src/constraints/Rattle.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
#include "constraints/Rattle.hpp"
#include "primitives/Molecule.hpp"
#include "utils/simError.h"
namespace OpenMD {

  Rattle::Rattle(SimInfo* info) : info_(info), maxConsIteration_(10), 
                                  consTolerance_(1.0e-6), doRattle_(false), 
                                  currConstraintTime_(0.0) {
    
    if (info_->getNGlobalConstraints() > 0)
      doRattle_ = true;
    
    if (!doRattle_) return;

    Globals* simParams = info_->getSimParams();

    if (simParams->haveDt()) {
      dt_ = simParams->getDt();
    } else {
      sprintf(painCave.errMsg,
              "Rattle Error: dt is not set\n");
      painCave.isFatal = 1;
      simError();
    }    

    currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
    if (simParams->haveConstraintTime()){
      constraintTime_ = simParams->getConstraintTime();
    } else {
      constraintTime_ = simParams->getStatusTime();
    }

    constraintOutputFile_ = getPrefix(info_->getFinalConfigFileName()) + 
      ".constraintForces";


    // create ConstraintWriter  
    constraintWriter_ = new ConstraintWriter(info_, 
                                             constraintOutputFile_.c_str());

    if (!constraintWriter_){
      sprintf(painCave.errMsg, "Failed to create ConstraintWriter\n");
      painCave.isFatal = 1;
      simError();
    }
  }

  void Rattle::constraintA() {
    if (!doRattle_) return;
    doConstraint(&Rattle::constraintPairA);
  }
  void Rattle::constraintB() {
    if (!doRattle_) return;    
    doConstraint(&Rattle::constraintPairB);

    if (currentSnapshot_->getTime() >= currConstraintTime_){
      Molecule* mol;
      SimInfo::MoleculeIterator mi;
      ConstraintPair* consPair;
      Molecule::ConstraintPairIterator cpi;
      std::list<ConstraintPair*> constraints;
      for (mol = info_->beginMolecule(mi); mol != NULL; 
           mol = info_->nextMolecule(mi)) {
        for (consPair = mol->beginConstraintPair(cpi); consPair != NULL; 
             consPair = mol->nextConstraintPair(cpi)) {
          
          constraints.push_back(consPair);
        }
      }
      constraintWriter_->writeConstraintForces(constraints);
      currConstraintTime_ += constraintTime_;
    }
  }

  void Rattle::doConstraint(ConstraintPairFuncPtr func) {
    if (!doRattle_) return;

    Molecule* mol;
    SimInfo::MoleculeIterator mi;
    ConstraintElem* consElem;
    Molecule::ConstraintElemIterator cei;
    ConstraintPair* consPair;
    Molecule::ConstraintPairIterator cpi;
    
    for (mol = info_->beginMolecule(mi); mol != NULL; 
         mol = info_->nextMolecule(mi)) {
      for (consElem = mol->beginConstraintElem(cei); consElem != NULL; 
           consElem = mol->nextConstraintElem(cei)) {
        consElem->setMoved(true);
        consElem->setMoving(false);
      }
    }
    
    //main loop of constraint algorithm
    bool done = false;
    int iteration = 0;
    while(!done && iteration < maxConsIteration_){
      done = true;

      //loop over every constraint pair

      for (mol = info_->beginMolecule(mi); mol != NULL; 
           mol = info_->nextMolecule(mi)) {
        for (consPair = mol->beginConstraintPair(cpi); consPair != NULL; 
             consPair = mol->nextConstraintPair(cpi)) {


          //dispatch constraint algorithm
          if(consPair->isMoved()) {
            int exeStatus = (this->*func)(consPair);

            switch(exeStatus){
            case consFail:
              sprintf(painCave.errMsg,
                      "Constraint failure in Rattle::constrainA, " 
                      "Constraint Fail\n");
              painCave.isFatal = 1;
              simError();                             
                            
              break;
            case consSuccess:
              // constrain the pair by moving two elements
              done = false;
              consPair->getConsElem1()->setMoving(true);
              consPair->getConsElem2()->setMoving(true);
              break;
            case consAlready:
              // current pair is already constrained, do not need to
              // move the elements
              break;
            default:          
              sprintf(painCave.errMsg, "ConstraintAlgorithm::doConstraint() "
                      "Error: unrecognized status");
              painCave.isFatal = 1;
              simError();                           
              break;
            }      
          }
        }
      }//end for(iter->first())


      for (mol = info_->beginMolecule(mi); mol != NULL; 
           mol = info_->nextMolecule(mi)) {
        for (consElem = mol->beginConstraintElem(cei); consElem != NULL; 
             consElem = mol->nextConstraintElem(cei)) {
          consElem->setMoved(consElem->getMoving());
          consElem->setMoving(false);
        }
      }

      iteration++;
    }//end while

    if (!done){
      sprintf(painCave.errMsg,
              "Constraint failure in Rattle::constrainA, "
              "too many iterations: %d\n",
              iteration);
      painCave.isFatal = 1;
      simError();    
    }
  }

  int Rattle::constraintPairA(ConstraintPair* consPair){

    ConstraintElem* consElem1 = consPair->getConsElem1();
    ConstraintElem* consElem2 = consPair->getConsElem2();

