hillclimber 0.1.6__cp313-cp313-macosx_15_0_x86_64.whl

plumed/_lib/include/plumed/core/PlumedMainInitializer.h

@@ -0,0 +1,118 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+   Copyright (c) 2018-2023 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_PlumedMainInitializer_h
+#define __PLUMED_core_PlumedMainInitializer_h
+
+#include <cstddef>
+
+// !!!!!!!!!!!!!!!!!!!!!!    DANGER   !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!11
+// THE FOLLOWING ARE DEFINITIONS WHICH ARE NECESSARY FOR DYNAMIC LOADING OF THE PLUMED KERNEL:
+// This section should be consistent with the Plumed.h file.
+// Since the Plumed.h file may be included in host MD codes, **NEVER** MODIFY THE CODE IN THIS FILE
+// unless you know exactly what you are doing
+
+/**
+  Container for plumedmain function pointers (create, cmd and finalize).
+*/
+typedef struct {
+  void*(*create)();
+  void(*cmd)(void*,const char*,const void*);
+  void(*finalize)(void*);
+} plumed_plumedmain_function_holder_x;
+
+typedef struct {
+  void* ptr;
+  void (*handler)(void*,int,const char*,const void*);
+} plumed_nothrow_handler_x;
+
+typedef struct {
+  const void* ptr;
+  std::size_t nelem;
+  const std::size_t* shape;
+  std::size_t flags;
+  void* opt;
+} plumed_safeptr_x;
+
+/**
+  Container for symbol table. Presently only contains a version number and a plumed_plumedmain_function_holder object.
+  The definition of this structure might change in the future. In particular, the structure might grow adding
+  new fields. However, in that case the version number should be updated as well.
+*/
+typedef struct {
+  int version;
+  plumed_plumedmain_function_holder_x functions;
+  void (*cmd_nothrow)(void*plumed,const char*key,const void*val,plumed_nothrow_handler_x nothrow);
+  void (*cmd_safe)(void*plumed,const char*key,plumed_safeptr_x ptr);
+  void (*cmd_safe_nothrow)(void*plumed,const char*key,plumed_safeptr_x,plumed_nothrow_handler_x);
+  unsigned (*create_reference)(void*plumed);
+  unsigned (*delete_reference)(void*plumed);
+  unsigned (*use_count)(void*plumed);
+} plumed_symbol_table_type_x;
+
+
+// additional definitions
+typedef void*(*plumed_create_pointer_x)(void);
+typedef void(*plumed_cmd_pointer_x)(void*,const char*,const void*);
+typedef void(*plumed_finalize_pointer_x)(void*);
+
+/* These functions should be accessible from C, since they might be statically
+   used from Plumed.c (for static binding) */
+
+/**
+  Constructs a plumed object.
+  This function returns a void pointer that can be used in \ref plumed_plumedmain_cmd and \ref plumed_plumedmain_finalize.
+*/
+extern "C" void*plumed_plumedmain_create();
+
+/**
+  Send a command `key` and a pointer `val` to a void pointer returned by \ref plumed_plumedmain_create.
+*/
+extern "C" void plumed_plumedmain_cmd(void*plumed,const char*key,const void*val);
+
+/**
+  Finalize a void pointer returned by \ref plumed_plumedmain_create
+*/
+extern "C" void plumed_plumedmain_finalize(void*plumed);
+
+/**
+  Static symbol table that is accessed by the plumed loader.
+  Notice that this table is initialized with a static object construction.
+  In principle, it should be accessed by other programs dlopening the plumed kernel.
+  In that case, it is guaranteed to be already initialized.
+  However, when accessed directly it might be safer to first call \ref plumed_symbol_table_init.
+*/
+
+extern "C" plumed_symbol_table_type_x plumed_symbol_table;
+
+/**
+  Function that makes sure that \ref plumed_symbol_table is initialized.
+  Can be called multiple times.
+*/
+extern "C" void plumed_symbol_table_init();
+
+namespace PLMD {
+// This is just to avoid plumedcheck warnings.
