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root/group/trunk/OOPSE/libmdtools/Thermo.cpp
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Comparing trunk/OOPSE/libmdtools/Thermo.cpp (file contents):
Revision 403 by chuckv, Wed Mar 26 15:37:05 2003 UTC vs.
Revision 574 by gezelter, Tue Jul 8 20:56:10 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
129 <  MPI::COMM_WORLD.Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM);
130 < #else
131 <  ndf = ndf_local;
132 < #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 >
155 >  double volume;
156 >  double Hmat[9];
157 >
158 >  entry_plug->getBoxM(Hmat);
159 >
160 >  // volume = h1 (dot) h2 (cross) h3
161 >
162 >  volume = Hmat[0] * ( (Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]) )
163 >         + Hmat[1] * ( (Hmat[5]*Hmat[6]) - (Hmat[8]*Hmat[3]) )
164 >         + Hmat[2] * ( (Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]) );
165 >
166 >  return volume;
167 > }
168 >
169 > double Thermo::getPressure() {
170 >
171 >  // Relies on the calculation of the full molecular pressure tensor
172    
173 <  temperature = ( 2.0 * this->getKinetic() ) / ( ndf * kb );
174 <  return temperature;
173 >  const double p_convert = 1.63882576e8;
174 >  double press[9];
175 >  double pressure;
176 >
177 >  this->getPressureTensor(press);
178 >
179 >  pressure = p_convert * (press[0] + press[4] + press[8]) / 3.0;
180 >
181 >  return pressure;
182   }
183  
140 – double Thermo::getPressure(){
184  
185 < //  const double conv_Pa_atm = 9.901E-6; // convert Pa -> atm
186 < // const double conv_internal_Pa = 1.661E-7; //convert amu/(fs^2 A) -> Pa
187 < //  const double conv_A_m = 1.0E-10; //convert A -> m
185 > void Thermo::getPressureTensor(double press[9]){
186 >  // returns pressure tensor in units amu*fs^-2*Ang^-1
187 >  // routine derived via viral theorem description in:
188 >  // Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
189  
190 <  return 0.0;
190 >  const double e_convert = 4.184e-4;
191 >
192 >  double molmass, volume;
193 >  double vcom[3];
194 >  double p_local[9], p_global[9];
195 >  double theBox[3];
196 >  //double* tau;
197 >  int i, nMols;
198 >  Molecule* molecules;
199 >
200 >  nMols = entry_plug->n_mol;
201 >  molecules = entry_plug->molecules;
202 >  //tau = entry_plug->tau;
203 >
204 >  // use velocities of molecular centers of mass and molecular masses:
205 >  for (i=0; i < 9; i++) {    
206 >    p_local[i] = 0.0;
207 >    p_global[i] = 0.0;
208 >  }
209 >
210 >  for (i=0; i < nMols; i++) {
211 >    molmass = molecules[i].getCOMvel(vcom);
212 >
213 >    p_local[0] += molmass * (vcom[0] * vcom[0]);
214 >    p_local[1] += molmass * (vcom[0] * vcom[1]);
215 >    p_local[2] += molmass * (vcom[0] * vcom[2]);
216 >    p_local[3] += molmass * (vcom[1] * vcom[0]);
217 >    p_local[4] += molmass * (vcom[1] * vcom[1]);
218 >    p_local[5] += molmass * (vcom[1] * vcom[2]);
219 >    p_local[6] += molmass * (vcom[2] * vcom[0]);
220 >    p_local[7] += molmass * (vcom[2] * vcom[1]);
221 >    p_local[8] += molmass * (vcom[2] * vcom[2]);
222 >  }
223 >
224 >  // Get total for entire system from MPI.
225 >
226 > #ifdef IS_MPI
227 >  MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
228 > #else
229 >  for (i=0; i<9; i++) {
230 >    p_global[i] = p_local[i];
231 >  }
232 > #endif // is_mpi
233 >
234 >  volume = entry_plug->boxVol;
235 >
236 >  for(i=0; i<9; i++) {
237 >    press[i] = (p_global[i] - entry_plug->tau[i]*e_convert) / volume;
238 >  }
239   }
240  
241   void Thermo::velocitize() {
# Line 157 | Line 249 | void Thermo::velocitize() {
249    const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
250    double av2;
251    double kebar;
160 –  int ndf, ndf_local; // number of degrees of freedom
161 –  int ndfRaw, ndfRaw_local; // the raw number of degrees of freedom
252    int n_atoms;
253    Atom** atoms;
254    DirectionalAtom* dAtom;
# Line 172 | Line 262 | void Thermo::velocitize() {
262    n_oriented    = entry_plug->n_oriented;
263    n_constraints = entry_plug->n_constraints;
264    
265 <  // Raw degrees of freedom that we have to set
266 <  ndfRaw_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented;
177 <
178 <  // Degrees of freedom that can contain kinetic energy
179 <  ndf_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented
180 <    - entry_plug->n_constraints;
265 >  kebar = kb * temperature * (double)entry_plug->ndf /
266 >    ( 2.0 * (double)entry_plug->ndfRaw );
267    
182 – #ifdef IS_MPI
183 –  MPI::COMM_WORLD.Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM);
184 –  MPI::COMM_WORLD.Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM);
185 – #else
186 –  ndfRaw = ndfRaw_local;
187 –  ndf = ndf_local;
188 – #endif
189 –  ndf = ndf - 3;
190 –
191 –  kebar = kb * temperature * (double)ndf / ( 2.0 * (double)ndfRaw );
192 –  
268    for(vr = 0; vr < n_atoms; vr++){
269      
270      // uses equipartition theory to solve for vbar in angstrom/fs
271  
272      av2 = 2.0 * kebar / atoms[vr]->getMass();
273      vbar = sqrt( av2 );
274 <
274 >
275   //     vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() );
276      
277      // picks random velocities from a gaussian distribution
# Line 245 | Line 320 | void Thermo::velocitize() {
320  
321          vbar = sqrt( 2.0 * kebar * dAtom->getIyy() );
322          jy = vbar * gaussStream->getGaussian();
323 <
323 >        
324          vbar = sqrt( 2.0 * kebar * dAtom->getIzz() );
325          jz = vbar * gaussStream->getGaussian();
326          
# Line 285 | Line 360 | void Thermo::getCOMVel(double vdrift[3]){
360    }
361  
362   #ifdef IS_MPI
363 <  MPI::COMM_WORLD.Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM);
364 <  MPI::COMM_WORLD.Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM);
363 >  MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
364 >  MPI_Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
365   #else
366    mtot = mtot_local;
367    for(vd = 0; vd < 3; vd++) {

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