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#include <iostream> |
2 |
#include <cstdlib> |
3 |
|
4 |
#include "Integrator.hpp" |
5 |
#include "Thermo.hpp" |
6 |
#include "ReadWrite.hpp" |
7 |
#include "ForceFields.hpp" |
8 |
#include "simError.h" |
9 |
|
10 |
extern "C"{ |
11 |
|
12 |
void v_constrain_a_( double &dt, int &n_atoms, double* mass, |
13 |
double* Rx, double* Ry, double* Rz, |
14 |
double* Vx, double* Vy, double* Vz, |
15 |
double* Fx, double* Fy, double* Fz, |
16 |
int &n_constrained, double *constr_sqr, |
17 |
int* constr_i, int* constr_j, |
18 |
double &box_x, double &box_y, double &box_z ); |
19 |
|
20 |
void v_constrain_b_( double &dt, int &n_atoms, double* mass, |
21 |
double* Rx, double* Ry, double* Rz, |
22 |
double* Vx, double* Vy, double* Vz, |
23 |
double* Fx, double* Fy, double* Fz, |
24 |
double &Kinetic, |
25 |
int &n_constrained, double *constr_sqr, |
26 |
int* constr_i, int* constr_j, |
27 |
double &box_x, double &box_y, double &box_z ); |
28 |
} |
29 |
|
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|
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|
32 |
|
33 |
Symplectic::Symplectic( SimInfo* the_entry_plug, ForceFields* the_ff ){ |
34 |
entry_plug = the_entry_plug; |
35 |
myFF = the_ff; |
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isFirst = 1; |
37 |
|
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molecules = entry_plug->molecules; |
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nMols = entry_plug->n_mol; |
40 |
|
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// give a little love back to the SimInfo object |
42 |
|
43 |
if( entry_plug->the_integrator != NULL ) delete entry_plug->the_integrator; |
44 |
entry_plug->the_integrator = this; |
45 |
|
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// grab the masses |
47 |
|
48 |
mass = new double[entry_plug->n_atoms]; |
49 |
for(int i = 0; i < entry_plug->n_atoms; i++){ |
50 |
mass[i] = entry_plug->atoms[i]->getMass(); |
51 |
} |
52 |
|
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|
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|
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// check for constraints |
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|
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is_constrained = 0; |
58 |
|
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Constraint *temp_con; |
60 |
Constraint *dummy_plug; |
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temp_con = new Constraint[entry_plug->n_SRI]; |
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n_constrained = 0; |
63 |
int constrained = 0; |
64 |
|
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SRI** theArray; |
66 |
for(int i = 0; i < nMols; i++){ |
67 |
|
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theArray = (SRI**) molecules[i].getMyBonds(); |
69 |
for(int j=0; j<molecules[i].getNBonds(); j++){ |
70 |
|
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constrained = theArray[j]->is_constrained(); |
72 |
|
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if(constrained){ |
74 |
|
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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() ); |
79 |
|
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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() ); |
96 |
|
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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].getMyTorsions(); |
