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, 234107 (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:	1879
Committed:	Sun Jun 16 15:15:42 2013 UTC (11 years, 10 months ago) by gezelter
File size:	8109 byte(s)
Log Message:	MERGE OpenMD development 1783:1878 into trunk
#	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, 234107 (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), doRattle_(false) {
49
50	if (info_->getNConstraints() > 0)
51	doRattle_ = true;
52
53
54	if (info_->getSimParams()->haveDt()) {
55	dt_ = info_->getSimParams()->getDt();
56	} else {
57	sprintf(painCave.errMsg,
58	"Integrator Error: dt is not set\n");
59	painCave.isFatal = 1;
60	simError();
61	}
62
63	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
64	}
65
66	void Rattle::constraintA() {
67	if (!doRattle_) return;
68	doConstraint(&Rattle::constraintPairA);
69	}
70	void Rattle::constraintB() {
71	if (!doRattle_) return;
72	doConstraint(&Rattle::constraintPairB);
73	}
74
75	void Rattle::doConstraint(ConstraintPairFuncPtr func) {
76	if (!doRattle_) return;
77
78	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	for (consElem = mol->beginConstraintElem(cei); consElem != NULL; consElem = mol->nextConstraintElem(cei)) {
87	consElem->setMoved(true);
88	consElem->setMoving(false);
89	}
90	}
91
92	//main loop of constraint algorithm
93	bool done = false;
94	int iteration = 0;
95	while(!done && iteration < maxConsIteration_){
96	done = true;
97
98	//loop over every constraint pair
99
100	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
101	for (consPair = mol->beginConstraintPair(cpi); consPair != NULL; consPair = mol->nextConstraintPair(cpi)) {
102
103
104	//dispatch constraint algorithm
105	if(consPair->isMoved()) {
106	int exeStatus = (this->*func)(consPair);
107
108	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
115	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
135
136	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
143	iteration++;
144	}//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	}
154
155	int Rattle::constraintPairA(ConstraintPair* consPair){
156
157	ConstraintElem* consElem1 = consPair->getConsElem1();
158	ConstraintElem* consElem2 = consPair->getConsElem2();
159
160	Vector3d posA = consElem1->getPos();
161	Vector3d posB = consElem2->getPos();
162
163	Vector3d pab = posA -posB;
164
165	//periodic boundary condition
166
167	currentSnapshot_->wrapVector(pab);
168
169	RealType pabsq = pab.lengthSquare();
170
171	RealType rabsq = consPair->getConsDistSquare();
172	RealType diffsq = rabsq - pabsq;
173
174	// the original rattle code from alan tidesley
175	if (fabs(diffsq) > (consTolerance_ * rabsq * 2)){
176
177	Vector3d oldPosA = consElem1->getPrevPos();
178	Vector3d oldPosB = consElem2->getPrevPos();
179
180	Vector3d rab = oldPosA - oldPosB;
181
182	currentSnapshot_->wrapVector(rab);
183
184	RealType rpab = dot(rab, pab);
185	RealType rpabsq = rpab * rpab;
186
187	if (rpabsq < (rabsq * -diffsq)){
188	return consFail;
189	}
190
191	RealType rma = 1.0 / consElem1->getMass();
192	RealType rmb = 1.0 / consElem2->getMass();
193
194	RealType gab = diffsq / (2.0 * (rma + rmb) * rpab);
195
196	Vector3d delta = rab * gab;
197
198	//set atom1's position
199	posA += rma * delta;
200	consElem1->setPos(posA);
201
202	//set atom2's position
203	posB -= rmb * delta;
204	consElem2->setPos(posB);
205
206	delta /= dt_;
207
208	//set atom1's velocity
209	Vector3d velA = consElem1->getVel();
210	velA += rma * delta;
211	consElem1->setVel(velA);
212
213	//set atom2's velocity
214	Vector3d velB = consElem2->getVel();
215	velB -= rmb * delta;
216	consElem2->setVel(velB);
217
218	return consSuccess;
219	}
220	else
221	return consAlready;
222
223	}
224
225
226	int Rattle::constraintPairB(ConstraintPair* consPair){
227	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	RealType rma = 1.0 / consElem1->getMass();
244	RealType rmb = 1.0 / consElem2->getMass();
245
246	RealType rvab = dot(rab, dv);
247
248	RealType gab = -rvab / ((rma + rmb) * consPair->getConsDistSquare());
249
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	}
265
266	}