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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 755 by mmeineke, Tue Sep 9 20:35:25 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 17 | Line 16 | using namespace std;
16   #include "mpiSimulation.hpp"
17   #endif // is_mpi
18  
19 <
20 < #define BASE_SEED 123456789
21 <
23 < Thermo::Thermo( SimInfo* the_entry_plug ) {
24 <  entry_plug = the_entry_plug;
25 <  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 34 | 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 46 | 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  
56    vx2 = atoms[kl]->get_vx() * atoms[kl]->get_vx();
57    vy2 = atoms[kl]->get_vy() * atoms[kl]->get_vy();
58    vz2 = atoms[kl]->get_vz() * atoms[kl]->get_vz();
59
60    v_sqr = vx2 + vy2 + vz2;
61    kinetic += atoms[kl]->getMass() * v_sqr;
62
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();
69 <      jz2 = dAtom->getJz() * dAtom->getJz();
65 >      for (j=0; j<3; j++)
66 >        kinetic += aJ[j]*aJ[j] / I[j][j];
67        
71      kinetic += (jx2 / dAtom->getIxx()) + (jy2 / dAtom->getIyy())
72        + (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 89 | Line 85 | double Thermo::getPotential(){
85    int el, nSRI;
86    Molecule* molecules;
87  
88 <  molecules = entry_plug->molecules;
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_local += entry_plug->lrPot;
93 >  potential_local += info->lrPot;
94  
95 <  for( el=0; el<entry_plug->n_mol; el++ ){    
95 >  for( el=0; el<info->n_mol; el++ ){    
96      potential_local += molecules[el].getPotential();
97    }
98  
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
99    // Get total potential for entire system from MPI.
100   #ifdef IS_MPI
101 <  MPI::COMM_WORLD.Allreduce(&potential_local,&potential,1,MPI_DOUBLE,MPI_SUM);
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
# Line 136 | Line 125 | double Thermo::getTemperature(){
125  
126    const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K)
127    double temperature;
139  int ndf_local, ndf;
128    
129 <  ndf_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented
130 <    - entry_plug->n_constraints;
129 >  temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb );
130 >  return temperature;
131 > }
132  
133 < #ifdef IS_MPI
145 <  MPI::COMM_WORLD.Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM);
146 < #else
147 <  ndf = ndf_local;
148 < #endif
133 > double Thermo::getEnthalpy() {
134  
135 <  ndf = ndf - 3;
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 >  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 <  temperature = ( 2.0 * this->getKinetic() ) / ( ndf * kb );
159 <  return temperature;
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 < double Thermo::getPressure(){
169 > double Thermo::getPressureX() {
170  
171 < //  const double conv_Pa_atm = 9.901E-6; // convert Pa -> atm
172 < // const double conv_internal_Pa = 1.661E-7; //convert amu/(fs^2 A) -> Pa
173 < //  const double conv_A_m = 1.0E-10; //convert A -> m
171 >  // Relies on the calculation of the full molecular pressure tensor
172 >  
173 >  const double p_convert = 1.63882576e8;
174 >  double press[3][3];
175 >  double pressureX;
176  
177 <  return 0.0;
177 >  this->getPressureTensor(press);
178 >
179 >  pressureX = p_convert * press[0][0];
180 >
181 >  return pressureX;
182 > }
183 >
184 > double Thermo::getPressureY() {
185 >
186 >  // Relies on the calculation of the full molecular pressure tensor
187 >  
188 >  const double p_convert = 1.63882576e8;
189 >  double press[3][3];
190 >  double pressureY;
191 >
192 >  this->getPressureTensor(press);
193 >
194 >  pressureY = p_convert * press[1][1];
195 >
196 >  return pressureY;
197 > }
198 >
199 > double Thermo::getPressureZ() {
200 >
201 >  // Relies on the calculation of the full molecular pressure tensor
202 >  
203 >  const double p_convert = 1.63882576e8;
204 >  double press[3][3];
205 >  double pressureZ;
206 >
207 >  this->getPressureTensor(press);
208 >
209 >  pressureZ = p_convert * press[2][2];
