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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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*/ |
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#include "io/MultipoleAtomTypesSectionParser.hpp" |
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#include "UseTheForce/ForceField.hpp" |
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#include "utils/NumericConstant.hpp" |
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#include "utils/simError.h" |
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namespace oopse { |
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MultipoleAtomTypesSectionParser::MultipoleAtomTypesSectionParser() { |
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setSectionName("MultipoleAtomTypes"); |
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} |
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void MultipoleAtomTypesSectionParser::parseLine(ForceField& ff,const std::string& line, int lineNo){ |
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StringTokenizer tokenizer(line); |
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int nTokens = tokenizer.countTokens(); |
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// name multipole_type theta phi psi |
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// "name" must match the name in the AtomTypes section |
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// avaliable multipole type is d (dipole), s (split dipole) , q (quadrupoles), dq(dipole plus quadrupole) |
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// and sq(split dipole plus quadrupole) |
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// Directionality for dipoles and quadrupoles is given by three euler angles (phi, theta, psi), |
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//because the body-fixed reference frame for directional atoms is determined by the *mass* |
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//distribution and not by the charge distribution. |
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// Dipoles are given in units of Debye |
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// Quadrupoles are given in units of |
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// examples: |
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// name d theta phi psi dipole_moment |
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// name s theta phi psi dipole_moment splitdipole_distance |
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// name q theta phi psi Qxx Qyy Qzz |
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// name dq theta phi psi dipole_moment Qxx Qyy Qzz |
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// name sq theta phi psi dipole_moment splitdipole_distance Qxx Qyy Qzz |
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if (nTokens < 5) { |
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sprintf(painCave.errMsg, "MultipoleAtomTypesSectionParser Error: Not enough tokens at line %d\n", |
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lineNo); |
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painCave.isFatal = 1; |
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simError(); |
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} else { |
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std::string atomTypeName = tokenizer.nextToken(); |
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std::string multipoleType = tokenizer.nextToken(); |
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double phi = tokenizer.nextTokenAsDouble() * NumericConstant::PI /180.0; |
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double theta = tokenizer.nextTokenAsDouble() * NumericConstant::PI /180.0; |
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double psi = tokenizer.nextTokenAsDouble() * NumericConstant::PI /180.0; |
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nTokens -= 5; |
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AtomType* atomType = ff.getAtomType(atomTypeName); |
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if (atomType == NULL) { |
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sprintf(painCave.errMsg, "MultipoleAtomTypesSectionParser Error: Can not find matched AtomType at line %d\n", |
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lineNo); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType); |
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if (dAtomType == NULL) { |
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sprintf(painCave.errMsg, "MultipoleAtomTypesSectionParser Error: Can not Cast Atom to DirectionalAtom at line \n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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RotMat3x3d electroBodyFrame(phi, theta, psi); |
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dAtomType->setElectroBodyFrame(electroBodyFrame); |
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if (multipoleType== "d") { |
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parseDipole(tokenizer, dAtomType, lineNo); |
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} else if (multipoleType== "s") { |
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parseSplitDipole(tokenizer, dAtomType, lineNo); |
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} else if (multipoleType== "q") { |
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parseQuadruple( tokenizer, dAtomType, lineNo); |
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} else if (multipoleType== "dq") { |
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parseDipole(tokenizer, dAtomType, lineNo); |
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parseQuadruple( tokenizer, dAtomType, lineNo); |
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} else if (multipoleType== "sq") { |
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parseSplitDipole(tokenizer, dAtomType, lineNo); |
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parseQuadruple( tokenizer, dAtomType, lineNo); |
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} else { |
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sprintf(painCave.errMsg, "MultipoleAtomTypesSectionParser Error: unrecognized multiple type at line %d\n", |
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lineNo); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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} |
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void MultipoleAtomTypesSectionParser::parseDipole(StringTokenizer& tokenizer, |
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DirectionalAtomType* dAtomType, int lineNo) { |
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if (tokenizer.hasMoreTokens()) { |
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double dipole = tokenizer.nextTokenAsDouble(); |
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dAtomType->addProperty(new DoubleGenericData("Dipole", dipole)); |
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dAtomType->setDipole(); |
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} else { |
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sprintf(painCave.errMsg, "MultipoleAtomTypesSectionParser Error: Not enough tokens at line %d\n", |
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lineNo); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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void MultipoleAtomTypesSectionParser::parseSplitDipole(StringTokenizer& tokenizer, |
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DirectionalAtomType* dAtomType, int lineNo) { |
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if (tokenizer.hasMoreTokens()) { |
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parseDipole(tokenizer, dAtomType, lineNo); |
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double splitDipoleDistance = tokenizer.nextTokenAsDouble(); |
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dAtomType->addProperty(new DoubleGenericData("SplitDipoleDistance", splitDipoleDistance)); |
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dAtomType->setSplitDipole(); |
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} else { |
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sprintf(painCave.errMsg, "MultipoleAtomTypesSectionParser Error: Not enough tokens at line %d\n", |
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lineNo); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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void MultipoleAtomTypesSectionParser::parseQuadruple(StringTokenizer& tokenizer, |
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DirectionalAtomType* dAtomType, int lineNo) { |
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int nTokens = tokenizer.countTokens(); |
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if (nTokens < 3) { |
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Vector3d Q; |
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Q[0] = tokenizer.nextTokenAsDouble(); |
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Q[1] = tokenizer.nextTokenAsDouble(); |
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Q[2] = tokenizer.nextTokenAsDouble(); |
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double trace = Q[0] + Q[1] + Q[2]; |
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if (fabs(trace) > oopse::epsilon) { |
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sprintf(painCave.errMsg, "MultipoleAtomTypesSectionParser Error: the trace of qudrupole moments is not zero at line %d\n", |
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lineNo); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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dAtomType->addProperty(new Vector3dGenericData("QuadrupoleMoments", Q)); |
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dAtomType->setQuadrupole(); |
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} else { |
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sprintf(painCave.errMsg, "MultipoleAtomTypesSectionParser Error: Not enough tokens at line %d\n", |
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lineNo); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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} //end namespace oopse |
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