# | Line 11 | Line 11 | |
---|---|---|
11 | #include "simError.h" | |
12 | ||
13 | ||
14 | < | template<typename T> Integrator<T>::Integrator( SimInfo *theInfo, ForceFields* the_ff ) { |
15 | < | |
14 | > | template<typename T> Integrator<T>::Integrator(SimInfo* theInfo, |
15 | > | ForceFields* the_ff){ |
16 | info = theInfo; | |
17 | myFF = the_ff; | |
18 | isFirst = 1; | |
# | Line 21 | Line 21 | template<typename T> Integrator<T>::Integrator( SimInf | |
21 | nMols = info->n_mol; | |
22 | ||
23 | // give a little love back to the SimInfo object | |
24 | < | |
25 | < | if( info->the_integrator != NULL ) delete info->the_integrator; |
24 | > | |
25 | > | if (info->the_integrator != NULL){ |
26 | > | delete info->the_integrator; |
27 | > | } |
28 | info->the_integrator = this; | |
29 | ||
30 | nAtoms = info->n_atoms; | |
31 | ||
32 | // check for constraints | |
33 | < | |
34 | < | constrainedA = NULL; |
35 | < | constrainedB = NULL; |
33 | > | |
34 | > | constrainedA = NULL; |
35 | > | constrainedB = NULL; |
36 | constrainedDsqr = NULL; | |
37 | < | moving = NULL; |
38 | < | moved = NULL; |
39 | < | oldPos = NULL; |
40 | < | |
37 | > | moving = NULL; |
38 | > | moved = NULL; |
39 | > | oldPos = NULL; |
40 | > | |
41 | nConstrained = 0; | |
42 | ||
43 | checkConstraints(); | |
44 | } | |
45 | ||
46 | < | template<typename T> Integrator<T>::~Integrator() { |
47 | < | |
46 | < | if( nConstrained ){ |
46 | > | template<typename T> Integrator<T>::~Integrator(){ |
47 | > | if (nConstrained){ |
48 | delete[] constrainedA; | |
49 | delete[] constrainedB; | |
50 | delete[] constrainedDsqr; | |
# | Line 51 | Line 52 | template<typename T> Integrator<T>::~Integrator() { | |
52 | delete[] moved; | |
53 | delete[] oldPos; | |
54 | } | |
54 | – | |
55 | } | |
56 | ||
57 | < | template<typename T> void Integrator<T>::checkConstraints( void ){ |
58 | < | |
59 | < | |
57 | > | template<typename T> void Integrator<T>::checkConstraints(void){ |
58 | isConstrained = 0; | |
59 | ||
60 | < | Constraint *temp_con; |
61 | < | Constraint *dummy_plug; |
60 | > | Constraint* temp_con; |
61 | > | Constraint* dummy_plug; |
62 | temp_con = new Constraint[info->n_SRI]; | |
63 | nConstrained = 0; | |
64 | int constrained = 0; | |
65 | < | |
65 | > | |
66 | SRI** theArray; | |
67 | < | for(int i = 0; i < nMols; i++){ |
68 | < | |
69 | < | theArray = (SRI**) molecules[i].getMyBonds(); |
72 | < | for(int j=0; j<molecules[i].getNBonds(); j++){ |
73 | < | |
67 | > | for (int i = 0; i < nMols; i++){ |
68 | > | theArray = (SRI * *) molecules[i].getMyBonds(); |
69 | > | for (int j = 0; j < molecules[i].getNBonds(); j++){ |
70 | constrained = theArray[j]->is_constrained(); | |
71 | ||
72 | < | if(constrained){ |
72 | > | if (constrained){ |
73 | > | dummy_plug = theArray[j]->get_constraint(); |
74 | > | temp_con[nConstrained].set_a(dummy_plug->get_a()); |
75 | > | temp_con[nConstrained].set_b(dummy_plug->get_b()); |
76 | > | temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr()); |
77 | ||
78 | < | dummy_plug = theArray[j]->get_constraint(); |
79 | < | temp_con[nConstrained].set_a( dummy_plug->get_a() ); |
80 | < | temp_con[nConstrained].set_b( dummy_plug->get_b() ); |
81 | < | temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() ); |
82 | < | |
83 | < | nConstrained++; |
84 | < | constrained = 0; |
85 | < | } |
78 | > | nConstrained++; |
79 | > | constrained = 0; |
80 | > | } |
81 | } | |
82 | ||
83 | < | theArray = (SRI**) molecules[i].getMyBends(); |
84 | < | for(int j=0; j<molecules[i].getNBends(); j++){ |
90 | < | |
83 | > | theArray = (SRI * *) molecules[i].getMyBends(); |
84 | > | for (int j = 0; j < molecules[i].getNBends(); j++){ |
85 | constrained = theArray[j]->is_constrained(); | |
86 | < | |
87 | < | if(constrained){ |
88 | < | |
89 | < | dummy_plug = theArray[j]->get_constraint(); |
90 | < | temp_con[nConstrained].set_a( dummy_plug->get_a() ); |
91 | < | temp_con[nConstrained].set_b( dummy_plug->get_b() ); |
92 | < | temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() ); |
93 | < | |
94 | < | nConstrained++; |
101 | < | constrained = 0; |
86 | > | |
