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#include <cmath> |
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#include <math.h> |
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#include <iostream> |
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using namespace std; |
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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 "mpiSimulation.hpp" |
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#endif // is_mpi |
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|
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#define BASE_SEED 123456789 |
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|
23 |
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Thermo::Thermo( SimInfo* the_entry_plug ) { |
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entry_plug = the_entry_plug; |
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int baseSeed = BASE_SEED; |
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Thermo::Thermo( SimInfo* the_info ) { |
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info = the_info; |
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int baseSeed = the_info->getSeed(); |
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|
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gaussStream = new gaussianSPRNG( baseSeed ); |
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} |
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double Thermo::getKinetic(){ |
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|
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const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2 |
33 |
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double vx2, vy2, vz2; |
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double kinetic, v_sqr; |
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int kl; |
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double jx2, jy2, jz2; // the square of the angular momentums |
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double kinetic; |
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double amass; |
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double aVel[3], aJ[3], I[3][3]; |
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int j, kl; |
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|
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DirectionalAtom *dAtom; |
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Atom** atoms; |
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n_atoms = entry_plug->n_atoms; |
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atoms = entry_plug->atoms; |
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n_atoms = info->n_atoms; |
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atoms = info->atoms; |
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|
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kinetic = 0.0; |
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kinetic_global = 0.0; |
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for( kl=0; kl < n_atoms; kl++ ){ |
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|
52 |
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atoms[kl]->getVel(aVel); |
53 |
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amass = atoms[kl]->getMass(); |
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|
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for (j=0; j < 3; j++) |
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kinetic += amass * aVel[j] * aVel[j]; |
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|
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vx2 = atoms[kl]->get_vx() * atoms[kl]->get_vx(); |
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vy2 = atoms[kl]->get_vy() * atoms[kl]->get_vy(); |
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vz2 = atoms[kl]->get_vz() * atoms[kl]->get_vz(); |
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|
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v_sqr = vx2 + vy2 + vz2; |
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kinetic += atoms[kl]->getMass() * v_sqr; |
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|
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if( atoms[kl]->isDirectional() ){ |
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|
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dAtom = (DirectionalAtom *)atoms[kl]; |
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|
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dAtom->getJ( aJ ); |
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dAtom->getI( I ); |
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|
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jx2 = dAtom->getJx() * dAtom->getJx(); |
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jy2 = dAtom->getJy() * dAtom->getJy(); |
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jz2 = dAtom->getJz() * dAtom->getJz(); |
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for (j=0; j<3; j++) |
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kinetic += aJ[j]*aJ[j] / I[j][j]; |
