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. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. 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.
 */
 
#include "constraints/Rattle.hpp"
#include "primitives/Molecule.hpp"
#include "utils/simError.h"
namespace oopse {

  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);

    double pabsq = pab.lengthSquare();

    double rabsq = consPair->getConsDistSquare();
    double 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);

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

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

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

      double 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);

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

    double rvab = dot(rab, dv);

    double 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:	2204
Committed:	Fri Apr 15 22:04:00 2005 UTC (19 years, 2 months ago) by gezelter
File size:	7896 byte(s)
Log Message:	xemacs has been drafted to perform our indentation services
#	User	Rev	Content
1	gezelter	2204	/*
2	gezelter	1930	* 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. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42			#include "constraints/Rattle.hpp"
43			#include "primitives/Molecule.hpp"
44			#include "utils/simError.h"
45			namespace oopse {
46
47	gezelter	2204	Rattle::Rattle(SimInfo* info) : info_(info), maxConsIteration_(10), consTolerance_(1.0e-6) {
48	gezelter	1930
49			if (info_->getSimParams()->haveDt()) {
50	gezelter	2204	dt_ = info_->getSimParams()->getDt();
51	gezelter	1930	} else {
52	gezelter	2204	sprintf(painCave.errMsg,
53			"Integrator Error: dt is not set\n");
54			painCave.isFatal = 1;
55			simError();
56	gezelter	1930	}
57
58			currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
59	gezelter	2204	}
60	gezelter	1930
61	gezelter	2204	void Rattle::constraintA() {
62	gezelter	1930	if (info_->getNConstraints() > 0) {
63	gezelter	2204	doConstraint(&Rattle::constraintPairA);
64	gezelter	1930	}
65	gezelter	2204	}
66			void Rattle::constraintB() {
67	gezelter	1930	if (info_->getNConstraints() > 0) {
68	gezelter	2204	doConstraint(&Rattle::constraintPairB);
69	gezelter	1930	}
70	gezelter	2204	}
71	gezelter	1930
72	gezelter	2204	void Rattle::doConstraint(ConstraintPairFuncPtr func) {
73	gezelter	1930	Molecule* mol;
74			SimInfo::MoleculeIterator mi;
75			ConstraintElem* consElem;
76			Molecule::ConstraintElemIterator cei;
77			ConstraintPair* consPair;
78			Molecule::ConstraintPairIterator cpi;
79
80			for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
81	gezelter	2204	for (consElem = mol->beginConstraintElem(cei); consElem != NULL; consElem = mol->nextConstraintElem(cei)) {
82			consElem->setMoved(true);
83			consElem->setMoving(false);
84			}
85	gezelter	1930	}
86
87			//main loop of constraint algorithm
88			bool done = false;
89			int iteration = 0;
90			while(!done && iteration < maxConsIteration_){
91	gezelter	2204	done = true;
92	gezelter	1930
93	gezelter	2204	//loop over every constraint pair
94	gezelter	1930
95	gezelter	2204	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
96			for (consPair = mol->beginConstraintPair(cpi); consPair != NULL; consPair = mol->nextConstraintPair(cpi)) {
97	gezelter	1930
98
99	gezelter	2204	//dispatch constraint algorithm
100			if(consPair->isMoved()) {
101			int exeStatus = (this->*func)(consPair);
102	gezelter	1930
103	gezelter	2204	switch(exeStatus){
104			case consFail:
105			sprintf(painCave.errMsg,
106			"Constraint failure in Rattle::constrainA, Constraint Fail\n");
107			painCave.isFatal = 1;
108			simError();
109	gezelter	1930
110	gezelter	2204	break;
111			case consSuccess:
112			//constrain the pair by moving two elements
113			done = false;
114			consPair->getConsElem1()->setMoving(true);
115			consPair->getConsElem2()->setMoving(true);
116			break;
117			case consAlready:
118			//current pair is already constrained, do not need to move the elements
119			break;
120			default:
121			sprintf(painCave.errMsg, "ConstraintAlgorithm::doConstrain() Error: unrecognized status");
