# | Line 1 | Line 1 | |
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1 | #include <iostream> | |
2 | < | #include <cstdlib> |
3 | < | #include <cmath> |
2 | > | #include <stdlib.h> |
3 | > | #include <math.h> |
4 | ||
5 | #ifdef IS_MPI | |
6 | #include "mpiSimulation.hpp" | |
7 | #include <unistd.h> | |
8 | #endif //is_mpi | |
9 | ||
10 | + | #ifdef PROFILE |
11 | + | #include "mdProfile.hpp" |
12 | + | #endif // profile |
13 | + | |
14 | #include "Integrator.hpp" | |
15 | #include "simError.h" | |
16 | ||
17 | ||
18 | < | template<typename T> Integrator<T>::Integrator( SimInfo *theInfo, ForceFields* the_ff ) { |
19 | < | |
18 | > | template<typename T> Integrator<T>::Integrator(SimInfo* theInfo, |
19 | > | ForceFields* the_ff){ |
20 | info = theInfo; | |
21 | myFF = the_ff; | |
22 | isFirst = 1; | |
# | Line 21 | Line 25 | template<typename T> Integrator<T>::Integrator( SimInf | |
25 | nMols = info->n_mol; | |
26 | ||
27 | // give a little love back to the SimInfo object | |
24 | – | |
25 | – | if( info->the_integrator != NULL ) delete info->the_integrator; |
26 | – | info->the_integrator = this; |
28 | ||
29 | + | if (info->the_integrator != NULL){ |
30 | + | delete info->the_integrator; |
31 | + | } |
32 | + | |
33 | nAtoms = info->n_atoms; | |
34 | + | integrableObjects = info->integrableObjects; |
35 | ||
36 | // check for constraints | |
37 | < | |
38 | < | constrainedA = NULL; |
39 | < | constrainedB = NULL; |
37 | > | |
38 | > | constrainedA = NULL; |
39 | > | constrainedB = NULL; |
40 | constrainedDsqr = NULL; | |
41 | < | moving = NULL; |
42 | < | moved = NULL; |
43 | < | oldPos = NULL; |
44 | < | |
41 | > | moving = NULL; |
42 | > | moved = NULL; |
43 | > | oldPos = NULL; |
44 | > | |
45 | nConstrained = 0; | |
46 | ||
47 | checkConstraints(); | |
48 | } | |
49 | ||
50 | < | template<typename T> Integrator<T>::~Integrator() { |
51 | < | |
46 | < | if( nConstrained ){ |
50 | > | template<typename T> Integrator<T>::~Integrator(){ |
51 | > | if (nConstrained){ |
52 | delete[] constrainedA; | |
53 | delete[] constrainedB; | |
54 | delete[] constrainedDsqr; | |
# | Line 51 | Line 56 | template<typename T> Integrator<T>::~Integrator() { | |
56 | delete[] moved; | |
57 | delete[] oldPos; | |
58 | } | |
54 | – | |
59 | } | |
60 | ||
61 | < | template<typename T> void Integrator<T>::checkConstraints( void ){ |
58 | < | |
59 | < | |
61 | > | template<typename T> void Integrator<T>::checkConstraints(void){ |
62 | isConstrained = 0; | |
63 | ||
64 | < | Constraint *temp_con; |
65 | < | Constraint *dummy_plug; |
64 | > | Constraint* temp_con; |
65 | > | Constraint* dummy_plug; |
66 | temp_con = new Constraint[info->n_SRI]; | |
67 | nConstrained = 0; | |
68 | int constrained = 0; | |
69 | < | |
69 | > | |
70 | SRI** theArray; | |
71 | < | for(int i = 0; i < nMols; i++){ |
72 | < | |
73 | < | theArray = (SRI**) molecules[i].getMyBonds(); |
74 | < | for(int j=0; j<molecules[i].getNBonds(); j++){ |
73 | < | |
71 | > | for (int i = 0; i < nMols; i++){ |
72 | > | |
73 | > | theArray = (SRI * *) molecules[i].getMyBonds(); |
74 | > | for (int j = 0; j < molecules[i].getNBonds(); j++){ |
75 | constrained = theArray[j]->is_constrained(); | |
76 | ||
77 | < | if(constrained){ |
77 | > | if (constrained){ |
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 | < | dummy_plug = theArray[j]->get_constraint(); |
84 | < | temp_con[nConstrained].set_a( dummy_plug->get_a() ); |
85 | < | 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 | < | } |
83 | > | nConstrained++; |
84 | > | constrained = 0; |
85 | > | } |
86 | } | |
87 | ||
88 | < | theArray = (SRI**) molecules[i].getMyBends(); |
89 | < | for(int j=0; j<molecules[i].getNBends(); j++){ |
90 | < | |
88 | > | theArray = (SRI * *) molecules[i].getMyBends(); |
89 | > | for (int j = 0; j < molecules[i].getNBends(); j++){ |
90 | constrained = theArray[j]->is_constrained(); | |
91 | < | |
92 | < | if(constrained){ |
93 | < | |
94 | < | dummy_plug = theArray[j]->get_constraint(); |
95 | < | temp_con[nConstrained].set_a( dummy_plug->get_a() ); |
96 | < | temp_con[nConstrained].set_b( dummy_plug->get_b() ); |
97 | < | temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() ); |
98 | < | |
99 | < | nConstrained++; |
101 | < | constrained = 0; |
91 | > | |
92 | > | if (constrained){ |
93 | > | dummy_plug = theArray[j]->get_constraint(); |
94 | > | temp_con[nConstrained].set_a(dummy_plug->get_a()); |
95 | > | temp_con[nConstrained].set_b(dummy_plug->get_b()); |
96 | > | temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr()); |
97 | > | |
