891 lines
35 KiB
Cython
891 lines
35 KiB
Cython
"""@package qpms_c
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Cythonized parts of QPMS; mostly wrappers over the C data structures
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to make them available in Python.
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"""
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# Cythonized parts of QPMS here
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# -----------------------------
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import numpy as np
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from .qpms_cdefs cimport *
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from .cyquaternions cimport IRot3, CQuat
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from .cybspec cimport BaseSpec
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from .cycommon cimport make_c_string
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from .cycommon import string_c2py, PointGroupClass
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from .cytmatrices cimport CTMatrix, TMatrixFunction, TMatrixGenerator
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from libc.stdlib cimport malloc, free, calloc
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import warnings
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# Set custom GSL error handler. N.B. this is obviously not thread-safe.
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cdef char *pgsl_err_reason
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cdef char *pgsl_err_file
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cdef int pgsl_err_line
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cdef int pgsl_errno = 0
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cdef int *pgsl_errno_ignorelist = NULL # list of ignored error codes, terminated by zero
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# This error handler only sets the variables above
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cdef void pgsl_error_handler(const char *reason, const char *_file, const int line, const int gsl_errno):
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global pgsl_err_reason, pgsl_err_file, pgsl_err_line, pgsl_errno, pgsl_errno_ignorelist
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cdef size_t i
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if(pgsl_errno_ignorelist):
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i = 0
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while pgsl_errno_ignorelist[i] != 0:
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if gsl_errno == pgsl_errno_ignorelist[i]:
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return
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i += 1
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pgsl_err_file = _file
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pgsl_err_reason = reason
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pgsl_errno = gsl_errno
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pgsl_err_line = line
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return
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cdef const int* pgsl_set_ignorelist(const int *new_ignorelist):
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global pgsl_errno_ignorelist
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cdef const int *oldlist = pgsl_errno_ignorelist
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pgsl_errno_ignorelist = new_ignorelist
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return oldlist
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cdef class pgsl_ignore_error():
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'''Context manager for setting a temporary list of errnos ignored by pgsl_error_handler.
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Always sets pgsl_error_handler.
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Performs pgsl_check_err() on exit unless
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'''
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cdef const int *ignorelist_old
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cdef gsl_error_handler_t *old_handler
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cdef bint final_check
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cdef object ignorelist_python
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cdef int *ignorelist
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def __cinit__(self, *ignorelist, **kwargs):
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self.ignorelist = <int*>calloc((len(ignorelist)+1), sizeof(int))
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self.ignorelist_python = ignorelist
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for i in range(len(ignorelist)):
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self.ignorelist[i] = ignorelist[i]
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if "final_check" in kwargs.keys() and not kwargs["final_check"]:
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final_check = True
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final_check = False
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def __enter__(self):
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global pgsl_error_handler
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self.ignorelist_old = pgsl_set_ignorelist(self.ignorelist)
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self.old_handler = gsl_set_error_handler(pgsl_error_handler)
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return
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def __exit__(self, type, value, traceback):
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global pgsl_errno_ignorelist, pgsl_error_handler
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pgsl_set_ignorelist(self.ignorelist_old)
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gsl_set_error_handler(self.old_handler)
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if self.final_check:
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pgsl_check_err(retval = None, ignore = self.ignorelist_python)
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def __dealloc__(self):
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free(self.ignorelist)
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def pgsl_check_err(retval = None, ignorelist = None):
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global pgsl_err_reason, pgsl_err_file, pgsl_err_line, pgsl_errno
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'''Check for possible errors encountered by pgsl_error_handler.
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Takes return value of a function as an optional argument, which is now ignored.
