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root/group/branches/no-template-branch/OOPSE/libmdtools/Thermo.cpp
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Comparing trunk/OOPSE/libmdtools/Thermo.cpp (file contents):
Revision 444 by gezelter, Thu Apr 3 13:43:02 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"
# Line 73 | 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 100 | Line 100 | double Thermo::getPotential(){
100      potential_local += molecules[el].getPotential();
101    }
102  
103 – #ifdef IS_MPI
104 –  /*
105 –  std::cerr << "node " << worldRank << ": before LONG RANGE pot = " << entry_plug->lrPot
106 –            << "; pot_local = " << potential_local
107 –            << "; pot = " << potential << "\n";
108 –  */
109 – #endif
110 –
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
# Line 136 | Line 129 | double Thermo::getTemperature(){
129  
130    const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K)
131    double temperature;
139 –  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
147 <  ndf = ndf_local;
148 < #endif
149 <
150 <  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  
156 – 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 173 | Line 219 | void Thermo::velocitize() {
219    const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
220    double av2;
221    double kebar;
176 –  int ndf, ndf_local; // number of degrees of freedom
177 –  int ndfRaw, ndfRaw_local; // the raw number of degrees of freedom
222    int n_atoms;
223    Atom** atoms;
224    DirectionalAtom* dAtom;
# Line 188 | Line 232 | void Thermo::velocitize() {
232    n_oriented    = entry_plug->n_oriented;
233    n_constraints = entry_plug->n_constraints;
234    
235 <  // Raw degrees of freedom that we have to set
236 <  ndfRaw_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented;
193 <
194 <  // Degrees of freedom that can contain kinetic energy
195 <  ndf_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented
196 <    - entry_plug->n_constraints;
235 >  kebar = kb * temperature * (double)entry_plug->ndf /
236 >    ( 2.0 * (double)entry_plug->ndfRaw );
237    
198 – #ifdef IS_MPI
199 –  MPI::COMM_WORLD.Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM);
200 –  MPI::COMM_WORLD.Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM);
201 – #else
202 –  ndfRaw = ndfRaw_local;
203 –  ndf = ndf_local;
204 – #endif
205 –  ndf = ndf - 3;
206 –
207 –  kebar = kb * temperature * (double)ndf / ( 2.0 * (double)ndfRaw );
208 –  
238    for(vr = 0; vr < n_atoms; vr++){
239      
240      // uses equipartition theory to solve for vbar in angstrom/fs
# Line 261 | 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 301 | Line 330 | void Thermo::getCOMVel(double vdrift[3]){
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++) {

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