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 |
|
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|
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|
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 |
|
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constrained = theArray[j]->is_constrained(); |
73 |
|
74 |
if(constrained){ |
75 |
|
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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() ); |
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(); |
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for(int j=0; j<molecules[i].getNBends(); j++){ |
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|
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constrained = theArray[j]->is_constrained(); |
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|
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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 |
|
108 |
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 ){ |
153 |
|
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const double e_convert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2 |
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|
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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 |
|
164 |
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 |
|
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int time; |
175 |
|
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double dt = entry_plug->dt; |
177 |
double runTime = entry_plug->run_time; |
178 |
double sampleTime = entry_plug->sampleTime; |
179 |
double statusTime = entry_plug->statusTime; |
180 |
double thermalTime = entry_plug->thermalTime; |
181 |
|
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int n_loops = (int)( runTime / dt ); |
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int sample_n = (int)( sampleTime / dt ); |
184 |
int status_n = (int)( statusTime / dt ); |
185 |
int vel_n = (int)( thermalTime / dt ); |
186 |
|
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int calcPot; |
188 |
|
189 |
Thermo *tStats = new Thermo( entry_plug ); |
190 |
|
191 |
StatWriter* e_out = new StatWriter( entry_plug ); |
192 |
DumpWriter* dump_out = new DumpWriter( entry_plug ); |
193 |
|
194 |
Atom** atoms = entry_plug->atoms; |
195 |
DirectionalAtom* dAtom; |
196 |
dt2 = 0.5 * dt; |
197 |
|
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// initialize the forces the before the first step |
199 |
|
200 |
myFF->doForces(1,0); |
201 |
|
202 |
if( entry_plug->setTemp ){ |
203 |
|
204 |
tStats->velocitize(); |
205 |
} |
206 |
|
207 |
dump_out->writeDump( 0.0 ); |
208 |
e_out->writeStat( 0.0 ); |
209 |
|
210 |
calcPot = 0; |
211 |
|
212 |
if( n_constrained ){ |
213 |
|
214 |
double *Rx = new double[nAtoms]; |
215 |
double *Ry = new double[nAtoms]; |
216 |
double *Rz = new double[nAtoms]; |
217 |
|
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double *Vx = new double[nAtoms]; |
219 |
double *Vy = new double[nAtoms]; |
220 |
double *Vz = new double[nAtoms]; |
221 |
|
