| 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; |
| 38 |
myES = the_es; |
| 39 |
isFirst = 1; |
| 40 |
|
| 41 |
std::cerr<< "calling symplectic constructor\n"; |
| 42 |
|
| 43 |
molecules = entry_plug->molecules; |
| 44 |
nMols = entry_plug->n_mol; |
| 45 |
|
| 46 |
// give a little love back to the SimInfo object |
| 47 |
|
| 48 |
if( entry_plug->the_integrator != NULL ) delete entry_plug->the_integrator; |
| 49 |
entry_plug->the_integrator = this; |
| 50 |
|
| 51 |
// grab the masses |
| 52 |
|
| 53 |
mass = new double[entry_plug->n_atoms]; |
| 54 |
for(int i = 0; i < entry_plug->n_atoms; i++){ |
| 55 |
mass[i] = entry_plug->atoms[i]->getMass(); |
| 56 |
} |
| 57 |
|
| 58 |
// check for constraints |
| 59 |
|
| 60 |
is_constrained = 0; |
| 61 |
|
| 62 |
Constraint *temp_con; |
| 63 |
Constraint *dummy_plug; |
| 64 |
temp_con = new Constraint[entry_plug->n_SRI]; |
| 65 |
n_constrained = 0; |
| 66 |
int constrained = 0; |
| 67 |
|
| 68 |
SRI** theArray; |
| 69 |
for(int i = 0; i < nMols; i++){ |
| 70 |
|
| 71 |
theArray = (SRI**) molecules[i].getMyBonds(); |
| 72 |
for(int j=0; j<molecules[i].getNBonds(); j++){ |
| 73 |
|
| 74 |
constrained = theArray[j]->is_constrained(); |
| 75 |
|
| 76 |
if(constrained){ |
| 77 |
|
| 78 |
dummy_plug = theArray[j]->get_constraint(); |
| 79 |
temp_con[n_constrained].set_a( dummy_plug->get_a() ); |
| 80 |
temp_con[n_constrained].set_b( dummy_plug->get_b() ); |
| 81 |
temp_con[n_constrained].set_dsqr( dummy_plug->get_dsqr() ); |
| 82 |
|
| 83 |
n_constrained++; |
| 84 |
constrained = 0; |
| 85 |
} |
| 86 |
} |
| 87 |
|
| 88 |
theArray = (SRI**) molecules[i].getMyBends(); |
| 89 |
for(int j=0; j<molecules[i].getNBends(); j++){ |
| 90 |
|
| 91 |
constrained = theArray[j]->is_constrained(); |
| 92 |
|
| 93 |
if(constrained){ |
| 94 |
|
| 95 |
dummy_plug = theArray[j]->get_constraint(); |
| 96 |
temp_con[n_constrained].set_a( dummy_plug->get_a() ); |
| 97 |
temp_con[n_constrained].set_b( dummy_plug->get_b() ); |
| 98 |
temp_con[n_constrained].set_dsqr( dummy_plug->get_dsqr() ); |
| 99 |
|
| 100 |
n_constrained++; |
| 101 |
constrained = 0; |
| 102 |
} |
| 103 |
} |
| 104 |
|
| 105 |
theArray = (SRI**) molecules[i].getMyTorsions(); |
| 106 |
for(int j=0; j<molecules[i].getNTorsions(); j++){ |
| 107 |
|
| 108 |
constrained = theArray[j]->is_constrained(); |
| 109 |
|
| 110 |
if(constrained){ |
| 111 |
|
| 112 |
dummy_plug = theArray[j]->get_constraint(); |
| 113 |
temp_con[n_constrained].set_a( dummy_plug->get_a() ); |
| 114 |
temp_con[n_constrained].set_b( dummy_plug->get_b() ); |
| 115 |
temp_con[n_constrained].set_dsqr( dummy_plug->get_dsqr() ); |
