1 |
#include <iostream> |
2 |
#include <cstdlib> |
3 |
|
4 |
#include "Integrator.hpp" |
5 |
#include "Thermo.hpp" |
6 |
#include "ReadWrite.hpp" |
7 |
#include "ForceFields.hpp" |
8 |
#include "ExtendedSystem.hpp" |
9 |
#include "simError.h" |
10 |
|
11 |
extern "C"{ |
12 |
|
13 |
void v_constrain_a_( double &dt, int &n_atoms, double* mass, |
14 |
double* Rx, double* Ry, double* Rz, |
15 |
double* Vx, double* Vy, double* Vz, |
16 |
double* Fx, double* Fy, double* Fz, |
17 |
int &n_constrained, double *constr_sqr, |
18 |
int* constr_i, int* constr_j, |
19 |
double &box_x, double &box_y, double &box_z ); |
20 |
|
21 |
void v_constrain_b_( double &dt, int &n_atoms, double* mass, |
22 |
double* Rx, double* Ry, double* Rz, |
23 |
double* Vx, double* Vy, double* Vz, |
24 |
double* Fx, double* Fy, double* Fz, |
25 |
double &Kinetic, |
26 |
int &n_constrained, double *constr_sqr, |
27 |
int* constr_i, int* constr_j, |
28 |
double &box_x, double &box_y, double &box_z ); |
29 |
} |
30 |
|
31 |
|
32 |
|
33 |
|
34 |
Symplectic::Symplectic( SimInfo* the_entry_plug, ForceFields* the_ff, |
35 |
ExtendedSystem* the_es ){ |
36 |
entry_plug = the_entry_plug; |
37 |
myFF = the_ff; |
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myES = the_es; |
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isFirst = 1; |
40 |
|
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molecules = entry_plug->molecules; |
42 |
nMols = entry_plug->n_mol; |
43 |
|
44 |
// give a little love back to the SimInfo object |
45 |
|
46 |
if( entry_plug->the_integrator != NULL ) delete entry_plug->the_integrator; |
47 |
entry_plug->the_integrator = this; |
48 |
|
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// grab the masses |
50 |
|
51 |
mass = new double[entry_plug->n_atoms]; |
52 |
for(int i = 0; i < entry_plug->n_atoms; i++){ |
53 |
mass[i] = entry_plug->atoms[i]->getMass(); |
54 |
} |
55 |
|
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// check for constraints |
57 |
|
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is_constrained = 0; |
59 |
|
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Constraint *temp_con; |
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Constraint *dummy_plug; |
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temp_con = new Constraint[entry_plug->n_SRI]; |
63 |
n_constrained = 0; |
64 |
int constrained = 0; |
65 |
|
66 |
SRI** theArray; |
67 |
for(int i = 0; i < nMols; i++){ |
68 |
|
69 |
theArray = (SRI**) molecules[i].getMyBonds(); |
70 |
for(int j=0; j<molecules[i].getNBonds(); j++){ |
71 |
|
72 |
constrained = theArray[j]->is_constrained(); |
73 |
|
74 |
if(constrained){ |
75 |
|
76 |
dummy_plug = theArray[j]->get_constraint(); |
77 |
temp_con[n_constrained].set_a( dummy_plug->get_a() ); |
78 |
temp_con[n_constrained].set_b( dummy_plug->get_b() ); |
79 |
temp_con[n_constrained].set_dsqr( dummy_plug->get_dsqr() ); |
80 |
|
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n_constrained++; |
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constrained = 0; |
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} |
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} |
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|
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theArray = (SRI**) molecules[i].getMyBends(); |
87 |
for(int j=0; j<molecules[i].getNBends(); j++){ |
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|
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constrained = theArray[j]->is_constrained(); |
