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_->getNGlobalConstraints() > 0)
      doRattle_ = true;
    
    Globals* simParams = info_->getSimParams();

    if (simParams->haveDt()) {
      dt_ = simParams->getDt();
    } else {
      sprintf(painCave.errMsg,
              "Rattle 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:	1982
Committed:	Tue Apr 15 12:12:23 2014 UTC (11 years ago) by gezelter
File size:	9701 byte(s)
Log Message:	Migrated ConstraintWriter calls into Shake
#	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	1982	if (info_->getNGlobalConstraints() > 0)
51	gezelter	1782	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	gezelter	1982	"Rattle Error: dt is not set\n");
60	gezelter	507	painCave.isFatal = 1;
61			simError();
62	gezelter	246	}
63	gezelter	1982
64	gezelter	246	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
65	gezelter	1981	if (simParams->haveConstraintTime()){
66			constraintTime_ = simParams->getConstraintTime();
67			} else {
68			constraintTime_ = simParams->getStatusTime();
69			}
70
71			constraintOutputFile_ = getPrefix(info_->getFinalConfigFileName()) + ".constraintForces";
72
73			// create ConstraintWriter
74			constraintWriter_ = new ConstraintWriter(info_, constraintOutputFile_.c_str());
75
76			if (!constraintWriter_){
77			sprintf(painCave.errMsg, "Failed to create ConstraintWriter\n");
78			painCave.isFatal = 1;
79			simError();
80			}
81	gezelter	507	}
82	gezelter	246
83	gezelter	507	void Rattle::constraintA() {
84	gezelter	1782	if (!doRattle_) return;
85			doConstraint(&Rattle::constraintPairA);
86	gezelter	507	}
87			void Rattle::constraintB() {
88	gezelter	1782	if (!doRattle_) return;
89			doConstraint(&Rattle::constraintPairB);
90	gezelter	1981
91			if (currentSnapshot_->getTime() >= currConstraintTime_){
92			Molecule* mol;
93			SimInfo::MoleculeIterator mi;
94			ConstraintPair* consPair;
95			Molecule::ConstraintPairIterator cpi;
96			std::list<ConstraintPair*> constraints;
97			for (mol = info_->beginMolecule(mi); mol != NULL;
98			mol = info_->nextMolecule(mi)) {
99			for (consPair = mol->beginConstraintPair(cpi); consPair != NULL;
100			consPair = mol->nextConstraintPair(cpi)) {
101
102			constraints.push_back(consPair);
103			}
104			}
105
106			constraintWriter_->writeConstraintForces(constraints);
107			currConstraintTime_ += constraintTime_;
108			}
109	gezelter	507	}
110	gezelter	246
111	gezelter	507	void Rattle::doConstraint(ConstraintPairFuncPtr func) {
112	gezelter	1782	if (!doRattle_) return;
113
114	gezelter	246	Molecule* mol;
115			SimInfo::MoleculeIterator mi;
116			ConstraintElem* consElem;
117			Molecule::ConstraintElemIterator cei;
118			ConstraintPair* consPair;
119			Molecule::ConstraintPairIterator cpi;
120
121	gezelter	1979	for (mol = info_->beginMolecule(mi); mol != NULL;
122			mol = info_->nextMolecule(mi)) {
123			for (consElem = mol->beginConstraintElem(cei); consElem != NULL;
124			consElem = mol->nextConstraintElem(cei)) {
125	gezelter	507	consElem->setMoved(true);
126			consElem->setMoving(false);
127			}
128	gezelter	246	}
129
130			//main loop of constraint algorithm
131			bool done = false;
132			int iteration = 0;
133			while(!done && iteration < maxConsIteration_){
134	gezelter	507	done = true;
135	gezelter	246
136	gezelter	507	//loop over every constraint pair
137	gezelter	246
138	gezelter	1979	for (mol = info_->beginMolecule(mi); mol != NULL;
139			mol = info_->nextMolecule(mi)) {
140			for (consPair = mol->beginConstraintPair(cpi); consPair != NULL;
141			consPair = mol->nextConstraintPair(cpi)) {
142	gezelter	246
143
144	gezelter	507	//dispatch constraint algorithm
145			if(consPair->isMoved()) {
146			int exeStatus = (this->*func)(consPair);
147	gezelter	246
148	gezelter	507	switch(exeStatus){
149			case consFail:
150			sprintf(painCave.errMsg,
151	gezelter	1979	"Constraint failure in Rattle::constrainA, "
152			"Constraint Fail\n");
153	gezelter	507	painCave.isFatal = 1;
154			simError();
155	gezelter	246
156	gezelter	507	break;
157			case consSuccess:
158	gezelter	1979	// constrain the pair by moving two elements
159	gezelter	507	done = false;
160			consPair->getConsElem1()->setMoving(true);
161			consPair->getConsElem2()->setMoving(true);
162			break;
163			case consAlready:
164	gezelter	1979	// current pair is already constrained, do not need to
165			// move the elements
166	gezelter	507	break;
167			default:
168	gezelter	1979	sprintf(painCave.errMsg, "ConstraintAlgorithm::doConstraint() "