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'''
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cdef int errno_was
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if (pgsl_errno != 0):
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errno_was = pgsl_errno
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pgsl_errno = 0
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raise RuntimeError("Error %d in GSL calculation in %s:%d: %s" % (errno_was,
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string_c2py(pgsl_err_file), pgsl_err_line, string_c2py(pgsl_err_reason)))
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if (retval is not None and retval != 0 and ignorelist is not None and retval not in ignorelist):
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warnings.warn("Got non-zero return value %d" % retval)
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if retval is not None:
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return retval
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else:
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return 0
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def set_gsl_pythonic_error_handling():
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'''
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Sets pgsl_error_handler as the GSL error handler to avoid crashing.
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'''
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gsl_set_error_handler(pgsl_error_handler)
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cdef class PointGroup:
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cdef readonly qpms_pointgroup_t G
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def __init__(self, cls, qpms_gmi_t n = 0, IRot3 orientation = IRot3()):
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cls = PointGroupClass(cls)
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self.G.c = cls
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if n <= 0 and qpms_pg_is_finite_axial(cls):
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raise ValueError("For finite axial groups, n argument must be positive")
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self.G.n = n
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self.G.orientation = orientation.qd
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def __len__(self):
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return qpms_pg_order(self.G.c, self.G.n);
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def __le__(PointGroup self, PointGroup other):
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if qpms_pg_is_subgroup(self.G, other.G):
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return True
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else:
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return False
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def __ge__(PointGroup self, PointGroup other):
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if qpms_pg_is_subgroup(other.G, self.G):
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return True
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else:
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return False
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def __lt__(PointGroup self, PointGroup other):
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return qpms_pg_is_subgroup(self.G, other.G) and not qpms_pg_is_subgroup(other.G, self.G)
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def __eq__(PointGroup self, PointGroup other):
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return qpms_pg_is_subgroup(self.G, other.G) and qpms_pg_is_subgroup(other.G, self.G)
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def __gt__(PointGroup self, PointGroup other):
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return not qpms_pg_is_subgroup(self.G, other.G) and qpms_pg_is_subgroup(other.G, self.G)
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def elems(self):
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els = list()
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cdef qpms_irot3_t *arr
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arr = qpms_pg_elems(NULL, self.G)
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cdef IRot3 q
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for i in range(len(self)):
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q = IRot3()
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q.cset(arr[i])
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els.append(q)
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free(arr)
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return els
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cdef class FinitePointGroup:
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'''
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Wrapper over the qpms_finite_group_t structure.
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TODO more functionality to make it better usable in Python
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(group element class at least)
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'''
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def __cinit__(self, info):
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'''Constructs a FinitePointGroup from PointGroupInfo'''
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# TODO maybe I might use a try..finally statement to avoid leaks
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# First, generate all basic data from info
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permlist = info.deterministic_elemlist()
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cdef int order = len(permlist)
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permindices = {perm: i for i, perm in enumerate(permlist)} # 'invert' permlist
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identity = info.permgroup.identity
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# We use calloc to avoid calling free to unitialized pointers
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self.G = <qpms_finite_group_t *>calloc(1,sizeof(qpms_finite_group_t))
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if not self.G: raise MemoryError
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self.G[0].name = make_c_string(info.name)
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self.G[0].order = order
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self.G[0].idi = permindices[identity]
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self.G[0].mt = <qpms_gmi_t *>malloc(sizeof(qpms_gmi_t) * order * order)
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if not self.G[0].mt: raise MemoryError
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for i in range(order):
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for j in range(order):
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self.G[0].mt[i*order + j] = permindices[permlist[i] * permlist[j]]
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self.G[0].invi = <qpms_gmi_t *>malloc(sizeof(qpms_gmi_t) * order)
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if not self.G[0].invi: raise MemoryError
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for i in range(order):
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self.G[0].invi[i] = permindices[permlist[i]**-1]
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self.G[0].ngens = len(info.permgroupgens)
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self.G[0].gens = <qpms_gmi_t *>malloc(sizeof(qpms_gmi_t) * self.G[0].ngens)
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if not self.G[0].gens: raise MemoryError
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for i in range(self.G[0].ngens):
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self.G[0].gens[i] = permindices[info.permgroupgens[i]]
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self.G[0].permrep = <char **>calloc(order, sizeof(char *))
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if not self.G[0].permrep: raise MemoryError
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for i in range(order):
