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, 234107 (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_->getNGlobalConstraints() > 0)
      doShake_ = true;
    
    Globals* simParams = info_->getSimParams();

    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 Shake::constraintR() {
    if (!doShake_) return;
    doConstraint(&Shake::constraintPairR);
  }
  void Shake::constraintF() {
    if (!doShake_) return;    
    doConstraint(&Shake::constraintPairF);

    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 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::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 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);

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

      // 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:	9391 byte(s)
Log Message:	Migrated ConstraintWriter calls into Shake
#	User	Rev	Content
1	gezelter	1748	/*
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	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1748	* [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	gezelter	1982	if (info_->getNGlobalConstraints() > 0)
51	gezelter	1748	doShake_ = true;
52
53	gezelter	1982	Globals* simParams = info_->getSimParams();
54
55	gezelter	1748	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
56	gezelter	1982	if (simParams->haveConstraintTime()){
57			constraintTime_ = simParams->getConstraintTime();
58			} else {
59			constraintTime_ = simParams->getStatusTime();
60			}
61
62			constraintOutputFile_ = getPrefix(info_->getFinalConfigFileName()) + ".constraintForces";
63
64			// create ConstraintWriter
65			constraintWriter_ = new ConstraintWriter(info_, constraintOutputFile_.c_str());
66
67			if (!constraintWriter_){
68			sprintf(painCave.errMsg, "Failed to create ConstraintWriter\n");
69			painCave.isFatal = 1;
70			simError();
71			}
72	gezelter	1748	}
73
74			void Shake::constraintR() {
75			if (!doShake_) return;
76			doConstraint(&Shake::constraintPairR);
77			}
78			void Shake::constraintF() {
79			if (!doShake_) return;
80			doConstraint(&Shake::constraintPairF);
81	gezelter	1982
82			if (currentSnapshot_->getTime() >= currConstraintTime_){
83			Molecule* mol;
84			SimInfo::MoleculeIterator mi;
85			ConstraintPair* consPair;
86			Molecule::ConstraintPairIterator cpi;
87			std::list<ConstraintPair*> constraints;
88			for (mol = info_->beginMolecule(mi); mol != NULL;
89			mol = info_->nextMolecule(mi)) {
90			for (consPair = mol->beginConstraintPair(cpi); consPair != NULL;
91			consPair = mol->nextConstraintPair(cpi)) {
92
93			constraints.push_back(consPair);
94			}
95			}
96
97			constraintWriter_->writeConstraintForces(constraints);
98			currConstraintTime_ += constraintTime_;
99			}
100	gezelter	1748	}
101
102			void Shake::doConstraint(ConstraintPairFuncPtr func) {
103			if (!doShake_) return;
104
105			Molecule* mol;
106			SimInfo::MoleculeIterator mi;
107			ConstraintElem* consElem;
108			Molecule::ConstraintElemIterator cei;
109			ConstraintPair* consPair;
110			Molecule::ConstraintPairIterator cpi;
111
112	gezelter	1982	for (mol = info_->beginMolecule(mi); mol != NULL;
113			mol = info_->nextMolecule(mi)) {
114			for (consElem = mol->beginConstraintElem(cei); consElem != NULL;
115			consElem = mol->nextConstraintElem(cei)) {
116	gezelter	1748	consElem->setMoved(true);
117			consElem->setMoving(false);
118			}
119			}
120
121			//main loop of constraint algorithm
122			bool done = false;
123			int iteration = 0;
124			while(!done && iteration < maxConsIteration_){
125			done = true;
126
127			//loop over every constraint pair
128
129	gezelter	1982	for (mol = info_->beginMolecule(mi); mol != NULL;
130			mol = info_->nextMolecule(mi)) {
131			for (consPair = mol->beginConstraintPair(cpi); consPair != NULL;
132			consPair = mol->nextConstraintPair(cpi)) {
133
134	gezelter	1748
135			//dispatch constraint algorithm
136			if(consPair->isMoved()) {
137			int exeStatus = (this->*func)(consPair);
138
139			switch(exeStatus){
140			case consFail:
141			sprintf(painCave.errMsg,
142	gezelter	1982	"Constraint failure in Shake::constrainA, "
143			"Constraint Fail\n");
144	gezelter	1748	painCave.isFatal = 1;
145			simError();
146
147			break;
