hillclimber 0.1.6__cp313-cp313-macosx_15_0_x86_64.whl

plumed/_lib/include/plumed/lapack/lapack_limits.h

@@ -0,0 +1,79 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+These files are semi-automatic translations by f2c from the original netlib LAPACK library.
+The source has been modified to (mostly) use modern C formatting, and to get rid of
+compiler warnings. Any errors in doing this should be blamed on the GROMACS developers, and
+not the reference LAPACK implementation.
+
+The reference LAPACK implementation is available from http://www.netlib.org/lapack 
+
+LAPACK does not come with a formal named "license", but a general statement saying:
+
+"The reference LAPACK is a freely-available software package. It is available from netlib
+via anonymous ftp and the World Wide Web. Thus, it can be included in commercial software
+packages (and has been). We only ask that proper credit be given to the authors."
+
+While the rest of GROMACS is LGPL, we think it's only fair to give you the same rights to
+our modified LAPACK files as the original netlib versions, so do what you want with them.
+
+However, be warned that we have only tested that they to the right thing in the cases used
+in GROMACS (primarily full & sparse matrix diagonalization), so in most cases it is a much
+better idea to use the full reference implementation.
+
+Erik Lindahl, 2008-10-07.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_lapack_lapack_limits_h
+#define __PLUMED_lapack_lapack_limits_h
+
+#define DSTEBZ_BLOCKSIZE  1
+
+#define DORGBR_BLOCKSIZE    32
+#define DORGBR_MINBLOCKSIZE 2
+#define DORGBR_CROSSOVER    128
+
+#define DGEQRF_BLOCKSIZE    32
+#define DGEQRF_MINBLOCKSIZE 2  
+#define DGEQRF_CROSSOVER    128
+
+#define DORGQR_BLOCKSIZE    32
+#define DORGQR_MINBLOCKSIZE 2
+#define DORGQR_CROSSOVER    128
+
+#define DORMLQ_BLOCKSIZE    32
+#define DORMLQ_MINBLOCKSIZE 2
+#define DORMLQ_CROSSOVER    128
+
+#define DORMQL_BLOCKSIZE    32
+#define DORMQL_MINBLOCKSIZE 2
+#define DORMQL_CROSSOVER    128
+
+#define DSYTRD_BLOCKSIZE    32
+#define DSYTRD_MINBLOCKSIZE 2
+#define DSYTRD_CROSSOVER    128
+
+#define DGEBRD_BLOCKSIZE    32
+#define DGEBRD_MINBLOCKSIZE 2
+#define DGEBRD_CROSSOVER    128
+
+#define DORMQR_BLOCKSIZE    32
+#define DORMQR_MINBLOCKSIZE 2
+#define DORMQR_CROSSOVER    128
+
+#define DGELQF_BLOCKSIZE    32
+#define DGELQF_MINBLOCKSIZE 2  
+#define DGELQF_CROSSOVER    128
+
+#define DGETRF_BLOCKSIZE    64
+#define DGETRF_MINBLOCKSIZE 2
+
+#define DGETRI_BLOCKSIZE    64
+#define DGETRI_MINBLOCKSIZE 2
+
+#define DTRTRI_BLOCKSIZE    64
+
+#define DBDSDC_SMALLSIZE 25
+
+#define DBDSQR_MAXITR 6
+
+
+
+#endif /* _LAPACK_LIMITS_H_ */