87 | > | if (constrained){ |
88 | > | dummy_plug = theArray[j]->get_constraint(); |
89 | > | temp_con[nConstrained].set_a(dummy_plug->get_a()); |
90 | > | temp_con[nConstrained].set_b(dummy_plug->get_b()); |
91 | > | temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr()); |
92 | > | |
93 | > | nConstrained++; |
94 | > | constrained = 0; |
95 | } | |
96 | } | |
97 | ||
98 | < | theArray = (SRI**) molecules[i].getMyTorsions(); |
99 | < | for(int j=0; j<molecules[i].getNTorsions(); j++){ |
107 | < | |
98 | > | theArray = (SRI * *) molecules[i].getMyTorsions(); |
99 | > | for (int j = 0; j < molecules[i].getNTorsions(); j++){ |
100 | constrained = theArray[j]->is_constrained(); | |
101 | < | |
102 | < | if(constrained){ |
103 | < | |
104 | < | dummy_plug = theArray[j]->get_constraint(); |
105 | < | temp_con[nConstrained].set_a( dummy_plug->get_a() ); |
106 | < | temp_con[nConstrained].set_b( dummy_plug->get_b() ); |
107 | < | temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() ); |
108 | < | |
109 | < | nConstrained++; |
118 | < | constrained = 0; |
101 | > | |
102 | > | if (constrained){ |
103 | > | dummy_plug = theArray[j]->get_constraint(); |
104 | > | temp_con[nConstrained].set_a(dummy_plug->get_a()); |
105 | > | temp_con[nConstrained].set_b(dummy_plug->get_b()); |
106 | > | temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr()); |
107 | > | |
108 | > | nConstrained++; |
109 | > | constrained = 0; |
110 | } | |
111 | } | |
112 | } | |
113 | ||
114 | < | if(nConstrained > 0){ |
124 | < | |
114 | > | if (nConstrained > 0){ |
115 | isConstrained = 1; | |
116 | ||
117 | < | if(constrainedA != NULL ) delete[] constrainedA; |
118 | < | if(constrainedB != NULL ) delete[] constrainedB; |
119 | < | if(constrainedDsqr != NULL ) delete[] constrainedDsqr; |
117 | > | if (constrainedA != NULL) |
118 | > | delete[] constrainedA; |
119 | > | if (constrainedB != NULL) |
120 | > | delete[] constrainedB; |
121 | > | if (constrainedDsqr != NULL) |
122 | > | delete[] constrainedDsqr; |
123 | ||
124 | < | constrainedA = new int[nConstrained]; |
125 | < | constrainedB = new int[nConstrained]; |
124 | > | constrainedA = new int[nConstrained]; |
125 | > | constrainedB = new int[nConstrained]; |
126 | constrainedDsqr = new double[nConstrained]; | |
127 | < | |
128 | < | for( int i = 0; i < nConstrained; i++){ |
136 | < | |
127 | > | |
128 | > | for (int i = 0; i < nConstrained; i++){ |
129 | constrainedA[i] = temp_con[i].get_a(); | |
130 | constrainedB[i] = temp_con[i].get_b(); | |
131 | constrainedDsqr[i] = temp_con[i].get_dsqr(); | |
140 | – | |
132 | } | |
133 | ||
134 | < | |
134 | > | |
135 | // save oldAtoms to check for lode balanceing later on. | |
136 | < | |
136 | > | |
137 | oldAtoms = nAtoms; | |
138 | < | |
138 | > | |
139 | moving = new int[nAtoms]; | |
140 | < | moved = new int[nAtoms]; |
140 | > | moved = new int[nAtoms]; |
141 | ||
142 | < | oldPos = new double[nAtoms*3]; |
142 | > | oldPos = new double[nAtoms * 3]; |
143 | } | |
144 | < | |
144 | > | |
145 | delete[] temp_con; | |
146 | } | |
147 | ||
148 | ||
149 | < | template<typename T> void Integrator<T>::integrate( void ){ |
159 | < | |
149 | > | template<typename T> void Integrator<T>::integrate(void){ |
150 | int i, j; // loop counters | |
151 | ||
152 | < | double runTime = info->run_time; |
153 | < | double sampleTime = info->sampleTime; |
154 | < | double statusTime = info->statusTime; |
152 | > | double runTime = info->run_time; |
153 | > | double sampleTime = info->sampleTime; |
154 | > | double statusTime = info->statusTime; |
155 | double thermalTime = info->thermalTime; | |
156 | + | double resetTime = info->resetTime; |
157 | ||
158 | + | |
159 | double currSample; | |
160 | double currThermal; | |
161 | double currStatus; | |
162 | < | |
162 | > | double currReset; |
163 | > | |
164 | int calcPot, calcStress; | |
165 | int isError; | |
166 | ||
167 | < | tStats = new Thermo( info ); |
168 | < | statOut = new StatWriter( info ); |
169 | < | dumpOut = new DumpWriter( info ); |
167 | > | tStats = new Thermo(info); |
168 | > | statOut = new StatWriter(info); |