| 116 |
|
| 117 |
n_constrained++; |
| 118 |
constrained = 0; |
| 119 |
} |
| 120 |
} |
| 121 |
} |
| 122 |
|
| 123 |
if(n_constrained > 0){ |
| 124 |
|
| 125 |
is_constrained = 1; |
| 126 |
constrained_i = new int[n_constrained]; |
| 127 |
constrained_j = new int[n_constrained]; |
| 128 |
constrained_dsqr = new double[n_constrained]; |
| 129 |
|
| 130 |
for( int i = 0; i < n_constrained; i++){ |
| 131 |
|
| 132 |
/* add 1 to the index for the fortran arrays. */ |
| 133 |
|
| 134 |
constrained_i[i] = temp_con[i].get_a() + 1; |
| 135 |
constrained_j[i] = temp_con[i].get_b() + 1; |
| 136 |
constrained_dsqr[i] = temp_con[i].get_dsqr(); |
| 137 |
} |
| 138 |
} |
| 139 |
|
| 140 |
delete[] temp_con; |
| 141 |
} |
| 142 |
|
| 143 |
Symplectic::~Symplectic() { |
| 144 |
|
| 145 |
if( n_constrained ){ |
| 146 |
delete[] constrained_i; |
| 147 |
delete[] constrained_j; |
| 148 |
delete[] constrained_dsqr; |
| 149 |
} |
| 150 |
|
| 151 |
} |
| 152 |
|
| 153 |
|
| 154 |
void Symplectic::integrate( void ){ |
| 155 |
|
| 156 |
const double e_convert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2 |
| 157 |
|
| 158 |
int i, j; // loop counters |
| 159 |
int nAtoms = entry_plug->n_atoms; // the number of atoms |
| 160 |
double kE = 0.0; // the kinetic energy |
| 161 |
double rot_kE; |
| 162 |
double trans_kE; |
| 163 |
int tl; // the time loop conter |
| 164 |
double dt2; // half the dt |
| 165 |
|
| 166 |
double vx, vy, vz; // the velocities |
| 167 |
double vx2, vy2, vz2; // the square of the velocities |
| 168 |
double rx, ry, rz; // the postitions |
| 169 |
|
| 170 |
double ji[3]; // the body frame angular momentum |
| 171 |
double jx2, jy2, jz2; // the square of the angular momentums |
| 172 |
double Tb[3]; // torque in the body frame |
| 173 |
double angle; // the angle through which to rotate the rotation matrix |
| 174 |
double A[3][3]; // the rotation matrix |
| 175 |
|
| 176 |
int time; |
| 177 |
|
| 178 |
double dt = entry_plug->dt; |
| 179 |
double runTime = entry_plug->run_time; |
| 180 |
double sampleTime = entry_plug->sampleTime; |
| 181 |
double statusTime = entry_plug->statusTime; |
| 182 |
double thermalTime = entry_plug->thermalTime; |
| 183 |
|
| 184 |
int n_loops = (int)( runTime / dt ); |
| 185 |
int sample_n = (int)( sampleTime / dt ); |
| 186 |
int status_n = (int)( statusTime / dt ); |
| 187 |
int vel_n = (int)( thermalTime / dt ); |
| 188 |
|
| 189 |
int calcPot, calcStress; |
| 190 |
|
| 191 |
Thermo *tStats; |
| 192 |
StatWriter* e_out; |
| 193 |
DumpWriter* dump_out; |
| 194 |
|
| 195 |
std::cerr << "about to call new thermo\n"; |
