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_entry_plug ) { 
  entry_plug = the_entry_plug;
  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 vx2, vy2, vz2;
  double kinetic, v_sqr;
  int kl;
  double jx2, jy2, jz2; // the square of the angular momentums

  DirectionalAtom *dAtom;

  int n_atoms;
  double kinetic_global;
  Atom** atoms;

  
  n_atoms = entry_plug->n_atoms;
  atoms = entry_plug->atoms;

  kinetic = 0.0;
  kinetic_global = 0.0;
  for( kl=0; kl < n_atoms; kl++ ){

    vx2 = atoms[kl]->get_vx() * atoms[kl]->get_vx();
    vy2 = atoms[kl]->get_vy() * atoms[kl]->get_vy();
    vz2 = atoms[kl]->get_vz() * atoms[kl]->get_vz();

    v_sqr = vx2 + vy2 + vz2;
    kinetic += atoms[kl]->getMass() * v_sqr;

    if( atoms[kl]->isDirectional() ){
            
      dAtom = (DirectionalAtom *)atoms[kl];
      
      jx2 = dAtom->getJx() * dAtom->getJx();    
      jy2 = dAtom->getJy() * dAtom->getJy();
      jz2 = dAtom->getJz() * dAtom->getJz();
      
      kinetic += (jx2 / dAtom->getIxx()) + (jy2 / dAtom->getIyy()) 
        + (jz2 / dAtom->getIzz());
    }
  }
#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 = entry_plug->molecules;
  nSRI = entry_plug->n_SRI;

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

  for( el=0; el<entry_plug->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)entry_plug->ndf * kb );
  return temperature;
}

double Thermo::getPressure(){
  // returns pressure 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;
  const double p_convert = 1.63882576e8;
  double molmass;
  double vcom[3];
  double p_local, p_sum, p_mol, virial;
  double theBox[3];
  double* tau;
  int i, nMols;
  Molecule* molecules;

  nMols = entry_plug->n_mol;
  molecules = entry_plug->molecules;
  tau = entry_plug->tau;

  // use velocities of molecular centers of mass and molecular masses:
  p_local = 0.0;

  for (i=0; i < nMols; i++) {
    molmass = molecules[i].getCOMvel(vcom);
    p_local += (vcom[0]*vcom[0] + vcom[1]*vcom[1] + vcom[2]*vcom[2]) * molmass;
  }

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

  virial = tau[0] + tau[4] + tau[8];
  entry_plug->getBox(theBox);

  p_mol = p_convert * (p_sum - virial*e_convert) / 
    (3.0 * theBox[0] * theBox[1]* theBox[2]); 

  return p_mol;
}

void Thermo::velocitize() {
  
  double x,y;
  double vx, vy, vz;
  double jx, jy, jz;
  int i, 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         = entry_plug->atoms;
  n_atoms       = entry_plug->n_atoms;
  temperature   = entry_plug->target_temp;
  n_oriented    = entry_plug->n_oriented;
  n_constraints = entry_plug->n_constraints;
  
  kebar = kb * temperature * (double)entry_plug->ndf / 
    ( 2.0 * (double)entry_plug->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

    vx = vbar * gaussStream->getGaussian();
    vy = vbar * gaussStream->getGaussian();
    vz = vbar * gaussStream->getGaussian();

    atoms[vr]->set_vx( vx ); 
    atoms[vr]->set_vy( vy );
    atoms[vr]->set_vz( vz );
  }

