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, 7 months ago) by gezelter
File size:	10566 byte(s)
Log Message:	Merging changes from old branch into development branch
#	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/LJ.hpp"
47	#include "utils/simError.h"
48
49	namespace OpenMD {
50
51	LJ::LJ() : name_("LJ"), initialized_(false), forceField_(NULL) {}
52
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	string DistanceMix = fopts.getDistanceMixingRule();
100	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	ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
121	ForceField::AtomTypeContainer::MapTypeIterator i;
122	AtomType* at;
123
124	for (at = atomTypes->beginType(i); at != NULL;
125	at = atomTypes->nextType(i)) {
126
127	if (at->isLennardJones())
128	addType(at);
129	}
130
131	ForceField::NonBondedInteractionTypeContainer* nbiTypes = forceField_->getNonBondedInteractionTypes();
132	ForceField::NonBondedInteractionTypeContainer::MapTypeIterator j;
133	NonBondedInteractionType* nbt;
134
135	for (nbt = nbiTypes->beginType(j); nbt != NULL;
136	nbt = nbiTypes->nextType(j)) {
137
138	if (nbt->isLennardJones()) {
139
140	pair<AtomType, AtomType> atypes = nbt->getAtomTypes();
141
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
182	// add it to the map:
183	AtomTypeProperties atp = atomType->getATP();
184
185	pair<map<int,AtomType*>::iterator,bool> ret;
186	ret = LJMap.insert( pair<int, AtomType*>(atp.ident, atomType) );
187	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	void LJ::calcForce(InteractionData &idat) {
243
244	if (!initialized_) initialize();
245
246	map<pair<AtomType, AtomType>, LJInteractionData>::iterator it;
247	it = MixingMap.find( idat.atypes );
248
249	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	ros = (idat.rij) sigmai;
264
265	getLJfunc(ros, myPot, myDeriv);
266
267	if (idat.shiftedPot) {
268	rcos = (idat.rcut) sigmai;
269	getLJfunc(rcos, myPotC, myDerivC);
270	myDerivC = 0.0;
271	} else if (idat.shiftedForce) {
272	rcos = (idat.rcut) sigmai;
273	getLJfunc(rcos, myPotC, myDerivC);
274	myPotC = myPotC + myDerivC * ((idat.rij) - (idat.rcut)) * sigmai;
275	} else {
276	myPotC = 0.0;
277	myDerivC = 0.0;
278	}
279
280	RealType pot_temp = (idat.vdwMult) epsilon * (myPot - myPotC);
281	*(idat.vpair) += pot_temp;
282
283	RealType dudr = (idat.sw) (idat.vdwMult) epsilon * (myDeriv -
284	myDerivC)*sigmai;
285
286	((idat.pot))[VANDERWAALS_FAMILY] += (idat.sw) * pot_temp;
287	(idat.f1) += (idat.d) * dudr / *(idat.rij);
288	}
289	return;
290	}
291
292	void LJ::getLJfunc(RealType r, RealType &pot, RealType &deriv) {
293
294	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
301	pot = 4.0 * (ri12 - ri6);
302	deriv = 24.0 * (ri7 - 2.0 * ri13);
303
304	return;
305	}
306
307	RealType LJ::getSuggestedCutoffRadius(pair<AtomType, AtomType> atypes) {
308	if (!initialized_) initialize();
309	map<pair<AtomType, AtomType>, LJInteractionData>::iterator it;
310	it = MixingMap.find(atypes);
311	if (it == MixingMap.end())
312	return 0.0;
313	else {
314	LJInteractionData mixer = (*it).second;
315	return 2.5 * mixer.sigma;
316	}
317	}
318
319	}