src/flucq/FluctuatingChargeLangevin.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 "FluctuatingChargeLangevin.hpp"
#include "primitives/Molecule.hpp"
#include "utils/simError.h"
#include "utils/PhysicalConstants.hpp"


namespace OpenMD {

  FluctuatingChargeLangevin::FluctuatingChargeLangevin(SimInfo* info) : 
    FluctuatingChargePropagator(info), maxIterNum_(4),
    forceTolerance_(1e-6),
    snap(info->getSnapshotManager()->getCurrentSnapshot()) {    
  }

  void FluctuatingChargeLangevin::initialize() {
    FluctuatingChargePropagator::initialize();  
    if (hasFlucQ_) {
      if (info_->getSimParams()->haveDt()) {
        dt_ = info_->getSimParams()->getDt();
        dt2_ = dt_ * 0.5;
      } else {
        sprintf(painCave.errMsg,
                "FluctuatingChargeLangevin Error: dt is not set\n");
        painCave.isFatal = 1;
        simError();
      }
            
      if (!fqParams_->haveTargetTemp()) {
        sprintf(painCave.errMsg, "You can't use the FluctuatingChargeLangevin "
                "propagator without a flucQ.targetTemp!\n");
        painCave.isFatal = 1;
        painCave.severity = OPENMD_ERROR;
        simError();
      } else {
        targetTemp_ = fqParams_->getTargetTemp();
      }
      
      // We must set tauThermostat.
      
      if (!fqParams_->haveDragCoefficient()) {
        sprintf(painCave.errMsg, "If you use the FluctuatingChargeLangevin\n"
                "\tpropagator, you must set flucQ.dragCoefficient .\n");
        
        painCave.severity = OPENMD_ERROR;
        painCave.isFatal = 1;
        simError();
      } else {
        drag_ = fqParams_->getDragCoefficient();
      }
    }

    variance_ = 2.0 * PhysicalConstants::kb * targetTemp_ * drag_ / dt_;
  }


  void FluctuatingChargeLangevin::moveA() {

    if (!hasFlucQ_) return;

    SimInfo::MoleculeIterator i;
    Molecule::FluctuatingChargeIterator  j;
    Molecule* mol;
    Atom* atom;
    RealType cvel, cpos, cfrc, cmass;

    for (mol = info_->beginMolecule(i); mol != NULL; 
         mol = info_->nextMolecule(i)) {
      for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
           atom = mol->nextFluctuatingCharge(j)) {
        
        cvel = atom->getFlucQVel();
        cpos = atom->getFlucQPos();
        cfrc = atom->getFlucQFrc();
        cmass = atom->getChargeMass();       

        // velocity half step
        cvel += dt2_ * cfrc / cmass;
        // position whole step
        cpos += dt_ * cvel;
        
        atom->setFlucQVel(cvel);
        atom->setFlucQPos(cpos);
      }
    }   
  }

  void FluctuatingChargeLangevin::applyConstraints() {

    if (!hasFlucQ_) return;

    SimInfo::MoleculeIterator i;
    Molecule::FluctuatingChargeIterator  j;
    Molecule* mol;
    Atom* atom;
    RealType cvel, cfrc, cmass, randomForce, frictionForce;
    RealType velStep, oldFF;  // used to test for convergence

    for (mol = info_->beginMolecule(i); mol != NULL; 
         mol = info_->nextMolecule(i)) {
      for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
           atom = mol->nextFluctuatingCharge(j)) {

        cvel = atom->getFlucQVel();
        cfrc = atom->getFlucQFrc();
        cmass = atom->getChargeMass();       

        randomForce = randNumGen_.randNorm(0, variance_ );
        atom->addFlucQFrc(randomForce);        
        
        // What remains contains velocity explicitly, but the velocity
        // required is at the full step: v(t + h), while we have
        // initially the velocity at the half step: v(t + h/2).  We
        // need to iterate to converge the friction force vector.
          
