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) {}
  
  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();
    
    map<pair<AtomType*, AtomType*>, MorseInteractionData>::iterator it;
    it = MixingMap.find( idat.atypes );
    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 (idat.shiftedPot || idat.shiftedForce) {
        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 (idat.shiftedPot) {
          myPotC = De * (expfnc2C - 2.0 * expfncC);
          myDerivC = 0.0;
        } else if (idat.shiftedForce) {
          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 (idat.shiftedPot) {
          myPotC = De * expfnc2C;
          myDerivC = 0.0;
        } else if (idat.shiftedForce) {
          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))[VANDERWAALS_FAMILY] += *(idat.sw) * pot_temp;
      *(idat.f1) = *(idat.d) * dudr / *(idat.rij);
    }
    return;
    
  }
    
  RealType Morse::getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes) {
    if (!initialized_) initialize();   
    map<pair<AtomType*, AtomType*>, MorseInteractionData>::iterator it;
    it = MixingMap.find(atypes);
    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:	1583
Committed:	Thu Jun 16 22:00:08 2011 UTC (13 years, 11 months ago) by gezelter
File size:	8807 byte(s)
Log Message:	Bug squashing
#	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	1583	Morse::Morse() : name_("Morse"), initialized_(false), forceField_(NULL) {}
55	gezelter	1501
56			void Morse::initialize() {
57
58			stringToEnumMap_["shiftedMorse"] = shiftedMorse;
59			stringToEnumMap_["repulsiveMorse"] = repulsiveMorse;
60
61			ForceField::NonBondedInteractionTypeContainer* nbiTypes = forceField_->getNonBondedInteractionTypes();
62			ForceField::NonBondedInteractionTypeContainer::MapTypeIterator j;
63			NonBondedInteractionType* nbt;
64
65			for (nbt = nbiTypes->beginType(j); nbt != NULL;
66			nbt = nbiTypes->nextType(j)) {
67
68			if (nbt->isMorse()) {
69
70			pair<AtomType, AtomType> atypes = nbt->getAtomTypes();
71
72			GenericData* data = nbt->getPropertyByName("Morse");
73			if (data == NULL) {
74			sprintf( painCave.errMsg, "Morse::initialize could not find\n"
75			"\tMorse parameters for %s - %s interaction.\n",
76			atypes.first->getName().c_str(),
77			atypes.second->getName().c_str());
78			painCave.severity = OPENMD_ERROR;
79			painCave.isFatal = 1;
80			simError();
81			}
82
83			MorseData* morseData = dynamic_cast<MorseData*>(data);
84			if (morseData == NULL) {
85			sprintf( painCave.errMsg,
86			"Morse::initialize could not convert GenericData to\n"
87			"\tMorseData for %s - %s interaction.\n",
88			atypes.first->getName().c_str(),
89			atypes.second->getName().c_str());
90			painCave.severity = OPENMD_ERROR;
91			painCave.isFatal = 1;
92			simError();
93			}
94
95			MorseParam morseParam = morseData->getData();
96
97			RealType De = morseParam.De;
98			RealType Re = morseParam.Re;
99			RealType beta = morseParam.beta;
100			string interactionType = morseParam.interactionType;
101
102			toUpper(interactionType);
103			map<string, MorseInteractionType>::iterator i;
104			i = stringToEnumMap_.find(interactionType);
105			if (i != stringToEnumMap_.end()) {
106			addExplicitInteraction(atypes.first, atypes.second,
107			De, Re, beta, i->second );
108			} else {
109			sprintf( painCave.errMsg,
110			"Morse::initialize found unknown Morse interaction type\n"
111			"\t(%s) for %s - %s interaction.\n",
112			morseParam.interactionType.c_str(),
113			atypes.first->getName().c_str(),
114			atypes.second->getName().c_str());
115			painCave.severity = OPENMD_ERROR;
116			painCave.isFatal = 1;
117			simError();
118			}
119			}
120			}
121			initialized_ = true;
122			}
123
124			void Morse::addExplicitInteraction(AtomType* atype1, AtomType* atype2,
125			RealType De, RealType Re, RealType beta,
126			MorseInteractionType mit) {
127
128			MorseInteractionData mixer;
129			mixer.De = De;
