| 4 |
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|
| 5 |
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#ifdef IS_MPI |
| 6 |
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#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" |
| 10 |
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#include "SRI.hpp" |
| 11 |
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#include "Integrator.hpp" |
| 12 |
+ |
#include "simError.h" |
| 13 |
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|
| 14 |
+ |
#ifdef IS_MPI |
| 15 |
+ |
#define __C |
| 16 |
+ |
#include "mpiSimulation.hpp" |
| 17 |
+ |
#endif // is_mpi |
| 18 |
+ |
|
| 19 |
+ |
|
| 20 |
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#define BASE_SEED 123456789 |
| 21 |
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|
| 22 |
< |
Thermo::Thermo( SimInfo* the_entry_plug ) { |
| 23 |
< |
entry_plug = the_entry_plug; |
| 22 |
> |
Thermo::Thermo( SimInfo* the_info ) { |
| 23 |
> |
info = the_info; |
| 24 |
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int baseSeed = BASE_SEED; |
| 25 |
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|
| 26 |
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gaussStream = new gaussianSPRNG( baseSeed ); |
| 33 |
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double Thermo::getKinetic(){ |
| 34 |
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|
| 35 |
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const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2 |
| 36 |
< |
double vx2, vy2, vz2; |
| 37 |
< |
double kinetic, v_sqr; |
| 38 |
< |
int kl; |
| 39 |
< |
double jx2, jy2, jz2; // the square of the angular momentums |
| 36 |
> |
double kinetic; |
| 37 |
> |
double amass; |
| 38 |
> |
double aVel[3], aJ[3], I[3][3]; |
| 39 |
> |
int j, kl; |
| 40 |
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|
| 41 |
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DirectionalAtom *dAtom; |
| 42 |
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|
| 45 |
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Atom** atoms; |
| 46 |
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|
| 47 |
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|
| 48 |
< |
n_atoms = entry_plug->n_atoms; |
| 49 |
< |
atoms = entry_plug->atoms; |
| 48 |
> |
n_atoms = info->n_atoms; |
| 49 |
> |
atoms = info->atoms; |
| 50 |
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|
| 51 |
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kinetic = 0.0; |
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kinetic_global = 0.0; |
| 53 |
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for( kl=0; kl < n_atoms; kl++ ){ |
| 54 |
+ |
|
| 55 |
+ |
atoms[kl]->getVel(aVel); |
| 56 |
+ |
amass = atoms[kl]->getMass(); |
| 57 |
+ |
|
| 58 |
+ |
for (j=0; j < 3; j++) |
| 59 |
+ |
kinetic += amass * aVel[j] * aVel[j]; |
| 60 |
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|
| 49 |
– |
vx2 = atoms[kl]->get_vx() * atoms[kl]->get_vx(); |
| 50 |
– |
vy2 = atoms[kl]->get_vy() * atoms[kl]->get_vy(); |
| 51 |
– |
vz2 = atoms[kl]->get_vz() * atoms[kl]->get_vz(); |
| 52 |
– |
|
| 53 |
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v_sqr = vx2 + vy2 + vz2; |
| 54 |
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kinetic += atoms[kl]->getMass() * v_sqr; |
| 55 |
– |
|
| 61 |
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if( atoms[kl]->isDirectional() ){ |
| 62 |
