src/io/MultipoleAtomTypesSectionParser.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/MultipoleAtomTypesSectionParser.hpp"
#include "UseTheForce/ForceField.hpp"
#include "utils/NumericConstant.hpp"
#include "utils/simError.h"
namespace oopse {

  MultipoleAtomTypesSectionParser::MultipoleAtomTypesSectionParser() {
    setSectionName("MultipoleAtomTypes");
  }

  void MultipoleAtomTypesSectionParser::parseLine(ForceField& ff,const std::string& line, int lineNo){
    StringTokenizer tokenizer(line);
    int nTokens = tokenizer.countTokens();    

    // name multipole_type theta phi psi 
    // "name" must match the name in the AtomTypes section
    // avaliable multipole type is d (dipole), s (split dipole) ,  q (quadrupoles), dq(dipole plus quadrupole)
    // and sq(split dipole plus quadrupole)
    // Directionality for dipoles and quadrupoles is given by three euler angles (phi, theta, psi),
    //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 
    // examples:
    // name d phi theta psi dipole_moment
    // name s phi theta psi dipole_moment splitdipole_distance
    // name q phi theta psi Qxx Qyy Qzz
    // name dq phi theta psi dipole_moment Qxx Qyy Qzz
    // name sq phi theta psi dipole_moment splitdipole_distance Qxx Qyy Qzz
        
    if (nTokens < 5)  {
      sprintf(painCave.errMsg, "MultipoleAtomTypesSectionParser Error: Not enough tokens at line %d\n",
              lineNo);
      painCave.isFatal = 1;
      simError();
    } else {

      std::string atomTypeName = tokenizer.nextToken();    
      std::string multipoleType = tokenizer.nextToken();
      double phi = tokenizer.nextTokenAsDouble() * NumericConstant::PI /180.0;
      double theta = tokenizer.nextTokenAsDouble() * NumericConstant::PI /180.0;
      double psi = tokenizer.nextTokenAsDouble() * NumericConstant::PI /180.0;        
      nTokens -=  5;

      AtomType* atomType = ff.getAtomType(atomTypeName);
      if (atomType == NULL) {
        sprintf(painCave.errMsg, "MultipoleAtomTypesSectionParser Error: Can not find matched AtomType[%s] at line %d\n",
                atomTypeName.c_str(), lineNo);
        painCave.isFatal = 1;
        simError();
      }
        
      DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);            
      if (dAtomType == NULL) {
        sprintf(painCave.errMsg, "MultipoleAtomTypesSectionParser Error: Can not Cast Atom to DirectionalAtom at line %d\n", lineNo);
        painCave.isFatal = 1;
        simError();
      }        
        
      RotMat3x3d electroBodyFrame(phi, theta, psi);        
      dAtomType->setElectroBodyFrame(electroBodyFrame);        

      if (multipoleType== "d") {
        parseDipole(tokenizer, dAtomType, lineNo);
      } else if (multipoleType== "s") {
        parseSplitDipole(tokenizer, dAtomType, lineNo);
      } else if (multipoleType== "q") {
        parseQuadruple( tokenizer, dAtomType, lineNo);
      } else if (multipoleType== "dq") {
        parseDipole(tokenizer, dAtomType, lineNo);
        parseQuadruple( tokenizer, dAtomType, lineNo);
      } else if (multipoleType== "sq") {
        parseSplitDipole(tokenizer, dAtomType, lineNo);
        parseQuadruple( tokenizer, dAtomType, lineNo);
      } else {
        sprintf(painCave.errMsg, "MultipoleAtomTypesSectionParser Error: unrecognized multiple type at line %d\n",
                lineNo);
        painCave.isFatal = 1;
        simError();
      }
    }

  }

  void MultipoleAtomTypesSectionParser::parseDipole(StringTokenizer& tokenizer, 
                                                    DirectionalAtomType* dAtomType, int lineNo) {

    if (tokenizer.hasMoreTokens()) {
      double dipole = tokenizer.nextTokenAsDouble();

      dAtomType->addProperty(new DoubleGenericData("Dipole", dipole));
      dAtomType->setDipole();
    } else {
      sprintf(painCave.errMsg, "MultipoleAtomTypesSectionParser Error: Not enough tokens at line %d\n",
              lineNo);
      painCave.isFatal = 1;
      simError();
    }
  }

  void MultipoleAtomTypesSectionParser::parseSplitDipole(StringTokenizer& tokenizer, 
                                                         DirectionalAtomType* dAtomType, int lineNo) {