plumed/_lib/include/plumed/lapack/real.h

@@ -0,0 +1,50 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+These files are semi-automatic translations by f2c from the original netlib LAPACK library.
+The source has been modified to (mostly) use modern C formatting, and to get rid of
+compiler warnings. Any errors in doing this should be blamed on the GROMACS developers, and
+not the reference LAPACK implementation.
+
+The reference LAPACK implementation is available from http://www.netlib.org/lapack 
+
+LAPACK does not come with a formal named "license", but a general statement saying:
+
+"The reference LAPACK is a freely-available software package. It is available from netlib
+via anonymous ftp and the World Wide Web. Thus, it can be included in commercial software
+packages (and has been). We only ask that proper credit be given to the authors."
+
+While the rest of GROMACS is LGPL, we think it's only fair to give you the same rights to
+our modified LAPACK files as the original netlib versions, so do what you want with them.
+
+However, be warned that we have only tested that they to the right thing in the cases used
+in GROMACS (primarily full & sparse matrix diagonalization), so in most cases it is a much
+better idea to use the full reference implementation.
+
+Erik Lindahl, 2008-10-07.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_lapack_real_h
+#define __PLUMED_lapack_real_h
+    /*! \brief Double precision accuracy */
+#define PLUMED_GMX_DOUBLE_EPS   2.2204460492503131e-16
+
+    /*! \brief Maximum double precision value - reduced 1 unit in last digit for MSVC */
+#define PLUMED_GMX_DOUBLE_MAX   1.7976931348623157e+308
+
+    /*! \brief Minimum double precision value */
+#define PLUMED_GMX_DOUBLE_MIN   2.2250738585072014e-308
+
+    /*! \brief Single precision accuracy */
+#define PLUMED_GMX_FLOAT_EPS    1.19209290e-07F
+
+    /*! \brief Maximum single precision value - reduced 1 unit in last digit for MSVC */
+#define PLUMED_GMX_FLOAT_MAX    3.40282346E+38F
+
+    /*! \brief Minimum single precision value */
+#define PLUMED_GMX_FLOAT_MIN    1.175494351E-38F
+
+#if defined(F77_NO_UNDERSCORE)
+#define PLUMED_BLAS_F77_FUNC(lower,upper) lower
+#else
+#define PLUMED_BLAS_F77_FUNC(lower,upper) lower ## _
+#endif
+
+#endif

plumed/_lib/include/plumed/lepton/CompiledExpression.h

@@ -0,0 +1,164 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ * -------------------------------------------------------------------------- *
+ *                                   Lepton                                   *
+ * -------------------------------------------------------------------------- *
+ * This is part of the Lepton expression parser originating from              *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2013-2016 Stanford University and the Authors.      *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- *
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_lepton_CompiledExpression_h
+#define __PLUMED_lepton_CompiledExpression_h
+
+/* -------------------------------------------------------------------------- *
+ *                                   lepton                                   *
+ * -------------------------------------------------------------------------- *
+ * This is part of the lepton expression parser originating from              *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2013-2019 Stanford University and the Authors.      *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "ExpressionTreeNode.h"
+#include "windowsIncludes.h"
+#include <map>
+#include <set>
+#include <string>
+#include <utility>
+#include <vector>
+
+namespace PLMD {
+namespace lepton {
+
+bool useAsmJit();
+
+// Utility class.
+// Implement an unique pointer to asmjit::JitRuntime.
+// Needed to decouple asmjit header file from this one.
+class AsmJitRuntimePtr {
+/// if ASMJIT is not defined, just set the pointer to null
+  void* ptr=nullptr;
+public:
+/// constructor
+  AsmJitRuntimePtr();
+/// destructor
+  ~AsmJitRuntimePtr();
+/// deleted copy constructor
+  AsmJitRuntimePtr(const AsmJitRuntimePtr&) = delete;
+/// deleted assignment
+  AsmJitRuntimePtr & operator=(const AsmJitRuntimePtr&) = delete;
+/// get the pointer
+  void* get() {
+    return ptr;
+  }
+};
+
+class Operation;
+class ParsedExpression;
+
+/**
+ * A CompiledExpression is a highly optimized representation of an expression for cases when you want to evaluate
+ * it many times as quickly as possible.  You should treat it as an opaque object; none of the internal representation
+ * is visible.
+ * 
+ * A CompiledExpression is created by calling createCompiledExpression() on a ParsedExpression.
+ * 
+ * WARNING: CompiledExpression is NOT thread safe.  You should never access a CompiledExpression from two threads at
+ * the same time.
+ */
+
+class LEPTON_EXPORT CompiledExpression {
+public:
+    CompiledExpression();
+    CompiledExpression(const CompiledExpression& expression);
+    ~CompiledExpression();
+    CompiledExpression& operator=(const CompiledExpression& expression);
+    /**
+     * Get the names of all variables used by this expression.
+     */
+    const std::set<std::string>& getVariables() const;
+    /**
+     * Get a reference to the memory location where the value of a particular variable is stored.  This can be used
+     * to set the value of the variable before calling evaluate().
+     */
+    double& getVariableReference(const std::string& name);
+    /**
+     * You can optionally specify the memory locations from which the values of variables should be read.
+     * This is useful, for example, when several expressions all use the same variable.  You can then set
+     * the value of that variable in one place, and it will be seen by all of them.
+     */
+    void setVariableLocations(std::map<std::string, double*>& variableLocations);
+    /**
+     * Evaluate the expression.  The values of all variables should have been set before calling this.
+     */
+    double evaluate() const;
+private:
+    friend class ParsedExpression;
+    CompiledExpression(const ParsedExpression& expression);
+    void compileExpression(const ExpressionTreeNode& node, std::vector<std::pair<ExpressionTreeNode, int> >& temps);
+    int findTempIndex(const ExpressionTreeNode& node, std::vector<std::pair<ExpressionTreeNode, int> >& temps);
+    std::map<std::string, double*> variablePointers;
+    std::vector<std::pair<double*, double*> > variablesToCopy;
+    std::vector<std::vector<int> > arguments;
+    std::vector<int> target;
+    std::vector<Operation*> operation;
+    std::map<std::string, int> variableIndices;
+    std::set<std::string> variableNames;
+    mutable std::vector<double> workspace;
+    mutable std::vector<double> argValues;
+    std::map<std::string, double> dummyVariables;
+    void* jitCode;
+    void generateJitCode();
+    std::vector<double> constants;
+    AsmJitRuntimePtr runtimeptr;
+};
+
+} // namespace lepton
+} // namespace PLMD
+
+#endif /*LEPTON_COMPILED_EXPRESSION_H_*/