130			mixer.Re = Re;
131			mixer.beta = beta;
132			mixer.interactionType = mit;
133
134			pair<AtomType, AtomType> key1, key2;
135			key1 = make_pair(atype1, atype2);
136			key2 = make_pair(atype2, atype1);
137
138			MixingMap[key1] = mixer;
139			if (key2 != key1) {
140			MixingMap[key2] = mixer;
141			}
142			}
143
144	gezelter	1536	void Morse::calcForce(InteractionData &idat) {
145	gezelter	1501
146			if (!initialized_) initialize();
147
148	gezelter	1505	map<pair<AtomType, AtomType>, MorseInteractionData>::iterator it;
149	gezelter	1571	it = MixingMap.find( idat.atypes );
150	gezelter	1505	if (it != MixingMap.end()) {
151			MorseInteractionData mixer = (*it).second;
152
153			RealType myPot = 0.0;
154			RealType myPotC = 0.0;
155			RealType myDeriv = 0.0;
156			RealType myDerivC = 0.0;
157
158			RealType De = mixer.De;
159			RealType Re = mixer.Re;
160			RealType beta = mixer.beta;
161			MorseInteractionType interactionType = mixer.interactionType;
162
163			// V(r) = D_e exp(-a(r-re)(exp(-a(r-re))-2)
164
165	gezelter	1554	RealType expt = -beta( (idat.rij) - Re);
166	gezelter	1505	RealType expfnc = exp(expt);
167			RealType expfnc2 = expfnc*expfnc;
168
169			RealType exptC = 0.0;
170			RealType expfncC = 0.0;
171			RealType expfnc2C = 0.0;
172
173	gezelter	1583	if (idat.shiftedPot \|\| idat.shiftedForce) {
174	gezelter	1554	exptC = -beta( (idat.rcut) - Re);
175	gezelter	1505	expfncC = exp(exptC);
176			expfnc2C = expfncC*expfncC;
177	gezelter	1501	}
178	gezelter	1505
179
180			switch(interactionType) {
181			case shiftedMorse : {
182
183			myPot = De * (expfnc2 - 2.0 * expfnc);
184			myDeriv = 2.0 * De * beta * (expfnc - expfnc2);
185
186	gezelter	1583	if (idat.shiftedPot) {
187	gezelter	1505	myPotC = De * (expfnc2C - 2.0 * expfncC);
188			myDerivC = 0.0;
189	gezelter	1583	} else if (idat.shiftedForce) {
190	gezelter	1505	myPotC = De * (expfnc2C - 2.0 * expfncC);
191			myDerivC = 2.0 * De * beta * (expfnc2C - expfnc2C);
192	gezelter	1554	myPotC += myDerivC * ( (idat.rij) - (idat.rcut) );
193	gezelter	1505	} else {
194			myPotC = 0.0;
195			myDerivC = 0.0;
196			}
197
198			break;
199	gezelter	1501	}
200	gezelter	1505	case repulsiveMorse : {
201
202			myPot = De * expfnc2;
203			myDeriv = -2.0 * De * beta * expfnc2;
204
205	gezelter	1583	if (idat.shiftedPot) {
206	gezelter	1505	myPotC = De * expfnc2C;
207			myDerivC = 0.0;
208	gezelter	1583	} else if (idat.shiftedForce) {
209	gezelter	1505	myPotC = De * expfnc2C;
210			myDerivC = -2.0 * De * beta * expfnc2C;
211	gezelter	1554	myPotC += myDerivC * ( (idat.rij) - (idat.rcut));
212	gezelter	1505	} else {
213			myPotC = 0.0;
214			myDerivC = 0.0;
215			}
216
217			break;
218			}
219			}
220
221	gezelter	1554	RealType pot_temp = (idat.vdwMult) (myPot - myPotC);
222			*(idat.vpair) += pot_temp;
223	gezelter	1505
224	gezelter	1554	RealType dudr = (idat.sw) (idat.vdwMult) (myDeriv - myDerivC);
225	gezelter	1505
226	gezelter	1582	((idat.pot))[VANDERWAALS_FAMILY] += (idat.sw) * pot_temp;
227	gezelter	1554	(idat.f1) = (idat.d) * dudr / *(idat.rij);
228	gezelter	1501	}
229	gezelter	1505	return;
230	gezelter	1501
231	gezelter	1505	}
232
233	gezelter	1545	RealType Morse::getSuggestedCutoffRadius(pair<AtomType, AtomType> atypes) {
234	gezelter	1505	if (!initialized_) initialize();
235			map<pair<AtomType, AtomType>, MorseInteractionData>::iterator it;
236	gezelter	1545	it = MixingMap.find(atypes);
237	gezelter	1505	if (it == MixingMap.end())
238			return 0.0;
239			else {
240			MorseInteractionData mixer = (*it).second;
241	gezelter	1501
242	gezelter	1505	RealType Re = mixer.Re;
243			RealType beta = mixer.beta;
244			// This value of the r corresponds to an energy about 1.48% of
245			// the energy at the bottom of the Morse well. For comparison, the
246			// Lennard-Jones function is about 1.63% of it's minimum value at
247			// a distance of 2.5 sigma.
248			return (4.9 + beta * Re) / beta;
249			}
250	gezelter	1501	}
251			}
252