hillclimber 0.1.6__cp313-cp313-macosx_15_0_x86_64.whl

plumed/_lib/include/plumed/colvar/PathMSDBase.h

@@ -0,0 +1,101 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+   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_colvar_PathMSDBase_h
+#define __PLUMED_colvar_PathMSDBase_h
+
+#include "Colvar.h"
+#include "../core/ActionRegister.h"
+
+#include "../tools/PDB.h"
+#include "../tools/RMSD.h"
+
+namespace PLMD {
+namespace colvar {
+
+class PathMSDBase : public Colvar {
+/// this class is a general container for path stuff
+  class ImagePath {
+  public:
+    // cardinal indexing: needed to map over msd
+    unsigned index;
+    // spiwok indexing
+    std::vector<double> property;
+    // distance
+    double distance;
+    // similarity (exp - lambda distance) or other
+    double similarity;
+    // derivatives of the distance
+    std::vector<Vector> distder;
+    // here one can add a pointer to a value (hypothetically providing a distance from a point)
+  };
+  struct imgOrderByDist {
+    bool operator ()(ImagePath const& a, ImagePath const& b) {
+      return (a).distance < (b).distance;
+    }
+  };
+  struct imgOrderBySimilarity {
+    bool operator ()(ImagePath const& a, ImagePath const& b) {
+      return (a).similarity > (b).similarity;
+    }
+  };
+
+  bool nopbc;
+
+  double lambda;
+  int neigh_size;
+  int neigh_stride;
+  std::vector<RMSD> msdv;
+  std::string reference;
+  std::vector<Vector> derivs_s;
+  std::vector<Vector> derivs_z;
+  std::vector <ImagePath> imgVec; // this can be used for doing neighlist
+
+  //variables used for the close structure method, i is the number of reference structures
+  double epsilonClose; //the maximal distance between the close and the current structure before reassignment
+  int debugClose; //turns on debug mode
+  int logClose; //turns on logging
+  RMSD rmsdPosClose; //rmsd between the current and the close structure
+  bool firstPosClose; //flag indicating the first time we need to calculate the distance between the close and the current structure
+  bool computeRefClose; //flag indicating necessity to recompute accurately all distances and rotation matrices between the close structure and reference str
+  std::vector<Tensor> rotationRefClose; //Tensor[i] saved rotation matrices between the close structure and reference structures
+  Tensor rotationPosClose; //rotation matrix between the close and the current structure
+  std::array<std::array<Tensor,3>,3> drotationPosCloseDrr01; //Tensor[3][3]; //derivation of the rotation matrix w.r.t rr01, necessary for calculation of derivations
+  std::vector<unsigned> savedIndices; //saved indices of imgVec from previous steps, used for recalculating after neighbourlist update
+protected:
+  std::vector<PDB> pdbv;
+  std::vector<std::string> labels;
+  std::vector< std::vector<double> > indexvec; // use double to allow isomaps
+  unsigned nframes;
+public:
+  explicit PathMSDBase(const ActionOptions&);
+  ~PathMSDBase();
+// active methods:
+  void calculate() override;
+//  virtual void prepare();
+  static void registerKeywords(Keywords& keys);
+};
+
+}
+}
+
+#endif
+

