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), shiftedPot_(false), 
             shiftedFrc_(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;
      
      cerr << "ros = " << ros << "\n";
      
      getLJfunc(ros, myPot, myDeriv);
      
      if (shiftedPot_) {
        rcos = *(idat.rcut) * sigmai;
        getLJfunc(rcos, myPotC, myDerivC);
        myDerivC = 0.0;
      } else if (LJ::shiftedFrc_) {
        rcos = *(idat.rcut) * sigmai;
        getLJfunc(rcos, myPotC, myDerivC);
        myPotC = myPotC + myDerivC * (*(idat.rij) - *(idat.rcut)) * sigmai;
      } else {
        myPotC = 0.0;
        myDerivC = 0.0;        
      }

      cerr << "myPot =  " << myPot << "\n";
      cerr << "myPotC =  " << myPotC << "\n";
      cerr << "epsilon =  " << epsilon << "\n";
      cerr << "vdwm =  " << *(idat.vdwMult) << "\n";
      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:	1579
Committed:	Thu Jun 9 20:26:29 2011 UTC (13 years, 11 months ago) by gezelter
File size:	10843 byte(s)
Log Message:	bug fixes (not done yet)
#	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), shiftedPot_(false),
52	shiftedFrc_(false), forceField_(NULL) {}
53
54	LJParam LJ::getLJParam(AtomType* atomType) {
55
56	// Do sanity checking on the AtomType we were passed before
57	// building any data structures:
58	if (!atomType->isLennardJones()) {
59	sprintf( painCave.errMsg,
60	"LJ::getLJParam was passed an atomType (%s) that does not\n"
61	"\tappear to be a Lennard-Jones atom.\n",
62	atomType->getName().c_str());
63	painCave.severity = OPENMD_ERROR;
64	painCave.isFatal = 1;
65	simError();
66	}
67
68	GenericData* data = atomType->getPropertyByName("LennardJones");
69	if (data == NULL) {
70	sprintf( painCave.errMsg, "LJ::getLJParam could not find Lennard-Jones\n"
71	"\tparameters for atomType %s.\n", atomType->getName().c_str());
72	painCave.severity = OPENMD_ERROR;
73	painCave.isFatal = 1;
74	simError();
75	}
76
77	LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
78	if (ljData == NULL) {
79	sprintf( painCave.errMsg,
80	"LJ::getLJParam could not convert GenericData to LJParam for\n"
81	"\tatom type %s\n", atomType->getName().c_str());
82	painCave.severity = OPENMD_ERROR;
83	painCave.isFatal = 1;
84	simError();
85	}
86
87	return ljData->getData();
88	}
89
90	RealType LJ::getSigma(AtomType* atomType) {
91	LJParam ljParam = getLJParam(atomType);
92	return ljParam.sigma;
93	}
94
95	RealType LJ::getSigma(AtomType* atomType1, AtomType* atomType2) {
96	RealType sigma1 = getSigma(atomType1);
97	RealType sigma2 = getSigma(atomType2);
98
99	ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
100	string DistanceMix = fopts.getDistanceMixingRule();
101	toUpper(DistanceMix);
102
103	if (DistanceMix == "GEOMETRIC")
104	return sqrt(sigma1 * sigma2);
105	else
106	return 0.5 * (sigma1 + sigma2);
107	}
108
109	RealType LJ::getEpsilon(AtomType* atomType) {
110	LJParam ljParam = getLJParam(atomType);
111	return ljParam.epsilon;
112	}
113
114	RealType LJ::getEpsilon(AtomType* atomType1, AtomType* atomType2) {
115	RealType epsilon1 = getEpsilon(atomType1);
116	RealType epsilon2 = getEpsilon(atomType2);
117	return sqrt(epsilon1 * epsilon2);
118	}
119
120	void LJ::initialize() {
121	ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
122	ForceField::AtomTypeContainer::MapTypeIterator i;
123	AtomType* at;
124
125	for (at = atomTypes->beginType(i); at != NULL;
126	at = atomTypes->nextType(i)) {
127
128	if (at->isLennardJones())
129	addType(at);
130	}
131
132	ForceField::NonBondedInteractionTypeContainer* nbiTypes = forceField_->getNonBondedInteractionTypes();
133	ForceField::NonBondedInteractionTypeContainer::MapTypeIterator j;
134	NonBondedInteractionType* nbt;
135
136	for (nbt = nbiTypes->beginType(j); nbt != NULL;
137	nbt = nbiTypes->nextType(j)) {
138
139	if (nbt->isLennardJones()) {
140
141	pair<AtomType, AtomType> atypes = nbt->getAtomTypes();
142
143	GenericData* data = nbt->getPropertyByName("LennardJones");
144	if (data == NULL) {
145	sprintf( painCave.errMsg, "LJ::rebuildMixingMap could not find\n"
146	"\tLennard-Jones parameters for %s - %s interaction.\n",
147	atypes.first->getName().c_str(),
148	atypes.second->getName().c_str());
149	painCave.severity = OPENMD_ERROR;
150	painCave.isFatal = 1;
151	simError();
152	}
153
154	LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
155	if (ljData == NULL) {
156	sprintf( painCave.errMsg,
157	"LJ::rebuildMixingMap could not convert GenericData to\n"
