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


namespace OpenMD {

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

  void FluctuatingChargeNVT::initialize() {
    FluctuatingChargePropagator::initialize();  
    if (hasFlucQ_) {
      if (info_->getSimParams()->haveDt()) {
        dt_ = info_->getSimParams()->getDt();
        dt2_ = dt_ * 0.5;
      } else {
        sprintf(painCave.errMsg,
                "FluctuatingChargeNVT Error: dt is not set\n");
        painCave.isFatal = 1;
        simError();
      }
      
      if (!info_->getSimParams()->getUseIntialExtendedSystemState()) {
        snap->setElectronicThermostat(make_pair(0.0, 0.0));
      }
      
      if (!fqParams_->haveTargetTemp()) {
        sprintf(painCave.errMsg, "You can't use the FluctuatingChargeNVT "
                "propagator without a flucQ.targetTemp!\n");
        painCave.isFatal = 1;
        painCave.severity = OPENMD_ERROR;
        simError();
      } else {
        targetTemp_ = fqParams_->getTargetTemp();
      }
      
      // We must set tauThermostat.
      
      if (!fqParams_->haveTauThermostat()) {
        sprintf(painCave.errMsg, "If you use the FluctuatingChargeNVT\n"
                "\tpropagator, you must set flucQ.tauThermostat .\n");
        
        painCave.severity = OPENMD_ERROR;
        painCave.isFatal = 1;
        simError();
      } else {
        tauThermostat_ = fqParams_->getTauThermostat();
      }
      updateSizes(); 
    }
  }


  void FluctuatingChargeNVT::moveA() {

    if (!hasFlucQ_) return;

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

    pair<RealType, RealType> thermostat = snap->getElectronicThermostat();
    RealType chi = thermostat.first;
    RealType integralOfChidt = thermostat.second;
    RealType instTemp = thermo.getElectronicTemperature();

    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 - dt2_*chi*cvel;                    
        // position whole step
        cpos += dt_ * cvel;
        
        atom->setFlucQVel(cvel);
        atom->setFlucQPos(cpos);
      }
    }
    
    chi += dt2_ * (instTemp / targetTemp_ - 1.0) / 
      (tauThermostat_ * tauThermostat_);

    integralOfChidt += chi * dt2_;
    snap->setElectronicThermostat(make_pair(chi, integralOfChidt));
  }

  void FluctuatingChargeNVT::updateSizes() {
    oldVel_.resize(info_->getNFluctuatingCharges());
  }

  void FluctuatingChargeNVT::moveB() {
    if (!hasFlucQ_) return;
    SimInfo::MoleculeIterator i;
    Molecule::FluctuatingChargeIterator  j;
    Molecule* mol;
    Atom* atom;
    RealType instTemp;
    pair<RealType, RealType> thermostat = snap->getElectronicThermostat();
    RealType chi = thermostat.first;
    RealType oldChi = chi;
    RealType prevChi;
    RealType integralOfChidt = thermostat.second;
    int index;
    RealType cfrc, cvel, cmass;

    index = 0;
    for (mol = info_->beginMolecule(i); mol != NULL; 
         mol = info_->nextMolecule(i)) {
      for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
           atom = mol->nextFluctuatingCharge(j)) {
        
        oldVel_[index] = atom->getFlucQVel();
        ++index;
      }
    }
        
    // do the iteration:
    
    for(int k = 0; k < maxIterNum_; k++) {
      index = 0;
      instTemp = thermo.getElectronicTemperature();
      // evolve chi another half step using the temperature at t + dt/2
      prevChi = chi;
      chi = oldChi + dt2_ * (instTemp / targetTemp_ - 1.0) / 
        (tauThermostat_ * tauThermostat_);

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

          cfrc = atom->getFlucQFrc();
          cvel =atom->getFlucQVel();
          cmass = atom->getChargeMass();
          
          // velocity half step
          cvel = oldVel_[index] + dt2_ * cfrc / cmass - dt2_*chi*oldVel_[index];
          atom->setFlucQVel(cvel);      
          ++index;          
        }
      }
      if (fabs(prevChi - chi) <= chiTolerance_)
        break;
    }
    integralOfChidt += dt2_ * chi;
    snap->setElectronicThermostat(make_pair(chi, integralOfChidt));
  }
  
  void FluctuatingChargeNVT::resetPropagator() {
    if (!hasFlucQ_) return;
    snap->setElectronicThermostat(make_pair(0.0, 0.0));
  }
  
