hillclimber 0.1.6__cp313-cp313-macosx_15_0_x86_64.whl

plumed/_lib/lib/plumed/patches/gromacs-2025.0.diff/src/gromacs/mdrunutility/mdmodulesnotifiers.h.preplumed

@@ -0,0 +1,429 @@
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright 2019- The GROMACS Authors
+ * and the project initiators Erik Lindahl, Berk Hess and David van der Spoel.
+ * Consult the AUTHORS/COPYING files and https://www.gromacs.org for details.
+ *
+ * GROMACS 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 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS 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 GROMACS; if not, see
+ * https://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at https://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out https://www.gromacs.org.
+ */
+/*! \libinternal \file
+ * \brief
+ * Declares gmx::MDModulesNotifiers.
+ *
+ * \author Christian Blau <blau@kth.se>
+ * \inlibraryapi
+ * \ingroup module_mdrunutility
+ */
+
+#ifndef GMX_MDRUNUTILITY_MDMODULESNOTIFIERS_H
+#define GMX_MDRUNUTILITY_MDMODULESNOTIFIERS_H
+
+#include <cstdint>
+
+#include <optional>
+#include <string>
+#include <vector>
+
+#include "gromacs/math/arrayrefwithpadding.h"
+#include "gromacs/math/matrix.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/mdrunutility/mdmodulesnotifier.h"
+#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/real.h"
+
+
+struct t_commrec;
+struct gmx_mtop_t;
+class WarningHandler;
+enum class PbcType : int;
+struct t_inputrec;
+struct gmx_multisim_t;
+
+namespace gmx
+{
+
+class KeyValueTreeObject;
+class KeyValueTreeObjectBuilder;
+class LocalAtomSetManager;
+class MDLogger;
+class IndexGroupsAndNames;
+class SeparatePmeRanksPermitted;
+struct MDModulesCheckpointReadingDataOnMain;
+struct MDModulesCheckpointReadingBroadcast;
+struct MDModulesWriteCheckpointData;
+enum class StartingBehavior;
+
+/*! \libinternal \brief Notification that atoms may have been redistributed
+ *
+ * This notification is emitted at the end of the DD (re)partitioning
+ * or without DD right after atoms have put into the box.
+ * The local atom sets are updated for the new atom order when this signal is emitted.
+ * The coordinates of atoms can be shifted by periodic vectors
+ * before the signal was emitted.
+ */
+struct MDModulesAtomsRedistributedSignal
+{
+    MDModulesAtomsRedistributedSignal(const matrix box, gmx::ArrayRef<const RVec> x) :
+        box_(createMatrix3x3FromLegacyMatrix(box)), x_(x)
+    {
+    }
+
+    //! The simulation unit cell
+    const Matrix3x3 box_;
+    //! List of local atom coordinates after partitioning
+    gmx::ArrayRef<const RVec> x_;
+};
+
+/*! \libinternal \brief Check if module outputs energy to a specific field.
+ *
+ * Ensures that energy is output for this module.
+ */
+struct MDModulesEnergyOutputToDensityFittingRequestChecker
+{
+    //! Trigger output to density fitting energy field
+    bool energyOutputToDensityFitting_ = false;
+};
+
+/*! \libinternal \brief Check if QMMM module outputs energy to a specific field.
+ *
+ * Ensures that energy is output for QMMM module.
+ */
+struct MDModulesEnergyOutputToQMMMRequestChecker
+{
+    //! Trigger output to QMMM energy field
+    bool energyOutputToQMMM_ = false;
+};
+
+/*! \libinternal \brief Check if NNPot module outputs energy to a specific field.
+ *
+ * Ensures that energy is output for NNPot module.
+ */
+struct MDModulesEnergyOutputToNNPotRequestChecker
+{
+    //! Trigger output to NNPot energy field
+    bool energyOutputToNNPot_ = false;
+};
+
+/*! \libinternal
+ * \brief Collect errors for the energy calculation frequency.
+ *
+ * Collect errors regarding energy calculation frequencies as strings that then
+ * may be used to issue errors.
+ *
+ * \note The mdp option "nstcalcenergy" is altered after reading the .mdp input
+ *       and only used in certain integrators, thus this class is to be used
+ *       only after all these operations are done.