169 | > | dumpOut = new DumpWriter(info); |
170 | ||
171 | atoms = info->atoms; | |
172 | DirectionalAtom* dAtom; | |
# | Line 185 | Line 178 | template<typename T> void Integrator<T>::integrate( vo | |
178 | ||
179 | calcForce(1, 1); | |
180 | ||
181 | < | if( info->setTemp ){ |
189 | < | |
181 | > | if (info->setTemp){ |
182 | thermalize(); | |
183 | } | |
184 | < | |
184 | > | |
185 | calcPot = 0; | |
186 | calcStress = 0; | |
187 | < | currSample = sampleTime; |
188 | < | currThermal = thermalTime; |
189 | < | currStatus = statusTime; |
187 | > | currSample = sampleTime + info->getTime(); |
188 | > | currThermal = thermalTime+ info->getTime(); |
189 | > | currStatus = statusTime + info->getTime(); |
190 | > | currReset = resetTime + info->getTime(); |
191 | ||
192 | < | dumpOut->writeDump( info->getTime() ); |
193 | < | statOut->writeStat( info->getTime() ); |
192 | > | dumpOut->writeDump(info->getTime()); |
193 | > | statOut->writeStat(info->getTime()); |
194 | ||
195 | readyCheck(); | |
196 | ||
197 | #ifdef IS_MPI | |
198 | < | strcpy( checkPointMsg, |
206 | < | "The integrator is ready to go." ); |
198 | > | strcpy(checkPointMsg, "The integrator is ready to go."); |
199 | MPIcheckPoint(); | |
200 | #endif // is_mpi | |
201 | ||
202 | < | while( info->getTime() < runTime ){ |
203 | < | |
212 | < | if( (info->getTime()+dt) >= currStatus ){ |
202 | > | while (info->getTime() < runTime){ |
203 | > | if ((info->getTime() + dt) >= currStatus){ |
204 | calcPot = 1; | |
205 | calcStress = 1; | |
206 | } | |
207 | ||
208 | < | integrateStep( calcPot, calcStress ); |
209 | < | |
208 | > | integrateStep(calcPot, calcStress); |
209 | > | |
210 | info->incrTime(dt); | |
211 | ||
212 | < | if( info->setTemp ){ |
213 | < | if( info->getTime() >= currThermal ){ |
214 | < | thermalize(); |
215 | < | currThermal += thermalTime; |
212 | > | if (info->setTemp){ |
213 | > | if (info->getTime() >= currThermal){ |
214 | > | thermalize(); |
215 | > | currThermal += thermalTime; |
216 | } | |
217 | } | |
218 | ||
219 | < | if( info->getTime() >= currSample ){ |
220 | < | dumpOut->writeDump( info->getTime() ); |
219 | > | if (info->getTime() >= currSample){ |
220 | > | dumpOut->writeDump(info->getTime()); |
221 | currSample += sampleTime; | |
222 | } | |
223 | ||
224 | < | if( info->getTime() >= currStatus ){ |
225 | < | statOut->writeStat( info->getTime() ); |
224 | > | if (info->getTime() >= currStatus){ |
225 | > | statOut->writeStat(info->getTime()); |
226 | calcPot = 0; | |
227 | calcStress = 0; | |
228 | currStatus += statusTime; | |
229 | } | |
230 | ||
231 | + | if (info->resetIntegrator){ |
232 | + | if (info->getTime() >= currReset){ |
233 | + | this->resetIntegrator(); |
234 | + | currReset += resetTime; |
235 | + | } |
236 | + | } |
237 | + | |
238 | #ifdef IS_MPI | |
239 | < | strcpy( checkPointMsg, |
242 | < | "successfully took a time step." ); |
239 | > | strcpy(checkPointMsg, "successfully took a time step."); |
240 | MPIcheckPoint(); | |
241 | #endif // is_mpi | |
245 | – | |
242 | } | |
243 | ||
244 | dumpOut->writeFinal(info->getTime()); | |
# | Line 251 | Line 247 | template<typename T> void Integrator<T>::integrate( vo | |
247 | delete statOut; | |
248 | } | |
249 | ||
250 | < | template<typename T> void Integrator<T>::integrateStep( int calcPot, int calcStress ){ |
251 | < | |
256 | < | |
257 | < | |
250 | > | template<typename T> void Integrator<T>::integrateStep(int calcPot, |
251 | > | int calcStress){ |
252 | // Position full step, and velocity half step | |
259 | – | |
253 | preMove(); | |
254 | + | |
255 | moveA(); | |
262 | – | if( nConstrained ) constrainA(); |
256 | ||
257 | < | |
257 | > | if (nConstrained){ |
258 | > | constrainA(); |
259 | > | } |
260 | > | |
261 | > | |
262 | #ifdef IS_MPI | |
263 | < | strcpy( checkPointMsg, "Succesful moveA\n" ); |
263 | > | strcpy(checkPointMsg, "Succesful moveA\n"); |
264 | MPIcheckPoint(); | |
265 | #endif // is_mpi | |
269 | – | |
266 | ||
267 | + | |
268 | // calc forces | |
269 | ||
270 | < | calcForce(calcPot,calcStress); |
270 | > | calcForce(calcPot, calcStress); |
271 | ||
272 | #ifdef IS_MPI | |
