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root/group/trunk/OOPSE/libmdtools/Thermo.cpp
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Comparing trunk/OOPSE/libmdtools/Thermo.cpp (file contents):
Revision 378 by mmeineke, Fri Mar 21 17:42:12 2003 UTC vs.
Revision 574 by gezelter, Tue Jul 8 20:56:10 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"
17 + #endif // is_mpi
18 +
19 +
20   #define BASE_SEED 123456789
21  
22   Thermo::Thermo( SimInfo* the_entry_plug ) {
# Line 66 | Line 72 | double Thermo::getKinetic(){
72      }
73    }
74   #ifdef IS_MPI
75 <  MPI::COMM_WORLD.Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,MPI_SUM);
75 >  MPI_Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,
76 >                MPI_SUM, MPI_COMM_WORLD);
77    kinetic = kinetic_global;
78   #endif //is_mpi
79  
# Line 77 | Line 84 | double Thermo::getPotential(){
84  
85   double Thermo::getPotential(){
86    
87 +  double potential_local;
88    double potential;
81 –  double potential_global;
89    int el, nSRI;
90 <  SRI** sris;
90 >  Molecule* molecules;
91  
92 <  sris = entry_plug->sr_interactions;
92 >  molecules = entry_plug->molecules;
93    nSRI = entry_plug->n_SRI;
94  
95 +  potential_local = 0.0;
96    potential = 0.0;
97 <  potential_global = 0.0;
90 <  potential += entry_plug->lrPot;
97 >  potential_local += entry_plug->lrPot;
98  
99 <  for( el=0; el<nSRI; el++ ){
100 <    
94 <    potential += sris[el]->get_potential();
99 >  for( el=0; el<entry_plug->n_mol; el++ ){    
100 >    potential_local += molecules[el].getPotential();
101    }
102  
103    // Get total potential for entire system from MPI.
104   #ifdef IS_MPI
105 <  MPI::COMM_WORLD.Allreduce(&potential,&potential_global,1,MPI_DOUBLE,MPI_SUM);
106 <  potential = potential_global;
107 <
105 >  MPI_Allreduce(&potential_local,&potential,1,MPI_DOUBLE,
106 >                MPI_SUM, MPI_COMM_WORLD);
107 > #else
108 >  potential = potential_local;
109   #endif // is_mpi
110  
111 + #ifdef IS_MPI
112 +  /*
113 +  std::cerr << "node " << worldRank << ": after pot = " << potential << "\n";
114 +  */
115 + #endif
116 +
117    return potential;
118   }
119  
# Line 117 | Line 130 | double Thermo::getTemperature(){
130    const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K)
131    double temperature;
132    
133 <  int ndf = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented
121 <    - entry_plug->n_constraints - 3;
122 <
123 <  temperature = ( 2.0 * this->getKinetic() ) / ( ndf * kb );
133 >  temperature = ( 2.0 * this->getKinetic() ) / ((double)entry_plug->ndf * kb );
134    return temperature;
135   }
136  
137 < double Thermo::getPressure(){
137 > double Thermo::getEnthalpy() {
138  
139 < //  const double conv_Pa_atm = 9.901E-6; // convert Pa -> atm
140 < // const double conv_internal_Pa = 1.661E-7; //convert amu/(fs^2 A) -> Pa
141 < //  const double conv_A_m = 1.0E-10; //convert A -> m
139 >  const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2
140 >  double u, p, v;
141 >  double press[9];
142  
143 <  return 0.0;
143 >  u = this->getTotalE();
144 >
145 >  this->getPressureTensor(press);
146 >  p = (press[0] + press[4] + press[8]) / 3.0;
147 >
148 >  v = this->getVolume();
149 >
150 >  return (u + (p*v)/e_convert);
151   }
152  
153 + double Thermo::getVolume() {
154 +
155 +  double volume;
156 +  double Hmat[9];
157 +
158 +  entry_plug->getBoxM(Hmat);
159 +
160 +  // volume = h1 (dot) h2 (cross) h3
161 +
162 +  volume = Hmat[0] * ( (Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]) )
163 +         + Hmat[1] * ( (Hmat[5]*Hmat[6]) - (Hmat[8]*Hmat[3]) )
164 +         + Hmat[2] * ( (Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]) );
165 +
166 +  return volume;
