hillclimber 0.1.5__cp313-cp313-musllinux_1_2_aarch64.whl

plumed/_lib/lib/plumed/src/config/config.txt

@@ -0,0 +1,179 @@
+# version strings
+# syntax: version short/long/git number
+version short 2.11
+version long 2.11.0-dev
+version git Unknown
+
+# python executable
+# syntax: python_bin executable
+# empty string means that python has not been configured
+python_bin 
+
+# command to lauch mpi processes
+# syntax: mpiexec command
+# empty string means that mpiexec was not chosen at configure time
+mpiexec 
+
+# list of 'has' options
+# syntax: has name on/of
+# if option xx is on then plumed has beeen compiled with -D__PLUMED_HAS_XX
+has arrayfire off
+has arrayfire_cuda off
+has arrayfire_ocl off
+has asmjit off
+has boost_graph off
+has boost_serialization off
+has cregex on
+has dladdr on
+has dlopen on
+has execinfo off
+has external_blas off
+has external_lapack off
+has external_molfile_plugins off
+has fftw off
+has gsl off
+has libmetatomic off
+has libtorch off
+has molfile_plugins on
+has mpi off
+has openacc off
+has python off
+has rtld_default on
+has subprocess on
+has zlib on
+
+# other defines
+# syntax: define name=value
+define HAVE_INTTYPES_H=1
+define HAVE_MEMORY_H=1
+define HAVE_STDINT_H=1
+define HAVE_STDLIB_H=1
+define HAVE_STRINGS_H=1
+define HAVE_STRING_H=1
+define HAVE_SYS_STAT_H=1
+define HAVE_SYS_TYPES_H=1
+define HAVE_UNISTD_H=1
+define NDEBUG=1
+define PACKAGE_BUGREPORT=""
+define PACKAGE_NAME="PLUMED"
+define PACKAGE_STRING="PLUMED 2"
+define PACKAGE_TARNAME="plumed"
+define PACKAGE_URL=""
+define PACKAGE_VERSION="2"
+define STDC_HEADERS=1
+define _REENTRANT=1
+define __PLUMED_CXX17_FILESYSTEM=1
+define __PLUMED_PROGRAM_NAME="plumed"
+define __PLUMED_SOEXT="so"
+define __PLUMED_WRAPPER_LIBCXX11=1
+
+# list of modules
+# syntax: module name on/off (default-on/default-off/always)
+module adjmat on (default-off)
+module annfunc on (default-off)
+module asmjit on (always)
+module bias on (default-on)
+module blas on (always)
+module cltools on (default-on)
+module clusters on (default-off)
+module colvar on (default-on)
+module contour on (default-off)
+module core on (always)
+module crystdistrib on (default-off)
+module dimred on (default-off)
+module drr on (default-off)
+module eds on (default-off)
+module envsim on (default-off)
+module fisst on (default-off)
+module fourier on (default-off)
+module function on (default-on)
+module funnel on (default-off)
+module generic on (default-on)
+module gridtools on (default-on)
+module isdb on (default-on)
+module landmarks on (default-off)
+module lapack on (always)
+module lepton on (always)
+module liquid_crystal on (default-on)
+module logmfd on (default-off)
+module mapping on (default-off)
+module matrixtools on (default-on)
+module maze on (default-off)
+module membranefusion on (default-off)
+module metatomic on (default-off)
+module molfile on (default-on)
+module multicolvar on (default-on)
+module opes on (default-off)
+module pamm on (default-off)
+module piv on (default-off)
+module pytorch on (default-off)
+module refdist on (default-on)
+module s2cm on (default-off)
+module sasa on (default-off)
+module secondarystructure on (default-on)
+module setup on (default-on)