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self.G[0].permrep[i] = make_c_string(str(permlist[i]))
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if not self.G[0].permrep[i]: raise MemoryError
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self.G[0].permrep_nelem = info.permgroup.degree
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if info.rep3d is not None:
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self.G[0].rep3d = <qpms_irot3_t *>malloc(order * sizeof(qpms_irot3_t))
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for i in range(order):
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self.G[0].rep3d[i] = info.rep3d[permlist[i]].qd
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self.G[0].nirreps = len(info.irreps)
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self.G[0].irreps = <qpms_finite_group_irrep_t *>calloc(self.G[0].nirreps, sizeof(qpms_finite_group_irrep_t))
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if not self.G[0].irreps: raise MemoryError
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cdef int dim
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for iri, irname in enumerate(sorted(info.irreps.keys())):
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irrep = info.irreps[irname]
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is1d = isinstance(irrep[identity], (int, float, complex))
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dim = 1 if is1d else irrep[identity].shape[0]
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self.G[0].irreps[iri].dim = dim
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self.G[0].irreps[iri].name = <char *>make_c_string(irname)
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if not self.G[0].irreps[iri].name: raise MemoryError
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self.G[0].irreps[iri].m = <cdouble *>malloc(dim*dim*sizeof(cdouble)*order)
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if not self.G[0].irreps[iri].m: raise MemoryError
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if is1d:
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for i in range(order):
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self.G[0].irreps[iri].m[i] = irrep[permlist[i]]
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else:
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for i in range(order):
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for row in range(dim):
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for col in range(dim):
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self.G[0].irreps[iri].m[i*dim*dim + row*dim + col] = irrep[permlist[i]][row,col]
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self.G[0].elemlabels = <char **> 0 # Elem labels not yet implemented
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self.owns_data = True
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def __dealloc__(self):
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cdef qpms_gmi_t order
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if self.owns_data:
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if self.G:
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order = self.G[0].order
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free(self.G[0].name)
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free(self.G[0].mt)
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free(self.G[0].invi)
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free(self.G[0].gens)
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if self.G[0].permrep:
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for i in range(order): free(self.G[0].permrep[i])
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free(self.G[0].permrep)
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if self.G[0].elemlabels: # this is not even contructed right now
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for i in range(order): free(self.G[0].elemlabels[i])
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if self.G[0].irreps:
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for iri in range(self.G[0].nirreps):
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free(self.G[0].irreps[iri].name)
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free(self.G[0].irreps[iri].m)
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free(self.G[0].irreps)
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free(self.G)
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self.G = <qpms_finite_group_t *>0
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self.owns_data = False
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cdef class FinitePointGroupElement:
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'''TODO'''
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cdef readonly FinitePointGroup G
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cdef readonly qpms_gmi_t gmi
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def __cinit__(self, FinitePointGroup G, qpms_gmi_t gmi):
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self.G = G
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self.gmi = gmi
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cdef class Particle:
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'''
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Wrapper over the qpms_particle_t structure.
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'''
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cdef qpms_particle_t p
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cdef readonly TMatrixFunction f # Reference to ensure correct reference counting
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def __cinit__(Particle self, pos, t, bspec = None):
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cdef TMatrixGenerator tgen
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cdef BaseSpec spec
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if(len(pos)>=2 and len(pos) < 4):
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self.p.pos.x = pos[0]
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self.p.pos.y = pos[1]
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self.p.pos.z = pos[2] if len(pos)==3 else 0
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else:
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raise ValueError("Position argument has to contain 3 or 2 cartesian coordinates")
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if isinstance(t, CTMatrix):
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tgen = TMatrixGenerator(t)
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elif isinstance(t, TMatrixGenerator):
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tgen = <TMatrixGenerator>t
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else: raise TypeError('t must be either CTMatrix or TMatrixGenerator, was %s' % str(type(t)))
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if bspec is not None:
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spec = bspec
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else:
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if isinstance(tgen.holder, CTMatrix):
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spec = (<CTMatrix>tgen.holder).spec
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else:
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raise ValueError("bspec argument must be specified separately for str(type(t))")
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self.f = TMatrixFunction(tgen, spec)
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self.p.tmg = self.f.rawpointer()
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# TODO non-trivial transformations later; if modified, do not forget to update ScatteringSystem constructor
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self.p.op = qpms_tmatrix_operation_noop
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def __dealloc__(self):
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qpms_tmatrix_operation_clear(&self.p.op)
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cdef qpms_particle_t *rawpointer(Particle self):
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'''Pointer to the qpms_particle_p structure.
