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);

        if (atomType != NULL) {

            
            //parse charge
            if (biggestRank >= 1) {
                parseCharge(tokenizer, atomType);
            }
            
            DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);            
            if (dAtomType != NULL) {

            } else {
                std::cerr << "ElectrostaticAtomTypesSectionParser Warning:" << std::endl;
            }

            switch (biggestRank) {
                case 1 :
                    parseCharge(tokenizer, atomType);
                    break;

               case 2 :
                    parseCharge(tokenizer, dAtomType);
                    parseDipole(tokenizer, dAtomType);
                    parseElectroBodyFrame(tokenizer, dAtomType);
                    break;

               case 3:
                    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:	1815
Committed:	Wed Dec 1 18:42:45 2004 UTC (19 years, 7 months ago) by tim
File size:	5632 byte(s)
Log Message:	except integrator and constraint, other directories get 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
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	1770
64			if (atomType != NULL) {
65	tim	1815
66
67	tim	1770	//parse charge
68	tim	1815	if (biggestRank >= 1) {
69			parseCharge(tokenizer, atomType);
70			}
71
72	tim	1770	DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
73			if (dAtomType != NULL) {
74	tim	1813
75	tim	1770	} else {
76			std::cerr << "ElectrostaticAtomTypesSectionParser Warning:" << std::endl;
77			}
78
79	tim	1815	switch (biggestRank) {
80			case 1 :
81			parseCharge(tokenizer, atomType);
82			break;
83
84			case 2 :
85			parseCharge(tokenizer, dAtomType);
86			parseDipole(tokenizer, dAtomType);
87			parseElectroBodyFrame(tokenizer, dAtomType);
88			break;
89
90			case 3:
91			parseCharge(tokenizer, dAtomType);
92			parseDipole(tokenizer, dAtomType);
93			parseQuadruple(tokenizer, dAtomType);
94			parseElectroBodyFrame(tokenizer, dAtomType);
95			break;
96
97			default :
98			break;
99
100			}
101	tim	1770
102			} else {
103			std::cerr << "ElectrostaticAtomTypesSectionParser Error: Can not find matched AtomType " << atomTypeName
104			<< "at line " << lineNo << std::endl;
105			}
106
107			}
108
109
110			}
111
112	tim	1813
113			void ElectrostaticAtomTypesSectionParser::parseCharge(StringTokenizer& tokenizer,
114			AtomType* atomType) {
115
116			double charge = tokenizer.nextTokenAsDouble();
117			atomType->addProperty(new DoubleGenericData("Charge", charge));
118			atomType->setCharge();
119
120			}
121			void ElectrostaticAtomTypesSectionParser::parseDipole(StringTokenizer& tokenizer,
122			DirectionalAtomType* dAtomType) {
123
124			double Dipole = tokenizer.nextTokenAsDouble();
125			dAtomType->addProperty(new DoubleGenericData("Dipole", Dipole));
126			dAtomType->setDipole();
127			}
128
129			void ElectrostaticAtomTypesSectionParser::parseQuadruple(StringTokenizer& tokenizer,
130			DirectionalAtomType* dAtomType) {
131
132			Vector3d Q;
133	tim	1815	Q[0] = tokenizer.nextTokenAsDouble();
134			Q[1] = tokenizer.nextTokenAsDouble();
135			Q[2] = tokenizer.nextTokenAsDouble();
136	tim	1813
137			dAtomType->addProperty(new Vector3dGenericData("Quadrupole", Q));
138			dAtomType->setQuadrupole();
139			}
140			void ElectrostaticAtomTypesSectionParser::parseElectroBodyFrame(StringTokenizer& tokenizer,
141			DirectionalAtomType* dAtomType) {
142
143	tim	1815	double phi;
144			double theta;
145			double psi;
146	tim	1813
147	tim	1815	if (tokenizer.countTokens() >=3 ) {
148			phi = tokenizer.nextTokenAsDouble()/180.0;
149			theta = tokenizer.nextTokenAsDouble()/180.0;
150			psi = tokenizer.nextTokenAsDouble()/180.0;
151			} else {
152			phi = 0.0;
153			theta = 0.0;
154			psi = 0.0;
155			}
156
157	tim	1813	RotMat3x3d electroBodyFrame(phi, theta, psi);
158			dAtomType->setElectroBodyFrame(electroBodyFrame);
159
160			}
161
162	tim	1770	} //end namespace oopse
163
164
165