+module sizeshape on (default-off)
+module small_vector on (always)
+module sprint on (default-off)
+module symfunc on (default-off)
+module tools on (always)
+module valtools on (always)
+module vatom on (default-on)
+module ves on (default-off)
+module volumes on (default-off)
+module wham on (default-off)
+module xdrfile on (default-on)
+
+# Makefile.conf file
+# syntax: makefile_conf followed by a single space followed by a line from makefile_conf
+makefile_conf CC=gcc
+makefile_conf FC=gfortran
+makefile_conf LDF90=gfortran
+makefile_conf CFLAGS=-g -O2 -fPIC
+makefile_conf CXX=g++
+makefile_conf CXXFLAGS=-Wno-error -fPIC -Wall -pedantic -Wno-unknown-pragmas -std=c++17 -fno-gnu-unique -fopenmp
+makefile_conf CXXFLAGS_NOOPENMP=-Wno-error -fPIC -Wall -pedantic -Wno-unknown-pragmas -std=c++17 -fno-gnu-unique
+makefile_conf CPPFLAGS= -DPACKAGE_NAME=\"PLUMED\" -DPACKAGE_TARNAME=\"plumed\" -DPACKAGE_VERSION=\"2\" -DPACKAGE_STRING=\"PLUMED\ 2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -D__PLUMED_WRAPPER_LIBCXX11=1 -D__PLUMED_CXX17_FILESYSTEM=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_DLADDR=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_ZLIB=1 -DNDEBUG=1 -D_REENTRANT=1 -D__PLUMED_PROGRAM_NAME=\"plumed\" -D__PLUMED_SOEXT=\"so\"
+makefile_conf LDFLAGS=
+makefile_conf DYNAMIC_LIBS= -lstdc++ -lz -ldl  -Wl,-rpath,$ORIGIN/../lib -rdynamic -Wl,-Bsymbolic -fopenmp
+makefile_conf LIBS=-ldl 
+makefile_conf SOEXT=so
+makefile_conf # LD is used only to link the plumed executable, so should be equivalent to the C++ compiler
+makefile_conf LD=g++ -Wno-error -fPIC -Wall -pedantic -Wno-unknown-pragmas -std=c++17 -fno-gnu-unique
+makefile_conf LDSHARED=g++ -shared
+makefile_conf LD_MAIN_RUNPATH=
+makefile_conf GCCDEP=g++
+makefile_conf disable_dependency_tracking=yes
+makefile_conf prefix=/project/src/plumed/_lib
+makefile_conf # use this variable to double check that prefix is not changed after configure
+makefile_conf # (new in v2.5)
+makefile_conf prefix_double_check=/project/src/plumed/_lib
+makefile_conf program_name=plumed
+makefile_conf program_transform_name=s,x,x,
+makefile_conf program_can_run_mpi=
+makefile_conf program_can_run=yes
+makefile_conf make_pdfdoc=no
+makefile_conf make_doc=no
+makefile_conf PACKAGE_TARNAME=plumed
+makefile_conf LD_RO=/usr/lib/gcc/aarch64-alpine-linux-musl/14.2.0/../../../../aarch64-alpine-linux-musl/bin/ld -r -o
+makefile_conf AR_CR=/usr/lib/gcc/aarch64-alpine-linux-musl/14.2.0/../../../../aarch64-alpine-linux-musl/bin/ar cr
+makefile_conf exec_prefix=${prefix}
+makefile_conf bindir=${exec_prefix}/bin
+makefile_conf libdir=${exec_prefix}/lib
+makefile_conf includedir=${prefix}/include
+makefile_conf datarootdir=${prefix}/share
+makefile_conf datadir=${datarootdir}
+makefile_conf docdir=${datarootdir}/doc/${PACKAGE_TARNAME}
+makefile_conf htmldir=${docdir}
+makefile_conf python_bin=
+makefile_conf plumed_found_cython=
+makefile_conf canPyCV=
+makefile_conf pybind11_cflags=
+makefile_conf python_cf_embedded=
+makefile_conf python_ld_embedded=
+makefile_conf mpiexec=
+makefile_conf make_static_archive=yes
+makefile_conf use_absolute_soname=no
+makefile_conf use_loader_path=no
+makefile_conf use_debug_glibcxx=no
+makefile_conf BASH_COMPLETION_DIR=

