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#include <iostream> |
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#include <cstdlib> |
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#include <cmath> |
4 |
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5 |
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#ifdef IS_MPI |
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#include "mpiSimulation.hpp" |
11 |
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#include "simError.h" |
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13 |
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14 |
< |
Integrator::Integrator( SimInfo* theInfo, ForceFields* the_ff ){ |
14 |
> |
Integrator::Integrator( SimInfo *theInfo, ForceFields* the_ff ){ |
15 |
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|
16 |
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info = theInfo; |
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myFF = the_ff; |
27 |
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|
28 |
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nAtoms = info->n_atoms; |
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|
30 |
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std::cerr << "integ nAtoms = " << nAtoms << "\n"; |
31 |
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|
32 |
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// check for constraints |
33 |
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|
34 |
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constrainedA = NULL; |
36 |
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constrainedDsqr = NULL; |
37 |
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moving = NULL; |
38 |
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moved = NULL; |
39 |
< |
prePos = NULL; |
39 |
> |
oldPos = NULL; |
40 |
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|
41 |
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nConstrained = 0; |
42 |
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|
51 |
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delete[] constrainedDsqr; |
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delete[] moving; |
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delete[] moved; |
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delete[] prePos; |
54 |
> |
delete[] oldPos; |
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} |
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|
57 |
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} |
74 |
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for(int j=0; j<molecules[i].getNBonds(); j++){ |
75 |
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|
76 |
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constrained = theArray[j]->is_constrained(); |
77 |
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|
78 |
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std::cerr << "Is the folowing bond constrained \n"; |
79 |
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theArray[j]->printMe(); |
80 |
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|
81 |
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if(constrained){ |
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std::cerr << "Yes\n"; |
84 |
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|
85 |
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dummy_plug = theArray[j]->get_constraint(); |
86 |
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temp_con[nConstrained].set_a( dummy_plug->get_a() ); |
87 |
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temp_con[nConstrained].set_b( dummy_plug->get_b() ); |
