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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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#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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#ifdef IS_MPI |
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#define __C |
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} |
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} |
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#ifdef IS_MPI |
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< |
MPI::COMM_WORLD.Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,MPI_SUM); |
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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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potential_local = 0.0; |
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potential = 0.0; |
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potential_local += entry_plug->lrPot; |
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for( el=0; el<nSRI; el++ ){ |
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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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// 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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|
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#ifdef IS_MPI |
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/* |
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std::cerr << "node " << worldRank << ": after pot = " << potential << "\n"; |
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*/ |
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#endif |
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|
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return potential; |
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} |
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const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K) |
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double temperature; |
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int ndf_local, ndf; |
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|
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ndf_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented |
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- entry_plug->n_constraints; |
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temperature = ( 2.0 * this->getKinetic() ) / ((double)entry_plug->ndf * kb ); |
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return temperature; |
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} |
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|
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#ifdef IS_MPI |
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MPI::COMM_WORLD.Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM); |
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#else |
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ndf = ndf_local; |
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#endif |
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double Thermo::getEnthalpy() { |
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ndf = ndf - 3; |
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const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2 |
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double u, p, v; |
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double press[9]; |
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|
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u = this->getTotalE(); |
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|
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this->getPressureTensor(press); |
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p = (press[0] + press[4] + press[8]) / 3.0; |
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|
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v = this->getVolume(); |
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|
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return (u + (p*v)/e_convert); |
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} |
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|
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double Thermo::getVolume() { |
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|
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double volume; |
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double Hmat[9]; |
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|
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entry_plug->getBoxM(Hmat); |
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|
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// volume = h1 (dot) h2 (cross) h3 |
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|
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volume = Hmat[0] * ( (Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]) ) |
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+ Hmat[1] * ( (Hmat[5]*Hmat[6]) - (Hmat[8]*Hmat[3]) ) |
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+ Hmat[2] * ( (Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]) ); |
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|
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return volume; |
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} |
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|
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double Thermo::getPressure() { |
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|
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// Relies on the calculation of the full molecular pressure tensor |
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|
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temperature = ( 2.0 * this->getKinetic() ) / ( ndf * kb ); |
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return temperature; |
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const double p_convert = 1.63882576e8; |
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double press[9]; |
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double pressure; |
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|
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this->getPressureTensor(press); |
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|
