416 lines
11 KiB
Cython
416 lines
11 KiB
Cython
from libcpp cimport bool
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from libcpp cimport string as cppstring
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from libcpp.vector cimport vector as cppvector
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from cython.parallel cimport prange
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import numpy as np
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cimport numpy as np
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from cpython cimport PyObject, Py_INCREF
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cimport cython
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np.import_array()
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cdef extern from "loadSimu.hpp" namespace "CosmoTool":
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cdef cppclass SimuData:
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np.float_t BoxSize
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np.float_t time
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np.float_t Hubble
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np.float_t Omega_M
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np.float_t Omega_Lambda
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np.int64_t TotalNumPart
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np.int64_t NumPart
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np.int64_t *Id
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float *Pos[3]
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float *Vel[3]
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int *type
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float *Mass
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bool noAuto
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cdef const int NEED_GADGET_ID
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cdef const int NEED_POSITION
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cdef const int NEED_VELOCITY
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cdef const int NEED_TYPE
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cdef const int NEED_MASS
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cdef extern from "loadGadget.hpp" namespace "CosmoTool":
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SimuData *loadGadgetMulti(const char *fname, int id, int flags) nogil except +
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void cxx_writeGadget "CosmoTool::writeGadget" (const char * s, SimuData *data) except +
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cdef extern from "safe_gadget.hpp":
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SimuData *loadGadgetMulti_safe(cppstring.string s, int flags) nogil
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SimuData **alloc_simudata(int num) nogil
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void del_simudata(SimuData **d) nogil
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cdef extern from "loadRamses.hpp" namespace "CosmoTool":
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SimuData *loadRamsesSimu(const char *basename, int id, int cpuid, bool dp, int flags) except +
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class PySimulationBase(object):
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def getPositions(self):
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raise NotImplementedError("getPositions is not implemented")
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def getVelocities(self):
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raise NotImplementedError("getVelocities is not implemented")
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def getIdentifiers(self):
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raise NotImplementedError("getIdentifiers is not implemented")
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def getTypes(self):
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raise NotImplementedError("getTypes is not implemented")
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def getOmega_M(self):
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raise NotImplementedError("getOmega_M is not implemented")
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def getOmega_Lambda(self):
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raise NotImplementedError("getOmega_Lambda is not implemented")
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def getTime(self):
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raise NotImplementedError("getTime is not implemented")
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def getHubble(self):
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raise NotImplementedError("getHubble is not implemented")
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def getBoxsize(self):
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raise NotImplementedError("getBoxsize is not implemented")
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def getMasses(self):
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raise NotImplementedError("getMasses is not implemented")
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cdef class Simulation:
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cdef list positions
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cdef list velocities
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cdef object identifiers
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cdef object types
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cdef object masses
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cdef SimuData *data
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property BoxSize:
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def __get__(Simulation self):
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return self.data.BoxSize
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property time:
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def __get__(Simulation self):
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return self.data.time
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property Hubble:
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def __get__(Simulation self):
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return self.data.Hubble
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property Omega_M:
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def __get__(Simulation self):
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return self.data.Omega_M
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property Omega_Lambda:
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def __get__(Simulation self):
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return self.data.Omega_Lambda
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property positions:
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def __get__(Simulation self):
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return self.positions
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property velocities:
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def __get__(Simulation self):
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return self.velocities
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property identifiers:
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def __get__(Simulation self):
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return self.identifiers
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property types:
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def __get__(Simulation self):
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return self.types
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property masses:
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def __get__(Simulation self):
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return self.masses
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property numParticles:
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def __get__(Simulation self):
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return self.data.NumPart
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property totalNumParticles:
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def __get__(Simulation self):
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return self.data.TotalNumPart
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def __cinit__(Simulation self):
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self.data = <SimuData *>0
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def __dealloc__(Simulation self):
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if self.data != <SimuData *>0:
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print("Clearing simulation data")
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del self.data
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class _PySimulationAdaptor(PySimulationBase):
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def __init__(self,sim):
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self.simu = sim
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def getBoxsize(self):
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return self.simu.BoxSize
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def getPositions(self):
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return self.simu.positions
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def getTypes(self):
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return self.simu.types
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def getVelocities(self):
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return self.simu.velocities
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def getIdentifiers(self):
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return self.simu.identifiers
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def getTime(self):
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return self.simu.time
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def getHubble(self):
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return self.simu.Hubble
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def getOmega_M(self):
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return self.simu.Omega_M
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def getOmega_Lambda(self):
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return self.simu.Omega_Lambda
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def getMasses(self):
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return self.simu.masses
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cdef class ArrayWrapper:
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cdef void* data_ptr
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cdef np.uint64_t size
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cdef int type_array
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cdef set_data(self, np.uint64_t size, int type_array, void* data_ptr):
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""" Set the data of the array
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This cannot be done in the constructor as it must recieve C-level
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arguments.
