mdtools/md_code/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 "LRI.hpp"
#include "Integrator.hpp"

#define BASE_SEED 123456789

Thermo::Thermo( SimInfo* the_entry_plug ) { 
  entry_plug = the_entry_plug;
  int baseSeed = BASE_SEED;
  
  cerr << "creating thermo stream\n";
  gaussStream = new gaussianSPRNG( baseSeed );
  cerr << "created thermo stream\n";
}

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 );
  
  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);

#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:	254
Committed:	Thu Jan 30 20:03:37 2003 UTC (21 years, 5 months ago) by chuckv
File size:	7334 byte(s)
Log Message:	Bug fixes for mpi version of code
#	User	Rev	Content
1	mmeineke	10	#include <cmath>
2	chuckv	252	#include <iostream>
3	chuckv	253	using namespace std;
4	chuckv	249
5			#ifdef IS_MPI
6	chuckv	254	#include <mpi.h>
7	chuckv	218	#include <mpi++.h>
8	chuckv	249	#endif //is_mpi
9	mmeineke	10
10			#include "Thermo.hpp"
11			#include "SRI.hpp"
12			#include "LRI.hpp"
13			#include "Integrator.hpp"
14
15	chuckv	223	#define BASE_SEED 123456789
16	mmeineke	10
17	chuckv	223	Thermo::Thermo( SimInfo* the_entry_plug ) {
18			entry_plug = the_entry_plug;
19	chuckv	249	int baseSeed = BASE_SEED;
20	chuckv	253
21			cerr << "creating thermo stream\n";
22	chuckv	223	gaussStream = new gaussianSPRNG( baseSeed );
23	chuckv	253	cerr << "created thermo stream\n";
24	chuckv	223	}
25
26			Thermo::~Thermo(){
27			delete gaussStream;
28			}
29
30	mmeineke	10	double Thermo::getKinetic(){
31
32			const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2
33			double vx2, vy2, vz2;
34			double kinetic, v_sqr;
35			int kl;
36			double jx2, jy2, jz2; // the square of the angular momentums
37
38			DirectionalAtom *dAtom;
39
40			int n_atoms;
41	chuckv	218	double kinetic_global;
42	mmeineke	10	Atom** atoms;
43	chuckv	218
44	mmeineke	10
45			n_atoms = entry_plug->n_atoms;
46			atoms = entry_plug->atoms;
47
48			kinetic = 0.0;
49	chuckv	218	kinetic_global = 0.0;
50	mmeineke	10	for( kl=0; kl < n_atoms; kl++ ){
51
52			vx2 = atoms[kl]->get_vx() * atoms[kl]->get_vx();
53			vy2 = atoms[kl]->get_vy() * atoms[kl]->get_vy();
54			vz2 = atoms[kl]->get_vz() * atoms[kl]->get_vz();
55
56			v_sqr = vx2 + vy2 + vz2;
57			kinetic += atoms[kl]->getMass() * v_sqr;
58
59			if( atoms[kl]->isDirectional() ){
60
61			dAtom = (DirectionalAtom *)atoms[kl];
62
63			jx2 = dAtom->getJx() * dAtom->getJx();
64			jy2 = dAtom->getJy() * dAtom->getJy();
65			jz2 = dAtom->getJz() * dAtom->getJz();
66
67			kinetic += (jx2 / dAtom->getIxx()) + (jy2 / dAtom->getIyy())
68			+ (jz2 / dAtom->getIzz());
69			}
70			}
71	chuckv	218	#ifdef IS_MPI
72	chuckv	254	MPI::COMM_WORLD.Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,MPI_SUM);
73	chuckv	218	kinetic = kinetic_global;
74	chuckv	249	#endif //is_mpi
75	chuckv	218
76	mmeineke	10	kinetic = kinetic * 0.5 / e_convert;
77
78			return kinetic;
79			}
80
81			double Thermo::getPotential(){
82
83			double potential;
84	chuckv	218	double potential_global;
85	mmeineke	10	int el, nSRI;
86			SRI** sris;
87
88			sris = entry_plug->sr_interactions;
89			nSRI = entry_plug->n_SRI;
90
91			potential = 0.0;
92	chuckv	218	potential_global = 0.0;
