src/brains/ForceField.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. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. 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.
 */
 
 /**
  * @file ForceField.cpp
  * @author tlin
  * @date 11/04/2004
  * @time 22:51am
  * @version 1.0
  */
  
#include "UseTheForce/ForceField.hpp"
#include "utils/simError.h"
namespace oopse {

ForceField::ForceField() { 
    char* tempPath; 
    tempPath = getenv("FORCE_PARAM_PATH");

    if (tempPath == NULL) {
        //convert a macro from compiler to a string in c++
        STR_DEFINE(ffPath_, FRC_PATH );
    } else {
        ffPath_ = tempPath;
    }
}

AtomType* ForceField::getAtomType(const std::string &at) {
    std::vector<std::string> keys;
    keys.push_back(at);
    return atomTypeCont_.find(keys);
}

BondType* ForceField::getBondType(const std::string &at1, const std::string &at2) {
    std::vector<std::string> keys;
    keys.push_back(at1);
    keys.push_back(at2);    

    //try exact match first
    BondType* bondType = bondTypeCont_.find(keys);
    if (bondType) {
        return bondType;
    } else {
        //if no exact match found, try wild card match
        return bondTypeCont_.find(keys, wildCardAtomTypeName_);
    }

}

BendType* ForceField::getBendType(const std::string &at1, const std::string &at2,
                        const std::string &at3) {
    std::vector<std::string> keys;
    keys.push_back(at1);
    keys.push_back(at2);    
    keys.push_back(at3);    

    //try exact match first
    BendType* bendType = bendTypeCont_.find(keys);
    if (bendType) {
        return bendType;
    } else {
        //if no exact match found, try wild card match
        return bendTypeCont_.find(keys, wildCardAtomTypeName_);
    }
}

TorsionType* ForceField::getTorsionType(const std::string &at1, const std::string &at2,
                              const std::string &at3, const std::string &at4) {
    std::vector<std::string> keys;
    keys.push_back(at1);
    keys.push_back(at2);    
    keys.push_back(at3);    
    keys.push_back(at4);    

    TorsionType* torsionType = torsionTypeCont_.find(keys);
    if (torsionType) {
        return torsionType;
    } else {
        //if no exact match found, try wild card match
        return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
    }
    
    return torsionTypeCont_.find(keys, wildCardAtomTypeName_);

}

BondType* ForceField::getExactBondType(const std::string &at1, const std::string &at2){ 
    std::vector<std::string> keys;
    keys.push_back(at1);
    keys.push_back(at2);    
    return bondTypeCont_.find(keys);
}

BendType* ForceField::getExactBendType(const std::string &at1, const std::string &at2,
                            const std::string &at3){ 
    std::vector<std::string> keys;
    keys.push_back(at1);
    keys.push_back(at2);    
    keys.push_back(at3);    
    return bendTypeCont_.find(keys);
}

TorsionType* ForceField::getExactTorsionType(const std::string &at1, const std::string &at2,
                                  const std::string &at3, const std::string &at4){ 
    std::vector<std::string> keys;
    keys.push_back(at1);
    keys.push_back(at2);    
    keys.push_back(at3);    
    keys.push_back(at4);   
    return torsionTypeCont_.find(keys);
}
bool ForceField::addAtomType(const std::string &at, AtomType* atomType) {
    std::vector<std::string> keys;
    keys.push_back(at);
    return atomTypeCont_.add(keys, atomType);
}

bool ForceField::addBondType(const std::string &at1, const std::string &at2, BondType* bondType) {
    std::vector<std::string> keys;
    keys.push_back(at1);
    keys.push_back(at2);    
    return bondTypeCont_.add(keys, bondType);

}

bool ForceField::addBendType(const std::string &at1, const std::string &at2,
                        const std::string &at3, BendType* bendType) {
    std::vector<std::string> keys;
    keys.push_back(at1);
    keys.push_back(at2);    
    keys.push_back(at3);    
    return bendTypeCont_.add(keys, bendType);
}

bool ForceField::addTorsionType(const std::string &at1, const std::string &at2,
                              const std::string &at3, const std::string &at4, TorsionType* torsionType) {
    std::vector<std::string> keys;
    keys.push_back(at1);
    keys.push_back(at2);    
    keys.push_back(at3);    
    keys.push_back(at4);    
    return torsionTypeCont_.add(keys, torsionType);
}

double ForceField::getRcutFromAtomType(AtomType* at) {
    /**@todo */
    GenericData* data;
    double rcut = 0.0;

    if (at->isLennardJones()) {
        data = at->getPropertyByName("LennardJones");
        if (data != NULL) {
            LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);

            if (ljData != NULL) {
                LJParam ljParam = ljData->getData();

