hillclimber 0.1.6__cp313-cp313-macosx_15_0_x86_64.whl

plumed/_lib/include/plumed/lepton/ParsedExpression.h

@@ -0,0 +1,165 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ * -------------------------------------------------------------------------- *
+ *                                   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_ParsedExpression_h
+#define __PLUMED_lepton_ParsedExpression_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 "ExpressionTreeNode.h"
+#include "windowsIncludes.h"
+#include <map>
+#include <string>
+
+namespace PLMD {
+namespace lepton {
+
+class CompiledExpression;
+class ExpressionProgram;
+
+/**
+ * This class represents the result of parsing an expression.  It provides methods for working with the
+ * expression in various ways, such as evaluating it, getting the tree representation of the expresson, etc.
+ */
+
+class LEPTON_EXPORT ParsedExpression {
+public:
+    /**
+     * Create an uninitialized ParsedExpression.  This exists so that ParsedExpressions can be put in STL containers.
+     * Doing anything with it will produce an exception.
+     */
+    ParsedExpression();
+    /**
+     * Create a ParsedExpression.  Normally you will not call this directly.  Instead, use the Parser class
+     * to parse expression.
+     */
+    ParsedExpression(const ExpressionTreeNode& rootNode);
+    /**
+     * Get the root node of the expression's abstract syntax tree.
+     */
+    const ExpressionTreeNode& getRootNode() 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;
+    /**
+     * Create a new ParsedExpression which produces the same result as this one, but is faster to evaluate.
+     */
+    ParsedExpression optimize() const;
+    /**
+     * Create a new ParsedExpression which produces the same result as this one, but is faster to evaluate.
+     *
+     * @param variables    a map specifying values for a subset of variables that appear in the expression.
+     *                     All occurrences of these variables in the expression are replaced with the values
+     *                     specified.
+     */
+    ParsedExpression optimize(const std::map<std::string, double>& variables) const;
+    /**
+     * Create a new ParsedExpression which is the analytic derivative of this expression with respect to a
+     * particular variable.
+     *
+     * @param variable     the variable with respect to which the derivate should be taken
+     */
+    ParsedExpression differentiate(const std::string& variable) const;
+    /**
+     * Create an ExpressionProgram that represents the same calculation as this expression.
+     */
+    ExpressionProgram createProgram() const;
+    /**
+     * Create a CompiledExpression that represents the same calculation as this expression.
+     */
+    CompiledExpression createCompiledExpression() const;
+    /**
+     * Create a new ParsedExpression which is identical to this one, except that the names of some
+     * variables have been changed.
+     *
+     * @param replacements    a map whose keys are the names of variables, and whose values are the
+     *                        new names to replace them with
+     */
+    ParsedExpression renameVariables(const std::map<std::string, std::string>& replacements) const;
+private:
+    static double evaluate(const ExpressionTreeNode& node, const std::map<std::string, double>& variables);
+    static ExpressionTreeNode preevaluateVariables(const ExpressionTreeNode& node, const std::map<std::string, double>& variables);
+    static ExpressionTreeNode precalculateConstantSubexpressions(const ExpressionTreeNode& node, std::map<int, ExpressionTreeNode>& nodeCache);
+    static ExpressionTreeNode substituteSimplerExpression(const ExpressionTreeNode& node, std::map<int, ExpressionTreeNode>& nodeCache);
+    static ExpressionTreeNode differentiate(const ExpressionTreeNode& node, const std::string& variable, std::map<int, ExpressionTreeNode>& nodeCache);
+    static bool isConstant(const ExpressionTreeNode& node);
+    static double getConstantValue(const ExpressionTreeNode& node);
+    static ExpressionTreeNode renameNodeVariables(const ExpressionTreeNode& node, const std::map<std::string, std::string>& replacements);
+    ExpressionTreeNode rootNode;
+};
+
+LEPTON_EXPORT std::ostream& operator<<(std::ostream& out, const ExpressionTreeNode& node);
+
+LEPTON_EXPORT std::ostream& operator<<(std::ostream& out, const ParsedExpression& exp);
+
+} // namespace lepton
+} // namespace PLMD
+
+#endif /*LEPTON_PARSED_EXPRESSION_H_*/