273 | < | strcpy( checkPointMsg, "Succesful doForces\n" ); |
273 | > | strcpy(checkPointMsg, "Succesful doForces\n"); |
274 | MPIcheckPoint(); | |
275 | #endif // is_mpi | |
279 | – | |
276 | ||
277 | + | |
278 | // finish the velocity half step | |
279 | < | |
279 | > | |
280 | moveB(); | |
281 | < | if( nConstrained ) constrainB(); |
282 | < | |
281 | > | |
282 | > | if (nConstrained){ |
283 | > | constrainB(); |
284 | > | } |
285 | > | |
286 | #ifdef IS_MPI | |
287 | < | strcpy( checkPointMsg, "Succesful moveB\n" ); |
287 | > | strcpy(checkPointMsg, "Succesful moveB\n"); |
288 | MPIcheckPoint(); | |
289 | #endif // is_mpi | |
290 | – | |
291 | – | |
290 | } | |
291 | ||
292 | ||
293 | < | template<typename T> void Integrator<T>::moveA( void ){ |
296 | < | |
293 | > | template<typename T> void Integrator<T>::moveA(void){ |
294 | int i, j; | |
295 | DirectionalAtom* dAtom; | |
296 | double Tb[3], ji[3]; | |
# | Line 302 | Line 299 | template<typename T> void Integrator<T>::moveA( void ) | |
299 | double vel[3], pos[3], frc[3]; | |
300 | double mass; | |
301 | ||
302 | < | for( i=0; i<nAtoms; i++ ){ |
302 | > | for (i = 0; i < nAtoms; i++){ |
303 | > | atoms[i]->getVel(vel); |
304 | > | atoms[i]->getPos(pos); |
305 | > | atoms[i]->getFrc(frc); |
306 | ||
307 | – | atoms[i]->getVel( vel ); |
308 | – | atoms[i]->getPos( pos ); |
309 | – | atoms[i]->getFrc( frc ); |
310 | – | |
307 | mass = atoms[i]->getMass(); | |
308 | ||
309 | < | for (j=0; j < 3; j++) { |
309 | > | for (j = 0; j < 3; j++){ |
310 | // velocity half step | |
311 | < | vel[j] += ( dt2 * frc[j] / mass ) * eConvert; |
311 | > | vel[j] += (dt2 * frc[j] / mass) * eConvert; |
312 | // position whole step | |
313 | pos[j] += dt * vel[j]; | |
314 | } | |
315 | ||
316 | < | atoms[i]->setVel( vel ); |
317 | < | atoms[i]->setPos( pos ); |
316 | > | atoms[i]->setVel(vel); |
317 | > | atoms[i]->setPos(pos); |
318 | ||
319 | < | if( atoms[i]->isDirectional() ){ |
319 | > | if (atoms[i]->isDirectional()){ |
320 | > | dAtom = (DirectionalAtom *) atoms[i]; |
321 | ||
325 | – | dAtom = (DirectionalAtom *)atoms[i]; |
326 | – | |
322 | // get and convert the torque to body frame | |
328 | – | |
329 | – | dAtom->getTrq( Tb ); |
330 | – | dAtom->lab2Body( Tb ); |
323 | ||
324 | + | dAtom->getTrq(Tb); |
325 | + | dAtom->lab2Body(Tb); |
326 | + | |
327 | // get the angular momentum, and propagate a half step | |
328 | ||
329 | < | dAtom->getJ( ji ); |
329 | > | dAtom->getJ(ji); |
330 | ||
331 | < | for (j=0; j < 3; j++) |
331 | > | for (j = 0; j < 3; j++) |
332 | ji[j] += (dt2 * Tb[j]) * eConvert; | |
333 | < | |
333 | > | |
334 | // use the angular velocities to propagate the rotation matrix a | |
335 | // full time step | |
336 | ||
337 | dAtom->getA(A); | |
338 | dAtom->getI(I); | |
339 | < | |
339 | > | |
340 | // rotate about the x-axis | |
341 | angle = dt2 * ji[0] / I[0][0]; | |
342 | < | this->rotate( 1, 2, angle, ji, A ); |
342 | > | this->rotate(1, 2, angle, ji, A); |
343 | ||
344 | // rotate about the y-axis | |
345 | angle = dt2 * ji[1] / I[1][1]; | |
346 | < | this->rotate( 2, 0, angle, ji, A ); |
347 | < | |
346 | > | this->rotate(2, 0, angle, ji, A); |
347 | > | |
348 | // rotate about the z-axis | |
349 | angle = dt * ji[2] / I[2][2]; | |
350 | < | this->rotate( 0, 1, angle, ji, A); |
351 | < | |
350 | > | this->rotate(0, 1, angle, ji, A); |
351 | > | |
352 | // rotate about the y-axis | |
353 | angle = dt2 * ji[1] / I[1][1]; | |
354 | < | this->rotate( 2, 0, angle, ji, A ); |
355 | < | |
356 | < | // rotate about the x-axis |
354 | > | this->rotate(2, 0, angle, ji, A); |
355 | > | |
356 | > | // rotate about the x-axis |
357 | angle = dt2 * ji[0] / I[0][0]; | |
358 | < | this->rotate( 1, 2, angle, ji, A ); |
364 | < | |
358 | > | this->rotate(1, 2, angle, ji, A); |
359 | ||
360 | < | dAtom->setJ( ji ); |
361 | < | dAtom->setA( A ); |
362 | < | |
363 | < | } |
360 | > | |
361 | > | dAtom->setJ(ji); |
362 | > | dAtom->setA(A); |
363 | > | } |
364 | } | |
365 | } | |
366 | ||
367 | ||
368 | < | template<typename T> void Integrator<T>::moveB( void ){ |
