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/MorseInteractionType.hpp"

using namespace std;

namespace OpenMD {

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

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

    for (nbt = nbiTypes->beginType(j); nbt != NULL; 
         nbt = nbiTypes->nextType(j)) {
      
      if (nbt->isMorse()) {
        keys = nbiTypes->getKeys(j);
        AtomType* at1 = forceField_->getAtomType(keys[0]);
        AtomType* at2 = forceField_->getAtomType(keys[1]);

        MorseInteractionType* mit = dynamic_cast<MorseInteractionType*>(nbt);

        if (mit == NULL) {
          sprintf( painCave.errMsg,
                   "Morse::initialize could not convert NonBondedInteractionType\n"
                   "\tto MorseInteractionType for %s - %s interaction.\n", 
                   at1->getName().c_str(),
                   at2->getName().c_str());
          painCave.severity = OPENMD_ERROR;
          painCave.isFatal = 1;
          simError();          
        }
        
        RealType De = mit->getD();
        RealType Re = mit->getR();
        RealType beta = mit->getBeta();
   
        MorseType variant = mit->getInteractionType();
        addExplicitInteraction(at1, at2, De, Re, beta, variant );
      }
    }  
    initialized_ = true;
  }
      
  void Morse::addExplicitInteraction(AtomType* atype1, AtomType* atype2, 
                                     RealType De, RealType Re, RealType beta, 
                                     MorseType mt) {

    MorseInteractionData mixer;
    mixer.De = De;
    mixer.Re = Re;
    mixer.beta = beta;
    mixer.variant = mt;

    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;
      MorseType variant = mixer.variant;
      
      // 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(variant) {
      case mtShifted : {
        