| 196 |
|
| 197 |
tStats = new Thermo( entry_plug ); |
| 198 |
e_out = new StatWriter( entry_plug ); |
| 199 |
|
| 200 |
std::cerr << "calling dumpWriter \n"; |
| 201 |
dump_out = new DumpWriter( entry_plug ); |
| 202 |
std::cerr << "called dumpWriter \n"; |
| 203 |
|
| 204 |
Atom** atoms = entry_plug->atoms; |
| 205 |
DirectionalAtom* dAtom; |
| 206 |
dt2 = 0.5 * dt; |
| 207 |
|
| 208 |
// initialize the forces the before the first step |
| 209 |
|
| 210 |
myFF->doForces(1,1); |
| 211 |
|
| 212 |
if( entry_plug->setTemp ){ |
| 213 |
|
| 214 |
tStats->velocitize(); |
| 215 |
} |
| 216 |
|
| 217 |
dump_out->writeDump( 0.0 ); |
| 218 |
e_out->writeStat( 0.0 ); |
| 219 |
|
| 220 |
calcPot = 0; |
| 221 |
|
| 222 |
if (!strcasecmp( entry_plug->ensemble, "NPT")) { |
| 223 |
calcStress = 1; |
| 224 |
} else { |
| 225 |
calcStress = 0; |
| 226 |
} |
| 227 |
|
| 228 |
if( n_constrained ){ |
| 229 |
|
| 230 |
double *Rx = new double[nAtoms]; |
| 231 |
double *Ry = new double[nAtoms]; |
| 232 |
double *Rz = new double[nAtoms]; |
| 233 |
|
| 234 |
double *Vx = new double[nAtoms]; |
| 235 |
double *Vy = new double[nAtoms]; |
| 236 |
double *Vz = new double[nAtoms]; |
| 237 |
|
| 238 |
double *Fx = new double[nAtoms]; |
| 239 |
double *Fy = new double[nAtoms]; |
| 240 |
double *Fz = new double[nAtoms]; |
| 241 |
|
| 242 |
|
| 243 |
for( tl=0; tl < n_loops; tl++ ){ |
| 244 |
|
| 245 |
if (!strcasecmp( entry_plug->ensemble, "NVT")) |
| 246 |
myES->NoseHooverNVT( dt / 2.0 , tStats->getKinetic() ); |
| 247 |
|
| 248 |
for( j=0; j<nAtoms; j++ ){ |
| 249 |
|
| 250 |
Rx[j] = atoms[j]->getX(); |
| 251 |
Ry[j] = atoms[j]->getY(); |
| 252 |
Rz[j] = atoms[j]->getZ(); |
| 253 |
|
| 254 |
Vx[j] = atoms[j]->get_vx(); |
| 255 |
Vy[j] = atoms[j]->get_vy(); |
| 256 |
Vz[j] = atoms[j]->get_vz(); |
| 257 |
|
| 258 |
Fx[j] = atoms[j]->getFx(); |
| 259 |
Fy[j] = atoms[j]->getFy(); |
| 260 |
Fz[j] = atoms[j]->getFz(); |
| 261 |
|
| 262 |
} |
| 263 |
|
| 264 |
v_constrain_a_( dt, nAtoms, mass, Rx, Ry, Rz, Vx, Vy, Vz, |
| 265 |
Fx, Fy, Fz, |
| 266 |
n_constrained, constrained_dsqr, |
| 267 |
constrained_i, constrained_j, |
| 268 |
entry_plug->box_x, |
| 269 |
entry_plug->box_y, |
| 270 |
entry_plug->box_z ); |
| 271 |
|
| 272 |
for( j=0; j<nAtoms; j++ ){ |
| 273 |
|
| 274 |
atoms[j]->setX(Rx[j]); |
| 275 |
atoms[j]->setY(Ry[j]); |
| 276 |
atoms[j]->setZ(Rz[j]); |
| 277 |
|
| 278 |
atoms[j]->set_vx(Vx[j]); |
| 279 |
atoms[j]->set_vy(Vy[j]); |
| 280 |
atoms[j]->set_vz(Vz[j]); |
| 281 |
} |
| 282 |
|
| 283 |
|
| 284 |
for( i=0; i<nAtoms; i++ ){ |
| 285 |
if( atoms[i]->isDirectional() ){ |
| 286 |
