1 |
mmeineke |
377 |
#include <cmath> |
2 |
|
|
#include <iostream> |
3 |
|
|
using namespace std; |
4 |
|
|
|
5 |
|
|
#ifdef IS_MPI |
6 |
|
|
#include <mpi.h> |
7 |
|
|
#include <mpi++.h> |
8 |
|
|
#endif //is_mpi |
9 |
|
|
|
10 |
|
|
#include "Thermo.hpp" |
11 |
|
|
#include "SRI.hpp" |
12 |
|
|
#include "Integrator.hpp" |
13 |
chuckv |
401 |
#define __C |
14 |
|
|
//#include "mpiSimulation.hpp" |
15 |
mmeineke |
377 |
|
16 |
|
|
#define BASE_SEED 123456789 |
17 |
|
|
|
18 |
|
|
Thermo::Thermo( SimInfo* the_entry_plug ) { |
19 |
|
|
entry_plug = the_entry_plug; |
20 |
|
|
int baseSeed = BASE_SEED; |
21 |
|
|
|
22 |
|
|
gaussStream = new gaussianSPRNG( baseSeed ); |
23 |
|
|
} |
24 |
|
|
|
25 |
|
|
Thermo::~Thermo(){ |
26 |
|
|
delete gaussStream; |
27 |
|
|
} |
28 |
|
|
|
29 |
|
|
double Thermo::getKinetic(){ |
30 |
|
|
|
31 |
|
|
const double e_convert = 4.184E-4; // convert kcal/mol -> (amu A^2)/fs^2 |
32 |
|
|
double vx2, vy2, vz2; |
33 |
|
|
double kinetic, v_sqr; |
34 |
|
|
int kl; |
35 |
|
|
double jx2, jy2, jz2; // the square of the angular momentums |
36 |
|
|
|
37 |
|
|
DirectionalAtom *dAtom; |
38 |
|
|
|
39 |
|
|
int n_atoms; |
40 |
|
|
double kinetic_global; |
41 |
|
|
Atom** atoms; |
42 |
|
|
|
43 |
|
|
|
44 |
|
|
n_atoms = entry_plug->n_atoms; |
45 |
|
|
atoms = entry_plug->atoms; |
46 |
|
|
|
47 |
|
|
kinetic = 0.0; |
48 |
|
|
kinetic_global = 0.0; |
49 |
|
|
for( kl=0; kl < n_atoms; kl++ ){ |
50 |
|
|
|
51 |
|
|
vx2 = atoms[kl]->get_vx() * atoms[kl]->get_vx(); |
52 |
|
|
vy2 = atoms[kl]->get_vy() * atoms[kl]->get_vy(); |
53 |
|
|
vz2 = atoms[kl]->get_vz() * atoms[kl]->get_vz(); |
54 |
|
|
|
55 |
|
|
v_sqr = vx2 + vy2 + vz2; |
56 |
|
|
kinetic += atoms[kl]->getMass() * v_sqr; |
57 |
|
|
|
58 |
|
|
if( atoms[kl]->isDirectional() ){ |
59 |
|
|
|
60 |
|
|
dAtom = (DirectionalAtom *)atoms[kl]; |
61 |
|
|
|
62 |
|
|
jx2 = dAtom->getJx() * dAtom->getJx(); |
63 |
|
|
jy2 = dAtom->getJy() * dAtom->getJy(); |
64 |
|
|
jz2 = dAtom->getJz() * dAtom->getJz(); |
65 |
|
|
|
66 |
|
|
kinetic += (jx2 / dAtom->getIxx()) + (jy2 / dAtom->getIyy()) |
67 |
|
|
+ (jz2 / dAtom->getIzz()); |
68 |
|
|
} |
69 |
|
|
} |
70 |
|
|
#ifdef IS_MPI |
71 |
|
|
MPI::COMM_WORLD.Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE,MPI_SUM); |
72 |
|
|
kinetic = kinetic_global; |
73 |
|
|
#endif //is_mpi |
74 |
|
|
|
75 |
|
|
kinetic = kinetic * 0.5 / e_convert; |
76 |
|
|
|
77 |
|
|
return kinetic; |
78 |
|
|
} |
79 |
|
|
|
80 |
|
|
double Thermo::getPotential(){ |
81 |
|
|
|
82 |
chuckv |
401 |
double potential_local; |
83 |
mmeineke |
377 |
double potential; |
84 |
|
|
int el, nSRI; |
85 |
|
|
SRI** sris; |
86 |
|
|
|
87 |
|
|
sris = entry_plug->sr_interactions; |
88 |
|
|
nSRI = entry_plug->n_SRI; |
89 |
|
|
|
90 |
chuckv |
401 |
potential_local = 0.0; |
91 |
|
|
potential_local += entry_plug->lrPot; |
92 |
mmeineke |
377 |
|
93 |
chuckv |
401 |
for( el=0; el<nSRI; el++ ){ |
94 |
|
|
potential_local += sris[el]->get_potential(); |
95 |
mmeineke |
377 |
} |
96 |
|
|
|
97 |
|
|
// Get total potential for entire system from MPI. |
98 |
|
|
#ifdef IS_MPI |
99 |
chuckv |
401 |