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double *Fx = new double[nAtoms]; |
223 |
double *Fy = new double[nAtoms]; |
224 |
double *Fz = new double[nAtoms]; |
225 |
|
226 |
|
227 |
for( tl=0; tl < n_loops; tl++ ){ |
228 |
|
229 |
for( j=0; j<nAtoms; j++ ){ |
230 |
|
231 |
Rx[j] = atoms[j]->getX(); |
232 |
Ry[j] = atoms[j]->getY(); |
233 |
Rz[j] = atoms[j]->getZ(); |
234 |
|
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Vx[j] = atoms[j]->get_vx(); |
236 |
Vy[j] = atoms[j]->get_vy(); |
237 |
Vz[j] = atoms[j]->get_vz(); |
238 |
|
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Fx[j] = atoms[j]->getFx(); |
240 |
Fy[j] = atoms[j]->getFy(); |
241 |
Fz[j] = atoms[j]->getFz(); |
242 |
|
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} |
244 |
|
245 |
v_constrain_a_( dt, nAtoms, mass, Rx, Ry, Rz, Vx, Vy, Vz, |
246 |
Fx, Fy, Fz, |
247 |
n_constrained, constrained_dsqr, |
248 |
constrained_i, constrained_j, |
249 |
entry_plug->box_x, |
250 |
entry_plug->box_y, |
251 |
entry_plug->box_z ); |
252 |
|
253 |
for( j=0; j<nAtoms; j++ ){ |
254 |
|
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atoms[j]->setX(Rx[j]); |
256 |
atoms[j]->setY(Ry[j]); |
257 |
atoms[j]->setZ(Rz[j]); |
258 |
|
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atoms[j]->set_vx(Vx[j]); |
260 |
atoms[j]->set_vy(Vy[j]); |
261 |
atoms[j]->set_vz(Vz[j]); |
262 |
} |
263 |
|
264 |
|
265 |
for( i=0; i<nAtoms; i++ ){ |
266 |
if( atoms[i]->isDirectional() ){ |
267 |
|
268 |
dAtom = (DirectionalAtom *)atoms[i]; |
269 |
|
270 |
// get and convert the torque to body frame |
271 |
|
272 |
Tb[0] = dAtom->getTx(); |
273 |
Tb[1] = dAtom->getTy(); |
274 |
Tb[2] = dAtom->getTz(); |
275 |
|
276 |
dAtom->lab2Body( Tb ); |
277 |
|
278 |
// get the angular momentum, and propagate a half step |
279 |
|
280 |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * e_convert; |
281 |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * e_convert; |
282 |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * e_convert; |
283 |
|
284 |
// get the atom's rotation matrix |
285 |
|
286 |
A[0][0] = dAtom->getAxx(); |
287 |
A[0][1] = dAtom->getAxy(); |
288 |
A[0][2] = dAtom->getAxz(); |
289 |
|
290 |
A[1][0] = dAtom->getAyx(); |
291 |
A[1][1] = dAtom->getAyy(); |
292 |
A[1][2] = dAtom->getAyz(); |
293 |
|
294 |
A[2][0] = dAtom->getAzx(); |
295 |
A[2][1] = dAtom->getAzy(); |
296 |
A[2][2] = dAtom->getAzz(); |
297 |
|
298 |
|
299 |
// use the angular velocities to propagate the rotation matrix a |
300 |
// full time step |
301 |
|
302 |
|
303 |
angle = dt2 * ji[0] / dAtom->getIxx(); |
304 |
this->rotate( 1, 2, angle, ji, A ); // rotate about the x-axis |
305 |
|
306 |
angle = dt2 * ji[1] / dAtom->getIyy(); |
307 |
this->rotate( 2, 0, angle, ji, A ); // rotate about the y-axis |
308 |
|
309 |
angle = dt * ji[2] / dAtom->getIzz(); |
310 |
this->rotate( 0, 1, angle, ji, A ); // rotate about the z-axis |
311 |
|
312 |
angle = dt2 * ji[1] / dAtom->getIyy(); |
313 |
this->rotate( 2, 0, angle, ji, A ); // rotate about the y-axis |
314 |
|
315 |
angle = dt2 * ji[0] / dAtom->getIxx(); |
316 |
