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;
    
    Globals* simParams = info_->getSimParams();

    if (simParams->haveDt()) {
      dt_ = simParams->getDt();
    } else {
      sprintf(painCave.errMsg,
              "Integrator Error: dt is not set\n");
      painCave.isFatal = 1;
      simError();
    }    
    currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
    if (simParams->haveConstraintTime()){
      constraintTime_ = simParams->getConstraintTime();
    } else {
      constraintTime_ = simParams->getStatusTime();
    }

    constraintOutputFile_ = getPrefix(info_->getFinalConfigFileName()) + ".constraintForces";

    // create ConstraintWriter  
    constraintWriter_ = new ConstraintWriter(info_, constraintOutputFile_.c_str());   

    if (!constraintWriter_){
      sprintf(painCave.errMsg, "Failed to create ConstraintWriter\n");
      painCave.isFatal = 1;
      simError();
    }
  }

  void Rattle::constraintA() {
    if (!doRattle_) return;
    doConstraint(&Rattle::constraintPairA);
  }
  void Rattle::constraintB() {
    if (!doRattle_) return;    
    doConstraint(&Rattle::constraintPairB);

    if (currentSnapshot_->getTime() >= currConstraintTime_){
      Molecule* mol;
      SimInfo::MoleculeIterator mi;
      ConstraintPair* consPair;
      Molecule::ConstraintPairIterator cpi;
      std::list<ConstraintPair*> constraints;
      for (mol = info_->beginMolecule(mi); mol != NULL; 
           mol = info_->nextMolecule(mi)) {
        for (consPair = mol->beginConstraintPair(cpi); consPair != NULL; 
             consPair = mol->nextConstraintPair(cpi)) {
          
          constraints.push_back(consPair);
        }
      }
      
      constraintWriter_->writeConstraintForces(constraints);
      currConstraintTime_ += constraintTime_;
    }
  }