MPI::COMM_WORLD.Allreduce(&potential_local,&potential,1,MPI_DOUBLE,MPI_SUM); |
100 |
|
|
#else |
101 |
|
|
potential = potential_local; |
102 |
mmeineke |
377 |
#endif // is_mpi |
103 |
|
|
|
104 |
|
|
return potential; |
105 |
|
|
} |
106 |
|
|
|
107 |
|
|
double Thermo::getTotalE(){ |
108 |
|
|
|
109 |
|
|
double total; |
110 |
|
|
|
111 |
|
|
total = this->getKinetic() + this->getPotential(); |
112 |
|
|
return total; |
113 |
|
|
} |
114 |
|
|
|
115 |
|
|
double Thermo::getTemperature(){ |
116 |
|
|
|
117 |
|
|
const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K) |
118 |
|
|
double temperature; |
119 |
chuckv |
401 |
int ndf_local, ndf; |
120 |
mmeineke |
377 |
|
121 |
chuckv |
401 |
ndf_local = 3 * entry_plug->n_atoms + 3 * entry_plug->n_oriented |
122 |
|
|
- entry_plug->n_constraints; |
123 |
mmeineke |
377 |
|
124 |
chuckv |
401 |
#ifdef IS_MPI |
125 |
|
|
MPI::COMM_WORLD.Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM); |
126 |
|
|
#else |
127 |
|
|
ndf = ndf_local; |
128 |
|
|
#endif |
129 |
|
|
|
130 |
|
|
ndf = ndf - 3; |
131 |
|
|
|
132 |
mmeineke |
377 |
temperature = ( 2.0 * this->getKinetic() ) / ( ndf * kb ); |
133 |
|
|
return temperature; |
134 |
|
|
} |
135 |
|
|
|
136 |
|
|
double Thermo::getPressure(){ |
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 |
141 |
|
|
|
142 |
|
|
return 0.0; |
143 |
|
|
} |
144 |
|
|
|
145 |
|
|
void Thermo::velocitize() { |
146 |
|
|
|
147 |
|
|
double x,y; |
148 |
|
|
double vx, vy, vz; |
149 |
|
|
double jx, jy, jz; |
150 |
|
|
int i, vr, vd; // velocity randomizer loop counters |
151 |
chuckv |
401 |
double *vdrift; |
152 |
mmeineke |
377 |
double vbar; |
153 |
|
|
const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc. |
154 |
|
|
double av2; |
155 |
|
|
double kebar; |
156 |
|
|
int ndf; // number of degrees of freedom |
157 |
|
|
int ndfRaw; // the raw number of degrees of freedom |
158 |
|
|
int n_atoms; |
159 |
|
|
Atom** atoms; |
160 |
|
|
DirectionalAtom* dAtom; |
161 |
|
|
double temperature; |
162 |
|
|
int n_oriented; |
163 |
|
|
int n_constraints; |
164 |
|
|
|
165 |
|
|
atoms = entry_plug->atoms; |
166 |
|
|
n_atoms = entry_plug->n_atoms; |
167 |
|
|
temperature = entry_plug->target_temp; |
168 |
|
|
n_oriented = entry_plug->n_oriented; |
169 |
|
|
n_constraints = entry_plug->n_constraints; |
170 |
|
|
|
171 |
|
|
|
172 |
|
|
ndfRaw = 3 * n_atoms + 3 * n_oriented; |
173 |
|
|
ndf = ndfRaw - n_constraints - 3; |
174 |
|
|
kebar = kb * temperature * (double)ndf / ( 2.0 * (double)ndfRaw ); |
175 |
|
|
|
176 |
|
|
for(vr = 0; vr < n_atoms; vr++){ |
177 |
|
|
|
178 |
|
|
// uses equipartition theory to solve for vbar in angstrom/fs |
179 |
|
|
|
180 |
|
|
av2 = 2.0 * kebar / atoms[vr]->getMass(); |
181 |
|
|
vbar = sqrt( av2 ); |
182 |
|
|
|
183 |
|
|
// vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() ); |
184 |
|
|
|
185 |
|
|
// picks random velocities from a gaussian distribution |
186 |
|
|
// centered on vbar |
187 |
|
|
|
188 |
|
|
vx = vbar * gaussStream->getGaussian(); |
189 |
|
|
vy = vbar * gaussStream->getGaussian(); |
190 |
|
|
vz = vbar * gaussStream->getGaussian(); |
191 |
|
|
|
192 |
|
|