+ */
+class EnergyCalculationFrequencyErrors
+{
+public:
+    //! Construct by setting the energy calculation frequency
+    EnergyCalculationFrequencyErrors(int64_t energyCalculationIntervalInSteps);
+    //! Return the number of steps of an energy calculation interval
+    std::int64_t energyCalculationIntervalInSteps() const;
+    //! Collect error messages
+    void addError(const std::string& errorMessage);
+    //! Return error messages
+    const std::vector<std::string>& errorMessages() const;
+
+private:
+    //! The frequency of energy calculations
+    const std::int64_t energyCalculationIntervalInSteps_;
+    //! The error messages
+    std::vector<std::string> errorMessages_;
+};
+
+/*! \libinternal \brief Provides the simulation time step in ps.
+ */
+struct SimulationTimeStep
+{
+    //! Time step (ps)
+    const double delta_t;
+};
+
+/*! \libinternal \brief Provides coordinates and simulation box.
+ */
+struct CoordinatesAndBoxPreprocessed
+{
+    ArrayRefWithPadding<RVec> coordinates_;
+    matrix                    box_;
+    PbcType                   pbc_;
+};
+
+/*! \libinternal \brief Mdrun input filename.
+ */
+struct MdRunInputFilename
+{
+    //! The name of the run input file (.tpr) as output by grompp
+    std::string mdRunFilename_;
+};
+
+/*! \libinternal \brief Energy trajectory output filename from Mdrun.
+ */
+struct EdrOutputFilename
+{
+    //! The name of energy output file
+    std::string edrOutputFilename_;
+};
+
+/*! \libinternal \brief Notification for QM program input filename
+ *  provided by user as command-line argument for grompp
+ */
+struct QMInputFileName
+{
+    //! Flag if QM Input File has been provided by user
+    bool hasQMInputFileName_ = false;
+    //! The name of the QM Input file (.inp)
+    std::string qmInputFileName_;
+};
+
+/*! \libinternal \brief Notification for the optianal plumed input filename
+ *  provided by user as command-line argument for mdrun
+ */
+struct PlumedInputFilename
+{
+    //! The name of plumed input file, empty by default
+    std::optional<std::string> plumedFilename_{};
+};
+
+/*! \libinternal \brief Provides the constant ensemble temperature
+ */
+struct EnsembleTemperature
+{
+    /*! \libinternal
+     * \brief Check whether the constant ensemble temperature is available.
+     * Then, store the value as optional.
+     */
+    explicit EnsembleTemperature(const t_inputrec& ir);
+    //! The constant ensemble temperature
+    std::optional<real> constantEnsembleTemperature_;
+};
+
+/*! \libinternal
+ * \brief Group of notifers to organize that MDModules
+ * can receive callbacks they subscribe to.
+ *
+ * MDModules use members of this struct to subscribe to notifications
+ * of particular events. When the event occurs, the callback provided
+ * by a particular MDModule will be passed a parameter of the
+ * particular type they are interested in.
+ *
+ * Typically, during the setup phase, modules subscribe to notifiers
+ * that interest them by passing callbacks that expect a single parameter
+ * that describes the event. These are stored for later use. See the
+ * sequence diagram that follows:
+   \msc
+wordwraparcs=true,
+hscale="2";
+
+modules [label = "mdModules:\nMDModules"],
+notifiers [label="notifiers\nMDModulesNotifiers"],
+notifier [label="exampleNotifier:\nBuildMDModulesNotifier\n<EventX, EventY>::type"],
+moduleA [label="moduleA"],
+moduleB [label="moduleB"],
+moduleC [label="moduleC"];
+
+modules box moduleC [label = "mdModules creates and owns moduleA, moduleB, and moduleC"];
+modules =>> notifiers [label="creates"];
+notifiers =>> notifier [label="creates"];
+notifier =>> notifiers [label="returns"];
+notifiers =>> modules [label="returns"];
+
+modules =>> moduleA [label="provides notifiers"];
+moduleA =>> moduleA [label="unpacks\nnotifiers.exampleNotifier"];
+moduleA =>> notifier [label="subscribes with\ncallback(EventX&)"];
+notifier =>> notifier [label="records subscription\nto EventX"];
+moduleA =>> notifier [label="subscribes with\ncallback(EventY&)"];
+notifier =>> notifier [label="records subscription\nto EventY"];
+moduleA =>> modules [label="returns"];
+
+modules =>> moduleB [label="provides notifiers"];
+moduleB =>> moduleB [label="unpacks\nnotifiers.exampleNotifier"];
+moduleA =>> notifier [label="subscribes with\ncallback(EventY&)"];
+notifier =>> notifier [label="records subscription\nto EventY"];
+moduleB =>> modules [label="returns"];
+
+modules =>> moduleC [label="provides notifiers"];
+moduleC =>> moduleC [label="unpacks and keeps\nnotifiers.exampleNotifier"];
+moduleC =>> modules [label="returns"];
+
+   \endmsc
+
+   * When the event occurs later on, the stored callbacks are used to
+   * allow the modules to react. See the following sequence diagram,
+   * which assumes that exampleNotifier was configured as in the
+   * previous sequence diagram.
