src/io/ElectrostaticAtomTypesSectionParser.cpp

 /*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 */
 
#include "io/ElectrostaticAtomTypesSectionParser.hpp"
#include "UseTheForce/ForceField.hpp"
#include "utils/NumericConstant.hpp"
#include "utils/simError.h"
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)  {
        sprintf(painCave.errMsg, "ElectrostaticAtomTypesSectionParser Error: Not enough tokens at line %d\n",
                lineNo);
        painCave.isFatal = 1;
        simError();
    } 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) {
                        sprintf(painCave.errMsg, "ElectrostaticAtomTypesSectionParser Error: Can not Cast Atom to DirectionalAtom at line \n");
                        painCave.isFatal = 1;
                        simError();
                    }

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

               case 2:

                    dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);            
                    if (dAtomType == NULL) {
                        sprintf(painCave.errMsg, "ElectrostaticAtomTypesSectionParser Error: Can not Cast Atom to DirectionalAtom at line \n");
                        painCave.isFatal = 1;
                        simError();
                    }

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

            }
            
        } else {

            sprintf(painCave.errMsg, "ElectrostaticAtomTypesSectionParser Error: Can not find matched AtomType at line %d\n",
                    lineNo);
            painCave.isFatal = 1;
            simError();
        }
                       
    }    


}


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:	1957
Committed:	Tue Jan 25 17:45:23 2005 UTC (19 years, 5 months ago) by tim
File size:	7409 byte(s)
Log Message:	(1) complete section parser's error message (2) add GhostTorsion (3) accumulate inertial tensor from the directional atoms before calculate rigidbody's inertial tensor
#	User	Rev	Content
1	gezelter	1930	/*
2			* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9			* 1. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42			#include "io/ElectrostaticAtomTypesSectionParser.hpp"
43			#include "UseTheForce/ForceField.hpp"
44			#include "utils/NumericConstant.hpp"
45	tim	1957	#include "utils/simError.h"
46	gezelter	1930	namespace oopse {
47
48			ElectrostaticAtomTypesSectionParser::ElectrostaticAtomTypesSectionParser() {
49			setSectionName("ElectrostaticAtomTypes");
50			}
51
52			void ElectrostaticAtomTypesSectionParser::parseLine(ForceField& ff,const std::string& line, int lineNo){
53			StringTokenizer tokenizer(line);
54			int nTokens = tokenizer.countTokens();
55
56			//in AtomTypeSection, a line at least contains 2 tokens
57			//atomTypeName and biggest rank
58			//for the time being, we only support up to quadrupole
59			// "name" must match the name in the AtomTypes section
60			// charge is given in units of electrons (1.61 x 10^-19 C)
61			// Directionality for dipoles and quadrupoles must be given because the body-fixed
62			// reference frame for directional atoms is determined by the mass distribution and
63			// not by the charge distribution.
64			// Dipoles are given in units of Debye
65			// Quadrupoles are given in units of
66			// name 0 charge
67			// name 1 charge \|u\| [theta phi psi]
68			// name 2 charge \|u\| Qxx Qyy Qzz [theta phi psi]
69
70			if (nTokens < 2) {
71	tim	1957	sprintf(painCave.errMsg, "ElectrostaticAtomTypesSectionParser Error: Not enough tokens at line %d\n",
72			lineNo);
73			painCave.isFatal = 1;
