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), 
                                  currConstraintTime_(0.0) {
    
    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:	1983
Committed:	Tue Apr 15 20:36:19 2014 UTC (11 years ago) by gezelter
File size:	9843 byte(s)
Log Message:	Fixes for ConstraintWriter in parallel, some cppcheck cleanup starting preparation for 2.2 release
#	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	1983	Rattle::Rattle(SimInfo* info) : info_(info), maxConsIteration_(10),
49			consTolerance_(1.0e-6), doRattle_(false),
50			currConstraintTime_(0.0) {
51	gezelter	246
52	gezelter	1982	if (info_->getNGlobalConstraints() > 0)
53	gezelter	1782	doRattle_ = true;
54
55	gezelter	1981	Globals* simParams = info_->getSimParams();
56	gezelter	1782
57	gezelter	1981	if (simParams->haveDt()) {
58			dt_ = simParams->getDt();
59	gezelter	246	} else {
60	gezelter	507	sprintf(painCave.errMsg,
61	gezelter	1982	"Rattle Error: dt is not set\n");
62	gezelter	507	painCave.isFatal = 1;
63			simError();
64	gezelter	246	}
65	gezelter	1982
66	gezelter	246	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
67	gezelter	1981	if (simParams->haveConstraintTime()){
68			constraintTime_ = simParams->getConstraintTime();
69			} else {
70			constraintTime_ = simParams->getStatusTime();
71			}
72
73	gezelter	1983	constraintOutputFile_ = getPrefix(info_->getFinalConfigFileName()) +
74			".constraintForces";
75	gezelter	1981
76			// create ConstraintWriter
77	gezelter	1983	constraintWriter_ = new ConstraintWriter(info_,
78			constraintOutputFile_.c_str());
79	gezelter	1981
80			if (!constraintWriter_){
81			sprintf(painCave.errMsg, "Failed to create ConstraintWriter\n");
82			painCave.isFatal = 1;
83			simError();
84			}
85	gezelter	507	}
86	gezelter	246
87	gezelter	507	void Rattle::constraintA() {
88	gezelter	1782	if (!doRattle_) return;
89			doConstraint(&Rattle::constraintPairA);
90	gezelter	507	}
91			void Rattle::constraintB() {
92	gezelter	1782	if (!doRattle_) return;
93			doConstraint(&Rattle::constraintPairB);
94	gezelter	1981
95			if (currentSnapshot_->getTime() >= currConstraintTime_){
96			Molecule* mol;
97			SimInfo::MoleculeIterator mi;
98			ConstraintPair* consPair;
99			Molecule::ConstraintPairIterator cpi;
100			std::list<ConstraintPair*> constraints;
101			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
106			constraints.push_back(consPair);
107			}
108			}
109			constraintWriter_->writeConstraintForces(constraints);
110			currConstraintTime_ += constraintTime_;
111			}
112	gezelter	507	}
113	gezelter	246
114	gezelter	507	void Rattle::doConstraint(ConstraintPairFuncPtr func) {
115	gezelter	1782	if (!doRattle_) return;
116
117	gezelter	246	Molecule* mol;
118			SimInfo::MoleculeIterator mi;
119			ConstraintElem* consElem;
120			Molecule::ConstraintElemIterator cei;
121			ConstraintPair* consPair;
122			Molecule::ConstraintPairIterator cpi;
123
124	gezelter	1979	for (mol = info_->beginMolecule(mi); mol != NULL;
125			mol = info_->nextMolecule(mi)) {
126			for (consElem = mol->beginConstraintElem(cei); consElem != NULL;
127			consElem = mol->nextConstraintElem(cei)) {
128	gezelter	507	consElem->setMoved(true);
129			consElem->setMoving(false);
130			}
131	gezelter	246	}
132
133			//main loop of constraint algorithm
134			bool done = false;
135			int iteration = 0;
136			while(!done && iteration < maxConsIteration_){
137	gezelter	507	done = true;
138	gezelter	246
139	gezelter	507	//loop over every constraint pair
140	gezelter	246
141	gezelter	1979	for (mol = info_->beginMolecule(mi); mol != NULL;
142			mol = info_->nextMolecule(mi)) {
143			for (consPair = mol->beginConstraintPair(cpi); consPair != NULL;
144			consPair = mol->nextConstraintPair(cpi)) {
145	gezelter	246
146
147	gezelter	507	//dispatch constraint algorithm
148			if(consPair->isMoved()) {
149			int exeStatus = (this->*func)(consPair);
150	gezelter	246
151	gezelter	507	switch(exeStatus){
152			case consFail:
153			sprintf(painCave.errMsg,
154	gezelter	1979	"Constraint failure in Rattle::constrainA, "
155			"Constraint Fail\n");
156	gezelter	507	painCave.isFatal = 1;
157			simError();
158	gezelter	246
159	gezelter	507	break;
160			case consSuccess:
161	gezelter	1979	// constrain the pair by moving two elements
162	gezelter	507	done = false;
163			consPair->getConsElem1()->setMoving(true);
164			consPair->getConsElem2()->setMoving(true);
165			break;
166			case consAlready:
167	gezelter	1979	// current pair is already constrained, do not need to
168			// move the elements
169	gezelter	507	break;
170			default:
171	gezelter	1979	sprintf(painCave.errMsg, "ConstraintAlgorithm::doConstraint() "
172			"Error: unrecognized status");
173	gezelter	507	painCave.isFatal = 1;
174			simError();
175			break;
176			}
177			}
178			}
179			}//end for(iter->first())
180	gezelter	246
181
182	gezelter	1979	for (mol = info_->beginMolecule(mi); mol != NULL;
183			mol = info_->nextMolecule(mi)) {
184			for (consElem = mol->beginConstraintElem(cei); consElem != NULL;
185			consElem = mol->nextConstraintElem(cei)) {
186	gezelter	507	consElem->setMoved(consElem->getMoving());
187			consElem->setMoving(false);
188			}
189			}
190	gezelter	246
191	gezelter	507	iteration++;
192	gezelter	246	}//end while
193
194			if (!done){
195			sprintf(painCave.errMsg,
196	gezelter	1979	"Constraint failure in Rattle::constrainA, "
197			"too many iterations: %d\n",
198	gezelter	246	iteration);
199			painCave.isFatal = 1;
200			simError();
201			}
202	gezelter	507	}
203	gezelter	246
204	gezelter	507	int Rattle::constraintPairA(ConstraintPair* consPair){
205	gezelter	1782
206	gezelter	507	ConstraintElem* consElem1 = consPair->getConsElem1();
207			ConstraintElem* consElem2 = consPair->getConsElem2();
208	gezelter	246
209	gezelter	507	Vector3d posA = consElem1->getPos();
210			Vector3d posB = consElem2->getPos();
211	gezelter	246
212	gezelter	507	Vector3d pab = posA -posB;
213	gezelter	246
214	gezelter	507	//periodic boundary condition
215	gezelter	246
216	gezelter	507	currentSnapshot_->wrapVector(pab);
217	gezelter	246
218	tim	963	RealType pabsq = pab.lengthSquare();
219	gezelter	246
220	tim	963	RealType rabsq = consPair->getConsDistSquare();
221			RealType diffsq = rabsq - pabsq;
222	gezelter	246
223	gezelter	507	// the original rattle code from alan tidesley
224			if (fabs(diffsq) > (consTolerance_ * rabsq * 2)){
225	gezelter	246
226	gezelter	507	Vector3d oldPosA = consElem1->getPrevPos();
227			Vector3d oldPosB = consElem2->getPrevPos();
228	gezelter	246
229	gezelter	507	Vector3d rab = oldPosA - oldPosB;
230	gezelter	246
231	gezelter	507	currentSnapshot_->wrapVector(rab);
232	gezelter	246
233	tim	963	RealType rpab = dot(rab, pab);
234			RealType rpabsq = rpab * rpab;
235	gezelter	246
236	gezelter	507	if (rpabsq < (rabsq * -diffsq)){
237			return consFail;
238			}
239	gezelter	246
240	tim	963	RealType rma = 1.0 / consElem1->getMass();
241			RealType rmb = 1.0 / consElem2->getMass();
242	gezelter	246
243	tim	963	RealType gab = diffsq / (2.0 * (rma + rmb) * rpab);
244	gezelter	246
245	gezelter	507	Vector3d delta = rab * gab;
246	gezelter	246
247	gezelter	507	//set atom1's position
248			posA += rma * delta;
249			consElem1->setPos(posA);
250	gezelter	246
251	gezelter	507	//set atom2's position
252			posB -= rmb * delta;
253			consElem2->setPos(posB);
254	gezelter	246
255	gezelter	507	delta /= dt_;
256	gezelter	246
257	gezelter	507	//set atom1's velocity
258			Vector3d velA = consElem1->getVel();
259			velA += rma * delta;
260			consElem1->setVel(velA);
261	gezelter	246
262	gezelter	507	//set atom2's velocity
263			Vector3d velB = consElem2->getVel();
264			velB -= rmb * delta;
265			consElem2->setVel(velB);
266	gezelter	1979
267			// report the constraint force back to the constraint pair:
268			consPair->setConstraintForce(gab);
269	gezelter	507	return consSuccess;
270			}
271			else
272			return consAlready;
273
274	gezelter	246	}
275
276
277	gezelter	507	int Rattle::constraintPairB(ConstraintPair* consPair){
278	gezelter	246	ConstraintElem* consElem1 = consPair->getConsElem1();
279			ConstraintElem* consElem2 = consPair->getConsElem2();
280
281
282			Vector3d velA = consElem1->getVel();
283			Vector3d velB = consElem2->getVel();
284
285			Vector3d dv = velA - velB;
286
287			Vector3d posA = consElem1->getPos();
288			Vector3d posB = consElem2->getPos();
289
290			Vector3d rab = posA - posB;
291
292			currentSnapshot_->wrapVector(rab);
293
294	tim	963	RealType rma = 1.0 / consElem1->getMass();
295			RealType rmb = 1.0 / consElem2->getMass();
296	gezelter	246
297	tim	963	RealType rvab = dot(rab, dv);
298	gezelter	246
299	tim	963	RealType gab = -rvab / ((rma + rmb) * consPair->getConsDistSquare());
300	gezelter	246
301			if (fabs(gab) > consTolerance_){
302			Vector3d delta = rab * gab;
303
304			velA += rma * delta;
305			consElem1->setVel(velA);
306
307			velB -= rmb * delta;
308			consElem2->setVel(velB);
309
310	gezelter	1979	// report the constraint force back to the constraint pair:
311			consPair->setConstraintForce(gab);
312	gezelter	246	return consSuccess;
313			}
314			else
315			return consAlready;
316
317	gezelter	507	}
318	gezelter	246
319			}