src/nonbonded/Morse.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]  Vardeman & Gezelter, in progress (2009).                        
 */

#include <stdio.h>
#include <string.h>

#include <cmath>
#include "nonbonded/Morse.hpp"
#include "utils/simError.h"
#include "types/NonBondedInteractionType.hpp"

using namespace std;

namespace OpenMD {

  Morse::Morse() : name_("Morse"), initialized_(false), forceField_(NULL), 
                   shiftedPot_(false), shiftedFrc_(false) {}
  
  void Morse::initialize() {    

    stringToEnumMap_["shiftedMorse"] = shiftedMorse;
    stringToEnumMap_["repulsiveMorse"] = repulsiveMorse;

    ForceField::NonBondedInteractionTypeContainer* nbiTypes = forceField_->getNonBondedInteractionTypes();
    ForceField::NonBondedInteractionTypeContainer::MapTypeIterator j;
    NonBondedInteractionType* nbt;

    for (nbt = nbiTypes->beginType(j); nbt != NULL; 
         nbt = nbiTypes->nextType(j)) {
      
      if (nbt->isMorse()) {
        
        pair<AtomType*, AtomType*> atypes = nbt->getAtomTypes();
        
        GenericData* data = nbt->getPropertyByName("Morse");
        if (data == NULL) {
          sprintf( painCave.errMsg, "Morse::initialize could not find\n"
                   "\tMorse parameters for %s - %s interaction.\n", 
                   atypes.first->getName().c_str(),
                   atypes.second->getName().c_str());
          painCave.severity = OPENMD_ERROR;
          painCave.isFatal = 1;
          simError(); 
        }
        
        MorseData* morseData = dynamic_cast<MorseData*>(data);
        if (morseData == NULL) {
          sprintf( painCave.errMsg,
                   "Morse::initialize could not convert GenericData to\n"
                   "\tMorseData for %s - %s interaction.\n", 
                   atypes.first->getName().c_str(),
                   atypes.second->getName().c_str());
          painCave.severity = OPENMD_ERROR;
          painCave.isFatal = 1;
          simError();          
        }
        
        MorseParam morseParam = morseData->getData();

        RealType De = morseParam.De;
        RealType Re = morseParam.Re;
        RealType beta = morseParam.beta;
        string interactionType = morseParam.interactionType;

        toUpper(interactionType);
        map<string, MorseInteractionType>::iterator i;
        i = stringToEnumMap_.find(interactionType);
        if (i != stringToEnumMap_.end()) { 
          addExplicitInteraction(atypes.first, atypes.second, 
                                 De, Re, beta, i->second );
        } else {
          sprintf( painCave.errMsg,
                   "Morse::initialize found unknown Morse interaction type\n"
                   "\t(%s) for %s - %s interaction.\n", 
                   morseParam.interactionType.c_str(),
                   atypes.first->getName().c_str(),
                   atypes.second->getName().c_str());
          painCave.severity = OPENMD_ERROR;
          painCave.isFatal = 1;
          simError();          
        }
      }
    }  
    initialized_ = true;
  }
      
  void Morse::addExplicitInteraction(AtomType* atype1, AtomType* atype2, 
                                     RealType De, RealType Re, RealType beta, 
                                     MorseInteractionType mit) {

    MorseInteractionData mixer;
    mixer.De = De;
    mixer.Re = Re;
    mixer.beta = beta;
    mixer.interactionType = mit;

    pair<AtomType*, AtomType*> key1, key2;
    key1 = make_pair(atype1, atype2);
    key2 = make_pair(atype2, atype1);
    
    MixingMap[key1] = mixer;
    if (key2 != key1) {
      MixingMap[key2] = mixer;
    }    
  }
  
  void Morse::calcForce(InteractionData idat) {

    if (!initialized_) initialize();
    
    pair<AtomType*, AtomType*> key = make_pair(idat.atype1, idat.atype2); 
    map<pair<AtomType*, AtomType*>, MorseInteractionData>::iterator it;
    it = MixingMap.find(key);
    if (it != MixingMap.end()) {
      MorseInteractionData mixer = (*it).second;
      
