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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 484 by gezelter, Wed Apr 9 13:59:35 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 >  double theBox[3];
155 >
156 >  entry_plug->getBox(theBox);
157 >  return (theBox[0] * theBox[1] * theBox[2]);
158 > }
159 >
160 > double Thermo::getPressure() {
161 >  // returns the pressure in units of atm
162 >  // Relies on the calculation of the full molecular pressure tensor
163 >  
164 >  const double p_convert = 1.63882576e8;
165 >  double press[9];
166 >  double pressure;
167 >
168 >  this->getPressureTensor(press);
169 >
170 >  pressure = p_convert * (press[0] + press[4] + press[8]) / 3.0;
171 >
172 >  return pressure;
173 > }
174 >
175 >
176 > void Thermo::getPressureTensor(double press[9]){
177 >  // returns pressure tensor in units amu*fs^-2*Ang^-1
178 >  // routine derived via viral theorem description in:
179 >  // Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
180 >
181 >  const double e_convert = 4.184e-4;
182 >
183 >  double molmass, volume;
184 >  double vcom[3];
185 >  double p_local[9], p_global[9];
186 >  double theBox[3];
187 >  double* tau;
188 >  int i, nMols;
189 >  Molecule* molecules;
190 >
191 >  nMols = entry_plug->n_mol;
192 >  molecules = entry_plug->molecules;
193 >  tau = entry_plug->tau;
194 >
195 >  // use velocities of molecular centers of mass and molecular masses:
196 >  for (i=0; i < 9; i++) {    
197 >    p_local[i] = 0.0;
198 >    p_global[i] = 0.0;
199 >  }
200 >
201 >  for (i=0; i < nMols; i++) {
202 >    molmass = molecules[i].getCOMvel(vcom);
203 >
204 >    p_local[0] += molmass * (vcom[0] * vcom[0]);
205 >    p_local[1] += molmass * (vcom[0] * vcom[1]);
206 >    p_local[2] += molmass * (vcom[0] * vcom[2]);
207 >    p_local[3] += molmass * (vcom[1] * vcom[0]);
208 >    p_local[4] += molmass * (vcom[1] * vcom[1]);
209 >    p_local[5] += molmass * (vcom[1] * vcom[2]);
210 >    p_local[6] += molmass * (vcom[2] * vcom[0]);
211 >    p_local[7] += molmass * (vcom[2] * vcom[1]);
212 >    p_local[8] += molmass * (vcom[2] * vcom[2]);
213 >  }
214 >
215 >  // Get total for entire system from MPI.
216 >
217 > #ifdef IS_MPI
218 >  MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
219 > #else
220 >  for (i=0; i<9; i++) {
221 >    p_global[i] = p_local[i];
222 >  }
223 > #endif // is_mpi
224 >
225 >  entry_plug->getBox(theBox);
226 >
227 >  volume = theBox[0] * theBox[1] * theBox[2];
228 >
229 >  for(i=0; i<9; i++) {
230 >    press[i] = (p_global[i] - tau[i]*e_convert) / volume;
231 >  }
232   }
233  
234   void Thermo::velocitize() {
# Line 140 | Line 238 | void Thermo::velocitize() {
238    double jx, jy, jz;
239    int i, vr, vd; // velocity randomizer loop counters
240    double vdrift[3];
143 –  double mtot = 0.0;
241    double vbar;
242    const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
243    double av2;
244    double kebar;
148 –  int ndf; // number of degrees of freedom
149 –  int ndfRaw; // the raw number of degrees of freedom
245    int n_atoms;
246    Atom** atoms;
247    DirectionalAtom* dAtom;
# Line 160 | Line 255 | void Thermo::velocitize() {
255    n_oriented    = entry_plug->n_oriented;
256    n_constraints = entry_plug->n_constraints;
257    
258 <
259 <  ndfRaw = 3 * n_atoms + 3 * n_oriented;
165 <  ndf = ndfRaw - n_constraints - 3;
166 <  kebar = kb * temperature * (double)ndf / ( 2.0 * (double)ndfRaw );
258 >  kebar = kb * temperature * (double)entry_plug->ndf /
259 >    ( 2.0 * (double)entry_plug->ndfRaw );
260    
261    for(vr = 0; vr < n_atoms; vr++){
262      
# Line 171 | Line 264 | void Thermo::velocitize() {
264  
265      av2 = 2.0 * kebar / atoms[vr]->getMass();
266      vbar = sqrt( av2 );
267 <
267 >
268   //     vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() );
269      
270      // picks random velocities from a gaussian distribution
# Line 185 | Line 278 | void Thermo::velocitize() {
278      atoms[vr]->set_vy( vy );
279      atoms[vr]->set_vz( vz );
280    }
281 +
282 +  // Get the Center of Mass drift velocity.
283 +
284 +  getCOMVel(vdrift);
285    
286    //  Corrects for the center of mass drift.
287    // 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 –  
288  
289    for(vd = 0; vd < n_atoms; vd++){
290      
291      vx = atoms[vd]->get_vx();
292      vy = atoms[vd]->get_vy();
293      vz = atoms[vd]->get_vz();
294 <    
216 <    
294 >        
295      vx -= vdrift[0];
296      vy -= vdrift[1];
297      vz -= vdrift[2];
# Line 235 | Line 313 | void Thermo::velocitize() {
313  
314          vbar = sqrt( 2.0 * kebar * dAtom->getIyy() );
315          jy = vbar * gaussStream->getGaussian();
316 <
316 >        
317          vbar = sqrt( 2.0 * kebar * dAtom->getIzz() );
318          jz = vbar * gaussStream->getGaussian();
319          
# Line 246 | Line 324 | void Thermo::velocitize() {
324      }  
325    }
326   }
327 +
328 + void Thermo::getCOMVel(double vdrift[3]){
329 +
330 +  double mtot, mtot_local;
331 +  double vdrift_local[3];
332 +  int vd, n_atoms;
333 +  Atom** atoms;
334 +
335 +  // We are very careless here with the distinction between n_atoms and n_local
336 +  // We should really fix this before someone pokes an eye out.
337 +
338 +  n_atoms = entry_plug->n_atoms;  
339 +  atoms   = entry_plug->atoms;
340 +
341 +  mtot_local = 0.0;
342 +  vdrift_local[0] = 0.0;
343 +  vdrift_local[1] = 0.0;
344 +  vdrift_local[2] = 0.0;
345 +  
346 +  for(vd = 0; vd < n_atoms; vd++){
347 +    
348 +    vdrift_local[0] += atoms[vd]->get_vx() * atoms[vd]->getMass();
349 +    vdrift_local[1] += atoms[vd]->get_vy() * atoms[vd]->getMass();
350 +    vdrift_local[2] += atoms[vd]->get_vz() * atoms[vd]->getMass();
351 +    
352 +    mtot_local += atoms[vd]->getMass();
353 +  }
354 +
355 + #ifdef IS_MPI
356 +  MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
357 +  MPI_Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
358 + #else
359 +  mtot = mtot_local;
360 +  for(vd = 0; vd < 3; vd++) {
361 +    vdrift[vd] = vdrift_local[vd];
362 +  }
363 + #endif
364 +    
365 +  for (vd = 0; vd < 3; vd++) {
366 +    vdrift[vd] = vdrift[vd] / mtot;
367 +  }
368 +  
369 + }
370 +

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