210 >
211 >  return pressureZ;
212 > }
213 >
214 >
215 > void Thermo::getPressureTensor(double press[3][3]){
216 >  // returns pressure tensor in units amu*fs^-2*Ang^-1
217 >  // routine derived via viral theorem description in:
218 >  // Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
219 >
220 >  const double e_convert = 4.184e-4;
221 >
222 >  double molmass, volume;
223 >  double vcom[3];
224 >  double p_local[9], p_global[9];
225 >  int i, j, k, nMols;
226 >  Molecule* molecules;
227 >
228 >  nMols = info->n_mol;
229 >  molecules = info->molecules;
230 >  //tau = info->tau;
231 >
232 >  // use velocities of molecular centers of mass and molecular masses:
233 >  for (i=0; i < 9; i++) {    
234 >    p_local[i] = 0.0;
235 >    p_global[i] = 0.0;
236 >  }
237 >
238 >  for (i=0; i < nMols; i++) {
239 >    molmass = molecules[i].getCOMvel(vcom);
240 >
241 >    p_local[0] += molmass * (vcom[0] * vcom[0]);
242 >    p_local[1] += molmass * (vcom[0] * vcom[1]);
243 >    p_local[2] += molmass * (vcom[0] * vcom[2]);
244 >    p_local[3] += molmass * (vcom[1] * vcom[0]);
245 >    p_local[4] += molmass * (vcom[1] * vcom[1]);
246 >    p_local[5] += molmass * (vcom[1] * vcom[2]);
247 >    p_local[6] += molmass * (vcom[2] * vcom[0]);
248 >    p_local[7] += molmass * (vcom[2] * vcom[1]);
249 >    p_local[8] += molmass * (vcom[2] * vcom[2]);
250 >  }
251 >
252 >  // Get total for entire system from MPI.
253 >
254 > #ifdef IS_MPI
255 >  MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
256 > #else
257 >  for (i=0; i<9; i++) {
258 >    p_global[i] = p_local[i];
259 >  }
260 > #endif // is_mpi
261 >
262 >  volume = this->getVolume();
263 >
264 >  for(i = 0; i < 3; i++) {
265 >    for (j = 0; j < 3; j++) {
266 >      k = 3*i + j;
267 >      press[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume;
268 >
269 >    }
270 >  }
271   }
272  
273   void Thermo::velocitize() {
274    
275    double x,y;
276 <  double vx, vy, vz;
277 <  double jx, jy, jz;
170 <  int i, vr, vd; // velocity randomizer loop counters
276 >  double aVel[3], aJ[3], I[3][3];
277 >  int i, j, vr, vd; // velocity randomizer loop counters
278    double vdrift[3];
279    double vbar;
280    const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
281    double av2;
282    double kebar;
176  int ndf, ndf_local; // number of degrees of freedom
177  int ndfRaw, ndfRaw_local; // the raw number of degrees of freedom
283    int n_atoms;
284    Atom** atoms;
285    DirectionalAtom* dAtom;
# Line 182 | Line 287 | void Thermo::velocitize() {
287    int n_oriented;
288    int n_constraints;
289  
290 <  atoms         = entry_plug->atoms;
291 <  n_atoms       = entry_plug->n_atoms;
292 <  temperature   = entry_plug->target_temp;
293 <  n_oriented    = entry_plug->n_oriented;
294 <  n_constraints = entry_plug->n_constraints;
290 >  atoms         = info->atoms;
291 >  n_atoms       = info->n_atoms;
292 >  temperature   = info->target_temp;
293 >  n_oriented    = info->n_oriented;
294 >  n_constraints = info->n_constraints;
295    
296 <  // Raw degrees of freedom that we have to set
297 <  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;
296 >  kebar = kb * temperature * (double)info->ndf /
297 >    ( 2.0 * (double)info->ndfRaw );
298    
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  
299    for(vr = 0; vr < n_atoms; vr++){
300      
301      // uses equipartition theory to solve for vbar in angstrom/fs
# Line 218 | Line 308 | void Thermo::velocitize() {
308      // picks random velocities from a gaussian distribution
309      // centered on vbar
310  
311 <    vx = vbar * gaussStream->getGaussian();
312 <    vy = vbar * gaussStream->getGaussian();
313 <    vz = vbar * gaussStream->getGaussian();
311 >    for (j=0; j<3; j++)
312 >      aVel[j] = vbar * gaussStream->getGaussian();
313 >    
314 >    atoms[vr]->setVel( aVel );
315  
225    atoms[vr]->set_vx( vx );
226    atoms[vr]->set_vy( vy );
227    atoms[vr]->set_vz( vz );
316    }
317  
318    // Get the Center of Mass drift velocity.