+// Notice that the only define C-style objects here, so namespace is not needed
+}
+
+
+#endif

plumed/_lib/include/plumed/core/RegisterBase.h

@@ -0,0 +1,340 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+   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_RegisterBase_h
+#define __PLUMED_core_RegisterBase_h
+
+#include "../tools/Exception.h"
+#include <string>
+#include <string_view>
+#include <map>
+#include <memory>
+#include <iostream>
+#include <vector>
+#include <algorithm>
+#include <mutex>
+#include <shared_mutex>
+
+namespace PLMD {
+
+/// Base class, with type independent information.
+/// Actual registers should inherit through the RegisterBase class below
+class Register {
+  /// Initialize registration - only used by registrationLock()
+  static void pushDLRegistration(const std::string & fullpath);
+  /// Finalize registration - only used by registrationLock()
+  static void popDLRegistration() noexcept;
+
+protected:
+  /// Mutex protecting access to map
+  mutable std::shared_mutex mutex;
+  /// Internal tool to format image addresses
+  static std::string imageToString(void* image);
+  /// Check if we are in a dlopen section
+  static bool isDLRegistering() noexcept;
+  /// Return the path of the currently-loading library
+  static const std::string getRegisteringFullPath() noexcept;
+  /// Save all staged objects from a register
+  virtual void completeRegistration(void* image)=0;
+  /// Clear staged objects.
+  /// Should be used when leaving the dlopen section to remove
+  /// any dangling object.
+  virtual void clearStaged() noexcept =0;
+  /// Get all registered keys.
+  /// These are the keys in the map, not the plumed keywords!
+  virtual std::vector<std::string> getKeys() const =0;
+
+public:
+  /// Constructor.
+  /// This keeps track of all created instances.
+  Register();
+  /// Destructor.
+  virtual ~Register() noexcept;
+  /// Disable move
+  Register(Register &&) = delete;
+  /// Disable copy
+  Register(const Register &) = delete;
+
+  /// Small class to manage registration lock
+  /// This is used during dlopen, to avoid data races in registrations
+  class RegistrationLock {
+    bool active;
+  public:
+    RegistrationLock(const std::string & fullpath);
+    RegistrationLock(const RegistrationLock&) = delete;
+    RegistrationLock(RegistrationLock&& other) noexcept;
+    ~RegistrationLock() noexcept;
+  };
+
+  /// return a registration lock
+  static RegistrationLock registrationLock(const std::string & fullpath);
+
+  /// Save all staged objects in all registers
+  static void completeAllRegistrations(void* image);
+
+  /// Get only keys registered specifically by a given image
+  std::vector<std::string> getKeysWithDLHandle(void* handle) const;
+
+  friend std::ostream & operator<<(std::ostream &log,const Register &reg);
+};
+
+/// Class representing an error in a register
+class ExceptionRegisterError :
+  public Exception {
+  /// The missing key
+  std::string missingKey;
+public:
+  using Exception::Exception;
+  /// Sets the missing key
+  /// \param key The missing key
+  /// \return This exception
+  ///
+  /// ExceptionRegisterError can be used as a builder pattern:
+  /// `throw ExceptionRegisterError().setMissingKey(key);`
+  ///
+  /// the key can be retrieved with ExceptionRegisterError::getMissingKey()
+  ExceptionRegisterError& setMissingKey (std::string_view key) {
+    missingKey=key;
+    return *this;
+  }
+  /// Returns the missing key
+  const std::string& getMissingKey() const {
+    return missingKey;
+  }
+  template<typename T>
+  ExceptionRegisterError& operator<<(const T & x) {
+    *static_cast<Exception*>(this) <<x;
+    return *this;
+  }
+};
+
+/// General register.
