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),
                                currConstraintTime_(0.0)  {
    
    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:	1983
Committed:	Tue Apr 15 20:36:19 2014 UTC (11 years ago) by gezelter
File size:	9536 byte(s)
Log Message:	Fixes for ConstraintWriter in parallel, some cppcheck cleanup starting preparation for 2.2 release
#	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	gezelter	1983	Shake::Shake(SimInfo* info) : info_(info), maxConsIteration_(10),
49			consTolerance_(1.0e-6), doShake_(false),
50			currConstraintTime_(0.0) {
51	gezelter	1748
52	gezelter	1982	if (info_->getNGlobalConstraints() > 0)
53	gezelter	1748	doShake_ = true;
54
55	gezelter	1982	Globals* simParams = info_->getSimParams();
56
57	gezelter	1748	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
58	gezelter	1982	if (simParams->haveConstraintTime()){
59			constraintTime_ = simParams->getConstraintTime();
60			} else {
61			constraintTime_ = simParams->getStatusTime();
62			}
63
64	gezelter	1983	constraintOutputFile_ = getPrefix(info_->getFinalConfigFileName()) +
65			".constraintForces";
66	gezelter	1982
67			// create ConstraintWriter
68	gezelter	1983	constraintWriter_ = new ConstraintWriter(info_,
69			constraintOutputFile_.c_str());
70	gezelter	1982
71			if (!constraintWriter_){
72			sprintf(painCave.errMsg, "Failed to create ConstraintWriter\n");
73			painCave.isFatal = 1;
74			simError();
75			}
76	gezelter	1748	}
77
78			void Shake::constraintR() {
79			if (!doShake_) return;
80			doConstraint(&Shake::constraintPairR);
81			}
82			void Shake::constraintF() {
83			if (!doShake_) return;
84			doConstraint(&Shake::constraintPairF);
85	gezelter	1982
86			if (currentSnapshot_->getTime() >= currConstraintTime_){
87			Molecule* mol;
88			SimInfo::MoleculeIterator mi;
89			ConstraintPair* consPair;
90			Molecule::ConstraintPairIterator cpi;
91			std::list<ConstraintPair*> constraints;
92			for (mol = info_->beginMolecule(mi); mol != NULL;
93			mol = info_->nextMolecule(mi)) {
94			for (consPair = mol->beginConstraintPair(cpi); consPair != NULL;
95			consPair = mol->nextConstraintPair(cpi)) {
96
97			constraints.push_back(consPair);
98			}
99			}
100
101			constraintWriter_->writeConstraintForces(constraints);
102			currConstraintTime_ += constraintTime_;
103			}
104	gezelter	1748	}
105
106			void Shake::doConstraint(ConstraintPairFuncPtr func) {
107			if (!doShake_) return;
108
109			Molecule* mol;
110			SimInfo::MoleculeIterator mi;
111			ConstraintElem* consElem;
112			Molecule::ConstraintElemIterator cei;
113			ConstraintPair* consPair;
114			Molecule::ConstraintPairIterator cpi;
115
116	gezelter	1982	for (mol = info_->beginMolecule(mi); mol != NULL;
117			mol = info_->nextMolecule(mi)) {
118			for (consElem = mol->beginConstraintElem(cei); consElem != NULL;
119			consElem = mol->nextConstraintElem(cei)) {
120	gezelter	1748	consElem->setMoved(true);
121			consElem->setMoving(false);
122			}
123			}
124
125			//main loop of constraint algorithm
126			bool done = false;
127			int iteration = 0;
128			while(!done && iteration < maxConsIteration_){
129			done = true;
130
131			//loop over every constraint pair
132
133	gezelter	1982	for (mol = info_->beginMolecule(mi); mol != NULL;
134			mol = info_->nextMolecule(mi)) {
135			for (consPair = mol->beginConstraintPair(cpi); consPair != NULL;
136			consPair = mol->nextConstraintPair(cpi)) {
137
138	gezelter	1748
139			//dispatch constraint algorithm
140			if(consPair->isMoved()) {
141			int exeStatus = (this->*func)(consPair);
142
143			switch(exeStatus){
144			case consFail:
145			sprintf(painCave.errMsg,
146	gezelter	1982	"Constraint failure in Shake::constrainA, "
147			"Constraint Fail\n");
148	gezelter	1748	painCave.isFatal = 1;
149			simError();
150
151			break;
152			case consSuccess:
153	gezelter	1982	// constrain the pair by moving two elements
154	gezelter	1748	done = false;
155			consPair->getConsElem1()->setMoving(true);
156			consPair->getConsElem2()->setMoving(true);
