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, 6 months ago) by gezelter
File size:	9391 byte(s)
Log Message:	Migrated ConstraintWriter calls into Shake
#	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), consTolerance_(1.0e-6), doShake_(false) {
49
50	if (info_->getNGlobalConstraints() > 0)
51	doShake_ = true;
52
53	Globals* simParams = info_->getSimParams();
54
55	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
56	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	}
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
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	}
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	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	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	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
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	"Constraint failure in Shake::constrainA, "
143	"Constraint Fail\n");
144	painCave.isFatal = 1;
145	simError();
146
147	break;
148	case consSuccess:
149	// constrain the pair by moving two elements
150	done = false;
151	consPair->getConsElem1()->setMoving(true);
152	consPair->getConsElem2()->setMoving(true);
153	break;
154	case consAlready:
155	// current pair is already constrained, do not need to
156	// move the elements
157	break;
158	default:
159	sprintf(painCave.errMsg, "ConstraintAlgorithm::doConstraint() "
160	"Error: unrecognized status");
161	painCave.isFatal = 1;
162	simError();
163	break;
164	}
165	}
166	}
167	}//end for(iter->first())
168
169
170	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	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	"Constraint failure in Shake::constrainA, "
185	"too many iterations: %d\n",
186	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
246	// report the constraint force back to the constraint pair:
247	consPair->setConstraintForce(gab);
248	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	// report the constraint force back to the constraint pair:
292	consPair->setConstraintForce(gab);
293	return consSuccess;
294	}
295	else
296	return consAlready;
297	}
298	}