+/// This class provide a generic implementation based on the content of the Register
+template<class Content>
+class RegisterBase :
+  public Register {
+
+public:
+/// auxiliary class
+  struct ContentAndFullPath {
+    Content content;
+    std::string fullPath;
+  };
+
+private:
+/// Main register map
+  std::map<std::string,std::unique_ptr<ContentAndFullPath>> m;
+/// Map of staged keys
+  std::map<std::string,std::unique_ptr<ContentAndFullPath>> staged_m;
+
+public:
+
+  struct ID {
+    ContentAndFullPath* ptr{nullptr};
+  };
+/// Register a new class.
+/// \param key The name of the directive to be used in the input file
+/// \param content The registered content
+/// \param ID A returned ID that can be used to remove the directive later
+  ID add(std::string key,const Content & content);
+
+/// Verify if a key is present in the register, accessing to registered images
+  bool check(const std::vector<void*> & images,const std::string & key) const;
+
+/// Verify if a key is present in the register, only considering the default image
+  bool check(const std::string & key) const;
+
+/// Return the content associated to a key in the register, accessing to registerd images
+  const Content & get(const std::vector<void*> & images,const std::string & key) const;
+
+/// Return the full path associated to a key in the register, accessing to registerd images
+  const std::string & getFullPath(const std::vector<void*> & images,const std::string & key) const;
+
+/// Return the content associated to a key in the register, only considering the default image
+  const Content & get(const std::string & key) const;
+
+/// Remove a registered keyword.
+/// Use the ID returned by add().
+  void remove(ID id);
+
+/// Get a list of keys
+/// Notice that these are the keys in the map, not the plumed keywords!
+/// Also notice that this list includes keys from all images, including the
+/// textual version of the image void*
+  std::vector<std::string> getKeys() const override;
+
+  ~RegisterBase() noexcept override;
+
+  /// complete registration
+  /// all staged keys will be enabled
+  /// Should be called after dlopen has been completed correctly.
+  void completeRegistration(void*handle) override;
+
+  void clearStaged() noexcept override;
+
+};
+
+template<class Content>
+typename RegisterBase<Content>::ID RegisterBase<Content>::add(std::string key,const Content & content) {
+
+  auto ptr=std::make_unique<ContentAndFullPath>(ContentAndFullPath{content,getRegisteringFullPath()});
+  ID id{ptr.get()};
+
+  // lock map for writing
+  std::unique_lock<std::shared_mutex> lock(mutex);
+
+  if(isDLRegistering()) {
+    plumed_assert(!staged_m.count(key)) << "cannot stage key twice with the same name "<< key<<"\n";
+    staged_m.insert({key, std::move(ptr)});
+  } else {
+    plumed_assert(!m.count(key)) << "cannot register key twice with the same name "<< key<<"\n";
+    m.insert({key, std::move(ptr)});
+  }
+  return id;
+}
+std::ostream & operator<<(std::ostream &log,const Register &reg);
+
+template<class Content>
+bool RegisterBase<Content>::check(const std::vector<void*> & images,const std::string & key) const {
+  // lock map for reading
+  std::shared_lock<std::shared_mutex> lock(mutex);
+  if(m.count(key)>0) {
+    return true;
+  }
+  for(auto image : images) {
+    std::string k=imageToString(image)+":"+key;
+    if(m.count(k)>0) {
+      return true;
+    }
+  }
+  return false;
+}
+
+template<class Content>
+bool RegisterBase<Content>::check(const std::string & key) const {
+  // lock map for reading
+  std::shared_lock<std::shared_mutex> lock(mutex);
+  return m.count(key)>0;
+}
+
+template<class Content>
+const Content & RegisterBase<Content>::get(const std::vector<void*> & images,const std::string & key) const {
+  // lock map for reading
+  std::shared_lock<std::shared_mutex> lock(mutex);
