hillclimber 0.1.5__cp313-cp313-musllinux_1_2_aarch64.whl

plumed/_lib/include/plumed/tools/RMSD.h

@@ -0,0 +1,493 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+   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_tools_RMSD_h
+#define __PLUMED_tools_RMSD_h
+
+#include "Vector.h"
+#include "Matrix.h"
+#include "Tensor.h"
+#include "View.h"
+#include <vector>
+#include <string>
+#include <array>
+
+namespace PLMD {
+
+class Log;
+class PDB;
+
+/** \ingroup TOOLBOX
+A class that implements RMSD calculations
+This is a class that implements the various infrastructure to calculate the
+RMSD or MSD respect a given frame. It can be done through an optimal alignment scheme
+as Kearsley or, more simply, by resetting the center of mass.
+This is the class that decides this. A very simple use is
+\verbatim
+#include "../tools/PDB.h"
+#include "../tools/RMSD.h"
+#include "../tools/Vector.h"
+using namespace PLMD;
+RMSD rmsd;
+PDB pdb;
+// get the pdb (see PDB documentation)
+pdb.read("file.pdb",true,1.0);
+string type;
+type.assign("OPTIMAL");
+// set the reference and the type
+rmsd.set(pdb,type);
+// this calculates the rmsd and the derivatives
+vector<Vector> derivs;
+double val;
+val=rmsd.calculate(getPositions(),derivs,true);
+\endverbatim
+
+**/
+
+class RMSD {
+  enum AlignmentMethod {SIMPLE, OPTIMAL, OPTIMAL_FAST};
+  AlignmentMethod alignmentMethod=SIMPLE;
+// Reference coordinates
+  std::vector<Vector> reference;
+// Weights for alignment
+  std::vector<double> align;
+// Weights for deviation
+  std::vector<double> displace;
+// Center for reference and flag for its calculation
+  Vector reference_center;
+  bool reference_center_is_calculated=false;
+  bool reference_center_is_removed=false;
+// Center for running position (not used in principle but here to reflect reference/positio symmetry
+  Vector positions_center;
+  bool positions_center_is_calculated=false;
+  bool positions_center_is_removed=false;
+// calculates the center from the position provided
+  Vector calculateCenter(const std::vector<Vector>&p,const std::vector<double> &w) {
+    plumed_massert(p.size()==w.size(),"mismatch in dimension of position/align arrays while calculating the center");
+    unsigned n;
+    n=p.size();
+    Vector c;
+    c.zero();
+    for(unsigned i=0; i<n; i++) {
+      c+=p[i]*w[i];
+    }
+    return c;
+  };
+// removes the center for the position provided
+  void removeCenter(std::vector<Vector>&p, const Vector &c) {
+    unsigned n;
+    n=p.size();
+    for(unsigned i=0; i<n; i++) {
+      p[i]-=c;
+    }
+  };
+// add center
+  void addCenter(std::vector<Vector>&p, const Vector &c) {
+    Vector cc=c*-1.;
+    removeCenter(p,cc);
+  };
+
+public:
+/// Constructor
+  RMSD();
+/// clear the structure
+  void clear();
+/// set reference, align and displace from input pdb structure: evtl remove com from the initial structure and normalize the input weights from the pdb
+  void set(const PDB&,
+           const std::string & mytype,
+           bool remove_center=true,
+           bool normalize_weights=true);
+/// set align displace reference and type from input vectors
+  void set(const std::vector<double>& alignTo,
+           const std::vector<double>& displaceFrom,
+           const std::vector<Vector>& ref,
+           const std::string & mytype,
+           bool remove_center=true,
+           bool normalize_weights=true );
+/// set the type of alignment we are doing
+  void setType(const std::string & mytype);
+/// set reference coordinates, remove the com by using uniform weights
+  void setReference(const std::vector<Vector>& ref);
+  const std::vector<Vector>& getReference() const ;
+/// set weights and remove the center from reference with normalized weights. If the com has been removed, it resets to the new value
+  void setAlign(const std::vector<double>& alignTo,
+                bool normalize_weights=true,
+                bool remove_center=true);
+  std::vector<double> getAlign();
+/// set align
+  void setDisplace(const std::vector<double>& displaceFrom, bool normalize_weights=true);
+  std::vector<double> getDisplace();
+///
+  std::string getMethod() const ;
+/// workhorses
+  double simpleAlignment(const std::vector<double>& alignTo,
+                         const std::vector<double>& displaceFrom,
