OOPSE/libmdtools/Thermo.cpp

#include <cmath>
#include <iostream>
using namespace std;

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

#include "Thermo.hpp"
#include "SRI.hpp"
#include "Integrator.hpp"
#define __C
//#include "mpiSimulation.hpp"

#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::COMM_WORLD.Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,MPI_SUM);
  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;
  SRI** sris;

  sris = entry_plug->sr_interactions;
  nSRI = entry_plug->n_SRI;

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

  for( el=0; el<nSRI; el++ ){    
    potential_local += sris[el]->get_potential();
  }

  // Get total potential for entire system from MPI.
#ifdef IS_MPI
  MPI::COMM_WORLD.Allreduce(&potential_local,&potential,1,MPI_DOUBLE,MPI_SUM);
#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 = 1.9872179E-3; // boltzman's constant in kcal/(mol K)
  double temperature;
  int ndf_local, ndf;
  
  ndf_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented
    - entry_plug->n_constraints;

#ifdef IS_MPI
  MPI::COMM_WORLD.Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM);
#else
  ndf = ndf_local;
#endif

  ndf = ndf - 3;
  
  temperature = ( 2.0 * this->getKinetic() ) / ( ndf * kb );
  return temperature;
}

double Thermo::getPressure(){

//  const double conv_Pa_atm = 9.901E-6; // convert Pa -> atm
// const double conv_internal_Pa = 1.661E-7; //convert amu/(fs^2 A) -> Pa
//  const double conv_A_m = 1.0E-10; //convert A -> m

  return 0.0;
}

void Thermo::velocitize() {
  
  double x,y;
  double vx, vy, vz;
  double jx, jy, jz;
  int i, vr, vd; // velocity randomizer loop counters
  double *vdrift;
  double vbar;
  const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
  double av2;
  double kebar;
  int ndf; // number of degrees of freedom
  int ndfRaw; // the raw number of degrees of freedom
  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;
  

  ndfRaw = 3 * n_atoms + 3 * n_oriented;
  ndf = ndfRaw - n_constraints - 3;
  kebar = kb * temperature * (double)ndf / ( 2.0 * (double)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.

  vdrift = getCOMVel();
  
  //  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 );
      }
    }   
  }
}

double* Thermo::getCOMVel(){

  double mtot, mtot_local;
  double* vdrift;
  double vdrift_local[3];
  int vd, n_atoms;
  Atom** atoms;

  vdrift = new double[3];
  // 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::COMM_WORLD.Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM);
  MPI::COMM_WORLD.Allreduce(&vdrift_local,&vdrift,3,MPI_DOUBLE,MPI_SUM);
#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;
  }
  
