src/constraints/Shake.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/Shake.hpp"
#include "primitives/Molecule.hpp"
#include "utils/simError.h"
namespace OpenMD {

  Shake::Shake(SimInfo* info) : info_(info), maxConsIteration_(10), consTolerance_(1.0e-6), doShake_(false) {
    
    if (info_->getNConstraints() > 0)
      doShake_ = true;
    
    currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
  }
  
  void Shake::constraintR() {
    if (!doShake_) return;
    doConstraint(&Shake::constraintPairR);
  }
  void Shake::constraintF() {
    if (!doShake_) return;    
    doConstraint(&Shake::constraintPairF);
  }

  void Shake::doConstraint(ConstraintPairFuncPtr func) {
    if (!doShake_) 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 Shake::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 Shake::constrainA, too many iterations: %d\n",
              iteration);
      painCave.isFatal = 1;
      simError();    
    }
  }

  /**
   * remove constraint force along the bond direction
   */
  int Shake::constraintPairR(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);
      return consSuccess;
    }
    else
      return consAlready;
  }

  /**
   * remove constraint force along the bond direction
   */
  int Shake::constraintPairF(ConstraintPair* consPair){
    ConstraintElem* consElem1 = consPair->getConsElem1();
    ConstraintElem* consElem2 = consPair->getConsElem2();

    Vector3d posA = consElem1->getPos();
    Vector3d posB = consElem2->getPos();

    Vector3d rab = posA - posB;

    currentSnapshot_->wrapVector(rab);

    Vector3d frcA = consElem1->getFrc();
    Vector3d frcB = consElem2->getFrc();

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

    Vector3d fpab = frcA * rma - frcB * rmb;

    RealType gab = fpab.lengthSquare();
    if (gab < 1.0) gab = 1.0;
    
    RealType rabsq = rab.lengthSquare();
    RealType rfab = dot(rab, fpab);

    if (fabs(rfab) > sqrt(rabsq*gab) * consTolerance_){
      gab = -rfab / (rabsq * (rma + rmb));

      frcA += rab*gab;
      frcB -= rab*gab;
      
      consElem1->setFrc(frcA);
      consElem2->setFrc(frcB);