plumed/_lib/include/plumed/colvar/RMSDVector.h

@@ -0,0 +1,78 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+   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_colvar_RMSDVector_h
+#define __PLUMED_colvar_RMSDVector_h
+
+#include "../core/ActionWithVector.h"
+#include "../core/ParallelTaskManager.h"
+#include "../tools/RMSD.h"
+
+namespace PLMD {
+namespace colvar {
+
+class RMSDVectorData {
+public:
+  bool squared;
+  bool displacement;
+  std::string type;
+  std::vector<PLMD::RMSD> myrmsd;
+  std::vector<double> align, displace, sqrtdisplace;
+};
+
+class RMSDVector : public ActionWithVector {
+public:
+  using input_type = RMSDVectorData;
+  using PTM = ParallelTaskManager<RMSDVector>;
+private:
+  bool firststep;
+  bool norm_weights;
+  ParallelActionsInput input;
+  std::vector<double> force_stash;
+  std::vector<double> input_buffer;
+  PTM taskmanager;
+  static void getPositionsFromInputData( const ParallelActionsInput& input, std::vector<Vector>& pos );
+public:
+  static void registerKeywords(Keywords& keys);
+  explicit RMSDVector(const ActionOptions&);
+  unsigned getNumberOfDerivatives() override ;
+  int checkTaskIsActive( const unsigned& itask ) const override ;
+  void transferStashToValues( const std::vector<unsigned>& partialTaskList, const std::vector<double>& stash ) override ;
+  void transferForcesToStash( const std::vector<unsigned>& partialTaskList, std::vector<double>& stash ) const override ;
+  static void performTask( std::size_t task_index,
+                           const RMSDVectorData& actiondata,
+                           ParallelActionsInput& input,
+                           ParallelActionsOutput& output );
+  static void gatherForces( std::size_t task_index,
+                            const RMSDVectorData& actiondata,
+                            const ParallelActionsInput& input,
+                            View<const double,helpers::dynamic_extent> f,
+                            const std::vector<double>& deriv,
+                            std::vector<double>& outforces );
+  void setReferenceConfigurations();
+  void calculate() override ;
+  void applyNonZeroRankForces( std::vector<double>& outforces ) override ;
+  void apply() override ;
+};
+
+}
+}
+#endif

plumed/_lib/include/plumed/config/Config.h

@@ -0,0 +1,118 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+   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_config_Config_h
+#define __PLUMED_config_Config_h
+
+#include <string>
+
+namespace PLMD {
+namespace config {
+
+/// Return the extension of shared libraries on this system.
+/// It is either "so" or "dylib". In case shared libraries are disabled, it returns an empty string.
+std::string getSoExt();
+
+/// Return path to the root of the PLUMED package.
+std::string getPlumedRoot();
+
+/// Return path to documentation.
+/// User documentation is located in `getPlumedHtmldir()+"/user-doc/html/index.html"`
+/// Developer documentation is located in `getPlumedHtmldir()+"/developer-doc/html/index.html"`
+std::string getPlumedHtmldir();
+
+/// Return path to the include directory.
+/// The header file for PLUMED wrapper is in `getPlumedIncludedir()+getPlumedProgramName()+"/wrapper/Plumed.h"`
+std::string getPlumedIncludedir();
+
+/// Return the name used for installing PLUMED.
+/// E.g. if PLUMED has been compiled with `./configure --program-suffix _mpi`
+/// it returns "plumed_mpi"
+std::string getPlumedProgramName();
+
+/**
+Return a string containing a sequence of environment variables.
+
+The returned string has the form:
+\verbatim
+env PLUMED_ROOT=/path env PLUMED_HTMLDIR=/path ... etc
+\endverbatim
+This string is used internally in PLUMED to run scripts located in plumedroot/script.
+For instance, the `patch` script can be run executing the following command:
+\verbatim
+config::getEnvCommand()+" \""+getPlumedRoot()+"\"/scripts/patch.sh";
+\endverbatim
+Notice that the getPlumedRoot() output is enclosed in escaped quotes. This
+allows this directory to have spaces in its name.
+*/
+std::string getEnvCommand();
+
+/// Return the content of `Makefile.conf` in a single string.
+/// Can be used to inspect the variables used to customize PLUMED.
+/// Notice that this reflects the content of the `Makefile.conf` file.
+/// Since some of the there defined variables can be overwritten at install
+/// (e.g., one can use `make install prefix=/new/path` to change the installation path)
+/// their values could be not faithful
+std::string getMakefile();
+
+/// Return the short PLUMED version.
+/// E.g. "2.2"
+std::string getVersion();
+
+/// Return the long PLUMED version.
+/// E.g. "2.2.3"
+std::string getVersionLong();
+
+/// Return the git PLUMED version
+/// E.g. "c5badb091cd30"
+std::string getVersionGit();
+
+/// Return the day PLUMED was compiled.
+/// E.g. "Apr 16 2018"
+std::string getCompilationDate();
+
+/// Return the time at which PLUMED was compiled.
+/// E.g. "13:27:58"
+std::string getCompilationTime();
+
+bool hasMatheval();
+
+bool hasDlopen();
+
+bool isInstalled();
+
+/// This will always return true for backward compatibility
+constexpr bool hasCregex() {
+  return true;
+}
+
+bool hasMolfile();
+
+bool hasExternalMolfile();
+
+bool hasZlib();
+
+std::string getLibraryPath();
+
+}
+}
+
+#endif

