1 |
mmeineke |
377 |
#include <cmath> |
2 |
|
|
#include <iostream> |
3 |
|
|
using namespace std; |
4 |
|
|
|
5 |
|
|
#ifdef IS_MPI |
6 |
|
|
#include <mpi.h> |
7 |
|
|
#endif //is_mpi |
8 |
|
|
|
9 |
|
|
#include "Thermo.hpp" |
10 |
|
|
#include "SRI.hpp" |
11 |
|
|
#include "Integrator.hpp" |
12 |
chuckv |
438 |
#include "simError.h" |
13 |
mmeineke |
402 |
|
14 |
|
|
#ifdef IS_MPI |
15 |
chuckv |
401 |
#define __C |
16 |
mmeineke |
402 |
#include "mpiSimulation.hpp" |
17 |
|
|
#endif // is_mpi |
18 |
mmeineke |
377 |
|
19 |
mmeineke |
402 |
|
20 |
mmeineke |
377 |
#define BASE_SEED 123456789 |
21 |
|
|
|
22 |
|
|
Thermo::Thermo( SimInfo* the_entry_plug ) { |
23 |
|
|
entry_plug = the_entry_plug; |
24 |
|
|
int baseSeed = BASE_SEED; |
25 |
|
|
|
26 |
|
|
gaussStream = new gaussianSPRNG( baseSeed ); |
27 |
|
|
} |
28 |
|
|
|
29 |
|
|
Thermo::~Thermo(){ |
30 |
|
|
delete gaussStream; |
31 |
|
|
} |
32 |
|
|
|
33 |
|
|
double Thermo::getKinetic(){ |
34 |
|
|
|
35 |
|
|
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 |
40 |
|
|
|
41 |
|
|
DirectionalAtom *dAtom; |
42 |
|
|
|
43 |
|
|
int n_atoms; |
44 |
|
|
double kinetic_global; |
45 |
|
|
Atom** atoms; |
46 |
|
|
|
47 |
|
|
|
48 |
|
|
n_atoms = entry_plug->n_atoms; |
49 |
|
|
atoms = entry_plug->atoms; |
50 |
|
|
|
51 |
|
|
kinetic = 0.0; |
52 |
|
|
kinetic_global = 0.0; |
53 |
|
|
for( kl=0; kl < n_atoms; kl++ ){ |
54 |
|
|
|
55 |
|
|
vx2 = atoms[kl]->get_vx() * atoms[kl]->get_vx(); |
56 |
|
|
vy2 = atoms[kl]->get_vy() * atoms[kl]->get_vy(); |
57 |
|
|
vz2 = atoms[kl]->get_vz() * atoms[kl]->get_vz(); |
58 |
|
|
|
59 |
|
|
v_sqr = vx2 + vy2 + vz2; |
60 |
|
|
kinetic += atoms[kl]->getMass() * v_sqr; |
61 |
|
|
|
62 |
|
|
if( atoms[kl]->isDirectional() ){ |
63 |
|
|
|
64 |
|
|
dAtom = (DirectionalAtom *)atoms[kl]; |
65 |
|
|
|
66 |
|
|
jx2 = dAtom->getJx() * dAtom->getJx(); |
67 |
|
|
jy2 = dAtom->getJy() * dAtom->getJy(); |
68 |
|
|
jz2 = dAtom->getJz() * dAtom->getJz(); |
69 |
|
|
|
70 |
|
|
kinetic += (jx2 / dAtom->getIxx()) + (jy2 / dAtom->getIyy()) |
71 |
|
|
+ (jz2 / dAtom->getIzz()); |
72 |
|
|
} |
73 |
|
|
} |
74 |
|
|
#ifdef IS_MPI |
75 |
mmeineke |
447 |
MPI_Allreduce(&kinetic,&kinetic_global,1,MPI_DOUBLE, |
76 |
|
|
MPI_SUM, MPI_COMM_WORLD); |
77 |
mmeineke |
377 |
kinetic = kinetic_global; |
78 |
|
|
#endif //is_mpi |
79 |
|
|
|
80 |
|
|
kinetic = kinetic * 0.5 / e_convert; |
81 |
|
|
|
82 |
|
|
return kinetic; |
83 |
|
|
} |
84 |
|
|
|
85 |
|
|
double Thermo::getPotential(){ |
86 |
|
|
|
87 |
chuckv |
401 |
double potential_local; |
88 |
mmeineke |
377 |
double potential; |
89 |
|
|
int el, nSRI; |
90 |
mmeineke |
428 |
Molecule* molecules; |
