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 convert = 4.184e-4;
  double mtot;
  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++) {
    molecules[i].getCOMvel(mtot, vcom);
    p_local += mtot* (vcom[0]*vcom[0] + vcom[1]*vcom[1] + vcom[2]*vcom[2]);
  }

  // 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_sum - virial*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:	468
Committed:	Mon Apr 7 16:56:38 2003 UTC (21 years, 3 months ago) by gezelter
File size:	7182 byte(s)
Log Message:	Many fixes to add extended system
#	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	468	const double convert = 4.184e-4;
143			double mtot;
144			double vcom[3];
145			double p_local, p_sum, p_mol, virial;
146			double theBox[3];
147			double* tau;
148			int i, nMols;
149			Molecule* molecules;
150
151			nMols = entry_plug->n_mol;
152			molecules = entry_plug->molecules;
153			tau = entry_plug->tau;
154
155			// use velocities of molecular centers of mass and molecular masses:
156			p_local = 0.0;
157			for (i=0; i < nMols; i++) {
158			molecules[i].getCOMvel(mtot, vcom);
159			p_local += mtot* (vcom[0]vcom[0] + vcom[1]vcom[1] + vcom[2]*vcom[2]);
160			}
161
162			// Get total for entire system from MPI.
163			#ifdef IS_MPI
164			MPI_Allreduce(&p_local,&p_sum,1,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
165			#else
166			p_sum = p_local;
167			#endif // is_mpi
168
169			virial = tau[0] + tau[4] + tau[8];
170			entry_plug->getBox(theBox);
171
172			p_mol = (p_sum - virialconvert) / (3.0 theBox[0] * theBox[1]* theBox[2]);
173
174			return p_mol;
175	mmeineke	377	}
176
177			void Thermo::velocitize() {
178
179			double x,y;
180			double vx, vy, vz;
181			double jx, jy, jz;
182			int i, vr, vd; // velocity randomizer loop counters
183	chuckv	403	double vdrift[3];
184	mmeineke	377	double vbar;
185			const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
186			double av2;
187			double kebar;
188			int n_atoms;
189			Atom** atoms;
190			DirectionalAtom* dAtom;
191			double temperature;
192			int n_oriented;
193			int n_constraints;
194
195			atoms = entry_plug->atoms;
196			n_atoms = entry_plug->n_atoms;
197			temperature = entry_plug->target_temp;
198			n_oriented = entry_plug->n_oriented;
199			n_constraints = entry_plug->n_constraints;
200
201	gezelter	458	kebar = kb * temperature * (double)entry_plug->ndf /
202			( 2.0 * (double)entry_plug->ndfRaw );
203	chuckv	403
204	mmeineke	377	for(vr = 0; vr < n_atoms; vr++){
205
206			// uses equipartition theory to solve for vbar in angstrom/fs
207
208			av2 = 2.0 * kebar / atoms[vr]->getMass();
209			vbar = sqrt( av2 );
210	gezelter	444
211	mmeineke	377	// vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() );
212
213			// picks random velocities from a gaussian distribution
214			// centered on vbar
215
216			vx = vbar * gaussStream->getGaussian();
217			vy = vbar * gaussStream->getGaussian();
218			vz = vbar * gaussStream->getGaussian();
219
220			atoms[vr]->set_vx( vx );
221			atoms[vr]->set_vy( vy );
222			atoms[vr]->set_vz( vz );
223			}
224	chuckv	401
225			// Get the Center of Mass drift velocity.
226
227	chuckv	403	getCOMVel(vdrift);
228	mmeineke	377
229			// Corrects for the center of mass drift.
230			// sums all the momentum and divides by total mass.
231
232			for(vd = 0; vd < n_atoms; vd++){
233
234			vx = atoms[vd]->get_vx();
235			vy = atoms[vd]->get_vy();
236			vz = atoms[vd]->get_vz();
237	chuckv	401
238	mmeineke	377	vx -= vdrift[0];
239			vy -= vdrift[1];
240			vz -= vdrift[2];
241
242			atoms[vd]->set_vx(vx);
243			atoms[vd]->set_vy(vy);
244			atoms[vd]->set_vz(vz);
245			}
246			if( n_oriented ){
247
248			for( i=0; i<n_atoms; i++ ){
249
250			if( atoms[i]->isDirectional() ){
251
252			dAtom = (DirectionalAtom *)atoms[i];
253
254			vbar = sqrt( 2.0 * kebar * dAtom->getIxx() );
255			jx = vbar * gaussStream->getGaussian();
256
257			vbar = sqrt( 2.0 * kebar * dAtom->getIyy() );
258			jy = vbar * gaussStream->getGaussian();
259	gezelter	454
260	mmeineke	377	vbar = sqrt( 2.0 * kebar * dAtom->getIzz() );
261			jz = vbar * gaussStream->getGaussian();
262
263			dAtom->setJx( jx );
264			dAtom->setJy( jy );
265			dAtom->setJz( jz );
266			}
267			}
268			}
269			}
270	chuckv	401
271	chuckv	403	void Thermo::getCOMVel(double vdrift[3]){
272	chuckv	401
273			double mtot, mtot_local;
274			double vdrift_local[3];
275			int vd, n_atoms;
276			Atom** atoms;
277
278			// We are very careless here with the distinction between n_atoms and n_local
279			// We should really fix this before someone pokes an eye out.
280
281			n_atoms = entry_plug->n_atoms;
282			atoms = entry_plug->atoms;
283
284			mtot_local = 0.0;
285			vdrift_local[0] = 0.0;
286			vdrift_local[1] = 0.0;
287			vdrift_local[2] = 0.0;
288
289			for(vd = 0; vd < n_atoms; vd++){
290
291			vdrift_local[0] += atoms[vd]->get_vx() * atoms[vd]->getMass();
292			vdrift_local[1] += atoms[vd]->get_vy() * atoms[vd]->getMass();
293			vdrift_local[2] += atoms[vd]->get_vz() * atoms[vd]->getMass();
294
295			mtot_local += atoms[vd]->getMass();
296			}
297
298			#ifdef IS_MPI
299	mmeineke	447	MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
300			MPI_Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
301	chuckv	401	#else
302			mtot = mtot_local;
303			for(vd = 0; vd < 3; vd++) {
304			vdrift[vd] = vdrift_local[vd];
305			}
306			#endif
307
308			for (vd = 0; vd < 3; vd++) {
309			vdrift[vd] = vdrift[vd] / mtot;
310			}
311
312			}
313