      return consSuccess;
    }
    else
      return consAlready;
  }
}
Revision:	1748
Committed:	Wed Jun 6 19:54:09 2012 UTC (12 years, 10 months ago) by gezelter
File size:	7761 byte(s)
Log Message:	fixing some bugs, adding Shake
#	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/Shake.hpp"
44	#include "primitives/Molecule.hpp"
45	#include "utils/simError.h"
46	namespace OpenMD {
47
48	Shake::Shake(SimInfo* info) : info_(info), maxConsIteration_(10), consTolerance_(1.0e-6), doShake_(false) {
49
50	if (info_->getNConstraints() > 0)
51	doShake_ = true;
52
53	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
54	}
55
56	void Shake::constraintR() {
57	if (!doShake_) return;
58	doConstraint(&Shake::constraintPairR);
59	}
60	void Shake::constraintF() {
61	if (!doShake_) return;
62	doConstraint(&Shake::constraintPairF);
63	}
64
65	void Shake::doConstraint(ConstraintPairFuncPtr func) {
66	if (!doShake_) return;
67
68	Molecule* mol;
69	SimInfo::MoleculeIterator mi;
70	ConstraintElem* consElem;
71	Molecule::ConstraintElemIterator cei;
72	ConstraintPair* consPair;
73	Molecule::ConstraintPairIterator cpi;
74
75	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
76	for (consElem = mol->beginConstraintElem(cei); consElem != NULL; consElem = mol->nextConstraintElem(cei)) {
77	consElem->setMoved(true);
78	consElem->setMoving(false);
79	}
80	}
81
82	//main loop of constraint algorithm
83	bool done = false;
84	int iteration = 0;
85	while(!done && iteration < maxConsIteration_){
86	done = true;
87
88	//loop over every constraint pair
89
90	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
91	for (consPair = mol->beginConstraintPair(cpi); consPair != NULL; consPair = mol->nextConstraintPair(cpi)) {
92
93
94	//dispatch constraint algorithm
95	if(consPair->isMoved()) {
96	int exeStatus = (this->*func)(consPair);
97
98	switch(exeStatus){
99	case consFail:
100	sprintf(painCave.errMsg,
101	"Constraint failure in Shake::constrainA, Constraint Fail\n");
102	painCave.isFatal = 1;
103	simError();
104
105	break;
106	case consSuccess:
107	//constrain the pair by moving two elements
108	done = false;
109	consPair->getConsElem1()->setMoving(true);
110	consPair->getConsElem2()->setMoving(true);
111	break;
112	case consAlready:
113	//current pair is already constrained, do not need to move the elements
114	break;
115	default:
116	sprintf(painCave.errMsg, "ConstraintAlgorithm::doConstrain() Error: unrecognized status");
117	painCave.isFatal = 1;
118	simError();
119	break;
120	}
121	}
122	}
123	}//end for(iter->first())
124
125
126	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
127	for (consElem = mol->beginConstraintElem(cei); consElem != NULL; consElem = mol->nextConstraintElem(cei)) {
128	consElem->setMoved(consElem->getMoving());
129	consElem->setMoving(false);
130	}
131	}
132
133	iteration++;
134	}//end while
135
136	if (!done){
137	sprintf(painCave.errMsg,
138	"Constraint failure in Shake::constrainA, too many iterations: %d\n",
139	iteration);
140	painCave.isFatal = 1;
141	simError();
142	}
143	}
144
145	/**
146	* remove constraint force along the bond direction
147	*/
148	int Shake::constraintPairR(ConstraintPair* consPair){
149
150	ConstraintElem* consElem1 = consPair->getConsElem1();
151	ConstraintElem* consElem2 = consPair->getConsElem2();
152
153	Vector3d posA = consElem1->getPos();
154	Vector3d posB = consElem2->getPos();
155
156	Vector3d pab = posA -posB;
157
158	//periodic boundary condition
159
160	currentSnapshot_->wrapVector(pab);
161
162	RealType pabsq = pab.lengthSquare();
163
164	RealType rabsq = consPair->getConsDistSquare();
165	RealType diffsq = rabsq - pabsq;
166
167	// the original rattle code from alan tidesley
168	if (fabs(diffsq) > (consTolerance_ * rabsq * 2)){
169
170	Vector3d oldPosA = consElem1->getPrevPos();
171	Vector3d oldPosB = consElem2->getPrevPos();
172
173	Vector3d rab = oldPosA - oldPosB;
174
175	currentSnapshot_->wrapVector(rab);
176
177	RealType rpab = dot(rab, pab);
178	RealType rpabsq = rpab * rpab;
179
180	if (rpabsq < (rabsq * -diffsq)){
181	return consFail;
182	}
183
184	RealType rma = 1.0 / consElem1->getMass();
185	RealType rmb = 1.0 / consElem2->getMass();
186
187	RealType gab = diffsq / (2.0 * (rma + rmb) * rpab);
188
189	Vector3d delta = rab * gab;
190
191	//set atom1's position
192	posA += rma * delta;
193	consElem1->setPos(posA);
194
195	//set atom2's position
196	posB -= rmb * delta;
197	consElem2->setPos(posB);
198	return consSuccess;
199	}
200	else
201	return consAlready;
202	}
203
204	/**
205	* remove constraint force along the bond direction
206	*/
207	int Shake::constraintPairF(ConstraintPair* consPair){
208	ConstraintElem* consElem1 = consPair->getConsElem1();
209	ConstraintElem* consElem2 = consPair->getConsElem2();
210
211	Vector3d posA = consElem1->getPos();
212	Vector3d posB = consElem2->getPos();
213
214	Vector3d rab = posA - posB;
215
216	currentSnapshot_->wrapVector(rab);
217
218	Vector3d frcA = consElem1->getFrc();
219	Vector3d frcB = consElem2->getFrc();
220
221	RealType rma = 1.0 / consElem1->getMass();
222	RealType rmb = 1.0 / consElem2->getMass();
223
224	Vector3d fpab = frcA * rma - frcB * rmb;
225
226	RealType gab = fpab.lengthSquare();
227	if (gab < 1.0) gab = 1.0;
228
229	RealType rabsq = rab.lengthSquare();
230	RealType rfab = dot(rab, fpab);
231
232	if (fabs(rfab) > sqrt(rabsqgab) consTolerance_){
233	gab = -rfab / (rabsq * (rma + rmb));
234
235	frcA += rab*gab;
236	frcB -= rab*gab;
237
238	consElem1->setFrc(frcA);
239	consElem2->setFrc(frcB);
240
241	return consSuccess;
242	}
243	else
244	return consAlready;
245	}
246	}