    Vector3d posA = consElem1->getPos();
    Vector3d posB = consElem2->getPos();

    Vector3d pab = posA -posB;   

    //periodic boundary condition

    currentSnapshot_->wrapVector(pab);

    RealType pabsq = pab.lengthSquare();

    RealType rabsq = consPair->getConsDistSquare();
    RealType diffsq = rabsq - pabsq;

    // the original rattle code from alan tidesley
    if (fabs(diffsq) > (consTolerance_ * rabsq * 2)){
    
      Vector3d oldPosA = consElem1->getPrevPos();
      Vector3d oldPosB = consElem2->getPrevPos();      

      Vector3d rab = oldPosA - oldPosB;    

      currentSnapshot_->wrapVector(rab);

      RealType rpab = dot(rab, pab);
      RealType rpabsq = rpab * rpab;

      if (rpabsq < (rabsq * -diffsq)){
        return consFail;
      }

      RealType rma = 1.0 / consElem1->getMass();
      RealType rmb = 1.0 / consElem2->getMass();

      RealType gab = diffsq / (2.0 * (rma + rmb) * rpab);

      Vector3d delta = rab * gab;

      //set atom1's position
      posA += rma * delta;    
      consElem1->setPos(posA);

      //set atom2's position
      posB -= rmb * delta;
      consElem2->setPos(posB);

      delta /= dt_;
    
      //set atom1's velocity
      Vector3d velA = consElem1->getVel();
      velA += rma * delta;
      consElem1->setVel(velA);

      //set atom2's velocity
      Vector3d velB = consElem2->getVel();
      velB -= rmb * delta;
      consElem2->setVel(velB);
      
      // report the constraint force back to the constraint pair:
      consPair->setConstraintForce(gab);
      return consSuccess;
    }
    else
      return consAlready;
  
  }


  int Rattle::constraintPairB(ConstraintPair* consPair){
    ConstraintElem* consElem1 = consPair->getConsElem1();
    ConstraintElem* consElem2 = consPair->getConsElem2();

  
    Vector3d velA = consElem1->getVel();
    Vector3d velB = consElem2->getVel();

    Vector3d dv = velA - velB;

    Vector3d posA = consElem1->getPos();
    Vector3d posB = consElem2->getPos();

    Vector3d rab = posA - posB;

    currentSnapshot_->wrapVector(rab);

    RealType rma = 1.0 / consElem1->getMass();
    RealType rmb = 1.0 / consElem2->getMass();

    RealType rvab = dot(rab, dv);

    RealType gab = -rvab / ((rma + rmb) * consPair->getConsDistSquare());

    if (fabs(gab) > consTolerance_){
      Vector3d delta = rab * gab;
      
      velA += rma * delta;
      consElem1->setVel(velA);
      
      velB -= rmb * delta;
      consElem2->setVel(velB);

      // report the constraint force back to the constraint pair:
      consPair->setConstraintForce(gab);
      return consSuccess;
    }
    else
      return consAlready;

