mdtools/md_code/Thermo.cpp

#include <cmath>

#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 );
  
  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:	249
Committed:	Mon Jan 27 21:28:19 2003 UTC (21 years, 5 months ago) by chuckv
File size:	7187 byte(s)
Log Message:	For some unknown reason the Single processor builds. Has not been tested!
#	User	Rev	Content
1	mmeineke	10	#include <cmath>
2	chuckv	249
3			#ifdef IS_MPI
4	chuckv	218	#include <mpi++.h>
5	chuckv	249	#endif //is_mpi
6	mmeineke	10
7			#include "Thermo.hpp"
8			#include "SRI.hpp"
9			#include "LRI.hpp"
10			#include "Integrator.hpp"
11
12	chuckv	223	#define BASE_SEED 123456789
13	mmeineke	10
14	chuckv	223	Thermo::Thermo( SimInfo* the_entry_plug ) {
15			entry_plug = the_entry_plug;
16	chuckv	249	int baseSeed = BASE_SEED;
17	chuckv	223	gaussStream = new gaussianSPRNG( baseSeed );
18			}
19
20			Thermo::~Thermo(){
21			delete gaussStream;
22			}
23
24	mmeineke	10	double Thermo::getKinetic(){
25
26			const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2
27			double vx2, vy2, vz2;
28			double kinetic, v_sqr;
29			int kl;
30			double jx2, jy2, jz2; // the square of the angular momentums
31
32			DirectionalAtom *dAtom;
33
34			int n_atoms;
35	chuckv	218	double kinetic_global;
36	mmeineke	10	Atom** atoms;
37	chuckv	218
38	mmeineke	10
39			n_atoms = entry_plug->n_atoms;
40			atoms = entry_plug->atoms;
41
42			kinetic = 0.0;
43	chuckv	218	kinetic_global = 0.0;
44	mmeineke	10	for( kl=0; kl < n_atoms; kl++ ){
45
46			vx2 = atoms[kl]->get_vx() * atoms[kl]->get_vx();
47			vy2 = atoms[kl]->get_vy() * atoms[kl]->get_vy();
48			vz2 = atoms[kl]->get_vz() * atoms[kl]->get_vz();
49
50			v_sqr = vx2 + vy2 + vz2;
51			kinetic += atoms[kl]->getMass() * v_sqr;
52
53			if( atoms[kl]->isDirectional() ){
54
55			dAtom = (DirectionalAtom *)atoms[kl];
56
57			jx2 = dAtom->getJx() * dAtom->getJx();
58			jy2 = dAtom->getJy() * dAtom->getJy();
59			jz2 = dAtom->getJz() * dAtom->getJz();
60
61			kinetic += (jx2 / dAtom->getIxx()) + (jy2 / dAtom->getIyy())
62			+ (jz2 / dAtom->getIzz());
63			}
64			}
65	chuckv	218	#ifdef IS_MPI
66			MPI_COMM_WORLD.Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,MPI_SUM);
67			kinetic = kinetic_global;
68	chuckv	249	#endif //is_mpi
69	chuckv	218
70	mmeineke	10	kinetic = kinetic * 0.5 / e_convert;
71
72			return kinetic;
73			}
74
75			double Thermo::getPotential(){
76
77			double potential;
78	chuckv	218	double potential_global;
79	mmeineke	10	int el, nSRI;
80			SRI** sris;
81
82			sris = entry_plug->sr_interactions;
83			nSRI = entry_plug->n_SRI;
84
85			potential = 0.0;
86	chuckv	218	potential_global = 0.0;
87	chuckv	249	potential += entry_plug->lrPot;
88	mmeineke	10
89			// std::cerr << "long range potential: " << potential << "\n";
90			for( el=0; el<nSRI; el++ ){
91
92			potential += sris[el]->get_potential();
93			}
94
95	chuckv	218	// Get total potential for entire system from MPI.
96			#ifdef IS_MPI
97			MPI_COMM_WORLD.Allreduce(&potential,&potential_global,1,MPI_DOUBLE,MPI_SUM);
98			potential = potential_global;
99	chuckv	249	#endif // is_mpi
100	chuckv	218
101	mmeineke	10	return potential;
102			}
103
104			double Thermo::getTotalE(){
105
106			double total;
107
108			total = this->getKinetic() + this->getPotential();
109			return total;
110			}
111
112			double Thermo::getTemperature(){
113
114	mmeineke	25	const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K)
115	mmeineke	10	double temperature;
116
117			int ndf = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented
118			- entry_plug->n_constraints - 3;
119
120			temperature = ( 2.0 * this->getKinetic() ) / ( ndf * kb );
121			return temperature;
122			}
123
124			double Thermo::getPressure(){
125
126	mmeineke	117	// const double conv_Pa_atm = 9.901E-6; // convert Pa -> atm
127			// const double conv_internal_Pa = 1.661E-7; //convert amu/(fs^2 A) -> Pa
128			// const double conv_A_m = 1.0E-10; //convert A -> m
129	mmeineke	10
130			return 0.0;
131			}
132
133			void Thermo::velocitize() {
134
135			double x,y;
136			double vx, vy, vz;
137			double jx, jy, jz;
138			int i, vr, vd; // velocity randomizer loop counters
139			double vdrift[3];
140			double mtot = 0.0;
141			double vbar;
142			const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
143			double av2;
144			double kebar;
145			int ndf; // number of degrees of freedom
146			int ndfRaw; // the raw number of degrees of freedom
147			int n_atoms;
148			Atom** atoms;
149			DirectionalAtom* dAtom;
