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, 24107 (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) {
    
    if (info_->getSimParams()->haveDt()) {
      dt_ = info_->getSimParams()->getDt();
    } else {
      sprintf(painCave.errMsg,
              "Integrator Error: dt is not set\n");
      painCave.isFatal = 1;
      simError();
    }    
    
    currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
  }

  void Rattle::constraintA() {
    if (info_->getNConstraints() > 0) {
      doConstraint(&Rattle::constraintPairA);
    }
  }
  void Rattle::constraintB() {
    if (info_->getNConstraints() > 0) {
      doConstraint(&Rattle::constraintPairB);
    }
  }

  void Rattle::doConstraint(ConstraintPairFuncPtr func) {
    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::doConstrain() 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);

      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);

      return consSuccess;
    }
    else
      return consAlready;

  }

}
Revision:	1665
Committed:	Tue Nov 22 20:38:56 2011 UTC (13 years, 5 months ago) by gezelter
File size:	8028 byte(s)
Log Message:	updated copyright notices
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* 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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* 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	gezelter	1390	*
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, 24107 (2008).
39	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	246	*/
42
43			#include "constraints/Rattle.hpp"
44			#include "primitives/Molecule.hpp"
45			#include "utils/simError.h"
46	gezelter	1390	namespace OpenMD {
47	gezelter	246
48	gezelter	507	Rattle::Rattle(SimInfo* info) : info_(info), maxConsIteration_(10), consTolerance_(1.0e-6) {
49	gezelter	246
50			if (info_->getSimParams()->haveDt()) {
51	gezelter	507	dt_ = info_->getSimParams()->getDt();
52	gezelter	246	} else {
53	gezelter	507	sprintf(painCave.errMsg,
54			"Integrator Error: dt is not set\n");
55			painCave.isFatal = 1;
56			simError();
57	gezelter	246	}
58
59			currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
60	gezelter	507	}
61	gezelter	246
62	gezelter	507	void Rattle::constraintA() {
63	gezelter	246	if (info_->getNConstraints() > 0) {
64	gezelter	507	doConstraint(&Rattle::constraintPairA);
65	gezelter	246	}
66	gezelter	507	}
67			void Rattle::constraintB() {
68	gezelter	246	if (info_->getNConstraints() > 0) {
69	gezelter	507	doConstraint(&Rattle::constraintPairB);
70	gezelter	246	}
71	gezelter	507	}
72	gezelter	246
73	gezelter	507	void Rattle::doConstraint(ConstraintPairFuncPtr func) {
74	gezelter	246	Molecule* mol;
75			SimInfo::MoleculeIterator mi;
76			ConstraintElem* consElem;
77			Molecule::ConstraintElemIterator cei;
78			ConstraintPair* consPair;
79			Molecule::ConstraintPairIterator cpi;
80
81			for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
82	gezelter	507	for (consElem = mol->beginConstraintElem(cei); consElem != NULL; consElem = mol->nextConstraintElem(cei)) {
83			consElem->setMoved(true);
84			consElem->setMoving(false);
85			}
86	gezelter	246	}
87
88			//main loop of constraint algorithm
89			bool done = false;
90			int iteration = 0;
91			while(!done && iteration < maxConsIteration_){
92	gezelter	507	done = true;
93	gezelter	246
94	gezelter	507	//loop over every constraint pair
95	gezelter	246
96	gezelter	507	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
97			for (consPair = mol->beginConstraintPair(cpi); consPair != NULL; consPair = mol->nextConstraintPair(cpi)) {
98	gezelter	246
99
100	gezelter	507	//dispatch constraint algorithm
101			if(consPair->isMoved()) {
102			int exeStatus = (this->*func)(consPair);
103	gezelter	246
104	gezelter	507	switch(exeStatus){
105			case consFail:
106			sprintf(painCave.errMsg,
107			"Constraint failure in Rattle::constrainA, Constraint Fail\n");
108			painCave.isFatal = 1;
109			simError();
110	gezelter	246
111	gezelter	507	break;
112			case consSuccess:
113			//constrain the pair by moving two elements
114			done = false;
115			consPair->getConsElem1()->setMoving(true);
116			consPair->getConsElem2()->setMoving(true);
117			break;
118			case consAlready:
119			//current pair is already constrained, do not need to move the elements