98 | > | nConstrained++; |
99 | > | constrained = 0; |
100 | } | |
101 | } | |
102 | ||
103 | < | theArray = (SRI**) molecules[i].getMyTorsions(); |
104 | < | for(int j=0; j<molecules[i].getNTorsions(); j++){ |
107 | < | |
103 | > | theArray = (SRI * *) molecules[i].getMyTorsions(); |
104 | > | for (int j = 0; j < molecules[i].getNTorsions(); j++){ |
105 | constrained = theArray[j]->is_constrained(); | |
106 | < | |
107 | < | if(constrained){ |
108 | < | |
109 | < | dummy_plug = theArray[j]->get_constraint(); |
110 | < | temp_con[nConstrained].set_a( dummy_plug->get_a() ); |
111 | < | temp_con[nConstrained].set_b( dummy_plug->get_b() ); |
112 | < | temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() ); |
113 | < | |
114 | < | nConstrained++; |
118 | < | constrained = 0; |
106 | > | |
107 | > | if (constrained){ |
108 | > | dummy_plug = theArray[j]->get_constraint(); |
109 | > | temp_con[nConstrained].set_a(dummy_plug->get_a()); |
110 | > | temp_con[nConstrained].set_b(dummy_plug->get_b()); |
111 | > | temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr()); |
112 | > | |
113 | > | nConstrained++; |
114 | > | constrained = 0; |
115 | } | |
116 | } | |
117 | } | |
118 | ||
119 | < | if(nConstrained > 0){ |
120 | < | |
119 | > | |
120 | > | if (nConstrained > 0){ |
121 | isConstrained = 1; | |
122 | ||
123 | < | if(constrainedA != NULL ) delete[] constrainedA; |
124 | < | if(constrainedB != NULL ) delete[] constrainedB; |
125 | < | if(constrainedDsqr != NULL ) delete[] constrainedDsqr; |
126 | < | |
127 | < | constrainedA = new int[nConstrained]; |
128 | < | constrainedB = new int[nConstrained]; |
123 | > | if (constrainedA != NULL) |
124 | > | delete[] constrainedA; |
125 | > | if (constrainedB != NULL) |
126 | > | delete[] constrainedB; |
127 | > | if (constrainedDsqr != NULL) |
128 | > | delete[] constrainedDsqr; |
129 | > | |
130 | > | constrainedA = new int[nConstrained]; |
131 | > | constrainedB = new int[nConstrained]; |
132 | constrainedDsqr = new double[nConstrained]; | |
133 | < | |
134 | < | for( int i = 0; i < nConstrained; i++){ |
136 | < | |
133 | > | |
134 | > | for (int i = 0; i < nConstrained; i++){ |
135 | constrainedA[i] = temp_con[i].get_a(); | |
136 | constrainedB[i] = temp_con[i].get_b(); | |
137 | constrainedDsqr[i] = temp_con[i].get_dsqr(); | |
140 | – | |
138 | } | |
139 | ||
140 | < | |
141 | < | // save oldAtoms to check for lode balanceing later on. |
142 | < | |
140 | > | |
141 | > | // save oldAtoms to check for lode balancing later on. |
142 | > | |
143 | oldAtoms = nAtoms; | |
144 | < | |
144 | > | |
145 | moving = new int[nAtoms]; | |
146 | < | moved = new int[nAtoms]; |
146 | > | moved = new int[nAtoms]; |
147 | ||
148 | < | oldPos = new double[nAtoms*3]; |
148 | > | oldPos = new double[nAtoms * 3]; |
149 | } | |
150 | < | |
150 | > | |
151 | delete[] temp_con; | |
152 | } | |
153 | ||
154 | ||
155 | < | template<typename T> void Integrator<T>::integrate( void ){ |
155 | > | template<typename T> void Integrator<T>::integrate(void){ |
156 | ||
157 | < | int i, j; // loop counters |
158 | < | |
159 | < | double runTime = info->run_time; |
163 | < | double sampleTime = info->sampleTime; |
164 | < | double statusTime = info->statusTime; |
157 | > | double runTime = info->run_time; |
158 | > | double sampleTime = info->sampleTime; |
159 | > | double statusTime = info->statusTime; |
160 | double thermalTime = info->thermalTime; | |
161 | + | double resetTime = info->resetTime; |
162 | ||
163 | + | |
164 | double currSample; | |
165 | double currThermal; | |
166 | double currStatus; | |
167 | + | double currReset; |
168 | ||
169 | int calcPot, calcStress; | |
172 | – | int isError; |
170 | ||
171 | < | tStats = new Thermo( info ); |
172 | < | statOut = new StatWriter( info ); |
173 | < | dumpOut = new DumpWriter( info ); |
171 | > | tStats = new Thermo(info); |
172 | > | statOut = new StatWriter(info); |
173 | > | dumpOut = new DumpWriter(info); |
174 | ||
175 | atoms = info->atoms; | |
179 | – | DirectionalAtom* dAtom; |
176 | ||
177 | dt = info->dt; | |
178 | dt2 = 0.5 * dt; | |
179 | ||
180 | + | readyCheck(); |
181 | + | |
182 | // initialize the forces before the first step | |
183 | ||
184 | calcForce(1, 1); | |
185 | < | // myFF->doForces(1,1); |
186 | < | |
187 | < | if( info->setTemp ){ |
188 | < | |
189 | < | thermalize(); |
185 | > | |
186 | > | if (nConstrained){ |
187 | > | preMove(); |
188 | > | constrainA(); |
189 | > | calcForce(1, 1); |
190 | > | constrainB(); |
191 | } | |
192 | ||
193 | + | if (info->setTemp){ |
