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]  Vardeman & Gezelter, in progress (2009).                        
 */

#include <stdio.h>
#include <string.h>

#include <cmath>
#include "nonbonded/LJ.hpp"
#include "utils/simError.h"

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;

    for (nbt = nbiTypes->beginType(j); nbt != NULL; 
         nbt = nbiTypes->nextType(j)) {
      
      if (nbt->isLennardJones()) {
        
        pair<AtomType*, AtomType*> atypes = nbt->getAtomTypes();
        
        GenericData* data = nbt->getPropertyByName("LennardJones");
        if (data == NULL) {
          sprintf( painCave.errMsg, "LJ::rebuildMixingMap could not find\n"
               "\tLennard-Jones parameters for %s - %s interaction.\n", 
                   atypes.first->getName().c_str(),
                   atypes.second->getName().c_str());
          painCave.severity = OPENMD_ERROR;
          painCave.isFatal = 1;
          simError(); 
        }
    
        LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
        if (ljData == NULL) {
          sprintf( painCave.errMsg,
                   "LJ::rebuildMixingMap could not convert GenericData to\n"
                   "\tLJParam for %s - %s interaction.\n", 
                   atypes.first->getName().c_str(),
                   atypes.second->getName().c_str());
          painCave.severity = OPENMD_ERROR;
          painCave.isFatal = 1;
          simError();          
        }
        
        LJParam ljParam = ljData->getData();

        RealType sigma = ljParam.sigma;
        RealType epsilon = ljParam.epsilon;

        addExplicitInteraction(atypes.first, atypes.second, 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){
    
    // in case these weren't already in the map
    addType(atype1);
    addType(atype2);

