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::doConstraint() "
                      "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);
      
      // report the constraint force back to the constraint pair:
      consPair->setConstraintForce(gab);
      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);

      // report the constraint force back to the constraint pair:
      consPair->setConstraintForce(gab);
      return consSuccess;
    }
    else
      return consAlready;

  }

}
Revision:	1979
Committed:	Sat Apr 5 20:56:01 2014 UTC (11 years ago) by gezelter
File size:	8479 byte(s)
Log Message:	* Changed the stdDev printouts in RNEMD stats to the 95% confidence intervals * Added the ability to specify non-bonded constraints in a molecule * Added the ability to do selection offsets in the pAngle staticProps module
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* 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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* 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	gezelter	1390	*
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	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1782	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	246	*/
42
43			#include "constraints/Rattle.hpp"
44			#include "primitives/Molecule.hpp"
45			#include "utils/simError.h"
46	gezelter	1390	namespace OpenMD {
47	gezelter	246
48	gezelter	1782	Rattle::Rattle(SimInfo* info) : info_(info), maxConsIteration_(10), consTolerance_(1.0e-6), doRattle_(false) {
49	gezelter	246
50	gezelter	1782	if (info_->getNConstraints() > 0)
51			doRattle_ = true;
52
53
54	gezelter	246	if (info_->getSimParams()->haveDt()) {
55	gezelter	507	dt_ = info_->getSimParams()->getDt();
56	gezelter	246	} else {
57	gezelter	507	sprintf(painCave.errMsg,
58			"Integrator Error: dt is not set\n");
59			painCave.isFatal = 1;
60			simError();
61	gezelter	246	}
62			currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
63	gezelter	507	}
64	gezelter	246
65	gezelter	507	void Rattle::constraintA() {
66	gezelter	1782	if (!doRattle_) return;
67			doConstraint(&Rattle::constraintPairA);
68	gezelter	507	}
69			void Rattle::constraintB() {
70	gezelter	1782	if (!doRattle_) return;
71			doConstraint(&Rattle::constraintPairB);
72	gezelter	507	}
73	gezelter	246
74	gezelter	507	void Rattle::doConstraint(ConstraintPairFuncPtr func) {
75	gezelter	1782	if (!doRattle_) return;
76
77	gezelter	246	Molecule* mol;
78			SimInfo::MoleculeIterator mi;
79			ConstraintElem* consElem;
80			Molecule::ConstraintElemIterator cei;
81			ConstraintPair* consPair;
82			Molecule::ConstraintPairIterator cpi;
83
84	gezelter	1979	for (mol = info_->beginMolecule(mi); mol != NULL;
85			mol = info_->nextMolecule(mi)) {
86			for (consElem = mol->beginConstraintElem(cei); consElem != NULL;
87			consElem = mol->nextConstraintElem(cei)) {
88	gezelter	507	consElem->setMoved(true);
89			consElem->setMoving(false);
90			}
91	gezelter	246	}
92
93			//main loop of constraint algorithm
94			bool done = false;
95			int iteration = 0;
96			while(!done && iteration < maxConsIteration_){
97	gezelter	507	done = true;
98	gezelter	246
99	gezelter	507	//loop over every constraint pair
100	gezelter	246
101	gezelter	1979	for (mol = info_->beginMolecule(mi); mol != NULL;
102			mol = info_->nextMolecule(mi)) {
103			for (consPair = mol->beginConstraintPair(cpi); consPair != NULL;
104			consPair = mol->nextConstraintPair(cpi)) {
105	gezelter	246
106
107	gezelter	507	//dispatch constraint algorithm
108			if(consPair->isMoved()) {
109			int exeStatus = (this->*func)(consPair);
110	gezelter	246
111	gezelter	507	switch(exeStatus){
112			case consFail:
113			sprintf(painCave.errMsg,
114	gezelter	1979	"Constraint failure in Rattle::constrainA, "
115			"Constraint Fail\n");
116	gezelter	507	painCave.isFatal = 1;
117			simError();
118	gezelter	246
119	gezelter	507	break;
120			case consSuccess:
121	gezelter	1979	// constrain the pair by moving two elements
122	gezelter	507	done = false;
123			consPair->getConsElem1()->setMoving(true);
124			consPair->getConsElem2()->setMoving(true);
125			break;
126			case consAlready:
127	gezelter	1979	// current pair is already constrained, do not need to
128			// move the elements
129	gezelter	507	break;
130			default:
131	gezelter	1979	sprintf(painCave.errMsg, "ConstraintAlgorithm::doConstraint() "
132			"Error: unrecognized status");
133	gezelter	507	painCave.isFatal = 1;