194 | + | thermalize(); |
195 | + | } |
196 | + | |
197 | calcPot = 0; | |
198 | calcStress = 0; | |
199 | currSample = sampleTime + info->getTime(); | |
200 | currThermal = thermalTime+ info->getTime(); | |
201 | currStatus = statusTime + info->getTime(); | |
202 | + | currReset = resetTime + info->getTime(); |
203 | ||
204 | < | dumpOut->writeDump( info->getTime() ); |
205 | < | statOut->writeStat( info->getTime() ); |
204 | > | dumpOut->writeDump(info->getTime()); |
205 | > | statOut->writeStat(info->getTime()); |
206 | ||
203 | – | readyCheck(); |
207 | ||
208 | #ifdef IS_MPI | |
209 | < | strcpy( checkPointMsg, |
207 | < | "The integrator is ready to go." ); |
209 | > | strcpy(checkPointMsg, "The integrator is ready to go."); |
210 | MPIcheckPoint(); | |
211 | #endif // is_mpi | |
212 | ||
213 | < | while( info->getTime() < runTime ){ |
214 | < | |
213 | < | if( (info->getTime()+dt) >= currStatus ){ |
213 | > | while (info->getTime() < runTime && !stopIntegrator()){ |
214 | > | if ((info->getTime() + dt) >= currStatus){ |
215 | calcPot = 1; | |
216 | calcStress = 1; | |
217 | } | |
218 | ||
219 | < | integrateStep( calcPot, calcStress ); |
220 | < | |
219 | > | #ifdef PROFILE |
220 | > | startProfile( pro1 ); |
221 | > | #endif |
222 | > | |
223 | > | integrateStep(calcPot, calcStress); |
224 | > | |
225 | > | #ifdef PROFILE |
226 | > | endProfile( pro1 ); |
227 | > | |
228 | > | startProfile( pro2 ); |
229 | > | #endif // profile |
230 | > | |
231 | info->incrTime(dt); | |
232 | ||
233 | < | if( info->setTemp ){ |
234 | < | if( info->getTime() >= currThermal ){ |
235 | < | thermalize(); |
236 | < | currThermal += thermalTime; |
233 | > | if (info->setTemp){ |
234 | > | if (info->getTime() >= currThermal){ |
235 | > | thermalize(); |
236 | > | currThermal += thermalTime; |
237 | } | |
238 | } | |
239 | ||
240 | < | if( info->getTime() >= currSample ){ |
241 | < | dumpOut->writeDump( info->getTime() ); |
240 | > | if (info->getTime() >= currSample){ |
241 | > | dumpOut->writeDump(info->getTime()); |
242 | currSample += sampleTime; | |
243 | } | |
244 | ||
245 | < | if( info->getTime() >= currStatus ){ |
246 | < | statOut->writeStat( info->getTime() ); |
247 | < | calcPot = 0; |
245 | > | if (info->getTime() >= currStatus){ |
246 | > | statOut->writeStat(info->getTime()); |
247 | > | calcPot = 0; |
248 | calcStress = 0; | |
249 | currStatus += statusTime; | |
250 | < | } |
250 | > | } |
251 | ||
252 | + | if (info->resetIntegrator){ |
253 | + | if (info->getTime() >= currReset){ |
254 | + | this->resetIntegrator(); |
255 | + | currReset += resetTime; |
256 | + | } |
257 | + | } |
258 | + | |
259 | + | #ifdef PROFILE |
260 | + | endProfile( pro2 ); |
261 | + | #endif //profile |
262 | + | |
263 | #ifdef IS_MPI | |
264 | < | strcpy( checkPointMsg, |
243 | < | "successfully took a time step." ); |
264 | > | strcpy(checkPointMsg, "successfully took a time step."); |
265 | MPIcheckPoint(); | |
266 | #endif // is_mpi | |
246 | – | |
267 | } | |
268 | ||
249 | – | dumpOut->writeFinal(info->getTime()); |
250 | – | |
269 | delete dumpOut; | |
270 | delete statOut; | |
271 | } | |
272 | ||
273 | < | template<typename T> void Integrator<T>::integrateStep( int calcPot, int calcStress ){ |
274 | < | |
257 | < | |
258 | < | |
273 | > | template<typename T> void Integrator<T>::integrateStep(int calcPot, |
274 | > | int calcStress){ |
275 | // Position full step, and velocity half step | |
276 | ||
277 | + | #ifdef PROFILE |
278 | + | startProfile(pro3); |
279 | + | #endif //profile |
280 | + | |
281 | preMove(); | |
282 | + | |
283 | + | #ifdef PROFILE |
284 | + | endProfile(pro3); |
285 | + | |
286 | + | startProfile(pro4); |
287 | + | #endif // profile |
288 | + | |
289 | moveA(); | |
263 | – | if( nConstrained ) constrainA(); |
290 | ||
291 | + | #ifdef PROFILE |
292 | + | endProfile(pro4); |
293 | ||
294 | + | startProfile(pro5); |
295 | + | #endif//profile |
296 | + | |
297 | + | |
298 | #ifdef IS_MPI | |
299 | < | strcpy( checkPointMsg, "Succesful moveA\n" ); |
299 | > | strcpy(checkPointMsg, "Succesful moveA\n"); |
300 | MPIcheckPoint(); | |
301 | #endif // is_mpi | |
270 | – | |
302 | ||
303 | + | |
304 | // calc forces | |
305 | ||
306 | < | calcForce(calcPot,calcStress); |
306 | > | calcForce(calcPot, calcStress); |
307 | ||
308 | #ifdef IS_MPI | |
309 | < | strcpy( checkPointMsg, "Succesful doForces\n" ); |
309 | > | strcpy(checkPointMsg, "Succesful doForces\n"); |
310 | MPIcheckPoint(); | |
311 | #endif // is_mpi | |
280 | – | |
312 | ||
313 | + | #ifdef PROFILE |
314 | + | endProfile( pro5 ); |
