mdtools/md_code/Thermo.cpp

#include <cmath>
#include <iostream>


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

#include "Thermo.hpp"
#include "SRI.hpp"
#include "LRI.hpp"
#include "Integrator.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;
  double potential_global;
  int el, nSRI;
  SRI** sris;

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

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

  // std::cerr << "long range potential: " << potential << "\n";
  for( el=0; el<nSRI; el++ ){
    
    potential += sris[el]->get_potential();
  }

  // Get total potential for entire system from MPI.
#ifdef IS_MPI
  MPI_COMM_WORLD.Allreduce(&potential,&potential_global,1,MPI_DOUBLE,MPI_SUM);
  potential = potential_global;
#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 = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented
    - entry_plug->n_constraints - 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[3];
  double mtot = 0.0;
  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 );
  
  printf("Entered Velocitize\n");
  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
#ifndef USE_SPRNG
    /* If we are using mpi, we need to use the SPRNG random
       generator. The non drand48 generator will just repeat
       the same numbers for every node creating a non-gaussian
       distribution for the simulation. drand48 is fine for the
       single processor version of the code, but SPRNG should
       still be preferred for consistency.
    */

#ifdef IS_MPI
#error "SPRNG random number generator must be used for MPI"
#else
#warning "Using drand48 for random number generation"
#endif  // is_mpi 

    x = drand48();
    y = drand48();
    vx = vbar * sqrt( -2.0 * log(x)) * cos(2 * M_PI * y);
    
    x = drand48();
    y = drand48();
    vy = vbar * sqrt( -2.0 * log(x)) * cos(2 * M_PI * y);
    
    x = drand48();
    y = drand48();
    vz = vbar * sqrt( -2.0 * log(x)) * cos(2 * M_PI * y);
    printf("Setting new velocities vx: %f\n",vx);
#endif // use_spring

#ifdef USE_SPRNG
    vx = vbar * gaussStream->getGaussian();
    vy = vbar * gaussStream->getGaussian();
    vz = vbar * gaussStream->getGaussian();
#endif // use_spring

    atoms[vr]->set_vx( vx ); 
    atoms[vr]->set_vy( vy );
    atoms[vr]->set_vz( vz );
  }
  
  //  Corrects for the center of mass drift.
  // sums all the momentum and divides by total mass.
  
  mtot = 0.0;
  vdrift[0] = 0.0;
  vdrift[1] = 0.0;
  vdrift[2] = 0.0;
  for(vd = 0; vd < n_atoms; vd++){
    
    vdrift[0] += atoms[vd]->get_vx() * atoms[vd]->getMass();
    vdrift[1] += atoms[vd]->get_vy() * atoms[vd]->getMass();
    vdrift[2] += atoms[vd]->get_vz() * atoms[vd]->getMass();
    
    mtot = mtot + atoms[vd]->getMass();
  }
  
  for (vd = 0; vd < 3; vd++) {
    vdrift[vd] = vdrift[vd] / mtot;
  }
  
  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];

#ifndef USE_SPRNG

#ifdef IS_MPI
#error "SPRNG random number generator must be used for MPI"
#else  // is_mpi
#warning "Using drand48 for random number generation"
#endif   // is_MPI
        
        vbar = sqrt( 2.0 * kebar * dAtom->getIxx() );
        x = drand48();
        y = drand48();
        jx = vbar * sqrt( -2.0 * log(x)) * cos(2 * M_PI * y);
        
        vbar = sqrt( 2.0 * kebar * dAtom->getIyy() );
        x = drand48();
        y = drand48();
        jy = vbar * sqrt( -2.0 * log(x)) * cos(2 * M_PI * y);
        
        vbar = sqrt( 2.0 * kebar * dAtom->getIzz() );
        x = drand48();
        y = drand48();
        jz = vbar * sqrt( -2.0 * log(x)) * cos(2 * M_PI * y);