                //by default use 2.5*sigma as cutoff radius
                rcut = 2.5 * ljParam.sigma;
                
            } else {
                    sprintf( painCave.errMsg,
                           "Can not cast GenericData to LJParam\n");
                    painCave.severity = OOPSE_ERROR;
                    painCave.isFatal = 1;
                    simError();          
            }            
        } else {
            sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
            painCave.severity = OOPSE_ERROR;
            painCave.isFatal = 1;
            simError();          
        }
    }

    return rcut;    
}


ifstrstream* ForceField::openForceFieldFile(const std::string& filename) {
    std::string forceFieldFilename(filename);
    ifstrstream* ffStream = new ifstrstream();
    
    //try to open the force filed file in current directory first    
    ffStream->open(forceFieldFilename.c_str());
    if(!ffStream->is_open()){

        forceFieldFilename = ffPath_ + "/" + forceFieldFilename;
        ffStream->open( forceFieldFilename.c_str() );

        //if current directory does not contain the force field file,
        //try to open it in the path        
        if(!ffStream->is_open()){

            sprintf( painCave.errMsg,
               "Error opening the force field parameter file:\n"
               "\t%s\n"
               "\tHave you tried setting the FORCE_PARAM_PATH environment "
               "variable?\n",
               forceFieldFilename.c_str() );
            painCave.severity = OOPSE_ERROR;
            painCave.isFatal = 1;
            simError();
        }
    }  

    return ffStream;