  }

}
Revision:	1989
Committed:	Fri Apr 18 20:07:09 2014 UTC (11 years ago) by gezelter
File size:	9870 byte(s)
Log Message:	Fixed the creation of constraintForces files on simulations which don't have constraints
#	Content
1	/*
2	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	*
4	* The University of Notre Dame grants you ("Licensee") a
5	* non-exclusive, royalty free, license to use, modify and
6	* redistribute this software in source and binary code form, provided
7	* that the following conditions are met:
8	*
9	* 1. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
12	* 2. Redistributions in binary form must reproduce the above copyright
13	* notice, this list of conditions and the following disclaimer in the
14	* documentation and/or other materials provided with the
15	* distribution.
16	*
17	* This software is provided "AS IS," without a warranty of any
18	* kind. All express or implied conditions, representations and
19	* warranties, including any implied warranty of merchantability,
20	* fitness for a particular purpose or non-infringement, are hereby
21	* excluded. The University of Notre Dame and its licensors shall not
22	* be liable for any damages suffered by licensee as a result of
23	* using, modifying or distributing the software or its
24	* derivatives. In no event will the University of Notre Dame or its
25	* licensors be liable for any lost revenue, profit or data, or for
26	* direct, indirect, special, consequential, incidental or punitive
27	* damages, however caused and regardless of the theory of liability,
28	* arising out of the use of or inability to use software, even if the
29	* University of Notre Dame has been advised of the possibility of
30	* such damages.
31	*
32	* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33	* research, please cite the appropriate papers when you publish your
34	* work. Good starting points are:
35	*
36	* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
42
43	#include "constraints/Rattle.hpp"
44	#include "primitives/Molecule.hpp"
45	#include "utils/simError.h"
46	namespace OpenMD {
47
48	Rattle::Rattle(SimInfo* info) : info_(info), maxConsIteration_(10),
49	consTolerance_(1.0e-6), doRattle_(false),
50	currConstraintTime_(0.0) {
51
52	if (info_->getNGlobalConstraints() > 0)
53	doRattle_ = true;
54
55	if (!doRattle_) return;
56
57	Globals* simParams = info_->getSimParams();
58
59	if (simParams->haveDt()) {
60	dt_ = simParams->getDt();
61	} else {
62	sprintf(painCave.errMsg,
63	"Rattle Error: dt is not set\n");
64	painCave.isFatal = 1;
65	simError();
66	}
67
68	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
69	if (simParams->haveConstraintTime()){
70	constraintTime_ = simParams->getConstraintTime();
71	} else {
72	constraintTime_ = simParams->getStatusTime();
73	}
74
75	constraintOutputFile_ = getPrefix(info_->getFinalConfigFileName()) +
76	".constraintForces";
77
78
79	// create ConstraintWriter
80	constraintWriter_ = new ConstraintWriter(info_,
81	constraintOutputFile_.c_str());
82
83	if (!constraintWriter_){
84	sprintf(painCave.errMsg, "Failed to create ConstraintWriter\n");
85	painCave.isFatal = 1;
86	simError();
87	}
88	}
89
90	void Rattle::constraintA() {
91	if (!doRattle_) return;
92	doConstraint(&Rattle::constraintPairA);
93	}
94	void Rattle::constraintB() {
95	if (!doRattle_) return;
96	doConstraint(&Rattle::constraintPairB);
97
98	if (currentSnapshot_->getTime() >= currConstraintTime_){
99	Molecule* mol;
100	SimInfo::MoleculeIterator mi;
101	ConstraintPair* consPair;
102	Molecule::ConstraintPairIterator cpi;
103	std::list<ConstraintPair*> constraints;
104	for (mol = info_->beginMolecule(mi); mol != NULL;
105	mol = info_->nextMolecule(mi)) {
106	for (consPair = mol->beginConstraintPair(cpi); consPair != NULL;
107	consPair = mol->nextConstraintPair(cpi)) {
108
109	constraints.push_back(consPair);
110	}
111	}
112	constraintWriter_->writeConstraintForces(constraints);
113	currConstraintTime_ += constraintTime_;
114	}
115	}
116
117	void Rattle::doConstraint(ConstraintPairFuncPtr func) {
118	if (!doRattle_) return;
119
120	Molecule* mol;
121	SimInfo::MoleculeIterator mi;
122	ConstraintElem* consElem;
123	Molecule::ConstraintElemIterator cei;
124	ConstraintPair* consPair;
125	Molecule::ConstraintPairIterator cpi;
126
127	for (mol = info_->beginMolecule(mi); mol != NULL;
128	mol = info_->nextMolecule(mi)) {
129	for (consElem = mol->beginConstraintElem(cei); consElem != NULL;
130	consElem = mol->nextConstraintElem(cei)) {
131	consElem->setMoved(true);
132	consElem->setMoving(false);
133	}
134	}
135
136	//main loop of constraint algorithm