103 |
for(int j=0; j<molecules[i].getNTorsions(); j++){ |
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|
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constrained = theArray[j]->is_constrained(); |
106 |
|
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if(constrained){ |
108 |
|
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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() ); |
113 |
|
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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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} |
136 |
|
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delete[] temp_con; |
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} |
139 |
|
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Symplectic::~Symplectic() { |
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|
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if( n_constrained ){ |
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delete[] constrained_i; |
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delete[] constrained_j; |
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delete[] constrained_dsqr; |
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} |
147 |
|
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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 |
154 |
|
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int i, j; // loop counters |
156 |
int nAtoms = entry_plug->n_atoms; // the number of atoms |
157 |
double kE = 0.0; // the kinetic energy |
158 |
double rot_kE; |
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double trans_kE; |
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int tl; // the time loop conter |
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double dt2; // half the dt |
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|
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double vx, vy, vz; // the velocities |
164 |
// double vx2, vy2, vz2; // the square of the velocities |
165 |
double rx, ry, rz; // the postitions |
166 |
|
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double ji[3]; // the body frame angular momentum |
168 |
double jx2, jy2, jz2; // the square of the angular momentums |
169 |
double Tb[3]; // torque in the body frame |
170 |
double angle; // the angle through which to rotate the rotation matrix |
171 |
double A[3][3]; // the rotation matrix |
172 |
|
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int time; |
174 |
|
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double dt = entry_plug->dt; |
176 |
double runTime = entry_plug->run_time; |
177 |
double sampleTime = entry_plug->sampleTime; |
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double statusTime = entry_plug->statusTime; |
179 |
double thermalTime = entry_plug->thermalTime; |
180 |
|
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int n_loops = (int)( runTime / dt ); |
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int sample_n = (int)( sampleTime / dt ); |
183 |
int status_n = (int)( statusTime / dt ); |
184 |
int vel_n = (int)( thermalTime / dt ); |
185 |
|
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int calcPot; |
187 |
|
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Thermo *tStats = new Thermo( entry_plug ); |
189 |
|
190 |
StatWriter* e_out = new StatWriter( entry_plug ); |
191 |
DumpWriter* dump_out = new DumpWriter( entry_plug ); |
