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), 
    currentSnapshot_(info->getSnapshotManager()->getCurrentSnapshot()) {


    if (info_->usesFluctuatingCharges()) {
      if (info_->getNFluctuatingCharges() > 0) {

        hasFlucQ_ = true;
        Globals* simParams = info_->getSimParams();
        FluctuatingChargeParameters* fqParams = simParams->getFluctuatingChargeParameters();

        if (simParams->haveDt()) {
          dt_ = simParams->getDt();
          dt2_ = dt_ * 0.5;
        } else {
          sprintf(painCave.errMsg,
                  "FluctuatingChargeNVT Error: dt is not set\n");
          painCave.isFatal = 1;
          simError();
        }
        
        if (!simParams->getUseIntialExtendedSystemState()) {
          currentSnapshot_->setChiElectronic(0.0);
          currentSnapshot_->setIntegralOfChiElectronicDt(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::initialize() {

    if (!hasFlucQ_) return;

    SimInfo::MoleculeIterator i;
    Molecule::FluctuatingChargeIterator  j;
    Molecule* mol;
    Atom* atom;
    
    for (mol = info_->beginMolecule(i); mol != NULL; 
         mol = info_->nextMolecule(i)) {
      for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
           atom = mol->nextFluctuatingCharge(j)) {
        atom->setFlucQPos(0.0);
        atom->setFlucQVel(0.0);
      }
    }
    
    cerr << "Yeah, you should probably implement this\n";
  }

  void FluctuatingChargeNVT::moveA() {

    if (!hasFlucQ_) return;

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

    RealType chi = currentSnapshot_->getChiElectronic();
    RealType integralOfChidt = currentSnapshot_->getIntegralOfChiElectronicDt();
    RealType instTemp = thermo.getElectronicTemperature();

    cerr << "why are we here?\n";

    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_ *PhysicalConstants::energyConvert/cmass*cfrc - 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_;
    currentSnapshot_->setChiElectronic(chi);
    currentSnapshot_->setIntegralOfChiElectronicDt(integralOfChidt);
       
  }

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

  void FluctuatingChargeNVT::moveB() {
    if (!hasFlucQ_) return;
    SimInfo::MoleculeIterator i;
    Molecule::FluctuatingChargeIterator  j;
    Molecule* mol;
    Atom* atom;
    RealType instTemp;
    RealType chi = currentSnapshot_->getChiElectronic();
    RealType oldChi = chi;
    RealType prevChi;
    RealType integralOfChidt = currentSnapshot_->getIntegralOfChiElectronicDt();
    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_/cmass*PhysicalConstants::energyConvert * cfrc - dt2_*chi*oldVel_[index];
          
          atom->setFlucQVel(cvel);      
          ++index;          
        }
      }
      if (fabs(prevChi - chi) <= chiTolerance_)
        break;
    }
    integralOfChidt += dt2_ * chi;
    currentSnapshot_->setChiElectronic(chi);
    currentSnapshot_->setIntegralOfChiElectronicDt(integralOfChidt);
  }
  
  void FluctuatingChargeNVT::resetPropagator() {
    if (!hasFlucQ_) return;
    currentSnapshot_->setChiElectronic(0.0);
    currentSnapshot_->setIntegralOfChiElectronicDt(0.0);
  }
  
