OOPSE/libmdtools/Thermo.cpp

#include <cmath>
#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


#define BASE_SEED 123456789

Thermo::Thermo( SimInfo* the_info ) { 
  info = the_info;
  int baseSeed = BASE_SEED;
  
  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

#ifdef IS_MPI
  /*
  std::cerr << "node " << worldRank << ": after pot = " << potential << "\n";
  */
#endif

  return potential;
}

double Thermo::getTotalE(){

  double total;

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

double Thermo::getTemperature(){

  const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K)
  double temperature;
  
  temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb );
  return temperature;
}

double Thermo::getEnthalpy() {

  const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2
  double u, p, v;
  double press[3][3];

  u = this->getTotalE();

  this->getPressureTensor(press);
  p = (press[0][0] + press[1][1] + press[2][2]) / 3.0;

  v = this->getVolume();

  return (u + (p*v)/e_convert);
}

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;
}


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 x,y;
  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->ndf / 
    ( 2.0 * (double)info->ndfRaw );
  
  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 );
 
//     vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() );
    
    // 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;
  }
  
}

Revision:	614
Committed:	Tue Jul 15 17:57:04 2003 UTC (20 years, 11 months ago) by mmeineke
File size:	7609 byte(s)
Log Message:	fixed some bugs, Changed entry_plug to info where appropriate
#	User	Rev	Content
1	mmeineke	377	#include <cmath>
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	chuckv	438	#include "simError.h"
13	mmeineke	402
14			#ifdef IS_MPI
15	chuckv	401	#define __C
16	mmeineke	402	#include "mpiSimulation.hpp"
17			#endif // is_mpi
18	mmeineke	377
19	mmeineke	402
20	mmeineke	377	#define BASE_SEED 123456789
21
22	mmeineke	614	Thermo::Thermo( SimInfo* the_info ) {
23			info = the_info;
24	mmeineke	377	int baseSeed = BASE_SEED;
25
26			gaussStream = new gaussianSPRNG( baseSeed );
27			}
28
29			Thermo::~Thermo(){
30			delete gaussStream;
31			}
32
33			double Thermo::getKinetic(){
34
35			const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2
36	gezelter	608	double kinetic;
37			double amass;
38			double aVel[3], aJ[3], I[3][3];
39			int j, kl;
40	mmeineke	377
41			DirectionalAtom *dAtom;
42
43			int n_atoms;
44			double kinetic_global;
45			Atom** atoms;
46
47
48	mmeineke	614	n_atoms = info->n_atoms;
49			atoms = info->atoms;
50	mmeineke	377
51			kinetic = 0.0;
52			kinetic_global = 0.0;
53			for( kl=0; kl < n_atoms; kl++ ){
54	gezelter	608
55			atoms[kl]->getVel(aVel);
56			amass = atoms[kl]->getMass();
57
58			for (j=0; j < 3; j++)
59			kinetic += amass * aVel[j] * aVel[j];
60	mmeineke	377
61			if( atoms[kl]->isDirectional() ){
62
63			dAtom = (DirectionalAtom *)atoms[kl];
64	gezelter	608
65			dAtom->getJ( aJ );
66			dAtom->getI( I );
67	mmeineke	377
68	gezelter	608	for (j=0; j<3; j++)
69			kinetic += aJ[j]*aJ[j] / I[j][j];
70	mmeineke	377
71			}
72			}
73			#ifdef IS_MPI
74	mmeineke	447	MPI_Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,
75			MPI_SUM, MPI_COMM_WORLD);
76	mmeineke	377	kinetic = kinetic_global;
77			#endif //is_mpi
78
79			kinetic = kinetic * 0.5 / e_convert;
80
81			return kinetic;
82			}
83
84			double Thermo::getPotential(){
85
86	chuckv	401	double potential_local;
87	mmeineke	377	double potential;
88			int el, nSRI;
89	mmeineke	428	Molecule* molecules;
90	mmeineke	377
91	mmeineke	614	molecules = info->molecules;
92			nSRI = info->n_SRI;
93	mmeineke	377
94	chuckv	401	potential_local = 0.0;
95	chuckv	438	potential = 0.0;
96	mmeineke	614	potential_local += info->lrPot;