90 |
|
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if(constrained){ |
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|
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dummy_plug = theArray[j]->get_constraint(); |
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temp_con[n_constrained].set_a( dummy_plug->get_a() ); |
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temp_con[n_constrained].set_b( dummy_plug->get_b() ); |
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temp_con[n_constrained].set_dsqr( dummy_plug->get_dsqr() ); |
97 |
|
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n_constrained++; |
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constrained = 0; |
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} |
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} |
102 |
|
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theArray = (SRI**) molecules[i].getMyTorsions(); |
104 |
for(int j=0; j<molecules[i].getNTorsions(); j++){ |
105 |
|
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constrained = theArray[j]->is_constrained(); |
107 |
|
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if(constrained){ |
109 |
|
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dummy_plug = theArray[j]->get_constraint(); |
111 |
temp_con[n_constrained].set_a( dummy_plug->get_a() ); |
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temp_con[n_constrained].set_b( dummy_plug->get_b() ); |
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temp_con[n_constrained].set_dsqr( dummy_plug->get_dsqr() ); |
114 |
|
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n_constrained++; |
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constrained = 0; |
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} |
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} |
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} |
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|
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if(n_constrained > 0){ |
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|
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is_constrained = 1; |
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constrained_i = new int[n_constrained]; |
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constrained_j = new int[n_constrained]; |
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constrained_dsqr = new double[n_constrained]; |
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|
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for( int i = 0; i < n_constrained; i++){ |
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|
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/* add 1 to the index for the fortran arrays. */ |
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|
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constrained_i[i] = temp_con[i].get_a() + 1; |
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constrained_j[i] = temp_con[i].get_b() + 1; |
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constrained_dsqr[i] = temp_con[i].get_dsqr(); |
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} |
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} |
137 |
|
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delete[] temp_con; |
139 |
} |
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|
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Symplectic::~Symplectic() { |
142 |
|