  return vdrift;
}

Revision:	401
Committed:	Tue Mar 25 22:54:16 2003 UTC (21 years, 3 months ago) by chuckv
File size:	6582 byte(s)
Log Message:	Fixed bugs with calculation of potential energy and temperature.
#	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			#include <mpi++.h>
8			#endif //is_mpi
9
10			#include "Thermo.hpp"
11			#include "SRI.hpp"
12			#include "Integrator.hpp"
13	chuckv	401	#define __C
14			//#include "mpiSimulation.hpp"
15	mmeineke	377
16			#define BASE_SEED 123456789
17
18			Thermo::Thermo( SimInfo* the_entry_plug ) {
19			entry_plug = the_entry_plug;
20			int baseSeed = BASE_SEED;
21
22			gaussStream = new gaussianSPRNG( baseSeed );
23			}
24
25			Thermo::~Thermo(){
26			delete gaussStream;
27			}
28
29			double Thermo::getKinetic(){
30
31			const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2
32			double vx2, vy2, vz2;
33			double kinetic, v_sqr;
34			int kl;
35			double jx2, jy2, jz2; // the square of the angular momentums
36
37			DirectionalAtom *dAtom;
38
39			int n_atoms;
40			double kinetic_global;
41			Atom** atoms;
42
43
44			n_atoms = entry_plug->n_atoms;
45			atoms = entry_plug->atoms;
46
47			kinetic = 0.0;
48			kinetic_global = 0.0;
49			for( kl=0; kl < n_atoms; kl++ ){
50
51			vx2 = atoms[kl]->get_vx() * atoms[kl]->get_vx();
52			vy2 = atoms[kl]->get_vy() * atoms[kl]->get_vy();
53			vz2 = atoms[kl]->get_vz() * atoms[kl]->get_vz();
54
55			v_sqr = vx2 + vy2 + vz2;
56			kinetic += atoms[kl]->getMass() * v_sqr;
57
58			if( atoms[kl]->isDirectional() ){
59
60			dAtom = (DirectionalAtom *)atoms[kl];
61
62			jx2 = dAtom->getJx() * dAtom->getJx();
63			jy2 = dAtom->getJy() * dAtom->getJy();
64			jz2 = dAtom->getJz() * dAtom->getJz();
65
66			kinetic += (jx2 / dAtom->getIxx()) + (jy2 / dAtom->getIyy())
67			+ (jz2 / dAtom->getIzz());
68			}
69			}
70			#ifdef IS_MPI
71			MPI::COMM_WORLD.Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,MPI_SUM);
72			kinetic = kinetic_global;
73			#endif //is_mpi
74
75			kinetic = kinetic * 0.5 / e_convert;
76
77			return kinetic;
78			}
79
80			double Thermo::getPotential(){
81
82	chuckv	401	double potential_local;
83	mmeineke	377	double potential;
84			int el, nSRI;
85			SRI** sris;
86
87			sris = entry_plug->sr_interactions;
88			nSRI = entry_plug->n_SRI;
89
90	chuckv	401	potential_local = 0.0;
91			potential_local += entry_plug->lrPot;
92	mmeineke	377
93	chuckv	401	for( el=0; el<nSRI; el++ ){
94			potential_local += sris[el]->get_potential();
95	mmeineke	377	}
96
97			// Get total potential for entire system from MPI.
98			#ifdef IS_MPI
99	chuckv	401	MPI::COMM_WORLD.Allreduce(&potential_local,&potential,1,MPI_DOUBLE,MPI_SUM);
100			#else
101			potential = potential_local;
102	mmeineke	377	#endif // is_mpi
103
104			return potential;
105			}
106
107			double Thermo::getTotalE(){
108
109			double total;
110
111			total = this->getKinetic() + this->getPotential();
112			return total;
113			}
114
115			double Thermo::getTemperature(){
116
117			const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K)
118			double temperature;
119	chuckv	401	int ndf_local, ndf;
120	mmeineke	377
121	chuckv	401	ndf_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented
122			- entry_plug->n_constraints;
123	mmeineke	377
124	chuckv	401	#ifdef IS_MPI
125			MPI::COMM_WORLD.Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM);
126			#else
127			ndf = ndf_local;
128			#endif
129
130			ndf = ndf - 3;
131
132	mmeineke	377	temperature = ( 2.0 * this->getKinetic() ) / ( ndf * kb );
133			return temperature;
134			}
135
136			double Thermo::getPressure(){
137
138			// const double conv_Pa_atm = 9.901E-6; // convert Pa -> atm
139			// const double conv_internal_Pa = 1.661E-7; //convert amu/(fs^2 A) -> Pa
140			// const double conv_A_m = 1.0E-10; //convert A -> m
141
142			return 0.0;
143			}
144
145			void Thermo::velocitize() {
146
147			double x,y;
148			double vx, vy, vz;