  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:	1981
Committed:	Mon Apr 14 18:32:51 2014 UTC (11 years ago) by gezelter
File size:	9698 byte(s)
Log Message:	Added the ConstraintWriter
#	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	gezelter	1981	Globals* simParams = info_->getSimParams();
54	gezelter	1782
55	gezelter	1981	if (simParams->haveDt()) {
56			dt_ = simParams->getDt();
57	gezelter	246	} else {
58	gezelter	507	sprintf(painCave.errMsg,
59			"Integrator Error: dt is not set\n");
60			painCave.isFatal = 1;
61			simError();
62	gezelter	246	}
63			currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
64	gezelter	1981	if (simParams->haveConstraintTime()){
65			constraintTime_ = simParams->getConstraintTime();
66			} else {
67			constraintTime_ = simParams->getStatusTime();
68			}
69
70			constraintOutputFile_ = getPrefix(info_->getFinalConfigFileName()) + ".constraintForces";
71
72			// create ConstraintWriter
73			constraintWriter_ = new ConstraintWriter(info_, constraintOutputFile_.c_str());
74
75			if (!constraintWriter_){
76			sprintf(painCave.errMsg, "Failed to create ConstraintWriter\n");
77			painCave.isFatal = 1;
78			simError();
79			}
80	gezelter	507	}
81	gezelter	246
82	gezelter	507	void Rattle::constraintA() {
83	gezelter	1782	if (!doRattle_) return;
84			doConstraint(&Rattle::constraintPairA);
85	gezelter	507	}
86			void Rattle::constraintB() {
87	gezelter	1782	if (!doRattle_) return;
88			doConstraint(&Rattle::constraintPairB);
89	gezelter	1981
90			if (currentSnapshot_->getTime() >= currConstraintTime_){
91			Molecule* mol;
92			SimInfo::MoleculeIterator mi;
93			ConstraintPair* consPair;
94			Molecule::ConstraintPairIterator cpi;
95			std::list<ConstraintPair*> constraints;
96			for (mol = info_->beginMolecule(mi); mol != NULL;
97			mol = info_->nextMolecule(mi)) {
98			for (consPair = mol->beginConstraintPair(cpi); consPair != NULL;
99			consPair = mol->nextConstraintPair(cpi)) {
100
101			constraints.push_back(consPair);
102			}
103			}
104
105			constraintWriter_->writeConstraintForces(constraints);
106			currConstraintTime_ += constraintTime_;
107			}
108	gezelter	507	}
109	gezelter	246
110	gezelter	507	void Rattle::doConstraint(ConstraintPairFuncPtr func) {
111	gezelter	1782	if (!doRattle_) return;
112
113	gezelter	246	Molecule* mol;
114			SimInfo::MoleculeIterator mi;
115			ConstraintElem* consElem;
116			Molecule::ConstraintElemIterator cei;
117			ConstraintPair* consPair;
118			Molecule::ConstraintPairIterator cpi;
119
120	gezelter	1979	for (mol = info_->beginMolecule(mi); mol != NULL;
121			mol = info_->nextMolecule(mi)) {
122			for (consElem = mol->beginConstraintElem(cei); consElem != NULL;
123			consElem = mol->nextConstraintElem(cei)) {
124	gezelter	507	consElem->setMoved(true);
125			consElem->setMoving(false);
126			}
127	gezelter	246	}
128
129			//main loop of constraint algorithm
130			bool done = false;
131			int iteration = 0;
132			while(!done && iteration < maxConsIteration_){
133	gezelter	507	done = true;
134	gezelter	246
135	gezelter	507	//loop over every constraint pair
136	gezelter	246
137	gezelter	1979	for (mol = info_->beginMolecule(mi); mol != NULL;
138			mol = info_->nextMolecule(mi)) {
139			for (consPair = mol->beginConstraintPair(cpi); consPair != NULL;
140			consPair = mol->nextConstraintPair(cpi)) {
141	gezelter	246
142
143	gezelter	507	//dispatch constraint algorithm
144			if(consPair->isMoved()) {
145			int exeStatus = (this->*func)(consPair);
146	gezelter	246
147	gezelter	507	switch(exeStatus){
148			case consFail:
149			sprintf(painCave.errMsg,
150	gezelter	1979	"Constraint failure in Rattle::constrainA, "
151			"Constraint Fail\n");
152	gezelter	507	painCave.isFatal = 1;
153			simError();
154	gezelter	246
155	gezelter	507	break;
156			case consSuccess:
157	gezelter	1979	// constrain the pair by moving two elements
158	gezelter	507	done = false;
159			consPair->getConsElem1()->setMoving(true);
160			consPair->getConsElem2()->setMoving(true);
161			break;
162			case consAlready:
163	gezelter	1979	// current pair is already constrained, do not need to
164			// move the elements
165	gezelter	507	break;
166			default:
167	gezelter	1979	sprintf(painCave.errMsg, "ConstraintAlgorithm::doConstraint() "
168			"Error: unrecognized status");
169	gezelter	507	painCave.isFatal = 1;
170			simError();
171			break;
172			}
173			}
174			}