      RealType myPot = 0.0;
      RealType myPotC = 0.0;
      RealType myDeriv = 0.0;
      RealType myDerivC = 0.0;
      
      RealType De = mixer.De;
      RealType Re = mixer.Re;
      RealType beta = mixer.beta;
      MorseInteractionType interactionType = mixer.interactionType;
      
      // V(r) = D_e exp(-a(r-re)(exp(-a(r-re))-2)
      
      RealType expt     = -beta*(idat.rij - Re);
      RealType expfnc   = exp(expt);
      RealType expfnc2  = expfnc*expfnc;
      
      RealType exptC = 0.0;
      RealType expfncC = 0.0;
      RealType expfnc2C = 0.0;
      
      if (Morse::shiftedPot_ || Morse::shiftedFrc_) {
        exptC     = -beta*(idat.rcut - Re);
        expfncC   = exp(exptC);
        expfnc2C  = expfncC*expfncC;
      }
      
      
      switch(interactionType) {
      case shiftedMorse : {
        
        myPot  = De * (expfnc2  - 2.0 * expfnc);
        myDeriv   = 2.0 * De * beta * (expfnc - expfnc2);
        
        if (Morse::shiftedPot_) {
          myPotC = De * (expfnc2C - 2.0 * expfncC);
          myDerivC = 0.0;
        } else if (Morse::shiftedFrc_) {
          myPotC = De * (expfnc2C - 2.0 * expfncC);
          myDerivC  = 2.0 * De * beta * (expfnc2C - expfnc2C);
          myPotC += myDerivC * (idat.rij - idat.rcut);
        } else {
          myPotC = 0.0;
          myDerivC = 0.0;
        }
        
        break;
      }
      case repulsiveMorse : {
        
        myPot  = De * expfnc2;
        myDeriv  = -2.0 * De * beta * expfnc2;
        
        if (Morse::shiftedPot_) {
          myPotC = De * expfnc2C;
          myDerivC = 0.0;
        } else if (Morse::shiftedFrc_) {
          myPotC = De * expfnc2C;
          myDerivC = -2.0 * De * beta * expfnc2C;
          myPotC += myDerivC * (idat.rij - idat.rcut);
        } else {
          myPotC = 0.0;
          myDerivC = 0.0;
        }
        
        break;
      }
      }
      
      RealType pot_temp = idat.vdwMult * (myPot - myPotC);
      idat.vpair += pot_temp;
      
      RealType dudr = idat.sw * idat.vdwMult * (myDeriv - myDerivC);
      
      idat.pot += idat.sw * pot_temp;
      idat.f1 = idat.d * dudr / idat.rij;
    }
    return;
    
  }
    
  RealType Morse::getSuggestedCutoffRadius(AtomType* at1, AtomType* at2) {
    if (!initialized_) initialize();   
    pair<AtomType*, AtomType*> key = make_pair(at1, at2); 
    map<pair<AtomType*, AtomType*>, MorseInteractionData>::iterator it;
    it = MixingMap.find(key);
    if (it == MixingMap.end()) 
      return 0.0;
    else  {
      MorseInteractionData mixer = (*it).second;

      RealType Re = mixer.Re;
      RealType beta = mixer.beta;
      // This value of the r corresponds to an energy about 1.48% of 
      // the energy at the bottom of the Morse well.  For comparison, the
      // Lennard-Jones function is about 1.63% of it's minimum value at
      // a distance of 2.5 sigma.
      return (4.9 + beta * Re) / beta;
    }
  }
}

