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"
#include "utils/NumericConstant.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();

    if (fabs(charge) > NumericConstant::epsilon) {
        atomType->addProperty(new DoubleGenericData("Charge", charge));
        atomType->setCharge();
    }
}
void ElectrostaticAtomTypesSectionParser::parseDipole(StringTokenizer& tokenizer, 
    DirectionalAtomType* dAtomType) {

    double dipole = tokenizer.nextTokenAsDouble();

    if (fabs(dipole) > NumericConstant::epsilon) {

        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();

    if (fabs(Q[0]) > NumericConstant::epsilon && fabs(Q[1]) > NumericConstant::epsilon 
        && fabs(Q[2]) > NumericConstant::epsilon) {    
        
        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:	1883
Committed:	Mon Dec 13 22:30:27 2004 UTC (19 years, 7 months ago) by tim
File size:	6114 byte(s)
Log Message:	MPI version is built
#	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	tim	1790	#include "UseTheForce/ForceField.hpp"
28	tim	1883	#include "utils/NumericConstant.hpp"
29	tim	1770	namespace oopse {
30
31			ElectrostaticAtomTypesSectionParser::ElectrostaticAtomTypesSectionParser() {
32			setSectionName("ElectrostaticAtomTypes");
33			}
34
35			void ElectrostaticAtomTypesSectionParser::parseLine(ForceField& ff,const std::string& line, int lineNo){
36			StringTokenizer tokenizer(line);
37			int nTokens = tokenizer.countTokens();
38
39			//in AtomTypeSection, a line at least contains 2 tokens
40			//atomTypeName and biggest rank
41			//for the time being, we only support up to quadrupole
42	tim	1775	// "name" must match the name in the AtomTypes section
43			// charge is given in units of electrons (1.61 x 10^-19 C)
44			// Directionality for dipoles and quadrupoles must be given because the body-fixed
45			// reference frame for directional atoms is determined by the mass distribution and
46			// not by the charge distribution.
47			// Dipoles are given in units of Debye
48			// Quadrupoles are given in units of
49			// name 0 charge
50			// name 1 charge \|u\| [theta phi psi]
51			// name 2 charge \|u\| Qxx Qyy Qzz [theta phi psi]
52	tim	1770
53			if (nTokens < 2) {
54			std::cerr << "ElectrostaticAtomTypesSectionParser Error: Not enought Tokens at line " << lineNo << std::endl;
55			} else {
56
57			std::string atomTypeName = tokenizer.nextToken();
58			int biggestRank = tokenizer.nextTokenAsInt();
59			nTokens -= 2;
60
61	tim	1790	AtomType* atomType = ff.getAtomType(atomTypeName);
62	tim	1869	DirectionalAtomType* dAtomType;
63	tim	1770	if (atomType != NULL) {
64	tim	1869
65	tim	1815	switch (biggestRank) {
66	tim	1869	case 0 :
67	tim	1815	parseCharge(tokenizer, atomType);
68			break;
69
70	tim	1869	case 1 :
71
72			dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
73			if (dAtomType == NULL) {
74			std::cerr << "ElectrostaticAtomTypesSectionParser Warning:" << std::endl;
75			}
76
77	tim	1815	parseCharge(tokenizer, dAtomType);
78			parseDipole(tokenizer, dAtomType);
79			parseElectroBodyFrame(tokenizer, dAtomType);
80			break;
81
82	tim	1869	case 2:
83
84			dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
85			if (dAtomType == NULL) {
86			std::cerr << "ElectrostaticAtomTypesSectionParser Warning:" << std::endl;
87			}
88
89	tim	1815	parseCharge(tokenizer, dAtomType);
90			parseDipole(tokenizer, dAtomType);
91			parseQuadruple(tokenizer, dAtomType);
92			parseElectroBodyFrame(tokenizer, dAtomType);
93			break;
94
95			default :
96			break;
97
98			}
99	tim	1770
100			} else {
101			std::cerr << "ElectrostaticAtomTypesSectionParser Error: Can not find matched AtomType " << atomTypeName
102			<< "at line " << lineNo << std::endl;
103			}
104
105			}
106
107
108			}
109
110	tim	1813
111			void ElectrostaticAtomTypesSectionParser::parseCharge(StringTokenizer& tokenizer,
112			AtomType* atomType) {
113
114			double charge = tokenizer.nextTokenAsDouble();
115	tim	1883
116			if (fabs(charge) > NumericConstant::epsilon) {
117			atomType->addProperty(new DoubleGenericData("Charge", charge));
118			atomType->setCharge();
119			}
120	tim	1813	}
121			void ElectrostaticAtomTypesSectionParser::parseDipole(StringTokenizer& tokenizer,
122			DirectionalAtomType* dAtomType) {
123
124	tim	1883	double dipole = tokenizer.nextTokenAsDouble();
125
126			if (fabs(dipole) > NumericConstant::epsilon) {
127
128			dAtomType->addProperty(new DoubleGenericData("Dipole", dipole));
129			dAtomType->setDipole();
130			}
131	tim	1813	}
132
133			void ElectrostaticAtomTypesSectionParser::parseQuadruple(StringTokenizer& tokenizer,
134			DirectionalAtomType* dAtomType) {
135
136			Vector3d Q;
137	tim	1815	Q[0] = tokenizer.nextTokenAsDouble();
138			Q[1] = tokenizer.nextTokenAsDouble();
139			Q[2] = tokenizer.nextTokenAsDouble();
140	tim	1883
141			if (fabs(Q[0]) > NumericConstant::epsilon && fabs(Q[1]) > NumericConstant::epsilon
142			&& fabs(Q[2]) > NumericConstant::epsilon) {
143
144			dAtomType->addProperty(new Vector3dGenericData("Quadrupole", Q));
145			dAtomType->setQuadrupole();
146			}
147	tim	1813	}
148			void ElectrostaticAtomTypesSectionParser::parseElectroBodyFrame(StringTokenizer& tokenizer,
149			DirectionalAtomType* dAtomType) {
150
151	tim	1815	double phi;
152			double theta;
153			double psi;
154	tim	1813
155	tim	1815	if (tokenizer.countTokens() >=3 ) {
156			phi = tokenizer.nextTokenAsDouble()/180.0;
157			theta = tokenizer.nextTokenAsDouble()/180.0;
158			psi = tokenizer.nextTokenAsDouble()/180.0;
159			} else {
160			phi = 0.0;
161			theta = 0.0;
162			psi = 0.0;
163			}
164
165	tim	1813	RotMat3x3d electroBodyFrame(phi, theta, psi);
166			dAtomType->setElectroBodyFrame(electroBodyFrame);
167
168			}
169
170	tim	1770	} //end namespace oopse
171
172
173