+  for(auto image = images.rbegin(); image != images.rend(); ++image) {
+    auto qualified_key=imageToString(*image) + ":" + key;
+    if(m.count(qualified_key)>0) {
+      return m.find(qualified_key)->second->content;
+    }
+  }
+  if (m.count(key) == 0 ) {
+    throw ExceptionRegisterError().setMissingKey(key);
+  }
+  return m.find(key)->second->content;
+}
+
+template<class Content>
+const std::string & RegisterBase<Content>::getFullPath(const std::vector<void*> & images,const std::string & key) const {
+  // lock map for reading
+  std::shared_lock<std::shared_mutex> lock(mutex);
+  for(auto image = images.rbegin(); image != images.rend(); ++image) {
+    auto qualified_key=imageToString(*image) + ":" + key;
+    if(m.count(qualified_key)>0) {
+      return m.find(qualified_key)->second->fullPath;
+    }
+  }
+  if (m.count(key) == 0 ) {
+    throw ExceptionRegisterError().setMissingKey(key);
+  }
+  return m.find(key)->second->fullPath;
+}
+
+template<class Content>
+const Content & RegisterBase<Content>::get(const std::string & key) const {
+  // lock map for reading
+  std::shared_lock<std::shared_mutex> lock(mutex);
+  if (m.count(key) == 0 ) {
+    throw ExceptionRegisterError().setMissingKey(key);
+  }
+  return m.find(key)->second->content;
+}
+
+template<class Content>
+void RegisterBase<Content>::remove(ID id) {
+  // lock map for writing
+  std::unique_lock<std::shared_mutex> lock(mutex);
+  if(id.ptr) {
+    for(auto p=m.begin(); p!=m.end(); ++p) {
+      if(p->second.get()==id.ptr) {
+        m.erase(p);
+        break;
+      }
+    }
+  }
+}
+
+template<class Content>
+std::vector<std::string> RegisterBase<Content>::getKeys() const {
+  // lock map for reading
+  std::shared_lock<std::shared_mutex> lock(mutex);
+  std::vector<std::string> s;
+  for(const auto & it : m) {
+    s.push_back(it.first);
+  }
+  std::sort(s.begin(),s.end());
+  return s;
+}
+
+template<class Content>
+RegisterBase<Content>::~RegisterBase() noexcept {
+  if(m.size()>0) {
+    std::string names="";
+    for(const auto & p : m) {
+      names+=p.first+" ";
+    }
+    std::cerr<<"WARNING: Directive "+ names +" has not been properly unregistered. This might lead to memory leak!!\n";
+  }
+}
+
+template<class Content>
+void RegisterBase<Content>::completeRegistration(void*handle) {
+  // lock map for writing
+  std::unique_lock<std::shared_mutex> lock(mutex);
+  for (auto iter = staged_m.begin(); iter != staged_m.end(); ) {
+    auto key = imageToString(handle) + ":" + iter->first;
+    plumed_assert(!m.count(key)) << "cannot register key twice with the same name "<< key<<"\n";
+    m[key] = std::move(iter->second);
+    // Since we've moved out the value, we can safely erase the element from the original map
+    // This also avoids invalidating our iterator since erase returns the next iterator
+    iter = staged_m.erase(iter);
+  }
+  plumed_assert(staged_m.empty());
+}
+
+template<class Content>
+void RegisterBase<Content>::clearStaged() noexcept {
+  // lock map for writing
+  std::unique_lock<std::shared_mutex> lock(mutex);
+  staged_m.clear();
+}
+}
+
+#endif

plumed/_lib/include/plumed/core/TargetDist.h

@@ -0,0 +1,48 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+   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_TargetDist_h
+#define __PLUMED_core_TargetDist_h
+
+#include <vector>
+#include <string>
+
+namespace PLMD {
+
+class Log;
+class PDB;
+class Value;
+
+class TargetDist {
+private:
+  std::vector<Value*> args;
+  std::vector<double> target;
+  Log &log;
+public:
+  explicit TargetDist(Log& mylog) : log(mylog) {}
+  void read( const PDB& pdb, const std::vector<Value*> & myargs );
+  void read( const std::vector<double>& targ, const std::vector<Value*> & ar );
+  double calculate( std::vector<double>& derivs );
+};
+
+}
+
+#endif