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|
| 63 |
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dAtom = (DirectionalAtom *)atoms[kl]; |
| 64 |
+ |
|
| 65 |
+ |
dAtom->getJ( aJ ); |
| 66 |
+ |
dAtom->getI( I ); |
| 67 |
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|
| 68 |
< |
jx2 = dAtom->getJx() * dAtom->getJx(); |
| 69 |
< |
jy2 = dAtom->getJy() * dAtom->getJy(); |
| 62 |
< |
jz2 = dAtom->getJz() * dAtom->getJz(); |
| 68 |
> |
for (j=0; j<3; j++) |
| 69 |
> |
kinetic += aJ[j]*aJ[j] / I[j][j]; |
| 70 |
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|
| 64 |
– |
kinetic += (jx2 / dAtom->getIxx()) + (jy2 / dAtom->getIyy()) |
| 65 |
– |
+ (jz2 / dAtom->getIzz()); |
| 71 |
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} |
| 72 |
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} |
| 73 |
|
#ifdef IS_MPI |
| 74 |
< |
MPI::COMM_WORLD.Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,MPI_SUM); |
| 74 |
> |
MPI_Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE, |
| 75 |
> |
MPI_SUM, MPI_COMM_WORLD); |
| 76 |
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kinetic = kinetic_global; |
| 77 |
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#endif //is_mpi |
| 78 |
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|
| 83 |
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|
| 84 |
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double Thermo::getPotential(){ |
| 85 |
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|
| 86 |
+ |
double potential_local; |
| 87 |
|
double potential; |
| 81 |
– |
double potential_global; |
| 88 |
|
int el, nSRI; |
| 89 |
< |
SRI** sris; |
| 89 |
> |
Molecule* molecules; |
| 90 |
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|
| 91 |
< |
sris = entry_plug->sr_interactions; |
| 92 |
< |
nSRI = entry_plug->n_SRI; |
| 91 |
> |
molecules = info->molecules; |
| 92 |
> |
nSRI = info->n_SRI; |
| 93 |
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|
| 94 |
+ |
potential_local = 0.0; |
| 95 |
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potential = 0.0; |
| 96 |
< |
potential_global = 0.0; |
| 90 |
< |
potential += entry_plug->lrPot; |
| 96 |
> |
potential_local += info->lrPot; |
| 97 |
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|
| 98 |
< |
for( el=0; el<nSRI; el++ ){ |
| 99 |
< |
|
| 94 |
< |
potential += sris[el]->get_potential(); |
| 98 |
> |
for( el=0; el<info->n_mol; el++ ){ |
| 99 |
> |
potential_local += molecules[el].getPotential(); |
| 100 |
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} |
| 101 |
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|
| 102 |
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// Get total potential for entire system from MPI. |
| 103 |
|
#ifdef IS_MPI |
| 104 |
< |
MPI::COMM_WORLD.Allreduce(&potential,&potential_global,1,MPI_DOUBLE,MPI_SUM); |
| 105 |
< |
potential = potential_global; |
| 106 |
< |
|
| 104 |
> |
MPI_Allreduce(&potential_local,&potential,1,MPI_DOUBLE, |
| 105 |
> |
MPI_SUM, MPI_COMM_WORLD); |
| 106 |
> |
#else |
| 107 |
> |
potential = potential_local; |
| 108 |
|
#endif // is_mpi |
| 109 |
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|
| 110 |
+ |
#ifdef IS_MPI |
| 111 |
+ |
/* |
| 112 |
+ |
std::cerr << "node " << worldRank << ": after pot = " << potential << "\n"; |
| 113 |
+ |
*/ |
| 114 |
+ |
#endif |
| 115 |
+ |
|
| 116 |
|
return potential; |
| 117 |
|
} |
| 118 |
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|
| 129 |
|