368 | > | template<typename T> void Integrator<T>::moveB(void){ |
369 | int i, j; | |
370 | DirectionalAtom* dAtom; | |
371 | double Tb[3], ji[3]; | |
372 | double vel[3], frc[3]; | |
373 | double mass; | |
374 | ||
375 | < | for( i=0; i<nAtoms; i++ ){ |
376 | < | |
377 | < | atoms[i]->getVel( vel ); |
384 | < | atoms[i]->getFrc( frc ); |
375 | > | for (i = 0; i < nAtoms; i++){ |
376 | > | atoms[i]->getVel(vel); |
377 | > | atoms[i]->getFrc(frc); |
378 | ||
379 | mass = atoms[i]->getMass(); | |
380 | ||
381 | // velocity half step | |
382 | < | for (j=0; j < 3; j++) |
383 | < | vel[j] += ( dt2 * frc[j] / mass ) * eConvert; |
391 | < | |
392 | < | atoms[i]->setVel( vel ); |
393 | < | |
394 | < | if( atoms[i]->isDirectional() ){ |
382 | > | for (j = 0; j < 3; j++) |
383 | > | vel[j] += (dt2 * frc[j] / mass) * eConvert; |
384 | ||
385 | < | dAtom = (DirectionalAtom *)atoms[i]; |
385 | > | atoms[i]->setVel(vel); |
386 | ||
387 | + | if (atoms[i]->isDirectional()){ |
388 | + | dAtom = (DirectionalAtom *) atoms[i]; |
389 | + | |
390 | // get and convert the torque to body frame | |
391 | ||
392 | < | dAtom->getTrq( Tb ); |
393 | < | dAtom->lab2Body( Tb ); |
392 | > | dAtom->getTrq(Tb); |
393 | > | dAtom->lab2Body(Tb); |
394 | ||
395 | // get the angular momentum, and propagate a half step | |
396 | ||
397 | < | dAtom->getJ( ji ); |
397 | > | dAtom->getJ(ji); |
398 | ||
399 | < | for (j=0; j < 3; j++) |
399 | > | for (j = 0; j < 3; j++) |
400 | ji[j] += (dt2 * Tb[j]) * eConvert; | |
409 | – | |
401 | ||
402 | < | dAtom->setJ( ji ); |
402 | > | |
403 | > | dAtom->setJ(ji); |
404 | } | |
405 | } | |
406 | } | |
407 | ||
408 | < | template<typename T> void Integrator<T>::preMove( void ){ |
408 | > | template<typename T> void Integrator<T>::preMove(void){ |
409 | int i, j; | |
410 | double pos[3]; | |
411 | ||
412 | < | if( nConstrained ){ |
412 | > | if (nConstrained){ |
413 | > | for (i = 0; i < nAtoms; i++){ |
414 | > | atoms[i]->getPos(pos); |
415 | ||
416 | < | for(i=0; i < nAtoms; i++) { |
417 | < | |
424 | < | atoms[i]->getPos( pos ); |
425 | < | |
426 | < | for (j = 0; j < 3; j++) { |
427 | < | oldPos[3*i + j] = pos[j]; |
416 | > | for (j = 0; j < 3; j++){ |
417 | > | oldPos[3 * i + j] = pos[j]; |
418 | } | |
429 | – | |
419 | } | |
420 | < | } |
420 | > | } |
421 | } | |
422 | ||
423 | template<typename T> void Integrator<T>::constrainA(){ | |
424 | < | |
436 | < | int i,j,k; |
424 | > | int i, j, k; |
425 | int done; | |
426 | double posA[3], posB[3]; | |
427 | double velA[3], velB[3]; | |
# | Line 448 | Line 436 | template<typename T> void Integrator<T>::constrainA(){ | |
436 | double gab; | |
437 | int iteration; | |
438 | ||
439 | < | for( i=0; i<nAtoms; i++){ |
439 | > | for (i = 0; i < nAtoms; i++){ |
440 | moving[i] = 0; | |
441 | < | moved[i] = 1; |
441 | > | moved[i] = 1; |
442 | } | |
443 | ||
444 | iteration = 0; | |
445 | done = 0; | |
446 | < | while( !done && (iteration < maxIteration )){ |
447 | < | |
448 | < | done = 1; |
461 | < | for(i=0; i<nConstrained; i++){ |
462 | < | |
446 | > | while (!done && (iteration < maxIteration)){ |
447 | > | done = 1; |
448 | > | for (i = 0; i < nConstrained; i++){ |
449 | a = constrainedA[i]; | |
450 | b = constrainedB[i]; | |
465 | – | |
466 | – | ax = (a*3) + 0; |
467 | – | ay = (a*3) + 1; |
468 | – | az = (a*3) + 2; |
451 | ||
452 | < | bx = (b*3) + 0; |
453 | < | by = (b*3) + 1; |
454 | < | bz = (b*3) + 2; |
452 | > | ax = (a * 3) + 0; |
453 | > | ay = (a * 3) + 1; |
454 | > | az = (a * 3) + 2; |
455 | ||
456 | < | if( moved[a] || moved[b] ){ |
457 | < | |
458 | < | atoms[a]->getPos( posA ); |
459 | < | atoms[b]->getPos( posB ); |
460 | < | |
461 | < | for (j = 0; j < 3; j++ ) |
456 | > | bx = (b * 3) + 0; |
457 | > | by = (b * 3) + 1; |
458 | > | bz = (b * 3) + 2; |
459 | > | |
460 | > | if (moved[a] || moved[b]){ |
461 | > | atoms[a]->getPos(posA); |
462 | > | atoms[b]->getPos(posB); |
463 | > | |
464 | > | for (j = 0; j < 3; j++) |
465 | pab[j] = posA[j] - posB[j]; | |
481 | – | |
482 | – | //periodic boundary condition |
466 | ||
467 | < | info->wrapVector( pab ); |
467 | > | //periodic boundary condition |
468 | ||
