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, 6 months ago) by tim
File size:	6114 byte(s)
Log Message:	MPI version is built
#	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	#include "UseTheForce/ForceField.hpp"
28	#include "utils/NumericConstant.hpp"
29	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	// "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
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	AtomType* atomType = ff.getAtomType(atomTypeName);
62	DirectionalAtomType* dAtomType;
63	if (atomType != NULL) {
64
65	switch (biggestRank) {
66	case 0 :
67	parseCharge(tokenizer, atomType);
68	break;
69
70	case 1 :
71
72	dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
73	if (dAtomType == NULL) {
74	std::cerr << "ElectrostaticAtomTypesSectionParser Warning:" << std::endl;
75	}
76
77	parseCharge(tokenizer, dAtomType);
78	parseDipole(tokenizer, dAtomType);
79	parseElectroBodyFrame(tokenizer, dAtomType);
80	break;
81
82	case 2:
83
84	dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
85	if (dAtomType == NULL) {
86	std::cerr << "ElectrostaticAtomTypesSectionParser Warning:" << std::endl;
87	}
88
89	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
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
111	void ElectrostaticAtomTypesSectionParser::parseCharge(StringTokenizer& tokenizer,
112	AtomType* atomType) {
113
114	double charge = tokenizer.nextTokenAsDouble();
115
116	if (fabs(charge) > NumericConstant::epsilon) {
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
126	if (fabs(dipole) > NumericConstant::epsilon) {
127
128	dAtomType->addProperty(new DoubleGenericData("Dipole", dipole));
129	dAtomType->setDipole();
130	}
131	}
132
133	void ElectrostaticAtomTypesSectionParser::parseQuadruple(StringTokenizer& tokenizer,
134	DirectionalAtomType* dAtomType) {
135
136	Vector3d Q;
137	Q[0] = tokenizer.nextTokenAsDouble();
138	Q[1] = tokenizer.nextTokenAsDouble();
139	Q[2] = tokenizer.nextTokenAsDouble();
140
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	}
148	void ElectrostaticAtomTypesSectionParser::parseElectroBodyFrame(StringTokenizer& tokenizer,
149	DirectionalAtomType* dAtomType) {
150
151	double phi;
152	double theta;
153	double psi;
154
155	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	RotMat3x3d electroBodyFrame(phi, theta, psi);
166	dAtomType->setElectroBodyFrame(electroBodyFrame);
167
168	}
169
170	} //end namespace oopse
171
172
173