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), doRattle_(false) {
    
    if (info_->getNConstraints() > 0)
      doRattle_ = true;
    

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

  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::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:	1715
Committed:	Tue May 22 21:55:31 2012 UTC (12 years, 11 months ago) by gezelter
File size:	8108 byte(s)
Log Message:	Adding more support structure for Fluctuating Charges.
#	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	1715	Rattle::Rattle(SimInfo* info) : info_(info), maxConsIteration_(10), consTolerance_(1.0e-6), doRattle_(false) {
49	gezelter	246
50	gezelter	1715	if (info_->getNConstraints() > 0)
51			doRattle_ = true;
52
53
54	gezelter	246	if (info_->getSimParams()->haveDt()) {
55	gezelter	507	dt_ = info_->getSimParams()->getDt();
56	gezelter	246	} else {
57	gezelter	507	sprintf(painCave.errMsg,
58			"Integrator Error: dt is not set\n");
59			painCave.isFatal = 1;
60			simError();
61	gezelter	246	}
62
63			currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
64	gezelter	507	}
65	gezelter	246
66	gezelter	507	void Rattle::constraintA() {
67	gezelter	1715	if (!doRattle_) return;
68			doConstraint(&Rattle::constraintPairA);
69	gezelter	507	}
70			void Rattle::constraintB() {
71	gezelter	1715	if (!doRattle_) return;
72			doConstraint(&Rattle::constraintPairB);
73	gezelter	507	}
74	gezelter	246
75	gezelter	507	void Rattle::doConstraint(ConstraintPairFuncPtr func) {
76	gezelter	1715	if (!doRattle_) return;
77
78	gezelter	246	Molecule* mol;
79			SimInfo::MoleculeIterator mi;
80			ConstraintElem* consElem;
81			Molecule::ConstraintElemIterator cei;
82			ConstraintPair* consPair;
83			Molecule::ConstraintPairIterator cpi;
84
85			for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
86	gezelter	507	for (consElem = mol->beginConstraintElem(cei); consElem != NULL; consElem = mol->nextConstraintElem(cei)) {
87			consElem->setMoved(true);
88			consElem->setMoving(false);
89			}
90	gezelter	246	}
91
92			//main loop of constraint algorithm
93			bool done = false;
94			int iteration = 0;
95			while(!done && iteration < maxConsIteration_){
96	gezelter	507	done = true;
97	gezelter	246
98	gezelter	507	//loop over every constraint pair
99	gezelter	246
100	gezelter	507	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
101			for (consPair = mol->beginConstraintPair(cpi); consPair != NULL; consPair = mol->nextConstraintPair(cpi)) {
102	gezelter	246
103
104	gezelter	507	//dispatch constraint algorithm
105			if(consPair->isMoved()) {
106			int exeStatus = (this->*func)(consPair);
107	gezelter	246
108	gezelter	507	switch(exeStatus){
109			case consFail:
110			sprintf(painCave.errMsg,
111			"Constraint failure in Rattle::constrainA, Constraint Fail\n");
112			painCave.isFatal = 1;
113			simError();
114	gezelter	246
115	gezelter	507	break;
116			case consSuccess:
117			//constrain the pair by moving two elements
118			done = false;
119			consPair->getConsElem1()->setMoving(true);
120			consPair->getConsElem2()->setMoving(true);
121			break;
122			case consAlready:
123			//current pair is already constrained, do not need to move the elements
124			break;
125			default:
126			sprintf(painCave.errMsg, "ConstraintAlgorithm::doConstrain() Error: unrecognized status");
127			painCave.isFatal = 1;
128			simError();
129			break;
130			}
131			}
132			}
133			}//end for(iter->first())
134	gezelter	246
135
136	gezelter	507	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
137			for (consElem = mol->beginConstraintElem(cei); consElem != NULL; consElem = mol->nextConstraintElem(cei)) {
138			consElem->setMoved(consElem->getMoving());
139			consElem->setMoving(false);
