hillclimber 0.1.6__cp314-cp314t-manylinux_2_27_aarch64.manylinux_2_28_aarch64.whl

plumed/_lib/include/plumed/molfile/vmdplugin.h

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+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+University of Illinois Open Source License
+Copyright 2003 Theoretical and Computational Biophysics Group, 
+All rights reserved.
+
+Developed by:		Theoretical and Computational Biophysics Group
+			University of Illinois at Urbana-Champaign
+			http://www.ks.uiuc.edu/
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of
+this software and associated documentation files (the Software), to deal with 
+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:
+
+Redistributions of source code must retain the above copyright notice, 
+this list of conditions and the following disclaimers.
+
+Redistributions in binary form must reproduce the above copyright notice, 
+this list of conditions and the following disclaimers in the documentation 
+and/or other materials provided with the distribution.
+
+Neither the names of Theoretical and Computational Biophysics Group, 
+University of Illinois at Urbana-Champaign, nor the names of its contributors 
+may be used to endorse or promote products derived from this Software without 
+specific prior written permission.
+
+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 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 WITH THE SOFTWARE.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_molfile_vmdplugin_h
+#define __PLUMED_molfile_vmdplugin_h
+namespace PLMD{
+namespace molfile{
+/***************************************************************************
+ *cr
+ *cr            (C) Copyright 1995-2006 The Board of Trustees of the
+ *cr                        University of Illinois
+ *cr                         All Rights Reserved
+ *cr
+ ***************************************************************************/
+
+/***************************************************************************
+ * RCS INFORMATION:
+ *
+ *      $RCSfile: vmdplugin.h,v $
+ *      $Author: johns $       $Locker:  $             $State: Exp $
+ *      $Revision: 1.35 $       $Date: 2020/10/16 07:50:56 $
+ *
+ ***************************************************************************/
+
+/** @file
+ * This header must be included by every VMD plugin library.  It defines the
+ * API for every plugin so that VMD can organize the plugins it finds.  
+ */
+
+#ifndef VMD_PLUGIN_H
+#define VMD_PLUGIN_H
+
+
+/* 
+ * Preprocessor tricks to make it easier for us to redefine the names of
+ * functions when building static plugins.
+ */
+#if !defined(VMDPLUGIN)
+/** 
+  * macro defining VMDPLUGIN if it hasn't already been set to the name of 
+  * a static plugin that is being compiled.  This is the catch-all case.
+  */
+#define VMDPLUGIN vmdplugin
+#endif
+/** concatenation macro, joins args x and y together as a single string */
+#define xcat(x, y) cat(x, y)
+/** concatenation macro, joins args x and y together as a single string */
+#define cat(x, y) x ## y 
+
+/*
+ *  macros to correctly define plugin function names depending on whether 
+ *  the plugin is being compiled for static linkage or dynamic loading. 
+ *  When compiled for static linkage, each plugin needs to have unique
+ *  function names for all of its entry points.  When compiled for dynamic
+ *  loading, the plugins must name their entry points consistently so that
+ *  the plugin loading mechanism can find the register, register_tcl, init,
+ *  and fini routines via dlopen() or similar operating system interfaces.
+ */
+/*@{*/
+/** Macro names entry points correctly for static linkage or dynamic loading */
+#define VMDPLUGIN_register     xcat(VMDPLUGIN, _register)
+#define VMDPLUGIN_register_tcl xcat(VMDPLUGIN, _register_tcl)
+#define VMDPLUGIN_init         xcat(VMDPLUGIN, _init)
+#define VMDPLUGIN_fini         xcat(VMDPLUGIN, _fini)
+/*@}*/
+
+
+/** Detect compilations targeting Windows x86 and x64 platforms */
+#if (defined(WIN32) || defined(WIN64) || defined(_MSC_VER)) 
