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, 24107 (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/LennardJonesInteractionType.hpp"

namespace OpenMD {

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

  LJParam LJ::getLJParam(AtomType* atomType) {
    
    // Do sanity checking on the AtomType we were passed before
    // building any data structures:
    if (!atomType->isLennardJones()) {
      sprintf( painCave.errMsg,
               "LJ::getLJParam was passed an atomType (%s) that does not\n"
               "\tappear to be a Lennard-Jones atom.\n",
               atomType->getName().c_str());
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
    
    GenericData* data = atomType->getPropertyByName("LennardJones");
    if (data == NULL) {
      sprintf( painCave.errMsg, "LJ::getLJParam could not find Lennard-Jones\n"
               "\tparameters for atomType %s.\n", atomType->getName().c_str());
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError(); 
    }
    
    LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
    if (ljData == NULL) {
      sprintf( painCave.errMsg,
               "LJ::getLJParam could not convert GenericData to LJParam for\n"
               "\tatom type %s\n", atomType->getName().c_str());
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();          
    }
    
    return ljData->getData();
  }

  RealType LJ::getSigma(AtomType* atomType) {    
    LJParam ljParam = getLJParam(atomType);
    return ljParam.sigma;
  }

  RealType LJ::getSigma(AtomType* atomType1, AtomType* atomType2) {    
    RealType sigma1 = getSigma(atomType1);
    RealType sigma2 = getSigma(atomType2);
    
    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* atomType) {    
    LJParam ljParam = getLJParam(atomType);
    return ljParam.epsilon;
  }

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

  void LJ::initialize() {    
    ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
    ForceField::AtomTypeContainer::MapTypeIterator i;
    AtomType* at;

    for (at = atomTypes->beginType(i); at != NULL; 
         at = atomTypes->nextType(i)) {
      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){
    RealType sigma1 = getSigma(atomType);
    RealType epsilon1 = getEpsilon(atomType);
    
    // add it to the map:
    AtomTypeProperties atp = atomType->getATP();    

    pair<map<int,AtomType*>::iterator,bool> ret;    
    ret = LJMap.insert( pair<int, AtomType*>(atp.ident, atomType) );
    if (ret.second == false) {
      sprintf( painCave.errMsg,
               "LJ already had a previous entry with ident %d\n",
               atp.ident);
      painCave.severity = OPENMD_INFO;
      painCave.isFatal = 0;
      simError();         
    }
    
    // Now, iterate over all known types and add to the mixing map:
    
    std::map<int, AtomType*>::iterator it;
    for( it = LJMap.begin(); it != LJMap.end(); ++it) {
      
      AtomType* atype2 = (*it).second;

      LJInteractionData mixer;
      mixer.sigma = getSigma(atomType, atype2);
      mixer.epsilon = getEpsilon(atomType, atype2);
      mixer.sigmai = 1.0 / mixer.sigma;
      mixer.explicitlySet = false;

      std::pair<AtomType*, AtomType*> key1, key2;
      key1 = std::make_pair(atomType, atype2);
      key2 = std::make_pair(atype2, atomType);
      
      MixingMap[key1] = mixer;
      if (key2 != key1) {
        MixingMap[key2] = 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;

    std::pair<AtomType*, AtomType*> key1, key2;
    key1 = std::make_pair(atype1, atype2);
    key2 = std::make_pair(atype2, atype1);
    
    MixingMap[key1] = mixer;
    if (key2 != key1) {
      MixingMap[key2] = mixer;
    }    
  }
 
  void LJ::calcForce(InteractionData &idat) {
    if (!initialized_) initialize();
    map<pair<AtomType*, AtomType*>, LJInteractionData>::iterator it;
    it = MixingMap.find( idat.atypes );
    
    if (it != MixingMap.end())  {
      
      LJInteractionData mixer = (*it).second;
      