149			double jx, jy, jz;
150			int i, vr, vd; // velocity randomizer loop counters
151	chuckv	401	double *vdrift;
152	mmeineke	377	double vbar;
153			const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
154			double av2;
155			double kebar;
156			int ndf; // number of degrees of freedom
157			int ndfRaw; // the raw number of degrees of freedom
158			int n_atoms;
159			Atom** atoms;
160			DirectionalAtom* dAtom;
161			double temperature;
162			int n_oriented;
163			int n_constraints;
164
165			atoms = entry_plug->atoms;
166			n_atoms = entry_plug->n_atoms;
167			temperature = entry_plug->target_temp;
168			n_oriented = entry_plug->n_oriented;
169			n_constraints = entry_plug->n_constraints;
170
171
172			ndfRaw = 3 * n_atoms + 3 * n_oriented;
173			ndf = ndfRaw - n_constraints - 3;
174			kebar = kb * temperature * (double)ndf / ( 2.0 * (double)ndfRaw );
175
176			for(vr = 0; vr < n_atoms; vr++){
177
178			// uses equipartition theory to solve for vbar in angstrom/fs
179
180			av2 = 2.0 * kebar / atoms[vr]->getMass();
181			vbar = sqrt( av2 );
182
183			// vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() );
184
185			// picks random velocities from a gaussian distribution
186			// centered on vbar
187
188			vx = vbar * gaussStream->getGaussian();
189			vy = vbar * gaussStream->getGaussian();
190			vz = vbar * gaussStream->getGaussian();
191
192			atoms[vr]->set_vx( vx );
193			atoms[vr]->set_vy( vy );
194			atoms[vr]->set_vz( vz );
195			}
196	chuckv	401
197			// Get the Center of Mass drift velocity.
198
199			vdrift = getCOMVel();
200	mmeineke	377
201			// Corrects for the center of mass drift.
202			// sums all the momentum and divides by total mass.
203
204			for(vd = 0; vd < n_atoms; vd++){
205
206			vx = atoms[vd]->get_vx();
207			vy = atoms[vd]->get_vy();
208			vz = atoms[vd]->get_vz();
209	chuckv	401
210	mmeineke	377	vx -= vdrift[0];
211			vy -= vdrift[1];
212			vz -= vdrift[2];
213
214			atoms[vd]->set_vx(vx);
215			atoms[vd]->set_vy(vy);
216			atoms[vd]->set_vz(vz);
217			}
218			if( n_oriented ){
219
220			for( i=0; i<n_atoms; i++ ){
221
222			if( atoms[i]->isDirectional() ){
223
224			dAtom = (DirectionalAtom *)atoms[i];
225
226			vbar = sqrt( 2.0 * kebar * dAtom->getIxx() );
227			jx = vbar * gaussStream->getGaussian();
228
229			vbar = sqrt( 2.0 * kebar * dAtom->getIyy() );
230			jy = vbar * gaussStream->getGaussian();
231
232			vbar = sqrt( 2.0 * kebar * dAtom->getIzz() );
233			jz = vbar * gaussStream->getGaussian();
234
235			dAtom->setJx( jx );
236			dAtom->setJy( jy );
237			dAtom->setJz( jz );
238			}
239			}
240			}
241			}
242	chuckv	401
243			double* Thermo::getCOMVel(){
244
245			double mtot, mtot_local;
246			double* vdrift;
247			double vdrift_local[3];
248			int vd, n_atoms;
249			Atom** atoms;
250
251			vdrift = new double[3];
252			// We are very careless here with the distinction between n_atoms and n_local
253			// We should really fix this before someone pokes an eye out.
254
255			n_atoms = entry_plug->n_atoms;
256			atoms = entry_plug->atoms;
257
258			mtot_local = 0.0;
259			vdrift_local[0] = 0.0;
260			vdrift_local[1] = 0.0;
261			vdrift_local[2] = 0.0;
262
263			for(vd = 0; vd < n_atoms; vd++){
264
265			vdrift_local[0] += atoms[vd]->get_vx() * atoms[vd]->getMass();
266			vdrift_local[1] += atoms[vd]->get_vy() * atoms[vd]->getMass();
267			vdrift_local[2] += atoms[vd]->get_vz() * atoms[vd]->getMass();
268
269			mtot_local += atoms[vd]->getMass();
270			}
271
272			#ifdef IS_MPI
273			MPI::COMM_WORLD.Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM);
274			MPI::COMM_WORLD.Allreduce(&vdrift_local,&vdrift,3,MPI_DOUBLE,MPI_SUM);
275			#else
276			mtot = mtot_local;
277			for(vd = 0; vd < 3; vd++) {
278			vdrift[vd] = vdrift_local[vd];
279			}
280			#endif
281
282			for (vd = 0; vd < 3; vd++) {
283			vdrift[vd] = vdrift[vd] / mtot;
284			}
285
286			return vdrift;
287			}
288