src/io/ElectrostaticAtomTypesSectionParser.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.
 *
 */
 
#include "io/ElectrostaticAtomTypesSectionParser.hpp"

#include "UseTheForce/ForceField.hpp"

namespace oopse {

ElectrostaticAtomTypesSectionParser::ElectrostaticAtomTypesSectionParser() {
    setSectionName("ElectrostaticAtomTypes");
}

void ElectrostaticAtomTypesSectionParser::parseLine(ForceField& ff,const std::string& line, int lineNo){
    StringTokenizer tokenizer(line);
    int nTokens = tokenizer.countTokens();    

    //in AtomTypeSection, a line at least contains 2 tokens
    //atomTypeName and biggest rank
    //for the time being, we only support up to quadrupole
    // "name" must match the name in the AtomTypes section
    // charge is given in units of electrons (1.61 x 10^-19 C)
    // Directionality for dipoles and quadrupoles must be given because the body-fixed
    // reference frame for directional atoms is determined by the *mass* distribution and
    // not by the charge distribution.  
    // Dipoles are given in units of Debye  
    // Quadrupoles are given in units of 
    // name 0 charge
    // name 1 charge |u| [theta phi psi]
    // name 2 charge |u| Qxx Qyy Qzz [theta phi psi]
    
    if (nTokens < 2)  {
        std::cerr << "ElectrostaticAtomTypesSectionParser Error: Not enought Tokens at line " << lineNo << std::endl;                  
    } else {

        std::string atomTypeName = tokenizer.nextToken();    
        int biggestRank = tokenizer.nextTokenAsInt();
        nTokens -=  2;
        
        AtomType* atomType = ff.getAtomType(atomTypeName);
        DirectionalAtomType* dAtomType;
        if (atomType != NULL) {
                       
            switch (biggestRank) {
                case 0 :
                    parseCharge(tokenizer, atomType);
                    break;

               case 1 :

                    dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);            
                    if (dAtomType == NULL) {
                        std::cerr << "ElectrostaticAtomTypesSectionParser Warning:" << std::endl;
                    }

                    parseCharge(tokenizer, dAtomType);
                    parseDipole(tokenizer, dAtomType);
                    parseElectroBodyFrame(tokenizer, dAtomType);
                    break;

               case 2:

                    dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);            
                    if (dAtomType == NULL) {
                        std::cerr << "ElectrostaticAtomTypesSectionParser Warning:" << std::endl;
                    }

                    parseCharge(tokenizer, dAtomType);
                    parseDipole(tokenizer, dAtomType);
                    parseQuadruple(tokenizer, dAtomType);
                    parseElectroBodyFrame(tokenizer, dAtomType);
                    break;
                    
               default :
                    break;

            }
            
        } else {
            std::cerr << "ElectrostaticAtomTypesSectionParser Error: Can not find matched AtomType " << atomTypeName
                          << "at line " << lineNo << std::endl;
        }
                       
    }    


}


void ElectrostaticAtomTypesSectionParser::parseCharge(StringTokenizer& tokenizer,
    AtomType* atomType) {

    double charge = tokenizer.nextTokenAsDouble();
    atomType->addProperty(new DoubleGenericData("Charge", charge));
    atomType->setCharge();
    
}
void ElectrostaticAtomTypesSectionParser::parseDipole(StringTokenizer& tokenizer, 
    DirectionalAtomType* dAtomType) {

    double Dipole = tokenizer.nextTokenAsDouble();
    dAtomType->addProperty(new DoubleGenericData("Dipole", Dipole));
    dAtomType->setDipole();
}

void ElectrostaticAtomTypesSectionParser::parseQuadruple(StringTokenizer& tokenizer,
    DirectionalAtomType* dAtomType) {

    Vector3d Q;
    Q[0] = tokenizer.nextTokenAsDouble();
    Q[1] = tokenizer.nextTokenAsDouble();
    Q[2] = tokenizer.nextTokenAsDouble();
    
    dAtomType->addProperty(new Vector3dGenericData("Quadrupole", Q));
    dAtomType->setQuadrupole();
}
void ElectrostaticAtomTypesSectionParser::parseElectroBodyFrame(StringTokenizer& tokenizer,
    DirectionalAtomType* dAtomType) {

    double phi;
    double theta;
    double psi;

    if (tokenizer.countTokens() >=3 ) {
        phi = tokenizer.nextTokenAsDouble()/180.0;
        theta = tokenizer.nextTokenAsDouble()/180.0;
        psi = tokenizer.nextTokenAsDouble()/180.0;
    } else {
        phi = 0.0;
        theta = 0.0;
        psi = 0.0;    
    }
    
    RotMat3x3d electroBodyFrame(phi, theta, psi);
    dAtomType->setElectroBodyFrame(electroBodyFrame);
        