      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();   
    map<pair<AtomType*, AtomType*>, LJInteractionData>::iterator it;
    it = MixingMap.find(atypes);
    if (it == MixingMap.end()) 
      return 0.0;
    else  {
      LJInteractionData mixer = (*it).second;
      return 2.5 * mixer.sigma;
    }
  }

}
Revision:	1683
Committed:	Wed Feb 29 20:33:01 2012 UTC (13 years, 8 months ago) by jmichalk
File size:	10201 byte(s)
Log Message:	LJ.cpp has been updated to more correctly deal with nonbonded interactions (i.e. explicit interactions where the species are not necessarily defined to be lennardJones type atoms)
#	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			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (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	jmichalk	1683	#include "types/LennardJonesInteractionType.hpp"
50	gezelter	1471
51			namespace OpenMD {
52
53	gezelter	1583	LJ::LJ() : name_("LJ"), initialized_(false), forceField_(NULL) {}
54	gezelter	1471
55			LJParam LJ::getLJParam(AtomType* atomType) {
56
57			// Do sanity checking on the AtomType we were passed before
58			// building any data structures:
59			if (!atomType->isLennardJones()) {
60			sprintf( painCave.errMsg,
61			"LJ::getLJParam was passed an atomType (%s) that does not\n"
62			"\tappear to be a Lennard-Jones atom.\n",
63			atomType->getName().c_str());
64			painCave.severity = OPENMD_ERROR;
65			painCave.isFatal = 1;
66			simError();
67			}
68
69			GenericData* data = atomType->getPropertyByName("LennardJones");
70			if (data == NULL) {
71			sprintf( painCave.errMsg, "LJ::getLJParam could not find Lennard-Jones\n"
72			"\tparameters for atomType %s.\n", atomType->getName().c_str());
73			painCave.severity = OPENMD_ERROR;
74			painCave.isFatal = 1;
75			simError();
76			}
77
78			LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
79			if (ljData == NULL) {
80			sprintf( painCave.errMsg,
81			"LJ::getLJParam could not convert GenericData to LJParam for\n"
82			"\tatom type %s\n", atomType->getName().c_str());
83			painCave.severity = OPENMD_ERROR;
84			painCave.isFatal = 1;
85			simError();
86			}
87
88			return ljData->getData();
89			}
90
91			RealType LJ::getSigma(AtomType* atomType) {
92			LJParam ljParam = getLJParam(atomType);
93			return ljParam.sigma;
94			}
95
96			RealType LJ::getSigma(AtomType* atomType1, AtomType* atomType2) {
97			RealType sigma1 = getSigma(atomType1);
98			RealType sigma2 = getSigma(atomType2);
99
100			ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
101	gezelter	1502	string DistanceMix = fopts.getDistanceMixingRule();
102	gezelter	1471	toUpper(DistanceMix);
103
104			if (DistanceMix == "GEOMETRIC")
105			return sqrt(sigma1 * sigma2);
106			else
107			return 0.5 * (sigma1 + sigma2);
108			}
109
110			RealType LJ::getEpsilon(AtomType* atomType) {
111			LJParam ljParam = getLJParam(atomType);
112			return ljParam.epsilon;
113			}
114
115			RealType LJ::getEpsilon(AtomType* atomType1, AtomType* atomType2) {
116			RealType epsilon1 = getEpsilon(atomType1);
117			RealType epsilon2 = getEpsilon(atomType2);
118			return sqrt(epsilon1 * epsilon2);