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|
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nConstrained++; |
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constrained = 0; |
92 |
< |
} |
92 |
> |
} |
93 |
> |
else std::cerr << "No.\n"; |
94 |
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} |
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|
96 |
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theArray = (SRI**) molecules[i].getMyBends(); |
145 |
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constrainedA[i] = temp_con[i].get_a(); |
146 |
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constrainedB[i] = temp_con[i].get_b(); |
147 |
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constrainedDsqr[i] = temp_con[i].get_dsqr(); |
148 |
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|
149 |
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} |
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moving = new int[nAtoms]; |
157 |
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moved = new int[nAtoms]; |
158 |
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159 |
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prePos = new double[nAtoms*3]; |
159 |
> |
oldPos = new double[nAtoms*3]; |
160 |
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} |
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delete[] temp_con; |
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void Integrator::integrate( void ){ |
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int i, j; // loop counters |
159 |
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double kE = 0.0; // the kinetic energy |
160 |
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double rot_kE; |
161 |
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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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double vx, vy, vz; // the velocities |
166 |
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double vx2, vy2, vz2; // the square of the velocities |
167 |
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double rx, ry, rz; // the postitions |
168 |
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|
169 |
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double ji[3]; // the body frame angular momentum |
170 |
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double jx2, jy2, jz2; // the square of the angular momentums |
171 |
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double Tb[3]; // torque in the body frame |
172 |
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double angle; // the angle through which to rotate the rotation matrix |
173 |
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double A[3][3]; // the rotation matrix |
174 |
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double press[9]; |
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|
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double dt = info->dt; |
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double runTime = info->run_time; |
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double sampleTime = info->sampleTime; |
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double statusTime = info->statusTime; |
181 |
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int isError; |
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|
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tStats = new Thermo( info ); |
184 |
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e_out = new StatWriter( info ); |
185 |
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dump_out = new DumpWriter( info ); |