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Parameters:
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-----------
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size: int
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Length of the array.
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data_ptr: void*
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Pointer to the data
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"""
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self.data_ptr = data_ptr
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self.size = size
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self.type_array = type_array
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def __array__(self):
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""" Here we use the __array__ method, that is called when numpy
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tries to get an array from the object."""
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cdef np.npy_intp shape[1]
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shape[0] = <np.npy_intp> self.size
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# Create a 1D array, of length 'size'
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ndarray = np.PyArray_SimpleNewFromData(1, shape, self.type_array, self.data_ptr)
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return ndarray
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def __dealloc__(self):
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""" Frees the array. This is called by Python when all the
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references to the object are gone. """
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pass
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cdef object wrap_array(void *p, np.uint64_t s, int typ):
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cdef np.ndarray ndarray
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cdef ArrayWrapper wrapper
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wrapper = ArrayWrapper()
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wrapper.set_data(s, typ, p)
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ndarray = np.array(wrapper, copy=False)
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ndarray.base = <PyObject*> wrapper
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Py_INCREF(wrapper)
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return ndarray
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cdef object wrap_float_array(float *p, np.uint64_t s):
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return wrap_array(<void *>p, s, np.NPY_FLOAT32)
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cdef object wrap_int64_array(np.int64_t* p, np.uint64_t s):
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return wrap_array(<void *>p, s, np.NPY_INT64)
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cdef object wrap_int_array(int* p, np.uint64_t s):
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return wrap_array(<void *>p, s, np.NPY_INT)
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cdef object wrap_simudata(SimuData *data, int flags):
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cdef Simulation simu
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simu = Simulation()
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simu.data = data
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if flags & NEED_POSITION:
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simu.positions = [wrap_float_array(data.Pos[i], data.NumPart) for i in xrange(3)]
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else:
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simu.positions = None
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if flags & NEED_VELOCITY:
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simu.velocities = [wrap_float_array(data.Vel[i], data.NumPart) for i in xrange(3)]
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else:
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simu.velocities = None
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if flags & NEED_GADGET_ID:
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simu.identifiers = wrap_int64_array(data.Id, data.NumPart)
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else:
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simu.identifiers = None
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if flags & NEED_TYPE:
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simu.types = wrap_int_array(data.type, data.NumPart)
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else:
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simu.types = None
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if flags & NEED_MASS:
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simu.masses = wrap_float_array(data.Mass, data.NumPart)
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else:
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simu.masses = None
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return simu
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def loadGadget(str filename, int snapshot_id, bool loadPosition = True, bool loadVelocity = False, bool loadId = False, bool loadType = False, bool loadMass=False):
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"""loadGadget(filename, cpu_id, loadPosition=True, loadVelocity=False, loadId=False, loadType=False)
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It loads a gadget-1 snapshot and return a PySimulationBase object. If cpu_id is negative then the snapshot is considered not to be part of a set of snapshots written by different cpu. Otherwise the filename is modified to reflectt this cpu_id.