119			}
120
121			void LJ::initialize() {
122	gezelter	1476	ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
123	gezelter	1471	ForceField::AtomTypeContainer::MapTypeIterator i;
124			AtomType* at;
125
126	gezelter	1476	for (at = atomTypes->beginType(i); at != NULL;
127			at = atomTypes->nextType(i)) {
128	jmichalk	1683	if (at->isLennardJones()){
129			addType(at);
130			}
131	gezelter	1471	}
132	gezelter	1476	ForceField::NonBondedInteractionTypeContainer* nbiTypes = forceField_->getNonBondedInteractionTypes();
133	gezelter	1471	ForceField::NonBondedInteractionTypeContainer::MapTypeIterator j;
134			NonBondedInteractionType* nbt;
135	jmichalk	1683	ForceField::NonBondedInteractionTypeContainer::KeyType keys;
136	gezelter	1471
137	jmichalk	1683
138	gezelter	1476	for (nbt = nbiTypes->beginType(j); nbt != NULL;
139			nbt = nbiTypes->nextType(j)) {
140	jmichalk	1683
141	gezelter	1471	if (nbt->isLennardJones()) {
142	jmichalk	1683	keys = nbiTypes->getKeys(j);
143			AtomType* at1 = forceField_->getAtomType(keys[0]);
144			AtomType* at2 = forceField_->getAtomType(keys[1]);
145
146			LennardJonesInteractionType* ljit = dynamic_cast<LennardJonesInteractionType*>(nbt);
147
148			if (ljit == NULL) {
149	gezelter	1471	sprintf( painCave.errMsg,
150	jmichalk	1683	"LJ::initialize could not convert NonBondedInteractionType\n"
151			"\tto LennardJonesInteractionType for %s - %s interaction.\n",
152			at1->getName().c_str(),
153			at2->getName().c_str());
154	gezelter	1471	painCave.severity = OPENMD_ERROR;
155			painCave.isFatal = 1;
156			simError();
157			}
158
159	jmichalk	1683	RealType sigma = ljit->getSigma();
160			RealType epsilon = ljit->getEpsilon();
161			addExplicitInteraction(at1, at2, sigma, epsilon);
162	gezelter	1471	}
163			}
164			initialized_ = true;
165			}
166
167
168
169			void LJ::addType(AtomType* atomType){
170			RealType sigma1 = getSigma(atomType);
171			RealType epsilon1 = getEpsilon(atomType);
172	gezelter	1502
173	gezelter	1471	// add it to the map:
174			AtomTypeProperties atp = atomType->getATP();
175	gezelter	1473
176	gezelter	1502	pair<map<int,AtomType*>::iterator,bool> ret;
177			ret = LJMap.insert( pair<int, AtomType*>(atp.ident, atomType) );
178	gezelter	1471	if (ret.second == false) {
179			sprintf( painCave.errMsg,
180			"LJ already had a previous entry with ident %d\n",
181			atp.ident);
182			painCave.severity = OPENMD_INFO;
183			painCave.isFatal = 0;
184			simError();
185			}
186
187			// Now, iterate over all known types and add to the mixing map:
188
189			std::map<int, AtomType*>::iterator it;
190			for( it = LJMap.begin(); it != LJMap.end(); ++it) {
191
192			AtomType* atype2 = (*it).second;
193
194			LJInteractionData mixer;
195			mixer.sigma = getSigma(atomType, atype2);
196			mixer.epsilon = getEpsilon(atomType, atype2);
197			mixer.sigmai = 1.0 / mixer.sigma;
198			mixer.explicitlySet = false;
199
200			std::pair<AtomType, AtomType> key1, key2;
201			key1 = std::make_pair(atomType, atype2);
202			key2 = std::make_pair(atype2, atomType);
203
204			MixingMap[key1] = mixer;
205			if (key2 != key1) {
206			MixingMap[key2] = mixer;
