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Comparing trunk/OOPSE/libmdtools/Thermo.cpp (file contents):
Revision 447 by mmeineke, Thu Apr 3 20:21:54 2003 UTC vs.
Revision 708 by tim, Wed Aug 20 22:23:34 2003 UTC

# Line 16 | Line 16 | using namespace std;
16   #include "mpiSimulation.hpp"
17   #endif // is_mpi
18  
19 <
20 < #define BASE_SEED 123456789
21 <
22 < Thermo::Thermo( SimInfo* the_entry_plug ) {
23 <  entry_plug = the_entry_plug;
24 <  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 33 | 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 45 | 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  
55 –    vx2 = atoms[kl]->get_vx() * atoms[kl]->get_vx();
56 –    vy2 = atoms[kl]->get_vy() * atoms[kl]->get_vy();
57 –    vz2 = atoms[kl]->get_vz() * atoms[kl]->get_vz();
58 –
59 –    v_sqr = vx2 + vy2 + vz2;
60 –    kinetic += atoms[kl]->getMass() * v_sqr;
61 –
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();
68 <      jz2 = dAtom->getJz() * dAtom->getJz();
65 >      for (j=0; j<3; j++)
66 >        kinetic += aJ[j]*aJ[j] / I[j][j];
67        
70 –      kinetic += (jx2 / dAtom->getIxx()) + (jy2 / dAtom->getIyy())
71 –        + (jz2 / dAtom->getIzz());
68      }
69    }
70   #ifdef IS_MPI
# 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  
# Line 129 | Line 125 | double Thermo::getTemperature(){
125  
126    const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K)
127    double temperature;
132 –  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
138 <  MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
139 < #else
140 <  ndf = ndf_local;
141 < #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(){
170 <  // returns pressure in units amu*fs^-2*Ang^-1
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 <  return 0.0;
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;
162 <  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];
234    double vbar;
235    const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
236    double av2;
237    double kebar;
168 –  int ndf, ndf_local; // number of degrees of freedom
169 –  int ndfRaw, ndfRaw_local; // the raw number of degrees of freedom
238    int n_atoms;
239    Atom** atoms;
240    DirectionalAtom* dAtom;
# Line 174 | 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 <  // Raw degrees of freedom that we have to set
252 <  ndfRaw_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented;
185 <
186 <  // Degrees of freedom that can contain kinetic energy
187 <  ndf_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented
188 <    - entry_plug->n_constraints;
251 >  kebar = kb * temperature * (double)info->ndf /
252 >    ( 2.0 * (double)info->ndfRaw );
253    
190 – #ifdef IS_MPI
191 –  MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
192 –  MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
193 – #else
194 –  ndfRaw = ndfRaw_local;
195 –  ndf = ndf_local;
196 – #endif
197 –  ndf = ndf - 3;
198 –
199 –  kebar = kb * temperature * (double)ndf / ( 2.0 * (double)ndfRaw );
200 –  
254    for(vr = 0; vr < n_atoms; vr++){
255      
256      // uses equipartition theory to solve for vbar in angstrom/fs
# Line 210 | Line 263 | void Thermo::velocitize() {
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  
217 –    atoms[vr]->set_vx( vx );
218 –    atoms[vr]->set_vy( vy );
219 –    atoms[vr]->set_vz( vz );
271    }
272  
273    // Get the Center of Mass drift velocity.
# Line 228 | Line 279 | void Thermo::velocitize() {
279  
280    for(vd = 0; vd < n_atoms; vd++){
281      
282 <    vx = atoms[vd]->get_vx();
232 <    vy = atoms[vd]->get_vy();
233 <    vz = atoms[vd]->get_vz();
234 <        
235 <    vx -= vdrift[0];
236 <    vy -= vdrift[1];
237 <    vz -= vdrift[2];
282 >    atoms[vd]->getVel(aVel);
283      
284 <    atoms[vd]->set_vx(vx);
285 <    atoms[vd]->set_vy(vy);
286 <    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 247 | 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() );
255 <        jy = vbar * gaussStream->getGaussian();
303 >        }      
304  
305 <        vbar = sqrt( 2.0 * kebar * dAtom->getIzz() );
306 <        jz = vbar * gaussStream->getGaussian();
259 <        
260 <        dAtom->setJx( jx );
261 <        dAtom->setJy( jy );
262 <        dAtom->setJz( jz );
305 >        dAtom->setJ( aJ );
306 >
307        }
308      }  
309    }
# Line 268 | Line 312 | void Thermo::getCOMVel(double vdrift[3]){
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;
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 = entry_plug->n_atoms;  
324 <  atoms   = entry_plug->atoms;
323 >  n_atoms = info->n_atoms;  
324 >  atoms   = info->atoms;
325  
326    mtot_local = 0.0;
327    vdrift_local[0] = 0.0;
# Line 285 | Line 330 | void Thermo::getCOMVel(double vdrift[3]){
330    
331    for(vd = 0; vd < n_atoms; vd++){
332      
333 <    vdrift_local[0] += atoms[vd]->get_vx() * atoms[vd]->getMass();
334 <    vdrift_local[1] += atoms[vd]->get_vy() * atoms[vd]->getMass();
335 <    vdrift_local[2] += atoms[vd]->get_vz() * atoms[vd]->getMass();
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 += atoms[vd]->getMass();
339 >    mtot_local += amass;
340    }
341  
342   #ifdef IS_MPI

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