plumed/_lib/lib/plumed/src/lib/Plumed.cmake

@@ -0,0 +1,8 @@
+set(PLUMED_RUNTIME_LOAD  "/project/src/plumed/_lib/lib/libplumedWrapper.a" -ldl  )
+set(PLUMED_STATIC_LOAD  "/project/src/plumed/_lib/lib/libplumed.a" -ldl  -lstdc++ -lz -ldl  -Wl,-rpath,RIGIN/../lib -rdynamic -Wl,-Bsymbolic -fopenmp )
+set(PLUMED_SHARED_LOAD  "/project/src/plumed/_lib/lib/libplumed.so" -ldl  )
+set(PLUMED_RUNTIME_DEPENDENCIES )
+set(PLUMED_STATIC_DEPENDENCIES  "/project/src/plumed/_lib/lib/libplumed.a")
+set(PLUMED_SHARED_DEPENDENCIES  "/project/src/plumed/_lib/lib/libplumed.so")
+set(PLUMED_FORTRAN  "/project/src/plumed/_lib/lib/plumed/fortran/plumed.f90")
+set(PLUMED_FORTRAN08  "/project/src/plumed/_lib/lib/plumed/fortran/plumed_f08.f90")

plumed/_lib/lib/plumed/src/lib/Plumed.cmake.runtime

@@ -0,0 +1,5 @@
+# PLUMED: runtime installation
+set(PLUMED_LOAD  "/project/src/plumed/_lib/lib/libplumedWrapper.a" -ldl  )
+set(PLUMED_DEPENDENCIES )
+set(PLUMED_FORTRAN  "/project/src/plumed/_lib/lib/plumed/fortran/plumed.f90")
+set(PLUMED_FORTRAN08  "/project/src/plumed/_lib/lib/plumed/fortran/plumed_f08.f90")

plumed/_lib/lib/plumed/src/lib/Plumed.cmake.shared

@@ -0,0 +1,5 @@
+# PLUMED: shared installation
+set(PLUMED_LOAD  "/project/src/plumed/_lib/lib/libplumed.so" -ldl  )
+set(PLUMED_DEPENDENCIES  "/project/src/plumed/_lib/lib/libplumed.so")
+set(PLUMED_FORTRAN  "/project/src/plumed/_lib/lib/plumed/fortran/plumed.f90")
+set(PLUMED_FORTRAN08  "/project/src/plumed/_lib/lib/plumed/fortran/plumed_f08.f90")

plumed/_lib/lib/plumed/src/lib/Plumed.cmake.static

@@ -0,0 +1,5 @@
+# PLUMED: static installation
+set(PLUMED_LOAD  "/project/src/plumed/_lib/lib/libplumed.a" -ldl  -lstdc++ -lz -ldl  -Wl,-rpath,RIGIN/../lib -rdynamic -Wl,-Bsymbolic -fopenmp )
+set(PLUMED_DEPENDENCIES  "/project/src/plumed/_lib/lib/libplumed.a")
+set(PLUMED_FORTRAN  "/project/src/plumed/_lib/lib/plumed/fortran/plumed.f90")
+set(PLUMED_FORTRAN08  "/project/src/plumed/_lib/lib/plumed/fortran/plumed_f08.f90")

plumed/_lib/lib/plumed/src/lib/Plumed.inc

@@ -0,0 +1,8 @@
+PLUMED_RUNTIME_LOAD= "/project/src/plumed/_lib/lib/libplumedWrapper.a" -ldl  
+PLUMED_STATIC_LOAD= "/project/src/plumed/_lib/lib/libplumed.a" -ldl  -lstdc++ -lz -ldl  -Wl,-rpath,RIGIN/../lib -rdynamic -Wl,-Bsymbolic -fopenmp 
+PLUMED_SHARED_LOAD= "/project/src/plumed/_lib/lib/libplumed.so" -ldl  
+PLUMED_RUNTIME_DEPENDENCIES=
+PLUMED_STATIC_DEPENDENCIES= "/project/src/plumed/_lib/lib/libplumed.a"
+PLUMED_SHARED_DEPENDENCIES= "/project/src/plumed/_lib/lib/libplumed.so"
+PLUMED_FORTRAN= "/project/src/plumed/_lib/lib/plumed/fortran/plumed.f90"
+PLUMED_FORTRAN08= "/project/src/plumed/_lib/lib/plumed/fortran/plumed_f08.f90"