|
| 287 |
dAtom = (DirectionalAtom *)atoms[i]; |
| 288 |
|
| 289 |
// get and convert the torque to body frame |
| 290 |
|
| 291 |
Tb[0] = dAtom->getTx(); |
| 292 |
Tb[1] = dAtom->getTy(); |
| 293 |
Tb[2] = dAtom->getTz(); |
| 294 |
|
| 295 |
dAtom->lab2Body( Tb ); |
| 296 |
|
| 297 |
// get the angular momentum, and propagate a half step |
| 298 |
|
| 299 |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * e_convert; |
| 300 |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * e_convert; |
| 301 |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * e_convert; |
| 302 |
|
| 303 |
// get the atom's rotation matrix |
| 304 |
|
| 305 |
A[0][0] = dAtom->getAxx(); |
| 306 |
A[0][1] = dAtom->getAxy(); |
| 307 |
A[0][2] = dAtom->getAxz(); |
| 308 |
|
| 309 |
A[1][0] = dAtom->getAyx(); |
| 310 |
A[1][1] = dAtom->getAyy(); |
| 311 |
A[1][2] = dAtom->getAyz(); |
| 312 |
|
| 313 |
A[2][0] = dAtom->getAzx(); |
| 314 |
A[2][1] = dAtom->getAzy(); |
| 315 |
A[2][2] = dAtom->getAzz(); |
| 316 |
|
| 317 |
|
| 318 |
// use the angular velocities to propagate the rotation matrix a |
| 319 |
// full time step |
| 320 |
|
| 321 |
|
| 322 |
angle = dt2 * ji[0] / dAtom->getIxx(); |
| 323 |
this->rotate( 1, 2, angle, ji, A ); // rotate about the x-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 = dt * ji[2] / dAtom->getIzz(); |
| 329 |
this->rotate( 0, 1, angle, ji, A ); // rotate about the z-axis |
| 330 |
|
| 331 |
angle = dt2 * ji[1] / dAtom->getIyy(); |
| 332 |
this->rotate( 2, 0, angle, ji, A ); // rotate about the y-axis |
| 333 |
|
| 334 |
angle = dt2 * ji[0] / dAtom->getIxx(); |
| 335 |
this->rotate( 1, 2, angle, ji, A ); // rotate about the x-axis |
| 336 |
|
| 337 |
|
| 338 |
dAtom->setA( A ); |
| 339 |
dAtom->setJx( ji[0] ); |
| 340 |
dAtom->setJy( ji[1] ); |
| 341 |
dAtom->setJz( ji[2] ); |
| 342 |
} |
| 343 |
} |
| 344 |
|
| 345 |
// calculate the forces |
| 346 |
|
| 347 |
myFF->doForces(calcPot, calcStress); |
| 348 |
|
| 349 |
// move b |
| 350 |
|
| 351 |
for( j=0; j<nAtoms; j++ ){ |
| 352 |
|
| 353 |
Rx[j] = atoms[j]->getX(); |
| 354 |
Ry[j] = atoms[j]->getY(); |
| 355 |
Rz[j] = atoms[j]->getZ(); |
| 356 |
|
| 357 |
Vx[j] = atoms[j]->get_vx(); |
| 358 |
Vy[j] = atoms[j]->get_vy(); |
| 359 |
Vz[j] = atoms[j]->get_vz(); |
| 360 |
|
| 361 |
Fx[j] = atoms[j]->getFx(); |
| 362 |
Fy[j] = atoms[j]->getFy(); |
| 363 |
Fz[j] = atoms[j]->getFz(); |
| 364 |
} |
| 365 |
|
| 366 |
v_constrain_b_( dt, nAtoms, mass, Rx, Ry, Rz, Vx, Vy, Vz, |
| 367 |
Fx, Fy, Fz, |
| 368 |
kE, n_constrained, constrained_dsqr, |
| 369 |
constrained_i, constrained_j, |
| 370 |
entry_plug->box_x, |