192 |
|
193 |
Atom** atoms = entry_plug->atoms; |
194 |
DirectionalAtom* dAtom; |
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dt2 = 0.5 * dt; |
196 |
|
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// initialize the forces the before the first step |
198 |
|
199 |
myFF->doForces(1,0); |
200 |
|
201 |
if( entry_plug->setTemp ){ |
202 |
|
203 |
tStats->velocitize(); |
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} |
205 |
|
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dump_out->writeDump( 0.0 ); |
207 |
e_out->writeStat( 0.0 ); |
208 |
|
209 |
calcPot = 0; |
210 |
|
211 |
if( n_constrained ){ |
212 |
|
213 |
double *Rx = new double[nAtoms]; |
214 |
double *Ry = new double[nAtoms]; |
215 |
double *Rz = new double[nAtoms]; |
216 |
|
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double *Vx = new double[nAtoms]; |
218 |
double *Vy = new double[nAtoms]; |
219 |
double *Vz = new double[nAtoms]; |
220 |
|
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double *Fx = new double[nAtoms]; |
222 |
double *Fy = new double[nAtoms]; |
223 |
double *Fz = new double[nAtoms]; |
224 |
|
225 |
|
226 |
for( tl=0; tl < n_loops; tl++ ){ |
227 |
|
228 |
for( j=0; j<nAtoms; j++ ){ |
229 |
|
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Rx[j] = atoms[j]->getX(); |
231 |
Ry[j] = atoms[j]->getY(); |
232 |
Rz[j] = atoms[j]->getZ(); |
233 |
|
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Vx[j] = atoms[j]->get_vx(); |
235 |
Vy[j] = atoms[j]->get_vy(); |
236 |
Vz[j] = atoms[j]->get_vz(); |
237 |
|
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Fx[j] = atoms[j]->getFx(); |
239 |
Fy[j] = atoms[j]->getFy(); |
240 |
Fz[j] = atoms[j]->getFz(); |
241 |
|
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} |
243 |
|
244 |
v_constrain_a_( dt, nAtoms, mass, Rx, Ry, Rz, Vx, Vy, Vz, |
245 |
Fx, Fy, Fz, |
246 |
n_constrained, constrained_dsqr, |
247 |
constrained_i, constrained_j, |
248 |
entry_plug->box_x, |
249 |
entry_plug->box_y, |
250 |
entry_plug->box_z ); |
251 |
|
252 |
for( j=0; j<nAtoms; j++ ){ |
253 |
|
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atoms[j]->setX(Rx[j]); |
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atoms[j]->setY(Ry[j]); |
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atoms[j]->setZ(Rz[j]); |
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|
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atoms[j]->set_vx(Vx[j]); |
259 |
atoms[j]->set_vy(Vy[j]); |
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atoms[j]->set_vz(Vz[j]); |
261 |
} |
262 |
|
263 |
|
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for( i=0; i<nAtoms; i++ ){ |
265 |
if( atoms[i]->isDirectional() ){ |
266 |
|
267 |
dAtom = (DirectionalAtom *)atoms[i]; |
268 |
|
269 |
// get and convert the torque to body frame |
270 |
|
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Tb[0] = dAtom->getTx(); |
272 |
Tb[1] = dAtom->getTy(); |
273 |
Tb[2] = dAtom->getTz(); |
274 |
|
275 |
dAtom->lab2Body( Tb ); |
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|
277 |
// get the angular momentum, and propagate a half step |
278 |
|
279 |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * e_convert; |
280 |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * e_convert; |
281 |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * e_convert; |
282 |
|
283 |
// get the atom's rotation matrix |
284 |
|
285 |
A[0][0] = dAtom->getAxx(); |