plumed/_lib/lib/plumed/src/lib/Plumed.inc.runtime

@@ -0,0 +1,5 @@
+# PLUMED: runtime installation
+PLUMED_LOAD= "/project/src/plumed/_lib/lib/libplumedWrapper.a" -ldl  
+PLUMED_DEPENDENCIES=
+PLUMED_FORTRAN= "/project/src/plumed/_lib/lib/plumed/fortran/plumed.f90"
+PLUMED_FORTRAN08= "/project/src/plumed/_lib/lib/plumed/fortran/plumed_f08.f90"

plumed/_lib/lib/plumed/src/lib/Plumed.inc.shared

@@ -0,0 +1,5 @@
+# PLUMED: shared installation
+PLUMED_LOAD= "/project/src/plumed/_lib/lib/libplumed.so" -ldl  
+PLUMED_DEPENDENCIES= "/project/src/plumed/_lib/lib/libplumed.so"
+PLUMED_FORTRAN= "/project/src/plumed/_lib/lib/plumed/fortran/plumed.f90"
+PLUMED_FORTRAN08= "/project/src/plumed/_lib/lib/plumed/fortran/plumed_f08.f90"

plumed/_lib/lib/plumed/src/lib/Plumed.inc.static

@@ -0,0 +1,5 @@
+# PLUMED: static installation
+PLUMED_LOAD= "/project/src/plumed/_lib/lib/libplumed.a" -ldl  -lstdc++ -lz -ldl  -Wl,-rpath,RIGIN/../lib -rdynamic -Wl,-Bsymbolic -fopenmp 
+PLUMED_DEPENDENCIES= "/project/src/plumed/_lib/lib/libplumed.a"
+PLUMED_FORTRAN= "/project/src/plumed/_lib/lib/plumed/fortran/plumed.f90"
+PLUMED_FORTRAN08= "/project/src/plumed/_lib/lib/plumed/fortran/plumed_f08.f90"

plumed/_lib/lib/plumed/vim/scripts.vim

@@ -0,0 +1,6 @@
+if did_filetype()	" filetype already set..
+ finish		" ..don't do these checks
+endif
+if getline(1) =~ '^#! FIELDS .*$' || getline(1) =~ '^#! SET .*$'
+  setfiletype plumedf
+endif