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if( n_constrained ){ |
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delete[] constrained_i; |
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delete[] constrained_j; |
146 |
delete[] constrained_dsqr; |
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} |
148 |
|
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} |
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|
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|
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void Symplectic::integrate( void ){ |
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|
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const double e_convert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2 |
155 |
|
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int i, j; // loop counters |
157 |
int nAtoms = entry_plug->n_atoms; // the number of atoms |
158 |
double kE = 0.0; // the kinetic energy |
159 |
double rot_kE; |
160 |
double trans_kE; |
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int tl; // the time loop conter |
162 |
double dt2; // half the dt |
163 |
|
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double vx, vy, vz; // the velocities |
165 |
double vx2, vy2, vz2; // the square of the velocities |
166 |
double rx, ry, rz; // the postitions |
167 |
|
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double ji[3]; // the body frame angular momentum |
169 |
double jx2, jy2, jz2; // the square of the angular momentums |
170 |
double Tb[3]; // torque in the body frame |
171 |
double angle; // the angle through which to rotate the rotation matrix |
172 |
double A[3][3]; // the rotation matrix |
173 |
double press[9]; |
174 |
|
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int time; |
176 |
|
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double dt = entry_plug->dt; |
178 |
double runTime = entry_plug->run_time; |
179 |
double sampleTime = entry_plug->sampleTime; |
180 |
double statusTime = entry_plug->statusTime; |
181 |
double thermalTime = entry_plug->thermalTime; |
182 |
|
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int n_loops = (int)( runTime / dt ); |
184 |
int sample_n = (int)( sampleTime / dt ); |
185 |
int status_n = (int)( statusTime / dt ); |
186 |
int vel_n = (int)( thermalTime / dt ); |
187 |
|
188 |
int calcPot, calcStress; |
189 |
|
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Thermo *tStats; |
191 |
StatWriter* e_out; |
192 |
DumpWriter* dump_out; |
193 |
|
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tStats = new Thermo( entry_plug ); |
195 |
e_out = new StatWriter( entry_plug ); |
196 |
dump_out = new DumpWriter( entry_plug ); |
197 |
|
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Atom** atoms = entry_plug->atoms; |
199 |
DirectionalAtom* dAtom; |
200 |
dt2 = 0.5 * dt; |
201 |
|
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// initialize the forces the before the first step |
203 |
|
204 |
myFF->doForces(1,1); |
205 |
|
206 |
if( entry_plug->setTemp ){ |
207 |
|
208 |
tStats->velocitize(); |
209 |
} |
210 |
|
211 |
dump_out->writeDump( 0.0 ); |
212 |
e_out->writeStat( 0.0 ); |
213 |
|
214 |
calcPot = 0; |
215 |
|
216 |
if (!strcasecmp( entry_plug->ensemble, "NPT")) { |
217 |
calcStress = 1; |
218 |
} else { |
219 |
calcStress = 0; |
220 |
} |
221 |
|
222 |
if( n_constrained ){ |
223 |
|
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double *Rx = new double[nAtoms]; |
225 |