286 |
A[0][1] = dAtom->getAxy(); |
287 |
A[0][2] = dAtom->getAxz(); |
288 |
|
289 |
A[1][0] = dAtom->getAyx(); |
290 |
A[1][1] = dAtom->getAyy(); |
291 |
A[1][2] = dAtom->getAyz(); |
292 |
|
293 |
A[2][0] = dAtom->getAzx(); |
294 |
A[2][1] = dAtom->getAzy(); |
295 |
A[2][2] = dAtom->getAzz(); |
296 |
|
297 |
|
298 |
// use the angular velocities to propagate the rotation matrix a |
299 |
// full time step |
300 |
|
301 |
|
302 |
angle = dt2 * ji[0] / dAtom->getIxx(); |
303 |
this->rotate( 1, 2, angle, ji, A ); // rotate about the x-axis |
304 |
|
305 |
angle = dt2 * ji[1] / dAtom->getIyy(); |
306 |
this->rotate( 2, 0, angle, ji, A ); // rotate about the y-axis |
307 |
|
308 |
angle = dt * ji[2] / dAtom->getIzz(); |
309 |
this->rotate( 0, 1, angle, ji, A ); // rotate about the z-axis |
310 |
|
311 |
angle = dt2 * ji[1] / dAtom->getIyy(); |
312 |
this->rotate( 2, 0, angle, ji, A ); // rotate about the y-axis |
313 |
|
314 |
angle = dt2 * ji[0] / dAtom->getIxx(); |
315 |
this->rotate( 1, 2, angle, ji, A ); // rotate about the x-axis |
316 |
|
317 |
|
318 |
dAtom->setA( A ); |
319 |
dAtom->setJx( ji[0] ); |
320 |
dAtom->setJy( ji[1] ); |
321 |
dAtom->setJz( ji[2] ); |
322 |
} |
323 |
} |
324 |
|
325 |
// calculate the forces |
326 |
|
327 |
myFF->doForces(calcPot, 0); |
328 |
|
329 |
// move b |
330 |
|
331 |
for( j=0; j<nAtoms; j++ ){ |
332 |
|
333 |
Rx[j] = atoms[j]->getX(); |
334 |
Ry[j] = atoms[j]->getY(); |
335 |
Rz[j] = atoms[j]->getZ(); |
336 |
|
337 |
Vx[j] = atoms[j]->get_vx(); |
338 |
Vy[j] = atoms[j]->get_vy(); |
339 |
Vz[j] = atoms[j]->get_vz(); |
340 |
|
341 |
Fx[j] = atoms[j]->getFx(); |
342 |
Fy[j] = atoms[j]->getFy(); |
343 |
Fz[j] = atoms[j]->getFz(); |
344 |
} |
345 |
|
346 |
v_constrain_b_( dt, nAtoms, mass, Rx, Ry, Rz, Vx, Vy, Vz, |
347 |
Fx, Fy, Fz, |
348 |
kE, n_constrained, constrained_dsqr, |
349 |
constrained_i, constrained_j, |
350 |
entry_plug->box_x, |
351 |
entry_plug->box_y, |
352 |
entry_plug->box_z ); |
353 |
|
354 |
for( j=0; j<nAtoms; j++ ){ |
355 |
|
356 |
atoms[j]->setX(Rx[j]); |
357 |
atoms[j]->setY(Ry[j]); |
358 |
atoms[j]->setZ(Rz[j]); |
359 |
|
360 |
atoms[j]->set_vx(Vx[j]); |
361 |
atoms[j]->set_vy(Vy[j]); |
362 |
atoms[j]->set_vz(Vz[j]); |
363 |
} |
364 |
|
365 |
for( i=0; i< nAtoms; i++ ){ |
366 |
|
367 |
if( atoms[i]->isDirectional() ){ |
368 |
|
369 |
dAtom = (DirectionalAtom *)atoms[i]; |
370 |
|
371 |
// get and convert the torque to body frame |
372 |
|
373 |
Tb[0] = dAtom->getTx(); |
374 |
Tb[1] = dAtom->getTy(); |
375 |
Tb[2] = dAtom->getTz(); |
376 |
|
377 |
dAtom->lab2Body( Tb ); |
378 |
|
379 |
// get the angular momentum, and complete the angular momentum |
380 |
// half step |
381 |
|
382 |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * e_convert; |
383 |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * e_convert; |
384 |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * e_convert; |
385 |
|
386 |
dAtom->setJx( ji[0] ); |
387 |
dAtom->setJy( ji[1] ); |
388 |
dAtom->setJz( ji[2] ); |
389 |
} |
390 |
} |
391 |
|
392 |
time = tl + 1; |
393 |
|
394 |
if( entry_plug->setTemp ){ |
395 |
if( !(time % vel_n) ) tStats->velocitize(); |
396 |
} |
397 |
if( !(time % sample_n) ) dump_out->writeDump( time * dt ); |
398 |
if( !((time+1) % status_n) ) calcPot = 1; |
399 |
if( !(time % status_n) ){ e_out->writeStat( time * dt ); calcPot = 0; } |
400 |
} |
401 |
} |
402 |
else{ |
403 |
|
404 |
for( tl=0; tl<n_loops; tl++ ){ |
405 |
|
406 |
