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::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 entry_plug->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 = entry_plug->n_mol;
  molecules = entry_plug->molecules;
  //tau = entry_plug->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 = entry_plug->boxVol;

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

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:	588
Committed:	Thu Jul 10 17:10:56 2003 UTC (21 years ago) by gezelter
File size:	8409 byte(s)
Log Message:	Bunch of 1-d array -> 2-d array stuff
#	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	gezelter	484	double Thermo::getEnthalpy() {
138
139			const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2
140			double u, p, v;
141	gezelter	588	double press[3][3];
142	gezelter	484
143			u = this->getTotalE();
144
145			this->getPressureTensor(press);
146	gezelter	588	p = (press[0][0] + press[1][1] + press[2][2]) / 3.0;
147	gezelter	484
148			v = this->getVolume();
149
150			return (u + (p*v)/e_convert);
151			}
152
153			double Thermo::getVolume() {
154	gezelter	574
155	mmeineke	582	return entry_plug->boxVol;
156	gezelter	484	}
157
158	gezelter	483	double Thermo::getPressure() {
159	gezelter	574
160	gezelter	483	// Relies on the calculation of the full molecular pressure tensor
161
162			const double p_convert = 1.63882576e8;
163	gezelter	588	double press[3][3];
164	gezelter	483	double pressure;
165
166			this->getPressureTensor(press);
167
168	gezelter	588	pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
169	gezelter	483
170			return pressure;
171			}
172
173
174	gezelter	588	void Thermo::getPressureTensor(double press[3][3]){
175	gezelter	483	// returns pressure tensor in units amufs^-2Ang^-1
176	gezelter	445	// routine derived via viral theorem description in:
177			// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
178	mmeineke	377
179	gezelter	477	const double e_convert = 4.184e-4;
180	gezelter	483
181			double molmass, volume;
182	gezelter	468	double vcom[3];
183	gezelter	483	double p_local[9], p_global[9];
184	gezelter	588	int i, j, k, nMols;
185	gezelter	468	Molecule* molecules;
186
187			nMols = entry_plug->n_mol;
188			molecules = entry_plug->molecules;
189	mmeineke	486	//tau = entry_plug->tau;
190	gezelter	468
191			// use velocities of molecular centers of mass and molecular masses:
192	gezelter	483	for (i=0; i < 9; i++) {
193			p_local[i] = 0.0;
194			p_global[i] = 0.0;
195			}
196	gezelter	475
197	gezelter	468	for (i=0; i < nMols; i++) {
198	gezelter	475	molmass = molecules[i].getCOMvel(vcom);
199	gezelter	483
200			p_local[0] += molmass * (vcom[0] * vcom[0]);
201			p_local[1] += molmass * (vcom[0] * vcom[1]);
202			p_local[2] += molmass * (vcom[0] * vcom[2]);
203			p_local[3] += molmass * (vcom[1] * vcom[0]);
204			p_local[4] += molmass * (vcom[1] * vcom[1]);
205			p_local[5] += molmass * (vcom[1] * vcom[2]);
206			p_local[6] += molmass * (vcom[2] * vcom[0]);
207			p_local[7] += molmass * (vcom[2] * vcom[1]);
208			p_local[8] += molmass * (vcom[2] * vcom[2]);
209	gezelter	468	}
210
211			// Get total for entire system from MPI.
