src/UseTheForce/ForceField.cpp

/*
 * Copyright (C) 2000-2004  Object Oriented Parallel Simulation Engine (OOPSE) project
 * 
 * Contact: oopse@oopse.org
 * 
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
 * of the License, or (at your option) any later version.
 * All we ask is that proper credit is given for our work, which includes
 * - but is not limited to - adding the above copyright notice to the beginning
 * of your source code files, and to any copyright notice that you may distribute
 * with programs based on this work.
 * 
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU Lesser General Public License for more details.
 * 
 * You should have received a copy of the GNU Lesser General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
 *
 */
 
 /**
  * @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:	1847
Committed:	Sat Dec 4 05:24:07 2004 UTC (21 years, 2 months ago) by tim
File size:	7493 byte(s)
Log Message:	NVE conserved energy, however, potential is not the same as OOPSE-1.0 Step 1 argon in NVE, NVT, NPTi, NPTf and NPTxyz to test integrator Step 2 SSD in NVE to test DLM, dipole, sticky Step 3 Butane in NVE to test Bond Bend Torsion Step 4 EAM Step 5 Shape Step 6 Constraint & Restraint
#	User	Rev	Content
1	tim	1720	/*
2			* Copyright (C) 2000-2004 Object Oriented Parallel Simulation Engine (OOPSE) project
3			*
4			* Contact: oopse@oopse.org
5			*
6			* This program is free software; you can redistribute it and/or
7			* modify it under the terms of the GNU Lesser General Public License
8			* as published by the Free Software Foundation; either version 2.1
9			* of the License, or (at your option) any later version.
10			* All we ask is that proper credit is given for our work, which includes
11			* - but is not limited to - adding the above copyright notice to the beginning
12			* of your source code files, and to any copyright notice that you may distribute
13			* with programs based on this work.
14			*
15			* This program is distributed in the hope that it will be useful,
16			* but WITHOUT ANY WARRANTY; without even the implied warranty of
17			* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
18			* GNU Lesser General Public License for more details.
19			*
20			* You should have received a copy of the GNU Lesser General Public License
21			* along with this program; if not, write to the Free Software
22			* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
23			*
24			*/
25
26			/**
27			* @file ForceField.cpp
28			* @author tlin
29			* @date 11/04/2004
30			* @time 22:51am
31			* @version 1.0
32			*/
33
34	gezelter	1711	#include "UseTheForce/ForceField.hpp"
35	tim	1783	#include "utils/simError.h"
36	tim	1720	namespace oopse {
37	gezelter	1711
38	tim	1809	ForceField::ForceField() {
39	tim	1720	char* tempPath;
40			tempPath = getenv("FORCE_PARAM_PATH");
41	gezelter	1711
42	tim	1720	if (tempPath == NULL) {
43			//convert a macro from compiler to a string in c++
44			STR_DEFINE(ffPath_, FRC_PATH );
45			} else {
46			ffPath_ = tempPath;
47			}
48	gezelter	1711	}
49
50	tim	1720	AtomType* ForceField::getAtomType(const std::string &at) {
51			std::vector<std::string> keys;
52			keys.push_back(at);
53			return atomTypeCont_.find(keys);
54			}
55	gezelter	1711
56	tim	1720	BondType* ForceField::getBondType(const std::string &at1, const std::string &at2) {
57			std::vector<std::string> keys;
58			keys.push_back(at1);
59			keys.push_back(at2);
60	gezelter	1711
61	tim	1847	//try exact match first
62			BondType* bondType = bondTypeCont_.find(keys);
63			if (bondType) {
64			return bondType;
65			} else {
66			//if no exact match found, try wild card match
67			return bondTypeCont_.find(keys, wildCardAtomTypeName_);
68			}
69
70	tim	1720	}
71	gezelter	1711
72	tim	1720	BendType* ForceField::getBendType(const std::string &at1, const std::string &at2,
73			const std::string &at3) {
74			std::vector<std::string> keys;
75			keys.push_back(at1);
76			keys.push_back(at2);
77			keys.push_back(at3);
78	tim	1847
79			//try exact match first
80			BendType* bendType = bendTypeCont_.find(keys);
81			if (bendType) {
82			return bendType;
83			} else {
84			//if no exact match found, try wild card match
85			return bendTypeCont_.find(keys, wildCardAtomTypeName_);
86			}
87	tim	1720	}
88	gezelter	1711
89	tim	1720	TorsionType* ForceField::getTorsionType(const std::string &at1, const std::string &at2,
90			const std::string &at3, const std::string &at4) {
91			std::vector<std::string> keys;
92			keys.push_back(at1);
93			keys.push_back(at2);
94			keys.push_back(at3);
95			keys.push_back(at4);
96	tim	1847