this->rotate( 1, 2, angle, ji, A ); // rotate about the x-axis |
317 |
|
318 |
|
319 |
dAtom->setA( A ); |
320 |
dAtom->setJx( ji[0] ); |
321 |
dAtom->setJy( ji[1] ); |
322 |
dAtom->setJz( ji[2] ); |
323 |
} |
324 |
} |
325 |
|
326 |
// calculate the forces |
327 |
|
328 |
myFF->doForces(calcPot, 0); |
329 |
|
330 |
// move b |
331 |
|
332 |
for( j=0; j<nAtoms; j++ ){ |
333 |
|
334 |
Rx[j] = atoms[j]->getX(); |
335 |
Ry[j] = atoms[j]->getY(); |
336 |
Rz[j] = atoms[j]->getZ(); |
337 |
|
338 |
Vx[j] = atoms[j]->get_vx(); |
339 |
Vy[j] = atoms[j]->get_vy(); |
340 |
Vz[j] = atoms[j]->get_vz(); |
341 |
|
342 |
Fx[j] = atoms[j]->getFx(); |
343 |
Fy[j] = atoms[j]->getFy(); |
344 |
Fz[j] = atoms[j]->getFz(); |
345 |
} |
346 |
|
347 |
v_constrain_b_( dt, nAtoms, mass, Rx, Ry, Rz, Vx, Vy, Vz, |
348 |
Fx, Fy, Fz, |
349 |
kE, n_constrained, constrained_dsqr, |
350 |
constrained_i, constrained_j, |
351 |
entry_plug->box_x, |
352 |
entry_plug->box_y, |
353 |
entry_plug->box_z ); |
354 |
|
355 |
for( j=0; j<nAtoms; j++ ){ |
356 |
|
357 |
atoms[j]->setX(Rx[j]); |
358 |
atoms[j]->setY(Ry[j]); |
359 |
atoms[j]->setZ(Rz[j]); |
360 |
|
361 |
atoms[j]->set_vx(Vx[j]); |
362 |
atoms[j]->set_vy(Vy[j]); |
363 |
atoms[j]->set_vz(Vz[j]); |
364 |
} |
365 |
|
366 |
for( i=0; i< nAtoms; i++ ){ |
367 |
|
368 |
if( atoms[i]->isDirectional() ){ |
369 |
|
370 |
dAtom = (DirectionalAtom *)atoms[i]; |
371 |
|
372 |
// get and convert the torque to body frame |
373 |
|
374 |
Tb[0] = dAtom->getTx(); |
375 |
Tb[1] = dAtom->getTy(); |
376 |
Tb[2] = dAtom->getTz(); |
377 |
|
378 |
dAtom->lab2Body( Tb ); |
379 |
|
380 |
// get the angular momentum, and complete the angular momentum |
381 |
// half step |
382 |
|
383 |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * e_convert; |
384 |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * e_convert; |
385 |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * e_convert; |
386 |
|
387 |
dAtom->setJx( ji[0] ); |
388 |
dAtom->setJy( ji[1] ); |
389 |
dAtom->setJz( ji[2] ); |
390 |
} |
391 |
} |
392 |
|
393 |
time = tl + 1; |
394 |
|
395 |
if( entry_plug->setTemp ){ |
396 |
if( !(time % vel_n) ) tStats->velocitize(); |
397 |
} |
398 |
if( !(time % sample_n) ) dump_out->writeDump( time * dt ); |
399 |
if( !((time+1) % status_n) ) calcPot = 1; |
400 |
if( !(time % status_n) ){ e_out->writeStat( time * dt ); calcPot = 0; } |
401 |
} |
402 |
} |
403 |
else{ |
404 |
|
405 |
for( tl=0; tl<n_loops; tl++ ){ |
406 |
|
407 |
kE = 0.0; |
408 |
rot_kE= 0.0; |
409 |
trans_kE = 0.0; |
410 |
|
411 |
for( i=0; i<nAtoms; i++ ){ |
412 |
|
413 |
// velocity half step |
414 |
|
415 |
vx = atoms[i]->get_vx() + |
416 |
( dt2 * atoms[i]->getFx() / atoms[i]->getMass() ) * e_convert; |
417 |
vy = atoms[i]->get_vy() + |
418 |
( dt2 * atoms[i]->getFy() / atoms[i]->getMass() ) * e_convert; |
419 |
vz = atoms[i]->get_vz() + |
420 |
( dt2 * atoms[i]->getFz() / atoms[i]->getMass() ) * e_convert; |
421 |
|
422 |
// position whole step |
423 |
|
424 |
rx = atoms[i]->getX() + dt * vx; |
425 |
ry = atoms[i]->getY() + dt * vy; |
426 |
rz = atoms[i]->getZ() + dt * vz; |
427 |
|
428 |
atoms[i]->setX( rx ); |
429 |
