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), 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();
          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:	1874
Committed:	Wed May 15 15:09:35 2013 UTC (11 years, 11 months ago) by gezelter
File size:	7887 byte(s)
Log Message:	Fixed a bunch of cppcheck warnings.
#	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 "FluctuatingChargeNVT.hpp"
44	#include "primitives/Molecule.hpp"
45	#include "utils/simError.h"
46	#include "utils/PhysicalConstants.hpp"
47
48
49	namespace OpenMD {
50
51	FluctuatingChargeNVT::FluctuatingChargeNVT(SimInfo* info) :
52	FluctuatingChargePropagator(info), chiTolerance_ (1e-6),
53	maxIterNum_(4), thermo(info),
54	snap(info->getSnapshotManager()->getCurrentSnapshot()) {
55	}
56
57	void FluctuatingChargeNVT::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	"FluctuatingChargeNVT Error: dt is not set\n");
66	painCave.isFatal = 1;
67	simError();
68	}
69
70	if (!info_->getSimParams()->getUseIntialExtendedSystemState()) {
71	snap->setElectronicThermostat(make_pair(0.0, 0.0));
72	}
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
90	painCave.severity = OPENMD_ERROR;
91	painCave.isFatal = 1;
92	simError();
93	} else {
94	tauThermostat_ = fqParams_->getTauThermostat();
95	}
96	updateSizes();
97	}
98	}
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	pair<RealType, RealType> thermostat = snap->getElectronicThermostat();
112	RealType chi = thermostat.first;
113	RealType integralOfChidt = thermostat.second;
114	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	cmass = atom->getChargeMass();
125
126	// velocity half step
127	cvel += dt2_ * cfrc / cmass - dt2_chicvel;
128	// position whole step
129	cpos += dt_ * cvel;
130
131	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	snap->setElectronicThermostat(make_pair(chi, integralOfChidt));
141	}
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	pair<RealType, RealType> thermostat = snap->getElectronicThermostat();
155	RealType chi = thermostat.first;
156	RealType oldChi = chi;
157	RealType prevChi;
158	RealType integralOfChidt = thermostat.second;
159	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	cmass = atom->getChargeMass();
190
191	// velocity half step
192	cvel = oldVel_[index] + dt2_ * cfrc / cmass - dt2_chioldVel_[index];
193	atom->setFlucQVel(cvel);
194	++index;
195	}
196	}
197	if (fabs(prevChi - chi) <= chiTolerance_)
198	break;
199	}
200	integralOfChidt += dt2_ * chi;
201	snap->setElectronicThermostat(make_pair(chi, integralOfChidt));
202	}
203
204	void FluctuatingChargeNVT::resetPropagator() {
205	if (!hasFlucQ_) return;
206	snap->setElectronicThermostat(make_pair(0.0, 0.0));
207	}
208
209	RealType FluctuatingChargeNVT::calcConservedQuantity() {
210	if (!hasFlucQ_) return 0.0;
211	pair<RealType, RealType> thermostat = snap->getElectronicThermostat();
212	RealType chi = thermostat.first;
213	RealType integralOfChidt = thermostat.second;
214	RealType fkBT = info_->getNFluctuatingCharges() *
215	PhysicalConstants::kB *targetTemp_;
216
217	RealType thermostat_kinetic = fkBT * tauThermostat_ * tauThermostat_ *
218	chi * chi / (2.0 * PhysicalConstants::energyConvert);
219
220	RealType thermostat_potential = fkBT * integralOfChidt /
221	PhysicalConstants::energyConvert;
222
223	return thermostat_kinetic + thermostat_potential;
224	}
225	}