hillclimber 0.1.5__cp313-cp313-musllinux_1_2_aarch64.whl

plumed/_lib/include/plumed/lepton/ExpressionTreeNode.h

@@ -0,0 +1,145 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ * -------------------------------------------------------------------------- *
+ *                                   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_ExpressionTreeNode_h
+#define __PLUMED_lepton_ExpressionTreeNode_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) 2009-2021 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"
+#include <string>
+#include <vector>
+
+namespace PLMD {
+namespace lepton {
+
+class Operation;
+class ParsedExpression;
+
+/**
+ * This class represents a node in the abstract syntax tree representation of an expression.
+ * Each node is defined by an Operation and a set of children.  When the expression is
+ * evaluated, each child is first evaluated in order, then the resulting values are passed
+ * as the arguments to the Operation's evaluate() method.
+ */
+
+class LEPTON_EXPORT ExpressionTreeNode {
+public:
+    /**
+     * Create a new ExpressionTreeNode.
+     *
+     * @param operation    the operation for this node.  The ExpressionTreeNode takes over ownership
+     *                     of this object, and deletes it when the node is itself deleted.
+     * @param children     the children of this node
+     */
+    ExpressionTreeNode(Operation* operation, const std::vector<ExpressionTreeNode>& children);
+    /**
+     * Create a new ExpressionTreeNode with two children.
+     *
+     * @param operation    the operation for this node.  The ExpressionTreeNode takes over ownership
+     *                     of this object, and deletes it when the node is itself deleted.
+     * @param child1       the first child of this node
+     * @param child2       the second child of this node
+     */
+    ExpressionTreeNode(Operation* operation, const ExpressionTreeNode& child1, const ExpressionTreeNode& child2);
+    /**
+     * Create a new ExpressionTreeNode with one child.
+     *
+     * @param operation    the operation for this node.  The ExpressionTreeNode takes over ownership
+     *                     of this object, and deletes it when the node is itself deleted.
+     * @param child        the child of this node
+     */
+    ExpressionTreeNode(Operation* operation, const ExpressionTreeNode& child);
+    /**
+     * Create a new ExpressionTreeNode with no children.
+     *
+     * @param operation    the operation for this node.  The ExpressionTreeNode takes over ownership
+     *                     of this object, and deletes it when the node is itself deleted.
+     */
+    ExpressionTreeNode(Operation* operation);
+    ExpressionTreeNode(const ExpressionTreeNode& node);
+    ExpressionTreeNode(ExpressionTreeNode&& node);
+    ExpressionTreeNode();
+    ~ExpressionTreeNode();
+    bool operator==(const ExpressionTreeNode& node) const;
+    bool operator!=(const ExpressionTreeNode& node) const;
+    ExpressionTreeNode& operator=(const ExpressionTreeNode& node);
+    ExpressionTreeNode& operator=(ExpressionTreeNode&& node);
+    /**
+     * Get the Operation performed by this node.
+     */
+    const Operation& getOperation() const;
+    /**
+     * Get this node's child nodes.
+     */
+    const std::vector<ExpressionTreeNode>& getChildren() const;
+private:
+    friend class ParsedExpression;
+    void assignTags(std::vector<const ExpressionTreeNode*>& examples) const;
+    Operation* operation;
+    std::vector<ExpressionTreeNode> children;
+    mutable int tag;
+};
+
+} // namespace lepton
+} // namespace PLMD
+
+#endif /*LEPTON_EXPRESSION_TREE_NODE_H_*/

plumed/_lib/include/plumed/lepton/Lepton.h

@@ -0,0 +1,85 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ * -------------------------------------------------------------------------- *
+ *                                   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_Lepton_h
+#define __PLUMED_lepton_Lepton_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 <map>
+#include <cmath>
+#include <string>
+
+namespace PLMD {
+namespace lepton {
+const std::map<std::string, double> & Constants();
+}
+}
+
+#include "CompiledExpression.h"
+#include "CustomFunction.h"
+#include "ExpressionProgram.h"
+#include "ExpressionTreeNode.h"
+#include "Operation.h"
+#include "ParsedExpression.h"
+#include "Parser.h"
+
+#endif /*LEPTON_H_*/