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'''
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return &(self.p)
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property rawpointer:
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def __get__(self):
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return <uintptr_t> &(self.p)
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cdef qpms_particle_t cval(Particle self):
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'''Provides a copy for assigning in cython code'''
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return self.p
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property x:
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def __get__(self):
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return self.p.pos.x
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def __set__(self,x):
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self.p.pos.x = x
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property y:
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def __get__(self):
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return self.p.pos.y
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def __set__(self,y):
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self.p.pos.y = y
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property z:
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def __get__(self):
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return self.p.pos.z
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def __set__(self,z):
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self.p.pos.z = z
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property pos:
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def __get__(self):
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return (self.p.pos.x, self.p.pos.y, self.p.pos.z)
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def __set__(self, pos):
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if(len(pos)>=2 and len(pos) < 4):
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self.p.pos.x = pos[0]
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self.p.pos.y = pos[1]
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self.p.pos.z = pos[2] if len(pos)==3 else 0
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else:
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raise ValueError("Position argument has to contain 3 or 2 cartesian coordinates")
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cpdef void scatsystem_set_nthreads(long n):
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qpms_scatsystem_set_nthreads(n)
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return
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cdef class ScatteringSystem:
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'''
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Wrapper over the C qpms_scatsys_t structure.
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'''
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cdef list tmgobjs # here we keep the references to occuring TMatrixFunctions (and hence BaseSpecs and TMatrixGenerators)
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#cdef list Tmatrices # Here we keep the references to occuring T-matrices
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cdef qpms_scatsys_t *s
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def check_s(self): # cdef instead?
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if self.s == <qpms_scatsys_t *>NULL:
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raise ValueError("ScatteringSystem's s-pointer not set. You must not use the default constructor; use the create() method instead")
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#TODO is there a way to disable the constructor outside this module?
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@staticmethod # We don't have any "standard" constructor for this right now
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def create(particles, FinitePointGroup sym, cdouble omega): # TODO tolerances
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# These we are going to construct
