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, 5 months ago) by gezelter
File size:	7657 byte(s)
Log Message:	Modified some of the nonbonded interactions and types
#	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/MorseInteractionType.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	ForceField::NonBondedInteractionTypeContainer* nbiTypes = forceField_->getNonBondedInteractionTypes();
59	ForceField::NonBondedInteractionTypeContainer::MapTypeIterator j;
60	NonBondedInteractionType* nbt;
61	ForceField::NonBondedInteractionTypeContainer::KeyType keys;
62
63	for (nbt = nbiTypes->beginType(j); nbt != NULL;
64	nbt = nbiTypes->nextType(j)) {
65
66	if (nbt->isMorse()) {
67	keys = nbiTypes->getKeys(j);
68	AtomType* at1 = forceField_->getAtomType(keys[0]);
69	AtomType* at2 = forceField_->getAtomType(keys[1]);
70
71	MorseInteractionType* mit = dynamic_cast<MorseInteractionType*>(nbt);
72
73	if (mit == NULL) {
74	sprintf( painCave.errMsg,
75	"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	painCave.severity = OPENMD_ERROR;
80	painCave.isFatal = 1;
81	simError();
82	}
83
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	}
91	}
92	initialized_ = true;
93	}
94
95	void Morse::addExplicitInteraction(AtomType* atype1, AtomType* atype2,
96	RealType De, RealType Re, RealType beta,
97	MorseType mt) {
98
99	MorseInteractionData mixer;
100	mixer.De = De;
101	mixer.Re = Re;
102	mixer.beta = beta;
103	mixer.variant = mt;
104
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	void Morse::calcForce(InteractionData &idat) {
116
117	if (!initialized_) initialize();
118
119	map<pair<AtomType, AtomType>, MorseInteractionData>::iterator it;
120	it = MixingMap.find( idat.atypes );
121	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	MorseType variant = mixer.variant;
133
134	// V(r) = D_e exp(-a(r-re)(exp(-a(r-re))-2)
135
136	RealType expt = -beta( (idat.rij) - Re);
137	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	if (idat.shiftedPot \|\| idat.shiftedForce) {
145	exptC = -beta( (idat.rcut) - Re);
146	expfncC = exp(exptC);
147	expfnc2C = expfncC*expfncC;
148	}
149
150
151	switch(variant) {
152	case mtShifted : {
153
154	myPot = De * (expfnc2 - 2.0 * expfnc);
155	myDeriv = 2.0 * De * beta * (expfnc - expfnc2);
156
157	if (idat.shiftedPot) {
158	myPotC = De * (expfnc2C - 2.0 * expfncC);
159	myDerivC = 0.0;
160	} else if (idat.shiftedForce) {
161	myPotC = De * (expfnc2C - 2.0 * expfncC);
162	myDerivC = 2.0 * De * beta * (expfnc2C - expfnc2C);
163	myPotC += myDerivC * ( (idat.rij) - (idat.rcut) );
164	} else {
165	myPotC = 0.0;
166	myDerivC = 0.0;
167	}
168
169	break;
170	}
171	case mtRepulsive : {
172
173	myPot = De * expfnc2;
174	myDeriv = -2.0 * De * beta * expfnc2;
175
176	if (idat.shiftedPot) {
177	myPotC = De * expfnc2C;
178	myDerivC = 0.0;
179	} else if (idat.shiftedForce) {
180	myPotC = De * expfnc2C;
181	myDerivC = -2.0 * De * beta * expfnc2C;
182	myPotC += myDerivC * ( (idat.rij) - (idat.rcut));
183	} else {
184	myPotC = 0.0;
185	myDerivC = 0.0;
186	}
187
188	break;
189	}
190	case mtUnknown: {
191	// don't know what to do so don't do anything
192	break;
193	}
194	}
195
196	RealType pot_temp = (idat.vdwMult) (myPot - myPotC);
197	*(idat.vpair) += pot_temp;
198
199	RealType dudr = (idat.sw) (idat.vdwMult) (myDeriv - myDerivC);
200
201	((idat.pot))[VANDERWAALS_FAMILY] += (idat.sw) * pot_temp;
202	(idat.f1) = (idat.d) * dudr / *(idat.rij);
203	}
204	return;
205
206	}
207
208	RealType Morse::getSuggestedCutoffRadius(pair<AtomType, AtomType> atypes) {
209	if (!initialized_) initialize();
210	map<pair<AtomType, AtomType>, MorseInteractionData>::iterator it;
211	it = MixingMap.find(atypes);
212	if (it == MixingMap.end())
213	return 0.0;
214	else {
215	MorseInteractionData mixer = (*it).second;
216
217	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	}
226	}
227