4 |
|
|
5 |
|
#ifdef IS_MPI |
6 |
|
#include <mpi.h> |
7 |
– |
#include <mpi++.h> |
7 |
|
#endif //is_mpi |
8 |
|
|
9 |
|
#include "Thermo.hpp" |
10 |
|
#include "SRI.hpp" |
11 |
|
#include "Integrator.hpp" |
12 |
+ |
#include "simError.h" |
13 |
|
|
14 |
|
#ifdef IS_MPI |
15 |
|
#define __C |
72 |
|
} |
73 |
|
} |
74 |
|
#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 |
|
|
87 |
|
double potential_local; |
88 |
|
double potential; |
89 |
|
int el, nSRI; |
90 |
< |
SRI** sris; |
90 |
> |
Molecule* molecules; |
91 |
|
|
92 |
< |
sris = entry_plug->sr_interactions; |
92 |
> |
molecules = entry_plug->molecules; |
93 |
|
nSRI = entry_plug->n_SRI; |
94 |
|
|
95 |
|
potential_local = 0.0; |
96 |
+ |
potential = 0.0; |
97 |
|
potential_local += entry_plug->lrPot; |
98 |
|
|
99 |
< |
for( el=0; el<nSRI; el++ ){ |
100 |
< |
potential_local += sris[el]->get_potential(); |
99 |
> |
for( el=0; el<entry_plug->n_mol; el++ ){ |
100 |
> |
potential_local += molecules[el].getPotential(); |
101 |
|
} |
102 |
|
|
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 |
110 |
|
|
111 |
+ |
#ifdef IS_MPI |
112 |
+ |
/* |
113 |
+ |
std::cerr << "node " << worldRank << ": after pot = " << potential << "\n"; |
114 |
+ |
*/ |
115 |
+ |
#endif |
116 |
+ |
|
117 |
|
return potential; |
118 |
|
} |
119 |
|
|
125 |
|
return total; |
126 |
|
} |
127 |
|
|
128 |
< |
double Thermo::getTemperature(){ |
120 |
< |
|
121 |
< |
const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K) |
122 |
< |
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 |
|
|
142 |
– |
// const double conv_Pa_atm = 9.901E-6; // convert Pa -> atm |
143 |
– |
// const double conv_internal_Pa = 1.661E-7; //convert amu/(fs^2 A) -> Pa |
144 |
– |
// const double conv_A_m = 1.0E-10; //convert A -> m |
145 |
– |
|
175 |
|
return 0.0; |
176 |
|
} |
177 |
|
|
181 |
|
double vx, vy, vz; |
182 |
|
double jx, jy, jz; |
183 |
|
int i, vr, vd; // velocity randomizer loop counters |
184 |
< |
double *vdrift; |
184 |
> |
double vdrift[3]; |
185 |
|
double vbar; |
186 |
|
const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc. |
187 |
|
double av2; |
188 |
|
double kebar; |
189 |
< |
int ndf; // number of degrees of freedom |
190 |
< |
int ndfRaw; // the raw number of degrees of freedom |
189 |
> |
int ndf, ndf_local; // number of degrees of freedom |
190 |
> |
int ndfRaw, ndfRaw_local; // the raw number of degrees of freedom |
191 |
|
int n_atoms; |
192 |
|
Atom** atoms; |
193 |
|
DirectionalAtom* dAtom; |
201 |
|
n_oriented = entry_plug->n_oriented; |
202 |
|
n_constraints = entry_plug->n_constraints; |
203 |
|
|
204 |
< |
|
205 |
< |
ndfRaw = 3 * n_atoms + 3 * n_oriented; |
177 |
< |
ndf = ndfRaw - n_constraints - 3; |
178 |
< |
kebar = kb * temperature * (double)ndf / ( 2.0 * (double)ndfRaw ); |
204 |
> |
kebar = kb * temperature * (double)this->getNDF() / |
205 |
> |
( 2.0 * (double)this->getNDFraw() ); |
206 |
|
|
207 |
|
for(vr = 0; vr < n_atoms; vr++){ |
208 |
|
|
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 |
227 |
|
|
228 |
|
// Get the Center of Mass drift velocity. |
229 |
|
|
230 |
< |
vdrift = getCOMVel(); |
230 |
> |
getCOMVel(vdrift); |
231 |
|
|
232 |
|
// Corrects for the center of mass drift. |
233 |
|
// sums all the momentum and divides by total mass. |
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 |
|
|
271 |
|
} |
272 |
|
} |
273 |
|
|
274 |
< |
double* Thermo::getCOMVel(){ |
274 |
> |
void Thermo::getCOMVel(double vdrift[3]){ |
275 |
|
|
276 |
|
double mtot, mtot_local; |
250 |
– |
double* vdrift; |
277 |
|
double vdrift_local[3]; |
278 |
|
int vd, n_atoms; |
279 |
|
Atom** atoms; |
280 |
|
|
255 |
– |
vdrift = new double[3]; |
281 |
|
// We are very careless here with the distinction between n_atoms and n_local |
282 |
|
// We should really fix this before someone pokes an eye out. |
283 |
|
|
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++) { |
312 |
|
vdrift[vd] = vdrift[vd] / mtot; |
313 |
|
} |
314 |
|
|
290 |
– |
return vdrift; |
315 |
|
} |
316 |
|
|