  RealType FluctuatingChargeNVT::calcConservedQuantity() {
    if (!hasFlucQ_) return 0.0;
    pair<RealType, RealType> thermostat = snap->getElectronicThermostat();
    RealType chi = thermostat.first;
    RealType integralOfChidt = thermostat.second;
    RealType fkBT = info_->getNFluctuatingCharges() * 
      PhysicalConstants::kB *targetTemp_;

    RealType thermostat_kinetic = fkBT * tauThermostat_ * tauThermostat_ * 
      chi * chi / (2.0 * PhysicalConstants::energyConvert);

    RealType thermostat_potential = fkBT * integralOfChidt / 
      PhysicalConstants::energyConvert;

    return thermostat_kinetic + thermostat_potential;
  }
}
Revision:	1764
Committed:	Tue Jul 3 18:32:27 2012 UTC (13 years, 3 months ago) by gezelter
File size:	7925 byte(s)
Log Message:	Refactored Snapshot and Stats to use the Accumulator classes. Collected a number of methods into Thermo that belonged there.
#	User	Rev	Content
1	gezelter	1716	/*
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 "FluctuatingChargeNVT.hpp"
44			#include "primitives/Molecule.hpp"
45			#include "utils/simError.h"
46			#include "utils/PhysicalConstants.hpp"
47
48	gezelter	1761
49	gezelter	1716	namespace OpenMD {
50
51	gezelter	1760	FluctuatingChargeNVT::FluctuatingChargeNVT(SimInfo* info) :
52			FluctuatingChargePropagator(info), chiTolerance_ (1e-6),
53	gezelter	1761	maxIterNum_(4), thermo(info),
54	gezelter	1764	snap(info->getSnapshotManager()->getCurrentSnapshot()) {
55	gezelter	1761	}
56
57			void FluctuatingChargeNVT::initialize() {
58			FluctuatingChargePropagator::initialize();
59			if (hasFlucQ_) {
60	gezelter	1739	if (info_->getSimParams()->haveDt()) {
61			dt_ = info_->getSimParams()->getDt();
62			dt2_ = dt_ * 0.5;
63			} else {
64			sprintf(painCave.errMsg,
65			"FluctuatingChargeNVT Error: dt is not set\n");
66			painCave.isFatal = 1;
67			simError();
68			}
69
70			if (!info_->getSimParams()->getUseIntialExtendedSystemState()) {
71	gezelter	1764	snap->setElectronicThermostat(make_pair(0.0, 0.0));
72	gezelter	1739	}
73
74			if (!fqParams_->haveTargetTemp()) {
75			sprintf(painCave.errMsg, "You can't use the FluctuatingChargeNVT "
76			"propagator without a flucQ.targetTemp!\n");
77			painCave.isFatal = 1;
78			painCave.severity = OPENMD_ERROR;
79			simError();
80			} else {
81			targetTemp_ = fqParams_->getTargetTemp();
82			}
83
84			// We must set tauThermostat.
85
86			if (!fqParams_->haveTauThermostat()) {
87			sprintf(painCave.errMsg, "If you use the FluctuatingChargeNVT\n"
88			"\tpropagator, you must set flucQ.tauThermostat .\n");
89	gezelter	1716
90	gezelter	1739	painCave.severity = OPENMD_ERROR;
91			painCave.isFatal = 1;
92			simError();
93			} else {
94			tauThermostat_ = fqParams_->getTauThermostat();
95	gezelter	1716	}
96	gezelter	1761	updateSizes();
97	gezelter	1739	}
98	gezelter	1716	}
99
100
101			void FluctuatingChargeNVT::moveA() {
102
103			if (!hasFlucQ_) return;
104
105			SimInfo::MoleculeIterator i;
106			Molecule::FluctuatingChargeIterator j;
107			Molecule* mol;
108			Atom* atom;
109			RealType cvel, cpos, cfrc, cmass;
110
111	gezelter	1764	pair<RealType, RealType> thermostat = snap->getElectronicThermostat();
112			RealType chi = thermostat.first;
113			RealType integralOfChidt = thermostat.second;
114	gezelter	1716	RealType instTemp = thermo.getElectronicTemperature();
115
116			for (mol = info_->beginMolecule(i); mol != NULL;
117			mol = info_->nextMolecule(i)) {
118			for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
119			atom = mol->nextFluctuatingCharge(j)) {
120