97			TorsionType* torsionType = torsionTypeCont_.find(keys);
98			if (torsionType) {
99			return torsionType;
100			} else {
101			//if no exact match found, try wild card match
102			return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
103			}
104
105	tim	1720	return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
106	gezelter	1711
107	tim	1720	}
108	gezelter	1711
109	tim	1783	BondType* ForceField::getExactBondType(const std::string &at1, const std::string &at2){
110	tim	1770	std::vector<std::string> keys;
111			keys.push_back(at1);
112			keys.push_back(at2);
113			return bondTypeCont_.find(keys);
114			}
115
116	tim	1783	BendType* ForceField::getExactBendType(const std::string &at1, const std::string &at2,
117	tim	1770	const std::string &at3){
118			std::vector<std::string> keys;
119			keys.push_back(at1);
120			keys.push_back(at2);
121			keys.push_back(at3);
122			return bendTypeCont_.find(keys);
123			}
124
125	tim	1783	TorsionType* ForceField::getExactTorsionType(const std::string &at1, const std::string &at2,
126	tim	1770	const std::string &at3, const std::string &at4){
127			std::vector<std::string> keys;
128			keys.push_back(at1);
129			keys.push_back(at2);
130			keys.push_back(at3);
131			keys.push_back(at4);
132			return torsionTypeCont_.find(keys);
133			}
134	tim	1758	bool ForceField::addAtomType(const std::string &at, AtomType* atomType) {
135	tim	1720	std::vector<std::string> keys;
136			keys.push_back(at);
137	tim	1783	return atomTypeCont_.add(keys, atomType);
138	tim	1720	}
139	gezelter	1711
140	tim	1758	bool ForceField::addBondType(const std::string &at1, const std::string &at2, BondType* bondType) {
141	tim	1720	std::vector<std::string> keys;
142			keys.push_back(at1);
143			keys.push_back(at2);
144	tim	1783	return bondTypeCont_.add(keys, bondType);
145	gezelter	1711
146	tim	1720	}
147	gezelter	1711
148	tim	1758	bool ForceField::addBendType(const std::string &at1, const std::string &at2,
149	tim	1720	const std::string &at3, BendType* bendType) {
150			std::vector<std::string> keys;
151			keys.push_back(at1);
152			keys.push_back(at2);
153			keys.push_back(at3);
154	tim	1783	return bendTypeCont_.add(keys, bendType);
155	tim	1720	}
156	gezelter	1711
157	tim	1758	bool ForceField::addTorsionType(const std::string &at1, const std::string &at2,
158	tim	1720	const std::string &at3, const std::string &at4, TorsionType* torsionType) {
159			std::vector<std::string> keys;
160			keys.push_back(at1);
161			keys.push_back(at2);
162			keys.push_back(at3);
163			keys.push_back(at4);
164	tim	1783	return torsionTypeCont_.add(keys, torsionType);
165	tim	1720	}
166	gezelter	1711
167	tim	1735	double ForceField::getRcutFromAtomType(AtomType* at) {
168	tim	1783	/*@todo /
169			GenericData* data;
170			double rcut = 0.0;
171
172			if (at->isLennardJones()) {
173			data = at->getPropertyByName("LennardJones");
174			if (data != NULL) {
175			LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
176
177			if (ljData != NULL) {
178			LJParam ljParam = ljData->getData();
179
180			//by default use 2.5*sigma as cutoff radius
181			rcut = 2.5 * ljParam.sigma;
182
183			} else {
184			sprintf( painCave.errMsg,
185			"Can not cast GenericData to LJParam\n");
186			painCave.severity = OOPSE_ERROR;
187			painCave.isFatal = 1;
188			simError();
189			}
190			} else {
191			sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
192			painCave.severity = OOPSE_ERROR;
193			painCave.isFatal = 1;
194			simError();
195			}
196			}
197
198			return rcut;
199	tim	1720	}
200	gezelter	1711
201	tim	1740
202	tim	1783	ifstrstream* ForceField::openForceFieldFile(const std::string& filename) {
203	tim	1740	std::string forceFieldFilename(filename);
204			ifstrstream* ffStream = new ifstrstream();
205
206			//try to open the force filed file in current directory first
207	tim	1783	ffStream->open(forceFieldFilename.c_str());
208			if(!ffStream->is_open()){
209	tim	1740
210			forceFieldFilename = ffPath_ + "/" + forceFieldFilename;
211	tim	1783	ffStream->open( forceFieldFilename.c_str() );
212	tim	1740
213			//if current directory does not contain the force field file,
214			//try to open it in the path
215	tim	1783	if(!ffStream->is_open()){
216	tim	1740
217			sprintf( painCave.errMsg,
218			"Error opening the force field parameter file:\n"
219			"\t%s\n"
220			"\tHave you tried setting the FORCE_PARAM_PATH environment "
221			"variable?\n",
222			forceFieldFilename.c_str() );
223			painCave.severity = OOPSE_ERROR;
224			painCave.isFatal = 1;
225			simError();
226			}
227			}
228
229			return ffStream;
230
231			}
232
233	tim	1720	} //end namespace oopse