const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K) |
| 130 |
|
double temperature; |
| 131 |
|
|
| 132 |
< |
int ndf = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented |
| 121 |
< |
- entry_plug->n_constraints - 3; |
| 122 |
< |
|
| 123 |
< |
temperature = ( 2.0 * this->getKinetic() ) / ( ndf * kb ); |
| 132 |
> |
temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb ); |
| 133 |
|
return temperature; |
| 134 |
|
} |
| 135 |
|
|
| 136 |
< |
double Thermo::getPressure(){ |
| 136 |
> |
double Thermo::getEnthalpy() { |
| 137 |
|
|
| 138 |
< |
// const double conv_Pa_atm = 9.901E-6; // convert Pa -> atm |
| 139 |
< |
// const double conv_internal_Pa = 1.661E-7; //convert amu/(fs^2 A) -> Pa |
| 140 |
< |
// const double conv_A_m = 1.0E-10; //convert A -> m |
| 138 |
> |
const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2 |
| 139 |
> |
double u, p, v; |
| 140 |
> |
double press[3][3]; |
| 141 |
|
|
| 142 |
< |
return 0.0; |
| 142 |
> |
u = this->getTotalE(); |
| 143 |
> |
|
| 144 |
> |
this->getPressureTensor(press); |
| 145 |
> |
p = (press[0][0] + press[1][1] + press[2][2]) / 3.0; |
| 146 |
> |
|
| 147 |
> |
v = this->getVolume(); |
| 148 |
> |
|
| 149 |
> |
return (u + (p*v)/e_convert); |
| 150 |
> |
} |
| 151 |
> |
|
| 152 |
> |
double Thermo::getVolume() { |
| 153 |
> |
|
| 154 |
> |
return info->boxVol; |
| 155 |
> |
} |
| 156 |
> |
|
| 157 |
> |
double Thermo::getPressure() { |
| 158 |
> |
|
| 159 |
> |
// Relies on the calculation of the full molecular pressure tensor |
| 160 |
> |
|
| 161 |
> |
const double p_convert = 1.63882576e8; |
| 162 |
> |
double press[3][3]; |
| 163 |
> |
double pressure; |
| 164 |
> |
|
| 165 |
> |
this->getPressureTensor(press); |
| 166 |
> |
|
| 167 |
> |
pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0; |
| 168 |
> |
|
| 169 |
> |
return pressure; |
| 170 |
> |
} |
| 171 |
> |
|
| 172 |
> |
|
| 173 |
> |
void Thermo::getPressureTensor(double press[3][3]){ |
| 174 |
> |
// returns pressure tensor in units amu*fs^-2*Ang^-1 |
| 175 |
> |
// routine derived via viral theorem description in: |
| 176 |
> |
// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322 |
| 177 |
> |
|
| 178 |
> |
const double e_convert = 4.184e-4; |
| 179 |
> |
|
| 180 |
> |
double molmass, volume; |
| 181 |
> |
double vcom[3]; |
| 182 |
> |
double p_local[9], p_global[9]; |
| 183 |
> |
int i, j, k, nMols; |
| 184 |
> |
Molecule* molecules; |
| 185 |
> |
|
| 186 |
> |
nMols = info->n_mol; |
| 187 |
> |
molecules = info->molecules; |
| 188 |
> |
//tau = info->tau; |
| 189 |
> |
|
| 190 |
> |
// use velocities of molecular centers of mass and molecular masses: |
| 191 |
> |
for (i=0; i < 9; i++) { |
| 192 |
> |
p_local[i] = 0.0; |
| 193 |
> |
p_global[i] = 0.0; |
| 194 |
> |
} |
| 195 |
> |
|
| 196 |
> |
for (i=0; i < nMols; i++) { |
| 197 |
> |
molmass = molecules[i].getCOMvel(vcom); |
| 198 |
> |
|
| 199 |
> |
p_local[0] += molmass * (vcom[0] * vcom[0]); |
| 200 |
> |
p_local[1] += molmass * (vcom[0] * vcom[1]); |
| 201 |
> |
p_local[2] += molmass * (vcom[0] * vcom[2]); |
| 202 |
> |
p_local[3] += molmass * (vcom[1] * vcom[0]); |
| 203 |
> |
p_local[4] += molmass * (vcom[1] * vcom[1]); |
| 204 |
> |
p_local[5] += molmass * (vcom[1] * vcom[2]); |
| 205 |
> |
p_local[6] += molmass * (vcom[2] * vcom[0]); |
| 206 |
> |
p_local[7] += molmass * (vcom[2] * vcom[1]); |
| 207 |
> |
p_local[8] += molmass * (vcom[2] * vcom[2]); |
| 208 |
> |
} |
| 209 |
> |
|
| 210 |
> |
// Get total for entire system from MPI. |
