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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. 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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* 2. 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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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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*/ |
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|
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#include <stack> |
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#include "selection/SelectionEvaluator.hpp" |
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#include "primitives/Atom.hpp" |
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#include "primitives/DirectionalAtom.hpp" |
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#include "primitives/RigidBody.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "io/ifstrstream.hpp" |
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|
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namespace OpenMD { |
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|
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|
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SelectionEvaluator::SelectionEvaluator(SimInfo* si) |
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: info(si), nameFinder(info), distanceFinder(info), hullFinder(info), |
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indexFinder(info), |
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isLoaded_(false){ |
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nStuntDouble = info->getNGlobalAtoms() + info->getNGlobalRigidBodies(); |
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} |
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|
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bool SelectionEvaluator::loadScript(const std::string& filename, |
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const std::string& script) { |
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clearDefinitionsAndLoadPredefined(); |
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this->filename = filename; |
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this->script = script; |
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if (! compiler.compile(filename, script)) { |
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error = true; |
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errorMessage = compiler.getErrorMessage(); |
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|
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sprintf( painCave.errMsg, |
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"SelectionCompiler Error: %s\n", errorMessage.c_str()); |
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painCave.severity = OPENMD_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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return false; |
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} |
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|
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pc = 0; |
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aatoken = compiler.getAatokenCompiled(); |
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linenumbers = compiler.getLineNumbers(); |
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lineIndices = compiler.getLineIndices(); |
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|
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std::vector<std::vector<Token> >::const_iterator i; |
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|
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isDynamic_ = false; |
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for (i = aatoken.begin(); i != aatoken.end(); ++i) { |
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if (containDynamicToken(*i)) { |
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isDynamic_ = true; |
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break; |
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} |
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} |
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|
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isLoaded_ = true; |
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return true; |
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} |
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|
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void SelectionEvaluator::clearState() { |
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error = false; |
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errorMessage = ""; |
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} |
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|
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bool SelectionEvaluator::loadScriptString(const std::string& script) { |
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clearState(); |
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return loadScript("", script); |
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} |
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|
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bool SelectionEvaluator::loadScriptFile(const std::string& filename) { |
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clearState(); |
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return loadScriptFileInternal(filename); |
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} |
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|
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bool SelectionEvaluator::loadScriptFileInternal(const std::string & filename) { |
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ifstrstream ifs(filename.c_str()); |
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if (!ifs.is_open()) { |
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return false; |
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} |
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|
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const int bufferSize = 65535; |
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char buffer[bufferSize]; |
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std::string script; |
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while(ifs.getline(buffer, bufferSize)) { |
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script += buffer; |
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} |
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return loadScript(filename, script); |
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} |
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|
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void SelectionEvaluator::instructionDispatchLoop(OpenMDBitSet& bs){ |
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|
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while ( pc < aatoken.size()) { |
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statement = aatoken[pc++]; |
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statementLength = statement.size(); |
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Token token = statement[0]; |
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switch (token.tok) { |
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case Token::define: |
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define(); |
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break; |
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case Token::select: |
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select(bs); |
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break; |
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default: |
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unrecognizedCommand(token); |
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return; |
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} |
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} |
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|
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} |
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|
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OpenMDBitSet SelectionEvaluator::expression(const std::vector<Token>& code, |
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int pcStart) { |
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OpenMDBitSet bs; |
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std::stack<OpenMDBitSet> stack; |
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|
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for (int pc = pcStart; pc < code.size(); ++pc) { |
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Token instruction = code[pc]; |
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|
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switch (instruction.tok) { |
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case Token::expressionBegin: |
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break; |
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case Token::expressionEnd: |
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break; |
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case Token::all: |
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bs = OpenMDBitSet(nStuntDouble); |
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bs.setAll(); |
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stack.push(bs); |
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break; |
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case Token::none: |
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bs = OpenMDBitSet(nStuntDouble); |
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stack.push(bs); |
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break; |
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case Token::opOr: |
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bs = stack.top(); |
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stack.pop(); |
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stack.top() |= bs; |
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break; |
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case Token::opAnd: |
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bs = stack.top(); |
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stack.pop(); |