+
+   \msc
+wordwraparcs=true,
+hscale="2";
+
+moduleC [label="moduleC"],
+notifier [label="exampleNotifier:\nBuildMDModulesNotifier\n<EventX, EventY>::type"],
+moduleA [label="moduleA"],
+moduleB [label="moduleB"];
+
+moduleC box moduleB [label = "Later, when ModuleC is doing work"];
+moduleC =>> moduleC [label="generates EventX"];
+moduleC =>> moduleC [label="generates EventY"];
+moduleC =>> notifier [label="calls notify(eventX)"];
+notifier =>> moduleA [label="calls callback(eventX)"];
+moduleA =>> moduleA [label="reacts to eventX"];
+moduleA =>> notifier [label="returns"];
+
+notifier =>> moduleC [label="returns"];
+moduleC =>> notifier [label="calls notify(eventY)"];
+notifier =>> moduleA [label="calls callback(eventY)"];
+moduleA =>> moduleA [label="reacts to eventY"];
+moduleA =>> notifier [label="returns"];
+notifier =>> moduleB [label="calls callback(eventY)"];
+moduleB =>> moduleB [label="reacts to eventY"];
+moduleB =>> notifier [label="returns"];
+notifier =>> moduleC [label="returns"];
+   \endmsc
+ *
+ * The template arguments to the members of this struct are the
+ * parameters passed to the callback functions, one type per
+ * callback. Arguments passed as pointers are always meant to be
+ * modified, but never meant to be stored (in line with the policy
+ * everywhere else).
+ *
+ */
+struct MDModulesNotifiers
+{
+    /*! \brief Pre-processing callback functions.
+     *
+     * \tparam CoordinatesAndBoxPreprocessed
+     *                              Allows modules to access coordinates,
+     *                              box and PBC during grompp
+     * \tparam MDLogger             Allows MdModule to use standard logging class for
+     *                              output of messages
+     * \tparam warninp*             Allows modules to make grompp warnings, notes and errors
+     * \tparam EnergyCalculationFrequencyErrors*
+     *                              Allows modules to check if they match their required calculation
+     *                              frequency and add their error message if needed to the
+     *                              collected error messages
+     * \tparam gmx_mtop_t*          Allows modules to modify the topology during pre-processing
+     * \tparam IndexGroupsAndNames  Provides modules with atom indices and their names
+     * \tparam KeyValueTreeObjectBuilder
+     *                              Enables writing of module internal data to .tpr files.
+     * \tparam QMInputFileName      Allows the QMMM module to know if the user has provided
+     *                              an external QM input file
+     * \tparam EnsembleTemperature  Provides modules with the constant ensemble temperature.
+     */
+    BuildMDModulesNotifier<const CoordinatesAndBoxPreprocessed&,
+                           const MDLogger&,
+                           WarningHandler*,
+                           EnergyCalculationFrequencyErrors*,
+                           gmx_mtop_t*,
+                           const IndexGroupsAndNames&,
+                           KeyValueTreeObjectBuilder,
+                           const QMInputFileName&,
+                           const EnsembleTemperature&>::type preProcessingNotifier_;
+
+    /*! \brief Handles subscribing and calling checkpointing callback functions.
+     *
+     * \tparam MDModulesCheckpointReadingDataOnMain
+     *                              Provides modules with their checkpointed data
+     *                              on the main node and checkpoint file version
+     * \tparam MDModulesCheckpointReadingBroadcast
+     *                              Provides modules with a communicator and the
+     *                              checkpoint file version to distribute their data
+     * \tparam MDModulesWriteCheckpointData
+     *                              Provides the modules with a key-value-tree
+     *                              builder to store their checkpoint data and
+     *                              the checkpoint file version
+     */
+    BuildMDModulesNotifier<MDModulesCheckpointReadingDataOnMain, MDModulesCheckpointReadingBroadcast, MDModulesWriteCheckpointData>::type
+            checkpointingNotifier_;
+
+    /*! \brief Handles subscribing and calling callbacks during simulation setup.