469 | < | pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2]; |
469 | > | info->wrapVector(pab); |
470 | ||
471 | < | rabsq = constrainedDsqr[i]; |
489 | < | diffsq = rabsq - pabsq; |
471 | > | pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2]; |
472 | ||
473 | < | // the original rattle code from alan tidesley |
474 | < | if (fabs(diffsq) > (tol*rabsq*2)) { |
493 | < | rab[0] = oldPos[ax] - oldPos[bx]; |
494 | < | rab[1] = oldPos[ay] - oldPos[by]; |
495 | < | rab[2] = oldPos[az] - oldPos[bz]; |
473 | > | rabsq = constrainedDsqr[i]; |
474 | > | diffsq = rabsq - pabsq; |
475 | ||
476 | < | info->wrapVector( rab ); |
476 | > | // the original rattle code from alan tidesley |
477 | > | if (fabs(diffsq) > (tol * rabsq * 2)){ |
478 | > | rab[0] = oldPos[ax] - oldPos[bx]; |
479 | > | rab[1] = oldPos[ay] - oldPos[by]; |
480 | > | rab[2] = oldPos[az] - oldPos[bz]; |
481 | ||
482 | < | rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
482 | > | info->wrapVector(rab); |
483 | ||
484 | < | rpabsq = rpab * rpab; |
484 | > | rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
485 | ||
486 | + | rpabsq = rpab * rpab; |
487 | ||
504 | – | if (rpabsq < (rabsq * -diffsq)){ |
488 | ||
489 | + | if (rpabsq < (rabsq * -diffsq)){ |
490 | #ifdef IS_MPI | |
491 | < | a = atoms[a]->getGlobalIndex(); |
492 | < | b = atoms[b]->getGlobalIndex(); |
491 | > | a = atoms[a]->getGlobalIndex(); |
492 | > | b = atoms[b]->getGlobalIndex(); |
493 | #endif //is_mpi | |
494 | < | sprintf( painCave.errMsg, |
495 | < | "Constraint failure in constrainA at atom %d and %d.\n", |
496 | < | a, b ); |
497 | < | painCave.isFatal = 1; |
498 | < | simError(); |
499 | < | } |
494 | > | sprintf(painCave.errMsg, |
495 | > | "Constraint failure in constrainA at atom %d and %d.\n", a, |
496 | > | b); |
497 | > | painCave.isFatal = 1; |
498 | > | simError(); |
499 | > | } |
500 | ||
501 | < | rma = 1.0 / atoms[a]->getMass(); |
502 | < | rmb = 1.0 / atoms[b]->getMass(); |
501 | > | rma = 1.0 / atoms[a]->getMass(); |
502 | > | rmb = 1.0 / atoms[b]->getMass(); |
503 | ||
504 | < | gab = diffsq / ( 2.0 * ( rma + rmb ) * rpab ); |
504 | > | gab = diffsq / (2.0 * (rma + rmb) * rpab); |
505 | ||
506 | dx = rab[0] * gab; | |
507 | dy = rab[1] * gab; | |
508 | dz = rab[2] * gab; | |
509 | ||
510 | < | posA[0] += rma * dx; |
511 | < | posA[1] += rma * dy; |
512 | < | posA[2] += rma * dz; |
510 | > | posA[0] += rma * dx; |
511 | > | posA[1] += rma * dy; |
512 | > | posA[2] += rma * dz; |
513 | ||
514 | < | atoms[a]->setPos( posA ); |
514 | > | atoms[a]->setPos(posA); |
515 | ||
516 | < | posB[0] -= rmb * dx; |
517 | < | posB[1] -= rmb * dy; |
518 | < | posB[2] -= rmb * dz; |
516 | > | posB[0] -= rmb * dx; |
517 | > | posB[1] -= rmb * dy; |
518 | > | posB[2] -= rmb * dz; |
519 | ||
520 | < | atoms[b]->setPos( posB ); |
520 | > | atoms[b]->setPos(posB); |
521 | ||
522 | dx = dx / dt; | |
523 | dy = dy / dt; | |
524 | dz = dz / dt; | |
525 | ||
526 | < | atoms[a]->getVel( velA ); |
526 | > | atoms[a]->getVel(velA); |
527 | ||
528 | < | velA[0] += rma * dx; |
529 | < | velA[1] += rma * dy; |
530 | < | velA[2] += rma * dz; |
528 | > | velA[0] += rma * dx; |
529 | > | velA[1] += rma * dy; |
530 | > | velA[2] += rma * dz; |
531 | ||
532 | < | atoms[a]->setVel( velA ); |
532 | > | atoms[a]->setVel(velA); |
533 | ||
534 | < | atoms[b]->getVel( velB ); |
534 | > | atoms[b]->getVel(velB); |
535 | ||
536 | < | velB[0] -= rmb * dx; |
537 | < | velB[1] -= rmb * dy; |
538 | < | velB[2] -= rmb * dz; |
536 | > | velB[0] -= rmb * dx; |
537 | > | velB[1] -= rmb * dy; |
538 | > | velB[2] -= rmb * dz; |
539 | ||
540 | < | atoms[b]->setVel( velB ); |
540 | > | atoms[b]->setVel(velB); |
541 | ||
542 | < | moving[a] = 1; |
543 | < | moving[b] = 1; |
544 | < | done = 0; |
545 | < | } |
542 | > | moving[a] = 1; |
543 | > | moving[b] = 1; |
544 | > | done = 0; |
545 | > | } |
546 | } | |
547 | } | |
548 | < | |
549 | < | for(i=0; i<nAtoms; i++){ |
566 | < | |
548 | > | |
549 | > | for (i = 0; i < nAtoms; i++){ |
550 | moved[i] = moving[i]; | |
551 | moving[i] = 0; | |
552 | } | |
