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, 10 months ago) by gezelter
File size:	8807 byte(s)
Log Message:	Bug squashing
#	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
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	void Morse::calcForce(InteractionData &idat) {
145
146	if (!initialized_) initialize();
147
148	map<pair<AtomType, AtomType>, MorseInteractionData>::iterator it;
149	it = MixingMap.find( idat.atypes );
150	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	RealType expt = -beta( (idat.rij) - Re);
166	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	if (idat.shiftedPot \|\| idat.shiftedForce) {
174	exptC = -beta( (idat.rcut) - Re);
175	expfncC = exp(exptC);
176	expfnc2C = expfncC*expfncC;
177	}
178
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	if (idat.shiftedPot) {
187	myPotC = De * (expfnc2C - 2.0 * expfncC);
188	myDerivC = 0.0;
189	} else if (idat.shiftedForce) {
190	myPotC = De * (expfnc2C - 2.0 * expfncC);
191	myDerivC = 2.0 * De * beta * (expfnc2C - expfnc2C);
192	myPotC += myDerivC * ( (idat.rij) - (idat.rcut) );
193	} else {
194	myPotC = 0.0;
195	myDerivC = 0.0;
196	}
197
198	break;
199	}
200	case repulsiveMorse : {
201
202	myPot = De * expfnc2;
203	myDeriv = -2.0 * De * beta * expfnc2;
204
205	if (idat.shiftedPot) {
206	myPotC = De * expfnc2C;
207	myDerivC = 0.0;
208	} else if (idat.shiftedForce) {
209	myPotC = De * expfnc2C;
210	myDerivC = -2.0 * De * beta * expfnc2C;
211	myPotC += myDerivC * ( (idat.rij) - (idat.rcut));
212	} else {
213	myPotC = 0.0;
214	myDerivC = 0.0;
215	}
216
217	break;
218	}
219	}
220
221	RealType pot_temp = (idat.vdwMult) (myPot - myPotC);
222	*(idat.vpair) += pot_temp;
223
224	RealType dudr = (idat.sw) (idat.vdwMult) (myDeriv - myDerivC);
225
226	((idat.pot))[VANDERWAALS_FAMILY] += (idat.sw) * pot_temp;
227	(idat.f1) = (idat.d) * dudr / *(idat.rij);
228	}
229	return;
230
231	}
232
233	RealType Morse::getSuggestedCutoffRadius(pair<AtomType, AtomType> atypes) {
234	if (!initialized_) initialize();
235	map<pair<AtomType, AtomType>, MorseInteractionData>::iterator it;
236	it = MixingMap.find(atypes);
237	if (it == MixingMap.end())
238	return 0.0;
239	else {
240	MorseInteractionData mixer = (*it).second;
241
242	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	}
251	}
252