| 371 |
entry_plug->box_y, |
| 372 |
entry_plug->box_z ); |
| 373 |
|
| 374 |
for( j=0; j<nAtoms; j++ ){ |
| 375 |
|
| 376 |
atoms[j]->setX(Rx[j]); |
| 377 |
atoms[j]->setY(Ry[j]); |
| 378 |
atoms[j]->setZ(Rz[j]); |
| 379 |
|
| 380 |
atoms[j]->set_vx(Vx[j]); |
| 381 |
atoms[j]->set_vy(Vy[j]); |
| 382 |
atoms[j]->set_vz(Vz[j]); |
| 383 |
} |
| 384 |
|
| 385 |
for( i=0; i< nAtoms; i++ ){ |
| 386 |
|
| 387 |
if( atoms[i]->isDirectional() ){ |
| 388 |
|
| 389 |
dAtom = (DirectionalAtom *)atoms[i]; |
| 390 |
|
| 391 |
// get and convert the torque to body frame |
| 392 |
|
| 393 |
Tb[0] = dAtom->getTx(); |
| 394 |
Tb[1] = dAtom->getTy(); |
| 395 |
Tb[2] = dAtom->getTz(); |
| 396 |
|
| 397 |
dAtom->lab2Body( Tb ); |
| 398 |
|
| 399 |
// get the angular momentum, and complete the angular momentum |
| 400 |
// half step |
| 401 |
|
| 402 |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * e_convert; |
| 403 |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * e_convert; |
| 404 |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * e_convert; |
| 405 |
|
| 406 |
dAtom->setJx( ji[0] ); |
| 407 |
dAtom->setJy( ji[1] ); |
| 408 |
dAtom->setJz( ji[2] ); |
| 409 |
} |
| 410 |
} |
| 411 |
|
| 412 |
|
| 413 |
if (!strcasecmp( entry_plug->ensemble, "NVT")) |
| 414 |
myES->NoseHooverNVT( dt / 2.0, tStats->getKinetic() ); |
| 415 |
|
| 416 |
if (!strcasecmp( entry_plug->ensemble, "NPT") ) |
| 417 |
myES->NoseHooverAndersonNPT( dt, |
| 418 |
tStats->getKinetic(), |
| 419 |
tStats->getPressure()); |
| 420 |
|
| 421 |
time = tl + 1; |
| 422 |
|
| 423 |
if( entry_plug->setTemp ){ |
| 424 |
if( !(time % vel_n) ) tStats->velocitize(); |
| 425 |
} |
| 426 |
if( !(time % sample_n) ) dump_out->writeDump( time * dt ); |
| 427 |
if( !((time+1) % status_n) ) { |
| 428 |
calcPot = 1; |
| 429 |
// bitwise masking in case we need it for NPT |
| 430 |
calcStress = (!strcasecmp(entry_plug->ensemble,"NPT")) && 1; |
| 431 |
} |
| 432 |
if( !(time % status_n) ){ |
| 433 |
e_out->writeStat( time * dt ); |
| 434 |
calcPot = 0; |
| 435 |
// bitwise masking in case we need it for NPT |
| 436 |
calcStress = (!strcasecmp(entry_plug->ensemble,"NPT")) && 0; |
| 437 |
} |
| 438 |
} |
| 439 |
} |
| 440 |
else{ |
| 441 |
|
| 442 |
for( tl=0; tl<n_loops; tl++ ){ |
| 443 |
|
| 444 |
kE = 0.0; |
| 445 |
rot_kE= 0.0; |
| 446 |
trans_kE = 0.0; |
| 447 |
|
| 448 |
if (!strcasecmp( entry_plug->ensemble, "NVT")) |
| 449 |
myES->NoseHooverNVT( dt / 2.0, tStats->getKinetic() ); |
| 450 |
|
| 451 |
for( i=0; i<nAtoms; i++ ){ |
| 452 |
|
| 453 |
// velocity half step |
| 454 |
|
| 455 |
vx = atoms[i]->get_vx() + |