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> |
statOut = new StatWriter( info ); |
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> |
dumpOut = new DumpWriter( info ); |
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|
187 |
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Atom** atoms = info->atoms; |
187 |
> |
atoms = info->atoms; |
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DirectionalAtom* dAtom; |
189 |
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|
190 |
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dt = info->dt; |
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dt2 = 0.5 * dt; |
192 |
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|
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// initialize the forces before the first step |
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tStats->velocitize(); |
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} |
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202 |
< |
dump_out->writeDump( 0.0 ); |
203 |
< |
e_out->writeStat( 0.0 ); |
202 |
> |
dumpOut->writeDump( 0.0 ); |
203 |
> |
statOut->writeStat( 0.0 ); |
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|
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calcPot = 0; |
206 |
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calcStress = 0; |
224 |
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calcPot = 1; |
225 |
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calcStress = 1; |
226 |
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} |
227 |
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|
227 |
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|
228 |
> |
std::cerr << currTime << "\n"; |
229 |
> |
|
230 |
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integrateStep( calcPot, calcStress ); |
231 |
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currTime += dt; |
239 |
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} |
240 |
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241 |
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if( currTime >= currSample ){ |
242 |
< |
dump_out->writeDump( currTime ); |
242 |
> |
dumpOut->writeDump( currTime ); |
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currSample += sampleTime; |
244 |
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} |
245 |
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|
246 |
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if( currTime >= currStatus ){ |
247 |
< |
e_out->writeStat( time * dt ); |
247 |
> |
statOut->writeStat( currTime ); |
248 |
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calcPot = 0; |
249 |
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calcStress = 0; |
250 |
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currStatus += statusTime; |
258 |
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|
259 |
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} |
260 |
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261 |
< |
dump_out->writeFinal(); |
261 |
> |
dumpOut->writeFinal(currTime); |
262 |
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263 |
< |
delete dump_out; |
264 |
< |
delete e_out; |
263 |
> |
delete dumpOut; |
264 |
> |
delete statOut; |
265 |
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} |
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267 |
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void Integrator::integrateStep( int calcPot, int calcStress ){ |
268 |
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269 |
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|
270 |
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|
271 |