double *Ry = new double[nAtoms]; |
226 |
double *Rz = new double[nAtoms]; |
227 |
|
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double *Vx = new double[nAtoms]; |
229 |
double *Vy = new double[nAtoms]; |
230 |
double *Vz = new double[nAtoms]; |
231 |
|
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double *Fx = new double[nAtoms]; |
233 |
double *Fy = new double[nAtoms]; |
234 |
double *Fz = new double[nAtoms]; |
235 |
|
236 |
|
237 |
for( tl=0; tl < n_loops; tl++ ){ |
238 |
|
239 |
if (!strcasecmp( entry_plug->ensemble, "NVT")) |
240 |
myES->NoseHooverNVT( dt / 2.0 , tStats->getKinetic() ); |
241 |
|
242 |
for( j=0; j<nAtoms; j++ ){ |
243 |
|
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Rx[j] = atoms[j]->getX(); |
245 |
Ry[j] = atoms[j]->getY(); |
246 |
Rz[j] = atoms[j]->getZ(); |
247 |
|
248 |
Vx[j] = atoms[j]->get_vx(); |
249 |
Vy[j] = atoms[j]->get_vy(); |
250 |
Vz[j] = atoms[j]->get_vz(); |
251 |
|
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Fx[j] = atoms[j]->getFx(); |
253 |
Fy[j] = atoms[j]->getFy(); |
254 |
Fz[j] = atoms[j]->getFz(); |
255 |
|
256 |
} |
257 |
|
258 |
v_constrain_a_( dt, nAtoms, mass, Rx, Ry, Rz, Vx, Vy, Vz, |
259 |
Fx, Fy, Fz, |
260 |
n_constrained, constrained_dsqr, |
261 |
constrained_i, constrained_j, |
262 |
entry_plug->box_x, |
263 |
entry_plug->box_y, |
264 |
entry_plug->box_z ); |
265 |
|
266 |
for( j=0; j<nAtoms; j++ ){ |
267 |
|
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atoms[j]->setX(Rx[j]); |
269 |
atoms[j]->setY(Ry[j]); |
270 |
atoms[j]->setZ(Rz[j]); |
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|
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atoms[j]->set_vx(Vx[j]); |
273 |
atoms[j]->set_vy(Vy[j]); |
274 |
atoms[j]->set_vz(Vz[j]); |
275 |
} |
276 |
|
277 |
|
278 |
for( i=0; i<nAtoms; i++ ){ |
279 |
if( atoms[i]->isDirectional() ){ |
280 |
|
281 |
dAtom = (DirectionalAtom *)atoms[i]; |
282 |
|
283 |
// get and convert the torque to body frame |
284 |
|
285 |
Tb[0] = dAtom->getTx(); |
286 |
Tb[1] = dAtom->getTy(); |
287 |
Tb[2] = dAtom->getTz(); |
288 |
|
289 |
dAtom->lab2Body( Tb ); |
290 |
|
291 |
// get the angular momentum, and propagate a half step |
292 |
|
293 |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * e_convert; |
294 |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * e_convert; |
295 |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * e_convert; |
296 |
|
297 |
// get the atom's rotation matrix |
298 |
|
299 |
A[0][0] = dAtom->getAxx(); |
300 |
A[0][1] = dAtom->getAxy(); |
301 |
A[0][2] = dAtom->getAxz(); |
302 |
|
303 |
A[1][0] = dAtom->getAyx(); |
304 |
A[1][1] = dAtom->getAyy(); |
305 |
A[1][2] = dAtom->getAyz(); |
306 |
|
307 |
A[2][0] = dAtom->getAzx(); |
308 |
A[2][1] = dAtom->getAzy(); |
309 |
A[2][2] = dAtom->getAzz(); |
310 |
|
311 |
|
312 |
// use the angular velocities to propagate the rotation matrix a |
313 |
// full time step |
314 |
|
315 |
|
316 |
angle = dt2 * ji[0] / dAtom->getIxx(); |
317 |
this->rotate( 1, 2, angle, ji, A ); // rotate about the x-axis |
318 |
|
319 |
angle = dt2 * ji[1] / dAtom->getIyy(); |
320 |
this->rotate( 2, 0, angle, ji, A ); // rotate about the y-axis |
321 |
|
322 |
angle = dt * ji[2] / dAtom->getIzz(); |
323 |
this->rotate( 0, 1, angle, ji, A ); // rotate about the z-axis |
324 |
|
325 |
angle = dt2 * ji[1] / dAtom->getIyy(); |
326 |
this->rotate( 2, 0, angle, ji, A ); // rotate about the y-axis |
327 |
|
328 |
angle = dt2 * ji[0] / dAtom->getIxx(); |
329 |
