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root/group/trunk/OOPSE/libmdtools/Thermo.cpp
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Comparing trunk/OOPSE/libmdtools/Thermo.cpp (file contents):
Revision 445 by gezelter, Thu Apr 3 19:58:24 2003 UTC vs.
Revision 590 by mmeineke, Thu Jul 10 22:15:53 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[3][3];
142 >
143 >  u = this->getTotalE();
144 >
145 >  this->getPressureTensor(press);
146 >  p = (press[0][0] + press[1][1] + press[2][2]) / 3.0;
147 >
148 >  v = this->getVolume();
149 >
150 >  return (u + (p*v)/e_convert);
151 > }
152 >
153 > double Thermo::getVolume() {
154 >
155 >  return entry_plug->boxVol;
156 > }
157 >
158 > double Thermo::getPressure() {
159 >
160 >  // Relies on the calculation of the full molecular pressure tensor
161    
162 <  temperature = ( 2.0 * this->getKinetic() ) / ( ndf * kb );
163 <  return temperature;
162 >  const double p_convert = 1.63882576e8;
163 >  double press[3][3];
164 >  double pressure;
165 >
166 >  this->getPressureTensor(press);
167 >
168 >  pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
169 >
170 >  return pressure;
171   }
172  
173 < double Thermo::getPressure(){
174 <  // returns pressure in units amu*fs^-2*Ang^-1
173 >
174 > void Thermo::getPressureTensor(double press[3][3]){
175 >  // returns pressure tensor in units amu*fs^-2*Ang^-1
176    // routine derived via viral theorem description in:
177    // Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
178  
179 <  return 0.0;
179 >  const double e_convert = 4.184e-4;
180 >
181 >  double molmass, volume;
182 >  double vcom[3];
183 >  double p_local[9], p_global[9];
184 >  int i, j, k, l, nMols;
185 >  Molecule* molecules;
186 >
187 >  nMols = entry_plug->n_mol;
188 >  molecules = entry_plug->molecules;
189 >  //tau = entry_plug->tau;
190 >
191 >  // use velocities of molecular centers of mass and molecular masses:
192 >  for (i=0; i < 9; i++) {    
193 >    p_local[i] = 0.0;
194 >    p_global[i] = 0.0;
195 >  }
196 >
197 >  for (i=0; i < nMols; i++) {
198 >    molmass = molecules[i].getCOMvel(vcom);
199 >
200 >    p_local[0] += molmass * (vcom[0] * vcom[0]);
201 >    p_local[1] += molmass * (vcom[0] * vcom[1]);
202 >    p_local[2] += molmass * (vcom[0] * vcom[2]);
203 >    p_local[3] += molmass * (vcom[1] * vcom[0]);
204 >    p_local[4] += molmass * (vcom[1] * vcom[1]);
205 >    p_local[5] += molmass * (vcom[1] * vcom[2]);
206 >    p_local[6] += molmass * (vcom[2] * vcom[0]);
207 >    p_local[7] += molmass * (vcom[2] * vcom[1]);
208 >    p_local[8] += molmass * (vcom[2] * vcom[2]);
209 >  }
210 >
211 >  // Get total for entire system from MPI.
212 >
213 > #ifdef IS_MPI
214 >  MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
215 > #else
216 >  for (i=0; i<9; i++) {
217 >    p_global[i] = p_local[i];
218 >  }
219 > #endif // is_mpi
220 >
221 >  volume = entry_plug->boxVol;
222 >
223 >  for(i = 0; i < 3; i++) {
224 >    for (j = 0; j < 3; j++) {
225 >      k = 3*i + j;
226 >      l = 3*j + i;
227 >      press[i][j] = (p_global[k] - entry_plug->tau[l]*e_convert) / volume;
228 >    }
229 >  }
230   }
231  
232   void Thermo::velocitize() {
# Line 172 | Line 240 | void Thermo::velocitize() {
240    const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
241    double av2;
242    double kebar;
175 –  int ndf, ndf_local; // number of degrees of freedom
176 –  int ndfRaw, ndfRaw_local; // the raw number of degrees of freedom
243    int n_atoms;
244    Atom** atoms;
245    DirectionalAtom* dAtom;
# Line 187 | Line 253 | void Thermo::velocitize() {
253    n_oriented    = entry_plug->n_oriented;
254    n_constraints = entry_plug->n_constraints;
255    
256 <  // Raw degrees of freedom that we have to set
257 <  ndfRaw_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented;
192 <
193 <  // Degrees of freedom that can contain kinetic energy
194 <  ndf_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented
195 <    - entry_plug->n_constraints;
256 >  kebar = kb * temperature * (double)entry_plug->ndf /
257 >    ( 2.0 * (double)entry_plug->ndfRaw );
258    
197 – #ifdef IS_MPI
198 –  MPI::COMM_WORLD.Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM);
199 –  MPI::COMM_WORLD.Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM);
200 – #else
201 –  ndfRaw = ndfRaw_local;
202 –  ndf = ndf_local;
203 – #endif
204 –  ndf = ndf - 3;
205 –
206 –  kebar = kb * temperature * (double)ndf / ( 2.0 * (double)ndfRaw );
207 –  
259    for(vr = 0; vr < n_atoms; vr++){
260      
261      // uses equipartition theory to solve for vbar in angstrom/fs
# Line 260 | Line 311 | void Thermo::velocitize() {
311  
312          vbar = sqrt( 2.0 * kebar * dAtom->getIyy() );
313          jy = vbar * gaussStream->getGaussian();
314 <
314 >        
315          vbar = sqrt( 2.0 * kebar * dAtom->getIzz() );
316          jz = vbar * gaussStream->getGaussian();
317          
# Line 300 | Line 351 | void Thermo::getCOMVel(double vdrift[3]){
351    }
352  
353   #ifdef IS_MPI
354 <  MPI::COMM_WORLD.Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM);
355 <  MPI::COMM_WORLD.Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM);
354 >  MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
355 >  MPI_Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
356   #else
357    mtot = mtot_local;
358    for(vd = 0; vd < 3; vd++) {

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