  RealType FluctuatingChargeNVT::calcConservedQuantity() {
    if (!hasFlucQ_) return 0.0;
    RealType chi = currentSnapshot_->getChiElectronic();
    RealType integralOfChidt = currentSnapshot_->getIntegralOfChiElectronicDt();
    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:	1731
Committed:	Thu May 31 12:25:30 2012 UTC (12 years, 11 months ago) by gezelter
File size:	8951 byte(s)
Log Message:	Reorganized source directories, added RNEMD and flucQ blocks for options parsing.
#	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 "FluctuatingChargeNVT.hpp"
44	#include "primitives/Molecule.hpp"
45	#include "utils/simError.h"
46	#include "utils/PhysicalConstants.hpp"
47
48	namespace OpenMD {
49
50	FluctuatingChargeNVT::FluctuatingChargeNVT(SimInfo* info) :
51	FluctuatingChargePropagator(info), chiTolerance_ (1e-6), maxIterNum_(4),
52	thermo(info),
53	currentSnapshot_(info->getSnapshotManager()->getCurrentSnapshot()) {
54
55
56	if (info_->usesFluctuatingCharges()) {
57	if (info_->getNFluctuatingCharges() > 0) {
58
59	hasFlucQ_ = true;
60	Globals* simParams = info_->getSimParams();
61	FluctuatingChargeParameters* fqParams = simParams->getFluctuatingChargeParameters();
62
63	if (simParams->haveDt()) {
64	dt_ = simParams->getDt();
65	dt2_ = dt_ * 0.5;
66	} else {
67	sprintf(painCave.errMsg,
68	"FluctuatingChargeNVT Error: dt is not set\n");
69	painCave.isFatal = 1;
70	simError();
71	}
72
73	if (!simParams->getUseIntialExtendedSystemState()) {
74	currentSnapshot_->setChiElectronic(0.0);
75	currentSnapshot_->setIntegralOfChiElectronicDt(0.0);
76	}
77
78	if (!fqParams->haveTargetTemp()) {
79	sprintf(painCave.errMsg, "You can't use the FluctuatingChargeNVT "
80	"propagator without a flucQ.targetTemp!\n");
81	painCave.isFatal = 1;
82	painCave.severity = OPENMD_ERROR;
83	simError();
84	} else {
85	targetTemp_ = fqParams->getTargetTemp();
86	}
87
88	// We must set tauThermostat.
89
90	if (!fqParams->haveTauThermostat()) {
91	sprintf(painCave.errMsg, "If you use the FluctuatingChargeNVT\n"
92	"\tpropagator, you must set flucQ.tauThermostat .\n");
93
94	painCave.severity = OPENMD_ERROR;
95	painCave.isFatal = 1;
96	simError();
97	} else {
98	tauThermostat_ = fqParams->getTauThermostat();
99	}
100	updateSizes();
101	}
102	}
103	}
104
105	void FluctuatingChargeNVT::initialize() {
106
107	if (!hasFlucQ_) return;
108
109	SimInfo::MoleculeIterator i;
110	Molecule::FluctuatingChargeIterator j;
111	Molecule* mol;
112	Atom* atom;
113
114	for (mol = info_->beginMolecule(i); mol != NULL;
115	mol = info_->nextMolecule(i)) {
116	for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
117	atom = mol->nextFluctuatingCharge(j)) {
118	atom->setFlucQPos(0.0);
119	atom->setFlucQVel(0.0);
120	}
121	}
122
123	cerr << "Yeah, you should probably implement this\n";
124	}
125
126	void FluctuatingChargeNVT::moveA() {
127
128	if (!hasFlucQ_) return;
129
130	SimInfo::MoleculeIterator i;
131	Molecule::FluctuatingChargeIterator j;
132	Molecule* mol;
133	Atom* atom;
134	RealType cvel, cpos, cfrc, cmass;
135
136	RealType chi = currentSnapshot_->getChiElectronic();
137	RealType integralOfChidt = currentSnapshot_->getIntegralOfChiElectronicDt();
138	RealType instTemp = thermo.getElectronicTemperature();
139
140	cerr << "why are we here?\n";
141
142	for (mol = info_->beginMolecule(i); mol != NULL;
143	mol = info_->nextMolecule(i)) {
144	for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