this->rotate( 1, 2, angle, ji, A ); // rotate about the x-axis |
330 |
|
331 |
|
332 |
dAtom->setA( A ); |
333 |
dAtom->setJx( ji[0] ); |
334 |
dAtom->setJy( ji[1] ); |
335 |
dAtom->setJz( ji[2] ); |
336 |
} |
337 |
} |
338 |
|
339 |
// calculate the forces |
340 |
|
341 |
myFF->doForces(calcPot, calcStress); |
342 |
|
343 |
// move b |
344 |
|
345 |
for( j=0; j<nAtoms; j++ ){ |
346 |
|
347 |
Rx[j] = atoms[j]->getX(); |
348 |
Ry[j] = atoms[j]->getY(); |
349 |
Rz[j] = atoms[j]->getZ(); |
350 |
|
351 |
Vx[j] = atoms[j]->get_vx(); |
352 |
Vy[j] = atoms[j]->get_vy(); |
353 |
Vz[j] = atoms[j]->get_vz(); |
354 |
|
355 |
Fx[j] = atoms[j]->getFx(); |
356 |
Fy[j] = atoms[j]->getFy(); |
357 |
Fz[j] = atoms[j]->getFz(); |
358 |
} |
359 |
|
360 |
v_constrain_b_( dt, nAtoms, mass, Rx, Ry, Rz, Vx, Vy, Vz, |
361 |
Fx, Fy, Fz, |
362 |
kE, n_constrained, constrained_dsqr, |
363 |
constrained_i, constrained_j, |
364 |
entry_plug->box_x, |
365 |
entry_plug->box_y, |
366 |
entry_plug->box_z ); |
367 |
|
368 |
for( j=0; j<nAtoms; j++ ){ |
369 |
|
370 |
atoms[j]->setX(Rx[j]); |
371 |
atoms[j]->setY(Ry[j]); |
372 |
atoms[j]->setZ(Rz[j]); |
373 |
|
374 |
atoms[j]->set_vx(Vx[j]); |
375 |
atoms[j]->set_vy(Vy[j]); |
376 |
atoms[j]->set_vz(Vz[j]); |
377 |
} |
378 |
|
379 |
for( i=0; i< nAtoms; i++ ){ |
380 |
|
381 |
if( atoms[i]->isDirectional() ){ |
382 |
|
383 |
dAtom = (DirectionalAtom *)atoms[i]; |
384 |
|
385 |
// get and convert the torque to body frame |
386 |
|
387 |
Tb[0] = dAtom->getTx(); |
388 |
Tb[1] = dAtom->getTy(); |
389 |
Tb[2] = dAtom->getTz(); |
390 |
|
391 |
dAtom->lab2Body( Tb ); |
392 |
|
393 |
// get the angular momentum, and complete the angular momentum |
394 |
// half step |
395 |
|
396 |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * e_convert; |
397 |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * e_convert; |
398 |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * e_convert; |
399 |
|
400 |
dAtom->setJx( ji[0] ); |
401 |
dAtom->setJy( ji[1] ); |
402 |
dAtom->setJz( ji[2] ); |
403 |
} |
404 |
} |
405 |
|
406 |
|
407 |
if (!strcasecmp( entry_plug->ensemble, "NVT")) |
408 |
myES->NoseHooverNVT( dt / 2.0, tStats->getKinetic() ); |
409 |
|
410 |
if (!strcasecmp( entry_plug->ensemble, "NPT") ) { |
411 |
tStats->getPressureTensor(press); |
412 |
myES->NoseHooverAndersonNPT( dt, |
413 |
tStats->getKinetic(), |
414 |
press); |
415 |
} |
416 |
|
417 |
time = tl + 1; |
418 |
|
419 |
if( entry_plug->setTemp ){ |
420 |
if( !(time % vel_n) ) tStats->velocitize(); |
421 |
} |
422 |
if( !(time % sample_n) ) dump_out->writeDump( time * dt ); |
423 |
if( !((time+1) % status_n) ) { |
424 |
calcPot = 1; |
425 |
calcStress = 1; |
426 |
} |
427 |
if( !(time % status_n) ){ |
428 |
e_out->writeStat( time * dt ); |
429 |
calcPot = 0; |
430 |
if (!strcasecmp(entry_plug->ensemble, "NPT")) calcStress = 1; |
431 |
else calcStress = 0; |
432 |
} |
433 |
} |
434 |
} |
435 |
else{ |
436 |
|
437 |
for( tl=0; tl<n_loops; tl++ ){ |
438 |
|
439 |
kE = 0.0; |
440 |
rot_kE= 0.0; |
441 |
trans_kE = 0.0; |
442 |
|
443 |
if (!strcasecmp( entry_plug->ensemble, "NVT")) |
444 |
myES->NoseHooverNVT( dt / 2.0, tStats->getKinetic() ); |
445 |
|
446 |
for( i=0; i<nAtoms; i++ ){ |
447 |
|
448 |
// velocity half step |
449 |
|
450 |
vx = atoms[i]->get_vx() + |
451 |
( dt2 * atoms[i]->getFx() / atoms[i]->getMass() ) * e_convert; |
452 |
vy = atoms[i]->get_vy() + |
453 |
( dt2 * atoms[i]->getFy() / atoms[i]->getMass() ) * e_convert; |
454 |
vz = atoms[i]->get_vz() + |
455 |
