| 6 |
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* redistribute this software in source and binary code form, provided |
| 7 |
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* that the following conditions are met: |
| 8 |
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* |
| 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 |
| 9 |
> |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
|
* notice, this list of conditions and the following disclaimer. |
| 11 |
|
* |
| 12 |
< |
* 3. Redistributions in binary form must reproduce the above copyright |
| 12 |
> |
* 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
|
* notice, this list of conditions and the following disclaimer in the |
| 14 |
|
* documentation and/or other materials provided with the |
| 15 |
|
* distribution. |
| 28 |
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* arising out of the use of or inability to use software, even if the |
| 29 |
|
* University of Notre Dame has been advised of the possibility of |
| 30 |
|
* such damages. |
| 31 |
+ |
* |
| 32 |
+ |
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
| 33 |
+ |
* research, please cite the appropriate papers when you publish your |
| 34 |
+ |
* work. Good starting points are: |
| 35 |
+ |
* |
| 36 |
+ |
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
+ |
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
+ |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
| 39 |
+ |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
+ |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 42 |
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|
| 43 |
|
#ifndef SELECTION_SELECTIONEVALUATOR_HPP |
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|
#include "selection/SelectionCompiler.hpp" |
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|
#include "selection/NameFinder.hpp" |
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|
#include "selection/DistanceFinder.hpp" |
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+ |
#include "selection/HullFinder.hpp" |
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|
#include "selection/IndexFinder.hpp" |
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< |
#include "utils/OOPSEBitSet.hpp" |
| 58 |
> |
#include "utils/OpenMDBitSet.hpp" |
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|
#include "primitives/StuntDouble.hpp" |
| 60 |
|
#include "utils/StringUtils.hpp" |
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< |
namespace oopse { |
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> |
namespace OpenMD { |
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|
| 63 |
|
|
| 64 |
|
/** |
| 65 |
|
* @class SelectionEvaluator SelectionEvaluator.hpp "selection/SelectionEvaluator" |
| 66 |
< |
* @brief Evalute the tokens compiled by SelectionCompiler and return a OOPSEBitSet |
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> |
* @brief Evalute the tokens compiled by SelectionCompiler and return a OpenMDBitSet |
| 67 |
|
*/ |
| 68 |
|
class SelectionEvaluator{ |
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public: |
| 70 |
|
|
| 71 |
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SelectionEvaluator(SimInfo* info); |
| 72 |
|
|
| 71 |
– |
|
| 73 |
|
bool loadScriptString(const std::string& script); |
| 74 |
|
bool loadScriptFile(const std::string& filename); |
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|
|
| 76 |
< |
OOPSEBitSet evaluate(); |
| 76 |
> |
OpenMDBitSet evaluate(); |
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> |
OpenMDBitSet evaluate(int frame); |
| 78 |
|
|
| 79 |
|
/** |
| 80 |
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* Tests if the result from evaluation of script is dynamic. |
| 105 |
|
} |
| 106 |
|
return script.substr(ichBegin, ichEnd); |
| 107 |
|
} |
| 108 |
+ |
bool hasSurfaceArea() { return hasSurfaceArea_; } |
| 109 |
+ |
RealType getSurfaceArea() { |
| 110 |
+ |
if (hasSurfaceArea_) { |
| 111 |
+ |
return surfaceArea_; |
| 112 |
+ |
} else { |
| 113 |
+ |
sprintf( painCave.errMsg, |
| 114 |
+ |
"SelectionEvaluator Error: %s\n", "No Surface Area For You!"); |
