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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 <sstream> |
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#include <fstream> |
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#include "visitors/AtomNameVisitor.hpp" |
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#include "utils/Trim.hpp" |
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#include "utils/StringTokenizer.hpp" |
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|
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|
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namespace oopse { |
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AtomNameVisitor::AtomNameVisitor(SimInfo* info) : BaseVisitor(), info_(info) { |
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visitorName = "AtomNameVisitor"; |
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std::stringstream ss(defaultAtomTypeTable); |
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readAtomTypes(ss); |
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} |
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|
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AtomNameVisitor::AtomNameVisitor(SimInfo* info, const std::string& atomTypeFile) : BaseVisitor(), info_(info) { |
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visitorName = "AtomNameVisitor"; |
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std::ifstream ifs(atomTypeFile.c_str()); |
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readAtomTypes(ifs); |
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} |
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|
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|
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void AtomNameVisitor::visitAtom(Atom* atom) { |
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AtomData* atomData; |
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GenericData* data; |
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bool haveAtomData; |
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|
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data = atom->getPropertyByName("ATOMDATA"); |
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if(data != NULL){ |
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atomData = dynamic_cast<AtomData*>(data); |
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if(atomData == NULL){ |
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std::cerr << "can not get Atom Data from " << atom->getType() << std::endl; |
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atomData = new AtomData; |
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haveAtomData = false; |
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} else { |
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haveAtomData = true; |
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} |
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} else { |
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atomData = new AtomData; |
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haveAtomData = false; |
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} |
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|
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std::vector<AtomInfo*>::iterator i; |
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for (AtomInfo* atomInfo = atomData->beginAtomInfo(i); atomInfo != NULL; atomInfo = atomData->nextAtomInfo(i)) { |
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atomInfo->atomTypeName = getBaseAtomTypeName(atomInfo->atomTypeName); |
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} |
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|
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} |
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|
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void AtomNameVisitor::visit(RigidBody* rb) { |
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std::vector<Atom*>::iterator i; |
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|
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for (Atom* atom = rb->beginAtom(i); atom != NULL; atom = rb->nextAtom(i)) { |
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visit(atom); |
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} |
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} |
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|
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|
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void AtomNameVisitor::readAtomTypes(std::istream& is) { |
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const int bufferSize = 65535; |
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char buffer[bufferSize]; |
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std::string line; |
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while(is.getline(buffer, bufferSize)) { |
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line = trimLeftCopy(buffer); |
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//a line begins with "//" is comment |
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// let's also call lines starting with # and ! as comments |
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if ( line.empty() || |
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(line.size() >= 2 && line[0] == '/' && line[1] == '/') || |
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(line.size() >= 1 && line[0] == '#') || |
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(line.size() >= 1 && line[0] == '!') ) { |
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continue; |
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} else { |
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StringTokenizer tokenizer(line); |
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if (tokenizer.countTokens() >= 2) { |
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std::string atomName = tokenizer.nextToken(); |
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std::string baseAtomName = tokenizer.nextToken(); |
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atomNames_.insert(MapType::value_type(atomName, baseAtomName)); |
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} |
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} |
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} |
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|
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} |
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|
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std::string AtomNameVisitor::getBaseAtomTypeName(const std::string& atomTypeName) { |
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MapType::iterator i; |
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i = atomNames_.find(atomTypeName); |
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return i != atomNames_.end() ? i->second : atomTypeName; |
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} |
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|
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|
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const std::string AtomNameVisitor::toString() { |
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char buffer[65535]; |
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std::string result; |
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|
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sprintf(buffer, |
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"------------------------------------------------------------------\n"); |
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result += buffer; |
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|
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sprintf(buffer, "Visitor name: %s\n", visitorName.c_str()); |
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result += buffer; |
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|
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sprintf(buffer, |
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"Visitor Description: print base atom types\n"); |
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result += buffer; |
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|
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sprintf(buffer, |
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"------------------------------------------------------------------\n"); |
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result += buffer; |
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return result; |
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} |
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|
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} |