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, 24107 (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:	1826
Committed:	Wed Jan 9 19:41:48 2013 UTC (12 years, 9 months ago) by gezelter
File size:	7577 byte(s)
Log Message:	Cleaning more cruft and unused variables.
#	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, 24107 (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 "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
131	if (!hasFlucQ_) return;
132
133	SimInfo::MoleculeIterator i;
134	Molecule::FluctuatingChargeIterator j;
135	Molecule* mol;
136	Atom* atom;
137	RealType cvel, cfrc, cmass, randomForce, frictionForce;
138	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	}