91 |
mmeineke |
377 |
|
92 |
mmeineke |
428 |
molecules = entry_plug->molecules; |
93 |
mmeineke |
377 |
nSRI = entry_plug->n_SRI; |
94 |
|
|
|
95 |
chuckv |
401 |
potential_local = 0.0; |
96 |
chuckv |
438 |
potential = 0.0; |
97 |
chuckv |
401 |
potential_local += entry_plug->lrPot; |
98 |
mmeineke |
377 |
|
99 |
mmeineke |
423 |
for( el=0; el<entry_plug->n_mol; el++ ){ |
100 |
mmeineke |
428 |
potential_local += molecules[el].getPotential(); |
101 |
mmeineke |
377 |
} |
102 |
|
|
|
103 |
|
|
// Get total potential for entire system from MPI. |
104 |
|
|
#ifdef IS_MPI |
105 |
mmeineke |
447 |
MPI_Allreduce(&potential_local,&potential,1,MPI_DOUBLE, |
106 |
|
|
MPI_SUM, MPI_COMM_WORLD); |
107 |
chuckv |
401 |
#else |
108 |
|
|
potential = potential_local; |
109 |
mmeineke |
377 |
#endif // is_mpi |
110 |
|
|
|
111 |
chuckv |
438 |
#ifdef IS_MPI |
112 |
|
|
/* |
113 |
|
|
std::cerr << "node " << worldRank << ": after pot = " << potential << "\n"; |
114 |
|
|
*/ |
115 |
|
|
#endif |
116 |
|
|
|
117 |
mmeineke |
377 |
return potential; |
118 |
|
|
} |
119 |
|
|
|
120 |
|
|
double Thermo::getTotalE(){ |
121 |
|
|
|
122 |
|
|
double total; |
123 |
|
|
|
124 |
|
|
total = this->getKinetic() + this->getPotential(); |
125 |
|
|
return total; |
126 |
|
|
} |
127 |
|
|
|
128 |
gezelter |
454 |
double Thermo::getTemperature(){ |
129 |
|
|
|
130 |
|
|
const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K) |
131 |
|
|
double temperature; |
132 |
|
|
|
133 |
gezelter |
458 |
temperature = ( 2.0 * this->getKinetic() ) / ((double)entry_plug->ndf * kb ); |
134 |
mmeineke |
377 |
return temperature; |
135 |
|
|
} |
136 |
|
|
|
137 |
|
|
double Thermo::getPressure(){ |
138 |
gezelter |
445 |
// 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 |
mmeineke |
377 |
|
142 |
gezelter |
468 |
const double convert = 4.184e-4; |
143 |
gezelter |
475 |
double molmass; |
144 |
gezelter |
468 |
double vcom[3]; |
145 |
|
|
double p_local, p_sum, p_mol, virial; |
146 |
|
|
double theBox[3]; |
147 |
|
|
double* tau; |
148 |
|
|
int i, nMols; |
149 |
|
|
Molecule* molecules; |
150 |
|
|
|
151 |
|
|
nMols = entry_plug->n_mol; |
152 |
|
|
molecules = entry_plug->molecules; |
153 |
|
|
tau = entry_plug->tau; |
154 |
|
|
|
155 |
|
|
// use velocities of molecular centers of mass and molecular masses: |
156 |
|
|
p_local = 0.0; |
157 |
gezelter |
475 |
|
158 |
gezelter |
468 |
for (i=0; i < nMols; i++) { |
159 |
gezelter |
475 |
molmass = molecules[i].getCOMvel(vcom); |
160 |
|
|
p_local += (vcom[0]*vcom[0] + vcom[1]*vcom[1] + vcom[2]*vcom[2]) * molmass; |
161 |
gezelter |
468 |
} |
162 |
|
|
|
163 |
|
|
// Get total for entire system from MPI. |