158	"\tLJParam for %s - %s interaction.\n",
159	atypes.first->getName().c_str(),
160	atypes.second->getName().c_str());
161	painCave.severity = OPENMD_ERROR;
162	painCave.isFatal = 1;
163	simError();
164	}
165
166	LJParam ljParam = ljData->getData();
167
168	RealType sigma = ljParam.sigma;
169	RealType epsilon = ljParam.epsilon;
170
171	addExplicitInteraction(atypes.first, atypes.second, sigma, epsilon);
172	}
173	}
174	initialized_ = true;
175	}
176
177
178
179	void LJ::addType(AtomType* atomType){
180	RealType sigma1 = getSigma(atomType);
181	RealType epsilon1 = getEpsilon(atomType);
182
183	// add it to the map:
184	AtomTypeProperties atp = atomType->getATP();
185
186	pair<map<int,AtomType*>::iterator,bool> ret;
187	ret = LJMap.insert( pair<int, AtomType*>(atp.ident, atomType) );
188	if (ret.second == false) {
189	sprintf( painCave.errMsg,
190	"LJ already had a previous entry with ident %d\n",
191	atp.ident);
192	painCave.severity = OPENMD_INFO;
193	painCave.isFatal = 0;
194	simError();
195	}
196
197	// Now, iterate over all known types and add to the mixing map:
198
199	std::map<int, AtomType*>::iterator it;
200	for( it = LJMap.begin(); it != LJMap.end(); ++it) {
201
202	AtomType* atype2 = (*it).second;
203
204	LJInteractionData mixer;
205	mixer.sigma = getSigma(atomType, atype2);
206	mixer.epsilon = getEpsilon(atomType, atype2);
207	mixer.sigmai = 1.0 / mixer.sigma;
208	mixer.explicitlySet = false;
209
210	std::pair<AtomType, AtomType> key1, key2;
211	key1 = std::make_pair(atomType, atype2);
212	key2 = std::make_pair(atype2, atomType);
213
214	MixingMap[key1] = mixer;
215	if (key2 != key1) {
216	MixingMap[key2] = mixer;
217	}
218	}
219	}
220
221	void LJ::addExplicitInteraction(AtomType* atype1, AtomType* atype2, RealType sigma, RealType epsilon){
222
223	// in case these weren't already in the map
224	addType(atype1);
225	addType(atype2);
226
227	LJInteractionData mixer;
228	mixer.sigma = sigma;
229	mixer.epsilon = epsilon;
230	mixer.sigmai = 1.0 / mixer.sigma;
231	mixer.explicitlySet = true;
232
233	std::pair<AtomType, AtomType> key1, key2;
234	key1 = std::make_pair(atype1, atype2);
235	key2 = std::make_pair(atype2, atype1);
236
237	MixingMap[key1] = mixer;
238	if (key2 != key1) {
239	MixingMap[key2] = mixer;
240	}
241	}
242
243	void LJ::calcForce(InteractionData &idat) {
244
245	if (!initialized_) initialize();
246
247	map<pair<AtomType, AtomType>, LJInteractionData>::iterator it;
248	it = MixingMap.find( idat.atypes );
249
250	if (it != MixingMap.end()) {
251
252	LJInteractionData mixer = (*it).second;
253
254	RealType sigmai = mixer.sigmai;
255	RealType epsilon = mixer.epsilon;
256
257	RealType ros;
258	RealType rcos;
259	RealType myPot = 0.0;
260	RealType myPotC = 0.0;
261	RealType myDeriv = 0.0;
262	RealType myDerivC = 0.0;
263
264	ros = (idat.rij) sigmai;
265
266	cerr << "ros = " << ros << "\n";
267
268	getLJfunc(ros, myPot, myDeriv);
269
270	if (shiftedPot_) {
271	rcos = (idat.rcut) sigmai;
272	getLJfunc(rcos, myPotC, myDerivC);
273	myDerivC = 0.0;
274	} else if (LJ::shiftedFrc_) {
275	rcos = (idat.rcut) sigmai;
276	getLJfunc(rcos, myPotC, myDerivC);
277	myPotC = myPotC + myDerivC * ((idat.rij) - (idat.rcut)) * sigmai;
278	} else {
279	myPotC = 0.0;
280	myDerivC = 0.0;
281	}
282
283	cerr << "myPot = " << myPot << "\n";
284	cerr << "myPotC = " << myPotC << "\n";
285	cerr << "epsilon = " << epsilon << "\n";
286	cerr << "vdwm = " << *(idat.vdwMult) << "\n";
287	RealType pot_temp = (idat.vdwMult) epsilon * (myPot - myPotC);
288	*(idat.vpair) += pot_temp;
289
290	RealType dudr = (idat.sw) (idat.vdwMult) epsilon * (myDeriv -
291	myDerivC)*sigmai;
292
293	(idat.pot)[VANDERWAALS_FAMILY] += (idat.sw) pot_temp;
294	(idat.f1) = (idat.d) * dudr / *(idat.rij);
295	}
296	return;
297	}
298
299	void LJ::getLJfunc(RealType r, RealType &pot, RealType &deriv) {
300
301	RealType ri = 1.0 / r;
302	RealType ri2 = ri * ri;
303	RealType ri6 = ri2 * ri2 * ri2;
304	RealType ri7 = ri6 * ri;
305	RealType ri12 = ri6 * ri6;
306	RealType ri13 = ri12 * ri;
307
308	pot = 4.0 * (ri12 - ri6);
309	deriv = 24.0 * (ri7 - 2.0 * ri13);
310
311	return;
312	}
313
314	RealType LJ::getSuggestedCutoffRadius(pair<AtomType, AtomType> atypes) {
315	if (!initialized_) initialize();
316	map<pair<AtomType, AtomType>, LJInteractionData>::iterator it;
317	it = MixingMap.find(atypes);
318	if (it == MixingMap.end())
319	return 0.0;
320	else {
321	LJInteractionData mixer = (*it).second;
322	return 2.5 * mixer.sigma;
323	}
324	}
325
326	}