167 + }
168 +
169 + double Thermo::getPressure() {
170 +
171 +  // Relies on the calculation of the full molecular pressure tensor
172 +  
173 +  const double p_convert = 1.63882576e8;
174 +  double press[9];
175 +  double pressure;
176 +
177 +  this->getPressureTensor(press);
178 +
179 +  pressure = p_convert * (press[0] + press[4] + press[8]) / 3.0;
180 +
181 +  return pressure;
182 + }
183 +
184 +
185 + void Thermo::getPressureTensor(double press[9]){
186 +  // returns pressure tensor in units amu*fs^-2*Ang^-1
187 +  // routine derived via viral theorem description in:
188 +  // Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
189 +
190 +  const double e_convert = 4.184e-4;
191 +
192 +  double molmass, volume;
193 +  double vcom[3];
194 +  double p_local[9], p_global[9];
195 +  double theBox[3];
196 +  //double* tau;
197 +  int i, nMols;
198 +  Molecule* molecules;
199 +
200 +  nMols = entry_plug->n_mol;
201 +  molecules = entry_plug->molecules;
202 +  //tau = entry_plug->tau;
203 +
204 +  // use velocities of molecular centers of mass and molecular masses:
205 +  for (i=0; i < 9; i++) {    
206 +    p_local[i] = 0.0;
207 +    p_global[i] = 0.0;
208 +  }
209 +
210 +  for (i=0; i < nMols; i++) {
211 +    molmass = molecules[i].getCOMvel(vcom);
212 +
213 +    p_local[0] += molmass * (vcom[0] * vcom[0]);
214 +    p_local[1] += molmass * (vcom[0] * vcom[1]);
215 +    p_local[2] += molmass * (vcom[0] * vcom[2]);
216 +    p_local[3] += molmass * (vcom[1] * vcom[0]);
217 +    p_local[4] += molmass * (vcom[1] * vcom[1]);
218 +    p_local[5] += molmass * (vcom[1] * vcom[2]);
219 +    p_local[6] += molmass * (vcom[2] * vcom[0]);
220 +    p_local[7] += molmass * (vcom[2] * vcom[1]);
221 +    p_local[8] += molmass * (vcom[2] * vcom[2]);
222 +  }
223 +
224 +  // Get total for entire system from MPI.
225 +
226 + #ifdef IS_MPI
227 +  MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
228 + #else
229 +  for (i=0; i<9; i++) {
230 +    p_global[i] = p_local[i];
231 +  }
232 + #endif // is_mpi
233 +
234 +  volume = entry_plug->boxVol;
235 +
236 +  for(i=0; i<9; i++) {
237 +    press[i] = (p_global[i] - entry_plug->tau[i]*e_convert) / volume;
238 +  }
239 + }
240 +
241   void Thermo::velocitize() {
242    
243    double x,y;
# Line 140 | Line 245 | void Thermo::velocitize() {
245    double jx, jy, jz;
246    int i, vr, vd; // velocity randomizer loop counters
247    double vdrift[3];
143 –  double mtot = 0.0;
248    double vbar;
249    const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
250    double av2;
251    double kebar;
148 –  int ndf; // number of degrees of freedom
149 –  int ndfRaw; // the raw number of degrees of freedom
252    int n_atoms;
253    Atom** atoms;
254    DirectionalAtom* dAtom;
# Line 160 | Line 262 | void Thermo::velocitize() {
262    n_oriented    = entry_plug->n_oriented;
263    n_constraints = entry_plug->n_constraints;
264    
265 <
266 <  ndfRaw = 3 * n_atoms + 3 * n_oriented;
165 <  ndf = ndfRaw - n_constraints - 3;
166 <  kebar = kb * temperature * (double)ndf / ( 2.0 * (double)ndfRaw );
265 >  kebar = kb * temperature * (double)entry_plug->ndf /
266 >    ( 2.0 * (double)entry_plug->ndfRaw );
267    
268    for(vr = 0; vr < n_atoms; vr++){
269      
# Line 171 | Line 271 | void Thermo::velocitize() {
271  
272      av2 = 2.0 * kebar / atoms[vr]->getMass();
273      vbar = sqrt( av2 );
274 <
274 >
275   //     vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() );
276      
277      // picks random velocities from a gaussian distribution
# Line 185 | Line 285 | void Thermo::velocitize() {
285      atoms[vr]->set_vy( vy );
286      atoms[vr]->set_vz( vz );
287    }
288 +
289 +  // Get the Center of Mass drift velocity.
