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"
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:	1930
Committed:	Wed Jan 12 22:41:40 2005 UTC (19 years, 5 months ago) by gezelter
File size:	8422 byte(s)
Log Message:	merging new_design branch into OOPSE-2.0
#	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. 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	#include "UseTheForce/ForceField.hpp"
51	#include "utils/simError.h"
52	namespace oopse {
53
54	ForceField::ForceField() {
55	char* tempPath;
56	tempPath = getenv("FORCE_PARAM_PATH");
57
58	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	}
65
66	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
72	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
77	//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
86	}
87
88	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
95	//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
105	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
113	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
121	return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
122
123	}
124
125	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
132	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
141	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
156	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
162	}
163
164	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
173	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
183	double ForceField::getRcutFromAtomType(AtomType* at) {
184	/*@todo /
185	GenericData* data;
186	double rcut = 0.0;
187
188	if (at->isLennardJones()) {
189	data = at->getPropertyByName("LennardJones");
190	if (data != NULL) {
191	LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
192
193	if (ljData != NULL) {
194	LJParam ljParam = ljData->getData();
195
196	//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
214	return rcut;
215	}
216
217
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