Revision:	1505
Committed:	Sun Oct 3 22:18:59 2010 UTC (15 years, 1 month ago) by gezelter
File size:	8922 byte(s)
Log Message:	Less busted than it was on last check-in, but still won't completely build.
#	User	Rev	Content
1	gezelter	1501	/*
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] Vardeman & Gezelter, in progress (2009).
40			*/
41
42			#include <stdio.h>
43			#include <string.h>
44
45			#include <cmath>
46			#include "nonbonded/Morse.hpp"
47			#include "utils/simError.h"
48			#include "types/NonBondedInteractionType.hpp"
49
50			using namespace std;
51
52			namespace OpenMD {
53
54	gezelter	1502	Morse::Morse() : name_("Morse"), initialized_(false), forceField_(NULL),
55			shiftedPot_(false), shiftedFrc_(false) {}
56	gezelter	1501
57			void Morse::initialize() {
58
59			stringToEnumMap_["shiftedMorse"] = shiftedMorse;
60			stringToEnumMap_["repulsiveMorse"] = repulsiveMorse;
61
62			ForceField::NonBondedInteractionTypeContainer* nbiTypes = forceField_->getNonBondedInteractionTypes();
63			ForceField::NonBondedInteractionTypeContainer::MapTypeIterator j;
64			NonBondedInteractionType* nbt;
65
66			for (nbt = nbiTypes->beginType(j); nbt != NULL;
67			nbt = nbiTypes->nextType(j)) {
68
69			if (nbt->isMorse()) {
70
71			pair<AtomType, AtomType> atypes = nbt->getAtomTypes();
72
73			GenericData* data = nbt->getPropertyByName("Morse");
74			if (data == NULL) {
75			sprintf( painCave.errMsg, "Morse::initialize could not find\n"
76			"\tMorse parameters for %s - %s interaction.\n",
77			atypes.first->getName().c_str(),
78			atypes.second->getName().c_str());
79			painCave.severity = OPENMD_ERROR;
80			painCave.isFatal = 1;
81			simError();
82			}
83
84			MorseData* morseData = dynamic_cast<MorseData*>(data);
85			if (morseData == NULL) {
86			sprintf( painCave.errMsg,
87			"Morse::initialize could not convert GenericData to\n"
88			"\tMorseData for %s - %s interaction.\n",
89			atypes.first->getName().c_str(),
90			atypes.second->getName().c_str());
91			painCave.severity = OPENMD_ERROR;
92			painCave.isFatal = 1;
93			simError();
94			}
95
96			MorseParam morseParam = morseData->getData();
97
98			RealType De = morseParam.De;
99			RealType Re = morseParam.Re;
100			RealType beta = morseParam.beta;
101			string interactionType = morseParam.interactionType;
102
103			toUpper(interactionType);
104			map<string, MorseInteractionType>::iterator i;
105			i = stringToEnumMap_.find(interactionType);
106			if (i != stringToEnumMap_.end()) {
107			addExplicitInteraction(atypes.first, atypes.second,
108			De, Re, beta, i->second );
109			} else {
110			sprintf( painCave.errMsg,
111			"Morse::initialize found unknown Morse interaction type\n"
112			"\t(%s) for %s - %s interaction.\n",
113			morseParam.interactionType.c_str(),
114			atypes.first->getName().c_str(),
115			atypes.second->getName().c_str());
116			painCave.severity = OPENMD_ERROR;
117			painCave.isFatal = 1;
118			simError();
119			}
120			}
121			}
122			initialized_ = true;
123			}
124
125			void Morse::addExplicitInteraction(AtomType* atype1, AtomType* atype2,
126			RealType De, RealType Re, RealType beta,
127			MorseInteractionType mit) {
128
129			MorseInteractionData mixer;
130			mixer.De = De;
131			mixer.Re = Re;
132			mixer.beta = beta;
133			mixer.interactionType = mit;
134
135			pair<AtomType, AtomType> key1, key2;
136			key1 = make_pair(atype1, atype2);
137			key2 = make_pair(atype2, atype1);
138