150			double temperature;
151			int n_oriented;
152			int n_constraints;
153
154			atoms = entry_plug->atoms;
155			n_atoms = entry_plug->n_atoms;
156			temperature = entry_plug->target_temp;
157			n_oriented = entry_plug->n_oriented;
158			n_constraints = entry_plug->n_constraints;
159
160
161			ndfRaw = 3 * n_atoms + 3 * n_oriented;
162			ndf = ndfRaw - n_constraints - 3;
163			kebar = kb * temperature * (double)ndf / ( 2.0 * (double)ndfRaw );
164
165			for(vr = 0; vr < n_atoms; vr++){
166
167			// uses equipartition theory to solve for vbar in angstrom/fs
168
169			av2 = 2.0 * kebar / atoms[vr]->getMass();
170			vbar = sqrt( av2 );
171
172			// vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() );
173
174			// picks random velocities from a gaussian distribution
175			// centered on vbar
176	chuckv	221	#ifndef USE_SPRNG
177			/* If we are using mpi, we need to use the SPRNG random
178			generator. The non drand48 generator will just repeat
179			the same numbers for every node creating a non-gaussian
180			distribution for the simulation. drand48 is fine for the
181			single processor version of the code, but SPRNG should
182			still be preferred for consistency.
183			*/
184	chuckv	249
185	chuckv	221	#ifdef IS_MPI
186			#error "SPRNG random number generator must be used for MPI"
187			#else
188			#warning "Using drand48 for random number generation"
189	chuckv	249	#endif // is_mpi
190
191	mmeineke	10	x = drand48();
192			y = drand48();
193			vx = vbar * sqrt( -2.0 * log(x)) * cos(2 * M_PI * y);
194
195			x = drand48();
196			y = drand48();
197			vy = vbar * sqrt( -2.0 * log(x)) * cos(2 * M_PI * y);
198
199			x = drand48();
200			y = drand48();
201			vz = vbar * sqrt( -2.0 * log(x)) * cos(2 * M_PI * y);
202	chuckv	249	#endif // use_spring
203	chuckv	221
204			#ifdef USE_SPRNG
205	chuckv	223	vx = vbar * gaussStream->getGaussian();
206			vy = vbar * gaussStream->getGaussian();
207			vz = vbar * gaussStream->getGaussian();
208	chuckv	249	#endif // use_spring
209	chuckv	221
210	mmeineke	10	atoms[vr]->set_vx( vx );
211			atoms[vr]->set_vy( vy );
212			atoms[vr]->set_vz( vz );
213			}
214
215			// Corrects for the center of mass drift.
216			// sums all the momentum and divides by total mass.
217
218			mtot = 0.0;
219			vdrift[0] = 0.0;
220			vdrift[1] = 0.0;
221			vdrift[2] = 0.0;
222			for(vd = 0; vd < n_atoms; vd++){
223
224			vdrift[0] += atoms[vd]->get_vx() * atoms[vd]->getMass();
225			vdrift[1] += atoms[vd]->get_vy() * atoms[vd]->getMass();
226			vdrift[2] += atoms[vd]->get_vz() * atoms[vd]->getMass();
227
228			mtot = mtot + atoms[vd]->getMass();
229			}
230
231			for (vd = 0; vd < 3; vd++) {
232			vdrift[vd] = vdrift[vd] / mtot;
233			}
234
235			for(vd = 0; vd < n_atoms; vd++){
236
237			vx = atoms[vd]->get_vx();
238			vy = atoms[vd]->get_vy();
239			vz = atoms[vd]->get_vz();
240
241
242			vx -= vdrift[0];
243			vy -= vdrift[1];
244			vz -= vdrift[2];
245
246			atoms[vd]->set_vx(vx);
247			atoms[vd]->set_vy(vy);
248			atoms[vd]->set_vz(vz);
249			}
250			if( n_oriented ){
251
252			for( i=0; i<n_atoms; i++ ){
253
254			if( atoms[i]->isDirectional() ){
255
256			dAtom = (DirectionalAtom *)atoms[i];
257	chuckv	249
258			#ifndef USE_SPRNG
259
260	chuckv	221	#ifdef IS_MPI
261			#error "SPRNG random number generator must be used for MPI"
262	chuckv	249	#else // is_mpi
263	chuckv	221	#warning "Using drand48 for random number generation"
264	chuckv	249	#endif // is_MPI
265	mmeineke	10
266			vbar = sqrt( 2.0 * kebar * dAtom->getIxx() );
267			x = drand48();
268			y = drand48();
269			jx = vbar * sqrt( -2.0 * log(x)) * cos(2 * M_PI * y);
270
271			vbar = sqrt( 2.0 * kebar * dAtom->getIyy() );
272			x = drand48();
273			y = drand48();
274			jy = vbar * sqrt( -2.0 * log(x)) * cos(2 * M_PI * y);
275
276			vbar = sqrt( 2.0 * kebar * dAtom->getIzz() );
277			x = drand48();
278			y = drand48();
279			jz = vbar * sqrt( -2.0 * log(x)) * cos(2 * M_PI * y);
280	chuckv	249
281			#else //use_sprng
282
283	chuckv	221	vbar = sqrt( 2.0 * kebar * dAtom->getIxx() );
284	chuckv	223	jx = vbar * gaussStream->getGaussian();
285	chuckv	221
286			vbar = sqrt( 2.0 * kebar * dAtom->getIyy() );
287	chuckv	223	jy = vbar * gaussStream->getGaussian();
288	chuckv	221
289			vbar = sqrt( 2.0 * kebar * dAtom->getIzz() );
290	chuckv	223	jz = vbar * gaussStream->getGaussian();
291	chuckv	249	#endif //use_sprng
292	mmeineke	10
293			dAtom->setJx( jx );
294			dAtom->setJy( jy );
295			dAtom->setJz( jz );
296			}
297			}
298			}
299			}