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, 9 months ago) by tim
File size:	5788 byte(s)
Log Message:	fix a parsing bug in ElectroStaticAtomTypesSectionParser
#	User	Rev	Content
1	tim	1770	/*
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	tim	1790	#include "UseTheForce/ForceField.hpp"
29	tim	1784
30	tim	1770	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	tim	1775	// "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	tim	1770
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	tim	1790	AtomType* atomType = ff.getAtomType(atomTypeName);
63	tim	1869	DirectionalAtomType* dAtomType;
64	tim	1770	if (atomType != NULL) {
65	tim	1869
66	tim	1815	switch (biggestRank) {
67	tim	1869	case 0 :
68	tim	1815	parseCharge(tokenizer, atomType);
69			break;
70
71	tim	1869	case 1 :
72
73			dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
74			if (dAtomType == NULL) {
75			std::cerr << "ElectrostaticAtomTypesSectionParser Warning:" << std::endl;
76			}
77
78	tim	1815	parseCharge(tokenizer, dAtomType);
79			parseDipole(tokenizer, dAtomType);
80			parseElectroBodyFrame(tokenizer, dAtomType);
81			break;
82
83	tim	1869	case 2:
84
85			dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
86			if (dAtomType == NULL) {
87			std::cerr << "ElectrostaticAtomTypesSectionParser Warning:" << std::endl;
88			}
89
90	tim	1815	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	tim	1770
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	tim	1813
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	tim	1815	Q[0] = tokenizer.nextTokenAsDouble();
133			Q[1] = tokenizer.nextTokenAsDouble();
134			Q[2] = tokenizer.nextTokenAsDouble();
135	tim	1813
136			dAtomType->addProperty(new Vector3dGenericData("Quadrupole", Q));
137			dAtomType->setQuadrupole();
138			}
139			void ElectrostaticAtomTypesSectionParser::parseElectroBodyFrame(StringTokenizer& tokenizer,
140			DirectionalAtomType* dAtomType) {
141
142	tim	1815	double phi;
143			double theta;
144			double psi;
145	tim	1813
146	tim	1815	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	tim	1813	RotMat3x3d electroBodyFrame(phi, theta, psi);
157			dAtomType->setElectroBodyFrame(electroBodyFrame);
158
159			}
160
161	tim	1770	} //end namespace oopse
162
163
164