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cdef ScatteringSystem self
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cdef _ScatteringSystemAtOmega pyssw
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cdef qpms_scatsys_t orig # This should be automatically init'd to 0 (CHECKME)
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cdef qpms_ss_pi_t pi, p_count = len(particles)
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cdef qpms_ss_tmi_t tmi, tm_count = 0
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cdef qpms_ss_tmgi_t tmgi, tmg_count = 0
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cdef qpms_scatsys_at_omega_t *ssw
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cdef qpms_scatsys_t *ss
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cdef Particle p
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tmgindices = dict()
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tmgobjs = list()
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tmindices = dict()
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tmlist = list()
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for p in particles: # find and enumerate unique t-matrix generators
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if p.p.op.typ != QPMS_TMATRIX_OPERATION_NOOP:
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raise NotImplementedError("currently, only no-op T-matrix operations are allowed in ScatteringSystem constructor")
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tmg_key = id(p.f)
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if tmg_key not in tmgindices:
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tmgindices[tmg_key] = tmg_count
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tmgobjs.append(p.f) # Save the references on BaseSpecs and TMatrixGenerators (via TMatrixFunctions)
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tmg_count += 1
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# Following lines have to be adjusted when nontrivial operations allowed:
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tm_derived_key = (tmg_key, None) # TODO unique representation of p.p.op instead of None
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if tm_derived_key not in tmindices:
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tmindices[tm_derived_key] = tm_count
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tmlist.append(tm_derived_key)
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tm_count += 1
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orig.tmg_count = tmg_count
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orig.tm_count = tm_count
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orig.p_count = p_count
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try:
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orig.tmg = <qpms_tmatrix_function_t *>malloc(orig.tmg_count * sizeof(orig.tmg[0]))
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if not orig.tmg: raise MemoryError
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orig.tm = <qpms_ss_derived_tmatrix_t *>malloc(orig.tm_count * sizeof(orig.tm[0]))
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if not orig.tm: raise MemoryError
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orig.p = <qpms_particle_tid_t *>malloc(orig.p_count * sizeof(orig.p[0]))
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if not orig.p: raise MemoryError
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for tmgi in range(orig.tmg_count):
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orig.tmg[tmgi] = (<TMatrixFunction?>tmgobjs[tmgi]).raw()
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for tmi in range(tm_count):
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tm_derived_key = tmlist[tmi]
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tmgi = tmgindices[tmg_key[0]]
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orig.tm[tmi].tmgi = tmgi
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orig.tm[tmi].op = qpms_tmatrix_operation_noop # TODO adjust when notrivial operations allowed
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for pi in range(p_count):