    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:	1629
Committed:	Wed Sep 14 21:15:17 2011 UTC (13 years, 9 months ago) by gezelter
File size:	10566 byte(s)
Log Message:	Merging changes from old branch into development branch
#	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			* [4] Vardeman & Gezelter, in progress (2009).
40			*/
41
42			#include <stdio.h>
43			#include <string.h>
44
45			#include <cmath>
46			#include "nonbonded/LJ.hpp"
47			#include "utils/simError.h"
48
49			namespace OpenMD {
50
51	gezelter	1583	LJ::LJ() : name_("LJ"), initialized_(false), forceField_(NULL) {}
52	gezelter	1471
53			LJParam LJ::getLJParam(AtomType* atomType) {
54
55			// Do sanity checking on the AtomType we were passed before
56			// building any data structures:
57			if (!atomType->isLennardJones()) {
58			sprintf( painCave.errMsg,
59			"LJ::getLJParam was passed an atomType (%s) that does not\n"
60			"\tappear to be a Lennard-Jones atom.\n",
61			atomType->getName().c_str());
62			painCave.severity = OPENMD_ERROR;
63			painCave.isFatal = 1;
64			simError();
65			}
66
67			GenericData* data = atomType->getPropertyByName("LennardJones");
68			if (data == NULL) {
69			sprintf( painCave.errMsg, "LJ::getLJParam could not find Lennard-Jones\n"
70			"\tparameters for atomType %s.\n", atomType->getName().c_str());
71			painCave.severity = OPENMD_ERROR;
72			painCave.isFatal = 1;
73			simError();
74			}
75
76			LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
77			if (ljData == NULL) {
78			sprintf( painCave.errMsg,
79			"LJ::getLJParam could not convert GenericData to LJParam for\n"
80			"\tatom type %s\n", atomType->getName().c_str());
81			painCave.severity = OPENMD_ERROR;
82			painCave.isFatal = 1;
83			simError();
84			}
85
86			return ljData->getData();
87			}
88
89			RealType LJ::getSigma(AtomType* atomType) {
90			LJParam ljParam = getLJParam(atomType);
91			return ljParam.sigma;
92			}
93
94			RealType LJ::getSigma(AtomType* atomType1, AtomType* atomType2) {
95			RealType sigma1 = getSigma(atomType1);
96			RealType sigma2 = getSigma(atomType2);
97
98			ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
99	gezelter	1502	string DistanceMix = fopts.getDistanceMixingRule();
100	gezelter	1471	toUpper(DistanceMix);
101
102			if (DistanceMix == "GEOMETRIC")
103			return sqrt(sigma1 * sigma2);
104			else
105			return 0.5 * (sigma1 + sigma2);
106			}
107
108			RealType LJ::getEpsilon(AtomType* atomType) {
109			LJParam ljParam = getLJParam(atomType);
110			return ljParam.epsilon;
111			}
112
113			RealType LJ::getEpsilon(AtomType* atomType1, AtomType* atomType2) {
114			RealType epsilon1 = getEpsilon(atomType1);
115			RealType epsilon2 = getEpsilon(atomType2);
116			return sqrt(epsilon1 * epsilon2);
117			}
118
119			void LJ::initialize() {
120	gezelter	1476	ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
121	gezelter	1471	ForceField::AtomTypeContainer::MapTypeIterator i;
122			AtomType* at;
123
124	gezelter	1476	for (at = atomTypes->beginType(i); at != NULL;
125			at = atomTypes->nextType(i)) {
126	gezelter	1471
127			if (at->isLennardJones())
128			addType(at);
129			}
130
131	gezelter	1476	ForceField::NonBondedInteractionTypeContainer* nbiTypes = forceField_->getNonBondedInteractionTypes();
132	gezelter	1471	ForceField::NonBondedInteractionTypeContainer::MapTypeIterator j;
133			NonBondedInteractionType* nbt;
134
135	gezelter	1476	for (nbt = nbiTypes->beginType(j); nbt != NULL;
136			nbt = nbiTypes->nextType(j)) {
137	gezelter	1471
138			if (nbt->isLennardJones()) {
139
140	gezelter	1502	pair<AtomType, AtomType> atypes = nbt->getAtomTypes();
141	gezelter	1471
142			GenericData* data = nbt->getPropertyByName("LennardJones");
143			if (data == NULL) {
144			sprintf( painCave.errMsg, "LJ::rebuildMixingMap could not find\n"
145			"\tLennard-Jones parameters for %s - %s interaction.\n",
146			atypes.first->getName().c_str(),
147			atypes.second->getName().c_str());
148			painCave.severity = OPENMD_ERROR;
149			painCave.isFatal = 1;
150			simError();
151			}
152
153			LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
154			if (ljData == NULL) {
155			sprintf( painCave.errMsg,
156			"LJ::rebuildMixingMap could not convert GenericData to\n"
157			"\tLJParam for %s - %s interaction.\n",
158			atypes.first->getName().c_str(),
159			atypes.second->getName().c_str());
160			painCave.severity = OPENMD_ERROR;
161			painCave.isFatal = 1;
162			simError();
163			}
164
165			LJParam ljParam = ljData->getData();
166
167			RealType sigma = ljParam.sigma;
168			RealType epsilon = ljParam.epsilon;
169
170			addExplicitInteraction(atypes.first, atypes.second, sigma, epsilon);
