src/nonbonded/LJ.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/LJ.hpp"
#include "utils/simError.h"
#include "types/LennardJonesAdapter.hpp"
#include "types/LennardJonesInteractionType.hpp"

namespace OpenMD {

  LJ::LJ() : name_("LJ"), initialized_(false), forceField_(NULL) {}

  RealType LJ::getSigma(AtomType* atomType1, AtomType* atomType2) {

    LennardJonesAdapter lja1 = LennardJonesAdapter(atomType1);
    LennardJonesAdapter lja2 = LennardJonesAdapter(atomType2);
    RealType sigma1 = lja1.getSigma();
    RealType sigma2 = lja2.getSigma();
    
    ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
    string DistanceMix = fopts.getDistanceMixingRule();
    toUpper(DistanceMix);

    if (DistanceMix == "GEOMETRIC") 
      return sqrt(sigma1 * sigma2);
    else 
      return 0.5 * (sigma1 + sigma2);
  }

  RealType LJ::getEpsilon(AtomType* atomType1, AtomType* atomType2) {  
    LennardJonesAdapter lja1 = LennardJonesAdapter(atomType1);
    LennardJonesAdapter lja2 = LennardJonesAdapter(atomType2);
  
    RealType epsilon1 = lja1.getEpsilon();
    RealType epsilon2 = lja2.getEpsilon();
    return sqrt(epsilon1 * epsilon2);
  }

  void LJ::initialize() {    

    LJtypes.clear();
    LJtids.clear();
    MixingMap.clear();
    nLJ_ = 0;

    LJtids.resize( forceField_->getNAtomType(), -1);

    set<AtomType*>::iterator at;
    for (at = simTypes_.begin(); at != simTypes_.end(); ++at) {
      if ((*at)->isLennardJones()) nLJ_++;
    }

    MixingMap.resize(nLJ_);

    for (at = simTypes_.begin(); at != simTypes_.end(); ++at) {
      if ((*at)->isLennardJones()) addType(*at);      
    }

    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->isLennardJones()) {
        keys = nbiTypes->getKeys(j);
        AtomType* at1 = forceField_->getAtomType(keys[0]);
        AtomType* at2 = forceField_->getAtomType(keys[1]);

        LennardJonesInteractionType* ljit = dynamic_cast<LennardJonesInteractionType*>(nbt);

        if (ljit == NULL) {
          sprintf( painCave.errMsg,
                   "LJ::initialize could not convert NonBondedInteractionType\n"
                   "\tto LennardJonesInteractionType for %s - %s interaction.\n", 
                   at1->getName().c_str(),
                   at2->getName().c_str());
          painCave.severity = OPENMD_ERROR;
          painCave.isFatal = 1;
          simError();          
        }

        RealType sigma = ljit->getSigma();
        RealType epsilon = ljit->getEpsilon();
        addExplicitInteraction(at1, at2, sigma, epsilon);
      }
    }  
    initialized_ = true;
  }


  void LJ::addType(AtomType* atomType){
    LennardJonesAdapter lja1 = LennardJonesAdapter(atomType);

    RealType sigma1 = lja1.getSigma();
    RealType epsilon1 = lja1.getEpsilon();
    
    // add it to the map:
    int atid = atomType->getIdent();
    int ljtid = LJtypes.size();
  
    pair<set<int>::iterator,bool> ret;    
    ret = LJtypes.insert( atid );
    if (ret.second == false) {
      sprintf( painCave.errMsg,
               "LJ already had a previous entry with ident %d\n",
               atid) ;
      painCave.severity = OPENMD_INFO;
      painCave.isFatal = 0;
      simError();         
    }

    LJtids[atid] = ljtid;
    MixingMap[ljtid].resize( nLJ_ );

    // Now, iterate over all known types and add to the mixing map:
    
    std::set<int>::iterator it;
    for( it = LJtypes.begin(); it != LJtypes.end(); ++it) {

      int ljtid2 = LJtids[ (*it) ];
      AtomType* atype2 = forceField_->getAtomType( (*it) );