157			break;
158			case consAlready:
159	gezelter	1982	// current pair is already constrained, do not need to
160			// move the elements
161	gezelter	1748	break;
162			default:
163	gezelter	1982	sprintf(painCave.errMsg, "ConstraintAlgorithm::doConstraint() "
164			"Error: unrecognized status");
165	gezelter	1748	painCave.isFatal = 1;
166			simError();
167			break;
168			}
169			}
170			}
171			}//end for(iter->first())
172
173
174	gezelter	1982	for (mol = info_->beginMolecule(mi); mol != NULL;
175			mol = info_->nextMolecule(mi)) {
176			for (consElem = mol->beginConstraintElem(cei); consElem != NULL;
177			consElem = mol->nextConstraintElem(cei)) {
178	gezelter	1748	consElem->setMoved(consElem->getMoving());
179			consElem->setMoving(false);
180			}
181			}
182
183			iteration++;
184			}//end while
185
186			if (!done){
187			sprintf(painCave.errMsg,
188	gezelter	1982	"Constraint failure in Shake::constrainA, "
189			"too many iterations: %d\n",
190	gezelter	1748	iteration);
191			painCave.isFatal = 1;
192			simError();
193			}
194			}
195
196			/**
197			* remove constraint force along the bond direction
198			*/
199			int Shake::constraintPairR(ConstraintPair* consPair){
200
201			ConstraintElem* consElem1 = consPair->getConsElem1();
202			ConstraintElem* consElem2 = consPair->getConsElem2();
203
204			Vector3d posA = consElem1->getPos();
205			Vector3d posB = consElem2->getPos();
206
207			Vector3d pab = posA -posB;
208
209			//periodic boundary condition
210
211			currentSnapshot_->wrapVector(pab);
212
213			RealType pabsq = pab.lengthSquare();
214
215			RealType rabsq = consPair->getConsDistSquare();
216			RealType diffsq = rabsq - pabsq;
217
218			// the original rattle code from alan tidesley
219			if (fabs(diffsq) > (consTolerance_ * rabsq * 2)){
220
221			Vector3d oldPosA = consElem1->getPrevPos();
222			Vector3d oldPosB = consElem2->getPrevPos();
223
224			Vector3d rab = oldPosA - oldPosB;
225
226			currentSnapshot_->wrapVector(rab);
227
228			RealType rpab = dot(rab, pab);
229			RealType rpabsq = rpab * rpab;
230
231			if (rpabsq < (rabsq * -diffsq)){
232			return consFail;
233			}
234
235			RealType rma = 1.0 / consElem1->getMass();
236			RealType rmb = 1.0 / consElem2->getMass();
237
238			RealType gab = diffsq / (2.0 * (rma + rmb) * rpab);
239
240			Vector3d delta = rab * gab;
241
242			//set atom1's position
243			posA += rma * delta;
244			consElem1->setPos(posA);
245
246			//set atom2's position
247			posB -= rmb * delta;
248			consElem2->setPos(posB);
249	gezelter	1982
250			// report the constraint force back to the constraint pair:
251			consPair->setConstraintForce(gab);
252	gezelter	1748	return consSuccess;
253			}
254			else
255			return consAlready;
256			}
257
258			/**
259			* remove constraint force along the bond direction
260			*/
261			int Shake::constraintPairF(ConstraintPair* consPair){
262			ConstraintElem* consElem1 = consPair->getConsElem1();
263			ConstraintElem* consElem2 = consPair->getConsElem2();
264
265			Vector3d posA = consElem1->getPos();
266			Vector3d posB = consElem2->getPos();
267
268			Vector3d rab = posA - posB;
269
270			currentSnapshot_->wrapVector(rab);
271
272			Vector3d frcA = consElem1->getFrc();
273			Vector3d frcB = consElem2->getFrc();
274
275			RealType rma = 1.0 / consElem1->getMass();
276			RealType rmb = 1.0 / consElem2->getMass();
277
278			Vector3d fpab = frcA * rma - frcB * rmb;
279
280			RealType gab = fpab.lengthSquare();
281			if (gab < 1.0) gab = 1.0;
282
283			RealType rabsq = rab.lengthSquare();
284			RealType rfab = dot(rab, fpab);
285
286			if (fabs(rfab) > sqrt(rabsqgab) consTolerance_){
287			gab = -rfab / (rabsq * (rma + rmb));
288
289			frcA += rab*gab;
290			frcB -= rab*gab;
291
292			consElem1->setFrc(frcA);
293			consElem2->setFrc(frcB);
294
295	gezelter	1982	// report the constraint force back to the constraint pair:
296			consPair->setConstraintForce(gab);
297	gezelter	1748	return consSuccess;
298			}
299			else
300			return consAlready;
301			}
302			}