315 | + | |
316 | + | startProfile( pro6 ); |
317 | + | #endif //profile |
318 | + | |
319 | // finish the velocity half step | |
320 | < | |
320 | > | |
321 | moveB(); | |
322 | < | if( nConstrained ) constrainB(); |
323 | < | |
322 | > | |
323 | > | #ifdef PROFILE |
324 | > | endProfile(pro6); |
325 | > | #endif // profile |
326 | > | |
327 | #ifdef IS_MPI | |
328 | < | strcpy( checkPointMsg, "Succesful moveB\n" ); |
328 | > | strcpy(checkPointMsg, "Succesful moveB\n"); |
329 | MPIcheckPoint(); | |
330 | #endif // is_mpi | |
291 | – | |
292 | – | |
331 | } | |
332 | ||
333 | ||
334 | < | template<typename T> void Integrator<T>::moveA( void ){ |
335 | < | |
298 | < | int i, j; |
334 | > | template<typename T> void Integrator<T>::moveA(void){ |
335 | > | size_t i, j; |
336 | DirectionalAtom* dAtom; | |
337 | double Tb[3], ji[3]; | |
301 | – | double A[3][3], I[3][3]; |
302 | – | double angle; |
338 | double vel[3], pos[3], frc[3]; | |
339 | double mass; | |
340 | + | |
341 | + | for (i = 0; i < integrableObjects.size() ; i++){ |
342 | + | integrableObjects[i]->getVel(vel); |
343 | + | integrableObjects[i]->getPos(pos); |
344 | + | integrableObjects[i]->getFrc(frc); |
345 | + | |
346 | + | mass = integrableObjects[i]->getMass(); |
347 | ||
348 | < | for( i=0; i<nAtoms; i++ ){ |
307 | < | |
308 | < | atoms[i]->getVel( vel ); |
309 | < | atoms[i]->getPos( pos ); |
310 | < | atoms[i]->getFrc( frc ); |
311 | < | |
312 | < | mass = atoms[i]->getMass(); |
313 | < | |
314 | < | for (j=0; j < 3; j++) { |
348 | > | for (j = 0; j < 3; j++){ |
349 | // velocity half step | |
350 | < | vel[j] += ( dt2 * frc[j] / mass ) * eConvert; |
350 | > | vel[j] += (dt2 * frc[j] / mass) * eConvert; |
351 | // position whole step | |
352 | pos[j] += dt * vel[j]; | |
353 | } | |
354 | ||
355 | < | atoms[i]->setVel( vel ); |
356 | < | atoms[i]->setPos( pos ); |
355 | > | integrableObjects[i]->setVel(vel); |
356 | > | integrableObjects[i]->setPos(pos); |
357 | ||
358 | < | if( atoms[i]->isDirectional() ){ |
358 | > | if (integrableObjects[i]->isDirectional()){ |
359 | ||
326 | – | dAtom = (DirectionalAtom *)atoms[i]; |
327 | – | |
360 | // get and convert the torque to body frame | |
329 | – | |
330 | – | dAtom->getTrq( Tb ); |
331 | – | dAtom->lab2Body( Tb ); |
361 | ||
362 | + | integrableObjects[i]->getTrq(Tb); |
363 | + | integrableObjects[i]->lab2Body(Tb); |
364 | + | |
365 | // get the angular momentum, and propagate a half step | |
366 | ||
367 | < | dAtom->getJ( ji ); |
367 | > | integrableObjects[i]->getJ(ji); |
368 | ||
369 | < | for (j=0; j < 3; j++) |
369 | > | for (j = 0; j < 3; j++) |
370 | ji[j] += (dt2 * Tb[j]) * eConvert; | |
339 | – | |
340 | – | // use the angular velocities to propagate the rotation matrix a |
341 | – | // full time step |
371 | ||
372 | < | dAtom->getA(A); |
344 | < | dAtom->getI(I); |
345 | < | |
346 | < | // rotate about the x-axis |
347 | < | angle = dt2 * ji[0] / I[0][0]; |
348 | < | this->rotate( 1, 2, angle, ji, A ); |
372 | > | this->rotationPropagation( integrableObjects[i], ji ); |
373 | ||
374 | < | // rotate about the y-axis |
375 | < | angle = dt2 * ji[1] / I[1][1]; |
376 | < | this->rotate( 2, 0, angle, ji, A ); |
353 | < | |
354 | < | // rotate about the z-axis |
355 | < | angle = dt * ji[2] / I[2][2]; |
356 | < | this->rotate( 0, 1, angle, ji, A); |
357 | < | |
358 | < | // rotate about the y-axis |
359 | < | angle = dt2 * ji[1] / I[1][1]; |
360 | < | this->rotate( 2, 0, angle, ji, A ); |
361 | < | |
362 | < | // rotate about the x-axis |
363 | < | angle = dt2 * ji[0] / I[0][0]; |
364 | < | this->rotate( 1, 2, angle, ji, A ); |
365 | < | |
374 | > | integrableObjects[i]->setJ(ji); |
375 | > | } |
376 | > | } |
377 | ||
378 | < | dAtom->setJ( ji ); |
379 | < | dAtom->setA( A ); |
369 | < | |
370 | < | } |
378 | > | if (nConstrained){ |
379 | > | constrainA(); |
380 | } | |
381 | } | |
382 | ||
383 | ||
384 | < | template<typename T> void Integrator<T>::moveB( void ){ |
384 | > | template<typename T> void Integrator<T>::moveB(void){ |
385 | int i, j; | |
377 | – | DirectionalAtom* dAtom; |
386 | double Tb[3], ji[3]; | |
387 | double vel[3], frc[3]; | |
388 | double mass; | |
389 | ||
390 | < | for( i=0; i<nAtoms; i++ ){ |
391 | < | |
392 | < | atoms[i]->getVel( vel ); |
385 | < | atoms[i]->getFrc( frc ); |
390 | > | for (i = 0; i < integrableObjects.size(); i++){ |
391 | > | integrableObjects[i]->getVel(vel); |
392 | > | integrableObjects[i]->getFrc(frc); |
393 | ||
394 | < | mass = atoms[i]->getMass(); |
394 | > | mass = integrableObjects[i]->getMass(); |