        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 mtRepulsive : {
        
        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;
      }
      case mtUnknown: {
        // don't know what to do so don't do anything
        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:	1664
Committed:	Tue Nov 22 14:37:41 2011 UTC (13 years, 6 months ago) by gezelter
File size:	7657 byte(s)
Log Message:	Modified some of the nonbonded interactions and types
#	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	gezelter	1664	#include "types/MorseInteractionType.hpp"
49	gezelter	1501
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			ForceField::NonBondedInteractionTypeContainer* nbiTypes = forceField_->getNonBondedInteractionTypes();
59			ForceField::NonBondedInteractionTypeContainer::MapTypeIterator j;
60			NonBondedInteractionType* nbt;
61	gezelter	1664	ForceField::NonBondedInteractionTypeContainer::KeyType keys;
62	gezelter	1501
63			for (nbt = nbiTypes->beginType(j); nbt != NULL;
64			nbt = nbiTypes->nextType(j)) {
65
66			if (nbt->isMorse()) {
67	gezelter	1664	keys = nbiTypes->getKeys(j);
68			AtomType* at1 = forceField_->getAtomType(keys[0]);
69			AtomType* at2 = forceField_->getAtomType(keys[1]);
70	gezelter	1501
71	gezelter	1664	MorseInteractionType* mit = dynamic_cast<MorseInteractionType*>(nbt);
72	gezelter	1501
73	gezelter	1664	if (mit == NULL) {
74	gezelter	1501	sprintf( painCave.errMsg,
75	gezelter	1664	"Morse::initialize could not convert NonBondedInteractionType\n"
76			"\tto MorseInteractionType for %s - %s interaction.\n",
77			at1->getName().c_str(),
78			at2->getName().c_str());
79	gezelter	1501	painCave.severity = OPENMD_ERROR;
80			painCave.isFatal = 1;
81			simError();
82			}
83	gezelter	1664
84			RealType De = mit->getD();
85			RealType Re = mit->getR();
86			RealType beta = mit->getBeta();
87
88			MorseType variant = mit->getInteractionType();
89			addExplicitInteraction(at1, at2, De, Re, beta, variant );
90	gezelter	1501	}
91			}
92			initialized_ = true;
93			}
94
95			void Morse::addExplicitInteraction(AtomType* atype1, AtomType* atype2,
96			RealType De, RealType Re, RealType beta,
97	gezelter	1664	MorseType mt) {
98	gezelter	1501
99			MorseInteractionData mixer;
100			mixer.De = De;
101			mixer.Re = Re;
102			mixer.beta = beta;
103	gezelter	1664	mixer.variant = mt;
104	gezelter	1501
105			pair<AtomType, AtomType> key1, key2;
106			key1 = make_pair(atype1, atype2);
107			key2 = make_pair(atype2, atype1);
108
109			MixingMap[key1] = mixer;
110			if (key2 != key1) {
111			MixingMap[key2] = mixer;
112			}
113			}
114
115	gezelter	1536	void Morse::calcForce(InteractionData &idat) {
116	gezelter	1501
117			if (!initialized_) initialize();
118
119	gezelter	1505	map<pair<AtomType, AtomType>, MorseInteractionData>::iterator it;
120	gezelter	1571	it = MixingMap.find( idat.atypes );
121	gezelter	1505	if (it != MixingMap.end()) {
122			MorseInteractionData mixer = (*it).second;
123
124			RealType myPot = 0.0;
125			RealType myPotC = 0.0;
126			RealType myDeriv = 0.0;
127			RealType myDerivC = 0.0;
128
129			RealType De = mixer.De;
130			RealType Re = mixer.Re;
131			RealType beta = mixer.beta;
132	gezelter	1664	MorseType variant = mixer.variant;
133	gezelter	1505
134			// V(r) = D_e exp(-a(r-re)(exp(-a(r-re))-2)
135
136	gezelter	1554	RealType expt = -beta( (idat.rij) - Re);
137	gezelter	1505	RealType expfnc = exp(expt);
138			RealType expfnc2 = expfnc*expfnc;
139
140			RealType exptC = 0.0;
141			RealType expfncC = 0.0;
142			RealType expfnc2C = 0.0;
143
144	gezelter	1583	if (idat.shiftedPot \|\| idat.shiftedForce) {
145	gezelter	1554	exptC = -beta( (idat.rcut) - Re);
146	gezelter	1505	expfncC = exp(exptC);
147			expfnc2C = expfncC*expfncC;
148	gezelter	1501	}
149	gezelter	1505
150
151	gezelter	1664	switch(variant) {
152			case mtShifted : {
153	gezelter	1505
154			myPot = De * (expfnc2 - 2.0 * expfnc);
155			myDeriv = 2.0 * De * beta * (expfnc - expfnc2);
156
157	gezelter	1583	if (idat.shiftedPot) {
158	gezelter	1505	myPotC = De * (expfnc2C - 2.0 * expfncC);
159			myDerivC = 0.0;
160	gezelter	1583	} else if (idat.shiftedForce) {
161	gezelter	1505	myPotC = De * (expfnc2C - 2.0 * expfncC);
162			myDerivC = 2.0 * De * beta * (expfnc2C - expfnc2C);
163	gezelter	1554	myPotC += myDerivC * ( (idat.rij) - (idat.rcut) );
164	gezelter	1505	} else {
165			myPotC = 0.0;
166			myDerivC = 0.0;
167			}
168
169			break;
170	gezelter	1501	}
171	gezelter	1664	case mtRepulsive : {
172	gezelter	1505
173			myPot = De * expfnc2;
174			myDeriv = -2.0 * De * beta * expfnc2;
175
176	gezelter	1583	if (idat.shiftedPot) {
177	gezelter	1505	myPotC = De * expfnc2C;
178			myDerivC = 0.0;
179	gezelter	1583	} else if (idat.shiftedForce) {
180	gezelter	1505	myPotC = De * expfnc2C;
181			myDerivC = -2.0 * De * beta * expfnc2C;
182	gezelter	1554	myPotC += myDerivC * ( (idat.rij) - (idat.rcut));
183	gezelter	1505	} else {
184			myPotC = 0.0;
185			myDerivC = 0.0;
186			}
187
188			break;
189			}
190	gezelter	1664	case mtUnknown: {
191			// don't know what to do so don't do anything
192			break;
193	gezelter	1505	}
194	gezelter	1664	}
195	gezelter	1505
196	gezelter	1554	RealType pot_temp = (idat.vdwMult) (myPot - myPotC);
197			*(idat.vpair) += pot_temp;
198	gezelter	1505
199	gezelter	1554	RealType dudr = (idat.sw) (idat.vdwMult) (myDeriv - myDerivC);
200	gezelter	1505
201	gezelter	1582	((idat.pot))[VANDERWAALS_FAMILY] += (idat.sw) * pot_temp;
202	gezelter	1554	(idat.f1) = (idat.d) * dudr / *(idat.rij);
203	gezelter	1501	}
204	gezelter	1505	return;
205	gezelter	1501
206	gezelter	1505	}
207
208	gezelter	1545	RealType Morse::getSuggestedCutoffRadius(pair<AtomType, AtomType> atypes) {
209	gezelter	1505	if (!initialized_) initialize();
210			map<pair<AtomType, AtomType>, MorseInteractionData>::iterator it;
211	gezelter	1545	it = MixingMap.find(atypes);
212	gezelter	1505	if (it == MixingMap.end())
213			return 0.0;
214			else {
215			MorseInteractionData mixer = (*it).second;
216	gezelter	1501
217	gezelter	1505	RealType Re = mixer.Re;
218			RealType beta = mixer.beta;
219			// This value of the r corresponds to an energy about 1.48% of
220			// the energy at the bottom of the Morse well. For comparison, the
221			// Lennard-Jones function is about 1.63% of it's minimum value at
222			// a distance of 2.5 sigma.
223			return (4.9 + beta * Re) / beta;
224			}
225	gezelter	1501	}
226			}
227