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root/group/trunk/OOPSE/libmdtools/Thermo.cpp
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Comparing trunk/OOPSE/libmdtools/Thermo.cpp (file contents):
Revision 402 by mmeineke, Wed Mar 26 14:55:50 2003 UTC vs.
Revision 483 by gezelter, Wed Apr 9 04:06:43 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
# Line 72 | 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 86 | Line 87 | double Thermo::getPotential(){
87    double potential_local;
88    double potential;
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_local += entry_plug->lrPot;
98  
99 <  for( el=0; el<nSRI; el++ ){    
100 <    potential_local += 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_local,&potential,1,MPI_DOUBLE,MPI_SUM);
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 120 | Line 129 | double Thermo::getTemperature(){
129  
130    const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K)
131    double temperature;
123 –  int ndf_local, ndf;
132    
133 <  ndf_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented
134 <    - entry_plug->n_constraints;
133 >  temperature = ( 2.0 * this->getKinetic() ) / ((double)entry_plug->ndf * kb );
134 >  return temperature;
135 > }
136  
137 < #ifdef IS_MPI
138 <  MPI::COMM_WORLD.Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM);
139 < #else
131 <  ndf = ndf_local;
132 < #endif
133 <
134 <  ndf = ndf - 3;
137 > double Thermo::getPressure() {
138 >  // returns the pressure in units of atm
139 >  // Relies on the calculation of the full molecular pressure tensor
140    
141 <  temperature = ( 2.0 * this->getKinetic() ) / ( ndf * kb );
142 <  return temperature;
141 >  const double p_convert = 1.63882576e8;
142 >  double press[9];
143 >  double pressure;
144 >
145 >  this->getPressureTensor(press);
146 >
147 >  pressure = p_convert * (press[0] + press[4] + press[8]) / 3.0;
148 >
149 >  return pressure;
150   }
151  
140 – double Thermo::getPressure(){
152  
153 < //  const double conv_Pa_atm = 9.901E-6; // convert Pa -> atm
154 < // const double conv_internal_Pa = 1.661E-7; //convert amu/(fs^2 A) -> Pa
155 < //  const double conv_A_m = 1.0E-10; //convert A -> m
153 > void Thermo::getPressureTensor(double press[9]){
154 >  // returns pressure tensor in units amu*fs^-2*Ang^-1
155 >  // routine derived via viral theorem description in:
156 >  // Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
157  
158 <  return 0.0;
158 >  const double e_convert = 4.184e-4;
159 >
160 >  double molmass, volume;
161 >  double vcom[3];
162 >  double p_local[9], p_global[9];
163 >  double theBox[3];
164 >  double* tau;
165 >  int i, nMols;
166 >  Molecule* molecules;
167 >
168 >  nMols = entry_plug->n_mol;
169 >  molecules = entry_plug->molecules;
170 >  tau = entry_plug->tau;
171 >
172 >  // use velocities of molecular centers of mass and molecular masses:
173 >  for (i=0; i < 9; i++) {    
174 >    p_local[i] = 0.0;
175 >    p_global[i] = 0.0;
176 >  }
177 >
178 >  for (i=0; i < nMols; i++) {
179 >    molmass = molecules[i].getCOMvel(vcom);
180 >
181 >    p_local[0] += molmass * (vcom[0] * vcom[0]);
182 >    p_local[1] += molmass * (vcom[0] * vcom[1]);
183 >    p_local[2] += molmass * (vcom[0] * vcom[2]);
184 >    p_local[3] += molmass * (vcom[1] * vcom[0]);
185 >    p_local[4] += molmass * (vcom[1] * vcom[1]);
186 >    p_local[5] += molmass * (vcom[1] * vcom[2]);
187 >    p_local[6] += molmass * (vcom[2] * vcom[0]);
188 >    p_local[7] += molmass * (vcom[2] * vcom[1]);
189 >    p_local[8] += molmass * (vcom[2] * vcom[2]);
190 >  }
191 >
192 >  // Get total for entire system from MPI.
