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Comparing trunk/OOPSE/libmdtools/Thermo.cpp (file contents):
Revision 378 by mmeineke, Fri Mar 21 17:42:12 2003 UTC vs.
Revision 708 by tim, Wed Aug 20 22:23:34 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 < #define BASE_SEED 123456789
14 > #ifdef IS_MPI
15 > #define __C
16 > #include "mpiSimulation.hpp"
17 > #endif // is_mpi
18  
19 < Thermo::Thermo( SimInfo* the_entry_plug ) {
20 <  entry_plug = the_entry_plug;
21 <  int baseSeed = BASE_SEED;
19 > Thermo::Thermo( SimInfo* the_info ) {
20 >  info = the_info;
21 >  int baseSeed = the_info->getSeed();
22    
23    gaussStream = new gaussianSPRNG( baseSeed );
24   }
# Line 27 | Line 30 | double Thermo::getKinetic(){
30   double Thermo::getKinetic(){
31  
32    const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2
33 <  double vx2, vy2, vz2;
34 <  double kinetic, v_sqr;
35 <  int kl;
36 <  double jx2, jy2, jz2; // the square of the angular momentums
33 >  double kinetic;
34 >  double amass;
35 >  double aVel[3], aJ[3], I[3][3];
36 >  int j, kl;
37  
38    DirectionalAtom *dAtom;
39  
# Line 39 | Line 42 | double Thermo::getKinetic(){
42    Atom** atoms;
43  
44    
45 <  n_atoms = entry_plug->n_atoms;
46 <  atoms = entry_plug->atoms;
45 >  n_atoms = info->n_atoms;
46 >  atoms = info->atoms;
47  
48    kinetic = 0.0;
49    kinetic_global = 0.0;
50    for( kl=0; kl < n_atoms; kl++ ){
51 +    
52 +    atoms[kl]->getVel(aVel);
53 +    amass = atoms[kl]->getMass();
54 +    
55 +    for (j=0; j < 3; j++)
56 +      kinetic += amass * aVel[j] * aVel[j];
57  
49 –    vx2 = atoms[kl]->get_vx() * atoms[kl]->get_vx();
50 –    vy2 = atoms[kl]->get_vy() * atoms[kl]->get_vy();
51 –    vz2 = atoms[kl]->get_vz() * atoms[kl]->get_vz();
52 –
53 –    v_sqr = vx2 + vy2 + vz2;
54 –    kinetic += atoms[kl]->getMass() * v_sqr;
55 –
58      if( atoms[kl]->isDirectional() ){
59              
60        dAtom = (DirectionalAtom *)atoms[kl];
61 +
62 +      dAtom->getJ( aJ );
63 +      dAtom->getI( I );
64        
65 <      jx2 = dAtom->getJx() * dAtom->getJx();    
66 <      jy2 = dAtom->getJy() * dAtom->getJy();
62 <      jz2 = dAtom->getJz() * dAtom->getJz();
65 >      for (j=0; j<3; j++)
66 >        kinetic += aJ[j]*aJ[j] / I[j][j];
67        
64 –      kinetic += (jx2 / dAtom->getIxx()) + (jy2 / dAtom->getIyy())
65 –        + (jz2 / dAtom->getIzz());
68      }
69    }
70   #ifdef IS_MPI
71 <  MPI::COMM_WORLD.Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,MPI_SUM);
71 >  MPI_Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,
72 >                MPI_SUM, MPI_COMM_WORLD);
73    kinetic = kinetic_global;
74   #endif //is_mpi
75  
# Line 77 | Line 80 | double Thermo::getPotential(){
80  
81   double Thermo::getPotential(){
82    
83 +  double potential_local;
84    double potential;
81 –  double potential_global;
85    int el, nSRI;
86 <  SRI** sris;
86 >  Molecule* molecules;
87  
88 <  sris = entry_plug->sr_interactions;
89 <  nSRI = entry_plug->n_SRI;
88 >  molecules = info->molecules;
89 >  nSRI = info->n_SRI;
90  
91 +  potential_local = 0.0;
92    potential = 0.0;
93 <  potential_global = 0.0;
90 <  potential += entry_plug->lrPot;
93 >  potential_local += info->lrPot;
94  
95 <  for( el=0; el<nSRI; el++ ){
96 <    
94 <    potential += sris[el]->get_potential();
95 >  for( el=0; el<info->n_mol; el++ ){    
96 >    potential_local += molecules[el].getPotential();
97    }
98  
99    // Get total potential for entire system from MPI.