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// Position full step, and velocity half step |
272 |
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|
273 |
< |
//preMove(); |
273 |
> |
preMove(); |
274 |
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moveA(); |
275 |
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if( nConstrained ) constrainA(); |
276 |
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288 |
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289 |
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void Integrator::moveA( void ){ |
290 |
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291 |
< |
int i,j,k; |
293 |
< |
int atomIndex, aMatIndex; |
291 |
> |
int i, j; |
292 |
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DirectionalAtom* dAtom; |
293 |
< |
double Tb[3]; |
294 |
< |
double ji[3]; |
293 |
> |
double Tb[3], ji[3]; |
294 |
> |
double A[3][3], I[3][3]; |
295 |
> |
double angle; |
296 |
> |
double vel[3], pos[3], frc[3]; |
297 |
> |
double mass; |
298 |
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|
299 |
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for( i=0; i<nAtoms; i++ ){ |
299 |
– |
atomIndex = i * 3; |
300 |
– |
aMatIndex = i * 9; |
301 |
– |
|
302 |
– |
// velocity half step |
303 |
– |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
304 |
– |
vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert; |
300 |
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|
301 |
< |
// position whole step |
302 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
301 |
> |
atoms[i]->getVel( vel ); |
302 |
> |
atoms[i]->getPos( pos ); |
303 |
> |
atoms[i]->getFrc( frc ); |
304 |
> |
|
305 |
> |
mass = atoms[i]->getMass(); |
306 |
> |
|
307 |
> |
for (j=0; j < 3; j++) { |
308 |
> |
// velocity half step |
309 |
> |
vel[j] += ( dt2 * frc[j] / mass ) * eConvert; |
310 |
> |
// position whole step |
311 |
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pos[j] += dt * vel[j]; |
312 |
+ |
} |
313 |
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|
314 |
< |
|
314 |
> |
atoms[i]->setVel( vel ); |
315 |
> |
atoms[i]->setPos( pos ); |
316 |
> |
|
317 |
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if( atoms[i]->isDirectional() ){ |
318 |
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319 |
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dAtom = (DirectionalAtom *)atoms[i]; |
320 |
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|
321 |
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// get and convert the torque to body frame |
322 |
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323 |
< |
Tb[0] = dAtom->getTx(); |
318 |
< |
Tb[1] = dAtom->getTy(); |
319 |
< |
Tb[2] = dAtom->getTz(); |
320 |
< |
|
323 |
> |
dAtom->getTrq( Tb ); |
324 |
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dAtom->lab2Body( Tb ); |
325 |
< |
|
325 |
> |
|
326 |
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// get the angular momentum, and propagate a half step |
327 |
+ |
|
328 |
+ |
dAtom->getJ( ji ); |
329 |
+ |
|
330 |
+ |
for (j=0; j < 3; j++) |
331 |
+ |
ji[j] += (dt2 * Tb[j]) * eConvert; |
332 |
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|
325 |
– |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert; |
326 |
– |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert; |
327 |
– |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert; |
328 |
– |
|
333 |
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// use the angular velocities to propagate the rotation matrix a |
334 |
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// full time step |
335 |
< |
|
335 |
> |
|
336 |
> |
dAtom->getA(A); |
337 |
> |
dAtom->getI(I); |
338 |
> |
|
339 |