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|
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kinetic += (jx2 / dAtom->getIxx()) + (jy2 / dAtom->getIyy()) |
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+ (jz2 / dAtom->getIzz()); |
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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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int el, nSRI; |
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Molecule* molecules; |
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|
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molecules = entry_plug->molecules; |
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nSRI = entry_plug->n_SRI; |
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molecules = info->molecules; |
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nSRI = info->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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potential_local += info->lrPot; |
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|
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for( el=0; el<entry_plug->n_mol; el++ ){ |
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for( el=0; el<info->n_mol; el++ ){ |
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potential_local += molecules[el].getPotential(); |
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} |
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|
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#ifdef IS_MPI |
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/* |
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std::cerr << "node " << worldRank << ": before LONG RANGE pot = " << entry_plug->lrPot |
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<< "; pot_local = " << potential_local |
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<< "; pot = " << potential << "\n"; |
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*/ |
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#endif |
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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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|
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|
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double Thermo::getTemperature(){ |
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|
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const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K) |
120 |
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const double kb = 1.9872156E-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 |
124 |
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- entry_plug->n_constraints; |
123 |
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temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb ); |
124 |
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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; |
148 |
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#endif |
127 |
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double Thermo::getVolume() { |
128 |
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|
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ndf = ndf - 3; |
129 |
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return info->boxVol; |
130 |
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} |
131 |
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|
132 |
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double Thermo::getPressure() { |
133 |
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|
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// Relies on the calculation of the full molecular pressure tensor |
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|
136 |
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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; |
137 |
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double press[3][3]; |
138 |
> |
double pressure; |
139 |
> |
|
140 |
> |
this->getPressureTensor(press); |
141 |
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|
142 |
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pressure = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0; |
143 |
> |
|
144 |
> |
return pressure; |
145 |
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} |
146 |
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|
147 |
< |
double Thermo::getPressure(){ |
147 |
> |
double Thermo::getPressureX() { |
148 |
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|
149 |
< |
// const double conv_Pa_atm = 9.901E-6; // convert Pa -> atm |
150 |
< |
// const double conv_internal_Pa = 1.661E-7; //convert amu/(fs^2 A) -> Pa |
151 |
< |
// const double conv_A_m = 1.0E-10; //convert A -> m |
149 |
> |
// Relies on the calculation of the full molecular pressure tensor |
150 |
> |
|
151 |
> |
const double p_convert = 1.63882576e8; |
152 |
> |
double press[3][3]; |
153 |
> |
double pressureX; |
154 |
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|
155 |
< |
return 0.0; |
155 |
> |
this->getPressureTensor(press); |
156 |
> |
|
157 |
> |
