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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 468 by gezelter, Mon Apr 7 16:56:38 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(){
138 +  // returns pressure in units amu*fs^-2*Ang^-1
139 +  // routine derived via viral theorem description in:
140 +  // Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
141  
142 < //  const double conv_Pa_atm = 9.901E-6; // convert Pa -> atm
143 < // const double conv_internal_Pa = 1.661E-7; //convert amu/(fs^2 A) -> Pa
144 < //  const double conv_A_m = 1.0E-10; //convert A -> m
142 >  const double convert = 4.184e-4;
143 >  double mtot;
144 >  double vcom[3];
145 >  double p_local, p_sum, p_mol, virial;
146 >  double theBox[3];
147 >  double* tau;
148 >  int i, nMols;
149 >  Molecule* molecules;
150  
151 <  return 0.0;
151 >  nMols = entry_plug->n_mol;
152 >  molecules = entry_plug->molecules;
153 >  tau = entry_plug->tau;
154 >
155 >  // use velocities of molecular centers of mass and molecular masses:
156 >  p_local = 0.0;
157 >  for (i=0; i < nMols; i++) {
158 >    molecules[i].getCOMvel(mtot, vcom);
159 >    p_local += mtot* (vcom[0]*vcom[0] + vcom[1]*vcom[1] + vcom[2]*vcom[2]);
160 >  }
161 >
162 >  // Get total for entire system from MPI.
163 > #ifdef IS_MPI
164 >  MPI_Allreduce(&p_local,&p_sum,1,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
165 > #else
166 >  p_sum = p_local;
167 > #endif // is_mpi
168 >
169 >  virial = tau[0] + tau[4] + tau[8];
170 >  entry_plug->getBox(theBox);
171 >
172 >  p_mol = (p_sum - virial*convert) / (3.0 * theBox[0] * theBox[1]* theBox[2]);
173 >  
174 >  return p_mol;
175   }
176  
177   void Thermo::velocitize() {
# Line 140 | Line 181 | void Thermo::velocitize() {
181    double jx, jy, jz;
182    int i, vr, vd; // velocity randomizer loop counters
183    double vdrift[3];
143 –  double mtot = 0.0;
184    double vbar;
185    const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
186    double av2;
187    double kebar;
148 –  int ndf; // number of degrees of freedom
149 –  int ndfRaw; // the raw number of degrees of freedom
188    int n_atoms;
189    Atom** atoms;
190    DirectionalAtom* dAtom;
# Line 160 | Line 198 | void Thermo::velocitize() {
198    n_oriented    = entry_plug->n_oriented;
199    n_constraints = entry_plug->n_constraints;
200    
201 <
202 <  ndfRaw = 3 * n_atoms + 3 * n_oriented;
165 <  ndf = ndfRaw - n_constraints - 3;
166 <  kebar = kb * temperature * (double)ndf / ( 2.0 * (double)ndfRaw );
201 >  kebar = kb * temperature * (double)entry_plug->ndf /
202 >    ( 2.0 * (double)entry_plug->ndfRaw );
203    
204    for(vr = 0; vr < n_atoms; vr++){
205      
# Line 171 | Line 207 | void Thermo::velocitize() {
207  
208      av2 = 2.0 * kebar / atoms[vr]->getMass();
209      vbar = sqrt( av2 );
210 <
210 >
211   //     vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() );
212      
213      // picks random velocities from a gaussian distribution
# Line 185 | Line 221 | void Thermo::velocitize() {
221      atoms[vr]->set_vy( vy );
222      atoms[vr]->set_vz( vz );
223    }
224 +
225 +  // Get the Center of Mass drift velocity.
226 +
227 +  getCOMVel(vdrift);
228    
229    //  Corrects for the center of mass drift.
230    // 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 –  
231  
232    for(vd = 0; vd < n_atoms; vd++){
233      
234      vx = atoms[vd]->get_vx();
235      vy = atoms[vd]->get_vy();
236      vz = atoms[vd]->get_vz();
237 <    
216 <    
237 >        
238      vx -= vdrift[0];
239      vy -= vdrift[1];
240      vz -= vdrift[2];
# Line 235 | Line 256 | void Thermo::velocitize() {
256  
257          vbar = sqrt( 2.0 * kebar * dAtom->getIyy() );
258          jy = vbar * gaussStream->getGaussian();
259 <
259 >        
260          vbar = sqrt( 2.0 * kebar * dAtom->getIzz() );
261          jz = vbar * gaussStream->getGaussian();
262          
# Line 246 | Line 267 | void Thermo::velocitize() {
267      }  
268    }
269   }
270 +
271 + void Thermo::getCOMVel(double vdrift[3]){
272 +
273 +  double mtot, mtot_local;
274 +  double vdrift_local[3];
275 +  int vd, n_atoms;
276 +  Atom** atoms;
277 +
278 +  // We are very careless here with the distinction between n_atoms and n_local
279 +  // We should really fix this before someone pokes an eye out.
280 +
281 +  n_atoms = entry_plug->n_atoms;  
282 +  atoms   = entry_plug->atoms;
283 +
284 +  mtot_local = 0.0;
285 +  vdrift_local[0] = 0.0;
286 +  vdrift_local[1] = 0.0;
287 +  vdrift_local[2] = 0.0;
288 +  
289 +  for(vd = 0; vd < n_atoms; vd++){
290 +    
291 +    vdrift_local[0] += atoms[vd]->get_vx() * atoms[vd]->getMass();
292 +    vdrift_local[1] += atoms[vd]->get_vy() * atoms[vd]->getMass();
293 +    vdrift_local[2] += atoms[vd]->get_vz() * atoms[vd]->getMass();
294 +    
295 +    mtot_local += atoms[vd]->getMass();
296 +  }
297 +
298 + #ifdef IS_MPI
299 +  MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
300 +  MPI_Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
301 + #else
302 +  mtot = mtot_local;
303 +  for(vd = 0; vd < 3; vd++) {
304 +    vdrift[vd] = vdrift_local[vd];
305 +  }
306 + #endif
307 +    
308 +  for (vd = 0; vd < 3; vd++) {
309 +    vdrift[vd] = vdrift[vd] / mtot;
310 +  }
311 +  
312 + }
313 +

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