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// rotate about the x-axis |
340 |
< |
angle = dt2 * ji[0] / dAtom->getIxx(); |
341 |
< |
this->rotate( 1, 2, angle, ji, &aMat[aMatIndex] ); |
342 |
< |
|
340 |
> |
angle = dt2 * ji[0] / I[0][0]; |
341 |
> |
this->rotate( 1, 2, angle, ji, A ); |
342 |
> |
|
343 |
|
// rotate about the y-axis |
344 |
< |
angle = dt2 * ji[1] / dAtom->getIyy(); |
345 |
< |
this->rotate( 2, 0, angle, ji, &aMat[aMatIndex] ); |
344 |
> |
angle = dt2 * ji[1] / I[1][1]; |
345 |
> |
this->rotate( 2, 0, angle, ji, A ); |
346 |
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|
347 |
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// rotate about the z-axis |
348 |
< |
angle = dt * ji[2] / dAtom->getIzz(); |
349 |
< |
this->rotate( 0, 1, angle, ji, &aMat[aMatIndex] ); |
348 |
> |
angle = dt * ji[2] / I[2][2]; |
349 |
> |
this->rotate( 0, 1, angle, ji, A); |
350 |
|
|
351 |
|
// rotate about the y-axis |
352 |
< |
angle = dt2 * ji[1] / dAtom->getIyy(); |
353 |
< |
this->rotate( 2, 0, angle, ji, &aMat[aMatIndex] ); |
352 |
> |
angle = dt2 * ji[1] / I[1][1]; |
353 |
> |
this->rotate( 2, 0, angle, ji, A ); |
354 |
|
|
355 |
|
// rotate about the x-axis |
356 |
< |
angle = dt2 * ji[0] / dAtom->getIxx(); |
357 |
< |
this->rotate( 1, 2, angle, ji, &aMat[aMatIndex] ); |
356 |
> |
angle = dt2 * ji[0] / I[0][0]; |
357 |
> |
this->rotate( 1, 2, angle, ji, A ); |
358 |
|
|
359 |
< |
dAtom->setJx( ji[0] ); |
360 |
< |
dAtom->setJy( ji[1] ); |
361 |
< |
dAtom->setJz( ji[2] ); |
362 |
< |
} |
363 |
< |
|
359 |
> |
|
360 |
> |
dAtom->setJ( ji ); |
361 |
> |
dAtom->setA( A ); |
362 |
> |
|
363 |
> |
} |
364 |
|
} |
365 |
|
} |
366 |
|
|
367 |
|
|
368 |
|
void Integrator::moveB( void ){ |
369 |
< |
int i,j,k; |
363 |
< |
int atomIndex; |
369 |
> |
int i, j; |
370 |
|
DirectionalAtom* dAtom; |
371 |
< |
double Tb[3]; |
372 |
< |
double ji[3]; |
371 |
> |
double Tb[3], ji[3]; |
372 |
> |
double vel[3], frc[3]; |
373 |
> |
double mass; |
374 |
|
|
375 |
|
for( i=0; i<nAtoms; i++ ){ |
376 |
< |
atomIndex = i * 3; |
376 |
> |
|
377 |
> |
atoms[i]->getVel( vel ); |
378 |
> |
atoms[i]->getFrc( frc ); |
379 |
|
|
380 |
< |
// velocity half step |
372 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
373 |
< |
vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert; |
380 |
> |
mass = atoms[i]->getMass(); |
381 |
|
|
382 |
+ |
// velocity half step |
383 |
+ |
for (j=0; j < 3; j++) |
384 |
+ |
vel[j] += ( dt2 * frc[j] / mass ) * eConvert; |
385 |
+ |
|
386 |
+ |
atoms[i]->setVel( vel ); |
387 |
+ |
|
388 |
|
if( atoms[i]->isDirectional() ){ |
389 |
< |
|
389 |
> |
|
390 |
|
dAtom = (DirectionalAtom *)atoms[i]; |
391 |
< |
|
392 |
< |
// get and convert the torque to body frame |
393 |
< |
|
394 |
< |
Tb[0] = dAtom->getTx(); |
382 |
< |
Tb[1] = dAtom->getTy(); |
383 |
< |
Tb[2] = dAtom->getTz(); |
384 |
< |
|
391 |
> |
|
392 |
> |
// get and convert the torque to body frame |
393 |
> |
|
394 |
> |
dAtom->getTrq( Tb ); |
395 |
|
dAtom->lab2Body( Tb ); |
396 |
+ |
|
397 |
+ |
// get the angular momentum, and propagate a half step |
398 |
+ |
|
399 |
+ |
dAtom->getJ( ji ); |
400 |
+ |
|
401 |
+ |
for (j=0; j < 3; j++) |
402 |
+ |
ji[j] += (dt2 * Tb[j]) * eConvert; |
403 |
|
|
404 |
< |
// get the angular momentum, and complete the angular momentum |
405 |
< |
// half step |
389 |
< |
|
390 |
< |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert; |
391 |
< |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert; |
392 |
< |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert; |
393 |
< |
|
394 |
< |
jx2 = ji[0] * ji[0]; |
395 |
< |
jy2 = ji[1] * ji[1]; |
396 |
< |
jz2 = ji[2] * ji[2]; |
397 |
< |
|
398 |
< |
