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
#	Content
1	/*
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	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	* [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),
49	consTolerance_(1.0e-6), doShake_(false),
50	currConstraintTime_(0.0) {
51
52	if (info_->getNGlobalConstraints() > 0)
53	doShake_ = true;
54
55	Globals* simParams = info_->getSimParams();
56
57	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
58	if (simParams->haveConstraintTime()){
59	constraintTime_ = simParams->getConstraintTime();
60	} else {
61	constraintTime_ = simParams->getStatusTime();
62	}
63
64	constraintOutputFile_ = getPrefix(info_->getFinalConfigFileName()) +
65	".constraintForces";
66
67	// create ConstraintWriter
68	constraintWriter_ = new ConstraintWriter(info_,
69	constraintOutputFile_.c_str());
70
71	if (!constraintWriter_){
72	sprintf(painCave.errMsg, "Failed to create ConstraintWriter\n");
73	painCave.isFatal = 1;
74	simError();
75	}
76	}
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
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	}
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	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	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	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
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	"Constraint failure in Shake::constrainA, "
147	"Constraint Fail\n");
148	painCave.isFatal = 1;
149	simError();
150
151	break;
152	case consSuccess:
153	// constrain the pair by moving two elements
154	done = false;
155	consPair->getConsElem1()->setMoving(true);
156	consPair->getConsElem2()->setMoving(true);
157	break;
158	case consAlready:
159	// current pair is already constrained, do not need to
160	// move the elements
161	break;
162	default:
163	sprintf(painCave.errMsg, "ConstraintAlgorithm::doConstraint() "
164	"Error: unrecognized status");
165	painCave.isFatal = 1;
166	simError();
167	break;
168	}
169	}
170	}
171	}//end for(iter->first())
172
173
174	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	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	"Constraint failure in Shake::constrainA, "
189	"too many iterations: %d\n",
190	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
250	// report the constraint force back to the constraint pair:
251	consPair->setConstraintForce(gab);
252	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	// report the constraint force back to the constraint pair:
296	consPair->setConstraintForce(gab);
297	return consSuccess;
298	}
299	else
300	return consAlready;
301	}
302	}