduce(COM_local,COM,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
411	#else
412	mtot = mtot_local;
413	for(i = 0; i < 3; i++) {
414	COM[i] = COM_local[i];
415	}
416	#endif
417
418	for (i = 0; i < 3; i++) {
419	COM[i] = COM[i] / mtot;
420	}
421	}