| 115 |
+ |
painCave.severity = OPENMD_ERROR; |
| 116 |
+ |
painCave.isFatal = 1; |
| 117 |
+ |
simError(); |
| 118 |
+ |
return 0.0; |
| 119 |
+ |
} |
| 120 |
+ |
} |
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+ |
|
| 122 |
|
|
| 123 |
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private: |
| 124 |
|
|
| 132 |
|
void clearDefinitionsAndLoadPredefined(); |
| 133 |
|
|
| 134 |
|
void define(); |
| 135 |
< |
void select(OOPSEBitSet& bs); |
| 135 |
> |
void select(OpenMDBitSet& bs); |
| 136 |
> |
void select(OpenMDBitSet& bs, int frame); |
| 137 |
|
void predefine(const std::string& script); |
| 138 |
|
|
| 139 |
< |
void instructionDispatchLoop(OOPSEBitSet& bs); |
| 139 |
> |
void instructionDispatchLoop(OpenMDBitSet& bs); |
| 140 |
> |
void instructionDispatchLoop(OpenMDBitSet& bs, int frame); |
| 141 |
|
|
| 142 |
< |
void withinInstruction(const Token& instruction, OOPSEBitSet& bs); |
| 142 |
> |
void withinInstruction(const Token& instruction, OpenMDBitSet& bs); |
| 143 |
> |
void withinInstruction(const Token& instruction, OpenMDBitSet& bs, int frame); |
| 144 |
> |
OpenMDBitSet allInstruction(); |
| 145 |
|
|
| 146 |
< |
OOPSEBitSet comparatorInstruction(const Token& instruction); |
| 147 |
< |
void compareProperty(StuntDouble* sd, OOPSEBitSet& bs, int property, int comparator, float comparisonValue); |
| 148 |
< |
OOPSEBitSet nameInstruction(const std::string& name); |
| 149 |
< |
OOPSEBitSet indexInstruction(const boost::any& value); |
| 150 |
< |
OOPSEBitSet expression(const std::vector<Token>& tokens, int pc); |
| 146 |
> |
OpenMDBitSet comparatorInstruction(const Token& instruction); |
| 147 |
> |
OpenMDBitSet comparatorInstruction(const Token& instruction, int frame); |
| 148 |
> |
void compareProperty(StuntDouble* sd, OpenMDBitSet& bs, int property, int comparator, float comparisonValue); |
| 149 |
> |
void compareProperty(StuntDouble* sd, OpenMDBitSet& bs, int property, int comparator, float comparisonValue, int frame); |
| 150 |
> |
OpenMDBitSet nameInstruction(const std::string& name); |
| 151 |
> |
OpenMDBitSet indexInstruction(const boost::any& value); |
| 152 |
> |
OpenMDBitSet expression(const std::vector<Token>& tokens, int pc); |
| 153 |
> |
OpenMDBitSet expression(const std::vector<Token>& tokens, int pc, int frame); |
| 154 |
|
|
| 155 |
< |
OOPSEBitSet lookupValue(const std::string& variable); |
| 155 |
> |
OpenMDBitSet lookupValue(const std::string& variable); |
| 156 |
> |
|
| 157 |
> |
OpenMDBitSet hull(); |
| 158 |
> |
OpenMDBitSet hull(int frame); |
| 159 |
|
|
| 160 |
|
void evalError(const std::string& message) { |
| 161 |
< |
std::cerr << "SelectionEvaulator Error: " << message << std::endl; |
| 161 |
> |
sprintf( painCave.errMsg, |
| 162 |
> |
"SelectionEvaluator Error: %s\n", message.c_str()); |
| 163 |
> |
painCave.severity = OPENMD_ERROR; |
| 164 |
> |
painCave.isFatal = 1; |
| 165 |
> |
simError(); |
| 166 |
|
} |
| 167 |
|
|
| 168 |
|
void unrecognizedCommand(const Token& token) { |
| 193 |
|
bool containDynamicToken(const std::vector<Token>& tokens); |
| 194 |
|
|
| 195 |
|
RealType getCharge(Atom* atom); |
| 196 |
+ |
RealType getCharge(Atom* atom, int frame); |
| 197 |
|
|
| 198 |
|
SelectionCompiler compiler; |
| 199 |
|
|
| 207 |
|
std::vector<int> linenumbers; |
| 208 |
|
std::vector<int> lineIndices; |
| 209 |
|
std::vector<std::vector<Token> > aatoken; |
| 210 |
< |
int pc; // program counter |
| 210 |
> |
unsigned int pc; // program counter |
| 211 |
|
|
| 212 |
|
bool error; |
| 213 |
|
std::string errorMessage; |
| 218 |
|
SimInfo* info; |
| 219 |
|
NameFinder nameFinder; |
| 220 |
|
DistanceFinder distanceFinder; |
| 221 |
+ |
HullFinder hullFinder; |
| 222 |
|
IndexFinder indexFinder; |
| 223 |
< |
int nStuntDouble; //natoms + nrigidbodies |
| 223 |
> |
int nStuntDouble; //nGLOBALatoms + nGLOBALrigidbodies |
| 224 |
|
|
| 225 |
|
typedef std::map<std::string, boost::any > VariablesType; |
| 226 |
|
VariablesType variables; |
| 227 |
|
|
| 228 |
|
bool isDynamic_; |
| 229 |
|
bool isLoaded_; |
| 230 |
+ |
bool hasSurfaceArea_; |
| 231 |
+ |
RealType surfaceArea_; |
| 232 |
|
|
| 233 |
|
}; |
| 234 |
|
|