atoms[i]->setY( ry ); |
430 |
atoms[i]->setZ( rz ); |
431 |
|
432 |
atoms[i]->set_vx( vx ); |
433 |
atoms[i]->set_vy( vy ); |
434 |
atoms[i]->set_vz( vz ); |
435 |
|
436 |
if( atoms[i]->isDirectional() ){ |
437 |
|
438 |
dAtom = (DirectionalAtom *)atoms[i]; |
439 |
|
440 |
// get and convert the torque to body frame |
441 |
|
442 |
Tb[0] = dAtom->getTx(); |
443 |
Tb[1] = dAtom->getTy(); |
444 |
Tb[2] = dAtom->getTz(); |
445 |
|
446 |
dAtom->lab2Body( Tb ); |
447 |
|
448 |
// get the angular momentum, and propagate a half step |
449 |
|
450 |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * e_convert; |
451 |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * e_convert; |
452 |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * e_convert; |
453 |
|
454 |
// get the atom's rotation matrix |
455 |
|
456 |
A[0][0] = dAtom->getAxx(); |
457 |
A[0][1] = dAtom->getAxy(); |
458 |
A[0][2] = dAtom->getAxz(); |
459 |
|
460 |
A[1][0] = dAtom->getAyx(); |
461 |
A[1][1] = dAtom->getAyy(); |
462 |
A[1][2] = dAtom->getAyz(); |
463 |
|
464 |
A[2][0] = dAtom->getAzx(); |
465 |
A[2][1] = dAtom->getAzy(); |
466 |
A[2][2] = dAtom->getAzz(); |
467 |
|
468 |
|
469 |
// use the angular velocities to propagate the rotation matrix a |
470 |
// full time step |
471 |
|
472 |
|
473 |
angle = dt2 * ji[0] / dAtom->getIxx(); |
474 |
this->rotate( 1, 2, angle, ji, A ); // rotate about the x-axis |
475 |
|
476 |
angle = dt2 * ji[1] / dAtom->getIyy(); |
477 |
this->rotate( 2, 0, angle, ji, A ); // rotate about the y-axis |
478 |
|
479 |
angle = dt * ji[2] / dAtom->getIzz(); |
480 |
this->rotate( 0, 1, angle, ji, A ); // rotate about the z-axis |
481 |
|
482 |
angle = dt2 * ji[1] / dAtom->getIyy(); |
483 |
this->rotate( 2, 0, angle, ji, A ); // rotate about the y-axis |
484 |
|
485 |
angle = dt2 * ji[0] / dAtom->getIxx(); |
486 |
this->rotate( 1, 2, angle, ji, A ); // rotate about the x-axis |
487 |
|
488 |
|
489 |
dAtom->setA( A ); |
490 |
dAtom->setJx( ji[0] ); |
491 |
dAtom->setJy( ji[1] ); |
492 |
dAtom->setJz( ji[2] ); |
493 |
} |
494 |
} |
495 |
|
496 |
// calculate the forces |
497 |
|
498 |
myFF->doForces(calcPot,0); |
499 |
|
500 |
for( i=0; i< nAtoms; i++ ){ |
501 |
|
502 |
// complete the velocity half step |
503 |
|
504 |
vx = atoms[i]->get_vx() + |
505 |
( dt2 * atoms[i]->getFx() / atoms[i]->getMass() ) * e_convert; |
506 |
vy = atoms[i]->get_vy() + |
507 |
( dt2 * atoms[i]->getFy() / atoms[i]->getMass() ) * e_convert; |
508 |
vz = atoms[i]->get_vz() + |
509 |
( dt2 * atoms[i]->getFz() / atoms[i]->getMass() ) * e_convert; |
510 |
|
511 |
atoms[i]->set_vx( vx ); |
512 |
atoms[i]->set_vy( vy ); |
513 |
atoms[i]->set_vz( vz ); |
514 |
|
515 |
// vx2 = vx * vx; |
516 |
// vy2 = vy * vy; |
517 |
// vz2 = vz * vz; |
518 |
|
519 |
if( atoms[i]->isDirectional() ){ |
520 |
|
521 |
dAtom = (DirectionalAtom *)atoms[i]; |
522 |
|
523 |
// get and convert the torque to body frame |
524 |
|
525 |
Tb[0] = dAtom->getTx(); |
526 |
Tb[1] = dAtom->getTy(); |
527 |
Tb[2] = dAtom->getTz(); |
528 |
|
529 |
dAtom->lab2Body( Tb ); |
530 |
|
531 |
// get the angular momentum, and complete the angular momentum |
