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, 11 months ago) by gezelter
File size:	8028 byte(s)
Log Message:	updated copyright notices
#	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, 24107 (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), consTolerance_(1.0e-6) {
49
50	if (info_->getSimParams()->haveDt()) {
51	dt_ = info_->getSimParams()->getDt();
52	} else {
53	sprintf(painCave.errMsg,
54	"Integrator Error: dt is not set\n");
55	painCave.isFatal = 1;
56	simError();
57	}
58
59	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
60	}
61
62	void Rattle::constraintA() {
63	if (info_->getNConstraints() > 0) {
64	doConstraint(&Rattle::constraintPairA);
65	}
66	}
67	void Rattle::constraintB() {
68	if (info_->getNConstraints() > 0) {
69	doConstraint(&Rattle::constraintPairB);
70	}
71	}
72
73	void Rattle::doConstraint(ConstraintPairFuncPtr func) {
74	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	for (consElem = mol->beginConstraintElem(cei); consElem != NULL; consElem = mol->nextConstraintElem(cei)) {
83	consElem->setMoved(true);
84	consElem->setMoving(false);
85	}
86	}
87
88	//main loop of constraint algorithm
89	bool done = false;
90	int iteration = 0;
91	while(!done && iteration < maxConsIteration_){
92	done = true;
93
94	//loop over every constraint pair
95
96	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
97	for (consPair = mol->beginConstraintPair(cpi); consPair != NULL; consPair = mol->nextConstraintPair(cpi)) {
98
99
100	//dispatch constraint algorithm
101	if(consPair->isMoved()) {
102	int exeStatus = (this->*func)(consPair);
103
104	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
111	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
131
132	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
139	iteration++;
140	}//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	}
150
151	int Rattle::constraintPairA(ConstraintPair* consPair){
152	ConstraintElem* consElem1 = consPair->getConsElem1();
153	ConstraintElem* consElem2 = consPair->getConsElem2();
154
155	Vector3d posA = consElem1->getPos();
156	Vector3d posB = consElem2->getPos();
157
158	Vector3d pab = posA -posB;
159
160	//periodic boundary condition
161
162	currentSnapshot_->wrapVector(pab);
163
164	RealType pabsq = pab.lengthSquare();
165
166	RealType rabsq = consPair->getConsDistSquare();
167	RealType diffsq = rabsq - pabsq;
168
169	// the original rattle code from alan tidesley
170	if (fabs(diffsq) > (consTolerance_ * rabsq * 2)){
171
172	Vector3d oldPosA = consElem1->getPrevPos();
173	Vector3d oldPosB = consElem2->getPrevPos();
174
175	Vector3d rab = oldPosA - oldPosB;
176
177	currentSnapshot_->wrapVector(rab);
178
179	RealType rpab = dot(rab, pab);
180	RealType rpabsq = rpab * rpab;
181
182	if (rpabsq < (rabsq * -diffsq)){
183	return consFail;
184	}
185
186	RealType rma = 1.0 / consElem1->getMass();
187	RealType rmb = 1.0 / consElem2->getMass();
188
189	RealType gab = diffsq / (2.0 * (rma + rmb) * rpab);
190
191	Vector3d delta = rab * gab;
192
193	//set atom1's position
194	posA += rma * delta;
195	consElem1->setPos(posA);
196
197	//set atom2's position
198	posB -= rmb * delta;
199	consElem2->setPos(posB);
200
201	delta /= dt_;
202
203	//set atom1's velocity
204	Vector3d velA = consElem1->getVel();
205	velA += rma * delta;
206	consElem1->setVel(velA);
207
208	//set atom2's velocity
209	Vector3d velB = consElem2->getVel();
210	velB -= rmb * delta;
211	consElem2->setVel(velB);
212
213	return consSuccess;
214	}
215	else
216	return consAlready;
217
218	}
219
220
221	int Rattle::constraintPairB(ConstraintPair* consPair){
222	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	RealType rma = 1.0 / consElem1->getMass();
239	RealType rmb = 1.0 / consElem2->getMass();
240
241	RealType rvab = dot(rab, dv);
242
243	RealType gab = -rvab / ((rma + rmb) * consPair->getConsDistSquare());
244
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	}
260
261	}