plumedCommunications.pyi

@@ -0,0 +1,431 @@
+"""Type stubs for plumedCommunications module.
+
+This module is a pybind11 C++ extension that provides Python bindings
+for PLUMED's PythonCVInterface and PythonFunction classes.
+
+See: https://joss.theoj.org/papers/10.21105/joss.01773
+"""
+
+from typing import Any
+
+import numpy as np
+import numpy.typing as npt
+
+class defaults:
+    """Default definitions for PLUMED components."""
+
+    COMPONENT: dict[str, Any]
+    """Default component settings with derivative=True and period=None."""
+
+    COMPONENT_NODEV: dict[str, Any]
+    """Component settings with derivative=False and period=None."""
+
+class Pbc:
+    """Interface to PLUMED periodic boundary conditions."""
+
+    def apply(self, deltas: npt.NDArray[np.float64]) -> npt.NDArray[np.float64]:
+        """Apply PBC to a set of positions or distance vectors.
+
+        Parameters
+        ----------
+        deltas : np.ndarray
+            Array of shape (n, 3) containing distance vectors.
+
+        Returns
+        -------
+        np.ndarray
+            The input array with PBC applied (modified in-place).
+        """
+        ...
+
+    def getBox(self) -> npt.NDArray[np.float64]:
+        """Get the simulation box vectors.
+
+        Returns
+        -------
+        np.ndarray
+            Array of shape (3, 3) with the box vectors.
+        """
+        ...
+
+    def getInvBox(self) -> npt.NDArray[np.float64]:
+        """Get the inverted box vectors.
+
+        Returns
+        -------
+        np.ndarray
+            Array of shape (3, 3) with the inverted box vectors.
+        """
+        ...
+
+class NeighborList:
+    """Interface to PLUMED neighbor list."""
+
+    @property
+    def size(self) -> int:
+        """The number of atom pairs in the neighbor list."""
+        ...
+
+    def __len__(self) -> int:
+        """Return the number of atom pairs."""
+        ...
+
+    def getClosePairs(self) -> npt.NDArray[np.uint64]:
+        """Get the list of close atom pairs.
+
+        Returns
+        -------
+        np.ndarray
+            Array of shape (n_pairs, 2) with atom pair indices.
+        """
+        ...
+
+class PythonCVInterface:
+    """Interface for defining collective variables in Python.
+
+    This class provides access to atomic data and simulation information
+    when implementing custom collective variables via PYCVINTERFACE.
+    """
+
+    data: dict[str, Any]
+    """Persistent dictionary that survives across simulation steps."""
+
+    @property
+    def label(self) -> str:
+        """The label of this action."""
+        ...
+
+    @property
+    def nat(self) -> int:
+        """The number of atoms requested by this action."""
+        ...
+
+    def getStep(self) -> int:
+        """Get the current simulation step.
+
+        Returns
+        -------
+        int
+            The current step number.
+        """
+        ...
+
+    def getTime(self) -> float:
+        """Get the current simulation time.
+
+        Returns
+        -------
+        float
+            The current time.
+        """
+        ...
+
+    def getTimeStep(self) -> float:
+        """Get the simulation timestep.
+
+        Returns
+        -------
+        float
+            The timestep.
+        """
+        ...
+
+    def isRestart(self) -> bool:
+        """Check if this is a restart simulation.
+
+        Returns
+        -------
+        bool
+            True if restarting from a previous simulation.
+        """
+        ...
+
+    def isExchangeStep(self) -> bool:
+        """Check if this is a replica exchange step.
+
+        Returns
+        -------
+        bool
+            True if on an exchange step.
+        """
+        ...
+
+    def log(self, s: object) -> None:
+        """Write a message to the PLUMED log.
+
+        Parameters
+        ----------
+        s : object
+            Message to write (will be converted to string).
+        """
+        ...
+
+    def lognl(self, s: object) -> None:
+        """Write a message to the PLUMED log with newline.
+
+        Parameters
+        ----------
+        s : object
+            Message to write (will be converted to string).
+        """
+        ...
+
+    def getPosition(self, i: int) -> npt.NDArray[np.float64]:
+        """Get the position of atom i.
+
+        Parameters
+        ----------
+        i : int
+            Atom index (0-based, relative to atoms requested by action).
+
+        Returns
+        -------
+        np.ndarray
+            Array of shape (3,) with x, y, z coordinates.
+        """
+        ...
+
+    def getPositions(self) -> npt.NDArray[np.float64]:
+        """Get positions of all atoms requested by this action.
+
+        Returns
+        -------
+        np.ndarray
+            Array of shape (n_atoms, 3) with atomic positions.
+        """
+        ...
+
+    def getPbc(self) -> Pbc:
+        """Get the periodic boundary conditions interface.
+
+        Returns