dAtom->setJx( ji[0] ); |
399 |
< |
dAtom->setJy( ji[1] ); |
400 |
< |
dAtom->setJz( ji[2] ); |
404 |
> |
|
405 |
> |
dAtom->setJ( ji ); |
406 |
|
} |
407 |
|
} |
403 |
– |
|
408 |
|
} |
409 |
|
|
410 |
|
void Integrator::preMove( void ){ |
411 |
< |
int i; |
411 |
> |
int i, j; |
412 |
> |
double pos[3]; |
413 |
|
|
414 |
|
if( nConstrained ){ |
415 |
< |
if( oldAtoms != nAtoms ){ |
416 |
< |
|
417 |
< |
// save oldAtoms to check for lode balanceing later on. |
418 |
< |
|
419 |
< |
oldAtoms = nAtoms; |
420 |
< |
|
421 |
< |
delete[] moving; |
422 |
< |
delete[] moved; |
423 |
< |
delete[] oldPos; |
419 |
< |
|
420 |
< |
moving = new int[nAtoms]; |
421 |
< |
moved = new int[nAtoms]; |
422 |
< |
|
423 |
< |
oldPos = new double[nAtoms*3]; |
415 |
> |
|
416 |
> |
for(i=0; i < nAtoms; i++) { |
417 |
> |
|
418 |
> |
atoms[i]->getPos( pos ); |
419 |
> |
|
420 |
> |
for (j = 0; j < 3; j++) { |
421 |
> |
oldPos[3*i + j] = pos[j]; |
422 |
> |
} |
423 |
> |
|
424 |
|
} |
425 |
< |
|
426 |
< |
for(i=0; i<(nAtoms*3); i++) oldPos[i] = pos[i]; |
427 |
< |
} |
428 |
< |
} |
425 |
> |
} |
426 |
> |
} |
427 |
|
|
428 |
|
void Integrator::constrainA(){ |
429 |
|
|
430 |
|
int i,j,k; |
431 |
|
int done; |
432 |
< |
double pxab, pyab, pzab; |
433 |
< |
double rxab, ryab, rzab; |
434 |
< |
int a, b; |
432 |
> |
double posA[3], posB[3]; |
433 |
> |
double velA[3], velB[3]; |
434 |
> |
double pab[3]; |
435 |
> |
double rab[3]; |
436 |
> |
int a, b, ax, ay, az, bx, by, bz; |
437 |
|
double rma, rmb; |
438 |
|
double dx, dy, dz; |
439 |
+ |
double rpab; |
440 |
|
double rabsq, pabsq, rpabsq; |
441 |
|
double diffsq; |
442 |
|
double gab; |
443 |
|
int iteration; |
444 |
|
|
445 |
< |
|
445 |
< |
|
446 |
< |
for( i=0; i<nAtoms; i++){ |
447 |
< |
|
445 |
> |
for( i=0; i<nAtoms; i++){ |
446 |
|
moving[i] = 0; |
447 |
|
moved[i] = 1; |
448 |
|
} |
449 |
< |
|
452 |
< |
|
449 |
> |
|
450 |
|
iteration = 0; |
451 |
|
done = 0; |
452 |
|
while( !done && (iteration < maxIteration )){ |
456 |
|
|
457 |
|
a = constrainedA[i]; |
458 |
|
b = constrainedB[i]; |
459 |
< |
|
459 |
> |
|
460 |
> |
ax = (a*3) + 0; |
461 |
> |
ay = (a*3) + 1; |
462 |
> |
az = (a*3) + 2; |
463 |
> |
|
464 |
> |
bx = (b*3) + 0; |
465 |
> |
by = (b*3) + 1; |
466 |
> |
bz = (b*3) + 2; |
467 |
> |
|
468 |
|
if( moved[a] || moved[b] ){ |
469 |
< |
|
470 |
< |
pxab = pos[3*a+0] - pos[3*b+0]; |
471 |
< |
pyab = pos[3*a+1] - pos[3*b+1]; |
472 |
< |
pzab = pos[3*a+2] - pos[3*b+2]; |
469 |
> |
|
470 |
> |
atoms[a]->getPos( posA ); |
471 |
> |
atoms[b]->getPos( posB ); |
472 |
> |
|
473 |
> |
for (j = 0; j < 3; j++ ) |
474 |
> |
pab[j] = posA[j] - posB[j]; |
475 |
> |
|
476 |
> |
//periodic boundary condition |
477 |
|
|
478 |
< |
//periodic boundary condition |
470 |
< |
pxab = pxab - info->box_x * copysign(1, pxab) |
471 |
< |
* int(pxab / info->box_x + 0.5); |
472 |
< |
pyab = pyab - info->box_y * copysign(1, pyab) |
473 |
< |
* int(pyab / info->box_y + 0.5); |
474 |
< |
pzab = pzab - info->box_z * copysign(1, pzab) |
475 |
< |
* int(pzab / info->box_z + 0.5); |
476 |
< |
|
477 |
< |
pabsq = pxab * pxab + pyab * pyab + pzab * pzab; |
478 |
< |
rabsq = constraintedDsqr[i]; |
479 |
< |
diffsq = pabsq - rabsq; |
478 |
> |
info->wrapVector( pab ); |
479 |
|
|
480 |
+ |
pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2]; |
481 |
+ |
|
482 |
+ |
rabsq = constrainedDsqr[i]; |
483 |
+ |
diffsq = rabsq - pabsq; |
484 |
+ |
|
485 |
|
// the original rattle code from alan tidesley |
486 |
< |
if (fabs(diffsq) > tol*rabsq*2) { |
487 |
< |
rxab = oldPos[3*a+0] - oldPos[3*b+0]; |
488 |
< |
ryab = oldPos[3*a+1] - oldPos[3*b+1]; |
489 |
< |
rzab = oldPos[3*a+2] - oldPos[3*b+2]; |
486 |
< |
|
487 |
< |
rxab = rxab - info->box_x * copysign(1, rxab) |