      LJInteractionData mixer;
      mixer.sigma = getSigma(atomType, atype2);
      mixer.epsilon = getEpsilon(atomType, atype2);
      mixer.sigmai = 1.0 / mixer.sigma;
      mixer.explicitlySet = false;
      MixingMap[ljtid2].resize( nLJ_ );

      MixingMap[ljtid][ljtid2] = mixer;
      if (ljtid2 != ljtid) {
        MixingMap[ljtid2][ljtid] = mixer;
      }
    }      
  }
  
  void LJ::addExplicitInteraction(AtomType* atype1, AtomType* atype2, RealType sigma, RealType epsilon){
    
    LJInteractionData mixer;
    mixer.sigma = sigma;
    mixer.epsilon = epsilon;
    mixer.sigmai = 1.0 / mixer.sigma;
    mixer.explicitlySet = true;

    int atid1 = atype1->getIdent();
    int atid2 = atype2->getIdent();

    int ljtid1, ljtid2;

    pair<set<int>::iterator,bool> ret;    
    ret = LJtypes.insert( atid1 );
    if (ret.second == false) {
      // already had this type in the LJMap, just get the ljtid:
      ljtid1 = LJtids[ atid1 ];
    } else {
      // didn't already have it, so make a new one and assign it:
      ljtid1 = nLJ_;
      LJtids[atid1] = nLJ_;
      nLJ_++;
    }

    ret = LJtypes.insert( atid2 );
    if (ret.second == false) {
      // already had this type in the LJMap, just get the ljtid:
      ljtid2 = LJtids[ atid2 ];
    } else {
      // didn't already have it, so make a new one and assign it:
      ljtid2 = nLJ_;
      LJtids[atid2] = nLJ_;
      nLJ_++;
    }
    
    MixingMap.resize(nLJ_);
    MixingMap[ljtid1].resize(nLJ_);

    MixingMap[ljtid1][ljtid2] = mixer;
    if (ljtid2 != ljtid1) {
      MixingMap[ljtid2].resize(nLJ_);
      MixingMap[ljtid2][ljtid1] = mixer;
    }    
  }
 
  void LJ::calcForce(InteractionData &idat) {
    if (!initialized_) initialize();
    
    LJInteractionData &mixer = MixingMap[LJtids[idat.atid1]][LJtids[idat.atid2]];

    RealType sigmai = mixer.sigmai;
    RealType epsilon = mixer.epsilon;
    
    RealType ros;
    RealType rcos;
    RealType myPot = 0.0;
    RealType myPotC = 0.0;
    RealType myDeriv = 0.0;
    RealType myDerivC = 0.0;
    
    ros = *(idat.rij) * sigmai;     
    
    getLJfunc(ros, myPot, myDeriv);
    
    if (idat.shiftedPot) {
      rcos = *(idat.rcut) * sigmai;
      getLJfunc(rcos, myPotC, myDerivC);
      myDerivC = 0.0;
    } else if (idat.shiftedForce) {
      rcos = *(idat.rcut) * sigmai;
      getLJfunc(rcos, myPotC, myDerivC);
      myPotC = myPotC + myDerivC * (*(idat.rij) - *(idat.rcut)) * sigmai;
    } else {
      myPotC = 0.0;
      myDerivC = 0.0;        
    }
    
    RealType pot_temp = *(idat.vdwMult) * epsilon * (myPot - myPotC);
    *(idat.vpair) += pot_temp;
    
    RealType dudr = *(idat.sw) * *(idat.vdwMult) * epsilon * (myDeriv - 
                                                              myDerivC)*sigmai;      
    (*(idat.pot))[VANDERWAALS_FAMILY] += *(idat.sw) * pot_temp;
    *(idat.f1) += *(idat.d) * dudr / *(idat.rij);
    
    return;
  }
  
  void LJ::getLJfunc(RealType r, RealType &pot, RealType &deriv) {

    RealType ri = 1.0 / r;
    RealType ri2 = ri * ri;
    RealType ri6 = ri2 * ri2 * ri2;
    RealType ri7 = ri6 * ri;
    RealType ri12 = ri6 * ri6;
    RealType ri13 = ri12 * ri;
    
    pot = 4.0 * (ri12 - ri6);
    deriv = 24.0 * (ri7 - 2.0 * ri13);

    return;
  }
  
  RealType LJ::getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes) {
    if (!initialized_) initialize();   
    
    int atid1 = atypes.first->getIdent();
    int atid2 = atypes.second->getIdent();
    int ljtid1 = LJtids[atid1];
    int ljtid2 = LJtids[atid2];
    
    if (ljtid1 == -1 || ljtid2 == -1) return 0.0;
    else {      
      LJInteractionData mixer = MixingMap[ljtid1][ljtid2];
      return 2.5 * mixer.sigma;
    }
  }
  