175			}//end for(iter->first())
176	gezelter	246
177
178	gezelter	1979	for (mol = info_->beginMolecule(mi); mol != NULL;
179			mol = info_->nextMolecule(mi)) {
180			for (consElem = mol->beginConstraintElem(cei); consElem != NULL;
181			consElem = mol->nextConstraintElem(cei)) {
182	gezelter	507	consElem->setMoved(consElem->getMoving());
183			consElem->setMoving(false);
184			}
185			}
186	gezelter	246
187	gezelter	507	iteration++;
188	gezelter	246	}//end while
189
190			if (!done){
191			sprintf(painCave.errMsg,
192	gezelter	1979	"Constraint failure in Rattle::constrainA, "
193			"too many iterations: %d\n",
194	gezelter	246	iteration);
195			painCave.isFatal = 1;
196			simError();
197			}
198	gezelter	507	}
199	gezelter	246
200	gezelter	507	int Rattle::constraintPairA(ConstraintPair* consPair){
201	gezelter	1782
202	gezelter	507	ConstraintElem* consElem1 = consPair->getConsElem1();
203			ConstraintElem* consElem2 = consPair->getConsElem2();
204	gezelter	246
205	gezelter	507	Vector3d posA = consElem1->getPos();
206			Vector3d posB = consElem2->getPos();
207	gezelter	246
208	gezelter	507	Vector3d pab = posA -posB;
209	gezelter	246
210	gezelter	507	//periodic boundary condition
211	gezelter	246
212	gezelter	507	currentSnapshot_->wrapVector(pab);
213	gezelter	246
214	tim	963	RealType pabsq = pab.lengthSquare();
215	gezelter	246
216	tim	963	RealType rabsq = consPair->getConsDistSquare();
217			RealType diffsq = rabsq - pabsq;
218	gezelter	246
219	gezelter	507	// the original rattle code from alan tidesley
220			if (fabs(diffsq) > (consTolerance_ * rabsq * 2)){
221	gezelter	246
222	gezelter	507	Vector3d oldPosA = consElem1->getPrevPos();
223			Vector3d oldPosB = consElem2->getPrevPos();
224	gezelter	246
225	gezelter	507	Vector3d rab = oldPosA - oldPosB;
226	gezelter	246
227	gezelter	507	currentSnapshot_->wrapVector(rab);
228	gezelter	246
229	tim	963	RealType rpab = dot(rab, pab);
230			RealType rpabsq = rpab * rpab;
231	gezelter	246
232	gezelter	507	if (rpabsq < (rabsq * -diffsq)){
233			return consFail;
234			}
235	gezelter	246
236	tim	963	RealType rma = 1.0 / consElem1->getMass();
237			RealType rmb = 1.0 / consElem2->getMass();
238	gezelter	246
239	tim	963	RealType gab = diffsq / (2.0 * (rma + rmb) * rpab);
240	gezelter	246
241	gezelter	507	Vector3d delta = rab * gab;
242	gezelter	246
243	gezelter	507	//set atom1's position
244			posA += rma * delta;
245			consElem1->setPos(posA);
246	gezelter	246
247	gezelter	507	//set atom2's position
248			posB -= rmb * delta;
249			consElem2->setPos(posB);
250	gezelter	246
251	gezelter	507	delta /= dt_;
252	gezelter	246
253	gezelter	507	//set atom1's velocity
254			Vector3d velA = consElem1->getVel();
255			velA += rma * delta;
256			consElem1->setVel(velA);
257	gezelter	246
258	gezelter	507	//set atom2's velocity
259			Vector3d velB = consElem2->getVel();
260			velB -= rmb * delta;
261			consElem2->setVel(velB);
262	gezelter	1979
263			// report the constraint force back to the constraint pair:
264			consPair->setConstraintForce(gab);
265	gezelter	507	return consSuccess;
266			}
267			else
268			return consAlready;
269
270	gezelter	246	}
271
272
273	gezelter	507	int Rattle::constraintPairB(ConstraintPair* consPair){
274	gezelter	246	ConstraintElem* consElem1 = consPair->getConsElem1();
275			ConstraintElem* consElem2 = consPair->getConsElem2();
276
277
278			Vector3d velA = consElem1->getVel();
279			Vector3d velB = consElem2->getVel();
280
281			Vector3d dv = velA - velB;
282
283			Vector3d posA = consElem1->getPos();
284			Vector3d posB = consElem2->getPos();
285
286			Vector3d rab = posA - posB;
287
288			currentSnapshot_->wrapVector(rab);
289
290	tim	963	RealType rma = 1.0 / consElem1->getMass();
291			RealType rmb = 1.0 / consElem2->getMass();
292	gezelter	246
293	tim	963	RealType rvab = dot(rab, dv);
294	gezelter	246
295	tim	963	RealType gab = -rvab / ((rma + rmb) * consPair->getConsDistSquare());
296	gezelter	246
297			if (fabs(gab) > consTolerance_){
298			Vector3d delta = rab * gab;
299
300			velA += rma * delta;
301			consElem1->setVel(velA);
302
303			velB -= rmb * delta;
304			consElem2->setVel(velB);
305
306	gezelter	1979	// report the constraint force back to the constraint pair:
307			consPair->setConstraintForce(gab);
308	gezelter	246	return consSuccess;
309			}
310			else
311			return consAlready;
312
313	gezelter	507	}
314	gezelter	246
315			}