207			}
208			}
209			}
210
211			void LJ::addExplicitInteraction(AtomType* atype1, AtomType* atype2, RealType sigma, RealType epsilon){
212
213			LJInteractionData mixer;
214			mixer.sigma = sigma;
215			mixer.epsilon = epsilon;
216			mixer.sigmai = 1.0 / mixer.sigma;
217			mixer.explicitlySet = true;
218
219			std::pair<AtomType, AtomType> key1, key2;
220			key1 = std::make_pair(atype1, atype2);
221			key2 = std::make_pair(atype2, atype1);
222
223			MixingMap[key1] = mixer;
224			if (key2 != key1) {
225			MixingMap[key2] = mixer;
226			}
227			}
228
229	gezelter	1536	void LJ::calcForce(InteractionData &idat) {
230	gezelter	1471	if (!initialized_) initialize();
231	gezelter	1505	map<pair<AtomType, AtomType>, LJInteractionData>::iterator it;
232	gezelter	1571	it = MixingMap.find( idat.atypes );
233	gezelter	1471
234	gezelter	1505	if (it != MixingMap.end()) {
235
236			LJInteractionData mixer = (*it).second;
237
238			RealType sigmai = mixer.sigmai;
239			RealType epsilon = mixer.epsilon;
240
241			RealType ros;
242			RealType rcos;
243			RealType myPot = 0.0;
244			RealType myPotC = 0.0;
245			RealType myDeriv = 0.0;
246			RealType myDerivC = 0.0;
247
248	gezelter	1582	ros = (idat.rij) sigmai;
249	gezelter	1505
250			getLJfunc(ros, myPot, myDeriv);
251
252	gezelter	1583	if (idat.shiftedPot) {
253	gezelter	1554	rcos = (idat.rcut) sigmai;
254	gezelter	1505	getLJfunc(rcos, myPotC, myDerivC);
255			myDerivC = 0.0;
256	gezelter	1583	} else if (idat.shiftedForce) {
257	gezelter	1554	rcos = (idat.rcut) sigmai;
258	gezelter	1505	getLJfunc(rcos, myPotC, myDerivC);
259	gezelter	1554	myPotC = myPotC + myDerivC * ((idat.rij) - (idat.rcut)) * sigmai;
260	gezelter	1505	} else {
261			myPotC = 0.0;
262			myDerivC = 0.0;
263			}
264	gezelter	1473
265	gezelter	1554	RealType pot_temp = (idat.vdwMult) epsilon * (myPot - myPotC);
266			*(idat.vpair) += pot_temp;
267	gezelter	1505
268	gezelter	1554	RealType dudr = (idat.sw) (idat.vdwMult) epsilon * (myDeriv -
269	gezelter	1582	myDerivC)*sigmai;
270	gezelter	1583
271	gezelter	1582	((idat.pot))[VANDERWAALS_FAMILY] += (idat.sw) * pot_temp;
272	gezelter	1629	(idat.f1) += (idat.d) * dudr / *(idat.rij);
273	gezelter	1471	}
274			return;
275			}
276
277	gezelter	1472	void LJ::getLJfunc(RealType r, RealType &pot, RealType &deriv) {
278
279	gezelter	1471	RealType ri = 1.0 / r;
280			RealType ri2 = ri * ri;
281			RealType ri6 = ri2 * ri2 * ri2;
282			RealType ri7 = ri6 * ri;
283			RealType ri12 = ri6 * ri6;
284			RealType ri13 = ri12 * ri;
285	gezelter	1472
286	gezelter	1471	pot = 4.0 * (ri12 - ri6);
287			deriv = 24.0 * (ri7 - 2.0 * ri13);
288	gezelter	1472
289	gezelter	1471	return;
290			}
291	gezelter	1472
292	gezelter	1545	RealType LJ::getSuggestedCutoffRadius(pair<AtomType, AtomType> atypes) {
293	gezelter	1505	if (!initialized_) initialize();
294			map<pair<AtomType, AtomType>, LJInteractionData>::iterator it;
295	gezelter	1545	it = MixingMap.find(atypes);
296	gezelter	1505	if (it == MixingMap.end())
297			return 0.0;
298			else {
299			LJInteractionData mixer = (*it).second;
300			return 2.5 * mixer.sigma;
301			}
302			}
303	gezelter	1471
304			}