532 |
// half step |
533 |
|
534 |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * e_convert; |
535 |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * e_convert; |
536 |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * e_convert; |
537 |
|
538 |
jx2 = ji[0] * ji[0]; |
539 |
jy2 = ji[1] * ji[1]; |
540 |
jz2 = ji[2] * ji[2]; |
541 |
|
542 |
rot_kE += (jx2 / dAtom->getIxx()) + (jy2 / dAtom->getIyy()) |
543 |
+ (jz2 / dAtom->getIzz()); |
544 |
|
545 |
dAtom->setJx( ji[0] ); |
546 |
dAtom->setJy( ji[1] ); |
547 |
dAtom->setJz( ji[2] ); |
548 |
} |
549 |
} |
550 |
|
551 |
time = tl + 1; |
552 |
|
553 |
if( entry_plug->setTemp ){ |
554 |
if( !(time % vel_n) ) tStats->velocitize(); |
555 |
} |
556 |
if( !(time % sample_n) ) dump_out->writeDump( time * dt ); |
557 |
if( !((time+1) % status_n) ) calcPot = 1; |
558 |
if( !(time % status_n) ){ e_out->writeStat( time * dt ); calcPot = 0; } |
559 |
} |
560 |
} |
561 |
|
562 |
dump_out->writeFinal(); |
563 |
|
564 |
delete dump_out; |
565 |
delete e_out; |
566 |
} |
567 |
|
568 |
void Symplectic::rotate( int axes1, int axes2, double angle, double ji[3], |
569 |
double A[3][3] ){ |
570 |
|
571 |
int i,j,k; |
572 |
double sinAngle; |
573 |
double cosAngle; |
574 |
double angleSqr; |
575 |
double angleSqrOver4; |
576 |
double top, bottom; |
577 |
double rot[3][3]; |
578 |
double tempA[3][3]; |
579 |
double tempJ[3]; |
580 |
|
581 |
// initialize the tempA |
582 |
|
583 |
for(i=0; i<3; i++){ |
584 |
for(j=0; j<3; j++){ |
585 |
tempA[j][i] = A[i][j]; |
586 |
} |
587 |
} |
588 |
|
589 |
// initialize the tempJ |
590 |
|
591 |
for( i=0; i<3; i++) tempJ[i] = ji[i]; |
592 |
|
593 |
// initalize rot as a unit matrix |
594 |
|
595 |
rot[0][0] = 1.0; |
596 |
rot[0][1] = 0.0; |
597 |
rot[0][2] = 0.0; |
598 |
|
599 |
rot[1][0] = 0.0; |
600 |
rot[1][1] = 1.0; |
601 |
rot[1][2] = 0.0; |
602 |
|
603 |
rot[2][0] = 0.0; |
604 |
rot[2][1] = 0.0; |
605 |
rot[2][2] = 1.0; |
606 |
|
607 |
// use a small angle aproximation for sin and cosine |
608 |
|
609 |
angleSqr = angle * angle; |
610 |
angleSqrOver4 = angleSqr / 4.0; |
611 |
top = 1.0 - angleSqrOver4; |
612 |
bottom = 1.0 + angleSqrOver4; |
613 |
|
614 |
cosAngle = top / bottom; |
615 |
sinAngle = angle / bottom; |
616 |
|
617 |
rot[axes1][axes1] = cosAngle; |
618 |
rot[axes2][axes2] = cosAngle; |
619 |
|
620 |
rot[axes1][axes2] = sinAngle; |
621 |
rot[axes2][axes1] = -sinAngle; |
622 |
|
623 |
// rotate the momentum acoording to: ji[] = rot[][] * ji[] |
624 |
|
625 |
for(i=0; i<3; i++){ |
626 |
ji[i] = 0.0; |
627 |
for(k=0; k<3; k++){ |
628 |
ji[i] += rot[i][k] * tempJ[k]; |
629 |
} |
630 |
} |
631 |
|
632 |
// rotate the Rotation matrix acording to: |
633 |
// A[][] = A[][] * transpose(rot[][]) |
634 |
|
635 |
|
636 |
// NOte for as yet unknown reason, we are setting the performing the |
637 |
// calculation as: |
638 |
// transpose(A[][]) = transpose(A[][]) * transpose(rot[][]) |
639 |
|
640 |
for(i=0; i<3; i++){ |
641 |
for(j=0; j<3; j++){ |
642 |
A[j][i] = 0.0; |
643 |
for(k=0; k<3; k++){ |
644 |
A[j][i] += tempA[i][k] * rot[j][k]; |
645 |
} |
646 |
} |
647 |
} |
648 |
} |