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, 234107 (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), maxIterNum_(4), chiTolerance_ (1e-6), 
    snap(info->getSnapshotManager()->getCurrentSnapshot()), thermo(info) {  
  }

  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();
          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:	2071
Committed:	Sat Mar 7 21:41:51 2015 UTC (10 years, 4 months ago) by gezelter
File size:	7883 byte(s)
Log Message:	Reducing the number of warnings when using g++ to compile.
#	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	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1716	* [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	gezelter	2071	FluctuatingChargePropagator(info), maxIterNum_(4), chiTolerance_ (1e-6),
53			snap(info->getSnapshotManager()->getCurrentSnapshot()), thermo(info) {
54	gezelter	1761	}
55
56			void FluctuatingChargeNVT::initialize() {
57			FluctuatingChargePropagator::initialize();
58			if (hasFlucQ_) {
59	gezelter	1739	if (info_->getSimParams()->haveDt()) {
60			dt_ = info_->getSimParams()->getDt();
61			dt2_ = dt_ * 0.5;
62			} else {
63			sprintf(painCave.errMsg,
64			"FluctuatingChargeNVT Error: dt is not set\n");
65			painCave.isFatal = 1;
66			simError();
67			}
68
69			if (!info_->getSimParams()->getUseIntialExtendedSystemState()) {
70	gezelter	1764	snap->setElectronicThermostat(make_pair(0.0, 0.0));
71	gezelter	1739	}
72
73			if (!fqParams_->haveTargetTemp()) {
74			sprintf(painCave.errMsg, "You can't use the FluctuatingChargeNVT "
75			"propagator without a flucQ.targetTemp!\n");
76			painCave.isFatal = 1;
77			painCave.severity = OPENMD_ERROR;
78			simError();
79			} else {
80			targetTemp_ = fqParams_->getTargetTemp();
81			}
82
83			// We must set tauThermostat.
84
85			if (!fqParams_->haveTauThermostat()) {
86			sprintf(painCave.errMsg, "If you use the FluctuatingChargeNVT\n"
87			"\tpropagator, you must set flucQ.tauThermostat .\n");
88	gezelter	1716
89	gezelter	1739	painCave.severity = OPENMD_ERROR;
90			painCave.isFatal = 1;
91			simError();
92			} else {
93			tauThermostat_ = fqParams_->getTauThermostat();
94	gezelter	1716	}
95	gezelter	1761	updateSizes();
96	gezelter	1739	}
97	gezelter	1716	}
98
99
100			void FluctuatingChargeNVT::moveA() {
101
102			if (!hasFlucQ_) return;
103
104			SimInfo::MoleculeIterator i;
105			Molecule::FluctuatingChargeIterator j;
106			Molecule* mol;
107			Atom* atom;
108			RealType cvel, cpos, cfrc, cmass;
109
110	gezelter	1764	pair<RealType, RealType> thermostat = snap->getElectronicThermostat();
111			RealType chi = thermostat.first;
112			RealType integralOfChidt = thermostat.second;
113	gezelter	1716	RealType instTemp = thermo.getElectronicTemperature();
114
115			for (mol = info_->beginMolecule(i); mol != NULL;
116			mol = info_->nextMolecule(i)) {
117			for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
118			atom = mol->nextFluctuatingCharge(j)) {
119
120			cvel = atom->getFlucQVel();
121			cpos = atom->getFlucQPos();
122			cfrc = atom->getFlucQFrc();
123	gezelter	1761	cmass = atom->getChargeMass();
124
125	jmichalk	1735	// velocity half step
126			cvel += dt2_ * cfrc / cmass - dt2_chicvel;
127	gezelter	1716	// position whole step
128			cpos += dt_ * cvel;
129	jmichalk	1735
130	gezelter	1716	atom->setFlucQVel(cvel);
131			atom->setFlucQPos(cpos);
132			}
133			}
134
135			chi += dt2_ * (instTemp / targetTemp_ - 1.0) /
136			(tauThermostat_ * tauThermostat_);
137
138			integralOfChidt += chi * dt2_;
139	gezelter	1764	snap->setElectronicThermostat(make_pair(chi, integralOfChidt));
140	gezelter	1716	}
141
142			void FluctuatingChargeNVT::updateSizes() {
143			oldVel_.resize(info_->getNFluctuatingCharges());
144			}
145
146			void FluctuatingChargeNVT::moveB() {
147			if (!hasFlucQ_) return;
148			SimInfo::MoleculeIterator i;
149			Molecule::FluctuatingChargeIterator j;
150			Molecule* mol;
151			Atom* atom;
152			RealType instTemp;
153	gezelter	1764	pair<RealType, RealType> thermostat = snap->getElectronicThermostat();
154			RealType chi = thermostat.first;
155	gezelter	1716	RealType oldChi = chi;
156			RealType prevChi;
157	gezelter	1764	RealType integralOfChidt = thermostat.second;
158	gezelter	1716	int index;
159			RealType cfrc, cvel, cmass;
160
161			index = 0;
162			for (mol = info_->beginMolecule(i); mol != NULL;
163			mol = info_->nextMolecule(i)) {
164			for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
165			atom = mol->nextFluctuatingCharge(j)) {
166
167			oldVel_[index] = atom->getFlucQVel();
168			++index;
169			}
170			}
171
172			// do the iteration:
173
174			for(int k = 0; k < maxIterNum_; k++) {
175			index = 0;
176			instTemp = thermo.getElectronicTemperature();
177			// evolve chi another half step using the temperature at t + dt/2
178			prevChi = chi;
179			chi = oldChi + dt2_ * (instTemp / targetTemp_ - 1.0) /
180			(tauThermostat_ * tauThermostat_);
181
182			for (mol = info_->beginMolecule(i); mol != NULL;
183			mol = info_->nextMolecule(i)) {
184			for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
185			atom = mol->nextFluctuatingCharge(j)) {
186
187			cfrc = atom->getFlucQFrc();
188			cmass = atom->getChargeMass();
189
190			// velocity half step
191	jmichalk	1735	cvel = oldVel_[index] + dt2_ * cfrc / cmass - dt2_chioldVel_[index];
192	gezelter	1716	atom->setFlucQVel(cvel);
193			++index;
194			}
195			}
196			if (fabs(prevChi - chi) <= chiTolerance_)
197			break;
198			}
199			integralOfChidt += dt2_ * chi;
200	gezelter	1764	snap->setElectronicThermostat(make_pair(chi, integralOfChidt));
201	gezelter	1716	}
202
203			void FluctuatingChargeNVT::resetPropagator() {
204			if (!hasFlucQ_) return;
205	gezelter	1764	snap->setElectronicThermostat(make_pair(0.0, 0.0));
206	gezelter	1716	}
207
208			RealType FluctuatingChargeNVT::calcConservedQuantity() {
209			if (!hasFlucQ_) return 0.0;
210	gezelter	1764	pair<RealType, RealType> thermostat = snap->getElectronicThermostat();
211			RealType chi = thermostat.first;
212			RealType integralOfChidt = thermostat.second;
213	gezelter	1716	RealType fkBT = info_->getNFluctuatingCharges() *
214			PhysicalConstants::kB *targetTemp_;
215
216			RealType thermostat_kinetic = fkBT * tauThermostat_ * tauThermostat_ *
217			chi * chi / (2.0 * PhysicalConstants::energyConvert);
218
219			RealType thermostat_potential = fkBT * integralOfChidt /
220			PhysicalConstants::energyConvert;
221
222			return thermostat_kinetic + thermostat_potential;
223			}
224			}