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, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */

#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() {    

    Mtypes.clear();
    Mtids.clear();
    MixingMap.clear();
    Mtids.resize( forceField_->getNAtomType(), -1);

    ForceField::NonBondedInteractionTypeContainer* nbiTypes = forceField_->getNonBondedInteractionTypes();
    ForceField::NonBondedInteractionTypeContainer::MapTypeIterator j;
    ForceField::NonBondedInteractionTypeContainer::KeyType keys;
    NonBondedInteractionType* nbt;
    int mtid1, mtid2;

    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]);

        int atid1 = at1->getIdent();
        if (Mtids[atid1] == -1) {
          mtid1 = Mtypes.size();
          Mtypes.insert(atid1);
          Mtids[atid1] = mtid1;         
        }
        int atid2 = at2->getIdent();
        if (Mtids[atid2] == -1) {
          mtid2 = Mtypes.size();
          Mtypes.insert(atid2);
          Mtids[atid2] = mtid2;
        }
    
        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;

    int mtid1 = Mtids[atype1->getIdent()];
    int mtid2 = Mtids[atype2->getIdent()];
    int nM = Mtypes.size();

    MixingMap.resize(nM);
    MixingMap[mtid1].resize(nM);
    
    MixingMap[mtid1][mtid2] = mixer;
    if (mtid2 != mtid1) {
      MixingMap[mtid2].resize(nM);
      MixingMap[mtid2][mtid1] = mixer;
    }    
  }
  
  void Morse::calcForce(InteractionData &idat) {

    if (!initialized_) initialize();
    
    MorseInteractionData &mixer = MixingMap[Mtids[idat.atid1]][Mtids[idat.atid2]];

    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 * (expfncC - 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();   
    
    int atid1 = atypes.first->getIdent();
    int atid2 = atypes.second->getIdent();
    int mtid1 = Mtids[atid1];
    int mtid2 = Mtids[atid2];
    