| 211 |
> |
|
| 212 |
> |
#ifdef IS_MPI |
| 213 |
> |
MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
| 214 |
> |
#else |
| 215 |
> |
for (i=0; i<9; i++) { |
| 216 |
> |
p_global[i] = p_local[i]; |
| 217 |
> |
} |
| 218 |
> |
#endif // is_mpi |
| 219 |
> |
|
| 220 |
> |
volume = this->getVolume(); |
| 221 |
> |
|
| 222 |
> |
for(i = 0; i < 3; i++) { |
| 223 |
> |
for (j = 0; j < 3; j++) { |
| 224 |
> |
k = 3*i + j; |
| 225 |
> |
press[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume; |
| 226 |
> |
|
| 227 |
> |
} |
| 228 |
> |
} |
| 229 |
|
} |
| 230 |
|
|
| 231 |
|
void Thermo::velocitize() { |
| 232 |
|
|
| 233 |
|
double x,y; |
| 234 |
< |
double vx, vy, vz; |
| 235 |
< |
double jx, jy, jz; |
| 141 |
< |
int i, vr, vd; // velocity randomizer loop counters |
| 234 |
> |
double aVel[3], aJ[3], I[3][3]; |
| 235 |
> |
int i, j, vr, vd; // velocity randomizer loop counters |
| 236 |
|
double vdrift[3]; |
| 143 |
– |
double mtot = 0.0; |
| 237 |
|
double vbar; |
| 238 |
|
const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc. |
| 239 |
|
double av2; |
| 240 |
|
double kebar; |
| 148 |
– |
int ndf; // number of degrees of freedom |
| 149 |
– |
int ndfRaw; // the raw number of degrees of freedom |
| 241 |
|
int n_atoms; |
| 242 |
|
Atom** atoms; |
| 243 |
|
DirectionalAtom* dAtom; |
| 245 |
|
int n_oriented; |
| 246 |
|
int n_constraints; |
| 247 |
|
|
| 248 |
< |
atoms = entry_plug->atoms; |
| 249 |
< |
n_atoms = entry_plug->n_atoms; |
| 250 |
< |
temperature = entry_plug->target_temp; |
| 251 |
< |
n_oriented = entry_plug->n_oriented; |
| 252 |
< |
n_constraints = entry_plug->n_constraints; |
| 248 |
> |
atoms = info->atoms; |
| 249 |
> |
n_atoms = info->n_atoms; |
| 250 |
> |
temperature = info->target_temp; |
| 251 |
> |
n_oriented = info->n_oriented; |
| 252 |
> |
n_constraints = info->n_constraints; |
| 253 |
|
|
| 254 |
< |
|
| 255 |
< |
ndfRaw = 3 * n_atoms + 3 * n_oriented; |
| 165 |
< |
ndf = ndfRaw - n_constraints - 3; |
| 166 |
< |
kebar = kb * temperature * (double)ndf / ( 2.0 * (double)ndfRaw ); |
| 254 |
> |
kebar = kb * temperature * (double)info->ndf / |
| 255 |
> |
( 2.0 * (double)info->ndfRaw ); |
| 256 |
|
|
| 257 |
|
for(vr = 0; vr < n_atoms; vr++){ |
| 258 |
|
|
| 260 |
|
|
| 261 |
|
av2 = 2.0 * kebar / atoms[vr]->getMass(); |
| 262 |
|
vbar = sqrt( av2 ); |
| 263 |
< |
|
| 263 |
> |
|
| 264 |
|
// vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() ); |
| 265 |
|
|
| 266 |
|
// picks random velocities from a gaussian distribution |
| 267 |
|
// centered on vbar |
| 268 |
|
|
| 269 |
< |
vx = vbar * gaussStream->getGaussian(); |
| 270 |
< |
vy = vbar * gaussStream->getGaussian(); |
| 271 |
< |
vz = vbar * gaussStream->getGaussian(); |
| 269 |
> |
for (j=0; j<3; j++) |
| 270 |
> |
aVel[j] = vbar * gaussStream->getGaussian(); |
| 271 |
> |
|
| 272 |
> |
atoms[vr]->setVel( aVel ); |
| 273 |
|
|
| 184 |
– |
atoms[vr]->set_vx( vx ); |
| 185 |
– |
atoms[vr]->set_vy( vy ); |
| 186 |
– |
atoms[vr]->set_vz( vz ); |
| 274 |
|
} |
| 275 |
+ |
|
| 276 |
+ |
// Get the Center of Mass drift velocity. |
| 277 |
+ |
|
| 278 |
+ |
getCOMVel(vdrift); |
| 279 |
|
|
| 280 |
|
// Corrects for the center of mass drift. |
| 281 |
|
// sums all the momentum and divides by total mass. |
| 191 |
– |
|
| 192 |
– |
mtot = 0.0; |
| 193 |
– |
vdrift[0] = 0.0; |
| 194 |
– |
vdrift[1] = 0.0; |
| 195 |
– |
vdrift[2] = 0.0; |
| 196 |
– |
for(vd = 0; vd < n_atoms; vd++){ |
| 197 |
– |
|
| 198 |
– |