        // this is the velocity at the half-step:
            
        cvel = atom->getFlucQVel();

        // estimate velocity at full-step using everything but
        // friction forces:
        
        cfrc = atom->getFlucQFrc();
        velStep = cvel + dt2_ * cfrc / cmass;

        frictionForce = 0.0;
        //iteration starts here:
        
        for (int k = 0; k < maxIterNum_; k++) {
          
          oldFF = frictionForce;                            
          frictionForce = -drag_ * velStep;
          // re-estimate velocities at full-step using friction forces:
          
          velStep = cvel + dt2_ * (cfrc + frictionForce) / cmass;
          
          // check for convergence
          
          if (fabs(frictionForce - oldFF) <= forceTolerance_)
            break; // iteration ends here
        }
        //cerr << "rand = " << randomForce << " fric = " << frictionForce << "\n";
        atom->addFlucQFrc(frictionForce);
      }
    }        
    fqConstraints_->applyConstraints();
  }

  void FluctuatingChargeLangevin::moveB() {
    if (!hasFlucQ_) return;
    SimInfo::MoleculeIterator i;
    Molecule::FluctuatingChargeIterator  j;
    Molecule* mol;
    Atom* atom;
    RealType cfrc, cvel, cmass;

    for (mol = info_->beginMolecule(i); mol != NULL; 
         mol = info_->nextMolecule(i)) {
      for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
           atom = mol->nextFluctuatingCharge(j)) {        

        cvel =atom->getFlucQVel();
        cfrc = atom->getFlucQFrc();
        cmass = atom->getChargeMass();
                
        // velocity half step
        cvel += (dt2_ * cfrc) / cmass;
        