}

} //end namespace oopse
Revision:	246
Committed:	Wed Jan 12 22:41:40 2005 UTC (20 years, 9 months ago) by gezelter
Original Path:	*trunk/src/UseTheForce/ForceField.cpp*
File size:	8422 byte(s)
Log Message:	merging new_design branch into OOPSE-2.0
#	User	Rev	Content
1	gezelter	246	/*
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. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42			/**
43			* @file ForceField.cpp
44			* @author tlin
45			* @date 11/04/2004
46			* @time 22:51am
47			* @version 1.0
48			*/
49
50	gezelter	206	#include "UseTheForce/ForceField.hpp"
51	gezelter	246	#include "utils/simError.h"
52			namespace oopse {
53	gezelter	206
54	gezelter	246	ForceField::ForceField() {
55			char* tempPath;
56			tempPath = getenv("FORCE_PARAM_PATH");
57	gezelter	206
58	gezelter	246	if (tempPath == NULL) {
59			//convert a macro from compiler to a string in c++
60			STR_DEFINE(ffPath_, FRC_PATH );
61			} else {
62			ffPath_ = tempPath;
63			}
64	gezelter	206	}
65
66	gezelter	246	AtomType* ForceField::getAtomType(const std::string &at) {
67			std::vector<std::string> keys;
68			keys.push_back(at);
69			return atomTypeCont_.find(keys);
70			}
71	gezelter	206
72	gezelter	246	BondType* ForceField::getBondType(const std::string &at1, const std::string &at2) {
73			std::vector<std::string> keys;
74			keys.push_back(at1);
75			keys.push_back(at2);
76	gezelter	206
77	gezelter	246	//try exact match first
78			BondType* bondType = bondTypeCont_.find(keys);
79			if (bondType) {
80			return bondType;
81			} else {
82			//if no exact match found, try wild card match
83			return bondTypeCont_.find(keys, wildCardAtomTypeName_);
84			}
85	gezelter	206
86	gezelter	246	}
87	gezelter	206
88	gezelter	246	BendType* ForceField::getBendType(const std::string &at1, const std::string &at2,
89			const std::string &at3) {
90			std::vector<std::string> keys;
91			keys.push_back(at1);
92			keys.push_back(at2);
93			keys.push_back(at3);
94	gezelter	206
95	gezelter	246	//try exact match first
96			BendType* bendType = bendTypeCont_.find(keys);
97			if (bendType) {
98			return bendType;
99			} else {
100			//if no exact match found, try wild card match
101			return bendTypeCont_.find(keys, wildCardAtomTypeName_);
102			}
103			}
104	gezelter	206
105	gezelter	246	TorsionType* ForceField::getTorsionType(const std::string &at1, const std::string &at2,
106			const std::string &at3, const std::string &at4) {
107			std::vector<std::string> keys;
108			keys.push_back(at1);
109			keys.push_back(at2);
110			keys.push_back(at3);
111			keys.push_back(at4);
112	gezelter	206
113	gezelter	246	TorsionType* torsionType = torsionTypeCont_.find(keys);
114			if (torsionType) {
115			return torsionType;
116			} else {
117			//if no exact match found, try wild card match
118			return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
119			}
120	gezelter	206
121	gezelter	246	return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
122	gezelter	206
123	gezelter	246	}
124	gezelter	206
125	gezelter	246	BondType* ForceField::getExactBondType(const std::string &at1, const std::string &at2){
126			std::vector<std::string> keys;
127			keys.push_back(at1);
128			keys.push_back(at2);
129			return bondTypeCont_.find(keys);
130			}
131	gezelter	206
132	gezelter	246	BendType* ForceField::getExactBendType(const std::string &at1, const std::string &at2,
133			const std::string &at3){
134			std::vector<std::string> keys;
135			keys.push_back(at1);
136			keys.push_back(at2);
137			keys.push_back(at3);
138			return bendTypeCont_.find(keys);
139			}
140	gezelter	206
141	gezelter	246	TorsionType* ForceField::getExactTorsionType(const std::string &at1, const std::string &at2,
142			const std::string &at3, const std::string &at4){
143			std::vector<std::string> keys;
144			keys.push_back(at1);
145			keys.push_back(at2);
146			keys.push_back(at3);
147			keys.push_back(at4);
148			return torsionTypeCont_.find(keys);
149			}
150			bool ForceField::addAtomType(const std::string &at, AtomType* atomType) {
151			std::vector<std::string> keys;
152			keys.push_back(at);
153			return atomTypeCont_.add(keys, atomType);
154			}
155	gezelter	206
156	gezelter	246	bool ForceField::addBondType(const std::string &at1, const std::string &at2, BondType* bondType) {
157			std::vector<std::string> keys;
158			keys.push_back(at1);
159			keys.push_back(at2);
160			return bondTypeCont_.add(keys, bondType);
161	gezelter	206
162	gezelter	246	}
163	gezelter	206
164	gezelter	246	bool ForceField::addBendType(const std::string &at1, const std::string &at2,
165			const std::string &at3, BendType* bendType) {
166			std::vector<std::string> keys;
167			keys.push_back(at1);
168			keys.push_back(at2);
169			keys.push_back(at3);
170			return bendTypeCont_.add(keys, bendType);
171			}
172	gezelter	206
173	gezelter	246	bool ForceField::addTorsionType(const std::string &at1, const std::string &at2,
174			const std::string &at3, const std::string &at4, TorsionType* torsionType) {
175			std::vector<std::string> keys;
176			keys.push_back(at1);
177			keys.push_back(at2);
178			keys.push_back(at3);
179			keys.push_back(at4);
180			return torsionTypeCont_.add(keys, torsionType);
181			}
182	gezelter	206
183	gezelter	246	double ForceField::getRcutFromAtomType(AtomType* at) {
184			/*@todo /
185			GenericData* data;
186			double rcut = 0.0;
187	gezelter	206
188	gezelter	246	if (at->isLennardJones()) {
189			data = at->getPropertyByName("LennardJones");
190			if (data != NULL) {
191			LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
192	gezelter	206
193	gezelter	246	if (ljData != NULL) {
194			LJParam ljParam = ljData->getData();
195	gezelter	206
196	gezelter	246	//by default use 2.5*sigma as cutoff radius
197			rcut = 2.5 * ljParam.sigma;
198
199			} else {
200			sprintf( painCave.errMsg,
201			"Can not cast GenericData to LJParam\n");
202			painCave.severity = OOPSE_ERROR;
203			painCave.isFatal = 1;
204			simError();
205			}
206			} else {
207			sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
208			painCave.severity = OOPSE_ERROR;
209			painCave.isFatal = 1;
210			simError();
211			}
212			}
213	gezelter	206
214	gezelter	246	return rcut;
215			}
216	gezelter	206
217	gezelter	246
218			ifstrstream* ForceField::openForceFieldFile(const std::string& filename) {
219			std::string forceFieldFilename(filename);
220			ifstrstream* ffStream = new ifstrstream();
221
222			//try to open the force filed file in current directory first
223			ffStream->open(forceFieldFilename.c_str());
224			if(!ffStream->is_open()){
225
226			forceFieldFilename = ffPath_ + "/" + forceFieldFilename;
227			ffStream->open( forceFieldFilename.c_str() );
228
229			//if current directory does not contain the force field file,
230			//try to open it in the path
231			if(!ffStream->is_open()){
232
233			sprintf( painCave.errMsg,
234			"Error opening the force field parameter file:\n"
235			"\t%s\n"
236			"\tHave you tried setting the FORCE_PARAM_PATH environment "
237			"variable?\n",
238			forceFieldFilename.c_str() );
239			painCave.severity = OOPSE_ERROR;
240			painCave.isFatal = 1;
241			simError();
242			}
243			}
244
245			return ffStream;
246
247			}
248
249			} //end namespace oopse