  // 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++){
    
    vx = atoms[vd]->get_vx();
    vy = atoms[vd]->get_vy();
    vz = atoms[vd]->get_vz();
        
    vx -= vdrift[0];
    vy -= vdrift[1];
    vz -= vdrift[2];
    
    atoms[vd]->set_vx(vx);
    atoms[vd]->set_vy(vy);
    atoms[vd]->set_vz(vz);
  }
  if( n_oriented ){
  
    for( i=0; i<n_atoms; i++ ){
      
      if( atoms[i]->isDirectional() ){
        
        dAtom = (DirectionalAtom *)atoms[i];

        vbar = sqrt( 2.0 * kebar * dAtom->getIxx() );
        jx = vbar * gaussStream->getGaussian();

        vbar = sqrt( 2.0 * kebar * dAtom->getIyy() );
        jy = vbar * gaussStream->getGaussian();
        
        vbar = sqrt( 2.0 * kebar * dAtom->getIzz() );
        jz = vbar * gaussStream->getGaussian();
        
        dAtom->setJx( jx );
        dAtom->setJy( jy );
        dAtom->setJz( jz );
      }
    }   
  }
}

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

  double mtot, mtot_local;
  double vdrift_local[3];
  int vd, n_atoms;
  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 = entry_plug->n_atoms;  
  atoms   = entry_plug->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++){
    
    vdrift_local[0] += atoms[vd]->get_vx() * atoms[vd]->getMass();
    vdrift_local[1] += atoms[vd]->get_vy() * atoms[vd]->getMass();
    vdrift_local[2] += atoms[vd]->get_vz() * atoms[vd]->getMass();
    