+                         const View<Vector> positions,
+                         const std::vector<Vector>& ref,
+                         std::vector<Vector>& derivatives,
+                         std::vector<Vector>& displacement,
+                         bool squared=false)const;
+  template <bool safe,bool alEqDis>
+  double optimalAlignment(const std::vector<double>& alignTo,
+                          const std::vector<double>& displaceFrom,
+                          const View<Vector> positions,
+                          const std::vector<Vector>& ref,
+                          std::vector<Vector>& DDistDPos, bool squared=false)const;
+
+  template <bool safe, bool alEqDis>
+  double optimalAlignmentWithCloseStructure(const std::vector<double>& alignTo,
+      const std::vector<double>& displaceFrom,
+      const View<Vector> positions,
+      const std::vector<Vector>& ref,
+      std::vector<Vector>& derivatives,
+      const Tensor & rotationPosClose,
+      const Tensor & rotationRefClose,
+      std::array<std::array<Tensor,3>,3>& drotationPosCloseDrr01,
+      bool squared=false)const;
+
+  template <bool safe, bool alEqDis>
+  double optimalAlignment_Rot_DRotDRr01(const std::vector<double>& alignTo,
+                                        const std::vector<double>& displaceFrom,
+                                        const View<Vector> positions,
+                                        const std::vector<Vector>& ref,
+                                        Tensor & Rotation,
+                                        std::array<std::array<Tensor,3>,3>& drotationPosCloseDrr01,
+                                        bool squared=false)const;
+
+  template <bool safe, bool alEqDis>
+  double optimalAlignment_Rot(const std::vector<double>& alignTo,
+                              const std::vector<double>& displaceFrom,
+                              const View<Vector> positions,
+                              const std::vector<Vector>& ref,
+                              std::vector<Vector>& derivatives,
+                              Tensor & Rotation,
+                              bool squared=false)const;
+
+  template <bool safe,bool alEqDis>
+  double optimalAlignment_DDistDRef(const std::vector<double>& alignTo,
+                                    const std::vector<double>& displaceFrom,
+                                    const View<Vector> positions,
+                                    const std::vector<Vector>& ref,
+                                    std::vector<Vector>& DDistDPos,
+                                    std::vector<Vector>&  DDistDRef,
+                                    bool squared=false) const;
+
+  template <bool safe,bool alEqDis>
+  double optimalAlignment_SOMA(const std::vector<double>& alignTo,
+                               const std::vector<double>& displaceFrom,
+                               const View<Vector> positions,
+                               const std::vector<Vector>& ref,
+                               std::vector<Vector>& DDistDPos,
+                               std::vector<Vector>&  DDistDRef,
+                               bool squared=false) const;
+
+  template <bool safe,bool alEqDis>
+  double optimalAlignment_DDistDRef_Rot_DRotDPos(const std::vector<double>& alignTo,
+      const std::vector<double>& displaceFrom,
+      const View<Vector> positions,
+      const std::vector<Vector>& ref,
+      std::vector<Vector>& DDistDPos,
+      std::vector<Vector>&  DDistDRef,
+      Tensor & Rotation,
+      Matrix<std::vector<Vector> >&DRotDPos,
+      bool squared=false) const;
+
+  template <bool safe,bool alEqDis>
+  double optimalAlignment_DDistDRef_Rot_DRotDPos_DRotDRef(const std::vector<double>& alignTo,
+      const std::vector<double>& displaceFrom,
+      const View<Vector> positions,
+      const std::vector<Vector>& ref,
+      std::vector<Vector>& DDistDPos,
+      std::vector<Vector>&  DDistDRef,
+      Tensor & Rotation,
+      Matrix<std::vector<Vector> >&DRotDPos,
+      Matrix<std::vector<Vector> >&DRotDRef,
+      bool squared=false) const;
+
+  template <bool safe,bool alEqDis>
+  double optimalAlignment_PCA(const std::vector<double>& alignTo,
+                              const std::vector<double>& displaceFrom,