93	chuckv	249	potential += entry_plug->lrPot;
94	mmeineke	10
95			// std::cerr << "long range potential: " << potential << "\n";
96			for( el=0; el<nSRI; el++ ){
97
98			potential += sris[el]->get_potential();
99			}
100
101	chuckv	218	// Get total potential for entire system from MPI.
102			#ifdef IS_MPI
103	chuckv	254	MPI::COMM_WORLD.Allreduce(&potential,&potential_global,1,MPI_DOUBLE,MPI_SUM);
104	chuckv	218	potential = potential_global;
105	chuckv	249	#endif // is_mpi
106	chuckv	218
107	mmeineke	10	return potential;
108			}
109
110			double Thermo::getTotalE(){
111
112			double total;
113
114			total = this->getKinetic() + this->getPotential();
115			return total;
116			}
117
118			double Thermo::getTemperature(){
119
120	mmeineke	25	const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K)
121	mmeineke	10	double temperature;
122
123			int ndf = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented
124			- entry_plug->n_constraints - 3;
125
126			temperature = ( 2.0 * this->getKinetic() ) / ( ndf * kb );
127			return temperature;
128			}
129
130			double Thermo::getPressure(){
131
132	mmeineke	117	// const double conv_Pa_atm = 9.901E-6; // convert Pa -> atm
133			// const double conv_internal_Pa = 1.661E-7; //convert amu/(fs^2 A) -> Pa
134			// const double conv_A_m = 1.0E-10; //convert A -> m
135	mmeineke	10
136			return 0.0;
137			}
138
139			void Thermo::velocitize() {
140
141			double x,y;
142			double vx, vy, vz;
143			double jx, jy, jz;
144			int i, vr, vd; // velocity randomizer loop counters
145			double vdrift[3];
146			double mtot = 0.0;
147			double vbar;
148			const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
149			double av2;
150			double kebar;
151			int ndf; // number of degrees of freedom
152			int ndfRaw; // the raw number of degrees of freedom
153			int n_atoms;
154			Atom** atoms;
155			DirectionalAtom* dAtom;
156			double temperature;
157			int n_oriented;
158			int n_constraints;
159
160			atoms = entry_plug->atoms;
161			n_atoms = entry_plug->n_atoms;
162			temperature = entry_plug->target_temp;
163			n_oriented = entry_plug->n_oriented;
164			n_constraints = entry_plug->n_constraints;
165
166
167			ndfRaw = 3 * n_atoms + 3 * n_oriented;
168			ndf = ndfRaw - n_constraints - 3;
169			kebar = kb * temperature * (double)ndf / ( 2.0 * (double)ndfRaw );
170
171			for(vr = 0; vr < n_atoms; vr++){
172
173			// uses equipartition theory to solve for vbar in angstrom/fs
174
175			av2 = 2.0 * kebar / atoms[vr]->getMass();
176			vbar = sqrt( av2 );
177
178			// vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() );
179
180			// picks random velocities from a gaussian distribution
181			// centered on vbar
182	chuckv	221	#ifndef USE_SPRNG
183			/* If we are using mpi, we need to use the SPRNG random
184			generator. The non drand48 generator will just repeat
185			the same numbers for every node creating a non-gaussian
186			distribution for the simulation. drand48 is fine for the
187			single processor version of the code, but SPRNG should
188			still be preferred for consistency.
189			*/
190	chuckv	249
191	chuckv	221	#ifdef IS_MPI
192			#error "SPRNG random number generator must be used for MPI"
