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root/group/trunk/OOPSE/libmdtools/Thermo.cpp
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Comparing:
branches/mmeineke/OOPSE/libmdtools/Thermo.cpp (file contents), Revision 377 by mmeineke, Fri Mar 21 17:42:12 2003 UTC vs.
trunk/OOPSE/libmdtools/Thermo.cpp (file contents), 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
16 + #include "mpiSimulation.hpp"
17 + #endif // is_mpi
18 +
19 +
20   #define BASE_SEED 123456789
21  
22   Thermo::Thermo( SimInfo* the_entry_plug ) {
# Line 66 | 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 77 | Line 84 | double Thermo::getPotential(){
84  
85   double Thermo::getPotential(){
86    
87 +  double potential_local;
88    double potential;
81 –  double potential_global;
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_global = 0.0;
90 <  potential += entry_plug->lrPot;
97 >  potential_local += entry_plug->lrPot;
98  
99 <  for( el=0; el<nSRI; el++ ){
100 <    
94 <    potential += 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,&potential_global,1,MPI_DOUBLE,MPI_SUM);
106 <  potential = potential_global;
107 <
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 117 | Line 130 | double Thermo::getTemperature(){
130    const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K)
131    double temperature;
132    
133 <  int ndf = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented
121 <    - entry_plug->n_constraints - 3;
122 <
123 <  temperature = ( 2.0 * this->getKinetic() ) / ( ndf * kb );
133 >  temperature = ( 2.0 * this->getKinetic() ) / ((double)entry_plug->ndf * kb );
134    return temperature;
135   }
136  
137 < double Thermo::getPressure(){
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 >  const double p_convert = 1.63882576e8;
142 >  double press[9];
143 >  double pressure;
144  
145 < //  const double conv_Pa_atm = 9.901E-6; // convert Pa -> atm
130 < // const double conv_internal_Pa = 1.661E-7; //convert amu/(fs^2 A) -> Pa
131 < //  const double conv_A_m = 1.0E-10; //convert A -> m
145 >  this->getPressureTensor(press);
146  
147 <  return 0.0;
147 >  pressure = p_convert * (press[0] + press[4] + press[8]) / 3.0;
148 >
149 >  return pressure;
150   }
151  
152 +
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 +  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() {
212    
213    double x,y;
# Line 140 | Line 215 | void Thermo::velocitize() {
215    double jx, jy, jz;
216    int i, vr, vd; // velocity randomizer loop counters
217    double vdrift[3];
143 –  double mtot = 0.0;
218    double vbar;
219    const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
220    double av2;
221    double kebar;
148 –  int ndf; // number of degrees of freedom
149 –  int ndfRaw; // the raw number of degrees of freedom
222    int n_atoms;
223    Atom** atoms;
224    DirectionalAtom* dAtom;
# Line 160 | 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;
165 <  ndf = ndfRaw - n_constraints - 3;
166 <  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 171 | 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 185 | Line 255 | void Thermo::velocitize() {
255      atoms[vr]->set_vy( vy );
256      atoms[vr]->set_vz( vz );
257    }
258 +
259 +  // Get the Center of Mass drift velocity.
260 +
261 +  getCOMVel(vdrift);
262    
263    //  Corrects for the center of mass drift.
264    // sums all the momentum and divides by total mass.
191 –  
192 –  mtot = 0.0;
193 –  vdrift[0] = 0.0;
194 –  vdrift[1] = 0.0;
195 –  vdrift[2] = 0.0;
196 –  for(vd = 0; vd < n_atoms; vd++){
197 –    
198 –    vdrift[0] += atoms[vd]->get_vx() * atoms[vd]->getMass();
199 –    vdrift[1] += atoms[vd]->get_vy() * atoms[vd]->getMass();
200 –    vdrift[2] += atoms[vd]->get_vz() * atoms[vd]->getMass();
201 –    
202 –    mtot += atoms[vd]->getMass();
203 –  }
204 –  
205 –  for (vd = 0; vd < 3; vd++) {
206 –    vdrift[vd] = vdrift[vd] / mtot;
207 –  }
208 –  
265  
266    for(vd = 0; vd < n_atoms; vd++){
267      
268      vx = atoms[vd]->get_vx();
269      vy = atoms[vd]->get_vy();
270      vz = atoms[vd]->get_vz();
271 <    
216 <    
271 >        
272      vx -= vdrift[0];
273      vy -= vdrift[1];
274      vz -= vdrift[2];
# Line 235 | 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 246 | Line 301 | void Thermo::velocitize() {
301      }  
302    }
303   }
304 +
305 + void Thermo::getCOMVel(double vdrift[3]){
306 +
307 +  double mtot, mtot_local;
308 +  double vdrift_local[3];
309 +  int vd, n_atoms;
310 +  Atom** atoms;
311 +
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 +
315 +  n_atoms = entry_plug->n_atoms;  
316 +  atoms   = entry_plug->atoms;
317 +
318 +  mtot_local = 0.0;
319 +  vdrift_local[0] = 0.0;
320 +  vdrift_local[1] = 0.0;
321 +  vdrift_local[2] = 0.0;
322 +  
323 +  for(vd = 0; vd < n_atoms; vd++){
324 +    
325 +    vdrift_local[0] += atoms[vd]->get_vx() * atoms[vd]->getMass();
326 +    vdrift_local[1] += atoms[vd]->get_vy() * atoms[vd]->getMass();
327 +    vdrift_local[2] += atoms[vd]->get_vz() * atoms[vd]->getMass();
328 +    
329 +    mtot_local += atoms[vd]->getMass();
330 +  }
331 +
332 + #ifdef IS_MPI
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++) {
338 +    vdrift[vd] = vdrift_local[vd];
339 +  }
340 + #endif
341 +    
342 +  for (vd = 0; vd < 3; vd++) {
343 +    vdrift[vd] = vdrift[vd] / mtot;
344 +  }
345 +  
346 + }
347 +

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