| 456 |
( dt2 * atoms[i]->getFx() / atoms[i]->getMass() ) * e_convert; |
| 457 |
vy = atoms[i]->get_vy() + |
| 458 |
( dt2 * atoms[i]->getFy() / atoms[i]->getMass() ) * e_convert; |
| 459 |
vz = atoms[i]->get_vz() + |
| 460 |
( dt2 * atoms[i]->getFz() / atoms[i]->getMass() ) * e_convert; |
| 461 |
|
| 462 |
// position whole step |
| 463 |
|
| 464 |
rx = atoms[i]->getX() + dt * vx; |
| 465 |
ry = atoms[i]->getY() + dt * vy; |
| 466 |
rz = atoms[i]->getZ() + dt * vz; |
| 467 |
|
| 468 |
atoms[i]->setX( rx ); |
| 469 |
atoms[i]->setY( ry ); |
| 470 |
atoms[i]->setZ( rz ); |
| 471 |
|
| 472 |
atoms[i]->set_vx( vx ); |
| 473 |
atoms[i]->set_vy( vy ); |
| 474 |
atoms[i]->set_vz( vz ); |
| 475 |
|
| 476 |
if( atoms[i]->isDirectional() ){ |
| 477 |
|
| 478 |
dAtom = (DirectionalAtom *)atoms[i]; |
| 479 |
|
| 480 |
// get and convert the torque to body frame |
| 481 |
|
| 482 |
Tb[0] = dAtom->getTx(); |
| 483 |
Tb[1] = dAtom->getTy(); |
| 484 |
Tb[2] = dAtom->getTz(); |
| 485 |
|
| 486 |
dAtom->lab2Body( Tb ); |
| 487 |
|
| 488 |
// get the angular momentum, and propagate a half step |
| 489 |
|
| 490 |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * e_convert; |
| 491 |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * e_convert; |
| 492 |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * e_convert; |
| 493 |
|
| 494 |
// get the atom's rotation matrix |
| 495 |
|
| 496 |
A[0][0] = dAtom->getAxx(); |
| 497 |
A[0][1] = dAtom->getAxy(); |
| 498 |
A[0][2] = dAtom->getAxz(); |
| 499 |
|
| 500 |
A[1][0] = dAtom->getAyx(); |
| 501 |
A[1][1] = dAtom->getAyy(); |
| 502 |
A[1][2] = dAtom->getAyz(); |
| 503 |
|
| 504 |
A[2][0] = dAtom->getAzx(); |
| 505 |
A[2][1] = dAtom->getAzy(); |
| 506 |
A[2][2] = dAtom->getAzz(); |
| 507 |
|
| 508 |
|
| 509 |
// use the angular velocities to propagate the rotation matrix a |
| 510 |
// full time step |
| 511 |
|
| 512 |
|
| 513 |
angle = dt2 * ji[0] / dAtom->getIxx(); |
| 514 |
this->rotate( 1, 2, angle, ji, A ); // rotate about the x-axis |
| 515 |
|
| 516 |
angle = dt2 * ji[1] / dAtom->getIyy(); |
| 517 |
this->rotate( 2, 0, angle, ji, A ); // rotate about the y-axis |
| 518 |
|
| 519 |
angle = dt * ji[2] / dAtom->getIzz(); |
| 520 |
this->rotate( 0, 1, angle, ji, A ); // rotate about the z-axis |
| 521 |
|
| 522 |
angle = dt2 * ji[1] / dAtom->getIyy(); |
| 523 |
this->rotate( 2, 0, angle, ji, A ); // rotate about the y-axis |
| 524 |
|
| 525 |
angle = dt2 * ji[0] / dAtom->getIxx(); |
| 526 |
this->rotate( 1, 2, angle, ji, A ); // rotate about the x-axis |
| 527 |
|
| 528 |
|
| 529 |
dAtom->setA( A ); |
| 530 |