100   #ifdef IS_MPI
101 <  MPI::COMM_WORLD.Allreduce(&potential,&potential_global,1,MPI_DOUBLE,MPI_SUM);
102 <  potential = potential_global;
103 <
101 >  MPI_Allreduce(&potential_local,&potential,1,MPI_DOUBLE,
102 >                MPI_SUM, MPI_COMM_WORLD);
103 > #else
104 >  potential = potential_local;
105   #endif // is_mpi
106  
107 + #ifdef IS_MPI
108 +  /*
109 +  std::cerr << "node " << worldRank << ": after pot = " << potential << "\n";
110 +  */
111 + #endif
112 +
113    return potential;
114   }
115  
# Line 117 | Line 126 | double Thermo::getTemperature(){
126    const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K)
127    double temperature;
128    
129 <  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 );
129 >  temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb );
130    return temperature;
131   }
132  
133 < double Thermo::getPressure(){
133 > double Thermo::getEnthalpy() {
134  
135 < //  const double conv_Pa_atm = 9.901E-6; // convert Pa -> atm
136 < // const double conv_internal_Pa = 1.661E-7; //convert amu/(fs^2 A) -> Pa
137 < //  const double conv_A_m = 1.0E-10; //convert A -> m
135 >  const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2
136 >  double u, p, v;
137 >  double press[3][3];
138  
139 <  return 0.0;
139 >  u = this->getTotalE();
140 >
141 >  this->getPressureTensor(press);
142 >  p = (press[0][0] + press[1][1] + press[2][2]) / 3.0;
143 >
144 >  v = this->getVolume();
145 >
146 >  return (u + (p*v)/e_convert);
147   }
148  
149 + double Thermo::getVolume() {
150 +
151 +  return info->boxVol;
152 + }
153 +
154 + double Thermo::getPressure() {
155 +
156 +  // Relies on the calculation of the full molecular pressure tensor
157 +  
158 +  const double p_convert = 1.63882576e8;
159 +  double press[3][3];
160 +  double pressure;
161 +
162 +  this->getPressureTensor(press);
163 +
164 +  pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
165 +
166 +  return pressure;
167 + }
168 +
169 +
170 + void Thermo::getPressureTensor(double press[3][3]){
171 +  // returns pressure tensor in units amu*fs^-2*Ang^-1
172 +  // routine derived via viral theorem description in:
173 +  // Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
174 +
175 +  const double e_convert = 4.184e-4;
176 +
177 +  double molmass, volume;
178 +  double vcom[3];
179 +  double p_local[9], p_global[9];
180 +  int i, j, k, nMols;
181 +  Molecule* molecules;
182 +
183 +  nMols = info->n_mol;
184 +  molecules = info->molecules;
185 +  //tau = info->tau;
186 +
187 +  // use velocities of molecular centers of mass and molecular masses:
188 +  for (i=0; i < 9; i++) {    
189 +    p_local[i] = 0.0;
190 +    p_global[i] = 0.0;
191 +  }
192 +
193 +  for (i=0; i < nMols; i++) {
194 +    molmass = molecules[i].getCOMvel(vcom);
195 +
196 +    p_local[0] += molmass * (vcom[0] * vcom[0]);
197 +    p_local[1] += molmass * (vcom[0] * vcom[1]);
198 +    p_local[2] += molmass * (vcom[0] * vcom[2]);
199 +    p_local[3] += molmass * (vcom[1] * vcom[0]);
200 +    p_local[4] += molmass * (vcom[1] * vcom[1]);
201 +    p_local[5] += molmass * (vcom[1] * vcom[2]);
202 +    p_local[6] += molmass * (vcom[2] * vcom[0]);
203 +    p_local[7] += molmass * (vcom[2] * vcom[1]);
204 +    p_local[8] += molmass * (vcom[2] * vcom[2]);
205 +  }
206 +
207 +  // Get total for entire system from MPI.
208 +
209 + #ifdef IS_MPI
210 +  MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
211 + #else
212 +  for (i=0; i<9; i++) {
213 +    p_global[i] = p_local[i];
214 +  }
215 + #endif // is_mpi
216 +
217 +  volume = this->getVolume();
218 +
219 +  for(i = 0; i < 3; i++) {
220 +    for (j = 0; j < 3; j++) {
221 +      k = 3*i + j;
222 +      press[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume;
223 +
224 +    }
225 +  }
226 + }
227 +
228   void Thermo::velocitize() {
229    
230    double x,y;
231 <  double vx, vy, vz;
232 <  double jx, jy, jz;
141 <  int i, vr, vd; // velocity randomizer loop counters
231 >  double aVel[3], aJ[3], I[3][3];
232 >  int i, j, vr, vd; // velocity randomizer loop counters
233    double vdrift[3];
143 –  double mtot = 0.0;
234    double vbar;
235    const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
236    double av2;
237    double kebar;
148 –  int ndf; // number of degrees of freedom
149 –  int ndfRaw; // the raw number of degrees of freedom
238    int n_atoms;
239    Atom** atoms;
240    DirectionalAtom* dAtom;
# Line 154 | Line 242 | void Thermo::velocitize() {
242    int n_oriented;
243    int n_constraints;
244  
245 <  atoms         = entry_plug->atoms;
246 <  n_atoms       = entry_plug->n_atoms;
247 <  temperature   = entry_plug->target_temp;
248 <  n_oriented    = entry_plug->n_oriented;
249 <  n_constraints = entry_plug->n_constraints;
245 >  atoms         = info->atoms;
246 >  n_atoms       = info->n_atoms;
247 >  temperature   = info->target_temp;
248 >  n_oriented    = info->n_oriented;
249 >  n_constraints = info->n_constraints;
250    
251 <
252 <  ndfRaw = 3 * n_atoms + 3 * n_oriented;
165 <  ndf = ndfRaw - n_constraints - 3;
166 <  kebar = kb * temperature * (double)ndf / ( 2.0 * (double)ndfRaw );
251 >  kebar = kb * temperature * (double)info->ndf /
252 >    ( 2.0 * (double)info->ndfRaw );
253    
254    for(vr = 0; vr < n_atoms; vr++){
255      
# Line 171 | Line 257 | void Thermo::velocitize() {
257  
258      av2 = 2.0 * kebar / atoms[vr]->getMass();
259      vbar = sqrt( av2 );
260 <
260 >
261   //     vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() );
262      
263      // picks random velocities from a gaussian distribution
264      // centered on vbar
265  
266 <    vx = vbar * gaussStream->getGaussian();
267 <    vy = vbar * gaussStream->getGaussian();
268 <    vz = vbar * gaussStream->getGaussian();
266 >    for (j=0; j<3; j++)
267 >      aVel[j] = vbar * gaussStream->getGaussian();
268 >    
269 >    atoms[vr]->setVel( aVel );
270  
184 –    atoms[vr]->set_vx( vx );
185 –    atoms[vr]->set_vy( vy );
186 –    atoms[vr]->set_vz( vz );
271    }
272 +
273 +  // Get the Center of Mass drift velocity.