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stack.top() &= bs; |
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break; |
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case Token::opNot: |
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stack.top().flip(); |
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break; |
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case Token::within: |
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withinInstruction(instruction, stack.top()); |
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break; |
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case Token::hull: |
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stack.push(hull()); |
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break; |
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//case Token::selected: |
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// stack.push(getSelectionSet()); |
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// break; |
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case Token::name: |
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stack.push(nameInstruction(boost::any_cast<std::string>(instruction.value))); |
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break; |
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case Token::index: |
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stack.push(indexInstruction(instruction.value)); |
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break; |
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case Token::identifier: |
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stack.push(lookupValue(boost::any_cast<std::string>(instruction.value))); |
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break; |
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case Token::opLT: |
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case Token::opLE: |
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case Token::opGE: |
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case Token::opGT: |
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case Token::opEQ: |
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case Token::opNE: |
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stack.push(comparatorInstruction(instruction)); |
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break; |
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default: |
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unrecognizedExpression(); |
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} |
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} |
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if (stack.size() != 1) |
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evalError("atom expression compiler error - stack over/underflow"); |
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|
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return stack.top(); |
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} |
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|
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|
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|
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OpenMDBitSet SelectionEvaluator::comparatorInstruction(const Token& instruction) { |
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int comparator = instruction.tok; |
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int property = instruction.intValue; |
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float comparisonValue = boost::any_cast<float>(instruction.value); |
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float propertyValue; |
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OpenMDBitSet bs(nStuntDouble); |
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bs.clearAll(); |
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|
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SimInfo::MoleculeIterator mi; |
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Molecule* mol; |
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Molecule::AtomIterator ai; |
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Atom* atom; |
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Molecule::RigidBodyIterator rbIter; |
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RigidBody* rb; |
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|
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for (mol = info->beginMolecule(mi); mol != NULL; |
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mol = info->nextMolecule(mi)) { |
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|
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for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
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compareProperty(atom, bs, property, comparator, comparisonValue); |
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} |
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|
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for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
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rb = mol->nextRigidBody(rbIter)) { |
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compareProperty(rb, bs, property, comparator, comparisonValue); |
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} |
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} |
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|
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return bs; |
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} |
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|
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void SelectionEvaluator::compareProperty(StuntDouble* sd, OpenMDBitSet& bs, |
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int property, int comparator, |
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float comparisonValue) { |
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RealType propertyValue = 0.0; |
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switch (property) { |
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case Token::mass: |
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propertyValue = sd->getMass(); |
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break; |
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case Token::charge: |
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if (sd->isAtom()){ |
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Atom* atom = static_cast<Atom*>(sd); |
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propertyValue = getCharge(atom); |
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} else if (sd->isRigidBody()) { |
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RigidBody* rb = static_cast<RigidBody*>(sd); |
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RigidBody::AtomIterator ai; |
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Atom* atom; |
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for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) { |
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propertyValue+= getCharge(atom); |
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} |
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} |
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break; |
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case Token::x: |
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propertyValue = sd->getPos().x(); |
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break; |
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case Token::y: |
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propertyValue = sd->getPos().y(); |
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break; |
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case Token::z: |
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propertyValue = sd->getPos().z(); |
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break; |
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case Token::r: |
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propertyValue = sd->getPos().length(); |
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break; |
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default: |
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unrecognizedAtomProperty(property); |
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} |
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|
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bool match = false; |
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switch (comparator) { |
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case Token::opLT: |
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match = propertyValue < comparisonValue; |
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break; |
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case Token::opLE: |
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match = propertyValue <= comparisonValue; |
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break; |
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case Token::opGE: |
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match = propertyValue >= comparisonValue; |
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break; |
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case Token::opGT: |
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match = propertyValue > comparisonValue; |
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break; |
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case Token::opEQ: |
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match = propertyValue == comparisonValue; |
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break; |
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case Token::opNE: |
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match = propertyValue != comparisonValue; |
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break; |
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} |
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if (match) |
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bs.setBitOn(sd->getGlobalIndex()); |
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|
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} |
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|
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void SelectionEvaluator::withinInstruction(const Token& instruction, |