dAtom->setJx( ji[0] ); |
| 531 |
dAtom->setJy( ji[1] ); |
| 532 |
dAtom->setJz( ji[2] ); |
| 533 |
} |
| 534 |
} |
| 535 |
|
| 536 |
// calculate the forces |
| 537 |
|
| 538 |
myFF->doForces(calcPot,calcStress); |
| 539 |
|
| 540 |
for( i=0; i< nAtoms; i++ ){ |
| 541 |
|
| 542 |
// complete the velocity half step |
| 543 |
|
| 544 |
vx = atoms[i]->get_vx() + |
| 545 |
( dt2 * atoms[i]->getFx() / atoms[i]->getMass() ) * e_convert; |
| 546 |
vy = atoms[i]->get_vy() + |
| 547 |
( dt2 * atoms[i]->getFy() / atoms[i]->getMass() ) * e_convert; |
| 548 |
vz = atoms[i]->get_vz() + |
| 549 |
( dt2 * atoms[i]->getFz() / atoms[i]->getMass() ) * e_convert; |
| 550 |
|
| 551 |
atoms[i]->set_vx( vx ); |
| 552 |
atoms[i]->set_vy( vy ); |
| 553 |
atoms[i]->set_vz( vz ); |
| 554 |
|
| 555 |
vx2 = vx * vx; |
| 556 |
vy2 = vy * vy; |
| 557 |
vz2 = vz * vz; |
| 558 |
|
| 559 |
if( atoms[i]->isDirectional() ){ |
| 560 |
|
| 561 |
dAtom = (DirectionalAtom *)atoms[i]; |
| 562 |
|
| 563 |
// get and convert the torque to body frame |
| 564 |
|
| 565 |
Tb[0] = dAtom->getTx(); |
| 566 |
Tb[1] = dAtom->getTy(); |
| 567 |
Tb[2] = dAtom->getTz(); |
| 568 |
|
| 569 |
dAtom->lab2Body( Tb ); |
| 570 |
|
| 571 |
// get the angular momentum, and complete the angular momentum |
| 572 |
// half step |
| 573 |
|
| 574 |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * e_convert; |
| 575 |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * e_convert; |
| 576 |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * e_convert; |
| 577 |
|
| 578 |
jx2 = ji[0] * ji[0]; |
| 579 |
jy2 = ji[1] * ji[1]; |
| 580 |
jz2 = ji[2] * ji[2]; |
| 581 |
|
| 582 |
rot_kE += (jx2 / dAtom->getIxx()) + (jy2 / dAtom->getIyy()) |
| 583 |
+ (jz2 / dAtom->getIzz()); |
| 584 |
|
| 585 |
dAtom->setJx( ji[0] ); |
| 586 |
dAtom->setJy( ji[1] ); |
| 587 |
dAtom->setJz( ji[2] ); |
| 588 |
} |
| 589 |
} |
| 590 |
|
| 591 |
if (!strcasecmp( entry_plug->ensemble, "NVT")) |
| 592 |
myES->NoseHooverNVT( dt / 2.0, tStats->getKinetic() ); |
| 593 |
|
| 594 |
if (!strcasecmp( entry_plug->ensemble, "NPT") ) |
| 595 |
myES->NoseHooverAndersonNPT( dt, |
| 596 |
tStats->getKinetic(), |
| 597 |
tStats->getPressure()); |
| 598 |
|
| 599 |
time = tl + 1; |
| 600 |
|
| 601 |
if( entry_plug->setTemp ){ |
| 602 |
if( !(time % vel_n) ) tStats->velocitize(); |
| 603 |
} |
| 604 |
if( !(time % sample_n) ) dump_out->writeDump( time * dt ); |
| 605 |
if( !((time+1) % status_n) ) { |
| 606 |
calcPot = 1; |
| 607 |
// bitwise masking in case we need it for NPT |
| 608 |
calcStress = (!strcasecmp(entry_plug->ensemble,"NPT")) && 1; |
| 609 |
} |
| 610 |