    mtot_local += atoms[vd]->getMass();
  }

#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:	477
Committed:	Tue Apr 8 14:34:30 2003 UTC (21 years, 3 months ago) by gezelter
File size:	7255 byte(s)
Log Message:	dt/2 fix in nvt
#	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			Thermo::Thermo( SimInfo* the_entry_plug ) {
23			entry_plug = the_entry_plug;
24			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			double vx2, vy2, vz2;
37			double kinetic, v_sqr;
38			int kl;
39			double jx2, jy2, jz2; // the square of the angular momentums
40
41			DirectionalAtom *dAtom;
42
43			int n_atoms;
44			double kinetic_global;
45			Atom** atoms;
46
47
48			n_atoms = entry_plug->n_atoms;
49			atoms = entry_plug->atoms;
50
51			kinetic = 0.0;
52			kinetic_global = 0.0;
53			for( kl=0; kl < n_atoms; kl++ ){
54
55			vx2 = atoms[kl]->get_vx() * atoms[kl]->get_vx();
56			vy2 = atoms[kl]->get_vy() * atoms[kl]->get_vy();
57			vz2 = atoms[kl]->get_vz() * atoms[kl]->get_vz();
58
59			v_sqr = vx2 + vy2 + vz2;
60			kinetic += atoms[kl]->getMass() * v_sqr;
61
62			if( atoms[kl]->isDirectional() ){
63
64			dAtom = (DirectionalAtom *)atoms[kl];
65
66			jx2 = dAtom->getJx() * dAtom->getJx();
67			jy2 = dAtom->getJy() * dAtom->getJy();
68			jz2 = dAtom->getJz() * dAtom->getJz();
69
70			kinetic += (jx2 / dAtom->getIxx()) + (jy2 / dAtom->getIyy())
71			+ (jz2 / dAtom->getIzz());
72			}
73			}
74			#ifdef IS_MPI
75	mmeineke	447	MPI_Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,
76			MPI_SUM, MPI_COMM_WORLD);
77	mmeineke	377	kinetic = kinetic_global;
78			#endif //is_mpi
79
80			kinetic = kinetic * 0.5 / e_convert;
81
82			return kinetic;
83			}
84
85			double Thermo::getPotential(){
86
87	chuckv	401	double potential_local;
88	mmeineke	377	double potential;
89			int el, nSRI;
90	mmeineke	428	Molecule* molecules;
91	mmeineke	377
92	mmeineke	428	molecules = entry_plug->molecules;
93	mmeineke	377	nSRI = entry_plug->n_SRI;
94
95	chuckv	401	potential_local = 0.0;
96	chuckv	438	potential = 0.0;
97	chuckv	401	potential_local += entry_plug->lrPot;
98	mmeineke	377
99	mmeineke	423	for( el=0; el<entry_plug->n_mol; el++ ){
100	mmeineke	428	potential_local += molecules[el].getPotential();
101	mmeineke	377	}
102
103			// Get total potential for entire system from MPI.
104			#ifdef IS_MPI
105	mmeineke	447	MPI_Allreduce(&potential_local,&potential,1,MPI_DOUBLE,
106			MPI_SUM, MPI_COMM_WORLD);
107	chuckv	401	#else
108			potential = potential_local;
109	mmeineke	377	#endif // is_mpi
110
111	chuckv	438	#ifdef IS_MPI
112			/*
113			std::cerr << "node " << worldRank << ": after pot = " << potential << "\n";
114			*/
115			#endif
116
117	mmeineke	377	return potential;
118			}
119
120			double Thermo::getTotalE(){
121
122			double total;
123
124			total = this->getKinetic() + this->getPotential();
125			return total;
126			}
127
128	gezelter	454	double Thermo::getTemperature(){
129
130			const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K)
131			double temperature;
132
133	gezelter	458	temperature = ( 2.0 * this->getKinetic() ) / ((double)entry_plug->ndf * kb );
134	mmeineke	377	return temperature;
135			}
136
137			double Thermo::getPressure(){
138	gezelter	445	// returns pressure in units amufs^-2Ang^-1
139			// routine derived via viral theorem description in:
140			// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
141	mmeineke	377
142	gezelter	477	const double e_convert = 4.184e-4;
143			const double p_convert = 1.63882576e8;
144	gezelter	475	double molmass;
145	gezelter	468	double vcom[3];
146			double p_local, p_sum, p_mol, virial;
147			double theBox[3];
148			double* tau;
149			int i, nMols;
150			Molecule* molecules;
151
152			nMols = entry_plug->n_mol;
153			molecules = entry_plug->molecules;
154			tau = entry_plug->tau;
155
156			// use velocities of molecular centers of mass and molecular masses:
157			p_local = 0.0;
158	gezelter	475
159	gezelter	468	for (i=0; i < nMols; i++) {
160	gezelter	475	molmass = molecules[i].getCOMvel(vcom);
161			p_local += (vcom[0]vcom[0] + vcom[1]vcom[1] + vcom[2]vcom[2]) molmass;
162	gezelter	468	}
163
164			// Get total for entire system from MPI.
165			#ifdef IS_MPI
