src/constraints/Rattle.cpp


#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:	1916
Committed:	Tue Jan 11 15:52:45 2005 UTC (20 years, 3 months ago) by tim
File size:	6358 byte(s)
Log Message:	adding Rattle Algorithm
#	Content
1
2	#include "constraints/Rattle.hpp"
3	#include "primitives/Molecule.hpp"
4	#include "utils/simError.h"
5	namespace oopse {
6
7	Rattle::Rattle(SimInfo* info) : info_(info), maxConsIteration_(10), consTolerance_(1.0e-6) {
8
9	if (info_->getSimParams()->haveDt()) {
10	dt_ = info_->getSimParams()->getDt();
11	} else {
12	sprintf(painCave.errMsg,
13	"Integrator Error: dt is not set\n");
14	painCave.isFatal = 1;
15	simError();
16	}
17
18	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
19	}
20
21	void Rattle::constraintA() {
22	if (info_->getNConstraints() > 0) {
23	doConstraint(&Rattle::constraintPairA);
24	}
25	}
26	void Rattle::constraintB() {
27	if (info_->getNConstraints() > 0) {
28	doConstraint(&Rattle::constraintPairB);
29	}
30	}
31
32	void Rattle::doConstraint(ConstraintPairFuncPtr func) {
33	Molecule* mol;
34	SimInfo::MoleculeIterator mi;
35	ConstraintElem* consElem;
36	Molecule::ConstraintElemIterator cei;
37	ConstraintPair* consPair;
38	Molecule::ConstraintPairIterator cpi;
39
40	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
41	for (consElem = mol->beginConstraintElem(cei); consElem != NULL; consElem = mol->nextConstraintElem(cei)) {
42	consElem->setMoved(true);
43	consElem->setMoving(false);
44	}
45	}
46
47	//main loop of constraint algorithm
48	bool done = false;
49	int iteration = 0;
50	while(!done && iteration < maxConsIteration_){
51	done = true;
52
53	//loop over every constraint pair
54
55	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
56	for (consPair = mol->beginConstraintPair(cpi); consPair != NULL; consPair = mol->nextConstraintPair(cpi)) {
57
58
59	//dispatch constraint algorithm
60	if(consPair->isMoved()) {
61	int exeStatus = (this->*func)(consPair);
62
63	switch(exeStatus){
64	case consFail:
65	sprintf(painCave.errMsg,
66	"Constraint failure in Rattle::constrainA, Constraint Fail\n");
67	painCave.isFatal = 1;
68	simError();
69
70	break;
71	case consSuccess:
72	//constrain the pair by moving two elements
73	done = false;
74	consPair->getConsElem1()->setMoving(true);
75	consPair->getConsElem2()->setMoving(true);
76	break;
77	case consAlready:
78	//current pair is already constrained, do not need to move the elements
79	break;
80	default:
81	sprintf(painCave.errMsg, "ConstraintAlgorithm::doConstrain() Error: unrecognized status");
82	painCave.isFatal = 1;
83	simError();
84	break;
85	}
86	}
87	}
88	}//end for(iter->first())
89
90
91	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
92	for (consElem = mol->beginConstraintElem(cei); consElem != NULL; consElem = mol->nextConstraintElem(cei)) {
93	consElem->setMoved(consElem->getMoving());
94	consElem->setMoving(false);
95	}
96	}
97
98	iteration++;
99	}//end while
100
101	if (!done){
102	sprintf(painCave.errMsg,
103	"Constraint failure in Rattle::constrainA, too many iterations: %d\n",
104	iteration);
105	painCave.isFatal = 1;
106	simError();
107	}
108	}
109
110	int Rattle::constraintPairA(ConstraintPair* consPair){
111	ConstraintElem* consElem1 = consPair->getConsElem1();
112	ConstraintElem* consElem2 = consPair->getConsElem2();
113
114	Vector3d posA = consElem1->getPos();
115	Vector3d posB = consElem2->getPos();
116
117	Vector3d pab = posA -posB;
118
119	//periodic boundary condition
120
121	currentSnapshot_->wrapVector(pab);
122
123	double pabsq = pab.lengthSquare();
124
125	double rabsq = consPair->getConsDistSquare();
126	double diffsq = rabsq - pabsq;
127
128	// the original rattle code from alan tidesley
129	if (fabs(diffsq) > (consTolerance_ * rabsq * 2)){
130
131	Vector3d oldPosA = consElem1->getPrevPos();
132	Vector3d oldPosB = consElem2->getPrevPos();
133
134	Vector3d rab = oldPosA - oldPosB;
135
136	currentSnapshot_->wrapVector(rab);
137
138	double rpab = dot(rab, pab);
139	double rpabsq = rpab * rpab;
140
141	if (rpabsq < (rabsq * -diffsq)){
142	return consFail;
143	}
144
145	double rma = 1.0 / consElem1->getMass();
146	double rmb = 1.0 / consElem2->getMass();
147
148	double gab = diffsq / (2.0 * (rma + rmb) * rpab);
149
150	Vector3d delta = rab * gab;
151
152	//set atom1's position
153	posA += rma * delta;
154	consElem1->setPos(posA);
155
156	//set atom2's position
157	posB -= rmb * delta;
158	consElem2->setPos(posB);
159
160	delta /= dt_;
161
162	//set atom1's velocity
163	Vector3d velA = consElem1->getVel();
164	velA += rma * delta;
165	consElem1->setVel(velA);
166
167	//set atom2's velocity
168	Vector3d velB = consElem2->getVel();
169	velB -= rmb * delta;
170	consElem2->setVel(velB);
171
172	return consSuccess;
173	}
174	else
175	return consAlready;
176
177	}
178
179
180	int Rattle::constraintPairB(ConstraintPair* consPair){
181	ConstraintElem* consElem1 = consPair->getConsElem1();
182	ConstraintElem* consElem2 = consPair->getConsElem2();
183
184
185	Vector3d velA = consElem1->getVel();
186	Vector3d velB = consElem2->getVel();
187
188	Vector3d dv = velA - velB;
189
190	Vector3d posA = consElem1->getPos();
191	Vector3d posB = consElem2->getPos();
192
193	Vector3d rab = posA - posB;
194
195	currentSnapshot_->wrapVector(rab);
196
197	double rma = 1.0 / consElem1->getMass();
198	double rmb = 1.0 / consElem2->getMass();
199
200	double rvab = dot(rab, dv);
201
202	double gab = -rvab / ((rma + rmb) * consPair->getConsDistSquare());
203
204	if (fabs(gab) > consTolerance_){
205	Vector3d delta = rab * gab;
206
207	velA += rma * delta;
208	consElem1->setVel(velA);
209
210	velB -= rmb * delta;
211	consElem2->setVel(velB);
212
213	return consSuccess;
214	}
215	else
216	return consAlready;
217
218	}
219
220	}