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 (14 years, 7 months 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.
#	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] 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	Morse::Morse() : name_("Morse"), initialized_(false), forceField_(NULL),
55	shiftedPot_(false), shiftedFrc_(false) {}
56
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	void Morse::calcForce(InteractionData idat) {
146
147	if (!initialized_) initialize();
148
149	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	}
180
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	}
202	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	}
231	return;
232
233	}
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
245	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	}
254	}
255