kE = 0.0; |
407 |
rot_kE= 0.0; |
408 |
trans_kE = 0.0; |
409 |
|
410 |
for( i=0; i<nAtoms; i++ ){ |
411 |
|
412 |
// velocity half step |
413 |
|
414 |
vx = atoms[i]->get_vx() + |
415 |
( dt2 * atoms[i]->getFx() / atoms[i]->getMass() ) * e_convert; |
416 |
vy = atoms[i]->get_vy() + |
417 |
( dt2 * atoms[i]->getFy() / atoms[i]->getMass() ) * e_convert; |
418 |
vz = atoms[i]->get_vz() + |
419 |
( dt2 * atoms[i]->getFz() / atoms[i]->getMass() ) * e_convert; |
420 |
|
421 |
// position whole step |
422 |
|
423 |
rx = atoms[i]->getX() + dt * vx; |
424 |
ry = atoms[i]->getY() + dt * vy; |
425 |
rz = atoms[i]->getZ() + dt * vz; |
426 |
|
427 |
atoms[i]->setX( rx ); |
428 |
atoms[i]->setY( ry ); |
429 |
atoms[i]->setZ( rz ); |
430 |
|
431 |
atoms[i]->set_vx( vx ); |
432 |
atoms[i]->set_vy( vy ); |
433 |
atoms[i]->set_vz( vz ); |
434 |
|
435 |
if( atoms[i]->isDirectional() ){ |
436 |
|
437 |
dAtom = (DirectionalAtom *)atoms[i]; |
438 |
|
439 |
// get and convert the torque to body frame |
440 |
|
441 |
Tb[0] = dAtom->getTx(); |
442 |
Tb[1] = dAtom->getTy(); |
443 |
Tb[2] = dAtom->getTz(); |
444 |
|
445 |
dAtom->lab2Body( Tb ); |
446 |
|
447 |
// get the angular momentum, and propagate a half step |
448 |
|
449 |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * e_convert; |
450 |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * e_convert; |
451 |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * e_convert; |
452 |
|
453 |
// get the atom's rotation matrix |
454 |
|
455 |
A[0][0] = dAtom->getAxx(); |
456 |
A[0][1] = dAtom->getAxy(); |
457 |
A[0][2] = dAtom->getAxz(); |
458 |
|
459 |
A[1][0] = dAtom->getAyx(); |
460 |
A[1][1] = dAtom->getAyy(); |
461 |
A[1][2] = dAtom->getAyz(); |
462 |
|
463 |
A[2][0] = dAtom->getAzx(); |
464 |
A[2][1] = dAtom->getAzy(); |
465 |
A[2][2] = dAtom->getAzz(); |
466 |
|
467 |
|
468 |
// use the angular velocities to propagate the rotation matrix a |
469 |
// full time step |
470 |
|
471 |
|
472 |
angle = dt2 * ji[0] / dAtom->getIxx(); |
473 |
this->rotate( 1, 2, angle, ji, A ); // rotate about the x-axis |
474 |
|
475 |
angle = dt2 * ji[1] / dAtom->getIyy(); |
476 |
this->rotate( 2, 0, angle, ji, A ); // rotate about the y-axis |
477 |
|
478 |
angle = dt * ji[2] / dAtom->getIzz(); |
479 |
this->rotate( 0, 1, angle, ji, A ); // rotate about the z-axis |
480 |
|
481 |
angle = dt2 * ji[1] / dAtom->getIyy(); |
482 |
this->rotate( 2, 0, angle, ji, A ); // rotate about the y-axis |
483 |
|
484 |
angle = dt2 * ji[0] / dAtom->getIxx(); |
485 |
this->rotate( 1, 2, angle, ji, A ); // rotate about the x-axis |
486 |
|
487 |
|
488 |
dAtom->setA( A ); |
489 |
dAtom->setJx( ji[0] ); |
490 |
dAtom->setJy( ji[1] ); |
491 |
dAtom->setJz( ji[2] ); |
492 |
} |
493 |
} |
494 |
|
495 |
// calculate the forces |
496 |
|
497 |
myFF->doForces(calcPot,0); |
498 |
|
499 |
for( i=0; i< nAtoms; i++ ){ |
500 |
|
501 |
// complete the velocity half step |
502 |
|
503 |
vx = atoms[i]->get_vx() + |
504 |
( dt2 * atoms[i]->getFx() / atoms[i]->getMass() ) * e_convert; |
505 |
vy = atoms[i]->get_vy() + |
506 |
( dt2 * atoms[i]->getFy() / atoms[i]->getMass() ) * e_convert; |
507 |
vz = atoms[i]->get_vz() + |
508 |
( dt2 * atoms[i]->getFz() / atoms[i]->getMass() ) * e_convert; |
509 |
|
510 |
atoms[i]->set_vx( vx ); |
511 |
atoms[i]->set_vy( vy ); |
512 |
atoms[i]->set_vz( vz ); |
513 |
|
514 |
// vx2 = vx * vx; |
515 |
// vy2 = vy * vy; |
516 |
// vz2 = vz * vz; |
517 |
|
518 |
if( atoms[i]->isDirectional() ){ |