( dt2 * atoms[i]->getFz() / atoms[i]->getMass() ) * e_convert; |
456 |
|
457 |
// position whole step |
458 |
|
459 |
rx = atoms[i]->getX() + dt * vx; |
460 |
ry = atoms[i]->getY() + dt * vy; |
461 |
rz = atoms[i]->getZ() + dt * vz; |
462 |
|
463 |
atoms[i]->setX( rx ); |
464 |
atoms[i]->setY( ry ); |
465 |
atoms[i]->setZ( rz ); |
466 |
|
467 |
atoms[i]->set_vx( vx ); |
468 |
atoms[i]->set_vy( vy ); |
469 |
atoms[i]->set_vz( vz ); |
470 |
|
471 |
if( atoms[i]->isDirectional() ){ |
472 |
|
473 |
dAtom = (DirectionalAtom *)atoms[i]; |
474 |
|
475 |
// get and convert the torque to body frame |
476 |
|
477 |
Tb[0] = dAtom->getTx(); |
478 |
Tb[1] = dAtom->getTy(); |
479 |
Tb[2] = dAtom->getTz(); |
480 |
|
481 |
dAtom->lab2Body( Tb ); |
482 |
|
483 |
// get the angular momentum, and propagate a half step |
484 |
|
485 |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * e_convert; |
486 |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * e_convert; |
487 |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * e_convert; |
488 |
|
489 |
// get the atom's rotation matrix |
490 |
|
491 |
A[0][0] = dAtom->getAxx(); |
492 |
A[0][1] = dAtom->getAxy(); |
493 |
A[0][2] = dAtom->getAxz(); |
494 |
|
495 |
A[1][0] = dAtom->getAyx(); |
496 |
A[1][1] = dAtom->getAyy(); |
497 |
A[1][2] = dAtom->getAyz(); |
498 |
|
499 |
A[2][0] = dAtom->getAzx(); |
500 |
A[2][1] = dAtom->getAzy(); |
501 |
A[2][2] = dAtom->getAzz(); |
502 |
|
503 |
|
504 |
// use the angular velocities to propagate the rotation matrix a |
505 |
// full time step |
506 |
|
507 |
|
508 |
angle = dt2 * ji[0] / dAtom->getIxx(); |
509 |
this->rotate( 1, 2, angle, ji, A ); // rotate about the x-axis |
510 |
|
511 |
angle = dt2 * ji[1] / dAtom->getIyy(); |
512 |
this->rotate( 2, 0, angle, ji, A ); // rotate about the y-axis |
513 |
|
514 |
angle = dt * ji[2] / dAtom->getIzz(); |
515 |
this->rotate( 0, 1, angle, ji, A ); // rotate about the z-axis |
516 |
|
517 |
angle = dt2 * ji[1] / dAtom->getIyy(); |
518 |
this->rotate( 2, 0, angle, ji, A ); // rotate about the y-axis |
519 |
|
520 |
angle = dt2 * ji[0] / dAtom->getIxx(); |
521 |
this->rotate( 1, 2, angle, ji, A ); // rotate about the x-axis |
522 |
|
523 |
|
524 |
dAtom->setA( A ); |
525 |
dAtom->setJx( ji[0] ); |
526 |
dAtom->setJy( ji[1] ); |
527 |
dAtom->setJz( ji[2] ); |
528 |
} |
529 |
} |
530 |
|
531 |
// calculate the forces |
532 |
|
533 |
myFF->doForces(calcPot,calcStress); |
534 |
|
535 |
for( i=0; i< nAtoms; i++ ){ |
536 |
|
537 |
// complete the velocity half step |
538 |
|
539 |
vx = atoms[i]->get_vx() + |
540 |
( dt2 * atoms[i]->getFx() / atoms[i]->getMass() ) * e_convert; |
541 |
vy = atoms[i]->get_vy() + |
542 |
( dt2 * atoms[i]->getFy() / atoms[i]->getMass() ) * e_convert; |
543 |
vz = atoms[i]->get_vz() + |
544 |
( dt2 * atoms[i]->getFz() / atoms[i]->getMass() ) * e_convert; |
545 |
|
546 |
atoms[i]->set_vx( vx ); |
547 |
atoms[i]->set_vy( vy ); |
548 |
atoms[i]->set_vz( vz ); |
549 |
|
550 |
vx2 = vx * vx; |
551 |
vy2 = vy * vy; |
552 |
vz2 = vz * vz; |
553 |
|
554 |
if( atoms[i]->isDirectional() ){ |
555 |
|
556 |
dAtom = (DirectionalAtom *)atoms[i]; |
557 |
|
558 |
// get and convert the torque to body frame |
559 |
|
560 |
Tb[0] = dAtom->getTx(); |
561 |
Tb[1] = dAtom->getTy(); |
562 |
Tb[2] = dAtom->getTz(); |
563 |
|
564 |
dAtom->lab2Body( Tb ); |
565 |
|
566 |
// get the angular momentum, and complete the angular momentum |
567 |
// half step |
568 |
|
569 |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * e_convert; |