134			simError();
135			break;
136			}
137			}
138			}
139			}//end for(iter->first())
140	gezelter	246
141
142	gezelter	1979	for (mol = info_->beginMolecule(mi); mol != NULL;
143			mol = info_->nextMolecule(mi)) {
144			for (consElem = mol->beginConstraintElem(cei); consElem != NULL;
145			consElem = mol->nextConstraintElem(cei)) {
146	gezelter	507	consElem->setMoved(consElem->getMoving());
147			consElem->setMoving(false);
148			}
149			}
150	gezelter	246
151	gezelter	507	iteration++;
152	gezelter	246	}//end while
153
154			if (!done){
155			sprintf(painCave.errMsg,
156	gezelter	1979	"Constraint failure in Rattle::constrainA, "
157			"too many iterations: %d\n",
158	gezelter	246	iteration);
159			painCave.isFatal = 1;
160			simError();
161			}
162	gezelter	507	}
163	gezelter	246
164	gezelter	507	int Rattle::constraintPairA(ConstraintPair* consPair){
165	gezelter	1782
166	gezelter	507	ConstraintElem* consElem1 = consPair->getConsElem1();
167			ConstraintElem* consElem2 = consPair->getConsElem2();
168	gezelter	246
169	gezelter	507	Vector3d posA = consElem1->getPos();
170			Vector3d posB = consElem2->getPos();
171	gezelter	246
172	gezelter	507	Vector3d pab = posA -posB;
173	gezelter	246
174	gezelter	507	//periodic boundary condition
175	gezelter	246
176	gezelter	507	currentSnapshot_->wrapVector(pab);
177	gezelter	246
178	tim	963	RealType pabsq = pab.lengthSquare();
179	gezelter	246
180	tim	963	RealType rabsq = consPair->getConsDistSquare();
181			RealType diffsq = rabsq - pabsq;
182	gezelter	246
183	gezelter	507	// the original rattle code from alan tidesley
184			if (fabs(diffsq) > (consTolerance_ * rabsq * 2)){
185	gezelter	246
186	gezelter	507	Vector3d oldPosA = consElem1->getPrevPos();
187			Vector3d oldPosB = consElem2->getPrevPos();
188	gezelter	246
189	gezelter	507	Vector3d rab = oldPosA - oldPosB;
190	gezelter	246
191	gezelter	507	currentSnapshot_->wrapVector(rab);
192	gezelter	246
193	tim	963	RealType rpab = dot(rab, pab);
194			RealType rpabsq = rpab * rpab;
195	gezelter	246
196	gezelter	507	if (rpabsq < (rabsq * -diffsq)){
197			return consFail;
198			}
199	gezelter	246
200	tim	963	RealType rma = 1.0 / consElem1->getMass();
201			RealType rmb = 1.0 / consElem2->getMass();
202	gezelter	246
203	tim	963	RealType gab = diffsq / (2.0 * (rma + rmb) * rpab);
204	gezelter	246
205	gezelter	507	Vector3d delta = rab * gab;
206	gezelter	246
207	gezelter	507	//set atom1's position
208			posA += rma * delta;
209			consElem1->setPos(posA);
210	gezelter	246
211	gezelter	507	//set atom2's position
212			posB -= rmb * delta;
213			consElem2->setPos(posB);
214	gezelter	246
215	gezelter	507	delta /= dt_;
216	gezelter	246
217	gezelter	507	//set atom1's velocity
218			Vector3d velA = consElem1->getVel();
219			velA += rma * delta;
220			consElem1->setVel(velA);
221	gezelter	246
222	gezelter	507	//set atom2's velocity
223			Vector3d velB = consElem2->getVel();
224			velB -= rmb * delta;
225			consElem2->setVel(velB);
226	gezelter	1979
227			// report the constraint force back to the constraint pair:
228			consPair->setConstraintForce(gab);
229	gezelter	507	return consSuccess;
230			}
231			else
232			return consAlready;
233
234	gezelter	246	}
235
236
237	gezelter	507	int Rattle::constraintPairB(ConstraintPair* consPair){
238	gezelter	246	ConstraintElem* consElem1 = consPair->getConsElem1();
239			ConstraintElem* consElem2 = consPair->getConsElem2();
240
241
242			Vector3d velA = consElem1->getVel();
243			Vector3d velB = consElem2->getVel();
244
245			Vector3d dv = velA - velB;
246
247			Vector3d posA = consElem1->getPos();
248			Vector3d posB = consElem2->getPos();
249
250			Vector3d rab = posA - posB;
251
252			currentSnapshot_->wrapVector(rab);
253
254	tim	963	RealType rma = 1.0 / consElem1->getMass();
255			RealType rmb = 1.0 / consElem2->getMass();
256	gezelter	246
257	tim	963	RealType rvab = dot(rab, dv);
258	gezelter	246
259	tim	963	RealType gab = -rvab / ((rma + rmb) * consPair->getConsDistSquare());
260	gezelter	246
261			if (fabs(gab) > consTolerance_){
262			Vector3d delta = rab * gab;
263
264			velA += rma * delta;
265			consElem1->setVel(velA);
266
267			velB -= rmb * delta;
268			consElem2->setVel(velB);
269
270	gezelter	1979	// report the constraint force back to the constraint pair:
271			consPair->setConstraintForce(gab);
272	gezelter	246	return consSuccess;
273			}
274			else
275			return consAlready;
276
277	gezelter	507	}
278	gezelter	246
279			}