# | Line 571 | Line 554 | template<typename T> void Integrator<T>::constrainA(){ | |
554 | iteration++; | |
555 | } | |
556 | ||
557 | < | if( !done ){ |
558 | < | |
559 | < | sprintf( painCave.errMsg, |
560 | < | "Constraint failure in constrainA, too many iterations: %d\n", |
578 | < | iteration ); |
557 | > | if (!done){ |
558 | > | sprintf(painCave.errMsg, |
559 | > | "Constraint failure in constrainA, too many iterations: %d\n", |
560 | > | iteration); |
561 | painCave.isFatal = 1; | |
562 | simError(); | |
563 | } | |
582 | – | |
564 | } | |
565 | ||
566 | < | template<typename T> void Integrator<T>::constrainB( void ){ |
567 | < | |
587 | < | int i,j,k; |
566 | > | template<typename T> void Integrator<T>::constrainB(void){ |
567 | > | int i, j, k; |
568 | int done; | |
569 | double posA[3], posB[3]; | |
570 | double velA[3], velB[3]; | |
# | Line 598 | Line 578 | template<typename T> void Integrator<T>::constrainB( v | |
578 | double gab; | |
579 | int iteration; | |
580 | ||
581 | < | for(i=0; i<nAtoms; i++){ |
581 | > | for (i = 0; i < nAtoms; i++){ |
582 | moving[i] = 0; | |
583 | moved[i] = 1; | |
584 | } | |
585 | ||
586 | done = 0; | |
587 | iteration = 0; | |
588 | < | while( !done && (iteration < maxIteration ) ){ |
609 | < | |
588 | > | while (!done && (iteration < maxIteration)){ |
589 | done = 1; | |
590 | ||
591 | < | for(i=0; i<nConstrained; i++){ |
613 | < | |
591 | > | for (i = 0; i < nConstrained; i++){ |
592 | a = constrainedA[i]; | |
593 | b = constrainedB[i]; | |
594 | ||
595 | < | ax = (a*3) + 0; |
596 | < | ay = (a*3) + 1; |
597 | < | az = (a*3) + 2; |
595 | > | ax = (a * 3) + 0; |
596 | > | ay = (a * 3) + 1; |
597 | > | az = (a * 3) + 2; |
598 | ||
599 | < | bx = (b*3) + 0; |
600 | < | by = (b*3) + 1; |
601 | < | bz = (b*3) + 2; |
624 | < | |
625 | < | if( moved[a] || moved[b] ){ |
599 | > | bx = (b * 3) + 0; |
600 | > | by = (b * 3) + 1; |
601 | > | bz = (b * 3) + 2; |
602 | ||
603 | < | atoms[a]->getVel( velA ); |
604 | < | atoms[b]->getVel( velB ); |
605 | < | |
630 | < | vxab = velA[0] - velB[0]; |
631 | < | vyab = velA[1] - velB[1]; |
632 | < | vzab = velA[2] - velB[2]; |
603 | > | if (moved[a] || moved[b]){ |
604 | > | atoms[a]->getVel(velA); |
605 | > | atoms[b]->getVel(velB); |
606 | ||
607 | < | atoms[a]->getPos( posA ); |
608 | < | atoms[b]->getPos( posB ); |
607 | > | vxab = velA[0] - velB[0]; |
608 | > | vyab = velA[1] - velB[1]; |
609 | > | vzab = velA[2] - velB[2]; |
610 | ||
611 | < | for (j = 0; j < 3; j++) |
611 | > | atoms[a]->getPos(posA); |
612 | > | atoms[b]->getPos(posB); |
613 | > | |
614 | > | for (j = 0; j < 3; j++) |
615 | rab[j] = posA[j] - posB[j]; | |
639 | – | |
640 | – | info->wrapVector( rab ); |
641 | – | |
642 | – | rma = 1.0 / atoms[a]->getMass(); |
643 | – | rmb = 1.0 / atoms[b]->getMass(); |
616 | ||
617 | < | rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab; |
646 | < | |
647 | < | gab = -rvab / ( ( rma + rmb ) * constrainedDsqr[i] ); |
617 | > | info->wrapVector(rab); |
618 | ||
619 | < | if (fabs(gab) > tol) { |
620 | < | |
651 | < | dx = rab[0] * gab; |
652 | < | dy = rab[1] * gab; |
653 | < | dz = rab[2] * gab; |
654 | < | |
655 | < | velA[0] += rma * dx; |
656 | < | velA[1] += rma * dy; |
657 | < | velA[2] += rma * dz; |
619 | > | rma = 1.0 / atoms[a]->getMass(); |
620 | > | rmb = 1.0 / atoms[b]->getMass(); |
621 | ||
622 | < | atoms[a]->setVel( velA ); |
622 | > | rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab; |
623 | ||
624 | < | velB[0] -= rmb * dx; |
662 | < | velB[1] -= rmb * dy; |
663 | < | velB[2] -= rmb * dz; |
624 | > | gab = -rvab / ((rma + rmb) * constrainedDsqr[i]); |
625 | ||
626 | < | atoms[b]->setVel( velB ); |
627 | < | |
628 | < | moving[a] = 1; |
629 | < | moving[b] = 1; |
630 | < | done = 0; |
631 | < | } |
626 | > | if (fabs(gab) > tol){ |
627 | > | dx = rab[0] * gab; |
628 | > | dy = rab[1] * gab; |
629 | > | dz = rab[2] * gab; |
630 | > | |
631 | > | velA[0] += rma * dx; |
632 | > | velA[1] += rma * dy; |
633 | > | velA[2] += rma * dz; |
634 | > | |
635 | > | atoms[a]->setVel(velA); |
636 | > | |
637 | > | velB[0] -= rmb * dx; |
638 | > | velB[1] -= rmb * dy; |