plumed/_lib/include/plumed/lepton/Parser.h

@@ -0,0 +1,111 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ * -------------------------------------------------------------------------- *
+ *                                   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_Parser_h
+#define __PLUMED_lepton_Parser_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"
+#include <map>
+#include <string>
+#include <vector>
+
+namespace PLMD {
+namespace lepton {
+
+class CustomFunction;
+class ExpressionTreeNode;
+class Operation;
+class ParsedExpression;
+class ParseToken;
+
+/**
+ * This class provides the main interface for parsing expressions.
+ */
+
+class LEPTON_EXPORT Parser {
+public:
+    /**
+     * Parse a mathematical expression and return a representation of it as an abstract syntax tree.
+     */
+    static ParsedExpression parse(const std::string& expression);
+    /**
+     * Parse a mathematical expression and return a representation of it as an abstract syntax tree.
+     *
+     * @param customFunctions   a map specifying user defined functions that may appear in the expression.
+     *                          The key are function names, and the values are corresponding CustomFunction objects.
+     */
+    static ParsedExpression parse(const std::string& expression, const std::map<std::string, CustomFunction*>& customFunctions);
+private:
+    static std::string trim(const std::string& expression);
+    static std::vector<ParseToken> tokenize(const std::string& expression);
+    static ParseToken getNextToken(const std::string& expression, int start);
+    static ExpressionTreeNode parsePrecedence(const std::vector<ParseToken>& tokens, int& pos, const std::map<std::string, CustomFunction*>& customFunctions,
+            const std::map<std::string, ExpressionTreeNode>& subexpressionDefs, int precedence);
+    static Operation* getOperatorOperation(const std::string& name);
+    static Operation* getFunctionOperation(const std::string& name, const std::map<std::string, CustomFunction*>& customFunctions);
+};
+
+} // namespace lepton
+} // namespace PLMD
+
+#endif /*LEPTON_PARSER_H_*/

plumed/_lib/include/plumed/lepton/windowsIncludes.h

@@ -0,0 +1,73 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ * -------------------------------------------------------------------------- *
+ *                                   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_windowsIncludes_h
+#define __PLUMED_lepton_windowsIncludes_h
+
+/*
+ * Shared libraries are messy in Visual Studio. We have to distinguish three
+ * cases:
+ *   (1) this header is being used to build the lepton shared library
+ *       (dllexport)
+ *   (2) this header is being used by a *client* of the lepton shared
+ *       library (dllimport)
+ *   (3) we are building the lepton static library, or the client is
+ *       being compiled with the expectation of linking with the
+ *       lepton static library (nothing special needed)
+ * In the CMake script for building this library, we define one of the symbols
+ *     lepton_BUILDING_{SHARED|STATIC}_LIBRARY
+ * Client code normally has no special symbol defined, in which case we'll
+ * assume it wants to use the shared library. However, if the client defines
+ * the symbol LEPTON_USE_STATIC_LIBRARIES we'll suppress the dllimport so
+ * that the client code can be linked with static libraries. Note that
+ * the client symbol is not library dependent, while the library symbols
+ * affect only the lepton library, meaning that other libraries can
+ * be clients of this one. However, we are assuming all-static or all-shared.
+ */
+
+#ifdef _MSC_VER
+    // We don't want to hear about how sprintf is "unsafe".
+    #pragma warning(disable:4996)
+    // Keep MS VC++ quiet about lack of dll export of private members.
+    #pragma warning(disable:4251)
+    #if defined(LEPTON_BUILDING_SHARED_LIBRARY)
+        #define LEPTON_EXPORT __declspec(dllexport)
+    #elif defined(LEPTON_BUILDING_STATIC_LIBRARY) || defined(LEPTON_USE_STATIC_LIBRARIES)
+        #define LEPTON_EXPORT
+    #else
+        #define LEPTON_EXPORT __declspec(dllimport)   // i.e., a client of a shared library
+    #endif
+#else
+    #define LEPTON_EXPORT // Linux, Mac
+#endif
+
+#endif // LEPTON_WINDOW_INCLUDE_H_

plumed/_lib/include/plumed/mapping/Path.h

@@ -0,0 +1,44 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+   Copyright (c) 2013-2020 The plumed team
+   (see the PEOPLE file at the root of the distribution for a list of names)
+
+   See http://www.plumed.org for more information.
+
+   This file is part of plumed, version 2.
+
+   plumed is free software: you can redistribute it and/or modify
+   it under the terms of the GNU Lesser General Public License as published by
+   the Free Software Foundation, either version 3 of the License, or
+   (at your option) any later version.
+
+   plumed is distributed in the hope that it will be useful,
+   but WITHOUT ANY WARRANTY; without even the implied warranty of
+   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+   GNU Lesser General Public License for more details.
+
+   You should have received a copy of the GNU Lesser General Public License
+   along with plumed.  If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_mapping_Path_h
+#define __PLUMED_mapping_Path_h
+
+#include "../core/ActionShortcut.h"
+
+namespace PLMD {
+namespace mapping {
+
+class Path : public ActionShortcut {
+public:
+  static void registerKeywords(Keywords& keys);
+  static void registerInputFileKeywords( Keywords& keys );
+  static void readPropertyInformation( const std::vector<std::string>& pnames, const std::string& lab, const std::string& refname, ActionShortcut* action );
+  static void readInputFrames( const std::string& reference, const std::string& type, std::vector<std::string>& argnames, const bool& displacements, ActionShortcut* action, std::string& reference_data );
+  static std::string fixArgumentName( const std::string& argin );
+  explicit Path(const ActionOptions&);
+};
+
+}
+}
+
+
+#endif