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p = particles[pi]
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tmg_key = id(p.f)
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tm_derived_key = (tmg_key, None) # TODO unique representation of p.p.op instead of None
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orig.p[pi].pos = p.cval().pos
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orig.p[pi].tmatrix_id = tmindices[tm_derived_key]
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ssw = qpms_scatsys_apply_symmetry(&orig, sym.rawpointer(), omega, &QPMS_TOLERANCE_DEFAULT)
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ss = ssw[0].ss
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finally:
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free(orig.tmg)
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free(orig.tm)
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free(orig.p)
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self = ScatteringSystem()
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self.s = ss
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self.tmgobjs = tmgobjs
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pyssw = _ScatteringSystemAtOmega()
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pyssw.ssw = ssw
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pyssw.ss_pyref = self
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return self, pyssw
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def __call__(self, cdouble omega):
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self.check_s()
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cdef _ScatteringSystemAtOmega pyssw = _ScatteringSystemAtOmega()
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pyssw.ssw = qpms_scatsys_at_omega(self.s, omega)
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pyssw.ss_pyref = self
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def __dealloc__(self):
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if(self.s):
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qpms_scatsys_free(self.s)
|
|
|
|
property particles_tmi:
|
|
def __get__(self):
|
|
self.check_s()
|
|
r = list()
|
|
cdef qpms_ss_pi_t pi
|
|
for pi in range(self.s[0].p_count):
|
|
r.append(self.s[0].p[pi])
|
|
return r
|
|
|
|
property fecv_size:
|
|
def __get__(self):
|
|
self.check_s()
|
|
return self.s[0].fecv_size
|
|
property saecv_sizes:
|
|
def __get__(self):
|
|
self.check_s()
|
|
return [self.s[0].saecv_sizes[i]
|
|
for i in range(self.s[0].sym[0].nirreps)]
|
|
property irrep_names:
|
|
def __get__(self):
|
|
self.check_s()
|
|
return [string_c2py(self.s[0].sym[0].irreps[iri].name)
|
|
if (self.s[0].sym[0].irreps[iri].name) else None
|
|
for iri in range(self.s[0].sym[0].nirreps)]
|
|
property nirreps:
|
|
def __get__(self):
|
|
self.check_s()
|
|
return self.s[0].sym[0].nirreps
|
|
|
|
def pack_vector(self, vect, iri):
|
|
self.check_s()
|
|
if len(vect) != self.fecv_size:
|
|
raise ValueError("Length of a full vector has to be %d, not %d"
|
|
% (self.fecv_size, len(vect)))
|
|
vect = np.array(vect, dtype=complex, copy=False, order='C')
|
|
cdef cdouble[::1] vect_view = vect;
|
|
cdef np.ndarray[np.complex_t, ndim=1] target_np = np.empty(
|
|
(self.saecv_sizes[iri],), dtype=complex, order='C')
|
|
cdef cdouble[::1] target_view = target_np
|
|
qpms_scatsys_irrep_pack_vector(&target_view[0], &vect_view[0], self.s, iri)
|
|
return target_np
|
|
def unpack_vector(self, packed, iri):
|
|
self.check_s()
|
|
if len(packed) != self.saecv_sizes[iri]:
|
|
raise ValueError("Length of %d. irrep-packed vector has to be %d, not %d"
|
|
% (iri, self.saecv_sizes, len(packed)))
|
|
packed = np.array(packed, dtype=complex, copy=False, order='C')
|
|
cdef cdouble[::1] packed_view = packed
|
|
cdef np.ndarray[np.complex_t, ndim=1] target_np = np.empty(
|
|
(self.fecv_size,), dtype=complex)
|
|
cdef cdouble[::1] target_view = target_np
|
|
qpms_scatsys_irrep_unpack_vector(&target_view[0], &packed_view[0],
|
|
self.s, iri, 0)
|
|
return target_np
|
|
def pack_matrix(self, fullmatrix, iri):
|
|
self.check_s()
|
|
cdef size_t flen = self.s[0].fecv_size
|
|
cdef size_t rlen = self.saecv_sizes[iri]
|
|
fullmatrix = np.array(fullmatrix, dtype=complex, copy=False, order='C')