140			}
141			}
142	gezelter	246
143	gezelter	507	iteration++;
144	gezelter	246	}//end while
145
146			if (!done){
147			sprintf(painCave.errMsg,
148			"Constraint failure in Rattle::constrainA, too many iterations: %d\n",
149			iteration);
150			painCave.isFatal = 1;
151			simError();
152			}
153	gezelter	507	}
154	gezelter	246
155	gezelter	507	int Rattle::constraintPairA(ConstraintPair* consPair){
156	gezelter	1715
157	gezelter	507	ConstraintElem* consElem1 = consPair->getConsElem1();
158			ConstraintElem* consElem2 = consPair->getConsElem2();
159	gezelter	246
160	gezelter	507	Vector3d posA = consElem1->getPos();
161			Vector3d posB = consElem2->getPos();
162	gezelter	246
163	gezelter	507	Vector3d pab = posA -posB;
164	gezelter	246
165	gezelter	507	//periodic boundary condition
166	gezelter	246
167	gezelter	507	currentSnapshot_->wrapVector(pab);
168	gezelter	246
169	tim	963	RealType pabsq = pab.lengthSquare();
170	gezelter	246
171	tim	963	RealType rabsq = consPair->getConsDistSquare();
172			RealType diffsq = rabsq - pabsq;
173	gezelter	246
174	gezelter	507	// the original rattle code from alan tidesley
175			if (fabs(diffsq) > (consTolerance_ * rabsq * 2)){
176	gezelter	246
177	gezelter	507	Vector3d oldPosA = consElem1->getPrevPos();
178			Vector3d oldPosB = consElem2->getPrevPos();
179	gezelter	246
180	gezelter	507	Vector3d rab = oldPosA - oldPosB;
181	gezelter	246
182	gezelter	507	currentSnapshot_->wrapVector(rab);
183	gezelter	246
184	tim	963	RealType rpab = dot(rab, pab);
185			RealType rpabsq = rpab * rpab;
186	gezelter	246
187	gezelter	507	if (rpabsq < (rabsq * -diffsq)){
188			return consFail;
189			}
190	gezelter	246
191	tim	963	RealType rma = 1.0 / consElem1->getMass();
192			RealType rmb = 1.0 / consElem2->getMass();
193	gezelter	246
194	tim	963	RealType gab = diffsq / (2.0 * (rma + rmb) * rpab);
195	gezelter	246
196	gezelter	507	Vector3d delta = rab * gab;
197	gezelter	246
198	gezelter	507	//set atom1's position
199			posA += rma * delta;
200			consElem1->setPos(posA);
201	gezelter	246
202	gezelter	507	//set atom2's position
203			posB -= rmb * delta;
204			consElem2->setPos(posB);
205	gezelter	246
206	gezelter	507	delta /= dt_;
207	gezelter	246
208	gezelter	507	//set atom1's velocity
209			Vector3d velA = consElem1->getVel();
210			velA += rma * delta;
211			consElem1->setVel(velA);
212	gezelter	246
213	gezelter	507	//set atom2's velocity
214			Vector3d velB = consElem2->getVel();
215			velB -= rmb * delta;
216			consElem2->setVel(velB);
217	gezelter	246
218	gezelter	507	return consSuccess;
219			}
220			else
221			return consAlready;
222
223	gezelter	246	}
224
225
226	gezelter	507	int Rattle::constraintPairB(ConstraintPair* consPair){
227	gezelter	246	ConstraintElem* consElem1 = consPair->getConsElem1();
228			ConstraintElem* consElem2 = consPair->getConsElem2();
229
230
231			Vector3d velA = consElem1->getVel();
232			Vector3d velB = consElem2->getVel();
233
234			Vector3d dv = velA - velB;
235
236			Vector3d posA = consElem1->getPos();
237			Vector3d posB = consElem2->getPos();
238
239			Vector3d rab = posA - posB;
240
241			currentSnapshot_->wrapVector(rab);
242
243	tim	963	RealType rma = 1.0 / consElem1->getMass();
244			RealType rmb = 1.0 / consElem2->getMass();
245	gezelter	246
246	tim	963	RealType rvab = dot(rab, dv);
247	gezelter	246
248	tim	963	RealType gab = -rvab / ((rma + rmb) * consPair->getConsDistSquare());
249	gezelter	246
250			if (fabs(gab) > consTolerance_){
251			Vector3d delta = rab * gab;
252
253			velA += rma * delta;
254			consElem1->setVel(velA);
255
256			velB -= rmb * delta;
257			consElem2->setVel(velB);
258
259			return consSuccess;
260			}
261			else
262			return consAlready;
263
264	gezelter	507	}
265	gezelter	246
266			}