    if (tokenizer.hasMoreTokens()) {
      parseDipole(tokenizer, dAtomType, lineNo);    
      double splitDipoleDistance = tokenizer.nextTokenAsDouble();
      dAtomType->addProperty(new DoubleGenericData("SplitDipoleDistance", splitDipoleDistance));
      dAtomType->setSplitDipole();
    } else {
      sprintf(painCave.errMsg, "MultipoleAtomTypesSectionParser Error: Not enough tokens at line %d\n",
              lineNo);
      painCave.isFatal = 1;
      simError();
    }
  }

  void MultipoleAtomTypesSectionParser::parseQuadruple(StringTokenizer& tokenizer,
                                                       DirectionalAtomType* dAtomType, int lineNo) {
    int nTokens = tokenizer.countTokens();   
    if (nTokens >= 3) {
      Vector3d Q;
      Q[0] = tokenizer.nextTokenAsDouble();
      Q[1] = tokenizer.nextTokenAsDouble();
      Q[2] = tokenizer.nextTokenAsDouble();

      double trace =  Q[0] + Q[1] + Q[2];

      if (fabs(trace) > oopse::epsilon) {
        sprintf(painCave.errMsg, "MultipoleAtomTypesSectionParser Error: the trace of qudrupole moments is not zero at line %d\n",
                lineNo);
        painCave.isFatal = 1;
        simError();
      }

      dAtomType->addProperty(new Vector3dGenericData("QuadrupoleMoments", Q));
      dAtomType->setQuadrupole();
    } else {
      sprintf(painCave.errMsg, "MultipoleAtomTypesSectionParser Error: Not enough tokens at line %d\n",
              lineNo);
      painCave.isFatal = 1;
      simError();
    }
  }