139			MixingMap[key1] = mixer;
140			if (key2 != key1) {
141			MixingMap[key2] = mixer;
142			}
143			}
144
145	gezelter	1502	void Morse::calcForce(InteractionData idat) {
146	gezelter	1501
147			if (!initialized_) initialize();
148
149	gezelter	1505	pair<AtomType, AtomType> key = make_pair(idat.atype1, idat.atype2);
150			map<pair<AtomType, AtomType>, MorseInteractionData>::iterator it;
151			it = MixingMap.find(key);
152			if (it != MixingMap.end()) {
153			MorseInteractionData mixer = (*it).second;
154
155			RealType myPot = 0.0;
156			RealType myPotC = 0.0;
157			RealType myDeriv = 0.0;
158			RealType myDerivC = 0.0;
159
160			RealType De = mixer.De;
161			RealType Re = mixer.Re;
162			RealType beta = mixer.beta;
163			MorseInteractionType interactionType = mixer.interactionType;
164
165			// V(r) = D_e exp(-a(r-re)(exp(-a(r-re))-2)
166
167			RealType expt = -beta*(idat.rij - Re);
168			RealType expfnc = exp(expt);
169			RealType expfnc2 = expfnc*expfnc;
170
171			RealType exptC = 0.0;
172			RealType expfncC = 0.0;
173			RealType expfnc2C = 0.0;
174
175			if (Morse::shiftedPot_ \|\| Morse::shiftedFrc_) {
176			exptC = -beta*(idat.rcut - Re);
177			expfncC = exp(exptC);
178			expfnc2C = expfncC*expfncC;
179	gezelter	1501	}
180	gezelter	1505
181
182			switch(interactionType) {
183			case shiftedMorse : {
184
185			myPot = De * (expfnc2 - 2.0 * expfnc);
186			myDeriv = 2.0 * De * beta * (expfnc - expfnc2);
187
188			if (Morse::shiftedPot_) {
189			myPotC = De * (expfnc2C - 2.0 * expfncC);
190			myDerivC = 0.0;
191			} else if (Morse::shiftedFrc_) {
192			myPotC = De * (expfnc2C - 2.0 * expfncC);
193			myDerivC = 2.0 * De * beta * (expfnc2C - expfnc2C);
194			myPotC += myDerivC * (idat.rij - idat.rcut);
195			} else {
196			myPotC = 0.0;
197			myDerivC = 0.0;
198			}
199
200			break;
201	gezelter	1501	}
202	gezelter	1505	case repulsiveMorse : {
203
204			myPot = De * expfnc2;
205			myDeriv = -2.0 * De * beta * expfnc2;
206
207			if (Morse::shiftedPot_) {
208			myPotC = De * expfnc2C;
209			myDerivC = 0.0;
210			} else if (Morse::shiftedFrc_) {
211			myPotC = De * expfnc2C;
212			myDerivC = -2.0 * De * beta * expfnc2C;
213			myPotC += myDerivC * (idat.rij - idat.rcut);
214			} else {
215			myPotC = 0.0;
216			myDerivC = 0.0;
217			}
218
219			break;
220			}
221			}
222
223			RealType pot_temp = idat.vdwMult * (myPot - myPotC);
224			idat.vpair += pot_temp;
225
226			RealType dudr = idat.sw * idat.vdwMult * (myDeriv - myDerivC);
227
228			idat.pot += idat.sw * pot_temp;
229			idat.f1 = idat.d * dudr / idat.rij;
230	gezelter	1501	}
231	gezelter	1505	return;
232	gezelter	1501
233	gezelter	1505	}
234
235			RealType Morse::getSuggestedCutoffRadius(AtomType* at1, AtomType* at2) {
236			if (!initialized_) initialize();
237			pair<AtomType, AtomType> key = make_pair(at1, at2);
238			map<pair<AtomType, AtomType>, MorseInteractionData>::iterator it;
239			it = MixingMap.find(key);
240			if (it == MixingMap.end())
241			return 0.0;
242			else {
243			MorseInteractionData mixer = (*it).second;
244	gezelter	1501
245	gezelter	1505	RealType Re = mixer.Re;
246			RealType beta = mixer.beta;
247			// This value of the r corresponds to an energy about 1.48% of
248			// the energy at the bottom of the Morse well. For comparison, the
249			// Lennard-Jones function is about 1.63% of it's minimum value at
250			// a distance of 2.5 sigma.
251			return (4.9 + beta * Re) / beta;
252			}
253	gezelter	1501	}
254			}
255