}
Revision:	2017
Committed:	Tue Sep 2 18:31:44 2014 UTC (10 years, 9 months ago) by gezelter
File size:	9771 byte(s)
Log Message:	Latest
#	User	Rev	Content
1	gezelter	1471	/*
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	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	1471	*/
42
43			#include <stdio.h>
44			#include <string.h>
45
46			#include <cmath>
47			#include "nonbonded/LJ.hpp"
48			#include "utils/simError.h"
49	gezelter	1710	#include "types/LennardJonesAdapter.hpp"
50	jmichalk	1683	#include "types/LennardJonesInteractionType.hpp"
51	gezelter	1471
52			namespace OpenMD {
53
54	gezelter	1583	LJ::LJ() : name_("LJ"), initialized_(false), forceField_(NULL) {}
55	gezelter	1471
56	gezelter	1710	RealType LJ::getSigma(AtomType* atomType1, AtomType* atomType2) {
57	gezelter	1471
58	gezelter	1710	LennardJonesAdapter lja1 = LennardJonesAdapter(atomType1);
59			LennardJonesAdapter lja2 = LennardJonesAdapter(atomType2);
60			RealType sigma1 = lja1.getSigma();
61			RealType sigma2 = lja2.getSigma();
62	gezelter	1471
63			ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
64	gezelter	1502	string DistanceMix = fopts.getDistanceMixingRule();
65	gezelter	1471	toUpper(DistanceMix);
66
67			if (DistanceMix == "GEOMETRIC")
68			return sqrt(sigma1 * sigma2);
69			else
70			return 0.5 * (sigma1 + sigma2);
71			}
72
73	gezelter	1710	RealType LJ::getEpsilon(AtomType* atomType1, AtomType* atomType2) {
74			LennardJonesAdapter lja1 = LennardJonesAdapter(atomType1);
75			LennardJonesAdapter lja2 = LennardJonesAdapter(atomType2);
76
77			RealType epsilon1 = lja1.getEpsilon();
78			RealType epsilon2 = lja2.getEpsilon();
79	gezelter	1471	return sqrt(epsilon1 * epsilon2);
80			}
81
82			void LJ::initialize() {
83
84	gezelter	1895	LJtypes.clear();
85			LJtids.clear();
86			MixingMap.clear();
87			nLJ_ = 0;
88
89			LJtids.resize( forceField_->getNAtomType(), -1);
90
91			set<AtomType*>::iterator at;
92			for (at = simTypes_.begin(); at != simTypes_.end(); ++at) {
93			if ((*at)->isLennardJones()) nLJ_++;
94	gezelter	1471	}
95	gezelter	1895
96			MixingMap.resize(nLJ_);
97
98			for (at = simTypes_.begin(); at != simTypes_.end(); ++at) {
99			if ((at)->isLennardJones()) addType(at);
100			}
101
102	gezelter	1476	ForceField::NonBondedInteractionTypeContainer* nbiTypes = forceField_->getNonBondedInteractionTypes();
103	gezelter	1471	ForceField::NonBondedInteractionTypeContainer::MapTypeIterator j;
104			NonBondedInteractionType* nbt;
105	jmichalk	1683	ForceField::NonBondedInteractionTypeContainer::KeyType keys;
106	gezelter	1471
107	gezelter	1476	for (nbt = nbiTypes->beginType(j); nbt != NULL;
108			nbt = nbiTypes->nextType(j)) {
109	jmichalk	1683
110	gezelter	1471	if (nbt->isLennardJones()) {
111	jmichalk	1683	keys = nbiTypes->getKeys(j);
112			AtomType* at1 = forceField_->getAtomType(keys[0]);
113			AtomType* at2 = forceField_->getAtomType(keys[1]);
114
115			LennardJonesInteractionType* ljit = dynamic_cast<LennardJonesInteractionType*>(nbt);