164 |
|
|
#ifdef IS_MPI |
165 |
|
|
MPI_Allreduce(&p_local,&p_sum,1,MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
166 |
|
|
#else |
167 |
|
|
p_sum = p_local; |
168 |
|
|
#endif // is_mpi |
169 |
|
|
|
170 |
|
|
virial = tau[0] + tau[4] + tau[8]; |
171 |
|
|
entry_plug->getBox(theBox); |
172 |
|
|
|
173 |
|
|
p_mol = (p_sum - virial*convert) / (3.0 * theBox[0] * theBox[1]* theBox[2]); |
174 |
|
|
|
175 |
|
|
return p_mol; |
176 |
mmeineke |
377 |
} |
177 |
|
|
|
178 |
|
|
void Thermo::velocitize() { |
179 |
|
|
|
180 |
|
|
double x,y; |
181 |
|
|
double vx, vy, vz; |
182 |
|
|
double jx, jy, jz; |
183 |
|
|
int i, vr, vd; // velocity randomizer loop counters |
184 |
chuckv |
403 |
double vdrift[3]; |
185 |
mmeineke |
377 |
double vbar; |
186 |
|
|
const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc. |
187 |
|
|
double av2; |
188 |
|
|
double kebar; |
189 |
|
|
int n_atoms; |
190 |
|
|
Atom** atoms; |
191 |
|
|
DirectionalAtom* dAtom; |
192 |
|
|
double temperature; |
193 |
|
|
int n_oriented; |
194 |
|
|
int n_constraints; |
195 |
|
|
|
196 |
|
|
atoms = entry_plug->atoms; |
197 |
|
|
n_atoms = entry_plug->n_atoms; |
198 |
|
|
temperature = entry_plug->target_temp; |
199 |
|
|
n_oriented = entry_plug->n_oriented; |
200 |
|
|
n_constraints = entry_plug->n_constraints; |
201 |
|
|
|
202 |
gezelter |
458 |
kebar = kb * temperature * (double)entry_plug->ndf / |
203 |
|
|
( 2.0 * (double)entry_plug->ndfRaw ); |
204 |
chuckv |
403 |
|
205 |
mmeineke |
377 |
for(vr = 0; vr < n_atoms; vr++){ |
206 |
|
|
|
207 |
|
|
// uses equipartition theory to solve for vbar in angstrom/fs |
208 |
|
|
|
209 |
|
|
av2 = 2.0 * kebar / atoms[vr]->getMass(); |
210 |
|
|
vbar = sqrt( av2 ); |
211 |
gezelter |
444 |
|
212 |
mmeineke |
377 |
// vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() ); |
213 |
|
|
|
214 |
|
|
// picks random velocities from a gaussian distribution |
215 |
|
|
// centered on vbar |
216 |
|
|
|
217 |
|
|
vx = vbar * gaussStream->getGaussian(); |
218 |
|
|
vy = vbar * gaussStream->getGaussian(); |
219 |
|
|
vz = vbar * gaussStream->getGaussian(); |
220 |
|
|
|
221 |
|
|
atoms[vr]->set_vx( vx ); |
222 |
|
|
atoms[vr]->set_vy( vy ); |
223 |
|
|
atoms[vr]->set_vz( vz ); |
224 |
|
|
} |
225 |
chuckv |
401 |
|
226 |
|
|
// Get the Center of Mass drift velocity. |
227 |
|
|
|
228 |
chuckv |
403 |
getCOMVel(vdrift); |
229 |
mmeineke |
377 |
|
230 |
|
|
// Corrects for the center of mass drift. |
231 |
|
|
// sums all the momentum and divides by total mass. |
232 |
|
|
|
233 |
|
|
for(vd = 0; vd < n_atoms; vd++){ |
234 |
|
|
|
235 |
|
|
vx = atoms[vd]->get_vx(); |
236 |
|
|