#else //use_sprng

        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();
#endif //use_sprng
        
        dAtom->setJx( jx );
        dAtom->setJy( jy );
        dAtom->setJz( jz );
      }
    }   
  }
}
Revision:	252
Committed:	Tue Jan 28 22:16:55 2003 UTC (22 years, 9 months ago) by chuckv
File size:	7292 byte(s)
Log Message:	Force loops seems to work, velocitize never being called....
#	User	Rev	Content
1	mmeineke	10	#include <cmath>
2	chuckv	252	#include <iostream>
3	chuckv	249
4	chuckv	252
5	chuckv	249	#ifdef IS_MPI
6	chuckv	218	#include <mpi++.h>
7	chuckv	249	#endif //is_mpi
8	mmeineke	10
9			#include "Thermo.hpp"
10			#include "SRI.hpp"
11			#include "LRI.hpp"
12			#include "Integrator.hpp"
13
14	chuckv	223	#define BASE_SEED 123456789
15	mmeineke	10
16	chuckv	223	Thermo::Thermo( SimInfo* the_entry_plug ) {
17			entry_plug = the_entry_plug;
18	chuckv	249	int baseSeed = BASE_SEED;
19	chuckv	223	gaussStream = new gaussianSPRNG( baseSeed );
20			}
21
22			Thermo::~Thermo(){
23			delete gaussStream;
24			}
25
26	mmeineke	10	double Thermo::getKinetic(){
27
28			const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2
29			double vx2, vy2, vz2;
30			double kinetic, v_sqr;
31			int kl;
32			double jx2, jy2, jz2; // the square of the angular momentums
33
34			DirectionalAtom *dAtom;
35
36			int n_atoms;
37	chuckv	218	double kinetic_global;
38	mmeineke	10	Atom** atoms;
39	chuckv	218
40	mmeineke	10
41			n_atoms = entry_plug->n_atoms;
42			atoms = entry_plug->atoms;
43
44			kinetic = 0.0;
45	chuckv	218	kinetic_global = 0.0;
46	mmeineke	10	for( kl=0; kl < n_atoms; kl++ ){
47
48			vx2 = atoms[kl]->get_vx() * atoms[kl]->get_vx();
49			vy2 = atoms[kl]->get_vy() * atoms[kl]->get_vy();
50			vz2 = atoms[kl]->get_vz() * atoms[kl]->get_vz();
51
52			v_sqr = vx2 + vy2 + vz2;
53			kinetic += atoms[kl]->getMass() * v_sqr;
54
55			if( atoms[kl]->isDirectional() ){
56
57			dAtom = (DirectionalAtom *)atoms[kl];
58
59			jx2 = dAtom->getJx() * dAtom->getJx();
60			jy2 = dAtom->getJy() * dAtom->getJy();
61			jz2 = dAtom->getJz() * dAtom->getJz();
62
63			kinetic += (jx2 / dAtom->getIxx()) + (jy2 / dAtom->getIyy())
64			+ (jz2 / dAtom->getIzz());
65			}
66			}
67	chuckv	218	#ifdef IS_MPI
68			MPI_COMM_WORLD.Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,MPI_SUM);
69			kinetic = kinetic_global;
70	chuckv	249	#endif //is_mpi
71	chuckv	218
72	mmeineke	10	kinetic = kinetic * 0.5 / e_convert;
73
74			return kinetic;
75			}
76
77			double Thermo::getPotential(){
78
79			double potential;
80	chuckv	218	double potential_global;
81	mmeineke	10	int el, nSRI;
82			SRI** sris;
83
84			sris = entry_plug->sr_interactions;
85			nSRI = entry_plug->n_SRI;
86
87			potential = 0.0;
88	chuckv	218	potential_global = 0.0;
89	chuckv	249	potential += entry_plug->lrPot;
90	mmeineke	10
91			// std::cerr << "long range potential: " << potential << "\n";
92			for( el=0; el<nSRI; el++ ){
93
94			potential += sris[el]->get_potential();
95			}
96
97	chuckv	218	// Get total potential for entire system from MPI.
98			#ifdef IS_MPI
