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root/group/trunk/OOPSE/libmdtools/Thermo.cpp
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Comparing trunk/OOPSE/libmdtools/Thermo.cpp (file contents):
Revision 401 by chuckv, Tue Mar 25 22:54:16 2003 UTC vs.
Revision 611 by gezelter, Tue Jul 15 17:10:50 2003 UTC

# Line 4 | Line 4 | using namespace std;
4  
5   #ifdef IS_MPI
6   #include <mpi.h>
7 – #include <mpi++.h>
7   #endif //is_mpi
8  
9   #include "Thermo.hpp"
10   #include "SRI.hpp"
11   #include "Integrator.hpp"
12 + #include "simError.h"
13 +
14 + #ifdef IS_MPI
15   #define __C
16 < //#include "mpiSimulation.hpp"
16 > #include "mpiSimulation.hpp"
17 > #endif // is_mpi
18  
19 +
20   #define BASE_SEED 123456789
21  
22   Thermo::Thermo( SimInfo* the_entry_plug ) {
# Line 29 | Line 33 | double Thermo::getKinetic(){
33   double Thermo::getKinetic(){
34  
35    const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2
36 <  double vx2, vy2, vz2;
37 <  double kinetic, v_sqr;
38 <  int kl;
39 <  double jx2, jy2, jz2; // the square of the angular momentums
36 >  double kinetic;
37 >  double amass;
38 >  double aVel[3], aJ[3], I[3][3];
39 >  int j, kl;
40  
41    DirectionalAtom *dAtom;
42  
# Line 47 | Line 51 | double Thermo::getKinetic(){
51    kinetic = 0.0;
52    kinetic_global = 0.0;
53    for( kl=0; kl < n_atoms; kl++ ){
54 +    
55 +    atoms[kl]->getVel(aVel);
56 +    amass = atoms[kl]->getMass();
57 +    
58 +    for (j=0; j < 3; j++)
59 +      kinetic += amass * aVel[j] * aVel[j];
60  
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 –
61      if( atoms[kl]->isDirectional() ){
62              
63        dAtom = (DirectionalAtom *)atoms[kl];
64 +
65 +      dAtom->getJ( aJ );
66 +      dAtom->getI( I );
67        
68 <      jx2 = dAtom->getJx() * dAtom->getJx();    
69 <      jy2 = dAtom->getJy() * dAtom->getJy();
64 <      jz2 = dAtom->getJz() * dAtom->getJz();
68 >      for (j=0; j<3; j++)
69 >        kinetic += aJ[j]*aJ[j] / I[j][j];
70        
66 –      kinetic += (jx2 / dAtom->getIxx()) + (jy2 / dAtom->getIyy())
67 –        + (jz2 / dAtom->getIzz());
71      }
72    }
73   #ifdef IS_MPI
74 <  MPI::COMM_WORLD.Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,MPI_SUM);
74 >  MPI_Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,
75 >                MPI_SUM, MPI_COMM_WORLD);
76    kinetic = kinetic_global;
77   #endif //is_mpi
78  
# Line 82 | Line 86 | double Thermo::getPotential(){
86    double potential_local;
87    double potential;
88    int el, nSRI;
89 <  SRI** sris;
89 >  Molecule* molecules;
90  
91 <  sris = entry_plug->sr_interactions;
91 >  molecules = entry_plug->molecules;
92    nSRI = entry_plug->n_SRI;
93  
94    potential_local = 0.0;
95 +  potential = 0.0;
96    potential_local += entry_plug->lrPot;
97  
98 <  for( el=0; el<nSRI; el++ ){    
99 <    potential_local += sris[el]->get_potential();
98 >  for( el=0; el<entry_plug->n_mol; el++ ){    
99 >    potential_local += molecules[el].getPotential();
100    }
101  
102    // Get total potential for entire system from MPI.