137	bool done = false;
138	int iteration = 0;
139	while(!done && iteration < maxConsIteration_){
140	done = true;
141
142	//loop over every constraint pair
143
144	for (mol = info_->beginMolecule(mi); mol != NULL;
145	mol = info_->nextMolecule(mi)) {
146	for (consPair = mol->beginConstraintPair(cpi); consPair != NULL;
147	consPair = mol->nextConstraintPair(cpi)) {
148
149
150	//dispatch constraint algorithm
151	if(consPair->isMoved()) {
152	int exeStatus = (this->*func)(consPair);
153
154	switch(exeStatus){
155	case consFail:
156	sprintf(painCave.errMsg,
157	"Constraint failure in Rattle::constrainA, "
158	"Constraint Fail\n");
159	painCave.isFatal = 1;
160	simError();
161
162	break;
163	case consSuccess:
164	// constrain the pair by moving two elements
165	done = false;
166	consPair->getConsElem1()->setMoving(true);
167	consPair->getConsElem2()->setMoving(true);
168	break;
169	case consAlready:
170	// current pair is already constrained, do not need to
171	// move the elements
172	break;
173	default:
174	sprintf(painCave.errMsg, "ConstraintAlgorithm::doConstraint() "
175	"Error: unrecognized status");
176	painCave.isFatal = 1;
177	simError();
178	break;
179	}
180	}
181	}
182	}//end for(iter->first())
183
184
185	for (mol = info_->beginMolecule(mi); mol != NULL;
186	mol = info_->nextMolecule(mi)) {
187	for (consElem = mol->beginConstraintElem(cei); consElem != NULL;
188	consElem = mol->nextConstraintElem(cei)) {
189	consElem->setMoved(consElem->getMoving());
190	consElem->setMoving(false);
191	}
192	}
193
194	iteration++;
195	}//end while
196
197	if (!done){
198	sprintf(painCave.errMsg,
199	"Constraint failure in Rattle::constrainA, "
200	"too many iterations: %d\n",
201	iteration);
202	painCave.isFatal = 1;
203	simError();
204	}
205	}
206
207	int Rattle::constraintPairA(ConstraintPair* consPair){
208
209	ConstraintElem* consElem1 = consPair->getConsElem1();
210	ConstraintElem* consElem2 = consPair->getConsElem2();
211
212	Vector3d posA = consElem1->getPos();
213	Vector3d posB = consElem2->getPos();
214
215	Vector3d pab = posA -posB;
216
217	//periodic boundary condition
218
219	currentSnapshot_->wrapVector(pab);
220
221	RealType pabsq = pab.lengthSquare();
222
223	RealType rabsq = consPair->getConsDistSquare();
224	RealType diffsq = rabsq - pabsq;
225
226	// the original rattle code from alan tidesley
227	if (fabs(diffsq) > (consTolerance_ * rabsq * 2)){
228
229	Vector3d oldPosA = consElem1->getPrevPos();
230	Vector3d oldPosB = consElem2->getPrevPos();
231
232	Vector3d rab = oldPosA - oldPosB;
233
234	currentSnapshot_->wrapVector(rab);
235
236	RealType rpab = dot(rab, pab);
237	RealType rpabsq = rpab * rpab;
238
239	if (rpabsq < (rabsq * -diffsq)){
240	return consFail;
241	}
242
243	RealType rma = 1.0 / consElem1->getMass();
244	RealType rmb = 1.0 / consElem2->getMass();
245
246	RealType gab = diffsq / (2.0 * (rma + rmb) * rpab);
247
248	Vector3d delta = rab * gab;
249
250	//set atom1's position
251	posA += rma * delta;
252	consElem1->setPos(posA);
253
254	//set atom2's position
255	posB -= rmb * delta;
256	consElem2->setPos(posB);
257
258	delta /= dt_;
259
260	//set atom1's velocity
261	Vector3d velA = consElem1->getVel();
262	velA += rma * delta;
263	consElem1->setVel(velA);
264
265	//set atom2's velocity
266	Vector3d velB = consElem2->getVel();
267	velB -= rmb * delta;
268	consElem2->setVel(velB);
269
270	// report the constraint force back to the constraint pair:
271	consPair->setConstraintForce(gab);
272	return consSuccess;
273	}
274	else
275	return consAlready;
276
277	}
278
279
280	int Rattle::constraintPairB(ConstraintPair* consPair){
281	ConstraintElem* consElem1 = consPair->getConsElem1();
282	ConstraintElem* consElem2 = consPair->getConsElem2();
283
284
285	Vector3d velA = consElem1->getVel();
286	Vector3d velB = consElem2->getVel();
287
288	Vector3d dv = velA - velB;
289
290	Vector3d posA = consElem1->getPos();
291	Vector3d posB = consElem2->getPos();
292
293	Vector3d rab = posA - posB;
294
295	currentSnapshot_->wrapVector(rab);
296
297	RealType rma = 1.0 / consElem1->getMass();
298	RealType rmb = 1.0 / consElem2->getMass();
299
300	RealType rvab = dot(rab, dv);
301
302	RealType gab = -rvab / ((rma + rmb) * consPair->getConsDistSquare());
303
304	if (fabs(gab) > consTolerance_){
305	Vector3d delta = rab * gab;
306
307	velA += rma * delta;
308	consElem1->setVel(velA);
309
310	velB -= rmb * delta;
311	consElem2->setVel(velB);
312
313	// report the constraint force back to the constraint pair:
314	consPair->setConstraintForce(gab);
315	return consSuccess;
316	}
317	else
318	return consAlready;
319
320	}
321
322	}