99			MPI_COMM_WORLD.Allreduce(&potential,&potential_global,1,MPI_DOUBLE,MPI_SUM);
100			potential = potential_global;
101	chuckv	249	#endif // is_mpi
102	chuckv	218
103	mmeineke	10	return potential;
104			}
105
106			double Thermo::getTotalE(){
107
108			double total;
109
110			total = this->getKinetic() + this->getPotential();
111			return total;
112			}
113
114			double Thermo::getTemperature(){
115
116	mmeineke	25	const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K)
117	mmeineke	10	double temperature;
118
119			int ndf = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented
120			- entry_plug->n_constraints - 3;
121
122			temperature = ( 2.0 * this->getKinetic() ) / ( ndf * kb );
123			return temperature;
124			}
125
126			double Thermo::getPressure(){
127
128	mmeineke	117	// const double conv_Pa_atm = 9.901E-6; // convert Pa -> atm
129			// const double conv_internal_Pa = 1.661E-7; //convert amu/(fs^2 A) -> Pa
130			// const double conv_A_m = 1.0E-10; //convert A -> m
131	mmeineke	10
132			return 0.0;
133			}
134
135			void Thermo::velocitize() {
136
137			double x,y;
138			double vx, vy, vz;
139			double jx, jy, jz;
140			int i, vr, vd; // velocity randomizer loop counters
141			double vdrift[3];
142			double mtot = 0.0;
143			double vbar;
144			const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
145			double av2;
146			double kebar;
147			int ndf; // number of degrees of freedom
148			int ndfRaw; // the raw number of degrees of freedom
149			int n_atoms;
150			Atom** atoms;
151			DirectionalAtom* dAtom;
152			double temperature;
153			int n_oriented;
154			int n_constraints;
155
156			atoms = entry_plug->atoms;
157			n_atoms = entry_plug->n_atoms;
158			temperature = entry_plug->target_temp;
159			n_oriented = entry_plug->n_oriented;
160			n_constraints = entry_plug->n_constraints;
161
162
163			ndfRaw = 3 * n_atoms + 3 * n_oriented;
164			ndf = ndfRaw - n_constraints - 3;
165			kebar = kb * temperature * (double)ndf / ( 2.0 * (double)ndfRaw );
166
167	chuckv	252	printf("Entered Velocitize\n");
168	mmeineke	10	for(vr = 0; vr < n_atoms; vr++){
169
170			// uses equipartition theory to solve for vbar in angstrom/fs
171
172			av2 = 2.0 * kebar / atoms[vr]->getMass();
173			vbar = sqrt( av2 );
174
175			// vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() );
176
177			// picks random velocities from a gaussian distribution
178			// centered on vbar
179	chuckv	221	#ifndef USE_SPRNG
180			/* If we are using mpi, we need to use the SPRNG random
181			generator. The non drand48 generator will just repeat
182			the same numbers for every node creating a non-gaussian
183			distribution for the simulation. drand48 is fine for the
184			single processor version of the code, but SPRNG should
185			still be preferred for consistency.
186			*/
187	chuckv	249
188	chuckv	221	#ifdef IS_MPI
189			#error "SPRNG random number generator must be used for MPI"
190			#else
191			#warning "Using drand48 for random number generation"
192	chuckv	249	#endif // is_mpi
193
194	mmeineke	10	x = drand48();
195			y = drand48();