169			"Error: unrecognized status");
170	gezelter	507	painCave.isFatal = 1;
171			simError();
172			break;
173			}
174			}
175			}
176			}//end for(iter->first())
177	gezelter	246
178
179	gezelter	1979	for (mol = info_->beginMolecule(mi); mol != NULL;
180			mol = info_->nextMolecule(mi)) {
181			for (consElem = mol->beginConstraintElem(cei); consElem != NULL;
182			consElem = mol->nextConstraintElem(cei)) {
183	gezelter	507	consElem->setMoved(consElem->getMoving());
184			consElem->setMoving(false);
185			}
186			}
187	gezelter	246
188	gezelter	507	iteration++;
189	gezelter	246	}//end while
190
191			if (!done){
192			sprintf(painCave.errMsg,
193	gezelter	1979	"Constraint failure in Rattle::constrainA, "
194			"too many iterations: %d\n",
195	gezelter	246	iteration);
196			painCave.isFatal = 1;
197			simError();
198			}
199	gezelter	507	}
200	gezelter	246
201	gezelter	507	int Rattle::constraintPairA(ConstraintPair* consPair){
202	gezelter	1782
203	gezelter	507	ConstraintElem* consElem1 = consPair->getConsElem1();
204			ConstraintElem* consElem2 = consPair->getConsElem2();
205	gezelter	246
206	gezelter	507	Vector3d posA = consElem1->getPos();
207			Vector3d posB = consElem2->getPos();
208	gezelter	246
209	gezelter	507	Vector3d pab = posA -posB;
210	gezelter	246
211	gezelter	507	//periodic boundary condition
212	gezelter	246
213	gezelter	507	currentSnapshot_->wrapVector(pab);
214	gezelter	246
215	tim	963	RealType pabsq = pab.lengthSquare();
216	gezelter	246
217	tim	963	RealType rabsq = consPair->getConsDistSquare();
218			RealType diffsq = rabsq - pabsq;
219	gezelter	246
220	gezelter	507	// the original rattle code from alan tidesley
221			if (fabs(diffsq) > (consTolerance_ * rabsq * 2)){
222	gezelter	246
223	gezelter	507	Vector3d oldPosA = consElem1->getPrevPos();
224			Vector3d oldPosB = consElem2->getPrevPos();
225	gezelter	246
226	gezelter	507	Vector3d rab = oldPosA - oldPosB;
227	gezelter	246
228	gezelter	507	currentSnapshot_->wrapVector(rab);
229	gezelter	246
230	tim	963	RealType rpab = dot(rab, pab);
231			RealType rpabsq = rpab * rpab;
232	gezelter	246
233	gezelter	507	if (rpabsq < (rabsq * -diffsq)){
234			return consFail;
235			}
236	gezelter	246
237	tim	963	RealType rma = 1.0 / consElem1->getMass();
238			RealType rmb = 1.0 / consElem2->getMass();
239	gezelter	246
240	tim	963	RealType gab = diffsq / (2.0 * (rma + rmb) * rpab);
241	gezelter	246
242	gezelter	507	Vector3d delta = rab * gab;
243	gezelter	246
244	gezelter	507	//set atom1's position
245			posA += rma * delta;
246			consElem1->setPos(posA);
247	gezelter	246
248	gezelter	507	//set atom2's position
249			posB -= rmb * delta;
250			consElem2->setPos(posB);
251	gezelter	246
252	gezelter	507	delta /= dt_;
253	gezelter	246
254	gezelter	507	//set atom1's velocity
255			Vector3d velA = consElem1->getVel();
256			velA += rma * delta;
257			consElem1->setVel(velA);
258	gezelter	246
259	gezelter	507	//set atom2's velocity
260			Vector3d velB = consElem2->getVel();
261			velB -= rmb * delta;
262			consElem2->setVel(velB);
263	gezelter	1979
264			// report the constraint force back to the constraint pair:
265			consPair->setConstraintForce(gab);
266	gezelter	507	return consSuccess;
267			}
268			else
269			return consAlready;
270
271	gezelter	246	}
272
273
274	gezelter	507	int Rattle::constraintPairB(ConstraintPair* consPair){
275	gezelter	246	ConstraintElem* consElem1 = consPair->getConsElem1();
276			ConstraintElem* consElem2 = consPair->getConsElem2();
277
278
279			Vector3d velA = consElem1->getVel();
280			Vector3d velB = consElem2->getVel();
281
282			Vector3d dv = velA - velB;
283
284			Vector3d posA = consElem1->getPos();
285			Vector3d posB = consElem2->getPos();
286
287			Vector3d rab = posA - posB;
288
289			currentSnapshot_->wrapVector(rab);
290
291	tim	963	RealType rma = 1.0 / consElem1->getMass();
292			RealType rmb = 1.0 / consElem2->getMass();
293	gezelter	246
294	tim	963	RealType rvab = dot(rab, dv);
295	gezelter	246
296	tim	963	RealType gab = -rvab / ((rma + rmb) * consPair->getConsDistSquare());
297	gezelter	246
298			if (fabs(gab) > consTolerance_){
299			Vector3d delta = rab * gab;
300
301			velA += rma * delta;
302			consElem1->setVel(velA);
303
304			velB -= rmb * delta;
305			consElem2->setVel(velB);
306
307	gezelter	1979	// report the constraint force back to the constraint pair:
308			consPair->setConstraintForce(gab);
309	gezelter	246	return consSuccess;
310			}
311			else
312			return consAlready;
313
314	gezelter	507	}
315	gezelter	246
316			}