290 +
291 +  getCOMVel(vdrift);
292    
293    //  Corrects for the center of mass drift.
294    // sums all the momentum and divides by total mass.
191 –  
192 –  mtot = 0.0;
193 –  vdrift[0] = 0.0;
194 –  vdrift[1] = 0.0;
195 –  vdrift[2] = 0.0;
196 –  for(vd = 0; vd < n_atoms; vd++){
197 –    
198 –    vdrift[0] += atoms[vd]->get_vx() * atoms[vd]->getMass();
199 –    vdrift[1] += atoms[vd]->get_vy() * atoms[vd]->getMass();
200 –    vdrift[2] += atoms[vd]->get_vz() * atoms[vd]->getMass();
201 –    
202 –    mtot += atoms[vd]->getMass();
203 –  }
204 –  
205 –  for (vd = 0; vd < 3; vd++) {
206 –    vdrift[vd] = vdrift[vd] / mtot;
207 –  }
208 –  
295  
296    for(vd = 0; vd < n_atoms; vd++){
297      
298      vx = atoms[vd]->get_vx();
299      vy = atoms[vd]->get_vy();
300      vz = atoms[vd]->get_vz();
301 <    
216 <    
301 >        
302      vx -= vdrift[0];
303      vy -= vdrift[1];
304      vz -= vdrift[2];
# Line 235 | Line 320 | void Thermo::velocitize() {
320  
321          vbar = sqrt( 2.0 * kebar * dAtom->getIyy() );
322          jy = vbar * gaussStream->getGaussian();
323 <
323 >        
324          vbar = sqrt( 2.0 * kebar * dAtom->getIzz() );
325          jz = vbar * gaussStream->getGaussian();
326          
# Line 246 | Line 331 | void Thermo::velocitize() {
331      }  
332    }
333   }
334 +
335 + void Thermo::getCOMVel(double vdrift[3]){
336 +
337 +  double mtot, mtot_local;
338 +  double vdrift_local[3];
339 +  int vd, n_atoms;
340 +  Atom** atoms;
341 +
342 +  // We are very careless here with the distinction between n_atoms and n_local
343 +  // We should really fix this before someone pokes an eye out.
344 +
345 +  n_atoms = entry_plug->n_atoms;  
346 +  atoms   = entry_plug->atoms;
347 +
348 +  mtot_local = 0.0;
349 +  vdrift_local[0] = 0.0;
350 +  vdrift_local[1] = 0.0;
351 +  vdrift_local[2] = 0.0;
352 +  
353 +  for(vd = 0; vd < n_atoms; vd++){
354 +    
355 +    vdrift_local[0] += atoms[vd]->get_vx() * atoms[vd]->getMass();
356 +    vdrift_local[1] += atoms[vd]->get_vy() * atoms[vd]->getMass();
357 +    vdrift_local[2] += atoms[vd]->get_vz() * atoms[vd]->getMass();
358 +    
359 +    mtot_local += atoms[vd]->getMass();
360 +  }
361 +
362 + #ifdef IS_MPI
363 +  MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
364 +  MPI_Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
365 + #else
366 +  mtot = mtot_local;
367 +  for(vd = 0; vd < 3; vd++) {
368 +    vdrift[vd] = vdrift_local[vd];
369 +  }
370 + #endif
371 +    
372 +  for (vd = 0; vd < 3; vd++) {
373 +    vdrift[vd] = vdrift[vd] / mtot;
374 +  }
375 +  
376 + }
377 +

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