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" |
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 |
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kinetic = kinetic_global; |
78 |
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#endif //is_mpi |
79 |
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|
100 |
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potential_local += molecules[el].getPotential(); |
101 |
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} |
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 |
– |
<< "; pot = " << potential << "\n"; |
108 |
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*/ |
109 |
– |
#endif |
110 |
– |
|
103 |
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// Get total potential for entire system from MPI. |
104 |
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#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 |
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#else |
108 |
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potential = potential_local; |
109 |
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#endif // is_mpi |
129 |
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|
130 |
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const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K) |
131 |
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double temperature; |
139 |
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int ndf_local, ndf; |
132 |
|
|
133 |
< |
ndf_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented |
142 |
< |
- entry_plug->n_constraints; |
143 |
< |
|
144 |
< |
#ifdef IS_MPI |
145 |
< |
MPI::COMM_WORLD.Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM); |
146 |
< |
#else |
147 |
< |
ndf = ndf_local; |
148 |
< |
#endif |
149 |
< |
|
150 |
< |
ndf = ndf - 3; |
151 |
< |
|
152 |
< |
temperature = ( 2.0 * this->getKinetic() ) / ( ndf * kb ); |
133 |
> |
temperature = ( 2.0 * this->getKinetic() ) / ((double)entry_plug->ndf * kb ); |
134 |
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return temperature; |
135 |
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} |
136 |
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|
137 |
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double Thermo::getPressure(){ |
138 |
< |
|
139 |
< |
// const double conv_Pa_atm = 9.901E-6; // convert Pa -> atm |
140 |
< |
// 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 |
138 |
> |
// returns pressure in units amu*fs^-2*Ang^-1 |
139 |
> |
// routine derived via viral theorem description in: |
140 |
> |
// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322 |
141 |
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|
142 |
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return 0.0; |
143 |
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} |
153 |
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const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc. |
154 |
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double av2; |
155 |
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double kebar; |
176 |
– |
int ndf, ndf_local; // number of degrees of freedom |
177 |
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int ndfRaw, ndfRaw_local; // the raw number of degrees of freedom |
156 |
|
int n_atoms; |
157 |
|
Atom** atoms; |
158 |
|
DirectionalAtom* dAtom; |
166 |
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n_oriented = entry_plug->n_oriented; |
167 |
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n_constraints = entry_plug->n_constraints; |
168 |
|
|
169 |
< |
// Raw degrees of freedom that we have to set |
170 |
< |
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; |
169 |
> |
kebar = kb * temperature * (double)entry_plug->ndf / |
170 |
> |
( 2.0 * (double)entry_plug->ndfRaw ); |
171 |
|
|
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 |
– |
|
172 |
|
for(vr = 0; vr < n_atoms; vr++){ |
173 |
|
|
174 |
|
// uses equipartition theory to solve for vbar in angstrom/fs |
175 |
|
|
176 |
|
av2 = 2.0 * kebar / atoms[vr]->getMass(); |
177 |
|
vbar = sqrt( av2 ); |
178 |
< |
|
178 |
> |
|
179 |
|
// vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() ); |
180 |
|
|
181 |
|
// picks random velocities from a gaussian distribution |
224 |
|
|
225 |
|
vbar = sqrt( 2.0 * kebar * dAtom->getIyy() ); |
226 |
|
jy = vbar * gaussStream->getGaussian(); |
227 |
< |
|
227 |
> |
|
228 |
|
vbar = sqrt( 2.0 * kebar * dAtom->getIzz() ); |
229 |
|
jz = vbar * gaussStream->getGaussian(); |
230 |
|
|
264 |
|
} |
265 |
|
|
266 |
|
#ifdef IS_MPI |
267 |
< |
MPI::COMM_WORLD.Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM); |
268 |
< |
MPI::COMM_WORLD.Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM); |
267 |
> |
MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
268 |
> |
MPI_Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
269 |
|
#else |
270 |
|
mtot = mtot_local; |
271 |
|
for(vd = 0; vd < 3; vd++) { |