488 |
< |
* int(rxab / info->box_x + 0.5); |
489 |
< |
ryab = ryab - info->box_y * copysign(1, ryab) |
490 |
< |
* int(ryab / info->box_y + 0.5); |
491 |
< |
rzab = rzab - info->box_z * copysign(1, rzab) |
492 |
< |
* int(rzab / info->box_z + 0.5); |
486 |
> |
if (fabs(diffsq) > (tol*rabsq*2)) { |
487 |
> |
rab[0] = oldPos[ax] - oldPos[bx]; |
488 |
> |
rab[1] = oldPos[ay] - oldPos[by]; |
489 |
> |
rab[2] = oldPos[az] - oldPos[bz]; |
490 |
|
|
491 |
< |
rpab = rxab * pxab + ryab * pyab + rzab * pzab; |
491 |
> |
info->wrapVector( rab ); |
492 |
> |
|
493 |
> |
rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
494 |
> |
|
495 |
|
rpabsq = rpab * rpab; |
496 |
|
|
497 |
|
|
498 |
|
if (rpabsq < (rabsq * -diffsq)){ |
499 |
+ |
|
500 |
|
#ifdef IS_MPI |
501 |
|
a = atoms[a]->getGlobalIndex(); |
502 |
|
b = atoms[b]->getGlobalIndex(); |
503 |
|
#endif //is_mpi |
504 |
|
sprintf( painCave.errMsg, |
505 |
< |
"Constraint failure in constrainA at atom %d and %d\n.", |
505 |
> |
"Constraint failure in constrainA at atom %d and %d.\n", |
506 |
|
a, b ); |
507 |
|
painCave.isFatal = 1; |
508 |
|
simError(); |
510 |
|
|
511 |
|
rma = 1.0 / atoms[a]->getMass(); |
512 |
|
rmb = 1.0 / atoms[b]->getMass(); |
513 |
< |
|
513 |
> |
|
514 |
|
gab = diffsq / ( 2.0 * ( rma + rmb ) * rpab ); |
514 |
– |
dx = rxab * gab; |
515 |
– |
dy = ryab * gab; |
516 |
– |
dz = rzab * gab; |
515 |
|
|
516 |
< |
pos[3*a+0] += rma * dx; |
517 |
< |
pos[3*a+1] += rma * dy; |
518 |
< |
pos[3*a+2] += rma * dz; |
516 |
> |
dx = rab[0] * gab; |
517 |
> |
dy = rab[1] * gab; |
518 |
> |
dz = rab[2] * gab; |
519 |
|
|
520 |
< |
pos[3*b+0] -= rmb * dx; |
521 |
< |
pos[3*b+1] -= rmb * dy; |
522 |
< |
pos[3*b+2] -= rmb * dz; |
520 |
> |
posA[0] += rma * dx; |
521 |
> |
posA[1] += rma * dy; |
522 |
> |
posA[2] += rma * dz; |
523 |
|
|
524 |
+ |
atoms[a]->setPos( posA ); |
525 |
+ |
|
526 |
+ |
posB[0] -= rmb * dx; |
527 |
+ |
posB[1] -= rmb * dy; |
528 |
+ |
posB[2] -= rmb * dz; |
529 |
+ |
|
530 |
+ |
atoms[b]->setPos( posB ); |
531 |
+ |
|
532 |
|
dx = dx / dt; |
533 |
|
dy = dy / dt; |
534 |
|
dz = dz / dt; |
535 |
|
|
536 |
< |
vel[3*a+0] += rma * dx; |
531 |
< |
vel[3*a+1] += rma * dy; |
532 |
< |
vel[3*a+2] += rma * dz; |
536 |
> |
atoms[a]->getVel( velA ); |
537 |
|
|
538 |
< |
vel[3*b+0] -= rmb * dx; |
539 |
< |
vel[3*b+1] -= rmb * dy; |
540 |
< |
vel[3*b+2] -= rmb * dz; |
538 |
> |
velA[0] += rma * dx; |
539 |
> |
velA[1] += rma * dy; |
540 |
> |
velA[2] += rma * dz; |
541 |
|
|
542 |
+ |
atoms[a]->setVel( velA ); |
543 |
+ |
|
544 |
+ |
atoms[b]->getVel( velB ); |
545 |
+ |
|
546 |
+ |
velB[0] -= rmb * dx; |
547 |
+ |
velB[1] -= rmb * dy; |
548 |
+ |
velB[2] -= rmb * dz; |
549 |
+ |
|
550 |
+ |
atoms[b]->setVel( velB ); |
551 |
+ |
|
552 |
|
moving[a] = 1; |
553 |
|
moving[b] = 1; |
554 |
|
done = 0; |
567 |
|
|
568 |
|
if( !done ){ |
569 |
|
|
570 |
< |
sprintf( painCae.errMsg, |
570 |
> |
sprintf( painCave.errMsg, |
571 |
|
"Constraint failure in constrainA, too many iterations: %d\n", |
572 |
< |
iterations ); |
572 |
> |
iteration ); |
573 |
|
painCave.isFatal = 1; |
574 |
|
simError(); |
575 |
|
} |
580 |
|
|
581 |
|
int i,j,k; |
582 |
|
int done; |
583 |
+ |
double posA[3], posB[3]; |
584 |
+ |
double velA[3], velB[3]; |
585 |
|
double vxab, vyab, vzab; |
586 |
< |
double rxab, ryab, rzab; |
587 |
< |
int a, b; |
586 |
> |
double rab[3]; |
587 |
> |
int a, b, ax, ay, az, bx, by, bz; |
588 |
|
double rma, rmb; |
589 |
|
double dx, dy, dz; |
590 |
|
double rabsq, pabsq, rvab; |
592 |
|
double gab; |
593 |
|
int iteration; |
594 |
|
|
595 |
< |
for(i=0; i<nAtom; i++){ |
595 |
> |
for(i=0; i<nAtoms; i++){ |
596 |
|
moving[i] = 0; |
597 |
|
moved[i] = 1; |