395 | ||
396 | // velocity half step | |
397 | < | for (j=0; j < 3; j++) |
398 | < | vel[j] += ( dt2 * frc[j] / mass ) * eConvert; |
392 | < | |
393 | < | atoms[i]->setVel( vel ); |
394 | < | |
395 | < | if( atoms[i]->isDirectional() ){ |
397 | > | for (j = 0; j < 3; j++) |
398 | > | vel[j] += (dt2 * frc[j] / mass) * eConvert; |
399 | ||
400 | < | dAtom = (DirectionalAtom *)atoms[i]; |
400 | > | integrableObjects[i]->setVel(vel); |
401 | ||
402 | < | // get and convert the torque to body frame |
402 | > | if (integrableObjects[i]->isDirectional()){ |
403 | ||
404 | < | dAtom->getTrq( Tb ); |
402 | < | dAtom->lab2Body( Tb ); |
404 | > | // get and convert the torque to body frame |
405 | ||
406 | + | integrableObjects[i]->getTrq(Tb); |
407 | + | integrableObjects[i]->lab2Body(Tb); |
408 | + | |
409 | // get the angular momentum, and propagate a half step | |
410 | ||
411 | < | dAtom->getJ( ji ); |
411 | > | integrableObjects[i]->getJ(ji); |
412 | ||
413 | < | for (j=0; j < 3; j++) |
413 | > | for (j = 0; j < 3; j++) |
414 | ji[j] += (dt2 * Tb[j]) * eConvert; | |
410 | – | |
415 | ||
416 | < | dAtom->setJ( ji ); |
416 | > | |
417 | > | integrableObjects[i]->setJ(ji); |
418 | } | |
419 | } | |
420 | + | |
421 | + | if (nConstrained){ |
422 | + | constrainB(); |
423 | + | } |
424 | } | |
425 | ||
426 | < | template<typename T> void Integrator<T>::preMove( void ){ |
426 | > | template<typename T> void Integrator<T>::preMove(void){ |
427 | int i, j; | |
428 | double pos[3]; | |
429 | ||
430 | < | if( nConstrained ){ |
430 | > | if (nConstrained){ |
431 | > | for (i = 0; i < nAtoms; i++){ |
432 | > | atoms[i]->getPos(pos); |
433 | ||
434 | < | for(i=0; i < nAtoms; i++) { |
435 | < | |
425 | < | atoms[i]->getPos( pos ); |
426 | < | |
427 | < | for (j = 0; j < 3; j++) { |
428 | < | oldPos[3*i + j] = pos[j]; |
434 | > | for (j = 0; j < 3; j++){ |
435 | > | oldPos[3 * i + j] = pos[j]; |
436 | } | |
430 | – | |
437 | } | |
438 | < | } |
438 | > | } |
439 | } | |
440 | ||
441 | template<typename T> void Integrator<T>::constrainA(){ | |
442 | < | |
437 | < | int i,j,k; |
442 | > | int i, j; |
443 | int done; | |
444 | double posA[3], posB[3]; | |
445 | double velA[3], velB[3]; | |
# | Line 449 | Line 454 | template<typename T> void Integrator<T>::constrainA(){ | |
454 | double gab; | |
455 | int iteration; | |
456 | ||
457 | < | for( i=0; i<nAtoms; i++){ |
457 | > | for (i = 0; i < nAtoms; i++){ |
458 | moving[i] = 0; | |
459 | < | moved[i] = 1; |
459 | > | moved[i] = 1; |
460 | } | |
461 | ||
462 | iteration = 0; | |
463 | done = 0; | |
464 | < | while( !done && (iteration < maxIteration )){ |
460 | < | |
464 | > | while (!done && (iteration < maxIteration)){ |
465 | done = 1; | |
466 | < | for(i=0; i<nConstrained; i++){ |
463 | < | |
466 | > | for (i = 0; i < nConstrained; i++){ |
467 | a = constrainedA[i]; | |
468 | b = constrainedB[i]; | |
466 | – | |
467 | – | ax = (a*3) + 0; |
468 | – | ay = (a*3) + 1; |
469 | – | az = (a*3) + 2; |
469 | ||
470 | < | bx = (b*3) + 0; |
471 | < | by = (b*3) + 1; |
472 | < | bz = (b*3) + 2; |
470 | > | ax = (a * 3) + 0; |
471 | > | ay = (a * 3) + 1; |
472 | > | az = (a * 3) + 2; |
473 | ||
474 | < | if( moved[a] || moved[b] ){ |
475 | < | |
476 | < | atoms[a]->getPos( posA ); |
477 | < | atoms[b]->getPos( posB ); |
478 | < | |
479 | < | for (j = 0; j < 3; j++ ) |
474 | > | bx = (b * 3) + 0; |
475 | > | by = (b * 3) + 1; |
476 | > | bz = (b * 3) + 2; |
477 | > | |
478 | > | if (moved[a] || moved[b]){ |
479 | > | atoms[a]->getPos(posA); |
480 | > | atoms[b]->getPos(posB); |
481 | > | |
482 | > | for (j = 0; j < 3; j++) |
483 | pab[j] = posA[j] - posB[j]; | |
482 | – | |
483 | – | //periodic boundary condition |
484 | ||
485 | < | info->wrapVector( pab ); |
485 | > | //periodic boundary condition |
486 | ||
487 | < | pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2]; |
487 | > | info->wrapVector(pab); |
488 | ||
489 | < | rabsq = constrainedDsqr[i]; |
490 | < | diffsq = rabsq - pabsq; |
489 | > | pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2]; |
490 | ||
491 | < | // the original rattle code from alan tidesley |
492 | < | if (fabs(diffsq) > (tol*rabsq*2)) { |
494 | < | rab[0] = oldPos[ax] - oldPos[bx]; |
495 | < | rab[1] = oldPos[ay] - oldPos[by]; |
496 | < | rab[2] = oldPos[az] - oldPos[bz]; |
491 | > | rabsq = constrainedDsqr[i]; |
492 | > | diffsq = rabsq - pabsq; |
493 | ||
494 | < | info->wrapVector( rab ); |
494 | > | // the original rattle code from alan tidesley |
495 | > | if (fabs(diffsq) > (tol * rabsq * 2)){ |