519 |
|
520 |
dAtom = (DirectionalAtom *)atoms[i]; |
521 |
|
522 |
// get and convert the torque to body frame |
523 |
|
524 |
Tb[0] = dAtom->getTx(); |
525 |
Tb[1] = dAtom->getTy(); |
526 |
Tb[2] = dAtom->getTz(); |
527 |
|
528 |
dAtom->lab2Body( Tb ); |
529 |
|
530 |
// get the angular momentum, and complete the angular momentum |
531 |
// half step |
532 |
|
533 |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * e_convert; |
534 |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * e_convert; |
535 |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * e_convert; |
536 |
|
537 |
jx2 = ji[0] * ji[0]; |
538 |
jy2 = ji[1] * ji[1]; |
539 |
jz2 = ji[2] * ji[2]; |
540 |
|
541 |
rot_kE += (jx2 / dAtom->getIxx()) + (jy2 / dAtom->getIyy()) |
542 |
+ (jz2 / dAtom->getIzz()); |
543 |
|
544 |
dAtom->setJx( ji[0] ); |
545 |
dAtom->setJy( ji[1] ); |
546 |
dAtom->setJz( ji[2] ); |
547 |
} |
548 |
} |
549 |
|
550 |
time = tl + 1; |
551 |
|
552 |
if( entry_plug->setTemp ){ |
553 |
if( !(time % vel_n) ) tStats->velocitize(); |
554 |
} |
555 |
if( !(time % sample_n) ) dump_out->writeDump( time * dt ); |
556 |
if( !((time+1) % status_n) ) calcPot = 1; |
557 |
if( !(time % status_n) ){ e_out->writeStat( time * dt ); calcPot = 0; } |
558 |
} |
559 |
} |
560 |
|
561 |
dump_out->writeFinal(); |
562 |
|
563 |
delete dump_out; |
564 |
delete e_out; |
565 |
} |
566 |
|
567 |
void Symplectic::rotate( int axes1, int axes2, double angle, double ji[3], |
568 |
double A[3][3] ){ |
569 |
|
570 |
int i,j,k; |
571 |
double sinAngle; |
572 |
double cosAngle; |
573 |
double angleSqr; |
574 |
double angleSqrOver4; |
575 |
double top, bottom; |
576 |
double rot[3][3]; |
577 |
double tempA[3][3]; |
578 |
double tempJ[3]; |
579 |
|
580 |
// initialize the tempA |
581 |
|
582 |
for(i=0; i<3; i++){ |
583 |
for(j=0; j<3; j++){ |
584 |
tempA[j][i] = A[i][j]; |
585 |
} |
586 |
} |
587 |
|
588 |
// initialize the tempJ |
589 |
|
590 |
for( i=0; i<3; i++) tempJ[i] = ji[i]; |
591 |
|
592 |
// initalize rot as a unit matrix |
593 |
|
594 |
rot[0][0] = 1.0; |
595 |
rot[0][1] = 0.0; |
596 |
rot[0][2] = 0.0; |
597 |
|
598 |
rot[1][0] = 0.0; |
599 |
rot[1][1] = 1.0; |
600 |
rot[1][2] = 0.0; |
601 |
|
602 |
rot[2][0] = 0.0; |
603 |
rot[2][1] = 0.0; |
604 |
rot[2][2] = 1.0; |
605 |
|
606 |
// use a small angle aproximation for sin and cosine |
607 |
|
608 |
angleSqr = angle * angle; |
609 |
angleSqrOver4 = angleSqr / 4.0; |
610 |
top = 1.0 - angleSqrOver4; |
611 |
bottom = 1.0 + angleSqrOver4; |
612 |
|
613 |
cosAngle = top / bottom; |
614 |
sinAngle = angle / bottom; |
615 |
|
616 |
rot[axes1][axes1] = cosAngle; |
617 |
rot[axes2][axes2] = cosAngle; |
618 |
|
619 |
rot[axes1][axes2] = sinAngle; |
620 |
rot[axes2][axes1] = -sinAngle; |
621 |
|
622 |
// rotate the momentum acoording to: ji[] = rot[][] * ji[] |
623 |
|
624 |
for(i=0; i<3; i++){ |
625 |
ji[i] = 0.0; |
626 |
for(k=0; k<3; k++){ |
627 |
ji[i] += rot[i][k] * tempJ[k]; |
628 |
} |
629 |
} |
630 |
|
631 |
// rotate the Rotation matrix acording to: |
632 |
// A[][] = A[][] * transpose(rot[][]) |
633 |
|
634 |
|
635 |
// NOte for as yet unknown reason, we are setting the performing the |
636 |
// calculation as: |
637 |
// transpose(A[][]) = transpose(A[][]) * transpose(rot[][]) |
638 |
|
639 |
for(i=0; i<3; i++){ |
640 |
for(j=0; j<3; j++){ |
641 |
A[j][i] = 0.0; |
642 |
for(k=0; k<3; k++){ |
643 |
A[j][i] += tempA[i][k] * rot[j][k]; |
644 |
} |
645 |
} |
646 |
} |
647 |
} |