+#define WIN32_LEAN_AND_MEAN
+}
+}
+#include <windows.h>
+namespace PLMD{
+namespace molfile{
+
+
+#if !defined(STATIC_PLUGIN)
+#if defined(VMDPLUGIN_EXPORTS)
+/** 
+ *  Only define DllMain for plugins, not in VMD or in statically linked plugins
+ *  VMDPLUGIN_EXPORTS is only defined when compiling dynamically loaded plugins
+ */
+BOOL APIENTRY DllMain( HANDLE hModule,
+                       DWORD ul_reason_for_call,
+                       LPVOID lpReserved
+                     )
+{
+  return TRUE;
+}
+
+#define VMDPLUGIN_API __declspec(dllexport)
+#else
+#define VMDPLUGIN_API __declspec(dllimport)
+#endif /* VMDPLUGIN_EXPORTS */
+#else  /* ! STATIC_PLUGIN */
+#define VMDPLUGIN_API
+#endif /* ! STATIC_PLUGIN */
+#else
+/** If we're not compiling on Windows, then this macro is defined empty */
+#define VMDPLUGIN_API 
+#endif
+
+//TONI  Plumed mod: never "extern", C++ namespace
+/** define plugin linkage correctly for both C and C++ based plugins */
+#define VMDPLUGIN_EXTERN VMDPLUGIN_API
+
+/* 
+ * Plugin API functions start here 
+ */
+
+
+/** 
+ * Init routine: called the first time the library is loaded by the 
+ * application and before any other API functions are referenced.
+ * Return 0 on success.
+ */
+VMDPLUGIN_EXTERN int VMDPLUGIN_init(void);
+
+/**
+ * Macro for creating a struct header used in all plugin structures.
+ * 
+ * This header should be placed at the top of every plugin API definition 
+ * so that it can be treated as a subtype of the base plugin type.
+ *
+ * abiversion: Defines the ABI for the base plugin type (not for other plugins)
+ * type: A string descriptor of the plugin type.
+ * name: A name for the plugin.
+ * author: A string identifier, possibly including newlines.
+ * Major and minor version.  
+ * is_reentrant: Whether this library can be run concurrently with itself.
+ */
+#define vmdplugin_HEAD \
+  int abiversion; \
+  const char *type; \
+  const char *name; \
+  const char *prettyname; \
+  const char *author; \
+  int majorv; \
+  int minorv; \
+  int is_reentrant; 
+
+/** 
+  * Typedef for generic plugin header, individual plugins can
+  * make their own structures as long as the header info remains 
+  * the same as the generic plugin header, most easily done by 
+  * using the vmdplugin_HEAD macro.
+  */
+typedef struct {
+  vmdplugin_HEAD
+} vmdplugin_t;
+
+/**
+ * Use this macro to initialize the abiversion member of each plugin
+ */
+#define vmdplugin_ABIVERSION  18
+
+/*@{*/
+/** Use this macro to indicate a plugin's thread-safety at registration time */
+#define VMDPLUGIN_THREADUNSAFE 0
+#define VMDPLUGIN_THREADSAFE   1
+/*@}*/
+
+/*@{*/
+/** Error return code for use in the plugin registration and init functions */
+#define VMDPLUGIN_SUCCESS      0
+#define VMDPLUGIN_ERROR       -1
+/*@}*/
+
+/** 
+ * Function pointer typedef for register callback functions
+ */
+typedef int (*vmdplugin_register_cb)(void *, vmdplugin_t *);
+
+/**
+ * Allow the library to register plugins with the application.
+ * The callback should be called using the passed-in void pointer, which
+ * should not be interpreted in any way by the library.  Each vmdplugin_t
+ * pointer passed to the application should point to statically-allocated
+ * or heap-allocated memory and should never be later modified by the plugin.
+ * Applications must be permitted to retain only a copy of the the plugin
+ * pointer, without making any deep copy of the items in the struct.
+ */
+VMDPLUGIN_EXTERN int VMDPLUGIN_register(void *, vmdplugin_register_cb);
+
+/**
+ * Allow the library to register Tcl extensions.  
+ * This API is optional; if found by dlopen, it will be called after first
+ * calling init and register.  
+ */
+VMDPLUGIN_EXTERN int VMDPLUGIN_register_tcl(void *, void *tcl_interp, 
+    vmdplugin_register_cb);
+
+/**
+ * The Fini method is called when the application will no longer use 
+ * any plugins in the library.  
+ */
+VMDPLUGIN_EXTERN int VMDPLUGIN_fini(void);
+
+#endif   /* VMD_PLUGIN_H */
+}
+}
+#endif