496 | > | rab[0] = oldPos[ax] - oldPos[bx]; |
497 | > | rab[1] = oldPos[ay] - oldPos[by]; |
498 | > | rab[2] = oldPos[az] - oldPos[bz]; |
499 | ||
500 | < | rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
500 | > | info->wrapVector(rab); |
501 | ||
502 | < | rpabsq = rpab * rpab; |
502 | > | rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
503 | ||
504 | + | rpabsq = rpab * rpab; |
505 | ||
505 | – | if (rpabsq < (rabsq * -diffsq)){ |
506 | ||
507 | + | if (rpabsq < (rabsq * -diffsq)){ |
508 | #ifdef IS_MPI | |
509 | < | a = atoms[a]->getGlobalIndex(); |
510 | < | b = atoms[b]->getGlobalIndex(); |
509 | > | a = atoms[a]->getGlobalIndex(); |
510 | > | b = atoms[b]->getGlobalIndex(); |
511 | #endif //is_mpi | |
512 | < | sprintf( painCave.errMsg, |
513 | < | "Constraint failure in constrainA at atom %d and %d.\n", |
514 | < | a, b ); |
515 | < | painCave.isFatal = 1; |
516 | < | simError(); |
517 | < | } |
512 | > | sprintf(painCave.errMsg, |
513 | > | "Constraint failure in constrainA at atom %d and %d.\n", a, |
514 | > | b); |
515 | > | painCave.isFatal = 1; |
516 | > | simError(); |
517 | > | } |
518 | ||
519 | < | rma = 1.0 / atoms[a]->getMass(); |
520 | < | rmb = 1.0 / atoms[b]->getMass(); |
519 | > | rma = 1.0 / atoms[a]->getMass(); |
520 | > | rmb = 1.0 / atoms[b]->getMass(); |
521 | ||
522 | < | gab = diffsq / ( 2.0 * ( rma + rmb ) * rpab ); |
522 | > | gab = diffsq / (2.0 * (rma + rmb) * rpab); |
523 | ||
524 | dx = rab[0] * gab; | |
525 | dy = rab[1] * gab; | |
526 | dz = rab[2] * gab; | |
527 | ||
528 | < | posA[0] += rma * dx; |
529 | < | posA[1] += rma * dy; |
530 | < | posA[2] += rma * dz; |
528 | > | posA[0] += rma * dx; |
529 | > | posA[1] += rma * dy; |
530 | > | posA[2] += rma * dz; |
531 | ||
532 | < | atoms[a]->setPos( posA ); |
532 | > | atoms[a]->setPos(posA); |
533 | ||
534 | < | posB[0] -= rmb * dx; |
535 | < | posB[1] -= rmb * dy; |
536 | < | posB[2] -= rmb * dz; |
534 | > | posB[0] -= rmb * dx; |
535 | > | posB[1] -= rmb * dy; |
536 | > | posB[2] -= rmb * dz; |
537 | ||
538 | < | atoms[b]->setPos( posB ); |
538 | > | atoms[b]->setPos(posB); |
539 | ||
540 | dx = dx / dt; | |
541 | dy = dy / dt; | |
542 | dz = dz / dt; | |
543 | ||
544 | < | atoms[a]->getVel( velA ); |
544 | > | atoms[a]->getVel(velA); |
545 | ||
546 | < | velA[0] += rma * dx; |
547 | < | velA[1] += rma * dy; |
548 | < | velA[2] += rma * dz; |
546 | > | velA[0] += rma * dx; |
547 | > | velA[1] += rma * dy; |
548 | > | velA[2] += rma * dz; |
549 | ||
550 | < | atoms[a]->setVel( velA ); |
550 | > | atoms[a]->setVel(velA); |
551 | ||
552 | < | atoms[b]->getVel( velB ); |
552 | > | atoms[b]->getVel(velB); |
553 | ||
554 | < | velB[0] -= rmb * dx; |
555 | < | velB[1] -= rmb * dy; |
556 | < | velB[2] -= rmb * dz; |
554 | > | velB[0] -= rmb * dx; |
555 | > | velB[1] -= rmb * dy; |
556 | > | velB[2] -= rmb * dz; |
557 | ||
558 | < | atoms[b]->setVel( velB ); |
558 | > | atoms[b]->setVel(velB); |
559 | ||
560 | < | moving[a] = 1; |
561 | < | moving[b] = 1; |
562 | < | done = 0; |
563 | < | } |
560 | > | moving[a] = 1; |
561 | > | moving[b] = 1; |
562 | > | done = 0; |
563 | > | } |
564 | } | |
565 | } | |
566 | < | |
567 | < | for(i=0; i<nAtoms; i++){ |
567 | < | |
566 | > | |
567 | > | for (i = 0; i < nAtoms; i++){ |
568 | moved[i] = moving[i]; | |
569 | moving[i] = 0; | |
570 | } | |
# | Line 572 | Line 572 | template<typename T> void Integrator<T>::constrainA(){ | |
572 | iteration++; | |
573 | } | |
574 | ||
575 | < | if( !done ){ |
576 | < | |
577 | < | sprintf( painCave.errMsg, |
578 | < | "Constraint failure in constrainA, too many iterations: %d\n", |
579 | < | iteration ); |
575 | > | if (!done){ |
576 | > | sprintf(painCave.errMsg, |
577 | > | "Constraint failure in constrainA, too many iterations: %d\n", |
578 | > | iteration); |
579 | painCave.isFatal = 1; | |
580 | simError(); | |
581 | } | |
582 | ||
583 | } | |
584 | ||
585 | < | template<typename T> void Integrator<T>::constrainB( void ){ |
586 | < | |
588 | < | int i,j,k; |
585 | > | template<typename T> void Integrator<T>::constrainB(void){ |
586 | > | int i, j; |
587 | int done; | |
588 | double posA[3], posB[3]; | |
589 | double velA[3], velB[3]; | |
# | Line 594 | Line 592 | template<typename T> void Integrator<T>::constrainB( v | |
592 | int a, b, ax, ay, az, bx, by, bz; | |
593 | double rma, rmb; | |
594 | double dx, dy, dz; | |
595 | < | double rabsq, pabsq, rvab; |
598 | < | double diffsq; |
595 | > | double rvab; |
596 | double gab; | |
597 | int iteration; | |
598 | ||
599 | < | for(i=0; i<nAtoms; i++){ |
599 | > | for (i = 0; i < nAtoms; i++){ |