116
117			if (ljit == NULL) {
118	gezelter	1471	sprintf( painCave.errMsg,
119	jmichalk	1683	"LJ::initialize could not convert NonBondedInteractionType\n"
120			"\tto LennardJonesInteractionType for %s - %s interaction.\n",
121			at1->getName().c_str(),
122			at2->getName().c_str());
123	gezelter	1471	painCave.severity = OPENMD_ERROR;
124			painCave.isFatal = 1;
125			simError();
126			}
127
128	jmichalk	1683	RealType sigma = ljit->getSigma();
129			RealType epsilon = ljit->getEpsilon();
130			addExplicitInteraction(at1, at2, sigma, epsilon);
131	gezelter	1471	}
132			}
133			initialized_ = true;
134			}
135
136
137			void LJ::addType(AtomType* atomType){
138	gezelter	1710	LennardJonesAdapter lja1 = LennardJonesAdapter(atomType);
139
140			RealType sigma1 = lja1.getSigma();
141			RealType epsilon1 = lja1.getEpsilon();
142	gezelter	1502
143	gezelter	1471	// add it to the map:
144	gezelter	1895	int atid = atomType->getIdent();
145			int ljtid = LJtypes.size();
146
147			pair<set<int>::iterator,bool> ret;
148			ret = LJtypes.insert( atid );
149	gezelter	1471	if (ret.second == false) {
150			sprintf( painCave.errMsg,
151			"LJ already had a previous entry with ident %d\n",
152	gezelter	1895	atid) ;
153	gezelter	1471	painCave.severity = OPENMD_INFO;
154			painCave.isFatal = 0;
155			simError();
156			}
157	gezelter	1895
158			LJtids[atid] = ljtid;
159			MixingMap[ljtid].resize( nLJ_ );
160
161	gezelter	1471	// Now, iterate over all known types and add to the mixing map:
162
163	gezelter	1895	std::set<int>::iterator it;
164			for( it = LJtypes.begin(); it != LJtypes.end(); ++it) {
165	gezelter	1471
166	gezelter	1895	int ljtid2 = LJtids[ (*it) ];
167			AtomType* atype2 = forceField_->getAtomType( (*it) );
168
169	gezelter	1471	LJInteractionData mixer;
170			mixer.sigma = getSigma(atomType, atype2);
171			mixer.epsilon = getEpsilon(atomType, atype2);
172			mixer.sigmai = 1.0 / mixer.sigma;
173			mixer.explicitlySet = false;
174	gezelter	1895	MixingMap[ljtid2].resize( nLJ_ );
175	gezelter	1471
176	gezelter	1895	MixingMap[ljtid][ljtid2] = mixer;
177			if (ljtid2 != ljtid) {
178			MixingMap[ljtid2][ljtid] = mixer;
179	gezelter	1471	}
180			}
181			}
182
183			void LJ::addExplicitInteraction(AtomType* atype1, AtomType* atype2, RealType sigma, RealType epsilon){
184
185			LJInteractionData mixer;
186			mixer.sigma = sigma;
187			mixer.epsilon = epsilon;
188			mixer.sigmai = 1.0 / mixer.sigma;
189			mixer.explicitlySet = true;
190
191	gezelter	1895	int atid1 = atype1->getIdent();
192			int atid2 = atype2->getIdent();
193
194			int ljtid1, ljtid2;
195
196			pair<set<int>::iterator,bool> ret;
197			ret = LJtypes.insert( atid1 );
198			if (ret.second == false) {
199			// already had this type in the LJMap, just get the ljtid:
200			ljtid1 = LJtids[ atid1 ];
201			} else {
202			// didn't already have it, so make a new one and assign it:
203			ljtid1 = nLJ_;
204			LJtids[atid1] = nLJ_;