        atom->setFlucQVel(cvel);
      }
    }    
  }
    
  void FluctuatingChargeLangevin::updateSizes() { }

  RealType FluctuatingChargeLangevin::calcConservedQuantity() {
    return 0.0;
  }
}
Revision:	1850
Committed:	Wed Feb 20 15:39:39 2013 UTC (12 years, 3 months ago) by gezelter
File size:	7578 byte(s)
Log Message:	Fixed a widespread typo in the license
#	User	Rev	Content
1	gezelter	1766	/*
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	1850	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1766	* [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 "FluctuatingChargeLangevin.hpp"
44			#include "primitives/Molecule.hpp"
45			#include "utils/simError.h"
46			#include "utils/PhysicalConstants.hpp"
47
48
49			namespace OpenMD {
50
51			FluctuatingChargeLangevin::FluctuatingChargeLangevin(SimInfo* info) :
52			FluctuatingChargePropagator(info), maxIterNum_(4),
53			forceTolerance_(1e-6),
54			snap(info->getSnapshotManager()->getCurrentSnapshot()) {
55			}
56
57			void FluctuatingChargeLangevin::initialize() {
58			FluctuatingChargePropagator::initialize();
59			if (hasFlucQ_) {
60			if (info_->getSimParams()->haveDt()) {
61			dt_ = info_->getSimParams()->getDt();
62			dt2_ = dt_ * 0.5;
63			} else {
64			sprintf(painCave.errMsg,
65			"FluctuatingChargeLangevin Error: dt is not set\n");
66			painCave.isFatal = 1;
67			simError();
68			}
69
70			if (!fqParams_->haveTargetTemp()) {
71			sprintf(painCave.errMsg, "You can't use the FluctuatingChargeLangevin "
72			"propagator without a flucQ.targetTemp!\n");
73			painCave.isFatal = 1;
74			painCave.severity = OPENMD_ERROR;
75			simError();
76			} else {
77			targetTemp_ = fqParams_->getTargetTemp();
78			}
79
80			// We must set tauThermostat.
81
82			if (!fqParams_->haveDragCoefficient()) {
83			sprintf(painCave.errMsg, "If you use the FluctuatingChargeLangevin\n"
84			"\tpropagator, you must set flucQ.dragCoefficient .\n");
85
86			painCave.severity = OPENMD_ERROR;
87			painCave.isFatal = 1;
88			simError();
89			} else {
90			drag_ = fqParams_->getDragCoefficient();
91			}
92			}
93
94			variance_ = 2.0 * PhysicalConstants::kb * targetTemp_ * drag_ / dt_;
95			}
96
97
98			void FluctuatingChargeLangevin::moveA() {
99
100			if (!hasFlucQ_) return;
101
102			SimInfo::MoleculeIterator i;
103			Molecule::FluctuatingChargeIterator j;
104			Molecule* mol;
105			Atom* atom;
106			RealType cvel, cpos, cfrc, cmass;
107
108			for (mol = info_->beginMolecule(i); mol != NULL;
109			mol = info_->nextMolecule(i)) {
110			for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
111			atom = mol->nextFluctuatingCharge(j)) {
112
113			cvel = atom->getFlucQVel();
114			cpos = atom->getFlucQPos();
115			cfrc = atom->getFlucQFrc();
116			cmass = atom->getChargeMass();
117
118			// velocity half step
119			cvel += dt2_ * cfrc / cmass;
120			// position whole step
121			cpos += dt_ * cvel;
122
123			atom->setFlucQVel(cvel);
124			atom->setFlucQPos(cpos);
125			}
126			}
127			}
128
129			void FluctuatingChargeLangevin::applyConstraints() {
130	gezelter	1768
131			if (!hasFlucQ_) return;
132
133	gezelter	1766	SimInfo::MoleculeIterator i;
134			Molecule::FluctuatingChargeIterator j;
135			Molecule* mol;
136			Atom* atom;
137	gezelter	1826	RealType cvel, cfrc, cmass, randomForce, frictionForce;
138	gezelter	1766	RealType velStep, oldFF; // used to test for convergence
139
140			for (mol = info_->beginMolecule(i); mol != NULL;
141			mol = info_->nextMolecule(i)) {
142			for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
143			atom = mol->nextFluctuatingCharge(j)) {
144
145			cvel = atom->getFlucQVel();
146			cfrc = atom->getFlucQFrc();
147			cmass = atom->getChargeMass();
148
149			randomForce = randNumGen_.randNorm(0, variance_ );
150			atom->addFlucQFrc(randomForce);
151
152			// What remains contains velocity explicitly, but the velocity
153			// required is at the full step: v(t + h), while we have
154			// initially the velocity at the half step: v(t + h/2). We
155			// need to iterate to converge the friction force vector.
156
157			// this is the velocity at the half-step:
158
159			cvel = atom->getFlucQVel();
160
161			// estimate velocity at full-step using everything but
162			// friction forces:
163
164			cfrc = atom->getFlucQFrc();
165			velStep = cvel + dt2_ * cfrc / cmass;
166
167			frictionForce = 0.0;
168			//iteration starts here:
169
170			for (int k = 0; k < maxIterNum_; k++) {
171
172			oldFF = frictionForce;
173			frictionForce = -drag_ * velStep;
174			// re-estimate velocities at full-step using friction forces:
175
176			velStep = cvel + dt2_ * (cfrc + frictionForce) / cmass;
177
178			// check for convergence
179
180			if (fabs(frictionForce - oldFF) <= forceTolerance_)
181			break; // iteration ends here
182			}
183			//cerr << "rand = " << randomForce << " fric = " << frictionForce << "\n";
184			atom->addFlucQFrc(frictionForce);
185			}
186			}
187			fqConstraints_->applyConstraints();
188			}
189
190			void FluctuatingChargeLangevin::moveB() {
191			if (!hasFlucQ_) return;
192			SimInfo::MoleculeIterator i;
193			Molecule::FluctuatingChargeIterator j;
194			Molecule* mol;
195			Atom* atom;
196			RealType cfrc, cvel, cmass;
197
198			for (mol = info_->beginMolecule(i); mol != NULL;
199			mol = info_->nextMolecule(i)) {
200			for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
201			atom = mol->nextFluctuatingCharge(j)) {
202
203			cvel =atom->getFlucQVel();
204			cfrc = atom->getFlucQFrc();
205			cmass = atom->getChargeMass();
206
207			// velocity half step
208			cvel += (dt2_ * cfrc) / cmass;
209
210			atom->setFlucQVel(cvel);
211			}
212			}
213			}
214
215			void FluctuatingChargeLangevin::updateSizes() { }
216
217			RealType FluctuatingChargeLangevin::calcConservedQuantity() {
218			return 0.0;
219			}
220			}