600 | moving[i] = 0; | |
601 | moved[i] = 1; | |
602 | } | |
603 | ||
604 | done = 0; | |
605 | iteration = 0; | |
606 | < | while( !done && (iteration < maxIteration ) ){ |
610 | < | |
606 | > | while (!done && (iteration < maxIteration)){ |
607 | done = 1; | |
608 | ||
609 | < | for(i=0; i<nConstrained; i++){ |
614 | < | |
609 | > | for (i = 0; i < nConstrained; i++){ |
610 | a = constrainedA[i]; | |
611 | b = constrainedB[i]; | |
612 | ||
613 | < | ax = (a*3) + 0; |
614 | < | ay = (a*3) + 1; |
615 | < | az = (a*3) + 2; |
613 | > | ax = (a * 3) + 0; |
614 | > | ay = (a * 3) + 1; |
615 | > | az = (a * 3) + 2; |
616 | ||
617 | < | bx = (b*3) + 0; |
618 | < | by = (b*3) + 1; |
619 | < | bz = (b*3) + 2; |
617 | > | bx = (b * 3) + 0; |
618 | > | by = (b * 3) + 1; |
619 | > | bz = (b * 3) + 2; |
620 | ||
621 | < | if( moved[a] || moved[b] ){ |
621 | > | if (moved[a] || moved[b]){ |
622 | > | atoms[a]->getVel(velA); |
623 | > | atoms[b]->getVel(velB); |
624 | ||
625 | < | atoms[a]->getVel( velA ); |
626 | < | atoms[b]->getVel( velB ); |
627 | < | |
631 | < | vxab = velA[0] - velB[0]; |
632 | < | vyab = velA[1] - velB[1]; |
633 | < | vzab = velA[2] - velB[2]; |
625 | > | vxab = velA[0] - velB[0]; |
626 | > | vyab = velA[1] - velB[1]; |
627 | > | vzab = velA[2] - velB[2]; |
628 | ||
629 | < | atoms[a]->getPos( posA ); |
630 | < | atoms[b]->getPos( posB ); |
629 | > | atoms[a]->getPos(posA); |
630 | > | atoms[b]->getPos(posB); |
631 | ||
632 | < | for (j = 0; j < 3; j++) |
632 | > | for (j = 0; j < 3; j++) |
633 | rab[j] = posA[j] - posB[j]; | |
640 | – | |
641 | – | info->wrapVector( rab ); |
642 | – | |
643 | – | rma = 1.0 / atoms[a]->getMass(); |
644 | – | rmb = 1.0 / atoms[b]->getMass(); |
634 | ||
635 | < | rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab; |
647 | < | |
648 | < | gab = -rvab / ( ( rma + rmb ) * constrainedDsqr[i] ); |
635 | > | info->wrapVector(rab); |
636 | ||
637 | < | if (fabs(gab) > tol) { |
638 | < | |
652 | < | dx = rab[0] * gab; |
653 | < | dy = rab[1] * gab; |
654 | < | dz = rab[2] * gab; |
655 | < | |
656 | < | velA[0] += rma * dx; |
657 | < | velA[1] += rma * dy; |
658 | < | velA[2] += rma * dz; |
637 | > | rma = 1.0 / atoms[a]->getMass(); |
638 | > | rmb = 1.0 / atoms[b]->getMass(); |
639 | ||
640 | < | atoms[a]->setVel( velA ); |
640 | > | rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab; |
641 | ||
642 | < | velB[0] -= rmb * dx; |
663 | < | velB[1] -= rmb * dy; |
664 | < | velB[2] -= rmb * dz; |
642 | > | gab = -rvab / ((rma + rmb) * constrainedDsqr[i]); |
643 | ||
644 | < | atoms[b]->setVel( velB ); |
645 | < | |
646 | < | moving[a] = 1; |
647 | < | moving[b] = 1; |
648 | < | done = 0; |
649 | < | } |
644 | > | if (fabs(gab) > tol){ |
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 | > | 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; |
663 | > | done = 0; |
664 | > | } |
665 | } | |
666 | } | |
667 | ||
668 | < | for(i=0; i<nAtoms; i++){ |
668 | > | for (i = 0; i < nAtoms; i++){ |
669 | moved[i] = moving[i]; | |
670 | moving[i] = 0; | |
671 | } | |
672 | < | |
672 | > | |
673 | iteration++; | |
674 | } | |
682 | – | |
683 | – | if( !done ){ |
675 | ||
676 | < | |
677 | < | sprintf( painCave.errMsg, |
678 | < | "Constraint failure in constrainB, too many iterations: %d\n", |
679 | < | iteration ); |
676 | > | if (!done){ |
677 | > | sprintf(painCave.errMsg, |
678 | > | "Constraint failure in constrainB, too many iterations: %d\n", |
679 | > | iteration); |
680 | painCave.isFatal = 1; | |
681 | simError(); | |
682 | < | } |
692 | < | |
682 | > | } |
683 | } | |
684 | ||
685 | < | template<typename T> void Integrator<T>::rotate( int axes1, int axes2, double angle, double ji[3], |
686 | < | double A[3][3] ){ |
685 | > | template<typename T> void Integrator<T>::rotationPropagation |
686 | > | ( StuntDouble* sd, double ji[3] ){ |
687 | ||
688 | < | int i,j,k; |
688 | > | double angle; |
689 | > | double A[3][3], I[3][3]; |
690 | > | int i, j, k; |
691 | > | |
692 | > | // use the angular velocities to propagate the rotation matrix a |
693 | > | // full time step |
694 | > | |
695 | > | sd->getA(A); |
696 | > | sd->getI(I); |
697 | > | |
698 | > | if (sd->isLinear()) { |
699 | > | i = sd->linearAxis(); |
700 | > | j = (i+1)%3; |
701 | > | k = (i+2)%3; |
702 | > | |
703 | > | angle = dt2 * ji[j] / I[j][j]; |
704 | > | this->rotate( k, i, angle, ji, A ); |
705 | > | |
706 | > | angle = dt * ji[k] / I[k][k]; |
707 | > | this->rotate( i, j, angle, ji, A); |
708 | > | |
709 | > | angle = dt2 * ji[j] / I[j][j]; |