+                              const View<Vector> positions,
+                              const std::vector<Vector>& ref,
+                              std::vector<Vector>& alignedpositions,
+                              std::vector<Vector>& centeredpositions,
+                              std::vector<Vector>& centeredreference,
+                              Tensor & Rotation,
+                              std::vector<Vector>& DDistDPos,
+                              Matrix<std::vector<Vector> >& DRotDPos,
+                              bool squared=false) const ;
+
+  template <bool safe,bool alEqDis>
+  double optimalAlignment_Fit(const std::vector<double>& alignTo,
+                              const std::vector<double>& displaceFrom,
+                              const View<Vector> positions,
+                              const std::vector<Vector>& ref,
+                              Tensor & Rotation,
+                              Matrix<std::vector<Vector> >& DRotDPos,
+                              std::vector<Vector>& centeredpositions,
+                              Vector & center_positions,
+                              bool squared=false);
+
+
+/// Compute rmsd: note that this is an intermediate layer which is kept in order to evtl expand with more alignment types/user options to be called while keeping the workhorses separated
+//#pragma acc routine
+  double calculate(const View<Vector> positions,
+                   std::vector<Vector>&derivatives,
+                   bool squared=false)const;
+  double calculate(const std::vector<Vector>& positions,
+                   std::vector<Vector>&derivatives,
+                   bool squared=false)const;
+/// Other convenience methods:
+/// calculate the derivative of distance respect to position(DDistDPos) and reference (DDistDPos)
+  double calc_DDistDRef( const std::vector<Vector>& positions, std::vector<Vector> &DDistDPos, std::vector<Vector>& DDistDRef, const bool squared=false   );
+/// calculate the derivative for SOMA (i.e. derivative respect to reference frame without the matrix derivative)
+  double calc_SOMA( const std::vector<Vector>& positions,
+                    std::vector<Vector>&DDistDPos,
+                    std::vector<Vector>& DDistDRef,
+                    const bool squared=false);
+///
+  double calc_DDistDRef_Rot_DRotDPos( const std::vector<Vector>& positions,
+                                      std::vector<Vector>&DDistDPos,
+                                      std::vector<Vector>& DDistDRef,
+                                      Tensor & Rotation,Matrix<std::vector<Vector> >&DRotDPos,
+                                      const bool squared=false);
+  double calc_DDistDRef_Rot_DRotDPos_DRotDRef( const std::vector<Vector>& positions,
+      std::vector<Vector>&DDistDPos,
+      std::vector<Vector>& DDistDRef,
+      Tensor & Rotation,Matrix<std::vector<Vector> >&DRotDPos,Matrix<std::vector<Vector> > &DRotDRef,
+      const bool squared=false);
+/// convenience method to retrieve all the bits and pieces for PCA
+  double calc_PCAelements( const std::vector<Vector>& pos,
+                           std::vector<Vector>&DDistDPos,
+                           Tensor & Rotation,
+                           Matrix<std::vector<Vector> >& DRotDPos,std::vector<Vector>  & alignedpositions,
+                           std::vector<Vector>& centeredpositions,
+                           std::vector<Vector>&centeredreference,
+                           bool squared=false) const ;
+/// convenience method to retrieve all the bits and pieces needed by FitToTemplate
+  double calc_FitElements( const std::vector<Vector>& pos,
+                           Tensor & Rotation,
+                           Matrix<std::vector<Vector> >& DRotDPos,std::vector<Vector> & centeredpositions,Vector & center_positions,
+                           bool squared=false );
+///calculate rotation matrix, derivative of rotation matrix w.r.t. positions, derivative of rotation matrix w.r.t. rr01
+  double calc_Rot_DRotDRr01( const std::vector<Vector>& positions,
+                             Tensor & Rotation,
+                             std::array<std::array<Tensor,3>,3>& DRotDRr01,
+                             const bool squared=false   );
