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 (19 years, 7 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
#	Content
1	/*
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	#include "UseTheForce/ForceField.hpp"
35	#include "utils/simError.h"
36	namespace oopse {
37
38	ForceField::ForceField() {
39	char* tempPath;
40	tempPath = getenv("FORCE_PARAM_PATH");
41
42	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	}
49
50	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
56	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
61	//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	}
71
72	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
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	}
88
89	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
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	return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
106
107	}
108
109	BondType* ForceField::getExactBondType(const std::string &at1, const std::string &at2){
110	std::vector<std::string> keys;
111	keys.push_back(at1);
112	keys.push_back(at2);
113	return bondTypeCont_.find(keys);
114	}
115
116	BendType* ForceField::getExactBendType(const std::string &at1, const std::string &at2,
117	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	TorsionType* ForceField::getExactTorsionType(const std::string &at1, const std::string &at2,
126	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	bool ForceField::addAtomType(const std::string &at, AtomType* atomType) {
135	std::vector<std::string> keys;
136	keys.push_back(at);
137	return atomTypeCont_.add(keys, atomType);
138	}
139
140	bool ForceField::addBondType(const std::string &at1, const std::string &at2, BondType* bondType) {
141	std::vector<std::string> keys;
142	keys.push_back(at1);
143	keys.push_back(at2);
144	return bondTypeCont_.add(keys, bondType);
145
146	}
147
148	bool ForceField::addBendType(const std::string &at1, const std::string &at2,
149	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	return bendTypeCont_.add(keys, bendType);
155	}
156
157	bool ForceField::addTorsionType(const std::string &at1, const std::string &at2,
158	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	return torsionTypeCont_.add(keys, torsionType);
165	}
166
167	double ForceField::getRcutFromAtomType(AtomType* at) {
168	/*@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	}
200
201
202	ifstrstream* ForceField::openForceFieldFile(const std::string& filename) {
203	std::string forceFieldFilename(filename);
204	ifstrstream* ffStream = new ifstrstream();
205
206	//try to open the force filed file in current directory first
207	ffStream->open(forceFieldFilename.c_str());
208	if(!ffStream->is_open()){
209
210	forceFieldFilename = ffPath_ + "/" + forceFieldFilename;
211	ffStream->open( forceFieldFilename.c_str() );
212
213	//if current directory does not contain the force field file,
214	//try to open it in the path
215	if(!ffStream->is_open()){
216
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	} //end namespace oopse