plumed/_lib/include/plumed/mapping/PathProjectionCalculator.h

@@ -0,0 +1,57 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+   Copyright (c) 2016,2017 The plumed team
+   (see the PEOPLE file at the root of the distribution for a list of names)
+
+   See http://www.plumed.org for more information.
+
+   This file is part of plumed, version 2.
+
+   plumed is free software: you can redistribute it and/or modify
+   it under the terms of the GNU Lesser General Public License as published by
+   the Free Software Foundation, either version 3 of the License, or
+   (at your option) any later version.
+
+   plumed is distributed in the hope that it will be useful,
+   but WITHOUT ANY WARRANTY; without even the implied warranty of
+   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+   GNU Lesser General Public License for more details.
+
+   You should have received a copy of the GNU Lesser General Public License
+   along with plumed.  If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_mapping_PathProjectionCalculator_h
+#define __PLUMED_mapping_PathProjectionCalculator_h
+
+#include "../core/Value.h"
+#include "../core/PlumedMain.h"
+#include "../tools/Keywords.h"
+#include "../colvar/RMSDVector.h"
+
+namespace PLMD {
+namespace mapping {
+
+class PathProjectionCalculator {
+private:
+  Value* mypath_obj;
+  PlumedMain metric;
+  std::vector<double> data;
+  std::vector<Value*> refargs;
+  std::vector<colvar::RMSDVector*> rmsd_objects;
+/// Compute the vector connecting two of the frames in the path
+  void computeVectorBetweenFrames( const unsigned& ifrom, const unsigned& ito );
+public:
+  static void registerKeywords( Keywords& keys );
+  PathProjectionCalculator( Action* act );
+/// Get the number of frames in the path
+  unsigned getNumberOfFrames() const ;
+/// Get the displacement between two reference frames
+  void getDisplaceVector( const unsigned& ifrom, const unsigned& ito, std::vector<double>& displace );
+/// Transfer data in and out of the reference configurations (used for reparamerization)
+  void getReferenceConfiguration( const unsigned& iframe, std::vector<double>& refpos ) const ;
+  void setReferenceConfiguration( const unsigned& iframe, std::vector<double>& refpos );
+  void updateDepedentRMSDObjects();
+};
+
+}
+}
+#endif

plumed/_lib/include/plumed/matrixtools/MatrixOperationBase.h

@@ -0,0 +1,54 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+   Copyright (c) 2011-2023 The plumed team
+   (see the PEOPLE file at the root of the distribution for a list of names)
+
+   See http://www.plumed.org for more information.
+
+   This file is part of plumed, version 2.
+
+   plumed is free software: you can redistribute it and/or modify
+   it under the terms of the GNU Lesser General Public License as published by
+   the Free Software Foundation, either version 3 of the License, or
+   (at your option) any later version.
+
+   plumed is distributed in the hope that it will be useful,
+   but WITHOUT ANY WARRANTY; without even the implied warranty of
+   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+   GNU Lesser General Public License for more details.
+
+   You should have received a copy of the GNU Lesser General Public License
+   along with plumed.  If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_matrixtools_MatrixOperationBase_h
+#define __PLUMED_matrixtools_MatrixOperationBase_h
+
+#include "../core/ActionWithValue.h"
+#include "../core/ActionWithArguments.h"
+#include "../tools/Matrix.h"
+
+namespace PLMD {
+namespace matrixtools {
+
+class MatrixOperationBase :
+  public ActionWithArguments,
+  public ActionWithValue {
+private:
+/// These are used to hold the matrix
+  std::vector<double> MOBvals;
+  std::vector<std::pair<unsigned,unsigned> > MOBpairs;
+protected:
+/// Retrieve a dense version of the ith matrix that is used by this action
+  void retrieveFullMatrix( Matrix<double>& mymatrix );
+public:
+  static void registerKeywords( Keywords& keys );
+///
+  explicit MatrixOperationBase(const ActionOptions&);
+/// Apply the forces
+  virtual void apply() override;
+/// Get the force on a matrix element
+  virtual double getForceOnMatrixElement( const unsigned& jrow, const unsigned& krow ) const = 0 ;
+};
+
+}
+}
+#endif