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OpenMDBitSet& bs){ |
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|
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boost::any withinSpec = instruction.value; |
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float distance; |
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if (withinSpec.type() == typeid(float)){ |
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distance = boost::any_cast<float>(withinSpec); |
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} else if (withinSpec.type() == typeid(int)) { |
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distance = boost::any_cast<int>(withinSpec); |
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} else { |
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evalError("casting error in withinInstruction"); |
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bs.clearAll(); |
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} |
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|
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bs = distanceFinder.find(bs, distance); |
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} |
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|
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void SelectionEvaluator::define() { |
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assert(statement.size() >= 3); |
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|
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std::string variable = boost::any_cast<std::string>(statement[1].value); |
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|
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variables.insert(VariablesType::value_type(variable, |
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expression(statement, 2))); |
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} |
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|
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|
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/** @todo */ |
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void SelectionEvaluator::predefine(const std::string& script) { |
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|
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if (compiler.compile("#predefine", script)) { |
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std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled(); |
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if (aatoken.size() != 1) { |
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evalError("predefinition does not have exactly 1 command:" |
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+ script); |
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return; |
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} |
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std::vector<Token> statement = aatoken[0]; |
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if (statement.size() > 2) { |
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int tok = statement[1].tok; |
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if (tok == Token::identifier || |
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(tok & Token::predefinedset) == Token::predefinedset) { |
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std::string variable = boost::any_cast<std::string>(statement[1].value); |
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variables.insert(VariablesType::value_type(variable, statement)); |
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|
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} else { |
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evalError("invalid variable name:" + script); |
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} |
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}else { |
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evalError("bad predefinition length:" + script); |
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} |
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|
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} else { |
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evalError("predefined set compile error:" + script + |
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"\ncompile error:" + compiler.getErrorMessage()); |
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} |
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} |
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|
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void SelectionEvaluator::select(OpenMDBitSet& bs){ |
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bs = expression(statement, 1); |
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} |
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|
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OpenMDBitSet SelectionEvaluator::lookupValue(const std::string& variable){ |
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|
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OpenMDBitSet bs(nStuntDouble); |
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std::map<std::string, boost::any>::iterator i = variables.find(variable); |
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|
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if (i != variables.end()) { |
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if (i->second.type() == typeid(OpenMDBitSet)) { |
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return boost::any_cast<OpenMDBitSet>(i->second); |
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} else if (i->second.type() == typeid(std::vector<Token>)){ |
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bs = expression(boost::any_cast<std::vector<Token> >(i->second), 2); |
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i->second = bs; /**@todo fixme */ |
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return bs; |
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} |
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} else { |
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unrecognizedIdentifier(variable); |
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} |
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|
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return bs; |
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} |
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|
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OpenMDBitSet SelectionEvaluator::nameInstruction(const std::string& name){ |
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return nameFinder.match(name); |
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} |
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|
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bool SelectionEvaluator::containDynamicToken(const std::vector<Token>& tokens){ |
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std::vector<Token>::const_iterator i; |
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for (i = tokens.begin(); i != tokens.end(); ++i) { |
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if (i->tok & Token::dynamic) { |
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return true; |
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} |
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} |
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|
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return false; |
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} |
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|
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void SelectionEvaluator::clearDefinitionsAndLoadPredefined() { |
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variables.clear(); |
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//load predefine |
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//predefine(); |
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} |
| 417 |
|
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OpenMDBitSet SelectionEvaluator::evaluate() { |
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OpenMDBitSet bs(nStuntDouble); |
| 420 |
if (isLoaded_) { |
| 421 |
pc = 0; |
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instructionDispatchLoop(bs); |
| 423 |
} |
| 424 |
|
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return bs; |
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} |
| 427 |
|
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OpenMDBitSet SelectionEvaluator::indexInstruction(const boost::any& value) { |
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OpenMDBitSet bs(nStuntDouble); |
| 430 |
|
| 431 |
if (value.type() == typeid(int)) { |
| 432 |
int index = boost::any_cast<int>(value); |
| 433 |
if (index < 0 || index >= bs.size()) { |
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invalidIndex(index); |
| 435 |
} else { |
| 436 |
bs = indexFinder.find(index); |
| 437 |
} |
| 438 |
} else if (value.type() == typeid(std::pair<int, int>)) { |
| 439 |
std::pair<int, int> indexRange= boost::any_cast<std::pair<int, int> >(value); |
| 440 |
assert(indexRange.first <= indexRange.second); |
| 441 |
if (indexRange.first < 0 || indexRange.second >= bs.size()) { |
| 442 |
invalidIndexRange(indexRange); |
| 443 |
}else { |
| 444 |
bs = indexFinder.find(indexRange.first, indexRange.second); |
| 445 |
} |
| 446 |
} |
| 447 |
|
| 448 |
return bs; |
| 449 |
} |
| 450 |
|
| 451 |
|
| 452 |
OpenMDBitSet SelectionEvaluator::hull() { |
| 453 |
OpenMDBitSet bs(nStuntDouble); |
| 454 |
|
| 455 |
bs = hullFinder.findHull(); |
| 456 |
|
| 457 |
return bs; |
| 458 |
} |
| 459 |
|
| 460 |
|
| 461 |
|
| 462 |
RealType SelectionEvaluator::getCharge(Atom* atom) { |
| 463 |
RealType charge =0.0; |
| 464 |
AtomType* atomType = atom->getAtomType(); |
| 465 |
if (atomType->isCharge()) { |
| 466 |
GenericData* data = atomType->getPropertyByName("Charge"); |
| 467 |
if (data != NULL) { |
| 468 |
DoubleGenericData* doubleData= dynamic_cast<DoubleGenericData*>(data); |
| 469 |
|
| 470 |
if (doubleData != NULL) { |
| 471 |
charge = doubleData->getData(); |
| 472 |
|
| 473 |
} else { |
| 474 |
sprintf( painCave.errMsg, |
| 475 |
"Can not cast GenericData to DoubleGenericData\n"); |
| 476 |
painCave.severity = OPENMD_ERROR; |
| 477 |
painCave.isFatal = 1; |
| 478 |
simError(); |
| 479 |
} |
| 480 |
} |
| 481 |
} |
| 482 |
|
| 483 |
return charge; |
| 484 |
} |
| 485 |
|
| 486 |
} |