639 | > | velB[2] -= rmb * dz; |
640 | > | |
641 | > | atoms[b]->setVel(velB); |
642 | > | |
643 | > | moving[a] = 1; |
644 | > | moving[b] = 1; |
645 | > | done = 0; |
646 | > | } |
647 | } | |
648 | } | |
649 | ||
650 | < | for(i=0; i<nAtoms; i++){ |
650 | > | for (i = 0; i < nAtoms; i++){ |
651 | moved[i] = moving[i]; | |
652 | moving[i] = 0; | |
653 | } | |
654 | < | |
654 | > | |
655 | iteration++; | |
656 | } | |
681 | – | |
682 | – | if( !done ){ |
657 | ||
658 | < | |
659 | < | sprintf( painCave.errMsg, |
660 | < | "Constraint failure in constrainB, too many iterations: %d\n", |
661 | < | iteration ); |
658 | > | if (!done){ |
659 | > | sprintf(painCave.errMsg, |
660 | > | "Constraint failure in constrainB, too many iterations: %d\n", |
661 | > | iteration); |
662 | painCave.isFatal = 1; | |
663 | simError(); | |
664 | < | } |
691 | < | |
664 | > | } |
665 | } | |
666 | ||
667 | < | template<typename T> void Integrator<T>::rotate( int axes1, int axes2, double angle, double ji[3], |
668 | < | double A[3][3] ){ |
669 | < | |
670 | < | int i,j,k; |
667 | > | template<typename T> void Integrator<T>::rotate(int axes1, int axes2, |
668 | > | double angle, double ji[3], |
669 | > | double A[3][3]){ |
670 | > | int i, j, k; |
671 | double sinAngle; | |
672 | double cosAngle; | |
673 | double angleSqr; | |
# | Line 706 | Line 679 | template<typename T> void Integrator<T>::rotate( int a | |
679 | ||
680 | // initialize the tempA | |
681 | ||
682 | < | for(i=0; i<3; i++){ |
683 | < | for(j=0; j<3; j++){ |
682 | > | for (i = 0; i < 3; i++){ |
683 | > | for (j = 0; j < 3; j++){ |
684 | tempA[j][i] = A[i][j]; | |
685 | } | |
686 | } | |
687 | ||
688 | // initialize the tempJ | |
689 | ||
690 | < | for( i=0; i<3; i++) tempJ[i] = ji[i]; |
691 | < | |
690 | > | for (i = 0; i < 3; i++) |
691 | > | tempJ[i] = ji[i]; |
692 | > | |
693 | // initalize rot as a unit matrix | |
694 | ||
695 | rot[0][0] = 1.0; | |
# | Line 725 | Line 699 | template<typename T> void Integrator<T>::rotate( int a | |
699 | rot[1][0] = 0.0; | |
700 | rot[1][1] = 1.0; | |
701 | rot[1][2] = 0.0; | |
702 | < | |
702 | > | |
703 | rot[2][0] = 0.0; | |
704 | rot[2][1] = 0.0; | |
705 | rot[2][2] = 1.0; | |
706 | < | |
706 | > | |
707 | // use a small angle aproximation for sin and cosine | |
708 | ||
709 | < | angleSqr = angle * angle; |
709 | > | angleSqr = angle * angle; |
710 | angleSqrOver4 = angleSqr / 4.0; | |
711 | top = 1.0 - angleSqrOver4; | |
712 | bottom = 1.0 + angleSqrOver4; | |
# | Line 745 | Line 719 | template<typename T> void Integrator<T>::rotate( int a | |
719 | ||
720 | rot[axes1][axes2] = sinAngle; | |
721 | rot[axes2][axes1] = -sinAngle; | |
722 | < | |
722 | > | |
723 | // rotate the momentum acoording to: ji[] = rot[][] * ji[] | |
724 | < | |
725 | < | for(i=0; i<3; i++){ |
724 | > | |
725 | > | for (i = 0; i < 3; i++){ |
726 | ji[i] = 0.0; | |
727 | < | for(k=0; k<3; k++){ |
727 | > | for (k = 0; k < 3; k++){ |
728 | ji[i] += rot[i][k] * tempJ[k]; | |
729 | } | |
730 | } | |
# | Line 763 | Line 737 | template<typename T> void Integrator<T>::rotate( int a | |
737 | // calculation as: | |
738 | // transpose(A[][]) = transpose(A[][]) * transpose(rot[][]) | |
739 | ||
740 | < | for(i=0; i<3; i++){ |
741 | < | for(j=0; j<3; j++){ |
740 | > | for (i = 0; i < 3; i++){ |
741 | > | for (j = 0; j < 3; j++){ |
742 | A[j][i] = 0.0; | |
743 | < | for(k=0; k<3; k++){ |
744 | < | A[j][i] += tempA[i][k] * rot[j][k]; |
743 | > | for (k = 0; k < 3; k++){ |
744 | > | A[j][i] += tempA[i][k] * rot[j][k]; |
745 | } | |
746 | } | |
747 | } | |
748 | } | |
749 | ||
750 | < | template<typename T> void Integrator<T>::calcForce( int calcPot, int calcStress ){ |
751 | < | myFF->doForces(calcPot,calcStress); |
778 | < | |
750 | > | template<typename T> void Integrator<T>::calcForce(int calcPot, int calcStress){ |
751 | > | myFF->doForces(calcPot, calcStress); |
752 | } | |
753 | ||
754 | template<typename T> void Integrator<T>::thermalize(){ | |
755 | < | tStats->velocitize(); |
755 | > | tStats->velocitize(); |
756 | } |
– | Removed lines |
+ | Added lines |
< | Changed lines |
> | Changed lines |