# Line 236 | Line 324 | void Thermo::velocitize() {
324  
325    for(vd = 0; vd < n_atoms; vd++){
326      
327 <    vx = atoms[vd]->get_vx();
240 <    vy = atoms[vd]->get_vy();
241 <    vz = atoms[vd]->get_vz();
242 <        
243 <    vx -= vdrift[0];
244 <    vy -= vdrift[1];
245 <    vz -= vdrift[2];
327 >    atoms[vd]->getVel(aVel);
328      
329 <    atoms[vd]->set_vx(vx);
330 <    atoms[vd]->set_vy(vy);
331 <    atoms[vd]->set_vz(vz);
329 >    for (j=0; j < 3; j++)
330 >      aVel[j] -= vdrift[j];
331 >        
332 >    atoms[vd]->setVel( aVel );
333    }
334    if( n_oriented ){
335    
# Line 255 | Line 338 | void Thermo::velocitize() {
338        if( atoms[i]->isDirectional() ){
339          
340          dAtom = (DirectionalAtom *)atoms[i];
341 +        dAtom->getI( I );
342 +        
343 +        for (j = 0 ; j < 3; j++) {
344  
345 <        vbar = sqrt( 2.0 * kebar * dAtom->getIxx() );
346 <        jx = vbar * gaussStream->getGaussian();
345 >          vbar = sqrt( 2.0 * kebar * I[j][j] );
346 >          aJ[j] = vbar * gaussStream->getGaussian();
347  
348 <        vbar = sqrt( 2.0 * kebar * dAtom->getIyy() );
263 <        jy = vbar * gaussStream->getGaussian();
348 >        }      
349  
350 <        vbar = sqrt( 2.0 * kebar * dAtom->getIzz() );
351 <        jz = vbar * gaussStream->getGaussian();
267 <        
268 <        dAtom->setJx( jx );
269 <        dAtom->setJy( jy );
270 <        dAtom->setJz( jz );
350 >        dAtom->setJ( aJ );
351 >
352        }
353      }  
354    }
# Line 276 | Line 357 | void Thermo::getCOMVel(double vdrift[3]){
357   void Thermo::getCOMVel(double vdrift[3]){
358  
359    double mtot, mtot_local;
360 +  double aVel[3], amass;
361    double vdrift_local[3];
362 <  int vd, n_atoms;
362 >  int vd, n_atoms, j;
363    Atom** atoms;
364  
365    // We are very careless here with the distinction between n_atoms and n_local
366    // We should really fix this before someone pokes an eye out.
367  
368 <  n_atoms = entry_plug->n_atoms;  
369 <  atoms   = entry_plug->atoms;
368 >  n_atoms = info->n_atoms;  
369 >  atoms   = info->atoms;
370  
371    mtot_local = 0.0;
372    vdrift_local[0] = 0.0;
# Line 293 | Line 375 | void Thermo::getCOMVel(double vdrift[3]){
375    
376    for(vd = 0; vd < n_atoms; vd++){
377      
378 <    vdrift_local[0] += atoms[vd]->get_vx() * atoms[vd]->getMass();
379 <    vdrift_local[1] += atoms[vd]->get_vy() * atoms[vd]->getMass();
380 <    vdrift_local[2] += atoms[vd]->get_vz() * atoms[vd]->getMass();
378 >    amass = atoms[vd]->getMass();
379 >    atoms[vd]->getVel( aVel );
380 >
381 >    for(j = 0; j < 3; j++)
382 >      vdrift_local[j] += aVel[j] * amass;
383      
384 <    mtot_local += atoms[vd]->getMass();
384 >    mtot_local += amass;
385    }
386  
387   #ifdef IS_MPI
388 <  MPI::COMM_WORLD.Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM);
389 <  MPI::COMM_WORLD.Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM);
388 >  MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
389 >  MPI_Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
390   #else
391    mtot = mtot_local;
392    for(vd = 0; vd < 3; vd++) {

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