570 |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * e_convert; |
571 |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * e_convert; |
572 |
|
573 |
jx2 = ji[0] * ji[0]; |
574 |
jy2 = ji[1] * ji[1]; |
575 |
jz2 = ji[2] * ji[2]; |
576 |
|
577 |
rot_kE += (jx2 / dAtom->getIxx()) + (jy2 / dAtom->getIyy()) |
578 |
+ (jz2 / dAtom->getIzz()); |
579 |
|
580 |
dAtom->setJx( ji[0] ); |
581 |
dAtom->setJy( ji[1] ); |
582 |
dAtom->setJz( ji[2] ); |
583 |
} |
584 |
|
585 |
} |
586 |
|
587 |
if (!strcasecmp( entry_plug->ensemble, "NVT")) |
588 |
myES->NoseHooverNVT( dt / 2.0, tStats->getKinetic() ); |
589 |
|
590 |
if (!strcasecmp( entry_plug->ensemble, "NPT") ) { |
591 |
tStats->getPressureTensor(press); |
592 |
myES->NoseHooverAndersonNPT( dt, |
593 |
tStats->getKinetic(), |
594 |
press); |
595 |
} |
596 |
|
597 |
time = tl + 1; |
598 |
|
599 |
if( entry_plug->setTemp ){ |
600 |
if( !(time % vel_n) ) tStats->velocitize(); |
601 |
} |
602 |
if( !(time % sample_n) ) dump_out->writeDump( time * dt ); |
603 |
if( !((time+1) % status_n) ) { |
604 |
calcPot = 1; |
605 |
calcStress = 1; |
606 |
} |
607 |
if( !(time % status_n) ){ |
608 |
e_out->writeStat( time * dt ); |
609 |
calcPot = 0; |
610 |
if (!strcasecmp(entry_plug->ensemble, "NPT")) calcStress = 1; |
611 |
else calcStress = 0; |
612 |
} |
613 |
} |
614 |
} |
615 |
|
616 |
dump_out->writeFinal(); |
617 |
|
618 |
delete dump_out; |
619 |
delete e_out; |
620 |
} |
621 |
|
622 |
void Symplectic::rotate( int axes1, int axes2, double angle, double ji[3], |
623 |
double A[3][3] ){ |
624 |
|
625 |
int i,j,k; |
626 |
double sinAngle; |
627 |
double cosAngle; |
628 |
double angleSqr; |
629 |
double angleSqrOver4; |
630 |
double top, bottom; |
631 |
double rot[3][3]; |
632 |
double tempA[3][3]; |
633 |
double tempJ[3]; |
634 |
|
635 |
// initialize the tempA |
636 |
|
637 |
for(i=0; i<3; i++){ |
638 |
for(j=0; j<3; j++){ |
639 |
tempA[j][i] = A[i][j]; |
640 |
} |
641 |
} |
642 |
|
643 |
// initialize the tempJ |
644 |
|
645 |
for( i=0; i<3; i++) tempJ[i] = ji[i]; |
646 |
|
647 |
// initalize rot as a unit matrix |
648 |
|
649 |
rot[0][0] = 1.0; |
650 |
rot[0][1] = 0.0; |
651 |
rot[0][2] = 0.0; |
652 |
|
653 |
rot[1][0] = 0.0; |
654 |
rot[1][1] = 1.0; |
655 |
rot[1][2] = 0.0; |
656 |
|
657 |
rot[2][0] = 0.0; |
658 |
rot[2][1] = 0.0; |
659 |
rot[2][2] = 1.0; |
660 |
|
661 |
// use a small angle aproximation for sin and cosine |
662 |
|
663 |
angleSqr = angle * angle; |
664 |
angleSqrOver4 = angleSqr / 4.0; |
665 |
top = 1.0 - angleSqrOver4; |
666 |
bottom = 1.0 + angleSqrOver4; |
667 |
|
668 |
cosAngle = top / bottom; |
669 |
sinAngle = angle / bottom; |
670 |
|
671 |
rot[axes1][axes1] = cosAngle; |
672 |
rot[axes2][axes2] = cosAngle; |
673 |
|
674 |
rot[axes1][axes2] = sinAngle; |
675 |
rot[axes2][axes1] = -sinAngle; |
676 |
|
677 |
// rotate the momentum acoording to: ji[] = rot[][] * ji[] |
678 |
|
679 |
for(i=0; i<3; i++){ |
680 |
ji[i] = 0.0; |
681 |
for(k=0; k<3; k++){ |
682 |
ji[i] += rot[i][k] * tempJ[k]; |
683 |
} |
684 |
} |
685 |
|
686 |
// rotate the Rotation matrix acording to: |
687 |
// A[][] = A[][] * transpose(rot[][]) |
688 |
|
689 |
|
690 |
// NOte for as yet unknown reason, we are setting the performing the |
691 |
// calculation as: |
692 |
// transpose(A[][]) = transpose(A[][]) * transpose(rot[][]) |
693 |
|
694 |
for(i=0; i<3; i++){ |
695 |
for(j=0; j<3; j++){ |
696 |
A[j][i] = 0.0; |
697 |
for(k=0; k<3; k++){ |
698 |
A[j][i] += tempA[i][k] * rot[j][k]; |
699 |
} |
700 |
} |
701 |
} |
702 |
} |