    if ( mtid1 == -1 || mtid2 == -1) return 0.0;
    else {      
      MorseInteractionData mixer = MixingMap[mtid1][mtid2];
      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:	2017
Committed:	Tue Sep 2 18:31:44 2014 UTC (10 years, 8 months ago) by gezelter
File size:	8125 byte(s)
Log Message:	Latest
#	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, 234107 (2008).
39	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
42
43	#include <stdio.h>
44	#include <string.h>
45
46	#include <cmath>
47	#include "nonbonded/Morse.hpp"
48	#include "utils/simError.h"
49	#include "types/MorseInteractionType.hpp"
50
51	using namespace std;
52
53	namespace OpenMD {
54
55	Morse::Morse() : name_("Morse"), initialized_(false), forceField_(NULL) {}
56
57	void Morse::initialize() {
58
59	Mtypes.clear();
60	Mtids.clear();
61	MixingMap.clear();
62	Mtids.resize( forceField_->getNAtomType(), -1);
63
64	ForceField::NonBondedInteractionTypeContainer* nbiTypes = forceField_->getNonBondedInteractionTypes();
65	ForceField::NonBondedInteractionTypeContainer::MapTypeIterator j;
66	ForceField::NonBondedInteractionTypeContainer::KeyType keys;
67	NonBondedInteractionType* nbt;
68	int mtid1, mtid2;
69
70	for (nbt = nbiTypes->beginType(j); nbt != NULL;
71	nbt = nbiTypes->nextType(j)) {
72
73	if (nbt->isMorse()) {
74	keys = nbiTypes->getKeys(j);
75	AtomType* at1 = forceField_->getAtomType(keys[0]);
76	AtomType* at2 = forceField_->getAtomType(keys[1]);
77
78	int atid1 = at1->getIdent();
79	if (Mtids[atid1] == -1) {
80	mtid1 = Mtypes.size();
81	Mtypes.insert(atid1);
82	Mtids[atid1] = mtid1;
83	}
84	int atid2 = at2->getIdent();
85	if (Mtids[atid2] == -1) {
86	mtid2 = Mtypes.size();
87	Mtypes.insert(atid2);
88	Mtids[atid2] = mtid2;
89	}
90
91	MorseInteractionType* mit = dynamic_cast<MorseInteractionType*>(nbt);
92
93	if (mit == NULL) {
94	sprintf( painCave.errMsg,
95	"Morse::initialize could not convert NonBondedInteractionType\n"
96	"\tto MorseInteractionType for %s - %s interaction.\n",
97	at1->getName().c_str(),
98	at2->getName().c_str());
99	painCave.severity = OPENMD_ERROR;
100	painCave.isFatal = 1;
101	simError();
102	}
103
104	RealType De = mit->getD();
105	RealType Re = mit->getR();
106	RealType beta = mit->getBeta();
107
108	MorseType variant = mit->getInteractionType();
109	addExplicitInteraction(at1, at2, De, Re, beta, variant );
110	}
111	}
112	initialized_ = true;
113	}
114
115	void Morse::addExplicitInteraction(AtomType* atype1, AtomType* atype2,
116	RealType De, RealType Re, RealType beta,
117	MorseType mt) {
118
119	MorseInteractionData mixer;
120	mixer.De = De;
121	mixer.Re = Re;
122	mixer.beta = beta;
123	mixer.variant = mt;
124
125	int mtid1 = Mtids[atype1->getIdent()];
126	int mtid2 = Mtids[atype2->getIdent()];
127	int nM = Mtypes.size();
128
129	MixingMap.resize(nM);
130	MixingMap[mtid1].resize(nM);
131
132	MixingMap[mtid1][mtid2] = mixer;
133	if (mtid2 != mtid1) {
134	MixingMap[mtid2].resize(nM);
135	MixingMap[mtid2][mtid1] = mixer;
136	}
137	}
138
139	void Morse::calcForce(InteractionData &idat) {
140
141	if (!initialized_) initialize();
142
143	MorseInteractionData &mixer = MixingMap[Mtids[idat.atid1]][Mtids[idat.atid2]];
144
145	RealType myPot = 0.0;
146	RealType myPotC = 0.0;
147	RealType myDeriv = 0.0;
148	RealType myDerivC = 0.0;
149
150	RealType De = mixer.De;
151	RealType Re = mixer.Re;
152	RealType beta = mixer.beta;
153	MorseType variant = mixer.variant;
154
155	// V(r) = D_e exp(-a(r-re)(exp(-a(r-re))-2)
156
157	RealType expt = -beta( (idat.rij) - Re);
158	RealType expfnc = exp(expt);
159	RealType expfnc2 = expfnc*expfnc;
160
161	RealType exptC = 0.0;
162	RealType expfncC = 0.0;
163	RealType expfnc2C = 0.0;
164
165	if (idat.shiftedPot \|\| idat.shiftedForce) {
166	exptC = -beta( (idat.rcut) - Re);
167	expfncC = exp(exptC);
168	expfnc2C = expfncC*expfncC;
169	}
170
171
172	switch(variant) {
173	case mtShifted : {
174
175	myPot = De * (expfnc2 - 2.0 * expfnc);
176	myDeriv = 2.0 * De * beta * (expfnc - expfnc2);
177
178	if (idat.shiftedPot) {
179	myPotC = De * (expfnc2C - 2.0 * expfncC);
180	myDerivC = 0.0;
181	} else if (idat.shiftedForce) {
182	myPotC = De * (expfnc2C - 2.0 * expfncC);
183	myDerivC = 2.0 * De * beta * (expfncC - expfnc2C);
184	myPotC += myDerivC * ( (idat.rij) - (idat.rcut) );
185	} else {
186	myPotC = 0.0;
187	myDerivC = 0.0;
188	}
189
190	break;
191	}
192	case mtRepulsive : {
193
194	myPot = De * expfnc2;
195	myDeriv = -2.0 * De * beta * expfnc2;
196
197	if (idat.shiftedPot) {
198	myPotC = De * expfnc2C;
199	myDerivC = 0.0;
200	} else if (idat.shiftedForce) {
201	myPotC = De * expfnc2C;
202	myDerivC = -2.0 * De * beta * expfnc2C;
203	myPotC += myDerivC * ( (idat.rij) - (idat.rcut));
204	} else {
205	myPotC = 0.0;
206	myDerivC = 0.0;
207	}
208
209	break;
210	}
211	case mtUnknown: {
212	// don't know what to do so don't do anything
213	break;
214	}
215	}
216
217
218	RealType pot_temp = (idat.vdwMult) (myPot - myPotC);
219	*(idat.vpair) += pot_temp;
220
221	RealType dudr = (idat.sw) (idat.vdwMult) (myDeriv - myDerivC);
222
223
224	((idat.pot))[VANDERWAALS_FAMILY] += (idat.sw) * pot_temp;
225	(idat.f1) = (idat.d) * dudr / *(idat.rij);
226
227	return;
228	}
229
230	RealType Morse::getSuggestedCutoffRadius(pair<AtomType, AtomType> atypes) {
231	if (!initialized_) initialize();
232
233	int atid1 = atypes.first->getIdent();
234	int atid2 = atypes.second->getIdent();
235	int mtid1 = Mtids[atid1];
236	int mtid2 = Mtids[atid2];
237
238	if ( mtid1 == -1 \|\| mtid2 == -1) return 0.0;
239	else {
240	MorseInteractionData mixer = MixingMap[mtid1][mtid2];
241	RealType Re = mixer.Re;
242	RealType beta = mixer.beta;
243	// This value of the r corresponds to an energy about 1.48% of
244	// the energy at the bottom of the Morse well. For comparison, the
245	// Lennard-Jones function is about 1.63% of it's minimum value at
246	// a distance of 2.5 sigma.
247	return (4.9 + beta * Re) / beta;
248	}
249	}
250	}
251