|
|
if fullmatrix.shape != (flen, flen):
|
|
raise ValueError("Full matrix shape should be (%d,%d), is %s."
|
|
% (flen, flen, repr(fullmatrix.shape)))
|
|
cdef cdouble[:,::1] fullmatrix_view = fullmatrix
|
|
cdef np.ndarray[np.complex_t, ndim=2] target_np = np.empty(
|
|
(rlen, rlen), dtype=complex, order='C')
|
|
cdef cdouble[:,::1] target_view = target_np
|
|
qpms_scatsys_irrep_pack_matrix(&target_view[0][0], &fullmatrix_view[0][0],
|
|
self.s, iri)
|
|
return target_np
|
|
def unpack_matrix(self, packedmatrix, iri):
|
|
self.check_s()
|
|
cdef size_t flen = self.s[0].fecv_size
|
|
cdef size_t rlen = self.saecv_sizes[iri]
|
|
packedmatrix = np.array(packedmatrix, dtype=complex, copy=False, order='C')
|
|
if packedmatrix.shape != (rlen, rlen):
|
|
raise ValueError("Packed matrix shape should be (%d,%d), is %s."
|
|
% (rlen, rlen, repr(packedmatrix.shape)))
|
|
cdef cdouble[:,::1] packedmatrix_view = packedmatrix
|
|
cdef np.ndarray[np.complex_t, ndim=2] target_np = np.empty(
|
|
(flen, flen), dtype=complex, order='C')
|
|
cdef cdouble[:,::1] target_view = target_np
|
|
qpms_scatsys_irrep_unpack_matrix(&target_view[0][0], &packedmatrix_view[0][0],
|
|
self.s, iri, 0)
|
|
return target_np
|
|
|
|
def translation_matrix_full(self, double k, J = QPMS_HANKEL_PLUS):
|
|
self.check_s()
|
|
cdef size_t flen = self.s[0].fecv_size
|
|
cdef np.ndarray[np.complex_t, ndim=2] target = np.empty(
|
|
(flen,flen),dtype=complex, order='C')
|
|
cdef cdouble[:,::1] target_view = target
|
|
qpms_scatsys_build_translation_matrix_e_full(&target_view[0][0], self.s, k, J)
|
|
return target
|
|
|
|
def translation_matrix_packed(self, double k, qpms_iri_t iri, J = QPMS_HANKEL_PLUS):
|
|
self.check_s()
|
|
cdef size_t rlen = self.saecv_sizes[iri]
|
|
cdef np.ndarray[np.complex_t, ndim=2] target = np.empty(
|
|
(rlen,rlen),dtype=complex, order='C')
|
|
cdef cdouble[:,::1] target_view = target
|
|
qpms_scatsys_build_translation_matrix_e_irrep_packed(&target_view[0][0],
|
|
self.s, iri, k, J)
|
|
return target
|
|
|
|
property fullvec_psizes:
|
|
def __get__(self):
|
|
self.check_s()
|
|
cdef np.ndarray[int32_t, ndim=1] ar = np.empty((self.s[0].p_count,), dtype=np.int32)
|
|
cdef int32_t[::1] ar_view = ar
|
|
for pi in range(self.s[0].p_count):
|
|
ar_view[pi] = self.s[0].tm[self.s[0].p[pi].tmatrix_id].spec[0].n
|
|
return ar
|
|
|
|
|
|
property fullvec_poffsets:
|
|
def __get__(self):
|
|
self.check_s()
|
|
cdef np.ndarray[intptr_t, ndim=1] ar = np.empty((self.s[0].p_count,), dtype=np.intp)
|
|
cdef intptr_t[::1] ar_view = ar
|
|
cdef intptr_t offset = 0
|
|
for pi in range(self.s[0].p_count):
|
|
ar_view[pi] = offset
|
|
offset += self.s[0].tm[self.s[0].p[pi].tmatrix_id].spec[0].n
|
|
return ar
|
|
|
|
property positions:
|
|
def __get__(self):
|
|
self.check_s()
|
|
cdef np.ndarray[np.double_t, ndim=2] ar = np.empty((self.s[0].p_count, 3), dtype=float)
|
|
cdef np.double_t[:,::1] ar_view = ar
|
|
for pi in range(self.s[0].p_count):
|
|
ar_view[pi,0] = self.s[0].p[pi].pos.x
|
|
ar_view[pi,1] = self.s[0].p[pi].pos.y
|
|
ar_view[pi,2] = self.s[0].p[pi].pos.z
|
|
return ar
|
|
|
|
def planewave_full(self, k_cart, E_cart):
|
|
self.check_s()
|
|
k_cart = np.array(k_cart)
|
|
E_cart = np.array(E_cart)
|
|
if k_cart.shape != (3,) or E_cart.shape != (3,):
|
|
raise ValueError("k_cart and E_cart must be ndarrays of shape (3,)")
|
|
cdef qpms_incfield_planewave_params_t p
|
|
p.use_cartesian = 1
|
|
p.k.cart.x = <cdouble>k_cart[0]
|
|
p.k.cart.y = <cdouble>k_cart[1]
|
|
p.k.cart.z = <cdouble>k_cart[2]
|
|
p.E.cart.x = <cdouble>E_cart[0]
|
|
p.E.cart.y = <cdouble>E_cart[1]
|
|
p.E.cart.z = <cdouble>E_cart[2]
|
|
cdef np.ndarray[np.complex_t, ndim=1] target_np = np.empty(
|
|
(self.fecv_size,), dtype=complex)
|
|
cdef cdouble[::1] target_view = target_np
|
|
qpms_scatsys_incident_field_vector_full(&target_view[0],
|
|
self.s, qpms_incfield_planewave, <void *>&p, 0)
|
|
return target_np
|
|
|
|
cdef class _ScatteringSystemAtOmega:
|
|
'''
|
|
Wrapper over the C qpms_scatsys_at_omega_t structure
|
|
that keeps the T-matrix and background data evaluated
|
|
at specific frequency.
|
|
'''
|
|
cdef qpms_scatsys_at_omega_t *ssw
|
|
cdef ScatteringSystem ss_pyref
|
|
|
|
def check(self): # cdef instead?