710 | > | this->rotate( k, i, angle, ji, A ); |
711 | > | |
712 | > | } else { |
713 | > | // rotate about the x-axis |
714 | > | angle = dt2 * ji[0] / I[0][0]; |
715 | > | this->rotate( 1, 2, angle, ji, A ); |
716 | > | |
717 | > | // rotate about the y-axis |
718 | > | angle = dt2 * ji[1] / I[1][1]; |
719 | > | this->rotate( 2, 0, angle, ji, A ); |
720 | > | |
721 | > | // rotate about the z-axis |
722 | > | angle = dt * ji[2] / I[2][2]; |
723 | > | this->rotate( 0, 1, angle, ji, A); |
724 | > | |
725 | > | // rotate about the y-axis |
726 | > | angle = dt2 * ji[1] / I[1][1]; |
727 | > | this->rotate( 2, 0, angle, ji, A ); |
728 | > | |
729 | > | // rotate about the x-axis |
730 | > | angle = dt2 * ji[0] / I[0][0]; |
731 | > | this->rotate( 1, 2, angle, ji, A ); |
732 | > | |
733 | > | } |
734 | > | sd->setA( A ); |
735 | > | } |
736 | > | |
737 | > | template<typename T> void Integrator<T>::rotate(int axes1, int axes2, |
738 | > | double angle, double ji[3], |
739 | > | double A[3][3]){ |
740 | > | int i, j, k; |
741 | double sinAngle; | |
742 | double cosAngle; | |
743 | double angleSqr; | |
# | Line 707 | Line 749 | template<typename T> void Integrator<T>::rotate( int a | |
749 | ||
750 | // initialize the tempA | |
751 | ||
752 | < | for(i=0; i<3; i++){ |
753 | < | for(j=0; j<3; j++){ |
752 | > | for (i = 0; i < 3; i++){ |
753 | > | for (j = 0; j < 3; j++){ |
754 | tempA[j][i] = A[i][j]; | |
755 | } | |
756 | } | |
757 | ||
758 | // initialize the tempJ | |
759 | ||
760 | < | for( i=0; i<3; i++) tempJ[i] = ji[i]; |
761 | < | |
760 | > | for (i = 0; i < 3; i++) |
761 | > | tempJ[i] = ji[i]; |
762 | > | |
763 | // initalize rot as a unit matrix | |
764 | ||
765 | rot[0][0] = 1.0; | |
# | Line 726 | Line 769 | template<typename T> void Integrator<T>::rotate( int a | |
769 | rot[1][0] = 0.0; | |
770 | rot[1][1] = 1.0; | |
771 | rot[1][2] = 0.0; | |
772 | < | |
772 | > | |
773 | rot[2][0] = 0.0; | |
774 | rot[2][1] = 0.0; | |
775 | rot[2][2] = 1.0; | |
776 | < | |
776 | > | |
777 | // use a small angle aproximation for sin and cosine | |
778 | ||
779 | < | angleSqr = angle * angle; |
779 | > | angleSqr = angle * angle; |
780 | angleSqrOver4 = angleSqr / 4.0; | |
781 | top = 1.0 - angleSqrOver4; | |
782 | bottom = 1.0 + angleSqrOver4; | |
# | Line 746 | Line 789 | template<typename T> void Integrator<T>::rotate( int a | |
789 | ||
790 | rot[axes1][axes2] = sinAngle; | |
791 | rot[axes2][axes1] = -sinAngle; | |
792 | < | |
792 | > | |
793 | // rotate the momentum acoording to: ji[] = rot[][] * ji[] | |
794 | < | |
795 | < | for(i=0; i<3; i++){ |
794 | > | |
795 | > | for (i = 0; i < 3; i++){ |
796 | ji[i] = 0.0; | |
797 | < | for(k=0; k<3; k++){ |
797 | > | for (k = 0; k < 3; k++){ |
798 | ji[i] += rot[i][k] * tempJ[k]; | |
799 | } | |
800 | } | |
801 | ||
802 | < | // rotate the Rotation matrix acording to: |
802 | > | // rotate the Rotation matrix acording to: |
803 | // A[][] = A[][] * transpose(rot[][]) | |
804 | ||
805 | ||
# | Line 764 | Line 807 | template<typename T> void Integrator<T>::rotate( int a | |
807 | // calculation as: | |
808 | // transpose(A[][]) = transpose(A[][]) * transpose(rot[][]) | |
809 | ||
810 | < | for(i=0; i<3; i++){ |
811 | < | for(j=0; j<3; j++){ |
810 | > | for (i = 0; i < 3; i++){ |
811 | > | for (j = 0; j < 3; j++){ |
812 | A[j][i] = 0.0; | |
813 | < | for(k=0; k<3; k++){ |
814 | < | A[j][i] += tempA[i][k] * rot[j][k]; |
813 | > | for (k = 0; k < 3; k++){ |
814 | > | A[j][i] += tempA[i][k] * rot[j][k]; |
815 | } | |
816 | } | |
817 | } | |
818 | } | |
819 | ||
820 | < | template<typename T> void Integrator<T>::calcForce( int calcPot, int calcStress ){ |
821 | < | myFF->doForces(calcPot,calcStress); |
779 | < | |
820 | > | template<typename T> void Integrator<T>::calcForce(int calcPot, int calcStress){ |
821 | > | myFF->doForces(calcPot, calcStress); |
822 | } | |
823 | ||
824 | template<typename T> void Integrator<T>::thermalize(){ | |
825 | < | tStats->velocitize(); |
825 | > | tStats->velocitize(); |
826 | } | |
827 | + | |
828 | + | template<typename T> double Integrator<T>::getConservedQuantity(void){ |
829 | + | return tStats->getTotalE(); |
830 | + | } |
831 | + | template<typename T> string Integrator<T>::getAdditionalParameters(void){ |
832 | + | //By default, return a null string |
833 | + | //The reason we use string instead of char* is that if we use char*, we will |
834 | + | //return a pointer point to local variable which might cause problem |
835 | + | return string(); |
836 | + | } |
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