145	atom = mol->nextFluctuatingCharge(j)) {
146
147	cvel = atom->getFlucQVel();
148	cpos = atom->getFlucQPos();
149	cfrc = atom->getFlucQFrc();
150	cmass = atom->getChargeMass();
151
152	// velocity half step
153	cvel += dt2_ PhysicalConstants::energyConvert/cmasscfrc - dt2_chicvel;
154	// position whole step
155	cpos += dt_ * cvel;
156
157	atom->setFlucQVel(cvel);
158	atom->setFlucQPos(cpos);
159	}
160	}
161
162	chi += dt2_ * (instTemp / targetTemp_ - 1.0) /
163	(tauThermostat_ * tauThermostat_);
164
165	integralOfChidt += chi * dt2_;
166	currentSnapshot_->setChiElectronic(chi);
167	currentSnapshot_->setIntegralOfChiElectronicDt(integralOfChidt);
168
169	}
170
171	void FluctuatingChargeNVT::updateSizes() {
172	if (!hasFlucQ_) return;
173	oldVel_.resize(info_->getNFluctuatingCharges());
174	}
175
176	void FluctuatingChargeNVT::moveB() {
177	if (!hasFlucQ_) return;
178	SimInfo::MoleculeIterator i;
179	Molecule::FluctuatingChargeIterator j;
180	Molecule* mol;
181	Atom* atom;
182	RealType instTemp;
183	RealType chi = currentSnapshot_->getChiElectronic();
184	RealType oldChi = chi;
185	RealType prevChi;
186	RealType integralOfChidt = currentSnapshot_->getIntegralOfChiElectronicDt();
187	int index;
188	RealType cfrc, cvel, cmass;
189
190	index = 0;
191	for (mol = info_->beginMolecule(i); mol != NULL;
192	mol = info_->nextMolecule(i)) {
193	for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
194	atom = mol->nextFluctuatingCharge(j)) {
195
196	oldVel_[index] = atom->getFlucQVel();
197	++index;
198	}
199	}
200
201	// do the iteration:
202
203	for(int k = 0; k < maxIterNum_; k++) {
204	index = 0;
205	instTemp = thermo.getElectronicTemperature();
206
207	// evolve chi another half step using the temperature at t + dt/2
208	prevChi = chi;
209	chi = oldChi + dt2_ * (instTemp / targetTemp_ - 1.0) /
210	(tauThermostat_ * tauThermostat_);
211
212	for (mol = info_->beginMolecule(i); mol != NULL;
213	mol = info_->nextMolecule(i)) {
214	for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
215	atom = mol->nextFluctuatingCharge(j)) {
216
217	cfrc = atom->getFlucQFrc();
218	cvel =atom->getFlucQVel();
219	cmass = atom->getChargeMass();
220
221	// velocity half step
222	cvel = oldVel_[index] + dt2_/cmassPhysicalConstants::energyConvert cfrc - dt2_chioldVel_[index];
223
224	atom->setFlucQVel(cvel);
225	++index;
226	}
227	}
228	if (fabs(prevChi - chi) <= chiTolerance_)
229	break;
230	}
231	integralOfChidt += dt2_ * chi;
232	currentSnapshot_->setChiElectronic(chi);
233	currentSnapshot_->setIntegralOfChiElectronicDt(integralOfChidt);
234	}
235
236	void FluctuatingChargeNVT::resetPropagator() {
237	if (!hasFlucQ_) return;
238	currentSnapshot_->setChiElectronic(0.0);
239	currentSnapshot_->setIntegralOfChiElectronicDt(0.0);
240	}
241
242	RealType FluctuatingChargeNVT::calcConservedQuantity() {
243	if (!hasFlucQ_) return 0.0;
244	RealType chi = currentSnapshot_->getChiElectronic();
245	RealType integralOfChidt = currentSnapshot_->getIntegralOfChiElectronicDt();
246	RealType fkBT = info_->getNFluctuatingCharges() *
247	PhysicalConstants::kB *targetTemp_;
248
249	RealType thermostat_kinetic = fkBT * tauThermostat_ * tauThermostat_ *
250	chi * chi / (2.0 * PhysicalConstants::energyConvert);
251
252	RealType thermostat_potential = fkBT * integralOfChidt /
253	PhysicalConstants::energyConvert;
254
255	return thermostat_kinetic + thermostat_potential;
256	}
257	}