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;
    
    if (!doShake_) return;

    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:	1989
Committed:	Fri Apr 18 20:07:09 2014 UTC (11 years, 6 months ago) by gezelter
File size:	9564 byte(s)
Log Message:	Fixed the creation of constraintForces files on simulations which don't have constraints
#	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	if (!doShake_) return;
56
57	Globals* simParams = info_->getSimParams();
58
59	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
60	if (simParams->haveConstraintTime()){
61	constraintTime_ = simParams->getConstraintTime();
62	} else {
63	constraintTime_ = simParams->getStatusTime();
64	}
65
66	constraintOutputFile_ = getPrefix(info_->getFinalConfigFileName()) +
67	".constraintForces";
68
69	// create ConstraintWriter
70	constraintWriter_ = new ConstraintWriter(info_,
71	constraintOutputFile_.c_str());
72
73	if (!constraintWriter_){
74	sprintf(painCave.errMsg, "Failed to create ConstraintWriter\n");
75	painCave.isFatal = 1;
76	simError();
77	}
78	}
79
80	void Shake::constraintR() {
81	if (!doShake_) return;
82	doConstraint(&Shake::constraintPairR);
83	}
84	void Shake::constraintF() {
85	if (!doShake_) return;
86	doConstraint(&Shake::constraintPairF);
87
88	if (currentSnapshot_->getTime() >= currConstraintTime_){
89	Molecule* mol;
90	SimInfo::MoleculeIterator mi;
91	ConstraintPair* consPair;
92	Molecule::ConstraintPairIterator cpi;
93	std::list<ConstraintPair*> constraints;
94	for (mol = info_->beginMolecule(mi); mol != NULL;
95	mol = info_->nextMolecule(mi)) {
96	for (consPair = mol->beginConstraintPair(cpi); consPair != NULL;
97	consPair = mol->nextConstraintPair(cpi)) {
98
99	constraints.push_back(consPair);
100	}
101	}
102
103	constraintWriter_->writeConstraintForces(constraints);
104	currConstraintTime_ += constraintTime_;
105	}
106	}
107
108	void Shake::doConstraint(ConstraintPairFuncPtr func) {
109	if (!doShake_) return;
110
111	Molecule* mol;
112	SimInfo::MoleculeIterator mi;
113	ConstraintElem* consElem;
114	Molecule::ConstraintElemIterator cei;
115	ConstraintPair* consPair;
116	Molecule::ConstraintPairIterator cpi;
117
118	for (mol = info_->beginMolecule(mi); mol != NULL;
119	mol = info_->nextMolecule(mi)) {
120	for (consElem = mol->beginConstraintElem(cei); consElem != NULL;
121	consElem = mol->nextConstraintElem(cei)) {
122	consElem->setMoved(true);
123	consElem->setMoving(false);
124	}
125	}
126
127	//main loop of constraint algorithm
128	bool done = false;
129	int iteration = 0;
130	while(!done && iteration < maxConsIteration_){
131	done = true;
132
133	//loop over every constraint pair
134
135	for (mol = info_->beginMolecule(mi); mol != NULL;
136	mol = info_->nextMolecule(mi)) {
137	for (consPair = mol->beginConstraintPair(cpi); consPair != NULL;
138	consPair = mol->nextConstraintPair(cpi)) {
139
140
141	//dispatch constraint algorithm
142	if(consPair->isMoved()) {
143	int exeStatus = (this->*func)(consPair);
144
145	switch(exeStatus){
146	case consFail:
147	sprintf(painCave.errMsg,
148	"Constraint failure in Shake::constrainA, "
149	"Constraint Fail\n");
150	painCave.isFatal = 1;
151	simError();
152
153	break;
154	case consSuccess:
155	// constrain the pair by moving two elements
156	done = false;
157	consPair->getConsElem1()->setMoving(true);
158	consPair->getConsElem2()->setMoving(true);
159	break;
160	case consAlready:
161	// current pair is already constrained, do not need to
162	// move the elements
163	break;
164	default:
165	sprintf(painCave.errMsg, "ConstraintAlgorithm::doConstraint() "
166	"Error: unrecognized status");
167	painCave.isFatal = 1;
168	simError();
169	break;
170	}
171	}
172	}
173	}//end for(iter->first())
174
175
176	for (mol = info_->beginMolecule(mi); mol != NULL;
177	mol = info_->nextMolecule(mi)) {
178	for (consElem = mol->beginConstraintElem(cei); consElem != NULL;
179	consElem = mol->nextConstraintElem(cei)) {
180	consElem->setMoved(consElem->getMoving());
181	consElem->setMoving(false);
182	}
183	}
184
185	iteration++;
186	}//end while
187
188	if (!done){
189	sprintf(painCave.errMsg,
190	"Constraint failure in Shake::constrainA, "
191	"too many iterations: %d\n",
192	iteration);
193	painCave.isFatal = 1;
194	simError();
195	}
196	}
197
198	/**
199	* remove constraint force along the bond direction
200	*/
201	int Shake::constraintPairR(ConstraintPair* consPair){
202
203	ConstraintElem* consElem1 = consPair->getConsElem1();
204	ConstraintElem* consElem2 = consPair->getConsElem2();
205
206	Vector3d posA = consElem1->getPos();
207	Vector3d posB = consElem2->getPos();
208
209	Vector3d pab = posA -posB;
210
211	//periodic boundary condition
212
213	currentSnapshot_->wrapVector(pab);
214
215	RealType pabsq = pab.lengthSquare();
216
217	RealType rabsq = consPair->getConsDistSquare();
218	RealType diffsq = rabsq - pabsq;
219
220	// the original rattle code from alan tidesley
221	if (fabs(diffsq) > (consTolerance_ * rabsq * 2)){
222
223	Vector3d oldPosA = consElem1->getPrevPos();
224	Vector3d oldPosB = consElem2->getPrevPos();
225
226	Vector3d rab = oldPosA - oldPosB;
227
228	currentSnapshot_->wrapVector(rab);
229
230	RealType rpab = dot(rab, pab);
231	RealType rpabsq = rpab * rpab;
232
233	if (rpabsq < (rabsq * -diffsq)){
234	return consFail;
235	}
236
237	RealType rma = 1.0 / consElem1->getMass();
238	RealType rmb = 1.0 / consElem2->getMass();
239
240	RealType gab = diffsq / (2.0 * (rma + rmb) * rpab);
241
242	Vector3d delta = rab * gab;
243
244	//set atom1's position
245	posA += rma * delta;
246	consElem1->setPos(posA);
247
248	//set atom2's position
249	posB -= rmb * delta;
250	consElem2->setPos(posB);
251
252	// report the constraint force back to the constraint pair:
253	consPair->setConstraintForce(gab);
254	return consSuccess;
255	}
256	else
257	return consAlready;
258	}
259
260	/**
261	* remove constraint force along the bond direction
262	*/
263	int Shake::constraintPairF(ConstraintPair* consPair){
264	ConstraintElem* consElem1 = consPair->getConsElem1();
265	ConstraintElem* consElem2 = consPair->getConsElem2();
266
267	Vector3d posA = consElem1->getPos();
268	Vector3d posB = consElem2->getPos();
269
270	Vector3d rab = posA - posB;
271
272	currentSnapshot_->wrapVector(rab);
273
274	Vector3d frcA = consElem1->getFrc();
275	Vector3d frcB = consElem2->getFrc();
276
277	RealType rma = 1.0 / consElem1->getMass();
278	RealType rmb = 1.0 / consElem2->getMass();
279
280	Vector3d fpab = frcA * rma - frcB * rmb;
281
282	RealType gab = fpab.lengthSquare();
283	if (gab < 1.0) gab = 1.0;
284
285	RealType rabsq = rab.lengthSquare();
286	RealType rfab = dot(rab, fpab);
287
288	if (fabs(rfab) > sqrt(rabsqgab) consTolerance_){
289	gab = -rfab / (rabsq * (rma + rmb));
290
291	frcA += rab*gab;
292	frcB -= rab*gab;
293
294	consElem1->setFrc(frcA);
295	consElem2->setFrc(frcB);
296
297	// report the constraint force back to the constraint pair:
298	consPair->setConstraintForce(gab);
299	return consSuccess;
300	}
301	else
302	return consAlready;
303	}
304	}