212	chuckv	479
213	gezelter	468	#ifdef IS_MPI
214	gezelter	483	MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
215	gezelter	468	#else
216	gezelter	483	for (i=0; i<9; i++) {
217			p_global[i] = p_local[i];
218			}
219	gezelter	468	#endif // is_mpi
220
221	mmeineke	572	volume = entry_plug->boxVol;
222	gezelter	468
223	gezelter	588	for(i = 0; i < 3; i++) {
224			for (j = 0; j < 3; j++) {
225			k = 3*i + j;
226			press[i][j] = (p_global[k] - entry_plug->tau[k]*e_convert) / volume;
227			}
228	gezelter	483	}
229	mmeineke	377	}
230
231			void Thermo::velocitize() {
232
233			double x,y;
234			double vx, vy, vz;
235			double jx, jy, jz;
236			int i, vr, vd; // velocity randomizer loop counters
237	chuckv	403	double vdrift[3];
238	mmeineke	377	double vbar;
239			const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
240			double av2;
241			double kebar;
242			int n_atoms;
243			Atom** atoms;
244			DirectionalAtom* dAtom;
245			double temperature;
246			int n_oriented;
247			int n_constraints;
248
249			atoms = entry_plug->atoms;
250			n_atoms = entry_plug->n_atoms;
251			temperature = entry_plug->target_temp;
252			n_oriented = entry_plug->n_oriented;
253			n_constraints = entry_plug->n_constraints;
254
255	gezelter	458	kebar = kb * temperature * (double)entry_plug->ndf /
256			( 2.0 * (double)entry_plug->ndfRaw );
257	chuckv	403
258	mmeineke	377	for(vr = 0; vr < n_atoms; vr++){
259
260			// uses equipartition theory to solve for vbar in angstrom/fs
261
262			av2 = 2.0 * kebar / atoms[vr]->getMass();
263			vbar = sqrt( av2 );
264	gezelter	444
265	mmeineke	377	// vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() );
266
267			// picks random velocities from a gaussian distribution
268			// centered on vbar
269
270			vx = vbar * gaussStream->getGaussian();
271			vy = vbar * gaussStream->getGaussian();
272			vz = vbar * gaussStream->getGaussian();
273
274			atoms[vr]->set_vx( vx );
275			atoms[vr]->set_vy( vy );
276			atoms[vr]->set_vz( vz );
277			}
278	chuckv	401
279			// Get the Center of Mass drift velocity.
280
281	chuckv	403	getCOMVel(vdrift);
282	mmeineke	377
283			// Corrects for the center of mass drift.
284			// sums all the momentum and divides by total mass.
285
286			for(vd = 0; vd < n_atoms; vd++){
287
288			vx = atoms[vd]->get_vx();
289			vy = atoms[vd]->get_vy();
290			vz = atoms[vd]->get_vz();
291	chuckv	401
292	mmeineke	377	vx -= vdrift[0];
293			vy -= vdrift[1];
294			vz -= vdrift[2];
295
296			atoms[vd]->set_vx(vx);
297			atoms[vd]->set_vy(vy);
298			atoms[vd]->set_vz(vz);
299			}
300			if( n_oriented ){
301
302			for( i=0; i<n_atoms; i++ ){
303
304			if( atoms[i]->isDirectional() ){
305
306			dAtom = (DirectionalAtom *)atoms[i];
307
308			vbar = sqrt( 2.0 * kebar * dAtom->getIxx() );
309			jx = vbar * gaussStream->getGaussian();
310
311			vbar = sqrt( 2.0 * kebar * dAtom->getIyy() );
312			jy = vbar * gaussStream->getGaussian();
313	gezelter	454
314	mmeineke	377	vbar = sqrt( 2.0 * kebar * dAtom->getIzz() );
315			jz = vbar * gaussStream->getGaussian();
316
317			dAtom->setJx( jx );
318			dAtom->setJy( jy );
319			dAtom->setJz( jz );
320			}
321			}
322			}
323			}
324	chuckv	401
325	chuckv	403	void Thermo::getCOMVel(double vdrift[3]){
326	chuckv	401
327			double mtot, mtot_local;
328			double vdrift_local[3];
329			int vd, n_atoms;
330			Atom** atoms;
331
332			// We are very careless here with the distinction between n_atoms and n_local
333			// We should really fix this before someone pokes an eye out.
334
335			n_atoms = entry_plug->n_atoms;
336			atoms = entry_plug->atoms;
337
338			mtot_local = 0.0;
339			vdrift_local[0] = 0.0;
340			vdrift_local[1] = 0.0;
341			vdrift_local[2] = 0.0;
342
343			for(vd = 0; vd < n_atoms; vd++){
344
345			vdrift_local[0] += atoms[vd]->get_vx() * atoms[vd]->getMass();
346			vdrift_local[1] += atoms[vd]->get_vy() * atoms[vd]->getMass();
347			vdrift_local[2] += atoms[vd]->get_vz() * atoms[vd]->getMass();
348
349			mtot_local += atoms[vd]->getMass();
350			}
351
352			#ifdef IS_MPI
353	mmeineke	447	MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
354			MPI_Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
355	chuckv	401	#else
356			mtot = mtot_local;
357			for(vd = 0; vd < 3; vd++) {
358			vdrift[vd] = vdrift_local[vd];
359			}
360			#endif
361
362			for (vd = 0; vd < 3; vd++) {
363			vdrift[vd] = vdrift[vd] / mtot;
364			}
365
366			}
367