274 +
275 +  getCOMVel(vdrift);
276    
277    //  Corrects for the center of mass drift.
278    // 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 –  
279  
280    for(vd = 0; vd < n_atoms; vd++){
281      
282 <    vx = atoms[vd]->get_vx();
213 <    vy = atoms[vd]->get_vy();
214 <    vz = atoms[vd]->get_vz();
282 >    atoms[vd]->getVel(aVel);
283      
284 <    
285 <    vx -= vdrift[0];
286 <    vy -= vdrift[1];
287 <    vz -= vdrift[2];
220 <    
221 <    atoms[vd]->set_vx(vx);
222 <    atoms[vd]->set_vy(vy);
223 <    atoms[vd]->set_vz(vz);
284 >    for (j=0; j < 3; j++)
285 >      aVel[j] -= vdrift[j];
286 >        
287 >    atoms[vd]->setVel( aVel );
288    }
289    if( n_oriented ){
290    
# Line 229 | Line 293 | void Thermo::velocitize() {
293        if( atoms[i]->isDirectional() ){
294          
295          dAtom = (DirectionalAtom *)atoms[i];
296 +        dAtom->getI( I );
297 +        
298 +        for (j = 0 ; j < 3; j++) {
299  
300 <        vbar = sqrt( 2.0 * kebar * dAtom->getIxx() );
301 <        jx = vbar * gaussStream->getGaussian();
300 >          vbar = sqrt( 2.0 * kebar * I[j][j] );
301 >          aJ[j] = vbar * gaussStream->getGaussian();
302  
303 <        vbar = sqrt( 2.0 * kebar * dAtom->getIyy() );
237 <        jy = vbar * gaussStream->getGaussian();
303 >        }      
304  
305 <        vbar = sqrt( 2.0 * kebar * dAtom->getIzz() );
306 <        jz = vbar * gaussStream->getGaussian();
241 <        
242 <        dAtom->setJx( jx );
243 <        dAtom->setJy( jy );
244 <        dAtom->setJz( jz );
305 >        dAtom->setJ( aJ );
306 >
307        }
308      }  
309    }
310   }
311 +
312 + void Thermo::getCOMVel(double vdrift[3]){
313 +
314 +  double mtot, mtot_local;
315 +  double aVel[3], amass;
316 +  double vdrift_local[3];
317 +  int vd, n_atoms, j;
318 +  Atom** atoms;
319 +
320 +  // We are very careless here with the distinction between n_atoms and n_local
321 +  // We should really fix this before someone pokes an eye out.
322 +
323 +  n_atoms = info->n_atoms;  
324 +  atoms   = info->atoms;
325 +
326 +  mtot_local = 0.0;
327 +  vdrift_local[0] = 0.0;
328 +  vdrift_local[1] = 0.0;
329 +  vdrift_local[2] = 0.0;
330 +  
331 +  for(vd = 0; vd < n_atoms; vd++){
332 +    
333 +    amass = atoms[vd]->getMass();
334 +    atoms[vd]->getVel( aVel );
335 +
336 +    for(j = 0; j < 3; j++)
337 +      vdrift_local[j] += aVel[j] * amass;
338 +    
339 +    mtot_local += amass;
340 +  }
341 +
342 + #ifdef IS_MPI
343 +  MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
344 +  MPI_Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
345 + #else
346 +  mtot = mtot_local;
347 +  for(vd = 0; vd < 3; vd++) {
348 +    vdrift[vd] = vdrift_local[vd];
349 +  }
350 + #endif
351 +    
352 +  for (vd = 0; vd < 3; vd++) {
353 +    vdrift[vd] = vdrift[vd] / mtot;
354 +  }
355 +  
356 + }
357 +

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