193 >
194 > #ifdef IS_MPI
195 >  MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
196 > #else
197 >  for (i=0; i<9; i++) {
198 >    p_global[i] = p_local[i];
199 >  }
200 > #endif // is_mpi
201 >
202 >  entry_plug->getBox(theBox);
203 >
204 >  volume = theBox[0] * theBox[1] * theBox[2];
205 >
206 >  for(i=0; i<9; i++) {
207 >    press[i] = (p_global[i] - tau[i]*e_convert) / volume;
208 >  }
209   }
210  
211   void Thermo::velocitize() {
# Line 152 | Line 214 | void Thermo::velocitize() {
214    double vx, vy, vz;
215    double jx, jy, jz;
216    int i, vr, vd; // velocity randomizer loop counters
217 <  double *vdrift;
217 >  double vdrift[3];
218    double vbar;
219    const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
220    double av2;
221    double kebar;
160 –  int ndf; // number of degrees of freedom
161 –  int ndfRaw; // the raw number of degrees of freedom
222    int n_atoms;
223    Atom** atoms;
224    DirectionalAtom* dAtom;
# Line 172 | Line 232 | void Thermo::velocitize() {
232    n_oriented    = entry_plug->n_oriented;
233    n_constraints = entry_plug->n_constraints;
234    
235 <
236 <  ndfRaw = 3 * n_atoms + 3 * n_oriented;
177 <  ndf = ndfRaw - n_constraints - 3;
178 <  kebar = kb * temperature * (double)ndf / ( 2.0 * (double)ndfRaw );
235 >  kebar = kb * temperature * (double)entry_plug->ndf /
236 >    ( 2.0 * (double)entry_plug->ndfRaw );
237    
238    for(vr = 0; vr < n_atoms; vr++){
239      
# Line 183 | Line 241 | void Thermo::velocitize() {
241  
242      av2 = 2.0 * kebar / atoms[vr]->getMass();
243      vbar = sqrt( av2 );
244 <
244 >
245   //     vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() );
246      
247      // picks random velocities from a gaussian distribution
# Line 200 | Line 258 | void Thermo::velocitize() {
258  
259    // Get the Center of Mass drift velocity.
260  
261 <  vdrift = getCOMVel();
261 >  getCOMVel(vdrift);
262    
263    //  Corrects for the center of mass drift.
264    // sums all the momentum and divides by total mass.
# Line 232 | Line 290 | void Thermo::velocitize() {
290  
291          vbar = sqrt( 2.0 * kebar * dAtom->getIyy() );
292          jy = vbar * gaussStream->getGaussian();
293 <
293 >        
294          vbar = sqrt( 2.0 * kebar * dAtom->getIzz() );
295          jz = vbar * gaussStream->getGaussian();
296          
# Line 244 | Line 302 | double* Thermo::getCOMVel(){
302    }
303   }
304  
305 < double* Thermo::getCOMVel(){
305 > void Thermo::getCOMVel(double vdrift[3]){
306  
307    double mtot, mtot_local;
250 –  double* vdrift;
308    double vdrift_local[3];
309    int vd, n_atoms;
310    Atom** atoms;
311  
255 –  vdrift = new double[3];
312    // We are very careless here with the distinction between n_atoms and n_local
313    // We should really fix this before someone pokes an eye out.
314  
# Line 274 | Line 330 | double* Thermo::getCOMVel(){
330    }
331  
332   #ifdef IS_MPI
333 <  MPI::COMM_WORLD.Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM);
334 <  MPI::COMM_WORLD.Allreduce(&vdrift_local,&vdrift,3,MPI_DOUBLE,MPI_SUM);
333 >  MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
334 >  MPI_Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
335   #else
336    mtot = mtot_local;
337    for(vd = 0; vd < 3; vd++) {
# Line 287 | Line 343 | double* Thermo::getCOMVel(){
343      vdrift[vd] = vdrift[vd] / mtot;
344    }
345    
290 –  return vdrift;
346   }
347  

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