148			case consSuccess:
149	gezelter	1982	// constrain the pair by moving two elements
150	gezelter	1748	done = false;
151			consPair->getConsElem1()->setMoving(true);
152			consPair->getConsElem2()->setMoving(true);
153			break;
154			case consAlready:
155	gezelter	1982	// current pair is already constrained, do not need to
156			// move the elements
157	gezelter	1748	break;
158			default:
159	gezelter	1982	sprintf(painCave.errMsg, "ConstraintAlgorithm::doConstraint() "
160			"Error: unrecognized status");
161	gezelter	1748	painCave.isFatal = 1;
162			simError();
163			break;
164			}
165			}
166			}
167			}//end for(iter->first())
168
169
170	gezelter	1982	for (mol = info_->beginMolecule(mi); mol != NULL;
171			mol = info_->nextMolecule(mi)) {
172			for (consElem = mol->beginConstraintElem(cei); consElem != NULL;
173			consElem = mol->nextConstraintElem(cei)) {
174	gezelter	1748	consElem->setMoved(consElem->getMoving());
175			consElem->setMoving(false);
176			}
177			}
178
179			iteration++;
180			}//end while
181
182			if (!done){
183			sprintf(painCave.errMsg,
184	gezelter	1982	"Constraint failure in Shake::constrainA, "
185			"too many iterations: %d\n",
186	gezelter	1748	iteration);
187			painCave.isFatal = 1;
188			simError();
189			}
190			}
191
192			/**
193			* remove constraint force along the bond direction
194			*/
195			int Shake::constraintPairR(ConstraintPair* consPair){
196
197			ConstraintElem* consElem1 = consPair->getConsElem1();
198			ConstraintElem* consElem2 = consPair->getConsElem2();
199
200			Vector3d posA = consElem1->getPos();
201			Vector3d posB = consElem2->getPos();
202
203			Vector3d pab = posA -posB;
204
205			//periodic boundary condition
206
207			currentSnapshot_->wrapVector(pab);
208
209			RealType pabsq = pab.lengthSquare();
210
211			RealType rabsq = consPair->getConsDistSquare();
212			RealType diffsq = rabsq - pabsq;
213
214			// the original rattle code from alan tidesley
215			if (fabs(diffsq) > (consTolerance_ * rabsq * 2)){
216
217			Vector3d oldPosA = consElem1->getPrevPos();
218			Vector3d oldPosB = consElem2->getPrevPos();
219
220			Vector3d rab = oldPosA - oldPosB;
221
222			currentSnapshot_->wrapVector(rab);
223
224			RealType rpab = dot(rab, pab);
225			RealType rpabsq = rpab * rpab;
226
227			if (rpabsq < (rabsq * -diffsq)){
228			return consFail;
229			}
230
231			RealType rma = 1.0 / consElem1->getMass();
232			RealType rmb = 1.0 / consElem2->getMass();
233
234			RealType gab = diffsq / (2.0 * (rma + rmb) * rpab);
235
236			Vector3d delta = rab * gab;
237
238			//set atom1's position
239			posA += rma * delta;
240			consElem1->setPos(posA);
241
242			//set atom2's position
243			posB -= rmb * delta;
244			consElem2->setPos(posB);
245	gezelter	1982
246			// report the constraint force back to the constraint pair:
247			consPair->setConstraintForce(gab);
248	gezelter	1748	return consSuccess;
249			}
250			else
251			return consAlready;
252			}
253
254			/**
255			* remove constraint force along the bond direction
256			*/
257			int Shake::constraintPairF(ConstraintPair* consPair){
258			ConstraintElem* consElem1 = consPair->getConsElem1();
259			ConstraintElem* consElem2 = consPair->getConsElem2();
260
261			Vector3d posA = consElem1->getPos();
262			Vector3d posB = consElem2->getPos();
263
264			Vector3d rab = posA - posB;
265
266			currentSnapshot_->wrapVector(rab);
267
268			Vector3d frcA = consElem1->getFrc();
269			Vector3d frcB = consElem2->getFrc();
270
271			RealType rma = 1.0 / consElem1->getMass();
272			RealType rmb = 1.0 / consElem2->getMass();
273
274			Vector3d fpab = frcA * rma - frcB * rmb;
275
276			RealType gab = fpab.lengthSquare();
277			if (gab < 1.0) gab = 1.0;
278
279			RealType rabsq = rab.lengthSquare();
280			RealType rfab = dot(rab, fpab);
281
282			if (fabs(rfab) > sqrt(rabsqgab) consTolerance_){
283			gab = -rfab / (rabsq * (rma + rmb));
284
285			frcA += rab*gab;
286			frcB -= rab*gab;
287
288			consElem1->setFrc(frcA);
289			consElem2->setFrc(frcB);
290
291	gezelter	1982	// report the constraint force back to the constraint pair:
292			consPair->setConstraintForce(gab);
293	gezelter	1748	return consSuccess;
294			}
295			else
296			return consAlready;
297			}
298			}