if( !(time % status_n) ){ |
| 611 |
e_out->writeStat( time * dt ); |
| 612 |
calcPot = 0; |
| 613 |
// bitwise masking in case we need it for NPT |
| 614 |
calcStress = (!strcasecmp(entry_plug->ensemble,"NPT")) && 0; |
| 615 |
} |
| 616 |
} |
| 617 |
} |
| 618 |
|
| 619 |
dump_out->writeFinal(); |
| 620 |
|
| 621 |
delete dump_out; |
| 622 |
delete e_out; |
| 623 |
} |
| 624 |
|
| 625 |
void Symplectic::rotate( int axes1, int axes2, double angle, double ji[3], |
| 626 |
double A[3][3] ){ |
| 627 |
|
| 628 |
int i,j,k; |
| 629 |
double sinAngle; |
| 630 |
double cosAngle; |
| 631 |
double angleSqr; |
| 632 |
double angleSqrOver4; |
| 633 |
double top, bottom; |
| 634 |
double rot[3][3]; |
| 635 |
double tempA[3][3]; |
| 636 |
double tempJ[3]; |
| 637 |
|
| 638 |
// initialize the tempA |
| 639 |
|
| 640 |
for(i=0; i<3; i++){ |
| 641 |
for(j=0; j<3; j++){ |
| 642 |
tempA[j][i] = A[i][j]; |
| 643 |
} |
| 644 |
} |
| 645 |
|
| 646 |
// initialize the tempJ |
| 647 |
|
| 648 |
for( i=0; i<3; i++) tempJ[i] = ji[i]; |
| 649 |
|
| 650 |
// initalize rot as a unit matrix |
| 651 |
|
| 652 |
rot[0][0] = 1.0; |
| 653 |
rot[0][1] = 0.0; |
| 654 |
rot[0][2] = 0.0; |
| 655 |
|
| 656 |
rot[1][0] = 0.0; |
| 657 |
rot[1][1] = 1.0; |
| 658 |
rot[1][2] = 0.0; |
| 659 |
|
| 660 |
rot[2][0] = 0.0; |
| 661 |
rot[2][1] = 0.0; |
| 662 |
rot[2][2] = 1.0; |
| 663 |
|
| 664 |
// use a small angle aproximation for sin and cosine |
| 665 |
|
| 666 |
angleSqr = angle * angle; |
| 667 |
angleSqrOver4 = angleSqr / 4.0; |
| 668 |
top = 1.0 - angleSqrOver4; |
| 669 |
bottom = 1.0 + angleSqrOver4; |
| 670 |
|
| 671 |
cosAngle = top / bottom; |
| 672 |
sinAngle = angle / bottom; |
| 673 |
|
| 674 |
rot[axes1][axes1] = cosAngle; |
| 675 |
rot[axes2][axes2] = cosAngle; |
| 676 |
|
| 677 |
rot[axes1][axes2] = sinAngle; |
| 678 |
rot[axes2][axes1] = -sinAngle; |
| 679 |
|
| 680 |
// rotate the momentum acoording to: ji[] = rot[][] * ji[] |
| 681 |
|
| 682 |
for(i=0; i<3; i++){ |
| 683 |
ji[i] = 0.0; |
| 684 |
for(k=0; k<3; k++){ |
| 685 |
ji[i] += rot[i][k] * tempJ[k]; |
| 686 |
} |
| 687 |
} |
| 688 |
|
| 689 |
// rotate the Rotation matrix acording to: |
| 690 |
// A[][] = A[][] * transpose(rot[][]) |
| 691 |
|
| 692 |
|
| 693 |
// NOte for as yet unknown reason, we are setting the performing the |
| 694 |
// calculation as: |
| 695 |
// transpose(A[][]) = transpose(A[][]) * transpose(rot[][]) |
| 696 |
|
| 697 |
for(i=0; i<3; i++){ |
| 698 |
for(j=0; j<3; j++){ |
| 699 |
A[j][i] = 0.0; |
| 700 |
for(k=0; k<3; k++){ |
| 701 |
A[j][i] += tempA[i][k] * rot[j][k]; |
| 702 |
} |
| 703 |
} |
| 704 |
} |
| 705 |
} |