pressureX = p_convert * press[0][0]; |
158 |
> |
|
159 |
> |
return pressureX; |
160 |
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} |
161 |
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|
162 |
+ |
double Thermo::getPressureY() { |
163 |
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|
164 |
+ |
// Relies on the calculation of the full molecular pressure tensor |
165 |
+ |
|
166 |
+ |
const double p_convert = 1.63882576e8; |
167 |
+ |
double press[3][3]; |
168 |
+ |
double pressureY; |
169 |
+ |
|
170 |
+ |
this->getPressureTensor(press); |
171 |
+ |
|
172 |
+ |
pressureY = p_convert * press[1][1]; |
173 |
+ |
|
174 |
+ |
return pressureY; |
175 |
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} |
176 |
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|
177 |
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double Thermo::getPressureZ() { |
178 |
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|
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+ |
// Relies on the calculation of the full molecular pressure tensor |
180 |
+ |
|
181 |
+ |
const double p_convert = 1.63882576e8; |
182 |
+ |
double press[3][3]; |
183 |
+ |
double pressureZ; |
184 |
+ |
|
185 |
+ |
this->getPressureTensor(press); |
186 |
+ |
|
187 |
+ |
pressureZ = p_convert * press[2][2]; |
188 |
+ |
|
189 |
+ |
return pressureZ; |
190 |
+ |
} |
191 |
+ |
|
192 |
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|
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void Thermo::getPressureTensor(double press[3][3]){ |
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// returns pressure tensor in units amu*fs^-2*Ang^-1 |
195 |
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// routine derived via viral theorem description in: |
196 |
+ |
// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322 |
197 |
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|
198 |
+ |
const double e_convert = 4.184e-4; |
199 |
+ |
|
200 |
+ |
double molmass, volume; |
201 |
+ |
double vcom[3]; |
202 |
+ |
double p_local[9], p_global[9]; |
203 |
+ |
int i, j, k, nMols; |
204 |
+ |
Molecule* molecules; |
205 |
+ |
|
206 |
+ |
nMols = info->n_mol; |
207 |
+ |
molecules = info->molecules; |
208 |
+ |
//tau = info->tau; |
209 |
+ |
|
210 |
+ |
// use velocities of molecular centers of mass and molecular masses: |
211 |
+ |
for (i=0; i < 9; i++) { |
212 |
+ |
p_local[i] = 0.0; |
213 |
+ |
p_global[i] = 0.0; |
214 |
+ |
} |
215 |
+ |
|
216 |
+ |
for (i=0; i < nMols; i++) { |
217 |
+ |
molmass = molecules[i].getCOMvel(vcom); |
218 |
+ |
|
219 |
+ |
p_local[0] += molmass * (vcom[0] * vcom[0]); |
220 |
+ |
p_local[1] += molmass * (vcom[0] * vcom[1]); |
221 |
+ |
p_local[2] += molmass * (vcom[0] * vcom[2]); |
222 |
+ |
p_local[3] += molmass * (vcom[1] * vcom[0]); |
223 |
+ |
p_local[4] += molmass * (vcom[1] * vcom[1]); |
224 |
+ |
p_local[5] += molmass * (vcom[1] * vcom[2]); |
225 |
+ |
p_local[6] += molmass * (vcom[2] * vcom[0]); |
226 |
+ |
p_local[7] += molmass * (vcom[2] * vcom[1]); |
227 |
+ |
p_local[8] += molmass * (vcom[2] * vcom[2]); |
228 |
+ |
} |
229 |
+ |
|
230 |
+ |
// Get total for entire system from MPI. |
231 |
+ |
|
232 |
+ |
#ifdef IS_MPI |
233 |
+ |
MPI_Allreduce(p_local,p_global,9,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
234 |
+ |
#else |
235 |
+ |
for (i=0; i<9; i++) { |
236 |
+ |
p_global[i] = p_local[i]; |
237 |
+ |
} |
238 |
+ |
#endif // is_mpi |
239 |
+ |
|
240 |
+ |
volume = this->getVolume(); |
241 |
+ |
|
242 |
+ |
for(i = 0; i < 3; i++) { |
243 |
+ |
for (j = 0; j < 3; j++) { |
244 |
+ |
k = 3*i + j; |
245 |
+ |
press[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume; |
246 |
+ |
|
247 |
+ |
} |
248 |
+ |
} |
249 |
+ |
} |
250 |
+ |
|
251 |
|
void Thermo::velocitize() { |
252 |
|
|
253 |
< |
double x,y; |
254 |
< |
double vx, vy, vz; |
169 |
< |
double jx, jy, jz; |
170 |
< |
int i, vr, vd; // velocity randomizer loop counters |
253 |
> |
double aVel[3], aJ[3], I[3][3]; |
254 |
> |
int i, j, vr, vd; // velocity randomizer loop counters |
255 |
|
double vdrift[3]; |
256 |
|
double vbar; |
257 |
|
const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc. |
258 |
|
double av2; |
259 |
|
double kebar; |
176 |
– |
int ndf, ndf_local; // number of degrees of freedom |
177 |
– |
int ndfRaw, ndfRaw_local; // the raw number of degrees of freedom |
260 |
|
int n_atoms; |
261 |
|
Atom** atoms; |
262 |
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DirectionalAtom* dAtom; |
264 |
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int n_oriented; |
265 |
|
int n_constraints; |
266 |
|
|
267 |
< |
atoms = entry_plug->atoms; |
268 |
< |
n_atoms = entry_plug->n_atoms; |
269 |
< |
temperature = entry_plug->target_temp; |
270 |
< |
n_oriented = entry_plug->n_oriented; |
271 |
< |
n_constraints = entry_plug->n_constraints; |
267 |
> |
atoms = info->atoms; |
268 |
> |
n_atoms = info->n_atoms; |
269 |
> |
temperature = info->target_temp; |
270 |
> |
n_oriented = info->n_oriented; |
271 |
> |
n_constraints = info->n_constraints; |
272 |
|
|
273 |
< |
// Raw degrees of freedom that we have to set |
274 |
< |
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; |
273 |
> |