166			MPI_Allreduce(&p_local,&p_sum,1,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
167			#else
168			p_sum = p_local;
169			#endif // is_mpi
170
171			virial = tau[0] + tau[4] + tau[8];
172			entry_plug->getBox(theBox);
173
174	gezelter	477	p_mol = p_convert * (p_sum - virial*e_convert) /
175			(3.0 * theBox[0] * theBox[1]* theBox[2]);
176
177	gezelter	468	return p_mol;
178	mmeineke	377	}
179
180			void Thermo::velocitize() {
181
182			double x,y;
183			double vx, vy, vz;
184			double jx, jy, jz;
185			int i, vr, vd; // velocity randomizer loop counters
186	chuckv	403	double vdrift[3];
187	mmeineke	377	double vbar;
188			const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
189			double av2;
190			double kebar;
191			int n_atoms;
192			Atom** atoms;
193			DirectionalAtom* dAtom;
194			double temperature;
195			int n_oriented;
196			int n_constraints;
197
198			atoms = entry_plug->atoms;
199			n_atoms = entry_plug->n_atoms;
200			temperature = entry_plug->target_temp;
201			n_oriented = entry_plug->n_oriented;
202			n_constraints = entry_plug->n_constraints;
203
204	gezelter	458	kebar = kb * temperature * (double)entry_plug->ndf /
205			( 2.0 * (double)entry_plug->ndfRaw );
206	chuckv	403
207	mmeineke	377	for(vr = 0; vr < n_atoms; vr++){
208
209			// uses equipartition theory to solve for vbar in angstrom/fs
210
211			av2 = 2.0 * kebar / atoms[vr]->getMass();
212			vbar = sqrt( av2 );
213	gezelter	444
214	mmeineke	377	// vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() );
215
216			// picks random velocities from a gaussian distribution
217			// centered on vbar
218
219			vx = vbar * gaussStream->getGaussian();
220			vy = vbar * gaussStream->getGaussian();
221			vz = vbar * gaussStream->getGaussian();
222
223			atoms[vr]->set_vx( vx );
224			atoms[vr]->set_vy( vy );
225			atoms[vr]->set_vz( vz );
226			}
227	chuckv	401
228			// Get the Center of Mass drift velocity.
229
230	chuckv	403	getCOMVel(vdrift);
231	mmeineke	377
232			// Corrects for the center of mass drift.
233			// sums all the momentum and divides by total mass.
234
235			for(vd = 0; vd < n_atoms; vd++){
236
237			vx = atoms[vd]->get_vx();
238			vy = atoms[vd]->get_vy();
239			vz = atoms[vd]->get_vz();
240	chuckv	401
241	mmeineke	377	vx -= vdrift[0];
242			vy -= vdrift[1];
243			vz -= vdrift[2];
244
245			atoms[vd]->set_vx(vx);
246			atoms[vd]->set_vy(vy);
247			atoms[vd]->set_vz(vz);
248			}
249			if( n_oriented ){
250
251			for( i=0; i<n_atoms; i++ ){
252
253			if( atoms[i]->isDirectional() ){
254
255			dAtom = (DirectionalAtom *)atoms[i];
256
257			vbar = sqrt( 2.0 * kebar * dAtom->getIxx() );
258			jx = vbar * gaussStream->getGaussian();
259
260			vbar = sqrt( 2.0 * kebar * dAtom->getIyy() );
261			jy = vbar * gaussStream->getGaussian();
262	gezelter	454
263	mmeineke	377	vbar = sqrt( 2.0 * kebar * dAtom->getIzz() );
264			jz = vbar * gaussStream->getGaussian();
265
266			dAtom->setJx( jx );
267			dAtom->setJy( jy );
268			dAtom->setJz( jz );
269			}
270			}
271			}
272			}
273	chuckv	401
274	chuckv	403	void Thermo::getCOMVel(double vdrift[3]){
275	chuckv	401
276			double mtot, mtot_local;
277			double vdrift_local[3];
278			int vd, n_atoms;
279			Atom** atoms;
280
281			// We are very careless here with the distinction between n_atoms and n_local
282			// We should really fix this before someone pokes an eye out.
283
284			n_atoms = entry_plug->n_atoms;
285			atoms = entry_plug->atoms;
286
287			mtot_local = 0.0;
288			vdrift_local[0] = 0.0;
289			vdrift_local[1] = 0.0;
290			vdrift_local[2] = 0.0;
291
292			for(vd = 0; vd < n_atoms; vd++){
293
294			vdrift_local[0] += atoms[vd]->get_vx() * atoms[vd]->getMass();
295			vdrift_local[1] += atoms[vd]->get_vy() * atoms[vd]->getMass();
296			vdrift_local[2] += atoms[vd]->get_vz() * atoms[vd]->getMass();
297
298			mtot_local += atoms[vd]->getMass();
299			}
300
301			#ifdef IS_MPI
302	mmeineke	447	MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
303			MPI_Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
304	chuckv	401	#else
305			mtot = mtot_local;
306			for(vd = 0; vd < 3; vd++) {
307			vdrift[vd] = vdrift_local[vd];
308			}
309			#endif
310
311			for (vd = 0; vd < 3; vd++) {
312			vdrift[vd] = vdrift[vd] / mtot;
313			}
314
315			}
316