plumed/_lib/include/plumed/lepton/CustomFunction.h

@@ -0,0 +1,143 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ * -------------------------------------------------------------------------- *
+ *                                   Lepton                                   *
+ * -------------------------------------------------------------------------- *
+ * This is part of the Lepton expression parser originating from              *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2013-2016 Stanford University and the Authors.      *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- *
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_lepton_CustomFunction_h
+#define __PLUMED_lepton_CustomFunction_h
+
+/* -------------------------------------------------------------------------- *
+ *                                   lepton                                   *
+ * -------------------------------------------------------------------------- *
+ * This is part of the lepton expression parser originating from              *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2009 Stanford University and the Authors.           *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "windowsIncludes.h"
+
+namespace PLMD {
+namespace lepton {
+
+/**
+ * This class is the interface for defining your own function that may be included in expressions.
+ * To use it, create a concrete subclass that implements all of the virtual methods for each new function
+ * you want to define.  Then when you call Parser::parse() to parse an expression, pass a map of
+ * function names to CustomFunction objects.
+ */
+
+class LEPTON_EXPORT CustomFunction {
+public:
+    virtual ~CustomFunction() {
+    }
+    /**
+     * Get the number of arguments this function expects.
+     */
+    virtual int getNumArguments() const = 0;
+    /**
+     * Evaluate the function.
+     *
+     * @param arguments    the array of argument values
+     */
+    virtual double evaluate(const double* arguments) const = 0;
+    /**
+     * Evaluate a derivative of the function.
+     *
+     * @param arguments    the array of argument values
+     * @param derivOrder   an array specifying the number of times the function has been differentiated
+     *                     with respect to each of its arguments.  For example, the array {0, 2} indicates
+     *                     a second derivative with respect to the second argument.
+     */
+    virtual double evaluateDerivative(const double* arguments, const int* derivOrder) const = 0;
+    /**
+     * Create a new duplicate of this object on the heap using the "new" operator.
+     */
+    virtual CustomFunction* clone() const = 0;
+};
+
+/**
+ * This class is an implementation of CustomFunction that does no computation.  It just returns
+ * 0 for the value and derivatives.  This is useful when using the parser to analyze expressions
+ * rather than to evaluate them.  You can just create PlaceholderFunctions to represent any custom
+ * functions that may appear in expressions.
+ */
+
+class LEPTON_EXPORT PlaceholderFunction : public CustomFunction {
+public:
+    /**
+     * Create a Placeholder function.
+     * 
+     * @param numArgs    the number of arguments the function expects
+     */
+    PlaceholderFunction(int numArguments) : numArgs(numArguments) {
+    }
+    int getNumArguments() const {
+        return numArgs;
+    }
+    double evaluate(const double* arguments) const {
+        return 0.0;
+    }
+    double evaluateDerivative(const double* arguments, const int* derivOrder) const {
+        return 0.0;
+    }
+    CustomFunction* clone() const {
+        return new PlaceholderFunction(numArgs);
+    };
+private:
+    int numArgs;
+};
+
+} // namespace lepton
+} // namespace PLMD
+
+#endif /*LEPTON_CUSTOM_FUNCTION_H_*/