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"""
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cdef int flags
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cdef SimuData *data
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cdef Simulation simu
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flags = 0
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if loadPosition:
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flags |= NEED_POSITION
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if loadVelocity:
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flags |= NEED_VELOCITY
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if loadId:
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flags |= NEED_GADGET_ID
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if loadType:
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flags |= NEED_TYPE
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if loadMass:
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flags |= NEED_MASS
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data = loadGadgetMulti(filename, snapshot_id, flags)
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if data == <SimuData*>0:
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return None
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return _PySimulationAdaptor(wrap_simudata(data, flags))
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def loadParallelGadget(object filename_list, bool loadPosition = True, bool loadVelocity = False, bool loadId = False, bool loadType = False, bool loadMass=False):
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"""loadGadget(filename list, loadPosition=True, loadVelocity=False, loadId=False, loadType=False)
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Arguments:
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- filename list: a list or tuple of filenames to load in parallel
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Keywords:
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- loadPosition: indicate to load positions
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- loadVelocity: indicate to load velocities
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- loadId: indicate to load id
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- loadType: indicate to load particle types
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It loads a gadget-1 snapshot and return a PySimulationBase object.
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"""
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cdef int flags, i, num_files
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cdef list out_arrays
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cdef SimuData ** data
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cdef SimuData * local_data
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cdef Simulation simu
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cdef cppvector[cppstring.string] filenames
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flags = 0
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if loadPosition:
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flags |= NEED_POSITION
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if loadVelocity:
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flags |= NEED_VELOCITY
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if loadId:
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flags |= NEED_GADGET_ID
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if loadType:
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flags |= NEED_TYPE
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if loadMass:
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flags |= NEED_MASS
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num_files = len(filename_list)
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filenames.resize(num_files)
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data = alloc_simudata(num_files)
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for i,l in enumerate(filename_list):
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filenames[i] = l
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with nogil:
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for i in prange(num_files):
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local_data = loadGadgetMulti_safe(filenames[i], flags)
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data[i] = local_data
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# data[i] = loadGadgetMulti(filenames[i].c_str(), -1, flags)
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out_arrays = []
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for i in xrange(num_files):
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if data[i] == <SimuData*>0:
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out_arrays.append(None)
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else:
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out_arrays.append(_PySimulationAdaptor(wrap_simudata(data[i], flags)))
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del_simudata(data)
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return out_arrays
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def writeGadget(str filename, object simulation):
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cdef SimuData simdata
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cdef np.ndarray[np.float32_t, ndim=1] pos, vel
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cdef np.ndarray[np.int64_t, ndim=1] ids
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cdef np.int64_t NumPart
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cdef int j
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if not isinstance(simulation,PySimulationBase):
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raise TypeError("Second argument must be of type SimulationBase")
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NumPart = simulation.positions[0].size
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simdata.noAuto = True
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for j in xrange(3):
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pos = simulation.getPositions()[j]
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vel = simulation.getVelocities()[j]
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if pos.size != NumPart or vel.size != NumPart:
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raise ValueError("Invalid number of particles")
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simdata.Pos[j] = <float *>pos.data
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simdata.Vel[j] = <float *>vel.data
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ids = simulation.getIdentifiers()
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simdata.Id = <np.int64_t *>ids.data
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simdata.BoxSize = simulation.getBoxsize()
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simdata.time = simulation.getTime()
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simdata.Hubble = simulation.getHubble()
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simdata.Omega_M = simulation.getOmega_M()
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simdata.Omega_Lambda = simulation.getOmega_Lambda()
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simdata.TotalNumPart = NumPart
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simdata.NumPart = NumPart
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cxx_writeGadget(filename, &simdata)
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def loadRamses(str basepath, int snapshot_id, int cpu_id, bool doublePrecision = False, bool loadPosition = True, bool loadVelocity = False):
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""" loadRamses(basepath, snapshot_id, cpu_id, doublePrecision=False, loadPosition=True, loadVelocity=False)
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Loads the indicated snapshot based on the cpu id, snapshot id and basepath. It is important to specify the correct precision in doublePrecision.
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"""
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cdef int flags
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cdef SimuData *data
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cdef Simulation simu
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flags = 0
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if loadPosition:
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flags |= NEED_POSITION
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if loadVelocity:
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flags |= NEED_VELOCITY
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data = loadRamsesSimu(basepath, snapshot_id, cpu_id, doublePrecision, flags)
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if data == <SimuData*>0:
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return None
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return _PySimulationAdaptor(wrap_simudata(data, flags))
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