| 4 |
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|
| 5 |
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#ifdef IS_MPI |
| 6 |
|
#include <mpi.h> |
| 7 |
– |
#include <mpi++.h> |
| 7 |
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#endif //is_mpi |
| 8 |
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|
| 9 |
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#include "Thermo.hpp" |
| 72 |
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} |
| 73 |
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} |
| 74 |
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#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 |
|
|
| 100 |
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potential_local += molecules[el].getPotential(); |
| 101 |
|
} |
| 102 |
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|
| 103 |
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#ifdef IS_MPI |
| 104 |
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/* |
| 105 |
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std::cerr << "node " << worldRank << ": before LONG RANGE pot = " << entry_plug->lrPot |
| 106 |
– |
<< "; pot_local = " << potential_local |
| 107 |
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<< "; pot = " << potential << "\n"; |
| 108 |
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*/ |
| 109 |
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#endif |
| 110 |
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|
| 103 |
|
// Get total potential for entire system from MPI. |
| 104 |
|
#ifdef IS_MPI |
| 105 |
< |
MPI::COMM_WORLD.Allreduce(&potential_local,&potential,1,MPI_DOUBLE,MPI_SUM); |
| 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 |
| 125 |
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return total; |
| 126 |
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} |
| 127 |
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|
| 128 |
< |
double Thermo::getTemperature(){ |
| 136 |
< |
|
| 137 |
< |
const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K) |
| 138 |
< |
double temperature; |
| 128 |
> |
int Thermo::getNDF(){ |
| 129 |
|
int ndf_local, ndf; |
| 130 |
|
|
| 131 |
|
ndf_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented |
| 132 |
|
- entry_plug->n_constraints; |
| 133 |
|
|
| 134 |
|
#ifdef IS_MPI |
| 135 |
< |
MPI::COMM_WORLD.Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM); |
| 135 |
> |
MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
| 136 |
|
#else |
| 137 |
|
ndf = ndf_local; |
| 138 |
|
#endif |
| 139 |
|
|
| 140 |
|
ndf = ndf - 3; |
| 141 |
+ |
|
| 142 |
+ |
return ndf; |
| 143 |
+ |
} |
| 144 |
+ |
|
| 145 |
+ |
int Thermo::getNDFraw() { |
| 146 |
+ |
int ndfRaw_local, ndfRaw; |
| 147 |
+ |
|
| 148 |
+ |
// Raw degrees of freedom that we have to set |
| 149 |
+ |
ndfRaw_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented; |
| 150 |
|
|
| 151 |
< |
temperature = ( 2.0 * this->getKinetic() ) / ( ndf * kb ); |
| 151 |
> |
#ifdef IS_MPI |
| 152 |
> |
MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
| 153 |
> |
#else |
| 154 |
> |
ndfRaw = ndfRaw_local; |
| 155 |
> |
#endif |
| 156 |
> |
|
| 157 |
> |
return ndfRaw; |
| 158 |
> |
} |
| 159 |
> |
|
| 160 |
> |
|
| 161 |
> |
double Thermo::getTemperature(){ |
| 162 |
> |
|
| 163 |
> |
const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K) |
| 164 |
> |
double temperature; |
| 165 |
> |
|
| 166 |
> |
temperature = ( 2.0 * this->getKinetic() ) / ( (double)this->getNDF() * kb ); |
| 167 |
|
return temperature; |
| 168 |
|
} |
| 169 |
|
|
| 170 |
|
double Thermo::getPressure(){ |
| 171 |
+ |
// returns pressure 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 |
|
|
| 158 |
– |
// const double conv_Pa_atm = 9.901E-6; // convert Pa -> atm |
| 159 |
– |
// const double conv_internal_Pa = 1.661E-7; //convert amu/(fs^2 A) -> Pa |
| 160 |
– |
// const double conv_A_m = 1.0E-10; //convert A -> m |
| 161 |
– |
|
| 175 |
|
return 0.0; |
| 176 |
|
} |
| 177 |
|
|
| 201 |
|
n_oriented = entry_plug->n_oriented; |
| 202 |
|
n_constraints = entry_plug->n_constraints; |
| 203 |
|
|
| 204 |
< |
// Raw degrees of freedom that we have to set |
| 205 |
< |
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; |
| 204 |
> |
kebar = kb * temperature * (double)this->getNDF() / |
| 205 |
> |
( 2.0 * (double)this->getNDFraw() ); |
| 206 |
|
|
| 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 |
– |
|
| 207 |
|
for(vr = 0; vr < n_atoms; vr++){ |
| 208 |
|
|
| 209 |
|
// uses equipartition theory to solve for vbar in angstrom/fs |
| 210 |
|
|
| 211 |
|
av2 = 2.0 * kebar / atoms[vr]->getMass(); |
| 212 |
|
vbar = sqrt( av2 ); |
| 213 |
< |
|
| 213 |
> |
|
| 214 |
|
// vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() ); |
| 215 |
|
|
| 216 |
|
// picks random velocities from a gaussian distribution |
| 259 |
|
|
| 260 |
|
vbar = sqrt( 2.0 * kebar * dAtom->getIyy() ); |
| 261 |
|
jy = vbar * gaussStream->getGaussian(); |
| 262 |
< |
|
| 262 |
> |
|
| 263 |
|
vbar = sqrt( 2.0 * kebar * dAtom->getIzz() ); |
| 264 |
|
jz = vbar * gaussStream->getGaussian(); |
| 265 |
|
|
| 299 |
|
} |
| 300 |
|
|
| 301 |
|
#ifdef IS_MPI |
| 302 |
< |
MPI::COMM_WORLD.Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM); |
| 303 |
< |
MPI::COMM_WORLD.Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM); |
| 302 |
> |
MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
| 303 |
> |
MPI_Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
| 304 |
|
#else |
| 305 |
|
mtot = mtot_local; |
| 306 |
|
for(vd = 0; vd < 3; vd++) { |