vy = atoms[vd]->get_vy(); |
237 |
|
|
vz = atoms[vd]->get_vz(); |
238 |
chuckv |
401 |
|
239 |
mmeineke |
377 |
vx -= vdrift[0]; |
240 |
|
|
vy -= vdrift[1]; |
241 |
|
|
vz -= vdrift[2]; |
242 |
|
|
|
243 |
|
|
atoms[vd]->set_vx(vx); |
244 |
|
|
atoms[vd]->set_vy(vy); |
245 |
|
|
atoms[vd]->set_vz(vz); |
246 |
|
|
} |
247 |
|
|
if( n_oriented ){ |
248 |
|
|
|
249 |
|
|
for( i=0; i<n_atoms; i++ ){ |
250 |
|
|
|
251 |
|
|
if( atoms[i]->isDirectional() ){ |
252 |
|
|
|
253 |
|
|
dAtom = (DirectionalAtom *)atoms[i]; |
254 |
|
|
|
255 |
|
|
vbar = sqrt( 2.0 * kebar * dAtom->getIxx() ); |
256 |
|
|
jx = vbar * gaussStream->getGaussian(); |
257 |
|
|
|
258 |
|
|
vbar = sqrt( 2.0 * kebar * dAtom->getIyy() ); |
259 |
|
|
jy = vbar * gaussStream->getGaussian(); |
260 |
gezelter |
454 |
|
261 |
mmeineke |
377 |
vbar = sqrt( 2.0 * kebar * dAtom->getIzz() ); |
262 |
|
|
jz = vbar * gaussStream->getGaussian(); |
263 |
|
|
|
264 |
|
|
dAtom->setJx( jx ); |
265 |
|
|
dAtom->setJy( jy ); |
266 |
|
|
dAtom->setJz( jz ); |
267 |
|
|
} |
268 |
|
|
} |
269 |
|
|
} |
270 |
|
|
} |
271 |
chuckv |
401 |
|
272 |
chuckv |
403 |
void Thermo::getCOMVel(double vdrift[3]){ |
273 |
chuckv |
401 |
|
274 |
|
|
double mtot, mtot_local; |
275 |
|
|
double vdrift_local[3]; |
276 |
|
|
int vd, n_atoms; |
277 |
|
|
Atom** atoms; |
278 |
|
|
|
279 |
|
|
// We are very careless here with the distinction between n_atoms and n_local |
280 |
|
|
// We should really fix this before someone pokes an eye out. |
281 |
|
|
|
282 |
|
|
n_atoms = entry_plug->n_atoms; |
283 |
|
|
atoms = entry_plug->atoms; |
284 |
|
|
|
285 |
|
|
mtot_local = 0.0; |
286 |
|
|
vdrift_local[0] = 0.0; |
287 |
|
|
vdrift_local[1] = 0.0; |
288 |
|
|
vdrift_local[2] = 0.0; |
289 |
|
|
|
290 |
|
|
for(vd = 0; vd < n_atoms; vd++){ |
291 |
|
|
|
292 |
|
|
vdrift_local[0] += atoms[vd]->get_vx() * atoms[vd]->getMass(); |
293 |
|
|
vdrift_local[1] += atoms[vd]->get_vy() * atoms[vd]->getMass(); |
294 |
|
|
vdrift_local[2] += atoms[vd]->get_vz() * atoms[vd]->getMass(); |
295 |
|
|
|
296 |
|
|
mtot_local += atoms[vd]->getMass(); |
297 |
|
|
} |
298 |
|
|
|
299 |
|
|
#ifdef IS_MPI |
300 |
mmeineke |
447 |
MPI_Allreduce(&mtot_local,&mtot,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
301 |
|
|
MPI_Allreduce(vdrift_local,vdrift,3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
302 |
chuckv |
401 |
#else |
303 |
|
|
mtot = mtot_local; |
304 |
|
|
for(vd = 0; vd < 3; vd++) { |
305 |
|
|
vdrift[vd] = vdrift_local[vd]; |
306 |
|
|
} |
307 |
|
|
#endif |
308 |
|
|
|
309 |
|
|
for (vd = 0; vd < 3; vd++) { |
310 |
|
|
vdrift[vd] = vdrift[vd] / mtot; |
311 |
|
|
} |
312 |
|
|
|
313 |
|
|
} |
314 |
|
|
|