mdtools/md_code/Thermo.cpp

#include <cmath>
#include <mpi++.h>

#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;
  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

  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->longRange->get_potential();;

  // 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

  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 );
  
  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   
    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);
#endif

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

    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];
#ifdef IS_MPI
#error "SPRNG random number generator must be used for MPI"
#else
#warning "Using drand48 for random number generation"
#endif   
        
        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);
#endif
#ifdef 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
        
        dAtom->setJx( jx );
        dAtom->setJy( jy );
        dAtom->setJz( jz );
      }
    }   
  }
}
Revision:	223
Committed:	Fri Jan 3 22:04:50 2003 UTC (21 years, 7 months ago) by chuckv
File size:	7068 byte(s)
Log Message:	Finished thermo and randomSPRNG classes.
#	User	Rev	Content
1	mmeineke	10	#include <cmath>
2	chuckv	218	#include <mpi++.h>
3	mmeineke	10
4			#include "Thermo.hpp"
5			#include "SRI.hpp"
6			#include "LRI.hpp"
7			#include "Integrator.hpp"
8
9	chuckv	223	#define BASE_SEED 123456789
10	mmeineke	10
11	chuckv	223	Thermo::Thermo( SimInfo* the_entry_plug ) {
12			entry_plug = the_entry_plug;
13			baseSeed = BASE_SEED;
14			gaussStream = new gaussianSPRNG( baseSeed );
15			}
16
17			Thermo::~Thermo(){
18			delete gaussStream;
19			}
20
21	mmeineke	10	double Thermo::getKinetic(){
22
23			const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2
24			double vx2, vy2, vz2;
25			double kinetic, v_sqr;
26			int kl;
27			double jx2, jy2, jz2; // the square of the angular momentums
28
29			DirectionalAtom *dAtom;
30
31			int n_atoms;
32	chuckv	218	double kinetic_global;
33	mmeineke	10	Atom** atoms;
34	chuckv	218
35	mmeineke	10
36			n_atoms = entry_plug->n_atoms;
37			atoms = entry_plug->atoms;
38
39			kinetic = 0.0;
40	chuckv	218	kinetic_global = 0.0;
41	mmeineke	10	for( kl=0; kl < n_atoms; kl++ ){
42
43			vx2 = atoms[kl]->get_vx() * atoms[kl]->get_vx();
44			vy2 = atoms[kl]->get_vy() * atoms[kl]->get_vy();
45			vz2 = atoms[kl]->get_vz() * atoms[kl]->get_vz();
46
47			v_sqr = vx2 + vy2 + vz2;
48			kinetic += atoms[kl]->getMass() * v_sqr;
49
50			if( atoms[kl]->isDirectional() ){
51
52			dAtom = (DirectionalAtom *)atoms[kl];
53
54			jx2 = dAtom->getJx() * dAtom->getJx();
55			jy2 = dAtom->getJy() * dAtom->getJy();
56			jz2 = dAtom->getJz() * dAtom->getJz();
57
58			kinetic += (jx2 / dAtom->getIxx()) + (jy2 / dAtom->getIyy())
59			+ (jz2 / dAtom->getIzz());
60			}
61			}
62	chuckv	218	#ifdef IS_MPI
63			MPI_COMM_WORLD.Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,MPI_SUM);
64			kinetic = kinetic_global;
65			#endif
66
67	mmeineke	10	kinetic = kinetic * 0.5 / e_convert;
68
69			return kinetic;
70			}
71
72			double Thermo::getPotential(){
73
74			double potential;
75	chuckv	218	double potential_global;
76	mmeineke	10	int el, nSRI;
77			SRI** sris;
78
79			sris = entry_plug->sr_interactions;
80			nSRI = entry_plug->n_SRI;
81
82			potential = 0.0;
83	chuckv	218	potential_global = 0.0;
84	mmeineke	10	potential += entry_plug->longRange->get_potential();;
85
86			// std::cerr << "long range potential: " << potential << "\n";
87			for( el=0; el<nSRI; el++ ){
88
89			potential += sris[el]->get_potential();
90			}
91
92	chuckv	218	// Get total potential for entire system from MPI.
93			#ifdef IS_MPI
94			MPI_COMM_WORLD.Allreduce(&potential,&potential_global,1,MPI_DOUBLE,MPI_SUM);
95			potential = potential_global;
96			#endif
97
98	mmeineke	10	return potential;
99			}
100
101			double Thermo::getTotalE(){
102
103			double total;
104
105			total = this->getKinetic() + this->getPotential();
106			return total;
107			}
108
109			double Thermo::getTemperature(){
110
111	mmeineke	25	const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K)
112	mmeineke	10	double temperature;
113
114			int ndf = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented
115			- entry_plug->n_constraints - 3;
116
117			temperature = ( 2.0 * this->getKinetic() ) / ( ndf * kb );
118			return temperature;
119			}
120
121			double Thermo::getPressure(){
122
123	mmeineke	117	// const double conv_Pa_atm = 9.901E-6; // convert Pa -> atm
124			// const double conv_internal_Pa = 1.661E-7; //convert amu/(fs^2 A) -> Pa
125			// const double conv_A_m = 1.0E-10; //convert A -> m
126	mmeineke	10
127			return 0.0;
128			}
129
130			void Thermo::velocitize() {
131