103   #ifdef IS_MPI
104 <  MPI::COMM_WORLD.Allreduce(&potential_local,&potential,1,MPI_DOUBLE,MPI_SUM);
104 >  MPI_Allreduce(&potential_local,&potential,1,MPI_DOUBLE,
105 >                MPI_SUM, MPI_COMM_WORLD);
106   #else
107    potential = potential_local;
108   #endif // is_mpi
109  
110 + #ifdef IS_MPI
111 +  /*
112 +  std::cerr << "node " << worldRank << ": after pot = " << potential << "\n";
113 +  */
114 + #endif
115 +
116    return potential;
117   }
118  
# Line 116 | Line 128 | double Thermo::getTemperature(){
128  
129    const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K)
130    double temperature;
119 –  int ndf_local, ndf;
131    
132 <  ndf_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented
133 <    - entry_plug->n_constraints;
132 >  temperature = ( 2.0 * this->getKinetic() ) / ((double)entry_plug->ndf * kb );
133 >  return temperature;
134 > }
135  
136 < #ifdef IS_MPI
125 <  MPI::COMM_WORLD.Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM);
126 < #else
127 <  ndf = ndf_local;
128 < #endif
136 > double Thermo::getEnthalpy() {
137  
138 <  ndf = ndf - 3;
138 >  const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2
139 >  double u, p, v;
140 >  double press[3][3];
141 >
142 >  u = this->getTotalE();
143 >
144 >  this->getPressureTensor(press);
145 >  p = (press[0][0] + press[1][1] + press[2][2]) / 3.0;
146 >
147 >  v = this->getVolume();
148 >
149 >  return (u + (p*v)/e_convert);
150 > }
151 >
152 > double Thermo::getVolume() {
153 >
154 >  return entry_plug->boxVol;
155 > }
156 >
157 > double Thermo::getPressure() {
158 >
159 >  // Relies on the calculation of the full molecular pressure tensor
160    
161 <  temperature = ( 2.0 * this->getKinetic() ) / ( ndf * kb );
162 <  return temperature;
161 >  const double p_convert = 1.63882576e8;
162 >  double press[3][3];
163 >  double pressure;
164 >
165 >  this->getPressureTensor(press);
166 >
167 >  pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
168 >
169 >  return pressure;
170   }
171  
136 – double Thermo::getPressure(){
172  
173 < //  const double conv_Pa_atm = 9.901E-6; // convert Pa -> atm
174 < // const double conv_internal_Pa = 1.661E-7; //convert amu/(fs^2 A) -> Pa
175 < //  const double conv_A_m = 1.0E-10; //convert A -> m
173 > void Thermo::getPressureTensor(double press[3][3]){
174 >  // returns pressure tensor in units amu*fs^-2*Ang^-1
175 >  // routine derived via viral theorem description in:
176 >  // Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
177  
178 <  return 0.0;
178 >  const double e_convert = 4.184e-4;
179 >
180 >  double molmass, volume;
181 >  double vcom[3];
182 >  double p_local[9], p_global[9];
183 >  int i, j, k, l, nMols;
184 >  Molecule* molecules;
185 >
186 >  nMols = entry_plug->n_mol;
187 >  molecules = entry_plug->molecules;
188 >  //tau = entry_plug->tau;
189 >
190 >  // use velocities of molecular centers of mass and molecular masses:
191 >  for (i=0; i < 9; i++) {    
192 >    p_local[i] = 0.0;
193 >    p_global[i] = 0.0;
194 >  }
195 >
196 >  for (i=0; i < nMols; i++) {
197 >    molmass = molecules[i].getCOMvel(vcom);
198 >
199 >    p_local[0] += molmass * (vcom[0] * vcom[0]);
200 >    p_local[1] += molmass * (vcom[0] * vcom[1]);
201 >    p_local[2] += molmass * (vcom[0] * vcom[2]);
202 >    p_local[3] += molmass * (vcom[1] * vcom[0]);
203 >    p_local[4] += molmass * (vcom[1] * vcom[1]);
204 >    p_local[5] += molmass * (vcom[1] * vcom[2]);
205 >    p_local[6] += molmass * (vcom[2] * vcom[0]);
206 >    p_local[7] += molmass * (vcom[2] * vcom[1]);
207 >    p_local[8] += molmass * (vcom[2] * vcom[2]);
208 >  }
209 >
210 >  // Get total for entire system from MPI.
211 >
212 > #ifdef IS_MPI
213 >  MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
214 > #else
215 >  for (i=0; i<9; i++) {
216 >    p_global[i] = p_local[i];
217 >  }
218 > #endif // is_mpi
219 >
220 >  volume = this->getVolume();
221 >
222 >  for(i = 0; i < 3; i++) {
223 >    for (j = 0; j < 3; j++) {
224 >      k = 3*i + j;
225 >      press[i][j] = (p_global[k] + entry_plug->tau[k]*e_convert) / volume;
226 >    }
227 >  }
228   }
229  
230   void Thermo::velocitize() {
231    
232    double x,y;
233 <  double vx, vy, vz;
234 <  double jx, jy, jz;
235 <  int i, vr, vd; // velocity randomizer loop counters
151 <  double *vdrift;
233 >  double aVel[3], aJ[3], I[3][3];
234 >  int i, j, vr, vd; // velocity randomizer loop counters
235 >  double vdrift[3];
236    double vbar;
237    const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
238    double av2;
239    double kebar;
156 –  int ndf; // number of degrees of freedom
157 –  int ndfRaw; // the raw number of degrees of freedom
240    int n_atoms;
241    Atom** atoms;
242    DirectionalAtom* dAtom;
# Line 168 | Line 250 | void Thermo::velocitize() {
250    n_oriented    = entry_plug->n_oriented;
251    n_constraints = entry_plug->n_constraints;
252    
253 <
254 <  ndfRaw = 3 * n_atoms + 3 * n_oriented;
173 <  ndf = ndfRaw - n_constraints - 3;
174 <  kebar = kb * temperature * (double)ndf / ( 2.0 * (double)ndfRaw );
253 >  kebar = kb * temperature * (double)entry_plug->ndf /
254 >    ( 2.0 * (double)entry_plug->ndfRaw );
255    
256    for(vr = 0; vr < n_atoms; vr++){
257      
# Line 179 | Line 259 | void Thermo::velocitize() {
259  
260      av2 = 2.0 * kebar / atoms[vr]->getMass();
261      vbar = sqrt( av2 );
262 <
262 >
263   //     vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() );
264      
265      // picks random velocities from a gaussian distribution
266      // centered on vbar
267  
268 <    vx = vbar * gaussStream->getGaussian();
269 <    vy = vbar * gaussStream->getGaussian();
270 <    vz = vbar * gaussStream->getGaussian();
268 >    for (j=0; j<3; j++)
269 >      aVel[j] = vbar * gaussStream->getGaussian();
270 >    
271 >    atoms[vr]->setVel( aVel );
272  
192 –    atoms[vr]->set_vx( vx );
193 –    atoms[vr]->set_vy( vy );
194 –    atoms[vr]->set_vz( vz );
273    }
274  
275    // Get the Center of Mass drift velocity.