120			break;
121			default:
122			sprintf(painCave.errMsg, "ConstraintAlgorithm::doConstrain() Error: unrecognized status");
123			painCave.isFatal = 1;
124			simError();
125			break;
126			}
127			}
128			}
129			}//end for(iter->first())
130	gezelter	246
131
132	gezelter	507	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
133			for (consElem = mol->beginConstraintElem(cei); consElem != NULL; consElem = mol->nextConstraintElem(cei)) {
134			consElem->setMoved(consElem->getMoving());
135			consElem->setMoving(false);
136			}
137			}
138	gezelter	246
139	gezelter	507	iteration++;
140	gezelter	246	}//end while
141
142			if (!done){
143			sprintf(painCave.errMsg,
144			"Constraint failure in Rattle::constrainA, too many iterations: %d\n",
145			iteration);
146			painCave.isFatal = 1;
147			simError();
148			}
149	gezelter	507	}
150	gezelter	246
151	gezelter	507	int Rattle::constraintPairA(ConstraintPair* consPair){
152			ConstraintElem* consElem1 = consPair->getConsElem1();
153			ConstraintElem* consElem2 = consPair->getConsElem2();
154	gezelter	246
155	gezelter	507	Vector3d posA = consElem1->getPos();
156			Vector3d posB = consElem2->getPos();
157	gezelter	246
158	gezelter	507	Vector3d pab = posA -posB;
159	gezelter	246
160	gezelter	507	//periodic boundary condition
161	gezelter	246
162	gezelter	507	currentSnapshot_->wrapVector(pab);
163	gezelter	246
164	tim	963	RealType pabsq = pab.lengthSquare();
165	gezelter	246
166	tim	963	RealType rabsq = consPair->getConsDistSquare();
167			RealType diffsq = rabsq - pabsq;
168	gezelter	246
169	gezelter	507	// the original rattle code from alan tidesley
170			if (fabs(diffsq) > (consTolerance_ * rabsq * 2)){
171	gezelter	246
172	gezelter	507	Vector3d oldPosA = consElem1->getPrevPos();
173			Vector3d oldPosB = consElem2->getPrevPos();
174	gezelter	246
175	gezelter	507	Vector3d rab = oldPosA - oldPosB;
176	gezelter	246
177	gezelter	507	currentSnapshot_->wrapVector(rab);
178	gezelter	246
179	tim	963	RealType rpab = dot(rab, pab);
180			RealType rpabsq = rpab * rpab;
181	gezelter	246
182	gezelter	507	if (rpabsq < (rabsq * -diffsq)){
183			return consFail;
184			}
185	gezelter	246
186	tim	963	RealType rma = 1.0 / consElem1->getMass();
187			RealType rmb = 1.0 / consElem2->getMass();
188	gezelter	246
189	tim	963	RealType gab = diffsq / (2.0 * (rma + rmb) * rpab);
190	gezelter	246
191	gezelter	507	Vector3d delta = rab * gab;
192	gezelter	246
193	gezelter	507	//set atom1's position
194			posA += rma * delta;
195			consElem1->setPos(posA);
196	gezelter	246
197	gezelter	507	//set atom2's position
198			posB -= rmb * delta;
199			consElem2->setPos(posB);
200	gezelter	246
201	gezelter	507	delta /= dt_;
202	gezelter	246
203	gezelter	507	//set atom1's velocity
204			Vector3d velA = consElem1->getVel();
205			velA += rma * delta;
206			consElem1->setVel(velA);
207	gezelter	246
208	gezelter	507	//set atom2's velocity
209			Vector3d velB = consElem2->getVel();
210			velB -= rmb * delta;
211			consElem2->setVel(velB);
212	gezelter	246
213	gezelter	507	return consSuccess;
214			}
215			else
216			return consAlready;
217
218	gezelter	246	}
219
220
221	gezelter	507	int Rattle::constraintPairB(ConstraintPair* consPair){
222	gezelter	246	ConstraintElem* consElem1 = consPair->getConsElem1();
223			ConstraintElem* consElem2 = consPair->getConsElem2();
224
225
226			Vector3d velA = consElem1->getVel();
227			Vector3d velB = consElem2->getVel();
228
229			Vector3d dv = velA - velB;
230
231			Vector3d posA = consElem1->getPos();
232			Vector3d posB = consElem2->getPos();
233
234			Vector3d rab = posA - posB;
235
236			currentSnapshot_->wrapVector(rab);
237
238	tim	963	RealType rma = 1.0 / consElem1->getMass();
239			RealType rmb = 1.0 / consElem2->getMass();
240	gezelter	246
241	tim	963	RealType rvab = dot(rab, dv);
242	gezelter	246
243	tim	963	RealType gab = -rvab / ((rma + rmb) * consPair->getConsDistSquare());
244	gezelter	246
245			if (fabs(gab) > consTolerance_){
246			Vector3d delta = rab * gab;
247
248			velA += rma * delta;
249			consElem1->setVel(velA);
250
251			velB -= rmb * delta;
252			consElem2->setVel(velB);
253
254			return consSuccess;
255			}
256			else
257			return consAlready;
258
259	gezelter	507	}
260	gezelter	246
261			}