132			double x,y;
133			double vx, vy, vz;
134			double jx, jy, jz;
135			int i, vr, vd; // velocity randomizer loop counters
136			double vdrift[3];
137			double mtot = 0.0;
138			double vbar;
139			const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
140			double av2;
141			double kebar;
142			int ndf; // number of degrees of freedom
143			int ndfRaw; // the raw number of degrees of freedom
144			int n_atoms;
145			Atom** atoms;
146			DirectionalAtom* dAtom;
147			double temperature;
148			int n_oriented;
149			int n_constraints;
150
151			atoms = entry_plug->atoms;
152			n_atoms = entry_plug->n_atoms;
153			temperature = entry_plug->target_temp;
154			n_oriented = entry_plug->n_oriented;
155			n_constraints = entry_plug->n_constraints;
156
157
158			ndfRaw = 3 * n_atoms + 3 * n_oriented;
159			ndf = ndfRaw - n_constraints - 3;
160			kebar = kb * temperature * (double)ndf / ( 2.0 * (double)ndfRaw );
161
162			for(vr = 0; vr < n_atoms; vr++){
163
164			// uses equipartition theory to solve for vbar in angstrom/fs
165
166			av2 = 2.0 * kebar / atoms[vr]->getMass();
167			vbar = sqrt( av2 );
168
169			// vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() );
170
171			// picks random velocities from a gaussian distribution
172			// centered on vbar
173	chuckv	221	#ifndef USE_SPRNG
174			/* If we are using mpi, we need to use the SPRNG random
175			generator. The non drand48 generator will just repeat
176			the same numbers for every node creating a non-gaussian
177			distribution for the simulation. drand48 is fine for the
178			single processor version of the code, but SPRNG should
179			still be preferred for consistency.
180			*/
181			#ifdef IS_MPI
182			#error "SPRNG random number generator must be used for MPI"
183			#else
184			#warning "Using drand48 for random number generation"
185			#endif
186	mmeineke	10	x = drand48();
187			y = drand48();
188			vx = vbar * sqrt( -2.0 * log(x)) * cos(2 * M_PI * y);
189
190			x = drand48();
191			y = drand48();
192			vy = vbar * sqrt( -2.0 * log(x)) * cos(2 * M_PI * y);
193
194			x = drand48();
195			y = drand48();
196			vz = vbar * sqrt( -2.0 * log(x)) * cos(2 * M_PI * y);
197	chuckv	221	#endif
198
199			#ifdef USE_SPRNG
200	chuckv	223	vx = vbar * gaussStream->getGaussian();
201			vy = vbar * gaussStream->getGaussian();
202			vz = vbar * gaussStream->getGaussian();
203	chuckv	221	#endif
204
205	mmeineke	10	atoms[vr]->set_vx( vx );
206			atoms[vr]->set_vy( vy );
207			atoms[vr]->set_vz( vz );
208			}
209
210			// Corrects for the center of mass drift.
211			// sums all the momentum and divides by total mass.
212
213			mtot = 0.0;
214			vdrift[0] = 0.0;
215			vdrift[1] = 0.0;
216			vdrift[2] = 0.0;
217			for(vd = 0; vd < n_atoms; vd++){
218
219			vdrift[0] += atoms[vd]->get_vx() * atoms[vd]->getMass();
220			vdrift[1] += atoms[vd]->get_vy() * atoms[vd]->getMass();
221			vdrift[2] += atoms[vd]->get_vz() * atoms[vd]->getMass();
222
223			mtot = mtot + atoms[vd]->getMass();
224			}
225
226			for (vd = 0; vd < 3; vd++) {
227			vdrift[vd] = vdrift[vd] / mtot;
228			}
229
230			for(vd = 0; vd < n_atoms; vd++){
231
232			vx = atoms[vd]->get_vx();
233			vy = atoms[vd]->get_vy();
234			vz = atoms[vd]->get_vz();
235
236
237			vx -= vdrift[0];
238			vy -= vdrift[1];
239			vz -= vdrift[2];
240
241			atoms[vd]->set_vx(vx);
242			atoms[vd]->set_vy(vy);
243			atoms[vd]->set_vz(vz);
244			}
245			if( n_oriented ){
246
247			for( i=0; i<n_atoms; i++ ){
248
249			if( atoms[i]->isDirectional() ){
250
251			dAtom = (DirectionalAtom *)atoms[i];
252	chuckv	221	#ifdef IS_MPI
253			#error "SPRNG random number generator must be used for MPI"
254			#else
255			#warning "Using drand48 for random number generation"
256			#endif
257	mmeineke	10
258			vbar = sqrt( 2.0 * kebar * dAtom->getIxx() );
259			x = drand48();
260			y = drand48();
261			jx = vbar * sqrt( -2.0 * log(x)) * cos(2 * M_PI * y);
262
263			vbar = sqrt( 2.0 * kebar * dAtom->getIyy() );
264			x = drand48();
265			y = drand48();
266			jy = vbar * sqrt( -2.0 * log(x)) * cos(2 * M_PI * y);
267
268			vbar = sqrt( 2.0 * kebar * dAtom->getIzz() );
269			x = drand48();
270			y = drand48();
271			jz = vbar * sqrt( -2.0 * log(x)) * cos(2 * M_PI * y);
272	chuckv	221	#endif
273			#ifdef USE_SPRNG
274			vbar = sqrt( 2.0 * kebar * dAtom->getIxx() );
275	chuckv	223	jx = vbar * gaussStream->getGaussian();
276	chuckv	221
277			vbar = sqrt( 2.0 * kebar * dAtom->getIyy() );
278	chuckv	223	jy = vbar * gaussStream->getGaussian();
279	chuckv	221
280			vbar = sqrt( 2.0 * kebar * dAtom->getIzz() );
281	chuckv	223	jz = vbar * gaussStream->getGaussian();
282	chuckv	221	#endif
283	mmeineke	10
284			dAtom->setJx( jx );
285			dAtom->setJy( jy );
286			dAtom->setJz( jz );
287			}
288			}
289			}
290			}