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(ForceFieldOptions& options) : options_(options){
    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:	2501
Committed:	Thu Dec 8 15:38:49 2005 UTC (18 years, 6 months ago) by chuckv
File size:	7629 byte(s)
Log Message:	Wow thats alot o' files. Now passing forceFieldOptions to all of the parsers.
#	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/MultipoleAtomTypesSectionParser.hpp"
43	#include "UseTheForce/ForceField.hpp"
44	#include "utils/NumericConstant.hpp"
45	#include "utils/simError.h"
46	namespace oopse {
47
48	MultipoleAtomTypesSectionParser::MultipoleAtomTypesSectionParser(ForceFieldOptions& options) : options_(options){
49	setSectionName("MultipoleAtomTypes");
50	}
51
52	void MultipoleAtomTypesSectionParser::parseLine(ForceField& ff,const std::string& line, int lineNo){
53	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	// 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
72	if (nTokens < 5) {
73	sprintf(painCave.errMsg, "MultipoleAtomTypesSectionParser Error: Not enough tokens at line %d\n",
74	lineNo);
75	painCave.isFatal = 1;
76	simError();
77	} else {
78
79	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
86	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
94	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
101	RotMat3x3d electroBodyFrame(phi, theta, psi);
102	dAtomType->setElectroBodyFrame(electroBodyFrame);
103
104	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
124	}
125
126	void MultipoleAtomTypesSectionParser::parseDipole(StringTokenizer& tokenizer,
127	DirectionalAtomType* dAtomType, int lineNo) {
128
129	if (tokenizer.hasMoreTokens()) {
130	double dipole = tokenizer.nextTokenAsDouble();
131
132	dAtomType->addProperty(new DoubleGenericData("Dipole", dipole));
133	dAtomType->setDipole();
134	} else {
135	sprintf(painCave.errMsg, "MultipoleAtomTypesSectionParser Error: Not enough tokens at line %d\n",
136	lineNo);
137	painCave.isFatal = 1;
138	simError();
139	}
140	}
141
142	void MultipoleAtomTypesSectionParser::parseSplitDipole(StringTokenizer& tokenizer,
143	DirectionalAtomType* dAtomType, int lineNo) {
144
145	if (tokenizer.hasMoreTokens()) {
146	parseDipole(tokenizer, dAtomType, lineNo);
147	double splitDipoleDistance = tokenizer.nextTokenAsDouble();
148	dAtomType->addProperty(new DoubleGenericData("SplitDipoleDistance", splitDipoleDistance));
149	dAtomType->setSplitDipole();
150	} else {
151	sprintf(painCave.errMsg, "MultipoleAtomTypesSectionParser Error: Not enough tokens at line %d\n",
152	lineNo);
153	painCave.isFatal = 1;
154	simError();
155	}
156	}
157
158	void MultipoleAtomTypesSectionParser::parseQuadruple(StringTokenizer& tokenizer,
159	DirectionalAtomType* dAtomType, int lineNo) {
160	int nTokens = tokenizer.countTokens();
161	if (nTokens >= 3) {
162	Vector3d Q;
163	Q[0] = tokenizer.nextTokenAsDouble();
164	Q[1] = tokenizer.nextTokenAsDouble();
165	Q[2] = tokenizer.nextTokenAsDouble();
166
167	double trace = Q[0] + Q[1] + Q[2];
168
169	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
176	dAtomType->addProperty(new Vector3dGenericData("QuadrupoleMoments", Q));
177	dAtomType->setQuadrupole();
178	} else {
179	sprintf(painCave.errMsg, "MultipoleAtomTypesSectionParser Error: Not enough tokens at line %d\n",
180	lineNo);
181	painCave.isFatal = 1;
182	simError();
183	}
184	}
185
186
187	} //end namespace oopse
188
189
190