193			#else
194	chuckv	254	// warning "Using drand48 for random number generation"
195	chuckv	249	#endif // is_mpi
196
197	mmeineke	10	x = drand48();
198			y = drand48();
199			vx = vbar * sqrt( -2.0 * log(x)) * cos(2 * M_PI * y);
200
201			x = drand48();
202			y = drand48();
203			vy = vbar * sqrt( -2.0 * log(x)) * cos(2 * M_PI * y);
204
205			x = drand48();
206			y = drand48();
207			vz = vbar * sqrt( -2.0 * log(x)) * cos(2 * M_PI * y);
208	chuckv	253
209	chuckv	249	#endif // use_spring
210	chuckv	221
211			#ifdef USE_SPRNG
212	chuckv	223	vx = vbar * gaussStream->getGaussian();
213			vy = vbar * gaussStream->getGaussian();
214			vz = vbar * gaussStream->getGaussian();
215	chuckv	249	#endif // use_spring
216	chuckv	221
217	mmeineke	10	atoms[vr]->set_vx( vx );
218			atoms[vr]->set_vy( vy );
219			atoms[vr]->set_vz( vz );
220			}
221
222			// Corrects for the center of mass drift.
223			// sums all the momentum and divides by total mass.
224
225			mtot = 0.0;
226			vdrift[0] = 0.0;
227			vdrift[1] = 0.0;
228			vdrift[2] = 0.0;
229			for(vd = 0; vd < n_atoms; vd++){
230
231			vdrift[0] += atoms[vd]->get_vx() * atoms[vd]->getMass();
232			vdrift[1] += atoms[vd]->get_vy() * atoms[vd]->getMass();
233			vdrift[2] += atoms[vd]->get_vz() * atoms[vd]->getMass();
234
235			mtot = mtot + atoms[vd]->getMass();
236			}
237
238			for (vd = 0; vd < 3; vd++) {
239			vdrift[vd] = vdrift[vd] / mtot;
240			}
241
242			for(vd = 0; vd < n_atoms; vd++){
243
244			vx = atoms[vd]->get_vx();
245			vy = atoms[vd]->get_vy();
246			vz = atoms[vd]->get_vz();
247
248
249			vx -= vdrift[0];
250			vy -= vdrift[1];
251			vz -= vdrift[2];
252
253			atoms[vd]->set_vx(vx);
254			atoms[vd]->set_vy(vy);
255			atoms[vd]->set_vz(vz);
256			}
257			if( n_oriented ){
258
259			for( i=0; i<n_atoms; i++ ){
260
261			if( atoms[i]->isDirectional() ){
262
263			dAtom = (DirectionalAtom *)atoms[i];
264	chuckv	249
265			#ifndef USE_SPRNG
266
267	chuckv	221	#ifdef IS_MPI
268			#error "SPRNG random number generator must be used for MPI"
269	chuckv	249	#else // is_mpi
270	chuckv	254	//warning "Using drand48 for random number generation"
271	chuckv	249	#endif // is_MPI
272	mmeineke	10
273			vbar = sqrt( 2.0 * kebar * dAtom->getIxx() );
274			x = drand48();
275			y = drand48();
276			jx = vbar * sqrt( -2.0 * log(x)) * cos(2 * M_PI * y);
277
278			vbar = sqrt( 2.0 * kebar * dAtom->getIyy() );
279			x = drand48();
280			y = drand48();
281			jy = vbar * sqrt( -2.0 * log(x)) * cos(2 * M_PI * y);
282
283			vbar = sqrt( 2.0 * kebar * dAtom->getIzz() );
284			x = drand48();
285			y = drand48();
286			jz = vbar * sqrt( -2.0 * log(x)) * cos(2 * M_PI * y);
287	chuckv	249
288			#else //use_sprng
289
290	chuckv	221	vbar = sqrt( 2.0 * kebar * dAtom->getIxx() );
291	chuckv	223	jx = vbar * gaussStream->getGaussian();
292	chuckv	221
293			vbar = sqrt( 2.0 * kebar * dAtom->getIyy() );
294	chuckv	223	jy = vbar * gaussStream->getGaussian();
295	chuckv	221
296			vbar = sqrt( 2.0 * kebar * dAtom->getIzz() );
297	chuckv	223	jz = vbar * gaussStream->getGaussian();
298	chuckv	249	#endif //use_sprng
299	mmeineke	10
300			dAtom->setJx( jx );
301			dAtom->setJy( jy );
302			dAtom->setJz( jz );
303			}
304			}
305			}
306			}