276  
277 <  vdrift = getCOMVel();
277 >  getCOMVel(vdrift);
278    
279    //  Corrects for the center of mass drift.
280    // sums all the momentum and divides by total mass.
281  
282    for(vd = 0; vd < n_atoms; vd++){
283      
284 <    vx = atoms[vd]->get_vx();
207 <    vy = atoms[vd]->get_vy();
208 <    vz = atoms[vd]->get_vz();
209 <        
210 <    vx -= vdrift[0];
211 <    vy -= vdrift[1];
212 <    vz -= vdrift[2];
284 >    atoms[vd]->getVel(aVel);
285      
286 <    atoms[vd]->set_vx(vx);
287 <    atoms[vd]->set_vy(vy);
288 <    atoms[vd]->set_vz(vz);
286 >    for (j=0; j < 3; j++)
287 >      aVel[j] -= vdrift[j];
288 >        
289 >    atoms[vd]->setVel( aVel );
290    }
291    if( n_oriented ){
292    
# Line 222 | Line 295 | void Thermo::velocitize() {
295        if( atoms[i]->isDirectional() ){
296          
297          dAtom = (DirectionalAtom *)atoms[i];
298 +        dAtom->getI( I );
299 +        
300 +        for (j = 0 ; j < 3; j++) {
301  
302 <        vbar = sqrt( 2.0 * kebar * dAtom->getIxx() );
303 <        jx = vbar * gaussStream->getGaussian();
302 >          vbar = sqrt( 2.0 * kebar * I[j][j] );
303 >          aJ[j] = vbar * gaussStream->getGaussian();
304  
305 <        vbar = sqrt( 2.0 * kebar * dAtom->getIyy() );
230 <        jy = vbar * gaussStream->getGaussian();
305 >        }      
306  
307 <        vbar = sqrt( 2.0 * kebar * dAtom->getIzz() );
308 <        jz = vbar * gaussStream->getGaussian();
234 <        
235 <        dAtom->setJx( jx );
236 <        dAtom->setJy( jy );
237 <        dAtom->setJz( jz );
307 >        dAtom->setJ( aJ );
308 >
309        }
310      }  
311    }
312   }
313  
314 < double* Thermo::getCOMVel(){
314 > void Thermo::getCOMVel(double vdrift[3]){
315  
316    double mtot, mtot_local;
317 <  double* vdrift;
317 >  double aVel[3], amass;
318    double vdrift_local[3];
319 <  int vd, n_atoms;
319 >  int vd, n_atoms, j;
320    Atom** atoms;
321  
251 –  vdrift = new double[3];
322    // We are very careless here with the distinction between n_atoms and n_local
323    // We should really fix this before someone pokes an eye out.
324  
# Line 262 | Line 332 | double* Thermo::getCOMVel(){
332    
333    for(vd = 0; vd < n_atoms; vd++){
334      
335 <    vdrift_local[0] += atoms[vd]->get_vx() * atoms[vd]->getMass();
336 <    vdrift_local[1] += atoms[vd]->get_vy() * atoms[vd]->getMass();
337 <    vdrift_local[2] += atoms[vd]->get_vz() * atoms[vd]->getMass();
335 >    amass = atoms[vd]->getMass();
336 >    atoms[vd]->getVel( aVel );
337 >
338 >    for(j = 0; j < 3; j++)
339 >      vdrift_local[j] += aVel[j] * amass;
340      
341 <    mtot_local += atoms[vd]->getMass();
341 >    mtot_local += amass;
342    }
343  
344   #ifdef IS_MPI
345 <  MPI::COMM_WORLD.Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM);
346 <  MPI::COMM_WORLD.Allreduce(&vdrift_local,&vdrift,3,MPI_DOUBLE,MPI_SUM);
345 >  MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
346 >  MPI_Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
347   #else
348    mtot = mtot_local;
349    for(vd = 0; vd < 3; vd++) {
# Line 283 | Line 355 | double* Thermo::getCOMVel(){
355      vdrift[vd] = vdrift[vd] / mtot;
356    }
357    
286 –  return vdrift;
358   }
359  

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