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#ifdef IS_MPI |
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#include <mpi.h> |
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#include <mpi++.h> |
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#endif //is_mpi |
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|
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#include "Thermo.hpp" |
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#include "SRI.hpp" |
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#include "Integrator.hpp" |
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#include "simError.h" |
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|
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#ifdef IS_MPI |
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#define __C |
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} |
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} |
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#ifdef IS_MPI |
75 |
< |
MPI::COMM_WORLD.Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,MPI_SUM); |
75 |
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MPI_Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE, |
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> |
MPI_SUM, MPI_COMM_WORLD); |
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kinetic = kinetic_global; |
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#endif //is_mpi |
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|
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double potential_local; |
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double potential; |
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int el, nSRI; |
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< |
SRI** sris; |
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Molecule* molecules; |
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|
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sris = entry_plug->sr_interactions; |
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molecules = entry_plug->molecules; |
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nSRI = entry_plug->n_SRI; |
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|
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potential_local = 0.0; |
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potential = 0.0; |
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potential_local += entry_plug->lrPot; |
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|
99 |
< |
for( el=0; el<nSRI; el++ ){ |
100 |
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potential_local += sris[el]->get_potential(); |
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for( el=0; el<entry_plug->n_mol; el++ ){ |
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potential_local += molecules[el].getPotential(); |
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} |
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|
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// Get total potential for entire system from MPI. |
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#ifdef IS_MPI |
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< |
MPI::COMM_WORLD.Allreduce(&potential_local,&potential,1,MPI_DOUBLE,MPI_SUM); |
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> |
MPI_Allreduce(&potential_local,&potential,1,MPI_DOUBLE, |
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> |
MPI_SUM, MPI_COMM_WORLD); |
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#else |
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potential = potential_local; |
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#endif // is_mpi |
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|
111 |
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#ifdef IS_MPI |
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/* |
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std::cerr << "node " << worldRank << ": after pot = " << potential << "\n"; |
114 |
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*/ |
115 |
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#endif |
116 |
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|
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return potential; |
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} |
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|
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- entry_plug->n_constraints; |
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|
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#ifdef IS_MPI |
138 |
< |
MPI::COMM_WORLD.Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM); |
138 |
> |
MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
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#else |
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ndf = ndf_local; |
141 |
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#endif |
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} |
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|
149 |
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double Thermo::getPressure(){ |
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// returns pressure in units amu*fs^-2*Ang^-1 |
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// routine derived via viral theorem description in: |
152 |
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// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322 |
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|
142 |
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// const double conv_Pa_atm = 9.901E-6; // convert Pa -> atm |
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// const double conv_internal_Pa = 1.661E-7; //convert amu/(fs^2 A) -> Pa |
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// const double conv_A_m = 1.0E-10; //convert A -> m |
145 |
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|
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return 0.0; |
155 |
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} |
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|
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double vx, vy, vz; |
161 |
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double jx, jy, jz; |
162 |
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int i, vr, vd; // velocity randomizer loop counters |
163 |
< |
double *vdrift; |
163 |
> |
double vdrift[3]; |
164 |
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double vbar; |
165 |
|
const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc. |
166 |
|
double av2; |
167 |
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double kebar; |
168 |
< |
int ndf; // number of degrees of freedom |
169 |
< |
int ndfRaw; // the raw number of degrees of freedom |
168 |
> |
int ndf, ndf_local; // number of degrees of freedom |
169 |
> |
int ndfRaw, ndfRaw_local; // the raw number of degrees of freedom |
170 |
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int n_atoms; |
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Atom** atoms; |
172 |
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DirectionalAtom* dAtom; |
180 |
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n_oriented = entry_plug->n_oriented; |
181 |
|
n_constraints = entry_plug->n_constraints; |
182 |
|
|
183 |
+ |
// Raw degrees of freedom that we have to set |
184 |
+ |
ndfRaw_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented; |
185 |
|
|
186 |
< |
ndfRaw = 3 * n_atoms + 3 * n_oriented; |
187 |
< |
ndf = ndfRaw - n_constraints - 3; |
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; |
189 |
> |
|
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 |
|
|
201 |
|
for(vr = 0; vr < n_atoms; vr++){ |
204 |
|
|
205 |
|
av2 = 2.0 * kebar / atoms[vr]->getMass(); |
206 |
|
vbar = sqrt( av2 ); |
207 |
< |
|
207 |
> |
|
208 |
|
// vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() ); |
209 |
|
|
210 |
|
// picks random velocities from a gaussian distribution |
221 |
|
|
222 |
|
// Get the Center of Mass drift velocity. |
223 |
|
|
224 |
< |
vdrift = getCOMVel(); |
224 |
> |
getCOMVel(vdrift); |
225 |
|
|
226 |
|
// Corrects for the center of mass drift. |
227 |
|
// sums all the momentum and divides by total mass. |
265 |
|
} |
266 |
|
} |
267 |
|
|
268 |
< |
double* Thermo::getCOMVel(){ |
268 |
> |
void Thermo::getCOMVel(double vdrift[3]){ |
269 |
|
|
270 |
|
double mtot, mtot_local; |
250 |
– |
double* vdrift; |
271 |
|
double vdrift_local[3]; |
272 |
|
int vd, n_atoms; |
273 |
|
Atom** atoms; |
274 |
|
|
255 |
– |
vdrift = new double[3]; |
275 |
|
// We are very careless here with the distinction between n_atoms and n_local |
276 |
|
// We should really fix this before someone pokes an eye out. |
277 |
|
|
293 |
|
} |
294 |
|
|
295 |
|
#ifdef IS_MPI |
296 |
< |
MPI::COMM_WORLD.Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM); |
297 |
< |
MPI::COMM_WORLD.Allreduce(&vdrift_local,&vdrift,3,MPI_DOUBLE,MPI_SUM); |
296 |
> |
MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
297 |
> |
MPI_Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
298 |
|
#else |
299 |
|
mtot = mtot_local; |
300 |
|
for(vd = 0; vd < 3; vd++) { |
306 |
|
vdrift[vd] = vdrift[vd] / mtot; |
307 |
|
} |
308 |
|
|
290 |
– |
return vdrift; |
309 |
|
} |
310 |
|
|