171			}
172			}
173			initialized_ = true;
174			}
175
176
177
178			void LJ::addType(AtomType* atomType){
179			RealType sigma1 = getSigma(atomType);
180			RealType epsilon1 = getEpsilon(atomType);
181	gezelter	1502
182	gezelter	1471	// add it to the map:
183			AtomTypeProperties atp = atomType->getATP();
184	gezelter	1473
185	gezelter	1502	pair<map<int,AtomType*>::iterator,bool> ret;
186			ret = LJMap.insert( pair<int, AtomType*>(atp.ident, atomType) );
187	gezelter	1471	if (ret.second == false) {
188			sprintf( painCave.errMsg,
189			"LJ already had a previous entry with ident %d\n",
190			atp.ident);
191			painCave.severity = OPENMD_INFO;
192			painCave.isFatal = 0;
193			simError();
194			}
195
196			// Now, iterate over all known types and add to the mixing map:
197
198			std::map<int, AtomType*>::iterator it;
199			for( it = LJMap.begin(); it != LJMap.end(); ++it) {
200
201			AtomType* atype2 = (*it).second;
202
203			LJInteractionData mixer;
204			mixer.sigma = getSigma(atomType, atype2);
205			mixer.epsilon = getEpsilon(atomType, atype2);
206			mixer.sigmai = 1.0 / mixer.sigma;
207			mixer.explicitlySet = false;
208
209			std::pair<AtomType, AtomType> key1, key2;
210			key1 = std::make_pair(atomType, atype2);
211			key2 = std::make_pair(atype2, atomType);
212
213			MixingMap[key1] = mixer;
214			if (key2 != key1) {
215			MixingMap[key2] = mixer;
216			}
217			}
218			}
219
220			void LJ::addExplicitInteraction(AtomType* atype1, AtomType* atype2, RealType sigma, RealType epsilon){
221
222			// in case these weren't already in the map
223			addType(atype1);
224			addType(atype2);
225
226			LJInteractionData mixer;
227			mixer.sigma = sigma;
228			mixer.epsilon = epsilon;
229			mixer.sigmai = 1.0 / mixer.sigma;
230			mixer.explicitlySet = true;
231
232			std::pair<AtomType, AtomType> key1, key2;
233			key1 = std::make_pair(atype1, atype2);
234			key2 = std::make_pair(atype2, atype1);
235
236			MixingMap[key1] = mixer;
237			if (key2 != key1) {
238			MixingMap[key2] = mixer;
239			}
240			}
241
242	gezelter	1536	void LJ::calcForce(InteractionData &idat) {
243	gezelter	1502
244	gezelter	1471	if (!initialized_) initialize();
245	gezelter	1587
246	gezelter	1505	map<pair<AtomType, AtomType>, LJInteractionData>::iterator it;
247	gezelter	1571	it = MixingMap.find( idat.atypes );
248	gezelter	1471
249	gezelter	1505	if (it != MixingMap.end()) {
250
251			LJInteractionData mixer = (*it).second;
252
253			RealType sigmai = mixer.sigmai;
254			RealType epsilon = mixer.epsilon;
255
256			RealType ros;
257			RealType rcos;
258			RealType myPot = 0.0;
259			RealType myPotC = 0.0;
260			RealType myDeriv = 0.0;
261			RealType myDerivC = 0.0;
262
263	gezelter	1582	ros = (idat.rij) sigmai;
264	gezelter	1505
265			getLJfunc(ros, myPot, myDeriv);
266
267	gezelter	1583	if (idat.shiftedPot) {
268	gezelter	1554	rcos = (idat.rcut) sigmai;
269	gezelter	1505	getLJfunc(rcos, myPotC, myDerivC);
270			myDerivC = 0.0;
271	gezelter	1583	} else if (idat.shiftedForce) {
272	gezelter	1554	rcos = (idat.rcut) sigmai;
273	gezelter	1505	getLJfunc(rcos, myPotC, myDerivC);
274	gezelter	1554	myPotC = myPotC + myDerivC * ((idat.rij) - (idat.rcut)) * sigmai;
275	gezelter	1505	} else {
276			myPotC = 0.0;
277			myDerivC = 0.0;
278			}
279	gezelter	1473
280	gezelter	1554	RealType pot_temp = (idat.vdwMult) epsilon * (myPot - myPotC);
281			*(idat.vpair) += pot_temp;
282	gezelter	1505
283	gezelter	1554	RealType dudr = (idat.sw) (idat.vdwMult) epsilon * (myDeriv -
284	gezelter	1582	myDerivC)*sigmai;
285	gezelter	1583
286	gezelter	1582	((idat.pot))[VANDERWAALS_FAMILY] += (idat.sw) * pot_temp;
287	gezelter	1629	(idat.f1) += (idat.d) * dudr / *(idat.rij);
288	gezelter	1471	}
289			return;
290			}
291
292	gezelter	1472	void LJ::getLJfunc(RealType r, RealType &pot, RealType &deriv) {
293
294	gezelter	1471	RealType ri = 1.0 / r;
295			RealType ri2 = ri * ri;
296			RealType ri6 = ri2 * ri2 * ri2;
297			RealType ri7 = ri6 * ri;
298			RealType ri12 = ri6 * ri6;
299			RealType ri13 = ri12 * ri;
300	gezelter	1472
301	gezelter	1471	pot = 4.0 * (ri12 - ri6);
302			deriv = 24.0 * (ri7 - 2.0 * ri13);
303	gezelter	1472
304	gezelter	1471	return;
305			}
306	gezelter	1472
307	gezelter	1545	RealType LJ::getSuggestedCutoffRadius(pair<AtomType, AtomType> atypes) {
308	gezelter	1505	if (!initialized_) initialize();
309			map<pair<AtomType, AtomType>, LJInteractionData>::iterator it;
310	gezelter	1545	it = MixingMap.find(atypes);
311	gezelter	1505	if (it == MixingMap.end())
312			return 0.0;
313			else {
314			LJInteractionData mixer = (*it).second;
315			return 2.5 * mixer.sigma;
316			}
317			}
318	gezelter	1471
319			}