}

} //end namespace oopse


Revision:	1869
Committed:	Wed Dec 8 20:37:47 2004 UTC (19 years, 8 months ago) by tim
File size:	5788 byte(s)
Log Message:	fix a parsing bug in ElectroStaticAtomTypesSectionParser
#	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	#include "io/ElectrostaticAtomTypesSectionParser.hpp"
27
28	#include "UseTheForce/ForceField.hpp"
29
30	namespace oopse {
31
32	ElectrostaticAtomTypesSectionParser::ElectrostaticAtomTypesSectionParser() {
33	setSectionName("ElectrostaticAtomTypes");
34	}
35
36	void ElectrostaticAtomTypesSectionParser::parseLine(ForceField& ff,const std::string& line, int lineNo){
37	StringTokenizer tokenizer(line);
38	int nTokens = tokenizer.countTokens();
39
40	//in AtomTypeSection, a line at least contains 2 tokens
41	//atomTypeName and biggest rank
42	//for the time being, we only support up to quadrupole
43	// "name" must match the name in the AtomTypes section
44	// charge is given in units of electrons (1.61 x 10^-19 C)
45	// Directionality for dipoles and quadrupoles must be given because the body-fixed
46	// reference frame for directional atoms is determined by the mass distribution and
47	// not by the charge distribution.
48	// Dipoles are given in units of Debye
49	// Quadrupoles are given in units of
50	// name 0 charge
51	// name 1 charge \|u\| [theta phi psi]
52	// name 2 charge \|u\| Qxx Qyy Qzz [theta phi psi]
53
54	if (nTokens < 2) {
55	std::cerr << "ElectrostaticAtomTypesSectionParser Error: Not enought Tokens at line " << lineNo << std::endl;
56	} else {
57
58	std::string atomTypeName = tokenizer.nextToken();
59	int biggestRank = tokenizer.nextTokenAsInt();
60	nTokens -= 2;
61
62	AtomType* atomType = ff.getAtomType(atomTypeName);
63	DirectionalAtomType* dAtomType;
64	if (atomType != NULL) {
65
66	switch (biggestRank) {
67	case 0 :
68	parseCharge(tokenizer, atomType);
69	break;
70
71	case 1 :
72
73	dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
74	if (dAtomType == NULL) {
75	std::cerr << "ElectrostaticAtomTypesSectionParser Warning:" << std::endl;
76	}
77
78	parseCharge(tokenizer, dAtomType);
79	parseDipole(tokenizer, dAtomType);
80	parseElectroBodyFrame(tokenizer, dAtomType);
81	break;
82
83	case 2:
84
85	dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
86	if (dAtomType == NULL) {
87	std::cerr << "ElectrostaticAtomTypesSectionParser Warning:" << std::endl;
88	}
89
90	parseCharge(tokenizer, dAtomType);
91	parseDipole(tokenizer, dAtomType);
92	parseQuadruple(tokenizer, dAtomType);
93	parseElectroBodyFrame(tokenizer, dAtomType);
94	break;
95
96	default :
97	break;
98
99	}
100
101	} else {
102	std::cerr << "ElectrostaticAtomTypesSectionParser Error: Can not find matched AtomType " << atomTypeName
103	<< "at line " << lineNo << std::endl;
104	}
105
106	}
107
108
109	}
110
111
112	void ElectrostaticAtomTypesSectionParser::parseCharge(StringTokenizer& tokenizer,
113	AtomType* atomType) {
114
115	double charge = tokenizer.nextTokenAsDouble();
116	atomType->addProperty(new DoubleGenericData("Charge", charge));
117	atomType->setCharge();
118
119	}
120	void ElectrostaticAtomTypesSectionParser::parseDipole(StringTokenizer& tokenizer,
121	DirectionalAtomType* dAtomType) {
122
123	double Dipole = tokenizer.nextTokenAsDouble();
124	dAtomType->addProperty(new DoubleGenericData("Dipole", Dipole));
125	dAtomType->setDipole();
126	}
127
128	void ElectrostaticAtomTypesSectionParser::parseQuadruple(StringTokenizer& tokenizer,
129	DirectionalAtomType* dAtomType) {
130
131	Vector3d Q;
132	Q[0] = tokenizer.nextTokenAsDouble();
133	Q[1] = tokenizer.nextTokenAsDouble();
134	Q[2] = tokenizer.nextTokenAsDouble();
135
136	dAtomType->addProperty(new Vector3dGenericData("Quadrupole", Q));
137	dAtomType->setQuadrupole();
138	}
139	void ElectrostaticAtomTypesSectionParser::parseElectroBodyFrame(StringTokenizer& tokenizer,
140	DirectionalAtomType* dAtomType) {
141
142	double phi;
143	double theta;
144	double psi;
145
146	if (tokenizer.countTokens() >=3 ) {
147	phi = tokenizer.nextTokenAsDouble()/180.0;
148	theta = tokenizer.nextTokenAsDouble()/180.0;
149	psi = tokenizer.nextTokenAsDouble()/180.0;
150	} else {
151	phi = 0.0;
152	theta = 0.0;
153	psi = 0.0;
154	}
155
156	RotMat3x3d electroBodyFrame(phi, theta, psi);
157	dAtomType->setElectroBodyFrame(electroBodyFrame);
158
159	}
160
161	} //end namespace oopse
162
163
164