196			vx = vbar * sqrt( -2.0 * log(x)) * cos(2 * M_PI * y);
197
198			x = drand48();
199			y = drand48();
200			vy = vbar * sqrt( -2.0 * log(x)) * cos(2 * M_PI * y);
201
202			x = drand48();
203			y = drand48();
204			vz = vbar * sqrt( -2.0 * log(x)) * cos(2 * M_PI * y);
205	chuckv	252	printf("Setting new velocities vx: %f\n",vx);
206	chuckv	249	#endif // use_spring
207	chuckv	221
208			#ifdef USE_SPRNG
209	chuckv	223	vx = vbar * gaussStream->getGaussian();
210			vy = vbar * gaussStream->getGaussian();
211			vz = vbar * gaussStream->getGaussian();
212	chuckv	249	#endif // use_spring
213	chuckv	221
214	mmeineke	10	atoms[vr]->set_vx( vx );
215			atoms[vr]->set_vy( vy );
216			atoms[vr]->set_vz( vz );
217			}
218
219			// Corrects for the center of mass drift.
220			// sums all the momentum and divides by total mass.
221
222			mtot = 0.0;
223			vdrift[0] = 0.0;
224			vdrift[1] = 0.0;
225			vdrift[2] = 0.0;
226			for(vd = 0; vd < n_atoms; vd++){
227
228			vdrift[0] += atoms[vd]->get_vx() * atoms[vd]->getMass();
229			vdrift[1] += atoms[vd]->get_vy() * atoms[vd]->getMass();
230			vdrift[2] += atoms[vd]->get_vz() * atoms[vd]->getMass();
231
232			mtot = mtot + atoms[vd]->getMass();
233			}
234
235			for (vd = 0; vd < 3; vd++) {
236			vdrift[vd] = vdrift[vd] / mtot;
237			}
238
239			for(vd = 0; vd < n_atoms; vd++){
240
241			vx = atoms[vd]->get_vx();
242			vy = atoms[vd]->get_vy();
243			vz = atoms[vd]->get_vz();
244
245
246			vx -= vdrift[0];
247			vy -= vdrift[1];
248			vz -= vdrift[2];
249
250			atoms[vd]->set_vx(vx);
251			atoms[vd]->set_vy(vy);
252			atoms[vd]->set_vz(vz);
253			}
254			if( n_oriented ){
255
256			for( i=0; i<n_atoms; i++ ){
257
258			if( atoms[i]->isDirectional() ){
259
260			dAtom = (DirectionalAtom *)atoms[i];
261	chuckv	249
262			#ifndef USE_SPRNG
263
264	chuckv	221	#ifdef IS_MPI
265			#error "SPRNG random number generator must be used for MPI"
266	chuckv	249	#else // is_mpi
267	chuckv	221	#warning "Using drand48 for random number generation"
268	chuckv	249	#endif // is_MPI
269	mmeineke	10
270			vbar = sqrt( 2.0 * kebar * dAtom->getIxx() );
271			x = drand48();
272			y = drand48();
273			jx = vbar * sqrt( -2.0 * log(x)) * cos(2 * M_PI * y);
274
275			vbar = sqrt( 2.0 * kebar * dAtom->getIyy() );
276			x = drand48();
277			y = drand48();
278			jy = vbar * sqrt( -2.0 * log(x)) * cos(2 * M_PI * y);
279
280			vbar = sqrt( 2.0 * kebar * dAtom->getIzz() );
281			x = drand48();
282			y = drand48();
283			jz = vbar * sqrt( -2.0 * log(x)) * cos(2 * M_PI * y);
284	chuckv	249
285			#else //use_sprng
286
287	chuckv	221	vbar = sqrt( 2.0 * kebar * dAtom->getIxx() );
288	chuckv	223	jx = vbar * gaussStream->getGaussian();
289	chuckv	221
290			vbar = sqrt( 2.0 * kebar * dAtom->getIyy() );
291	chuckv	223	jy = vbar * gaussStream->getGaussian();
292	chuckv	221
293			vbar = sqrt( 2.0 * kebar * dAtom->getIzz() );
294	chuckv	223	jz = vbar * gaussStream->getGaussian();
295	chuckv	249	#endif //use_sprng
296	mmeineke	10
297			dAtom->setJx( jx );
298			dAtom->setJy( jy );
299			dAtom->setJz( jz );
300			}
301			}
302			}
303			}