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root/group/trunk/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 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"
# 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
145 <  MPI::COMM_WORLD.Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM);
146 < #else
147 <  ndf = ndf_local;
148 < #endif
137 > double Thermo::getEnthalpy() {
138  
139 <  ndf = ndf - 3;
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 >  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 <  temperature = ( 2.0 * this->getKinetic() ) / ( ndf * kb );
165 <  return temperature;
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  
156 – double Thermo::getPressure(){
175  
176 < //  const double conv_Pa_atm = 9.901E-6; // convert Pa -> atm
177 < // const double conv_internal_Pa = 1.661E-7; //convert amu/(fs^2 A) -> Pa
178 < //  const double conv_A_m = 1.0E-10; //convert A -> m
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 <  return 0.0;
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 173 | Line 242 | void Thermo::velocitize() {
242    const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
243    double av2;
244    double kebar;
176 –  int ndf, ndf_local; // number of degrees of freedom
177 –  int ndfRaw, ndfRaw_local; // the raw number of degrees of freedom
245    int n_atoms;
246    Atom** atoms;
247    DirectionalAtom* dAtom;
# Line 188 | Line 255 | void Thermo::velocitize() {
255    n_oriented    = entry_plug->n_oriented;
256    n_constraints = entry_plug->n_constraints;
257    
258 <  // Raw degrees of freedom that we have to set
259 <  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;
258 >  kebar = kb * temperature * (double)entry_plug->ndf /
259 >    ( 2.0 * (double)entry_plug->ndfRaw );
260    
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 –  
261    for(vr = 0; vr < n_atoms; vr++){
262      
263      // uses equipartition theory to solve for vbar in angstrom/fs
# Line 261 | 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 301 | Line 353 | void Thermo::getCOMVel(double vdrift[3]){
353    }
354  
355   #ifdef IS_MPI
356 <  MPI::COMM_WORLD.Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM);
357 <  MPI::COMM_WORLD.Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM);
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++) {

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