205			nLJ_++;
206			}
207
208			ret = LJtypes.insert( atid2 );
209			if (ret.second == false) {
210			// already had this type in the LJMap, just get the ljtid:
211			ljtid2 = LJtids[ atid2 ];
212			} else {
213			// didn't already have it, so make a new one and assign it:
214			ljtid2 = nLJ_;
215			LJtids[atid2] = nLJ_;
216			nLJ_++;
217			}
218	gezelter	1471
219	gezelter	1895	MixingMap.resize(nLJ_);
220			MixingMap[ljtid1].resize(nLJ_);
221
222			MixingMap[ljtid1][ljtid2] = mixer;
223			if (ljtid2 != ljtid1) {
224			MixingMap[ljtid2].resize(nLJ_);
225			MixingMap[ljtid2][ljtid1] = mixer;
226	gezelter	1471	}
227			}
228
229	gezelter	1536	void LJ::calcForce(InteractionData &idat) {
230	gezelter	1471	if (!initialized_) initialize();
231
232	gezelter	1895	LJInteractionData &mixer = MixingMap[LJtids[idat.atid1]][LJtids[idat.atid2]];
233	gezelter	1473
234	gezelter	1895	RealType sigmai = mixer.sigmai;
235			RealType epsilon = mixer.epsilon;
236
237			RealType ros;
238			RealType rcos;
239			RealType myPot = 0.0;
240			RealType myPotC = 0.0;
241			RealType myDeriv = 0.0;
242			RealType myDerivC = 0.0;
243
244			ros = (idat.rij) sigmai;
245
246			getLJfunc(ros, myPot, myDeriv);
247
248			if (idat.shiftedPot) {
249			rcos = (idat.rcut) sigmai;
250			getLJfunc(rcos, myPotC, myDerivC);
251			myDerivC = 0.0;
252			} else if (idat.shiftedForce) {
253			rcos = (idat.rcut) sigmai;
254			getLJfunc(rcos, myPotC, myDerivC);
255			myPotC = myPotC + myDerivC * ((idat.rij) - (idat.rcut)) * sigmai;
256			} else {
257			myPotC = 0.0;
258			myDerivC = 0.0;
259	gezelter	1471	}
260	gezelter	1895
261			RealType pot_temp = (idat.vdwMult) epsilon * (myPot - myPotC);
262			*(idat.vpair) += pot_temp;
263
264			RealType dudr = (idat.sw) (idat.vdwMult) epsilon * (myDeriv -
265			myDerivC)*sigmai;
266			((idat.pot))[VANDERWAALS_FAMILY] += (idat.sw) * pot_temp;
267			(idat.f1) += (idat.d) * dudr / *(idat.rij);
268
269	gezelter	1471	return;
270			}
271
272	gezelter	1472	void LJ::getLJfunc(RealType r, RealType &pot, RealType &deriv) {
273
274	gezelter	1471	RealType ri = 1.0 / r;
275			RealType ri2 = ri * ri;
276			RealType ri6 = ri2 * ri2 * ri2;
277			RealType ri7 = ri6 * ri;
278			RealType ri12 = ri6 * ri6;
279			RealType ri13 = ri12 * ri;
280	gezelter	1472
281	gezelter	1471	pot = 4.0 * (ri12 - ri6);
282			deriv = 24.0 * (ri7 - 2.0 * ri13);
283	gezelter	1472
284	gezelter	1471	return;
285			}
286	gezelter	1472
287	gezelter	1545	RealType LJ::getSuggestedCutoffRadius(pair<AtomType, AtomType> atypes) {
288	gezelter	1505	if (!initialized_) initialize();
289	gezelter	1895
290			int atid1 = atypes.first->getIdent();
291			int atid2 = atypes.second->getIdent();
292			int ljtid1 = LJtids[atid1];
293			int ljtid2 = LJtids[atid2];
294
295			if (ljtid1 == -1 \|\| ljtid2 == -1) return 0.0;
296			else {
297			LJInteractionData mixer = MixingMap[ljtid1][ljtid2];
298	gezelter	1505	return 2.5 * mixer.sigma;
299			}
300			}
301	gezelter	1895
302	gezelter	1471	}