+///calculate rotation matrix, derivative of rotation matrix w.r.t. positions
+  double calc_Rot( const std::vector<Vector>& positions,
+                   std::vector<Vector>&DDistDPos,
+                   Tensor & Rotation,
+                   const bool squared=false   );
+///calculate with close structure, i.e. approximate the RMSD without expensive computation of rotation matrix by reusing saved rotation matrices from previous iterations
+  double calculateWithCloseStructure( const std::vector<Vector>& positions,
+                                      std::vector<Vector>&DDistDPos,
+                                      const Tensor & rotationPosClose,
+                                      const Tensor & rotationRefClose,
+                                      std::array<std::array<Tensor,3>,3>& drotationPosCloseDrr01,
+                                      const bool squared=false   );
+/// static convenience method to get the matrix i,a from drotdpos (which is a bit tricky)
+  static Tensor getMatrixFromDRot(const Matrix< std::vector<Vector> >&drotdpos, const unsigned i, const unsigned a) {
+    Tensor t;
+    t[0][0]=drotdpos(0,0)[i][a];
+    t[0][1]=drotdpos(0,1)[i][a];
+    t[0][2]=drotdpos(0,2)[i][a];
+    t[1][0]=drotdpos(1,0)[i][a];
+    t[1][1]=drotdpos(1,1)[i][a];
+    t[1][2]=drotdpos(1,2)[i][a];
+    t[2][0]=drotdpos(2,0)[i][a];
+    t[2][1]=drotdpos(2,1)[i][a];
+    t[2][2]=drotdpos(2,2)[i][a];
+    return t;
+  };
+};
+
+/// this is a class which is needed to share information across the various non-threadsafe routines
+/// so that the public function of rmsd are threadsafe while the inner core can safely share information
+class RMSDCoreData {
+private:
+  //the parameters that are common to the two constructors
+  //are inititialized here at declaration,
+  //to underline differences in setups
+  bool alEqDis=false;
+  bool distanceIsMSD=false; // default is RMSD but can deliver the MSD
+  bool hasDistance=false;  // distance is already calculated
+  bool isInitialized=false;
+  bool safe=false;
+
+  // this need to be copied and they are small, should not affect the performance
+  Vector creference;
+  bool creference_is_calculated;
+  bool creference_is_removed;
+  Vector cpositions;
+  bool cpositions_is_calculated;
+  bool cpositions_is_removed;
+  bool retrieve_only_rotation;
+
+  // use reference assignment to speed up instead of copying
+  const View<Vector> positions;
+  const std::vector<Vector>&reference;
+  const std::vector<double>&align;
+  const std::vector<double>&displace;
+
+  // the needed stuff for distance and more (one could use eigenvecs components and eigenvals for some reason)
+  double dist=0.0;
+  Vector4d eigenvals;
+  Tensor4d eigenvecs;
+  double rr00=0.0; //  sum of positions squared (needed for dist calc)
+  double rr11=0.0; //  sum of reference squared (needed for dist calc)
+  Tensor rotation; // rotation derived from the eigenvector having the smallest eigenvalue
+  std::array<std::array<Tensor,3>,3> drotation_drr01; // derivative of the rotation only available when align!=displace
+  Tensor ddist_drr01;
+  Tensor ddist_drotation;
+  std::vector<Vector> d; // difference of components
+public:
+  /// the constructor (note: only references are passed, therefore is rather fast)
+  /// note: this aligns the reference onto the positions
+  ///
+  /// this method assumes that the centers are already calculated and subtracted
+  RMSDCoreData(const std::vector<double>&a,
+               const std::vector<double>&disp,
+               const View<Vector> p,
+               const std::vector<Vector>&r,
+               const Vector &cp,
+               const Vector &cr )
+    : creference(cr),
+      creference_is_calculated(true),
+      creference_is_removed(true),
+      cpositions(cp),
+      cpositions_is_calculated(true),
+      cpositions_is_removed(true),
+      retrieve_only_rotation(false),
+      positions(p),
+      reference(r),
+      align(a),
+      displace(disp) {}
+
+  // this constructor does not assume that the positions and reference have the center subtracted
+  RMSDCoreData(const std::vector<double>&a,
+               const std::vector<double>&disp,
+               const View<Vector> p,
+               const std::vector<Vector>&r)