kebar = kb * temperature * (double)info->ndfRaw / |
274 |
> |
( 2.0 * (double)info->ndf ); |
275 |
|
|
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 |
– |
|
276 |
|
for(vr = 0; vr < n_atoms; vr++){ |
277 |
|
|
278 |
|
// uses equipartition theory to solve for vbar in angstrom/fs |
280 |
|
av2 = 2.0 * kebar / atoms[vr]->getMass(); |
281 |
|
vbar = sqrt( av2 ); |
282 |
|
|
216 |
– |
// vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() ); |
217 |
– |
|
283 |
|
// picks random velocities from a gaussian distribution |
284 |
|
// centered on vbar |
285 |
|
|
286 |
< |
vx = vbar * gaussStream->getGaussian(); |
287 |
< |
vy = vbar * gaussStream->getGaussian(); |
288 |
< |
vz = vbar * gaussStream->getGaussian(); |
286 |
> |
for (j=0; j<3; j++) |
287 |
> |
aVel[j] = vbar * gaussStream->getGaussian(); |
288 |
> |
|
289 |
> |
atoms[vr]->setVel( aVel ); |
290 |
|
|
225 |
– |
atoms[vr]->set_vx( vx ); |
226 |
– |
atoms[vr]->set_vy( vy ); |
227 |
– |
atoms[vr]->set_vz( vz ); |
291 |
|
} |
292 |
|
|
293 |
|
// Get the Center of Mass drift velocity. |
299 |
|
|
300 |
|
for(vd = 0; vd < n_atoms; vd++){ |
301 |
|
|
302 |
< |
vx = atoms[vd]->get_vx(); |
240 |
< |
vy = atoms[vd]->get_vy(); |
241 |
< |
vz = atoms[vd]->get_vz(); |
242 |
< |
|
243 |
< |
vx -= vdrift[0]; |
244 |
< |
vy -= vdrift[1]; |
245 |
< |
vz -= vdrift[2]; |
302 |
> |
atoms[vd]->getVel(aVel); |
303 |
|
|
304 |
< |
atoms[vd]->set_vx(vx); |
305 |
< |
atoms[vd]->set_vy(vy); |
306 |
< |
atoms[vd]->set_vz(vz); |
304 |
> |
for (j=0; j < 3; j++) |
305 |
> |
aVel[j] -= vdrift[j]; |
306 |
> |
|
307 |
> |
atoms[vd]->setVel( aVel ); |
308 |
|
} |
309 |
|
if( n_oriented ){ |
310 |
|
|
313 |
|
if( atoms[i]->isDirectional() ){ |
314 |
|
|
315 |
|
dAtom = (DirectionalAtom *)atoms[i]; |
316 |
+ |
dAtom->getI( I ); |
317 |
+ |
|
318 |
+ |
for (j = 0 ; j < 3; j++) { |
319 |
|
|
320 |
< |
vbar = sqrt( 2.0 * kebar * dAtom->getIxx() ); |
321 |
< |
jx = vbar * gaussStream->getGaussian(); |
320 |
> |
vbar = sqrt( 2.0 * kebar * I[j][j] ); |
321 |
> |
aJ[j] = vbar * gaussStream->getGaussian(); |
322 |
|
|
323 |
< |
vbar = sqrt( 2.0 * kebar * dAtom->getIyy() ); |
263 |
< |
jy = vbar * gaussStream->getGaussian(); |
323 |
> |
} |
324 |
|
|
325 |
< |
vbar = sqrt( 2.0 * kebar * dAtom->getIzz() ); |
326 |
< |
jz = vbar * gaussStream->getGaussian(); |
267 |
< |
|
268 |
< |
dAtom->setJx( jx ); |
269 |
< |
dAtom->setJy( jy ); |
270 |
< |
dAtom->setJz( jz ); |
325 |
> |
dAtom->setJ( aJ ); |
326 |
> |
|
327 |
|
} |
328 |
|
} |
329 |
|
} |
332 |
|
void Thermo::getCOMVel(double vdrift[3]){ |
333 |
|
|
334 |
|
double mtot, mtot_local; |
335 |
+ |
double aVel[3], amass; |
336 |
|
double vdrift_local[3]; |
337 |
< |
int vd, n_atoms; |
337 |
> |
int vd, n_atoms, j; |
338 |
|
Atom** atoms; |
339 |
|
|
340 |
|
// We are very careless here with the distinction between n_atoms and n_local |
341 |
|
// We should really fix this before someone pokes an eye out. |
342 |
|
|
343 |
< |
n_atoms = entry_plug->n_atoms; |
344 |
< |
atoms = entry_plug->atoms; |
343 |
> |
n_atoms = info->n_atoms; |
344 |
> |
atoms = info->atoms; |
345 |
|
|
346 |
|
mtot_local = 0.0; |
347 |
|
vdrift_local[0] = 0.0; |
350 |
|
|
351 |
|
for(vd = 0; vd < n_atoms; vd++){ |
352 |
|
|
353 |
< |
vdrift_local[0] += atoms[vd]->get_vx() * atoms[vd]->getMass(); |
354 |
< |
vdrift_local[1] += atoms[vd]->get_vy() * atoms[vd]->getMass(); |
355 |
< |
vdrift_local[2] += atoms[vd]->get_vz() * atoms[vd]->getMass(); |
353 |
> |
amass = atoms[vd]->getMass(); |
354 |
> |
atoms[vd]->getVel( aVel ); |
355 |
> |
|
356 |
> |
for(j = 0; j < 3; j++) |
357 |
> |
vdrift_local[j] += aVel[j] * amass; |
358 |
|
|
359 |
< |
mtot_local += atoms[vd]->getMass(); |
359 |
> |
mtot_local += amass; |
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++) { |
375 |
|
|
376 |
|
} |
377 |
|
|
378 |
+ |
void Thermo::getCOM(double COM[3]){ |
379 |
+ |
|
380 |
+ |
double mtot, mtot_local; |
381 |
+ |
double aPos[3], amass; |
382 |
+ |
double COM_local[3]; |
383 |
+ |
int i, n_atoms, j; |
384 |
+ |
Atom** atoms; |
385 |
+ |
|
386 |
+ |
// We are very careless here with the distinction between n_atoms and n_local |
387 |
+ |
// We should really fix this before someone pokes an eye out. |
388 |
+ |
|
389 |
+ |
n_atoms = info->n_atoms; |
390 |
+ |
atoms = info->atoms; |
391 |
+ |
|
392 |
+ |
mtot_local = 0.0; |
393 |
+ |
COM_local[0] = 0.0; |
394 |
+ |
COM_local[1] = 0.0; |
395 |
+ |
COM_local[2] = 0.0; |
396 |
+ |
|
397 |
+ |
for(i = 0; i < n_atoms; i++){ |
398 |
+ |
|
399 |
+ |
amass = atoms[i]->getMass(); |
400 |
+ |
atoms[i]->getPos( aPos ); |
401 |
+ |
|
402 |
+ |
for(j = 0; j < 3; j++) |
403 |
+ |
COM_local[j] += aPos[j] * amass; |
404 |
+ |
|
405 |
+ |
mtot_local += amass; |
406 |
+ |
} |
407 |
+ |
|
408 |
+ |
#ifdef IS_MPI |
409 |
+ |
MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
410 |
+ |
MPI_Allreduce(COM_local,COM,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
411 |
+ |
#else |
412 |
+ |
mtot = mtot_local; |
413 |
+ |
for(i = 0; i < 3; i++) { |
414 |
+ |
COM[i] = COM_local[i]; |
415 |
+ |
} |
416 |
+ |
#endif |
417 |
+ |
|
418 |
+ |
for (i = 0; i < 3; i++) { |
419 |
+ |
COM[i] = COM[i] / mtot; |
420 |
+ |
} |
421 |
+ |
} |