plumed/_lib/include/plumed/multicolvar/MultiColvarShortcuts.h

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+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+   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_multicolvar_MultiColvarShortcuts_h
+#define __PLUMED_multicolvar_MultiColvarShortcuts_h
+
+#include <vector>
+#include "../core/ActionShortcut.h"
+
+namespace PLMD {
+
+namespace multicolvar {
+
+class MultiColvarShortcuts {
+public:
+  static void shortcutKeywords( Keywords& keys );
+  static void parseAtomList( const std::string& key, std::vector<std::string>& atoms, ActionShortcut* action );
+  static void readShortcutKeywords( std::map<std::string,std::string>& keymap, ActionShortcut* action );
+  static void expandFunctions( const std::string& labout, const std::string& argin, const std::string& weights,
+                               const std::map<std::string,std::string>& keymap, ActionShortcut* action );
+  static void expandFunctions( const std::string& labout, const std::string& argin, const std::string& weights, ActionShortcut* action );
+};
+
+}
+}
+
+#endif

plumed/_lib/include/plumed/opes/ExpansionCVs.h

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+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+   Copyright (c) 2020-2021 of Michele Invernizzi.
+
+   This file is part of the OPES plumed module.
+
+   The OPES plumed module 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.
+
+   The OPES plumed module 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_opes_ExpansionCVs_h
+#define __PLUMED_opes_ExpansionCVs_h
+
+#include "../core/ActionWithValue.h"
+#include "../core/ActionWithArguments.h"
+
+namespace PLMD {
+namespace opes {
+
+/*
+\ingroup INHERIT
+This is the abstract base class to use for implementing expansion CVs (ECVs).
+ECVs should be used together with the OPESexpanded action.
+They take as argument regular CVs, and output them as components without modification.
+*/
+
+class ExpansionCVs:
+  public ActionWithValue,
+  public ActionWithArguments {
+protected:
+  bool isReady_; //true only after initECVs
+  double kbt_;
+  unsigned totNumECVs_;
+
+//methods useful for linear expansions
+  std::vector<double> getSteps(double,double,const unsigned,const std::string&,const bool,const double) const;
+  unsigned estimateNumSteps(const double,const double,const std::vector<double>&,const std::string&) const;
+
+public:
+  explicit ExpansionCVs(const ActionOptions&);
+  virtual ~ExpansionCVs() {};
+  std::string getOutputComponentDescription( const std::string& cname, const Keywords& keys ) const override ;
+  void apply() override;
+  void calculate() override;
+  static void registerKeywords(Keywords&);
+  inline unsigned getNumberOfDerivatives() override {
+    return 1;
+  };
+
+  inline double getKbT() const {
+    return kbt_;
+  };
+  inline unsigned getTotNumECVs() const {
+    plumed_massert(isReady_,"cannot ask for totNumECVs before ECV isReady");
+    return totNumECVs_;
+  };
+  virtual std::vector< std::vector<unsigned> > getIndex_k() const; //might need to override this
+
+  virtual void calculateECVs(const double *) = 0;
+  virtual const double * getPntrToECVs(unsigned) = 0;
+  virtual const double * getPntrToDerECVs(unsigned) = 0;
+  virtual std::vector<std::string> getLambdas() const = 0;
+  virtual void initECVs_observ(const std::vector<double>&,const unsigned,const unsigned) = 0; //arg: all the observed CVs, the total numer of CVs, the first CV index referring to this ECV
+  virtual void initECVs_restart(const std::vector<std::string>&) = 0; //arg: the lambdas read from DeltaF_name relative to this ECV
+};
+
+}
+}
+
+#endif
+

plumed/_lib/include/plumed/sasa/Sasa.h

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+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+Copyright (c) 2021, Andrea Arsiccio
+
+This software is provided 'as-is', without any express or implied
+warranty. In no event will the authors be held liable for any damages
+arising from the use of this software.
+
+Permission is granted to anyone to use this software for any purpose,
+including commercial applications, and to alter it and redistribute it
+freely, subject to the following restrictions:
+
+1. The origin of this software must not be misrepresented; you must not
+   claim that you wrote the original software. If you use this software
+   in a product, an acknowledgment in the product documentation would be
+   appreciated but is not required.
+2. Altered source versions must be plainly marked as such, and must not be
+   misrepresented as being the original software.
+3. This notice may not be removed or altered from any source distribution.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_sasa_Sasa_h
+#define __PLUMED_sasa_Sasa_h
+#include "../core/Colvar.h"
+#include "../config/Config.h"
+
+namespace PLMD {
+namespace sasa {
+// Ideally core/Colvar.h should be moved to this directory and Colvar should stay in namespace PLMD::Sasa
+// With this trick, PLMD::Colvar is visible as PLMD::Sasa::Colvar
+using PLMD::Colvar;
+}
+}
+#endif