+    : creference(0.0,0.0,0.0),
+      creference_is_calculated(false),
+      creference_is_removed(false),
+      cpositions(0.0,0.0,0.0),
+      cpositions_is_calculated(false),
+      cpositions_is_removed(false),
+      retrieve_only_rotation(false),
+      positions(p),
+      reference(r),
+      align(a),
+      displace(disp) {}
+
+  // set the center on the fly without subtracting
+  void calcPositionsCenter() {
+    plumed_massert(!cpositions_is_calculated,"the center was already calculated");
+    cpositions.zero();
+    for(unsigned i=0; i<positions.size(); i++) {
+      cpositions+=positions[i]*align[i];
+    }
+    cpositions_is_calculated=true;
+  }
+
+  void calcReferenceCenter() {
+    plumed_massert(!creference_is_calculated,"the center was already calculated");
+    creference.zero();
+    for(unsigned i=0; i<reference.size(); i++) {
+      creference+=reference[i]*align[i];
+    }
+    creference_is_calculated=true;
+  }
+  // assume the center is given externally
+  // cppcheck-suppress passedByValue
+  void setPositionsCenter(Vector v) {
+    plumed_massert(!cpositions_is_calculated,"You are setting the center two times!");
+    cpositions=v;
+    cpositions_is_calculated=true;
+  }
+  // cppcheck-suppress passedByValue
+  void setReferenceCenter(Vector v) {
+    plumed_massert(!creference_is_calculated,"You are setting the center two times!");
+    creference=v;
+    creference_is_calculated=true;
+  }
+  // the center is already removed
+  void setPositionsCenterIsRemoved(bool t) {
+    cpositions_is_removed=t;
+  }
+  void setReferenceCenterIsRemoved(bool t) {
+    creference_is_removed=t;
+  }
+  bool getPositionsCenterIsRemoved() {
+    return cpositions_is_removed;
+  }
+  bool getReferenceCenterIsRemoved() {
+    return creference_is_removed;
+  }
+  //  does the core calc : first thing to call after the constructor:
+  // only_rotation=true does not retrieve the derivatives, just retrieve the optimal rotation (the same calc cannot be exploit further)
+  void doCoreCalc(bool setSafe,bool setAlEqDis, bool only_rotation=false);
+  // do calculation with close structure data structures
+  void doCoreCalcWithCloseStructure(bool setSafe,
+                                    bool setAlEqDis,
+                                    const Tensor & rotationPosClose,
+                                    const Tensor & rotationRefClose,
+                                    std::array<std::array<Tensor,3>,3>& drotationPosCloseDrr01);
+  // retrieve the distance if required after doCoreCalc
+  double getDistance(bool squared);
+  // retrieve the derivative of the distance respect to the position
+  std::vector<Vector> getDDistanceDPositions();
+  // retrieve the derivative of the distance respect to the reference
+  std::vector<Vector> getDDistanceDReference();
+  // specific version for SOMA calculation (i.e. does not need derivative respect to rotation matrix)
+  std::vector<Vector> getDDistanceDReferenceSOMA();
+  // get aligned reference onto position
+  std::vector<Vector> getAlignedReferenceToPositions();
+  // get aligned position onto reference
+  std::vector<Vector> getAlignedPositionsToReference();
+  // get centered positions
+  std::vector<Vector> getCenteredPositions();
+  // get centered reference
+  std::vector<Vector> getCenteredReference();
+  // get center of positions
+  Vector getPositionsCenter();
+  // get center of reference
+  Vector getReferenceCenter();
+  // get rotation matrix (reference ->positions)
+  Tensor getRotationMatrixReferenceToPositions();
+  // get rotation matrix (positions -> reference)
+  Tensor getRotationMatrixPositionsToReference();
+  // get the derivative of the rotation matrix respect to positions
+  // note that the this transformation overlap the  reference onto position
+  // if inverseTransform=true then aligns the positions onto reference
+  Matrix<std::vector<Vector> > getDRotationDPositions( bool inverseTransform=false );
+  // get the derivative of the rotation matrix respect to reference
+  // note that the this transformation overlap the  reference onto position
+  // if inverseTransform=true then aligns the positions onto reference
+  Matrix<std::vector<Vector> >  getDRotationDReference(bool inverseTransform=false );