plumed/_lib/include/plumed/config/version.h

@@ -0,0 +1,9 @@
+#ifndef __PLUMED_config_version_h
+#define __PLUMED_config_version_h
+#define PLUMED_VERSION_SHORT "2.11"
+#define PLUMED_VERSION_LONG "2.11.0-dev"
+#define PLUMED_VERSION_GIT "Unknown"
+#define PLUMED_VERSION_MAJOR 2
+#define PLUMED_VERSION_MINOR 11
+#define PLUMED_VERSION_PATCH 0
+#endif

plumed/_lib/include/plumed/contour/ContourFindingObject.h

@@ -0,0 +1,87 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+   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_contour_ContourFindingObject_h
+#define __PLUMED_contour_ContourFindingObject_h
+
+#include "../function/FunctionSetup.h"
+#include "../tools/RootFindingBase.h"
+
+namespace PLMD {
+namespace contour {
+
+template <class T>
+class ContourFindingObject {
+public:
+/// This is the object that does the root finding
+  RootFindingBase<ContourFindingObject<T>> mymin;
+/// This holds the input grid
+  // gridtools::EvaluateGridFunction
+  T function;
+/// Where you would like to find the contour
+  double contour;
+/// Get rid of constructor in future
+  explicit ContourFindingObject() : mymin(this), contour(0.0) {}
+/// Register keywords
+  static void registerKeywords( Keywords& keys );
+/// Get the contour value -- this will become static in future
+  double getDifferenceFromContour( const std::vector<double>& x, std::vector<double>& der ) const ;
+/// Read in the contour object
+  static void read( ContourFindingObject& func, ActionWithArguments* action, function::FunctionOptions& options );
+/// Find the contour
+  static void findContour( const ContourFindingObject& myobj, const std::vector<double>& direction, std::vector<double>& point );
+};
+
+template <class T>
+void ContourFindingObject<T>::registerKeywords( Keywords& keys ) {
+  keys.add("compulsory","CONTOUR","the value we would like to draw the contour at in the space");
+  T::registerKeywords(keys);
+  keys.remove("ZERO_OUTSIDE_GRID_RANGE");
+}
+
+template <class T>
+void ContourFindingObject<T>::read( ContourFindingObject& func, ActionWithArguments* action, function::FunctionOptions& options ) {
+  action->parse("CONTOUR",func.contour);
+  T::read( func.function, action, options );
+}
+
+template <class T>
+void ContourFindingObject<T>::findContour( const ContourFindingObject& myobj, const std::vector<double>& direction, std::vector<double>& point ) {
+  myobj.mymin.linesearch( direction, point, &ContourFindingObject<T>::getDifferenceFromContour );
+}
+
+template <class T>
+double ContourFindingObject<T>::getDifferenceFromContour( const std::vector<double>& x, std::vector<double>& der ) const {
+  std::vector<double> vals(1);
+  auto funcout = function::FunctionOutput::create( 1,
+                 vals.data(),
+                 x.size(),
+                 der.data() );
+  T::calc( function,
+           false,
+           View<const double>(x.data(),x.size()),
+           funcout );
+  return vals[0] - contour;
+}
+
+}
+}
+#endif