plumed/_lib/include/plumed/lepton/MSVC_erfc.h

@@ -0,0 +1,123 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ * -------------------------------------------------------------------------- *
+ *                                   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_MSVC_erfc_h
+#define __PLUMED_lepton_MSVC_erfc_h
+
+/*
+ * Up to version 11 (VC++ 2012), Microsoft does not support the
+ * standard C99 erf() and erfc() functions so we have to fake them here. 
+ * These were added in version 12 (VC++ 2013), which sets _MSC_VER=1800
+ * (VC11 has _MSC_VER=1700).
+ */
+
+#if defined(_MSC_VER) || defined(__MINGW32__)
+#if !defined(M_PI)
+#define M_PI 3.14159265358979323846264338327950288
+#endif
+#endif
+
+#if defined(_MSC_VER)
+#if _MSC_VER <= 1700 // 1700 is VC11, 1800 is VC12 
+/***************************
+*   erf.cpp
+*   author:  Steve Strand
+*   written: 29-Jan-04
+***************************/
+
+#include <cmath>
+
+static const double rel_error= 1E-12;        //calculate 12 significant figures
+//you can adjust rel_error to trade off between accuracy and speed
+//but don't ask for > 15 figures (assuming usual 52 bit mantissa in a double)
+
+static double erfc(double x);
+
+static double erf(double x)
+//erf(x) = 2/sqrt(pi)*integral(exp(-t^2),t,0,x)
+//       = 2/sqrt(pi)*[x - x^3/3 + x^5/5*2! - x^7/7*3! + ...]
+//       = 1-erfc(x)
+{
+    static const double two_sqrtpi=  1.128379167095512574;        // 2/sqrt(pi)
+    if (fabs(x) > 2.2) {
+        return 1.0 - erfc(x);        //use continued fraction when fabs(x) > 2.2
+    }
+    double sum= x, term= x, xsqr= x*x;
+    int j= 1;
+    do {
+        term*= xsqr/j;
+        sum-= term/(2*j+1);
+        ++j;
+        term*= xsqr/j;
+        sum+= term/(2*j+1);
+        ++j;
+    } while (fabs(term)/sum > rel_error);
+    return two_sqrtpi*sum;
+}
+
+
+static double erfc(double x)
+//erfc(x) = 2/sqrt(pi)*integral(exp(-t^2),t,x,inf)
+//        = exp(-x^2)/sqrt(pi) * [1/x+ (1/2)/x+ (2/2)/x+ (3/2)/x+ (4/2)/x+ ...]
+//        = 1-erf(x)
+//expression inside [] is a continued fraction so '+' means add to denominator only
+{
+    static const double one_sqrtpi=  0.564189583547756287;        // 1/sqrt(pi)
+    if (fabs(x) < 2.2) {
+        return 1.0 - erf(x);        //use series when fabs(x) < 2.2
+    }
+    // Don't look for x==0 here!
+    if (x < 0) {               //continued fraction only valid for x>0
+        return 2.0 - erfc(-x);
+    }
+    double a=1, b=x;                //last two convergent numerators
+    double c=x, d=x*x+0.5;          //last two convergent denominators
+    double q1, q2= b/d;             //last two convergents (a/c and b/d)
+    double n= 1.0, t;
+    do {
+        t= a*n+b*x;
+        a= b;
+        b= t;
+        t= c*n+d*x;
+        c= d;
+        d= t;
+        n+= 0.5;
+        q1= q2;
+        q2= b/d;
+      } while (fabs(q1-q2)/q2 > rel_error);
+    return one_sqrtpi*exp(-x*x)*q2;
+}
+
+#endif // _MSC_VER <= 1700
+#endif // _MSC_VER
+
+#endif // LEPTON_MSVC_ERFC_H_