+  const std::array<std::array<Tensor,3>,3>& getDRotationDRr01() const;
+};
+
+}
+
+#endif
+

plumed/_lib/include/plumed/tools/Random.h

@@ -0,0 +1,80 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+   Copyright (c) 2012-2023 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_tools_Random_h
+#define __PLUMED_tools_Random_h
+
+#include <string>
+#include <vector>
+#include <iosfwd>
+
+namespace PLMD {
+
+/// \ingroup TOOLBOX
+class Random {
+  static constexpr int IA=16807;
+  static constexpr int IM=2147483647;
+  static constexpr int IQ=127773;
+  static constexpr int IR=2836;
+  static constexpr int NTAB=32;
+  static constexpr int NDIV=(1+(IM-1)/NTAB);
+  static constexpr double fact=5.9604644775390625e-8;     /* 1 / 2^24  */
+  static constexpr double EPS=3.0e-16;
+  static constexpr double AM=1.0/IM;
+  static constexpr double RNMX=1.0-EPS;
+  static const std::string noname;
+  bool incPrec;
+  bool switchGaussian;
+  double saveGaussian;
+  int iy;
+  int iv[NTAB];
+  int idum;
+  std::string name;
+public:
+  explicit Random(const std::string & title=noname);
+  void setSeed(int idum);
+  double RandU01();
+  double U01();
+  double U01d();
+  int RandInt(int i);
+  void Shuffle(std::vector<unsigned>& vec);
+  void WriteStateFull(std::ostream &)const;
+  void ReadStateFull (std::istream &);
+  void fromString(const std::string & str);
+  void toString(std::string & str)const;
+  friend std::ostream & operator<<(std::ostream & out,const Random & rng) {
+    rng.WriteStateFull(out);
+    return out;
+  }
+  friend std::istream & operator>>(std::istream & in,Random & rng) {
+    rng.ReadStateFull(in);
+    return in;
+  }
+  double Gaussian();
+  void IncreasedPrecis(bool i) {
+    incPrec=i;
+  }
+};
+
+}
+
+#endif
+

plumed/_lib/include/plumed/tools/RootFindingBase.h

@@ -0,0 +1,79 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+   Copyright (c) 2016-2023 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_tools_RootFindingBase_h
+#define __PLUMED_tools_RootFindingBase_h
+
+#include "MinimiseBase.h"
+#include "Brent1DRootSearch.h"
+
+namespace PLMD {
+
+template <class FCLASS>
+class RootFindingBase {
+private:
+/// This is the pointer to the member function in the energy
+/// calculating class that calculates the energy
+  typedef double(FCLASS::*engf_pointer)( const std::vector<double>& p, std::vector<double>& der ) const ;
+  typedef double(FCLASS::*engfnc_pointer)( const std::vector<double>& p, std::vector<double>& der ) ;
+/// The class that calculates the energy given a position
+  FCLASS* myclass_func;
+/// This actually does the search for a root
+  void doSearch( const std::vector<double>& dir, std::vector<double>& p, F1dim<FCLASS>& f1dim  ) const ;
+public:
+  explicit RootFindingBase( FCLASS* funcc ) : myclass_func(funcc) {}
+/// This is the line minimiser
+  void linesearch( const std::vector<double>& dir, std::vector<double>& p, engf_pointer myfunc ) const ;
+  void lsearch( const std::vector<double>& dir, std::vector<double>& p, engfnc_pointer myfunc ) const ;
+};
+
+template <class FCLASS>
+void RootFindingBase<FCLASS>::doSearch( const std::vector<double>& dir, std::vector<double>& p, F1dim<FCLASS>& f1dim ) const {
+  // Construct an object that will do the line search for the minimum
+  Brent1DRootSearch<F1dim<FCLASS> > bb(f1dim);
+
+  // This does the actual search for the root
+  double ax=0.0, xx=1.0;
+  bb.bracket( ax, xx, &F1dim<FCLASS>::getEng );
+  double xmin=bb.search( &F1dim<FCLASS>::getEng );
+  for(unsigned i=0; i<p.size(); ++i) {
+    p[i] += xmin*dir[i];
+  }
+}
+
+template <class FCLASS>
+void RootFindingBase<FCLASS>::linesearch( const std::vector<double>& dir, std::vector<double>& p, engf_pointer myfunc ) const {
+  // Construct the object that turns points on a line into vectors
+  F1dim<FCLASS> f1dim( p, dir, myclass_func, myfunc, NULL );
+  // Actually do the search
+  doSearch( dir, p, f1dim );
+}
+
+template <class FCLASS>
+void RootFindingBase<FCLASS>::lsearch( const std::vector<double>& dir, std::vector<double>& p, engfnc_pointer myfunc ) const {
+  // Construct the object that turns points on a line into vectors
+  F1dim<FCLASS> f1dim( p, dir, myclass_func, NULL, myfunc );
+  // Actually do the search
+  doSearch( dir, p, f1dim );
+}
+
+}
+#endif