121			cvel = atom->getFlucQVel();
122			cpos = atom->getFlucQPos();
123			cfrc = atom->getFlucQFrc();
124	gezelter	1761	cmass = atom->getChargeMass();
125
126	jmichalk	1735	// velocity half step
127			cvel += dt2_ * cfrc / cmass - dt2_chicvel;
128	gezelter	1716	// position whole step
129			cpos += dt_ * cvel;
130	jmichalk	1735
131	gezelter	1716	atom->setFlucQVel(cvel);
132			atom->setFlucQPos(cpos);
133			}
134			}
135
136			chi += dt2_ * (instTemp / targetTemp_ - 1.0) /
137			(tauThermostat_ * tauThermostat_);
138
139			integralOfChidt += chi * dt2_;
140	gezelter	1764	snap->setElectronicThermostat(make_pair(chi, integralOfChidt));
141	gezelter	1716	}
142
143			void FluctuatingChargeNVT::updateSizes() {
144			oldVel_.resize(info_->getNFluctuatingCharges());
145			}
146
147			void FluctuatingChargeNVT::moveB() {
148			if (!hasFlucQ_) return;
149			SimInfo::MoleculeIterator i;
150			Molecule::FluctuatingChargeIterator j;
151			Molecule* mol;
152			Atom* atom;
153			RealType instTemp;
154	gezelter	1764	pair<RealType, RealType> thermostat = snap->getElectronicThermostat();
155			RealType chi = thermostat.first;
156	gezelter	1716	RealType oldChi = chi;
157			RealType prevChi;
158	gezelter	1764	RealType integralOfChidt = thermostat.second;
159	gezelter	1716	int index;
160			RealType cfrc, cvel, cmass;
161
162			index = 0;
163			for (mol = info_->beginMolecule(i); mol != NULL;
164			mol = info_->nextMolecule(i)) {
165			for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
166			atom = mol->nextFluctuatingCharge(j)) {
167
168			oldVel_[index] = atom->getFlucQVel();
169			++index;
170			}
171			}
172
173			// do the iteration:
174
175			for(int k = 0; k < maxIterNum_; k++) {
176			index = 0;
177			instTemp = thermo.getElectronicTemperature();
178			// evolve chi another half step using the temperature at t + dt/2
179			prevChi = chi;
180			chi = oldChi + dt2_ * (instTemp / targetTemp_ - 1.0) /
181			(tauThermostat_ * tauThermostat_);
182
183			for (mol = info_->beginMolecule(i); mol != NULL;
184			mol = info_->nextMolecule(i)) {
185			for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
186			atom = mol->nextFluctuatingCharge(j)) {
187
188			cfrc = atom->getFlucQFrc();
189			cvel =atom->getFlucQVel();
190			cmass = atom->getChargeMass();
191
192			// velocity half step
193	jmichalk	1735	cvel = oldVel_[index] + dt2_ * cfrc / cmass - dt2_chioldVel_[index];
194	gezelter	1716	atom->setFlucQVel(cvel);
195			++index;
196			}
197			}
198			if (fabs(prevChi - chi) <= chiTolerance_)
199			break;
200			}
201			integralOfChidt += dt2_ * chi;
202	gezelter	1764	snap->setElectronicThermostat(make_pair(chi, integralOfChidt));
203	gezelter	1716	}
204
205			void FluctuatingChargeNVT::resetPropagator() {
206			if (!hasFlucQ_) return;
207	gezelter	1764	snap->setElectronicThermostat(make_pair(0.0, 0.0));
208	gezelter	1716	}
209
210			RealType FluctuatingChargeNVT::calcConservedQuantity() {
211			if (!hasFlucQ_) return 0.0;
212	gezelter	1764	pair<RealType, RealType> thermostat = snap->getElectronicThermostat();
213			RealType chi = thermostat.first;
214			RealType integralOfChidt = thermostat.second;
215	gezelter	1716	RealType fkBT = info_->getNFluctuatingCharges() *
216			PhysicalConstants::kB *targetTemp_;
217
218			RealType thermostat_kinetic = fkBT * tauThermostat_ * tauThermostat_ *
219			chi * chi / (2.0 * PhysicalConstants::energyConvert);
220
221			RealType thermostat_potential = fkBT * integralOfChidt /
222			PhysicalConstants::energyConvert;
223
224			return thermostat_kinetic + thermostat_potential;
225			}
226			}