src/UseTheForce/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"
#include "UseTheForce/DarkSide/atype_interface.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;
    }
}


ForceField::~ForceField() {
    deleteAtypes();
}

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:	2172
Committed:	Tue Apr 12 18:30:37 2005 UTC (19 years, 3 months ago) by tim
File size:	8524 byte(s)
Log Message:	destory atom type in fortran side
#	User	Rev	Content
1	gezelter	1930	/*
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	1711	#include "UseTheForce/ForceField.hpp"
51	gezelter	1930	#include "utils/simError.h"
52	tim	2172	#include "UseTheForce/DarkSide/atype_interface.h"
53	gezelter	1930	namespace oopse {
54	gezelter	1711
55	gezelter	1930	ForceField::ForceField() {
56			char* tempPath;
57			tempPath = getenv("FORCE_PARAM_PATH");
58	gezelter	1711
59	gezelter	1930	if (tempPath == NULL) {
60			//convert a macro from compiler to a string in c++
61			STR_DEFINE(ffPath_, FRC_PATH );
62			} else {
63			ffPath_ = tempPath;
64			}
65	gezelter	1711	}
66
67	tim	2172
68			ForceField::~ForceField() {
69			deleteAtypes();
70			}
71
72	gezelter	1930	AtomType* ForceField::getAtomType(const std::string &at) {
73			std::vector<std::string> keys;
74			keys.push_back(at);
75			return atomTypeCont_.find(keys);
76			}
77	gezelter	1711
78	gezelter	1930	BondType* ForceField::getBondType(const std::string &at1, const std::string &at2) {
79			std::vector<std::string> keys;
80			keys.push_back(at1);
81			keys.push_back(at2);
82	gezelter	1711
83	gezelter	1930	//try exact match first
84			BondType* bondType = bondTypeCont_.find(keys);
85			if (bondType) {
86			return bondType;
87			} else {
88			//if no exact match found, try wild card match
89			return bondTypeCont_.find(keys, wildCardAtomTypeName_);
90			}
91	gezelter	1711
92	gezelter	1930	}
93	gezelter	1711
94	gezelter	1930	BendType* ForceField::getBendType(const std::string &at1, const std::string &at2,
95			const std::string &at3) {
96			std::vector<std::string> keys;
97			keys.push_back(at1);
98			keys.push_back(at2);
99			keys.push_back(at3);
100	gezelter	1711
101	gezelter	1930	//try exact match first
102			BendType* bendType = bendTypeCont_.find(keys);
103			if (bendType) {
104			return bendType;
105			} else {
106			//if no exact match found, try wild card match
107			return bendTypeCont_.find(keys, wildCardAtomTypeName_);
108			}
109			}
110	gezelter	1711
111	gezelter	1930	TorsionType* ForceField::getTorsionType(const std::string &at1, const std::string &at2,
112			const std::string &at3, const std::string &at4) {
113			std::vector<std::string> keys;
114			keys.push_back(at1);
115			keys.push_back(at2);
116			keys.push_back(at3);
117			keys.push_back(at4);
118	gezelter	1711
119	gezelter	1930	TorsionType* torsionType = torsionTypeCont_.find(keys);
120			if (torsionType) {
121			return torsionType;
122			} else {
123			//if no exact match found, try wild card match
124			return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
125			}
126	gezelter	1711
127	gezelter	1930	return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
128	gezelter	1711
129	gezelter	1930	}
130	gezelter	1711
131	gezelter	1930	BondType* ForceField::getExactBondType(const std::string &at1, const std::string &at2){
132			std::vector<std::string> keys;
133			keys.push_back(at1);
134			keys.push_back(at2);
135			return bondTypeCont_.find(keys);
136			}
137	gezelter	1711
138	gezelter	1930	BendType* ForceField::getExactBendType(const std::string &at1, const std::string &at2,
139			const std::string &at3){
140			std::vector<std::string> keys;
141			keys.push_back(at1);
142			keys.push_back(at2);
143			keys.push_back(at3);
