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() * NumericConstant::PI /180.0;
        theta = tokenizer.nextTokenAsDouble() * NumericConstant::PI /180.0;
        psi = tokenizer.nextTokenAsDouble() * NumericConstant::PI /180.0;
    } else {
        phi = 0.0;
        theta = 0.0;
        psi = 0.0;    
    }
    
    RotMat3x3d electroBodyFrame(phi, theta, psi);
    dAtomType->setElectroBodyFrame(electroBodyFrame);
        
}

} //end namespace oopse


Revision:	2053
Committed:	Fri Feb 18 23:07:32 2005 UTC (19 years, 4 months ago) by tim
File size:	7478 byte(s)
Log Message:	adding LipidTransVisitor, GofXyz is working now
#	Content
1	/*
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	#include "utils/simError.h"
46	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	sprintf(painCave.errMsg, "ElectrostaticAtomTypesSectionParser Error: Not enough tokens at line %d\n",
72	lineNo);
73	painCave.isFatal = 1;
74	simError();
75	} 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	sprintf(painCave.errMsg, "ElectrostaticAtomTypesSectionParser Error: Can not Cast Atom to DirectionalAtom at line \n");
95	painCave.isFatal = 1;
96	simError();
97	}
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	sprintf(painCave.errMsg, "ElectrostaticAtomTypesSectionParser Error: Can not Cast Atom to DirectionalAtom at line \n");
109	painCave.isFatal = 1;
110	simError();
111	}
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
126	sprintf(painCave.errMsg, "ElectrostaticAtomTypesSectionParser Error: Can not find matched AtomType at line %d\n",
127	lineNo);
128	painCave.isFatal = 1;
129	simError();
130	}
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() * NumericConstant::PI /180.0;
184	theta = tokenizer.nextTokenAsDouble() * NumericConstant::PI /180.0;
185	psi = tokenizer.nextTokenAsDouble() * NumericConstant::PI /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