atoms[vr]->set_vx( vx ); |
193 |
|
|
atoms[vr]->set_vy( vy ); |
194 |
|
|
atoms[vr]->set_vz( vz ); |
195 |
|
|
} |
196 |
chuckv |
401 |
|
197 |
|
|
// Get the Center of Mass drift velocity. |
198 |
|
|
|
199 |
|
|
vdrift = getCOMVel(); |
200 |
mmeineke |
377 |
|
201 |
|
|
// Corrects for the center of mass drift. |
202 |
|
|
// sums all the momentum and divides by total mass. |
203 |
|
|
|
204 |
|
|
for(vd = 0; vd < n_atoms; vd++){ |
205 |
|
|
|
206 |
|
|
vx = atoms[vd]->get_vx(); |
207 |
|
|
vy = atoms[vd]->get_vy(); |
208 |
|
|
vz = atoms[vd]->get_vz(); |
209 |
chuckv |
401 |
|
210 |
mmeineke |
377 |
vx -= vdrift[0]; |
211 |
|
|
vy -= vdrift[1]; |
212 |
|
|
vz -= vdrift[2]; |
213 |
|
|
|
214 |
|
|
atoms[vd]->set_vx(vx); |
215 |
|
|
atoms[vd]->set_vy(vy); |
216 |
|
|
atoms[vd]->set_vz(vz); |
217 |
|
|
} |
218 |
|
|
if( n_oriented ){ |
219 |
|
|
|
220 |
|
|
for( i=0; i<n_atoms; i++ ){ |
221 |
|
|
|
222 |
|
|
if( atoms[i]->isDirectional() ){ |
223 |
|
|
|
224 |
|
|
dAtom = (DirectionalAtom *)atoms[i]; |
225 |
|
|
|
226 |
|
|
vbar = sqrt( 2.0 * kebar * dAtom->getIxx() ); |
227 |
|
|
jx = vbar * gaussStream->getGaussian(); |
228 |
|
|
|
229 |
|
|
vbar = sqrt( 2.0 * kebar * dAtom->getIyy() ); |
230 |
|
|
jy = vbar * gaussStream->getGaussian(); |
231 |
|
|
|
232 |
|
|
vbar = sqrt( 2.0 * kebar * dAtom->getIzz() ); |
233 |
|
|
jz = vbar * gaussStream->getGaussian(); |
234 |
|
|
|
235 |
|
|
dAtom->setJx( jx ); |
236 |
|
|
dAtom->setJy( jy ); |
237 |
|
|
dAtom->setJz( jz ); |
238 |
|
|
} |
239 |
|
|
} |
240 |
|
|
} |
241 |
|
|
} |
242 |
chuckv |
401 |
|
243 |
|
|
double* Thermo::getCOMVel(){ |
244 |
|
|
|
245 |
|
|
double mtot, mtot_local; |
246 |
|
|
double* vdrift; |
247 |
|
|
double vdrift_local[3]; |
248 |
|
|
int vd, n_atoms; |
249 |
|
|
Atom** atoms; |
250 |
|
|
|
251 |
|
|
vdrift = new double[3]; |
252 |
|
|
// We are very careless here with the distinction between n_atoms and n_local |
253 |
|
|
// We should really fix this before someone pokes an eye out. |
254 |
|
|
|
255 |
|
|
n_atoms = entry_plug->n_atoms; |
256 |
|
|
atoms = entry_plug->atoms; |
257 |
|
|
|
258 |
|
|
mtot_local = 0.0; |
259 |
|
|
vdrift_local[0] = 0.0; |
260 |
|
|
vdrift_local[1] = 0.0; |
261 |
|
|
vdrift_local[2] = 0.0; |
262 |
|
|
|
263 |
|
|
for(vd = 0; vd < n_atoms; vd++){ |
264 |
|
|
|
265 |
|
|
vdrift_local[0] += atoms[vd]->get_vx() * atoms[vd]->getMass(); |
266 |
|
|
vdrift_local[1] += atoms[vd]->get_vy() * atoms[vd]->getMass(); |
267 |
|
|
vdrift_local[2] += atoms[vd]->get_vz() * atoms[vd]->getMass(); |
268 |
|
|
|
269 |
|
|
mtot_local += atoms[vd]->getMass(); |
270 |
|
|
} |
271 |
|
|
|
272 |
|
|
#ifdef IS_MPI |
273 |
|
|
MPI::COMM_WORLD.Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM); |
274 |
|
|
MPI::COMM_WORLD.Allreduce(&vdrift_local,&vdrift,3,MPI_DOUBLE,MPI_SUM); |
275 |
|
|
#else |
276 |
|
|
mtot = mtot_local; |
277 |
|
|
for(vd = 0; vd < 3; vd++) { |
278 |
|
|
vdrift[vd] = vdrift_local[vd]; |
279 |
|
|
} |
280 |
|
|
#endif |
281 |
|
|
|
282 |
|
|
for (vd = 0; vd < 3; vd++) { |
283 |
|
|
vdrift[vd] = vdrift[vd] / mtot; |
284 |
|
|
} |
285 |
|
|
|
286 |
|
|
return vdrift; |
287 |
|
|
} |
288 |
|
|
|