144			return bendTypeCont_.find(keys);
145			}
146	gezelter	1711
147	gezelter	1930	TorsionType* ForceField::getExactTorsionType(const std::string &at1, const std::string &at2,
148			const std::string &at3, const std::string &at4){
149			std::vector<std::string> keys;
150			keys.push_back(at1);
151			keys.push_back(at2);
152			keys.push_back(at3);
153			keys.push_back(at4);
154			return torsionTypeCont_.find(keys);
155			}
156			bool ForceField::addAtomType(const std::string &at, AtomType* atomType) {
157			std::vector<std::string> keys;
158			keys.push_back(at);
159			return atomTypeCont_.add(keys, atomType);
160			}
161	gezelter	1711
162	gezelter	1930	bool ForceField::addBondType(const std::string &at1, const std::string &at2, BondType* bondType) {
163			std::vector<std::string> keys;
164			keys.push_back(at1);
165			keys.push_back(at2);
166			return bondTypeCont_.add(keys, bondType);
167	gezelter	1711
168	gezelter	1930	}
169	gezelter	1711
170	gezelter	1930	bool ForceField::addBendType(const std::string &at1, const std::string &at2,
171			const std::string &at3, BendType* bendType) {
172			std::vector<std::string> keys;
173			keys.push_back(at1);
174			keys.push_back(at2);
175			keys.push_back(at3);
176			return bendTypeCont_.add(keys, bendType);
177			}
178	gezelter	1711
179	gezelter	1930	bool ForceField::addTorsionType(const std::string &at1, const std::string &at2,
180			const std::string &at3, const std::string &at4, TorsionType* torsionType) {
181			std::vector<std::string> keys;
182			keys.push_back(at1);
183			keys.push_back(at2);
184			keys.push_back(at3);
185			keys.push_back(at4);
186			return torsionTypeCont_.add(keys, torsionType);
187			}
188	gezelter	1711
189	gezelter	1930	double ForceField::getRcutFromAtomType(AtomType* at) {
190			/*@todo /
191			GenericData* data;
192			double rcut = 0.0;
193	gezelter	1711
194	gezelter	1930	if (at->isLennardJones()) {
195			data = at->getPropertyByName("LennardJones");
196			if (data != NULL) {
197			LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
198	gezelter	1711
199	gezelter	1930	if (ljData != NULL) {
200			LJParam ljParam = ljData->getData();
201	gezelter	1711
202	gezelter	1930	//by default use 2.5*sigma as cutoff radius
203			rcut = 2.5 * ljParam.sigma;
204
205			} else {
206			sprintf( painCave.errMsg,
207			"Can not cast GenericData to LJParam\n");
208			painCave.severity = OOPSE_ERROR;
209			painCave.isFatal = 1;
210			simError();
211			}
212			} else {
213			sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
214			painCave.severity = OOPSE_ERROR;
215			painCave.isFatal = 1;
216			simError();
217			}
218			}
219	gezelter	1711
220	gezelter	1930	return rcut;
221			}
222	gezelter	1711
223	gezelter	1930
224			ifstrstream* ForceField::openForceFieldFile(const std::string& filename) {
225			std::string forceFieldFilename(filename);
226			ifstrstream* ffStream = new ifstrstream();
227
228			//try to open the force filed file in current directory first
229			ffStream->open(forceFieldFilename.c_str());
230			if(!ffStream->is_open()){
231
232			forceFieldFilename = ffPath_ + "/" + forceFieldFilename;
233			ffStream->open( forceFieldFilename.c_str() );
234
235			//if current directory does not contain the force field file,
236			//try to open it in the path
237			if(!ffStream->is_open()){
238
239			sprintf( painCave.errMsg,
240			"Error opening the force field parameter file:\n"
241			"\t%s\n"
242			"\tHave you tried setting the FORCE_PARAM_PATH environment "
243			"variable?\n",
244			forceFieldFilename.c_str() );
245			painCave.severity = OOPSE_ERROR;
246			painCave.isFatal = 1;
247			simError();
248			}
249			}
250
251			return ffStream;
252
253			}
254
255			} //end namespace oopse