+        -------
+        Pbc
+            Interface to the current PBC.
+        """
+        ...
+
+    def getNeighbourList(self) -> NeighborList:
+        """Get the neighbor list interface.
+
+        Returns
+        -------
+        NeighborList
+            Interface to the current neighbor list.
+        """
+        ...
+
+    def makeWhole(self) -> None:
+        """Make atoms whole across periodic boundaries.
+
+        Assumes atoms are in proper order.
+        """
+        ...
+
+    def absoluteIndexes(self) -> npt.NDArray[np.uint32]:
+        """Get the absolute atom indices.
+
+        Returns
+        -------
+        np.ndarray
+            Array of absolute atom indices in the full system.
+        """
+        ...
+
+    def charge(self, i: int) -> float:
+        """Get the charge of atom i.
+
+        Parameters
+        ----------
+        i : int
+            Atom index.
+
+        Returns
+        -------
+        float
+            The atomic charge.
+        """
+        ...
+
+    def mass(self, i: int) -> float:
+        """Get the mass of atom i.
+
+        Parameters
+        ----------
+        i : int
+            Atom index.
+
+        Returns
+        -------
+        float
+            The atomic mass.
+        """
+        ...
+
+    def masses(self) -> npt.NDArray[np.float64]:
+        """Get masses of all atoms.
+
+        Returns
+        -------
+        np.ndarray
+            Array of atomic masses.
+        """
+        ...
+
+    def charges(self) -> npt.NDArray[np.float64]:
+        """Get charges of all atoms.
+
+        Returns
+        -------
+        np.ndarray
+            Array of atomic charges.
+        """
+        ...
+
+class PythonFunction:
+    """Interface for defining functions of collective variables in Python.
+
+    This class provides access to CV arguments when implementing
+    custom functions via PYFUNCTION.
+    """
+
+    @property
+    def label(self) -> str:
+        """The label of this action."""
+        ...
+
+    @property
+    def nargs(self) -> int:
+        """The number of arguments passed to this function."""
+        ...
+
+    def getStep(self) -> int:
+        """Get the current simulation step.
+
+        Returns
+        -------
+        int
+            The current step number.
+        """
+        ...
+
+    def getTime(self) -> float:
+        """Get the current simulation time.
+
+        Returns
+        -------
+        float
+            The current time.
+        """
+        ...
+
+    def getTimeStep(self) -> float:
+        """Get the simulation timestep.
+
+        Returns
+        -------
+        float
+            The timestep.
+        """
+        ...
+
+    def isRestart(self) -> bool:
+        """Check if this is a restart simulation.
+
+        Returns
+        -------
+        bool
+            True if restarting from a previous simulation.
+        """
+        ...
+
+    def isExchangeStep(self) -> bool:
+        """Check if this is a replica exchange step.
+
+        Returns
+        -------
+        bool
+            True if on an exchange step.
+        """
+        ...
+
+    def log(self, s: object) -> None:
+        """Write a message to the PLUMED log.
+
+        Parameters
+        ----------
+        s : object
+            Message to write (will be converted to string).
+        """
+        ...
+
+    def lognl(self, s: object) -> None:
+        """Write a message to the PLUMED log with newline.
+
+        Parameters
+        ----------
+        s : object
+            Message to write (will be converted to string).
+        """
+        ...
+
+    def argument(self, i: int) -> float:
+        """Get the value of argument i.
+
+        Parameters
+        ----------
+        i : int
+            Argument index.
+
+        Returns
+        -------
+        float
+            The argument value.
+        """
+        ...
+
+    def arguments(self) -> npt.NDArray[np.float64]:
+        """Get all argument values.
+
+        Returns
+        -------
+        np.ndarray
+            Array of argument values.
+        """
+        ...
+
+    def difference(self, i: int, x: float, y: float) -> float:
+        """Compute difference accounting for periodicity.
+
+        Parameters
+        ----------
+        i : int
+            Argument index (for periodicity info).
+        x : float
+            First value.
+        y : float
+            Second value.
+
+        Returns
+        -------
+        float
+            The difference y - x accounting for periodicity.
+        """
+        ...
+
+    def bringBackInPbc(self, i: int, x: float) -> float:
+        """Bring a value back into the periodic domain.
+
+        Parameters
+        ----------
+        i : int
+            Argument index (for periodicity info).
+        x : float
+            Value to wrap.
+
+        Returns
+        -------
+        float
+            The value wrapped into the periodic domain.
+        """
+        ...