97	mmeineke	377
98	mmeineke	614	for( el=0; el<info->n_mol; el++ ){
99	mmeineke	428	potential_local += molecules[el].getPotential();
100	mmeineke	377	}
101
102			// Get total potential for entire system from MPI.
103			#ifdef IS_MPI
104	mmeineke	447	MPI_Allreduce(&potential_local,&potential,1,MPI_DOUBLE,
105			MPI_SUM, MPI_COMM_WORLD);
106	chuckv	401	#else
107			potential = potential_local;
108	mmeineke	377	#endif // is_mpi
109
110	chuckv	438	#ifdef IS_MPI
111			/*
112			std::cerr << "node " << worldRank << ": after pot = " << potential << "\n";
113			*/
114			#endif
115
116	mmeineke	377	return potential;
117			}
118
119			double Thermo::getTotalE(){
120
121			double total;
122
123			total = this->getKinetic() + this->getPotential();
124			return total;
125			}
126
127	gezelter	454	double Thermo::getTemperature(){
128
129			const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K)
130			double temperature;
131
132	mmeineke	614	temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb );
133	mmeineke	377	return temperature;
134			}
135
136	gezelter	484	double Thermo::getEnthalpy() {
137
138			const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2
139			double u, p, v;
140	gezelter	588	double press[3][3];
141	gezelter	484
142			u = this->getTotalE();
143
144			this->getPressureTensor(press);
145	gezelter	588	p = (press[0][0] + press[1][1] + press[2][2]) / 3.0;
146	gezelter	484
147			v = this->getVolume();
148
149			return (u + (p*v)/e_convert);
150			}
151
152			double Thermo::getVolume() {
153	gezelter	574
154	mmeineke	614	return info->boxVol;
155	gezelter	484	}
156
157	gezelter	483	double Thermo::getPressure() {
158	gezelter	574
159	gezelter	483	// Relies on the calculation of the full molecular pressure tensor
160
161			const double p_convert = 1.63882576e8;
162	gezelter	588	double press[3][3];
163	gezelter	483	double pressure;
164
165			this->getPressureTensor(press);
166
167	gezelter	588	pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
168	gezelter	483
169			return pressure;
170			}
171
172
173	gezelter	588	void Thermo::getPressureTensor(double press[3][3]){
174	gezelter	483	// returns pressure tensor in units amufs^-2Ang^-1
175	gezelter	445	// routine derived via viral theorem description in:
176			// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
177	mmeineke	377
178	gezelter	477	const double e_convert = 4.184e-4;
179	gezelter	483
180			double molmass, volume;
181	gezelter	468	double vcom[3];
182	gezelter	483	double p_local[9], p_global[9];
183	mmeineke	614	int i, j, k, nMols;
184	gezelter	468	Molecule* molecules;
185
186	mmeineke	614	nMols = info->n_mol;
187			molecules = info->molecules;
188			//tau = info->tau;
189	gezelter	468
190			// use velocities of molecular centers of mass and molecular masses:
191	gezelter	483	for (i=0; i < 9; i++) {
192			p_local[i] = 0.0;
193			p_global[i] = 0.0;
194			}
195	gezelter	475
196	gezelter	468	for (i=0; i < nMols; i++) {
197	gezelter	475	molmass = molecules[i].getCOMvel(vcom);
198	gezelter	483
199			p_local[0] += molmass * (vcom[0] * vcom[0]);
200			p_local[1] += molmass * (vcom[0] * vcom[1]);
201			p_local[2] += molmass * (vcom[0] * vcom[2]);
202			p_local[3] += molmass * (vcom[1] * vcom[0]);
203			p_local[4] += molmass * (vcom[1] * vcom[1]);
204			p_local[5] += molmass * (vcom[1] * vcom[2]);
205			p_local[6] += molmass * (vcom[2] * vcom[0]);
206			p_local[7] += molmass * (vcom[2] * vcom[1]);
207			p_local[8] += molmass * (vcom[2] * vcom[2]);
208	gezelter	468	}
209
210			// Get total for entire system from MPI.
211	chuckv	479
212	gezelter	468	#ifdef IS_MPI
213	gezelter	483	MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
214	gezelter	468	#else
215	gezelter	483	for (i=0; i<9; i++) {
216			p_global[i] = p_local[i];
217			}
218	gezelter	468	#endif // is_mpi
219
