hillclimber 0.1.6__cp313-cp313-macosx_15_0_x86_64.whl

plumed/_lib/include/plumed/core/FlexibleBin.h

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+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+   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_core_FlexibleBin_h
+#define __PLUMED_core_FlexibleBin_h
+
+#include<vector>
+
+namespace PLMD {
+
+class ActionWithArguments;
+
+class FlexibleBin {
+private:
+  int type;
+  // this contains all the infos about the CVs including periodicity
+  ActionWithArguments *paction;
+  double sigma;
+  // variance is the matrix that really matters
+  std::vector<double> variance;
+  // this is only there
+  std::vector<double> average;
+  // minimum and maximum values
+  std::vector<double> sigmamin;
+  std::vector<double> sigmamax;
+  std::vector<bool>  limitmax;
+  std::vector<bool>  limitmin;
+public:
+  /// a constructor that takes the pointer of the action that contains it
+  FlexibleBin(int type,ActionWithArguments *paction, double const &d, std::vector<double> &sigmamin, const std::vector<double> &sigmamax );
+  /// a constructor for 1D FlexBin (for PBMETAD)
+  FlexibleBin(int type, ActionWithArguments *paction, unsigned iarg, double const &d, std::vector<double> &sigmamin, const std::vector<double> &sigmamax);
+  /// update the average (always for diffusion) or calculate the geom covariance (  only when do_when_zero is zero)
+  void update(bool nowAddAHill);
+  void update(bool nowAddAHill, unsigned iarg);
+  std::vector<double> getMatrix() const;
+  std::vector<double> getInverseMatrix() const;
+  std::vector<double> getInverseMatrix(unsigned iarg) const;
+  enum AdaptiveHillsType { none, diffusion, geometry };
+};
+
+
+
+}
+#endif

plumed/_lib/include/plumed/core/GREX.h

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+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+   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_core_GREX_h
+#define __PLUMED_core_GREX_h
+
+#include "WithCmd.h"
+#include "../tools/ForwardDecl.h"
+#include <string>
+#include <vector>
+
+namespace PLMD {
+
+class PlumedMain;
+class Communicator;
+
+class GREX:
+  public WithCmd {
+  bool initialized;
+  ForwardDecl<Communicator> intracomm_fwd;
+  Communicator& intracomm=*intracomm_fwd;
+  ForwardDecl<Communicator> intercomm_fwd;
+  Communicator& intercomm=*intercomm_fwd;
+  PlumedMain& plumedMain;
+  int partner;
+  double localDeltaBias;
+  double foreignDeltaBias;
+  double localUNow;
+  double localUSwap;
+  std::vector<double> allDeltaBias;
+  std::string buffer;
+  int myreplica;
+public:
+  explicit GREX(PlumedMain&);
+  ~GREX();
+  void cmd(std::string_view key,const TypesafePtr & val) override;
+  void calculate();
+  void savePositions();
+};
+
+}
+
+#endif

plumed/_lib/include/plumed/core/GenericMolInfo.h

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+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+   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_core_GenericMolInfo_h
+#define __PLUMED_core_GenericMolInfo_h
+
+#include "ActionSetup.h"
+#include "ActionPilot.h"
+#include "ActionAtomistic.h"
+#include "ActionAnyorder.h"
+#include "../tools/Exception.h"
+#include "../tools/ForwardDecl.h"
+#include "../tools/Subprocess.h"
+#include <memory>
+#include <map>
+
+namespace PLMD {
+
+class PDB;
+
+class GenericMolInfo :
+  public ActionAnyorder,
+  public ActionPilot,
+  public ActionAtomistic {
+private:
+  ForwardDecl<PDB> pdb_fwd;
+/// A pdb file containing the topology
+  PDB& pdb=*pdb_fwd;
+/// The type of molecule in the pdb
+  std::string mytype;
+/// The name of the reference pdb file
+  std::string reference;
+/// The backbone that was read in from the pdb file
+  std::vector< std::vector<AtomNumber> > read_backbone;
+/// Python interpreter is enabled
+  bool enablePythonInterpreter=false;
+/// Python command
+  std::string pythonCmd;
+/// Selector subprocess
+  std::unique_ptr<Subprocess> selector;
+/// Track is selector is running
+/// Needed on Get_rank()>0
+  bool selector_running=false;
+/// Structure in pdb file is whole
+  bool iswhole_;
+public:
+  ~GenericMolInfo();
+  void calculate() override {}
+  void apply() override {}
+  static void registerKeywords( Keywords& keys );
+  static std::map<std::string,std::string> getSpecialKeywords();
+  explicit GenericMolInfo(const ActionOptions&ao);
+  void getBackbone( std::vector<std::string>& resstrings, const std::string& fortype, std::vector< std::vector<AtomNumber> >& backbone );
+  std::string getAtomName(AtomNumber a)const;
+  bool checkForAtom(AtomNumber a)const;
+  unsigned getResidueNumber(AtomNumber a)const;
+  std::string getChainID(AtomNumber a)const;
+  Vector getPosition(AtomNumber a)const;
+  bool isWhole() const;
+  unsigned getPDBsize()const ;
+  std::string getResidueName(AtomNumber a)const;
+  void interpretSymbol( const std::string& symbol, std::vector<AtomNumber>& atoms );
+/// Calculate is used to kill the python interpreter.
+/// We do this in order to avoid possible interference or slowing down of the simulation
+/// due to the extra subprocess.
+  void prepare() override;
+};
+
+}
+
+#endif

plumed/_lib/include/plumed/core/Group.h

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+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+   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_core_Group_h
+#define __PLUMED_core_Group_h
+#include "ActionAtomistic.h"
+
+namespace PLMD {
+
+class Group : public ActionAtomistic {
+private:
+  std::vector<AtomNumber> atoms;
+public:
+  explicit Group(const ActionOptions&ao);
+  static void registerKeywords( Keywords& keys );
+  std::vector<std::string> getGroupAtoms() const ;
+  void calculate() override {}
+  void apply() override {}
+};
+
+}
+
+#endif

plumed/_lib/include/plumed/core/ModuleMap.h

@@ -0,0 +1,30 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+   Copyright (c) 2024-2024 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_core_ModuleMap_h
+#define __PLUMED_core_ModuleMap_h
+#include <map>
+#include <string>
+namespace PLMD {
+const std::map<std::string,std::string> & getModuleMap();
+} // namespace PLMD
+
+#endif //__PLUMED_core_ModuleMap_h