plumed/_lib/include/plumed/lepton/Exception.h

@@ -0,0 +1,93 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ * -------------------------------------------------------------------------- *
+ *                                   Lepton                                   *
+ * -------------------------------------------------------------------------- *
+ * This is part of the Lepton expression parser originating from              *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2013-2016 Stanford University and the Authors.      *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- *
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_lepton_Exception_h
+#define __PLUMED_lepton_Exception_h
+
+/* -------------------------------------------------------------------------- *
+ *                                   lepton                                   *
+ * -------------------------------------------------------------------------- *
+ * This is part of the lepton expression parser originating from              *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2009 Stanford University and the Authors.           *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include <exception>
+#include <string>
+
+namespace PLMD {
+namespace lepton {
+
+/**
+ * This class is used for all exceptions thrown by lepton.
+ */
+
+class Exception : public std::exception {
+public:
+    Exception(const std::string& msg) : message(msg) {
+    }
+    ~Exception() throw() {
+    }
+    const char* what() const throw() {
+        return message.c_str();
+    }
+private:
+    std::string message;
+};
+
+} // namespace lepton
+} // namespace PLMD
+
+#endif /*LEPTON_EXCEPTION_H_*/

plumed/_lib/include/plumed/lepton/ExpressionProgram.h

@@ -0,0 +1,137 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ * -------------------------------------------------------------------------- *
+ *                                   Lepton                                   *
+ * -------------------------------------------------------------------------- *
+ * This is part of the Lepton expression parser originating from              *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2013-2016 Stanford University and the Authors.      *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- *
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_lepton_ExpressionProgram_h
+#define __PLUMED_lepton_ExpressionProgram_h
+
+/* -------------------------------------------------------------------------- *
+ *                                   lepton                                   *
+ * -------------------------------------------------------------------------- *
+ * This is part of the lepton expression parser originating from              *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2009-2018 Stanford University and the Authors.      *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "ExpressionTreeNode.h"
+#include "windowsIncludes.h"
+#include <map>
+#include <string>
+#include <vector>
+
+namespace PLMD {
+namespace lepton {
+
+class ParsedExpression;
+
+/**
+ * An ExpressionProgram is a linear sequence of Operations for evaluating an expression.  The evaluation
+ * is done with a stack.  The arguments to each Operation are first taken off the stack in order, then it is
+ * evaluated and the result is pushed back onto the stack.  At the end, the stack contains a single value,
+ * which is the value of the expression.
+ *
+ * An ExpressionProgram is created by calling createProgram() on a ParsedExpression.
+ */
+
+class LEPTON_EXPORT ExpressionProgram {
+public:
+    ExpressionProgram();
+    ExpressionProgram(const ExpressionProgram& program);
+    ~ExpressionProgram();
+    ExpressionProgram& operator=(const ExpressionProgram& program);
+    /**
+     * Get the number of Operations that make up this program.
+     */
+    int getNumOperations() const;
+    /**
+     * Get an Operation in this program.
+     */
+    const Operation& getOperation(int index) const;
+    /**
+     * Change an Operation in this program.
+     * 
+     * The Operation must have been allocated on the heap with the "new" operator.
+     * The ExpressionProgram assumes ownership of it and will delete it when it
+     * is no longer needed.
+     */
+    void setOperation(int index, Operation* operation);
+    /**
+     * Get the size of the stack needed to execute this program.  This is the largest number of elements present
+     * on the stack at any point during evaluation.
+     */
+    int getStackSize() const;
+    /**
+     * Evaluate the expression.  If the expression involves any variables, this method will throw an exception.
+     */
+    double evaluate() const;
+    /**
+     * Evaluate the expression.
+     *
+     * @param variables    a map specifying the values of all variables that appear in the expression.  If any
+     *                     variable appears in the expression but is not included in this map, an exception
+     *                     will be thrown.
+     */
+    double evaluate(const std::map<std::string, double>& variables) const;
+private:
+    friend class ParsedExpression;
+    ExpressionProgram(const ParsedExpression& expression);
+    void buildProgram(const ExpressionTreeNode& node);
+    std::vector<Operation*> operations;
+    int maxArgs, stackSize;
+};
+
+} // namespace lepton
+} // namespace PLMD
+
+#endif /*LEPTON_EXPRESSION_PROGRAM_H_*/