} //end namespace oopse


Revision:	2204
Committed:	Fri Apr 15 22:04:00 2005 UTC (19 years, 2 months ago) by gezelter
File size:	7584 byte(s)
Log Message:	xemacs has been drafted to perform our indentation services
#	User	Rev	Content
1	gezelter	2204	/*
2	tim	2097	* 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/MultipoleAtomTypesSectionParser.hpp"
43			#include "UseTheForce/ForceField.hpp"
44			#include "utils/NumericConstant.hpp"
45			#include "utils/simError.h"
46			namespace oopse {
47
48	gezelter	2204	MultipoleAtomTypesSectionParser::MultipoleAtomTypesSectionParser() {
49	tim	2097	setSectionName("MultipoleAtomTypes");
50	gezelter	2204	}
51	tim	2097
52	gezelter	2204	void MultipoleAtomTypesSectionParser::parseLine(ForceField& ff,const std::string& line, int lineNo){
53	tim	2097	StringTokenizer tokenizer(line);
54			int nTokens = tokenizer.countTokens();
55
56			// name multipole_type theta phi psi
57			// "name" must match the name in the AtomTypes section
58			// avaliable multipole type is d (dipole), s (split dipole) , q (quadrupoles), dq(dipole plus quadrupole)
59			// and sq(split dipole plus quadrupole)
60			// Directionality for dipoles and quadrupoles is given by three euler angles (phi, theta, psi),
61			//because the body-fixed reference frame for directional atoms is determined by the mass
62			//distribution and not by the charge distribution.
63			// Dipoles are given in units of Debye
64			// Quadrupoles are given in units of
65			// examples:
66	tim	2102	// name d phi theta psi dipole_moment
67			// name s phi theta psi dipole_moment splitdipole_distance
68			// name q phi theta psi Qxx Qyy Qzz
69			// name dq phi theta psi dipole_moment Qxx Qyy Qzz
70			// name sq phi theta psi dipole_moment splitdipole_distance Qxx Qyy Qzz
71	tim	2097
72			if (nTokens < 5) {
73	gezelter	2204	sprintf(painCave.errMsg, "MultipoleAtomTypesSectionParser Error: Not enough tokens at line %d\n",
74			lineNo);
75			painCave.isFatal = 1;
76			simError();
77	tim	2097	} else {
78
79	gezelter	2204	std::string atomTypeName = tokenizer.nextToken();
80			std::string multipoleType = tokenizer.nextToken();
81			double phi = tokenizer.nextTokenAsDouble() * NumericConstant::PI /180.0;
82			double theta = tokenizer.nextTokenAsDouble() * NumericConstant::PI /180.0;
83			double psi = tokenizer.nextTokenAsDouble() * NumericConstant::PI /180.0;
84			nTokens -= 5;
85	tim	2097
86	gezelter	2204	AtomType* atomType = ff.getAtomType(atomTypeName);
87			if (atomType == NULL) {
88			sprintf(painCave.errMsg, "MultipoleAtomTypesSectionParser Error: Can not find matched AtomType[%s] at line %d\n",
89			atomTypeName.c_str(), lineNo);
90			painCave.isFatal = 1;
91			simError();
92			}
93	tim	2097
94	gezelter	2204	DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
95			if (dAtomType == NULL) {
96			sprintf(painCave.errMsg, "MultipoleAtomTypesSectionParser Error: Can not Cast Atom to DirectionalAtom at line %d\n", lineNo);
97			painCave.isFatal = 1;
98			simError();
99			}
100	tim	2097
101	gezelter	2204	RotMat3x3d electroBodyFrame(phi, theta, psi);
102			dAtomType->setElectroBodyFrame(electroBodyFrame);
103	tim	2097
104	gezelter	2204	if (multipoleType== "d") {
105			parseDipole(tokenizer, dAtomType, lineNo);
106			} else if (multipoleType== "s") {
107			parseSplitDipole(tokenizer, dAtomType, lineNo);
108			} else if (multipoleType== "q") {
109			parseQuadruple( tokenizer, dAtomType, lineNo);
110			} else if (multipoleType== "dq") {
111			parseDipole(tokenizer, dAtomType, lineNo);
112			parseQuadruple( tokenizer, dAtomType, lineNo);
113			} else if (multipoleType== "sq") {
114			parseSplitDipole(tokenizer, dAtomType, lineNo);
115			parseQuadruple( tokenizer, dAtomType, lineNo);
116			} else {
117			sprintf(painCave.errMsg, "MultipoleAtomTypesSectionParser Error: unrecognized multiple type at line %d\n",
118			lineNo);
119			painCave.isFatal = 1;
120			simError();
121			}
122			}
123	tim	2097
124	gezelter	2204	}
125	tim	2097
126	gezelter	2204	void MultipoleAtomTypesSectionParser::parseDipole(StringTokenizer& tokenizer,
127			DirectionalAtomType* dAtomType, int lineNo) {
128	tim	2097
129			if (tokenizer.hasMoreTokens()) {
130	gezelter	2204	double dipole = tokenizer.nextTokenAsDouble();
131	tim	2097
132	gezelter	2204	dAtomType->addProperty(new DoubleGenericData("Dipole", dipole));
133			dAtomType->setDipole();
134	tim	2097	} else {
135	gezelter	2204	sprintf(painCave.errMsg, "MultipoleAtomTypesSectionParser Error: Not enough tokens at line %d\n",
136			lineNo);
137			painCave.isFatal = 1;
138			simError();
139	tim	2097	}
140	gezelter	2204	}
141	tim	2097
142	gezelter	2204	void MultipoleAtomTypesSectionParser::parseSplitDipole(StringTokenizer& tokenizer,
143			DirectionalAtomType* dAtomType, int lineNo) {
144	tim	2097
145			if (tokenizer.hasMoreTokens()) {
146	gezelter	2204	parseDipole(tokenizer, dAtomType, lineNo);
147			double splitDipoleDistance = tokenizer.nextTokenAsDouble();
148			dAtomType->addProperty(new DoubleGenericData("SplitDipoleDistance", splitDipoleDistance));
149			dAtomType->setSplitDipole();
150	tim	2097	} else {
151	gezelter	2204	sprintf(painCave.errMsg, "MultipoleAtomTypesSectionParser Error: Not enough tokens at line %d\n",
152			lineNo);
153			painCave.isFatal = 1;
154			simError();
155	tim	2097	}
156	gezelter	2204	}
157	tim	2097
158	gezelter	2204	void MultipoleAtomTypesSectionParser::parseQuadruple(StringTokenizer& tokenizer,
159			DirectionalAtomType* dAtomType, int lineNo) {
160	tim	2097	int nTokens = tokenizer.countTokens();
161	tim	2120	if (nTokens >= 3) {
162	gezelter	2204	Vector3d Q;
163			Q[0] = tokenizer.nextTokenAsDouble();
164			Q[1] = tokenizer.nextTokenAsDouble();
165			Q[2] = tokenizer.nextTokenAsDouble();
166	tim	2097
167	gezelter	2204	double trace = Q[0] + Q[1] + Q[2];
168	tim	2097
169	gezelter	2204	if (fabs(trace) > oopse::epsilon) {
170			sprintf(painCave.errMsg, "MultipoleAtomTypesSectionParser Error: the trace of qudrupole moments is not zero at line %d\n",
171			lineNo);
172			painCave.isFatal = 1;
173			simError();
174			}
175	tim	2097
176	gezelter	2204	dAtomType->addProperty(new Vector3dGenericData("QuadrupoleMoments", Q));
177			dAtomType->setQuadrupole();
178	tim	2097	} else {
179	gezelter	2204	sprintf(painCave.errMsg, "MultipoleAtomTypesSectionParser Error: Not enough tokens at line %d\n",
180			lineNo);
181			painCave.isFatal = 1;
182			simError();
183	tim	2097	}
184	gezelter	2204	}
185	tim	2097
186
187			} //end namespace oopse
188
189
190