598 |
|
} |
599 |
|
|
600 |
|
done = 0; |
601 |
+ |
iteration = 0; |
602 |
|
while( !done && (iteration < maxIteration ) ){ |
603 |
|
|
604 |
+ |
done = 1; |
605 |
+ |
|
606 |
|
for(i=0; i<nConstrained; i++){ |
607 |
|
|
608 |
|
a = constrainedA[i]; |
609 |
|
b = constrainedB[i]; |
610 |
|
|
611 |
+ |
ax = (a*3) + 0; |
612 |
+ |
ay = (a*3) + 1; |
613 |
+ |
az = (a*3) + 2; |
614 |
+ |
|
615 |
+ |
bx = (b*3) + 0; |
616 |
+ |
by = (b*3) + 1; |
617 |
+ |
bz = (b*3) + 2; |
618 |
+ |
|
619 |
|
if( moved[a] || moved[b] ){ |
593 |
– |
|
594 |
– |
vxab = vel[3*a+0] - vel[3*b+0]; |
595 |
– |
vyab = vel[3*a+1] - vel[3*b+1]; |
596 |
– |
vzab = vel[3*a+2] - vel[3*b+2]; |
620 |
|
|
621 |
< |
rxab = pos[3*a+0] - pos[3*b+0];q |
622 |
< |
ryab = pos[3*a+1] - pos[3*b+1]; |
623 |
< |
rzab = pos[3*a+2] - pos[3*b+2]; |
624 |
< |
|
625 |
< |
rxab = rxab - info->box_x * copysign(1, rxab) |
626 |
< |
* int(rxab / info->box_x + 0.5); |
604 |
< |
ryab = ryab - info->box_y * copysign(1, ryab) |
605 |
< |
* int(ryab / info->box_y + 0.5); |
606 |
< |
rzab = rzab - info->box_z * copysign(1, rzab) |
607 |
< |
* int(rzab / info->box_z + 0.5); |
621 |
> |
atoms[a]->getVel( velA ); |
622 |
> |
atoms[b]->getVel( velB ); |
623 |
> |
|
624 |
> |
vxab = velA[0] - velB[0]; |
625 |
> |
vyab = velA[1] - velB[1]; |
626 |
> |
vzab = velA[2] - velB[2]; |
627 |
|
|
628 |
+ |
atoms[a]->getPos( posA ); |
629 |
+ |
atoms[b]->getPos( posB ); |
630 |
+ |
|
631 |
+ |
for (j = 0; j < 3; j++) |
632 |
+ |
rab[j] = posA[j] - posB[j]; |
633 |
+ |
|
634 |
+ |
info->wrapVector( rab ); |
635 |
+ |
|
636 |
|
rma = 1.0 / atoms[a]->getMass(); |
637 |
|
rmb = 1.0 / atoms[b]->getMass(); |
638 |
|
|
639 |
< |
rvab = rxab * vxab + ryab * vyab + rzab * vzab; |
639 |
> |
rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab; |
640 |
|
|
641 |
< |
gab = -rvab / ( ( rma + rmb ) * constraintsDsqr[i] ); |
641 |
> |
gab = -rvab / ( ( rma + rmb ) * constrainedDsqr[i] ); |
642 |
|
|
643 |
|
if (fabs(gab) > tol) { |
644 |
|
|
645 |
< |
dx = rxab * gab; |
646 |
< |
dy = ryab * gab; |
647 |
< |
dz = rzab * gab; |
648 |
< |
|
649 |
< |
vel[3*a+0] += rma * dx; |
650 |
< |
vel[3*a+1] += rma * dy; |
651 |
< |
vel[3*a+2] += rma * dz; |
645 |
> |
dx = rab[0] * gab; |
646 |
> |
dy = rab[1] * gab; |
647 |
> |
dz = rab[2] * gab; |
648 |
> |
|
649 |
> |
velA[0] += rma * dx; |
650 |
> |
velA[1] += rma * dy; |
651 |
> |
velA[2] += rma * dz; |
652 |
|
|
653 |
< |
vel[3*b+0] -= rmb * dx; |
654 |
< |
vel[3*b+1] -= rmb * dy; |
655 |
< |
vel[3*b+2] -= rmb * dz; |
653 |
> |
atoms[a]->setVel( velA ); |
654 |
> |
|
655 |
> |
velB[0] -= rmb * dx; |
656 |
> |
velB[1] -= rmb * dy; |
657 |
> |
velB[2] -= rmb * dz; |
658 |
> |
|
659 |
> |
atoms[b]->setVel( velB ); |
660 |
|
|
661 |
|
moving[a] = 1; |
662 |
|
moving[b] = 1; |
672 |
|
|
673 |
|
iteration++; |
674 |
|
} |
675 |
< |
|
675 |
> |
|
676 |
|
if( !done ){ |
677 |
|
|
678 |
|
|
679 |
< |
sprintf( painCae.errMsg, |
679 |
> |
sprintf( painCave.errMsg, |
680 |
|
"Constraint failure in constrainB, too many iterations: %d\n", |
681 |
< |
iterations ); |
681 |
> |
iteration ); |
682 |
|
painCave.isFatal = 1; |
683 |
|
simError(); |
684 |
|
} |
685 |
|
|
686 |
|
} |
687 |
|
|
657 |
– |
|
658 |
– |
|
659 |
– |
|
660 |
– |
|
661 |
– |
|
662 |
– |
|
688 |
|
void Integrator::rotate( int axes1, int axes2, double angle, double ji[3], |
689 |
|
double A[3][3] ){ |
690 |
|
|
753 |
|
// A[][] = A[][] * transpose(rot[][]) |
754 |
|
|
755 |
|
|
756 |
< |
// NOte for as yet unknown reason, we are setting the performing the |
756 |
> |
// NOte for as yet unknown reason, we are performing the |
757 |
|
// calculation as: |
758 |
|
// transpose(A[][]) = transpose(A[][]) * transpose(rot[][]) |
759 |
|
|