122			painCave.isFatal = 1;
123			simError();
124			break;
125			}
126			}
127			}
128			}//end for(iter->first())
129	gezelter	1930
130
131	gezelter	2204	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
132			for (consElem = mol->beginConstraintElem(cei); consElem != NULL; consElem = mol->nextConstraintElem(cei)) {
133			consElem->setMoved(consElem->getMoving());
134			consElem->setMoving(false);
135			}
136			}
137	gezelter	1930
138	gezelter	2204	iteration++;
139	gezelter	1930	}//end while
140
141			if (!done){
142			sprintf(painCave.errMsg,
143			"Constraint failure in Rattle::constrainA, too many iterations: %d\n",
144			iteration);
145			painCave.isFatal = 1;
146			simError();
147			}
148	gezelter	2204	}
149	gezelter	1930
150	gezelter	2204	int Rattle::constraintPairA(ConstraintPair* consPair){
151			ConstraintElem* consElem1 = consPair->getConsElem1();
152			ConstraintElem* consElem2 = consPair->getConsElem2();
153	gezelter	1930
154	gezelter	2204	Vector3d posA = consElem1->getPos();
155			Vector3d posB = consElem2->getPos();
156	gezelter	1930
157	gezelter	2204	Vector3d pab = posA -posB;
158	gezelter	1930
159	gezelter	2204	//periodic boundary condition
160	gezelter	1930
161	gezelter	2204	currentSnapshot_->wrapVector(pab);
162	gezelter	1930
163	gezelter	2204	double pabsq = pab.lengthSquare();
164	gezelter	1930
165	gezelter	2204	double rabsq = consPair->getConsDistSquare();
166			double diffsq = rabsq - pabsq;
167	gezelter	1930
168	gezelter	2204	// the original rattle code from alan tidesley
169			if (fabs(diffsq) > (consTolerance_ * rabsq * 2)){
170	gezelter	1930
171	gezelter	2204	Vector3d oldPosA = consElem1->getPrevPos();
172			Vector3d oldPosB = consElem2->getPrevPos();
173	gezelter	1930
174	gezelter	2204	Vector3d rab = oldPosA - oldPosB;
175	gezelter	1930
176	gezelter	2204	currentSnapshot_->wrapVector(rab);
177	gezelter	1930
178	gezelter	2204	double rpab = dot(rab, pab);
179			double rpabsq = rpab * rpab;
180	gezelter	1930
181	gezelter	2204	if (rpabsq < (rabsq * -diffsq)){
182			return consFail;
183			}
184	gezelter	1930
185	gezelter	2204	double rma = 1.0 / consElem1->getMass();
186			double rmb = 1.0 / consElem2->getMass();
187	gezelter	1930
188	gezelter	2204	double gab = diffsq / (2.0 * (rma + rmb) * rpab);
189	gezelter	1930
190	gezelter	2204	Vector3d delta = rab * gab;
191	gezelter	1930
192	gezelter	2204	//set atom1's position
193			posA += rma * delta;
194			consElem1->setPos(posA);
195	gezelter	1930
196	gezelter	2204	//set atom2's position
197			posB -= rmb * delta;
198			consElem2->setPos(posB);
199	gezelter	1930
200	gezelter	2204	delta /= dt_;
201	gezelter	1930
202	gezelter	2204	//set atom1's velocity
203			Vector3d velA = consElem1->getVel();
204			velA += rma * delta;
205			consElem1->setVel(velA);
206	gezelter	1930
207	gezelter	2204	//set atom2's velocity
208			Vector3d velB = consElem2->getVel();
209			velB -= rmb * delta;
210			consElem2->setVel(velB);
211	gezelter	1930
212	gezelter	2204	return consSuccess;
213			}
214			else
215			return consAlready;
216
217	gezelter	1930	}
218
219
220	gezelter	2204	int Rattle::constraintPairB(ConstraintPair* consPair){
221	gezelter	1930	ConstraintElem* consElem1 = consPair->getConsElem1();
222			ConstraintElem* consElem2 = consPair->getConsElem2();
223
224
225			Vector3d velA = consElem1->getVel();
226			Vector3d velB = consElem2->getVel();
227
228			Vector3d dv = velA - velB;
229
230			Vector3d posA = consElem1->getPos();
231			Vector3d posB = consElem2->getPos();
232
233			Vector3d rab = posA - posB;
234
235			currentSnapshot_->wrapVector(rab);
236
237			double rma = 1.0 / consElem1->getMass();
238			double rmb = 1.0 / consElem2->getMass();
239
240			double rvab = dot(rab, dv);
241
242			double gab = -rvab / ((rma + rmb) * consPair->getConsDistSquare());
243
244			if (fabs(gab) > consTolerance_){
245			Vector3d delta = rab * gab;
246
247			velA += rma * delta;
248			consElem1->setVel(velA);
249
250			velB -= rmb * delta;
251			consElem2->setVel(velB);
252
253			return consSuccess;
254			}
255			else
256			return consAlready;
257
258	gezelter	2204	}
259	gezelter	1930
260			}