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pressure = p_convert * (press[0] + press[4] + press[8]) / 3.0; |
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|
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return pressure; |
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} |
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|
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double Thermo::getPressure(){ |
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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 |
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> |
void Thermo::getPressureTensor(double press[9]){ |
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> |
// returns pressure tensor in units amu*fs^-2*Ang^-1 |
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> |
// routine derived via viral theorem description in: |
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> |
// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322 |
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|
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< |
return 0.0; |
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> |
const double e_convert = 4.184e-4; |
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> |
|
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> |
double molmass, volume; |
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> |
double vcom[3]; |
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> |
double p_local[9], p_global[9]; |
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> |
double theBox[3]; |
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> |
//double* tau; |
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> |
int i, nMols; |
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> |
Molecule* molecules; |
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> |
|
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> |
nMols = entry_plug->n_mol; |
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> |
molecules = entry_plug->molecules; |
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> |
//tau = entry_plug->tau; |
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> |
|
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> |
// use velocities of molecular centers of mass and molecular masses: |
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> |
for (i=0; i < 9; i++) { |
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> |
p_local[i] = 0.0; |
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> |
p_global[i] = 0.0; |
| 208 |
> |
} |
| 209 |
> |
|
| 210 |
> |
for (i=0; i < nMols; i++) { |
| 211 |
> |
molmass = molecules[i].getCOMvel(vcom); |
| 212 |
> |
|
| 213 |
> |
p_local[0] += molmass * (vcom[0] * vcom[0]); |
| 214 |
> |
p_local[1] += molmass * (vcom[0] * vcom[1]); |
| 215 |
> |
p_local[2] += molmass * (vcom[0] * vcom[2]); |
| 216 |
> |
p_local[3] += molmass * (vcom[1] * vcom[0]); |
| 217 |
> |
p_local[4] += molmass * (vcom[1] * vcom[1]); |
| 218 |
> |
p_local[5] += molmass * (vcom[1] * vcom[2]); |
| 219 |
> |
p_local[6] += molmass * (vcom[2] * vcom[0]); |
| 220 |
> |
p_local[7] += molmass * (vcom[2] * vcom[1]); |
| 221 |
> |
p_local[8] += molmass * (vcom[2] * vcom[2]); |
| 222 |
> |
} |
| 223 |
> |
|
| 224 |
> |
// Get total for entire system from MPI. |
| 225 |
> |
|
| 226 |
> |
#ifdef IS_MPI |
| 227 |
> |
MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
| 228 |
> |
#else |
| 229 |
> |
for (i=0; i<9; i++) { |
| 230 |
> |
p_global[i] = p_local[i]; |
| 231 |
> |
} |
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> |
#endif // is_mpi |
| 233 |
> |
|
| 234 |
> |
volume = entry_plug->boxVol; |
| 235 |
> |
|
| 236 |
> |
for(i=0; i<9; i++) { |
| 237 |
> |
press[i] = (p_global[i] - entry_plug->tau[i]*e_convert) / volume; |
| 238 |
> |
} |
| 239 |
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} |
| 240 |
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|
| 241 |
|
void Thermo::velocitize() { |
| 249 |
|
const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc. |
| 250 |
|
double av2; |
| 251 |
|
double kebar; |
| 160 |
– |
int ndf, ndf_local; // number of degrees of freedom |
| 161 |
– |
int ndfRaw, ndfRaw_local; // the raw number of degrees of freedom |
| 252 |
|
int n_atoms; |
| 253 |
|
Atom** atoms; |
| 254 |
|
DirectionalAtom* dAtom; |
| 262 |
|
n_oriented = entry_plug->n_oriented; |
| 263 |
|
n_constraints = entry_plug->n_constraints; |
| 264 |
|
|
| 265 |
< |
// Raw degrees of freedom that we have to set |
| 266 |
< |
ndfRaw_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented; |
| 177 |
< |
|
| 178 |
< |
// Degrees of freedom that can contain kinetic energy |
| 179 |
< |
ndf_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented |
| 180 |
< |
- entry_plug->n_constraints; |
| 265 |
> |
kebar = kb * temperature * (double)entry_plug->ndf / |
| 266 |
> |
( 2.0 * (double)entry_plug->ndfRaw ); |
| 267 |
|
|
| 182 |
– |
#ifdef IS_MPI |
| 183 |
– |
MPI::COMM_WORLD.Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM); |
| 184 |
– |
MPI::COMM_WORLD.Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM); |
| 185 |
– |
#else |
| 186 |
– |
ndfRaw = ndfRaw_local; |
| 187 |
– |
ndf = ndf_local; |
| 188 |
– |
#endif |
| 189 |
– |
ndf = ndf - 3; |
| 190 |
– |
|
| 191 |
– |
kebar = kb * temperature * (double)ndf / ( 2.0 * (double)ndfRaw ); |
| 192 |
– |
|
| 268 |
|
for(vr = 0; vr < n_atoms; vr++){ |
| 269 |
|
|
| 270 |
|
// uses equipartition theory to solve for vbar in angstrom/fs |
| 271 |
|
|
| 272 |
|
av2 = 2.0 * kebar / atoms[vr]->getMass(); |
| 273 |
|
vbar = sqrt( av2 ); |
| 274 |
< |
|
| 274 |
> |
|
| 275 |
|
// vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() ); |
| 276 |
|
|
| 277 |
|
// picks random velocities from a gaussian distribution |
| 320 |
|
|
| 321 |
|
vbar = sqrt( 2.0 * kebar * dAtom->getIyy() ); |
| 322 |
|
jy = vbar * gaussStream->getGaussian(); |
| 323 |
< |
|
| 323 |
> |
|
| 324 |
|
vbar = sqrt( 2.0 * kebar * dAtom->getIzz() ); |
| 325 |
|
jz = vbar * gaussStream->getGaussian(); |
| 326 |
|
|
| 360 |
|
} |
| 361 |
|
|
| 362 |
|
#ifdef IS_MPI |
| 363 |
< |
MPI::COMM_WORLD.Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM); |
| 364 |
< |
MPI::COMM_WORLD.Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM); |
| 363 |
> |
MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
| 364 |
> |
MPI_Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
| 365 |
|
#else |
| 366 |
|
mtot = mtot_local; |
| 367 |
|
for(vd = 0; vd < 3; vd++) { |