+     *
+     * \tparam KeyValueTreeObject&  Provides modules with the internal data they
+     *                              wrote to .tpr files
+     * \tparam LocalAtomSetManager* Enables modules to add atom indices to local atom sets
+     *                              to be managed
+     * \tparam StartingBehavio&     Provides modules with the starting behavior of the simulation
+     * \tparam MDLogger&            Allows MdModule to use standard logging class for messages
+     *                              output
+     * \tparam gmx_mtop_t&          Provides the topology of the system to the modules
+     * \tparam MDModulesEnergyOutputToDensityFittingRequestChecker*
+     *                              Enables modules to report if they want to write their
+     *                              energy output to the density fitting field in the energy files
+     * \tparam MDModulesEnergyOutputToQMMMRequestChecker*
+     *                              Enables QMMM module to report if it wants to write its energy
+     *                              output to the "Quantum En." field in the energy files
+     * \tparam MDModulesEnergyOutputToNNPotRequestChecker*
+     *                              Enables NNPot module to report if it wants to write its energy
+     *                              output to the "NN Potential" field in the energy files
+     * \tparam SeparatePmeRanksPermitted*
+     *                              Enables modules to report if they want to disable dedicated
+     *                              PME ranks
+     * \tparam PbcType&             Provides modules with the periodic boundary condition type
+     *                              that is used during the simulation
+     * \tparam SimulationTimeStep&  Provides modules with the simulation time-step that allows
+     *                              them to interconvert between step and time information
+     * \tparam EnsembleTemperature& Provides modules with the (eventual) constant ensemble
+     *                              temperature
+     * \tparam t_commrec&           Provides a communicator to the modules during simulation
+     *                              setup
+     *
+     * \tparam gmx_multisim_t&      Shares the multisim struct with the modules
+     *                              Subscribing to this notifier will sync checkpointing
+     *                              of simulations and will cause simulations to stop,
+     *                              due to signals or exceededing maximum time, at the same step.
+     *                              This ensures that the output and checkpoints of ensemble
+     *                              simulations are consistent and that ensemble simulations
+     *                              can be continued.
+     * \tparam MdRunInputFilename&  Allows modules to know .tpr filename during mdrun
+     * \tparam EdrOutputFilename&   Allows modules to know .edr filename during mdrun
+     * \tparam PlumedInputFilename& Allows modules to know the optional .dat filename to be read by plumed
+     */
+    BuildMDModulesNotifier<const KeyValueTreeObject&,
+                           LocalAtomSetManager*,
+                           const StartingBehavior&,
+                           const MDLogger&,
+                           const gmx_mtop_t&,
+                           const MDModulesAtomsRedistributedSignal,
+                           MDModulesEnergyOutputToDensityFittingRequestChecker*,
+                           MDModulesEnergyOutputToQMMMRequestChecker*,
+                           MDModulesEnergyOutputToNNPotRequestChecker*,
+                           SeparatePmeRanksPermitted*,
+                           const PbcType&,
+                           const SimulationTimeStep&,
+                           const EnsembleTemperature&,
+                           const t_commrec&,
+                           const gmx_multisim_t*,
+                           const MdRunInputFilename&,
+                           const EdrOutputFilename&,
+                           const PlumedInputFilename&>::type simulationSetupNotifier_;
+};
+
+} // namespace gmx
+
+#endif

plumed/_lib/lib/plumed/patches/namd-2.12.config

@@ -0,0 +1,30 @@
+
+
+function plumed_preliminary_test(){
+# check if the README.txt contains the word NAMD
+  grep -q NAMD README.txt 1>/dev/null 2>/dev/null && test -f */Make.config
+}
+
+function plumed_patch_info(){
+cat << EOF
+
+To enable PLUMED in a NAMD simulation one should add the following lines in the NAMD configuration file
+(often named as xxx.namd or xxx.conf) and run the plumed-patched version of NAMD with it:
+
+\verbatim
+plumed on
+plumedfile plumed.dat
+\endverbatim
+
+The first line tells NAMD to run with PLUMED and the second line specifies the PLUMED input file.
+
+\bug NAMD does not currently take into account virial contributions
+from PLUMED. Please use constant volume simulations only.
+
+For more information on NAMD you should visit http://www.ks.uiuc.edu/Research/namd/
+
+EOF
+}
+
+plumed_ignore_mpi=yes
+