vdrift[0] += atoms[vd]->get_vx() * atoms[vd]->getMass(); |
| 199 |
– |
vdrift[1] += atoms[vd]->get_vy() * atoms[vd]->getMass(); |
| 200 |
– |
vdrift[2] += atoms[vd]->get_vz() * atoms[vd]->getMass(); |
| 201 |
– |
|
| 202 |
– |
mtot += atoms[vd]->getMass(); |
| 203 |
– |
} |
| 204 |
– |
|
| 205 |
– |
for (vd = 0; vd < 3; vd++) { |
| 206 |
– |
vdrift[vd] = vdrift[vd] / mtot; |
| 207 |
– |
} |
| 208 |
– |
|
| 282 |
|
|
| 283 |
|
for(vd = 0; vd < n_atoms; vd++){ |
| 284 |
|
|
| 285 |
< |
vx = atoms[vd]->get_vx(); |
| 213 |
< |
vy = atoms[vd]->get_vy(); |
| 214 |
< |
vz = atoms[vd]->get_vz(); |
| 285 |
> |
atoms[vd]->getVel(aVel); |
| 286 |
|
|
| 287 |
< |
|
| 288 |
< |
vx -= vdrift[0]; |
| 289 |
< |
vy -= vdrift[1]; |
| 290 |
< |
vz -= vdrift[2]; |
| 220 |
< |
|
| 221 |
< |
atoms[vd]->set_vx(vx); |
| 222 |
< |
atoms[vd]->set_vy(vy); |
| 223 |
< |
atoms[vd]->set_vz(vz); |
| 287 |
> |
for (j=0; j < 3; j++) |
| 288 |
> |
aVel[j] -= vdrift[j]; |
| 289 |
> |
|
| 290 |
> |
atoms[vd]->setVel( aVel ); |
| 291 |
|
} |
| 292 |
|
if( n_oriented ){ |
| 293 |
|
|
| 296 |
|
if( atoms[i]->isDirectional() ){ |
| 297 |
|
|
| 298 |
|
dAtom = (DirectionalAtom *)atoms[i]; |
| 299 |
+ |
dAtom->getI( I ); |
| 300 |
+ |
|
| 301 |
+ |
for (j = 0 ; j < 3; j++) { |
| 302 |
|
|
| 303 |
< |
vbar = sqrt( 2.0 * kebar * dAtom->getIxx() ); |
| 304 |
< |
jx = vbar * gaussStream->getGaussian(); |
| 303 |
> |
vbar = sqrt( 2.0 * kebar * I[j][j] ); |
| 304 |
> |
aJ[j] = vbar * gaussStream->getGaussian(); |
| 305 |
|
|
| 306 |
< |
vbar = sqrt( 2.0 * kebar * dAtom->getIyy() ); |
| 237 |
< |
jy = vbar * gaussStream->getGaussian(); |
| 306 |
> |
} |
| 307 |
|
|
| 308 |
< |
vbar = sqrt( 2.0 * kebar * dAtom->getIzz() ); |
| 309 |
< |
jz = vbar * gaussStream->getGaussian(); |
| 241 |
< |
|
| 242 |
< |
dAtom->setJx( jx ); |
| 243 |
< |
dAtom->setJy( jy ); |
| 244 |
< |
dAtom->setJz( jz ); |
| 308 |
> |
dAtom->setJ( aJ ); |
| 309 |
> |
|
| 310 |
|
} |
| 311 |
|
} |
| 312 |
|
} |
| 313 |
|
} |
| 314 |
+ |
|
| 315 |
+ |
void Thermo::getCOMVel(double vdrift[3]){ |
| 316 |
+ |
|
| 317 |
+ |
double mtot, mtot_local; |
| 318 |
+ |
double aVel[3], amass; |
| 319 |
+ |
double vdrift_local[3]; |
| 320 |
+ |
int vd, n_atoms, j; |
| 321 |
+ |
Atom** atoms; |
| 322 |
+ |
|
| 323 |
+ |
// We are very careless here with the distinction between n_atoms and n_local |
| 324 |
+ |
// We should really fix this before someone pokes an eye out. |
| 325 |
+ |
|
| 326 |
+ |
n_atoms = info->n_atoms; |
| 327 |
+ |
atoms = info->atoms; |
| 328 |
+ |
|
| 329 |
+ |
mtot_local = 0.0; |
| 330 |
+ |
vdrift_local[0] = 0.0; |
| 331 |
+ |
vdrift_local[1] = 0.0; |
| 332 |
+ |
vdrift_local[2] = 0.0; |
| 333 |
+ |
|
| 334 |
+ |
for(vd = 0; vd < n_atoms; vd++){ |
| 335 |
+ |
|
| 336 |
+ |
amass = atoms[vd]->getMass(); |
| 337 |
+ |
atoms[vd]->getVel( aVel ); |
| 338 |
+ |
|
| 339 |
+ |
for(j = 0; j < 3; j++) |
| 340 |
+ |
vdrift_local[j] += aVel[j] * amass; |
| 341 |
+ |
|
| 342 |
+ |
mtot_local += amass; |
| 343 |
+ |
} |
| 344 |
+ |
|
| 345 |
+ |
#ifdef IS_MPI |
| 346 |
+ |
MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
| 347 |
+ |
MPI_Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
| 348 |
+ |
#else |
| 349 |
+ |
mtot = mtot_local; |
| 350 |
+ |
for(vd = 0; vd < 3; vd++) { |
| 351 |
+ |
vdrift[vd] = vdrift_local[vd]; |
| 352 |
+ |
} |
| 353 |
+ |
#endif |
| 354 |
+ |
|
| 355 |
+ |
for (vd = 0; vd < 3; vd++) { |
| 356 |
+ |
vdrift[vd] = vdrift[vd] / mtot; |
| 357 |
+ |
} |
| 358 |
+ |
|
| 359 |
+ |
} |
| 360 |
+ |
|