plumed/_lib/include/plumed/contour/DistanceFromContourBase.h

@@ -0,0 +1,82 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+   Copyright (c) 2013-2023 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_contour_DistanceFromContourBase_h
+#define __PLUMED_contour_DistanceFromContourBase_h
+
+#include "../core/ActionAtomistic.h"
+#include "../core/ActionWithValue.h"
+#include "../core/ActionWithArguments.h"
+#include "../tools/SwitchingFunction.h"
+#include "../tools/RootFindingBase.h"
+
+namespace PLMD {
+namespace contour {
+
+class DistanceFromContourBase :
+  public ActionWithValue,
+  public ActionAtomistic,
+  public ActionWithArguments {
+private:
+  double contour, gvol;
+  RootFindingBase<DistanceFromContourBase> mymin;
+protected:
+  std::string kerneltype;
+  std::vector<double> bw;
+  double rcut2;
+  unsigned nactive;
+  Vector pval;
+  std::vector<double> forcesToApply;
+  std::vector<unsigned> active_list;
+  SwitchingFunction switchingFunction;
+///
+  double evaluateKernel( const Vector& cpos, const Vector& apos, std::vector<double>& der ) const ;
+/// Find a contour along line specified by direction
+  void findContour( const std::vector<double>& direction, std::vector<double>& point ) const ;
+public:
+  static void registerKeywords( Keywords& keys );
+  explicit DistanceFromContourBase( const ActionOptions& );
+  unsigned getNumberOfDerivatives() override ;
+  void lockRequests() override;
+  void unlockRequests() override;
+  void calculateNumericalDerivatives( ActionWithValue* a ) override {
+    plumed_merror("numerical derivatives are not implemented for this action");
+  }
+  double getDifferenceFromContour( const std::vector<double>& x, std::vector<double>& der );
+  void apply() override;
+};
+
+inline
+unsigned DistanceFromContourBase::getNumberOfDerivatives() {
+  if( getNumberOfArguments()==1 ) {
+    return 4*getNumberOfAtoms() + 8;  // One derivative for each weight hence four times the number of atoms - 1
+  }
+  return 3*getNumberOfAtoms() + 9;
+}
+
+inline
+void DistanceFromContourBase::findContour( const std::vector<double>& direction, std::vector<double>& point ) const {
+  mymin.lsearch( direction, point, &DistanceFromContourBase::getDifferenceFromContour );
+}
+
+}
+}
+#endif

plumed/_lib/include/plumed/contour/FindContour.h

@@ -0,0 +1,67 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+   Copyright (c) 2015-2020 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_contour_FindContour_h
+#define __PLUMED_contour_FindContour_h
+
+#include "../core/ActionWithVector.h"
+#include "ContourFindingObject.h"
+#include "../gridtools/EvaluateGridFunction.h"
+#include "../core/ParallelTaskManager.h"
+
+namespace PLMD {
+namespace contour {
+
+class FindContour : public ActionWithVector {
+  friend class DumpContour;
+public:
+  using input_type = ContourFindingObject<gridtools::EvaluateGridFunction>;
+  using PTM = ParallelTaskManager<FindContour>;
+private:
+  bool firststep;
+/// The parallel task manager
+  PTM taskmanager;
+  unsigned gbuffer;
+  std::vector<unsigned> active_cells;
+public:
+  static void registerKeywords( Keywords& keys );
+  explicit FindContour(const ActionOptions&ao);
+  std::string getOutputComponentDescription( const std::string& cname, const Keywords& keys ) const override ;
+  const gridtools::GridCoordinatesObject& getInputGridObject() const ;
+  unsigned getNumberOfDerivatives() override ;
+  void getNumberOfTasks( unsigned& ntasks ) override ;
+  int checkTaskIsActive( const unsigned& taskno ) const override;
+  void calculate() override;
+  void getInputData( std::vector<double>& inputdata ) const override;
+  static void performTask( std::size_t task_index,
+                           const ContourFindingObject<gridtools::EvaluateGridFunction>& actiondata,
+                           ParallelActionsInput& input,
+                           ParallelActionsOutput& output );
+};
+
+inline
+const gridtools::GridCoordinatesObject& FindContour::getInputGridObject() const {
+  return taskmanager.getActionInput().function.getGridObject();
+}
+
+}
+}
+#endif