74			simError();
75	gezelter	1930	} else {
76
77			std::string atomTypeName = tokenizer.nextToken();
78			int biggestRank = tokenizer.nextTokenAsInt();
79			nTokens -= 2;
80
81			AtomType* atomType = ff.getAtomType(atomTypeName);
82			DirectionalAtomType* dAtomType;
83			if (atomType != NULL) {
84
85			switch (biggestRank) {
86			case 0 :
87			parseCharge(tokenizer, atomType);
88			break;
89
90			case 1 :
91
92			dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
93			if (dAtomType == NULL) {
94	tim	1957	sprintf(painCave.errMsg, "ElectrostaticAtomTypesSectionParser Error: Can not Cast Atom to DirectionalAtom at line \n");
95			painCave.isFatal = 1;
96			simError();
97	gezelter	1930	}
98
99			parseCharge(tokenizer, dAtomType);
100			parseDipole(tokenizer, dAtomType);
101			parseElectroBodyFrame(tokenizer, dAtomType);
102			break;
103
104			case 2:
105
106			dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
107			if (dAtomType == NULL) {
108	tim	1957	sprintf(painCave.errMsg, "ElectrostaticAtomTypesSectionParser Error: Can not Cast Atom to DirectionalAtom at line \n");
109			painCave.isFatal = 1;
110			simError();
111	gezelter	1930	}
112
113			parseCharge(tokenizer, dAtomType);
114			parseDipole(tokenizer, dAtomType);
115			parseQuadruple(tokenizer, dAtomType);
116			parseElectroBodyFrame(tokenizer, dAtomType);
117			break;
118
119			default :
120			break;
121
122			}
123
124			} else {
125	tim	1957
126			sprintf(painCave.errMsg, "ElectrostaticAtomTypesSectionParser Error: Can not find matched AtomType at line %d\n",
127			lineNo);
128			painCave.isFatal = 1;
129			simError();
130	gezelter	1930	}
131
132			}
133
134
135			}
136
137
138			void ElectrostaticAtomTypesSectionParser::parseCharge(StringTokenizer& tokenizer,
139			AtomType* atomType) {
140
141			double charge = tokenizer.nextTokenAsDouble();
142
143			if (fabs(charge) > NumericConstant::epsilon) {
144			atomType->addProperty(new DoubleGenericData("Charge", charge));
145			atomType->setCharge();
146			}
147			}
148			void ElectrostaticAtomTypesSectionParser::parseDipole(StringTokenizer& tokenizer,
149			DirectionalAtomType* dAtomType) {
150
151			double dipole = tokenizer.nextTokenAsDouble();
152
153			if (fabs(dipole) > NumericConstant::epsilon) {
154
155			dAtomType->addProperty(new DoubleGenericData("Dipole", dipole));
156			dAtomType->setDipole();
157			}
158			}
159
160			void ElectrostaticAtomTypesSectionParser::parseQuadruple(StringTokenizer& tokenizer,
161			DirectionalAtomType* dAtomType) {
162
163			Vector3d Q;
164			Q[0] = tokenizer.nextTokenAsDouble();
165			Q[1] = tokenizer.nextTokenAsDouble();
166			Q[2] = tokenizer.nextTokenAsDouble();
167
168			if (fabs(Q[0]) > NumericConstant::epsilon && fabs(Q[1]) > NumericConstant::epsilon
169			&& fabs(Q[2]) > NumericConstant::epsilon) {
170
171			dAtomType->addProperty(new Vector3dGenericData("Quadrupole", Q));
172			dAtomType->setQuadrupole();
173			}
174			}
175			void ElectrostaticAtomTypesSectionParser::parseElectroBodyFrame(StringTokenizer& tokenizer,
176			DirectionalAtomType* dAtomType) {
177
178			double phi;
179			double theta;
180			double psi;
181
182			if (tokenizer.countTokens() >=3 ) {
183			phi = tokenizer.nextTokenAsDouble()/180.0;
184			theta = tokenizer.nextTokenAsDouble()/180.0;
185			psi = tokenizer.nextTokenAsDouble()/180.0;
186			} else {
187			phi = 0.0;
188			theta = 0.0;
189			psi = 0.0;
190			}
191
192			RotMat3x3d electroBodyFrame(phi, theta, psi);
193			dAtomType->setElectroBodyFrame(electroBodyFrame);
194
195			}
196
197			} //end namespace oopse
198
199
200