220	gezelter	611	volume = this->getVolume();
221	gezelter	468
222	gezelter	588	for(i = 0; i < 3; i++) {
223			for (j = 0; j < 3; j++) {
224			k = 3*i + j;
225	mmeineke	614	press[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume;
226
227	gezelter	588	}
228	gezelter	483	}
229	mmeineke	377	}
230
231			void Thermo::velocitize() {
232
233			double x,y;
234	gezelter	608	double aVel[3], aJ[3], I[3][3];
235			int i, j, vr, vd; // velocity randomizer loop counters
236	chuckv	403	double vdrift[3];
237	mmeineke	377	double vbar;
238			const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
239			double av2;
240			double kebar;
241			int n_atoms;
242			Atom** atoms;
243			DirectionalAtom* dAtom;
244			double temperature;
245			int n_oriented;
246			int n_constraints;
247
248	mmeineke	614	atoms = info->atoms;
249			n_atoms = info->n_atoms;
250			temperature = info->target_temp;
251			n_oriented = info->n_oriented;
252			n_constraints = info->n_constraints;
253	mmeineke	377
254	mmeineke	614	kebar = kb * temperature * (double)info->ndf /
255			( 2.0 * (double)info->ndfRaw );
256	chuckv	403
257	mmeineke	377	for(vr = 0; vr < n_atoms; vr++){
258
259			// uses equipartition theory to solve for vbar in angstrom/fs
260
261			av2 = 2.0 * kebar / atoms[vr]->getMass();
262			vbar = sqrt( av2 );
263	gezelter	444
264	mmeineke	377	// vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() );
265
266			// picks random velocities from a gaussian distribution
267			// centered on vbar
268
269	gezelter	608	for (j=0; j<3; j++)
270			aVel[j] = vbar * gaussStream->getGaussian();
271
272			atoms[vr]->setVel( aVel );
273	mmeineke	377
274			}
275	chuckv	401
276			// Get the Center of Mass drift velocity.
277
278	chuckv	403	getCOMVel(vdrift);
279	mmeineke	377
280			// Corrects for the center of mass drift.
281			// sums all the momentum and divides by total mass.
282
283			for(vd = 0; vd < n_atoms; vd++){
284
285	gezelter	608	atoms[vd]->getVel(aVel);
286
287			for (j=0; j < 3; j++)
288			aVel[j] -= vdrift[j];
289	chuckv	401
290	gezelter	608	atoms[vd]->setVel( aVel );
291	mmeineke	377	}
292			if( n_oriented ){
293
294			for( i=0; i<n_atoms; i++ ){
295
296			if( atoms[i]->isDirectional() ){
297
298			dAtom = (DirectionalAtom *)atoms[i];
299	gezelter	608	dAtom->getI( I );
300
301			for (j = 0 ; j < 3; j++) {
302	mmeineke	377
303	gezelter	608	vbar = sqrt( 2.0 * kebar * I[j][j] );
304			aJ[j] = vbar * gaussStream->getGaussian();
305	mmeineke	377
306	gezelter	608	}
307
308			dAtom->setJ( aJ );
309
310	mmeineke	377	}
311			}
312			}
313			}
314	chuckv	401
315	chuckv	403	void Thermo::getCOMVel(double vdrift[3]){
316	chuckv	401
317			double mtot, mtot_local;
318	gezelter	608	double aVel[3], amass;
319	chuckv	401	double vdrift_local[3];
320	gezelter	608	int vd, n_atoms, j;
321	chuckv	401	Atom** atoms;
322
323			// We are very careless here with the distinction between n_atoms and n_local
324			// We should really fix this before someone pokes an eye out.
325
326	mmeineke	614	n_atoms = info->n_atoms;
327			atoms = info->atoms;
328	chuckv	401
329			mtot_local = 0.0;
330			vdrift_local[0] = 0.0;
331			vdrift_local[1] = 0.0;
332			vdrift_local[2] = 0.0;
333
334			for(vd = 0; vd < n_atoms; vd++){
335
336	gezelter	608	amass = atoms[vd]->getMass();
337			atoms[vd]->getVel( aVel );
338
339			for(j = 0; j < 3; j++)
340			vdrift_local[j] += aVel[j] * amass;
341	chuckv	401
342	gezelter	608	mtot_local += amass;
343	chuckv	401	}
344
345			#ifdef IS_MPI
346	mmeineke	447	MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
347			MPI_Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
348	chuckv	401	#else
349			mtot = mtot_local;
350			for(vd = 0; vd < 3; vd++) {
351			vdrift[vd] = vdrift_local[vd];
352			}
353			#endif
354
355			for (vd = 0; vd < 3; vd++) {
356			vdrift[vd] = vdrift[vd] / mtot;
357			}
358
359			}
360