|
|
if not self.ssw:
|
|
raise ValueError("_ScatteringSystemAtOmega's ssw-pointer not set. You must not use the default constructor; ScatteringSystem.create() instead")
|
|
self.ss_pyref.check_s()
|
|
#TODO is there a way to disable the constructor outside this module?
|
|
|
|
def __dealloc__(self):
|
|
if (self.ssw):
|
|
qpms_scatsys_at_omega_free(self.ssw)
|
|
|
|
def apply_Tmatrices_full(self, a):
|
|
self.check()
|
|
if len(a) != self.fecv_size:
|
|
raise ValueError("Length of a full vector has to be %d, not %d"
|
|
% (self.fecv_size, len(a)))
|
|
a = np.array(a, dtype=complex, copy=False, order='C')
|
|
cdef cdouble[::1] a_view = a;
|
|
cdef np.ndarray[np.complex_t, ndim=1] target_np = np.empty(
|
|
(self.fecv_size,), dtype=complex, order='C')
|
|
cdef cdouble[::1] target_view = target_np
|
|
qpms_scatsysw_apply_Tmatrices_full(&target_view[0], &a_view[0], self.ssw)
|
|
return target_np
|
|
|
|
cdef qpms_scatsys_at_omega_t *rawpointer(self):
|
|
return self.ssw
|
|
|
|
def scatter_solver(self, double k, iri=None):
|
|
self.check()
|
|
return ScatteringMatrix(self, iri)
|
|
|
|
property fecv_size:
|
|
def __get__(self): return self.ss_pyref.fecv_size
|
|
property saecv_sizes:
|
|
def __get__(self): return self.ss_pyref.saecv_sizes
|
|
property irrep_names:
|
|
def __get__(self): return self.ss_pyref.irrep_names
|
|
property nirreps:
|
|
def __get__(self): return self.ss_pyref.nirreps
|
|
|
|
def modeproblem_matrix_full(self):
|
|
self.check()
|
|
cdef size_t flen = self.s[0].fecv_size
|
|
cdef np.ndarray[np.complex_t, ndim=2] target = np.empty(
|
|
(flen,flen),dtype=complex, order='C')
|
|
cdef cdouble[:,::1] target_view = target
|
|
qpms_scatsysw_build_modeproblem_matrix_full(&target_view[0][0], self.ssw)
|
|
return target
|
|
|
|
def modeproblem_matrix_packed(self, qpms_iri_t iri, version='pR'):
|
|
self.check()
|
|
cdef size_t rlen = self.saecv_sizes[iri]
|
|
cdef np.ndarray[np.complex_t, ndim=2] target = np.empty(
|
|
(rlen,rlen),dtype=complex, order='C')
|
|
cdef cdouble[:,::1] target_view = target
|
|
if (version == 'R'):
|
|
qpms_scatsysw_build_modeproblem_matrix_irrep_packed_orbitorderR(&target_view[0][0], self.ssw, iri)
|
|
elif (version == 'pR'):
|
|
with nogil:
|
|
qpms_scatsysw_build_modeproblem_matrix_irrep_packed(&target_view[0][0], self.ssw, iri)
|
|
else:
|
|
qpms_scatsysw_build_modeproblem_matrix_irrep_packed_serial(&target_view[0][0], self.ssw, iri)
|
|
return target
|
|
|
|
|
|
cdef class ScatteringMatrix:
|
|
'''
|
|
Wrapper over the C qpms_ss_LU structure that keeps the factorised mode problem matrix.
|
|
'''
|
|
cdef _ScatteringSystemAtOmega ssw # Here we keep the reference to the parent scattering system
|
|
cdef qpms_ss_LU lu
|
|
|
|
def __cinit__(self, _ScatteringSystemAtOmega ssw, iri=None):
|
|
ssw.check()
|
|
self.ssw = ssw
|
|
# TODO? pre-allocate the matrix with numpy to make it transparent?
|
|
if iri is None:
|
|
self.lu = qpms_scatsysw_build_modeproblem_matrix_full_LU(
|
|
NULL, NULL, ssw.rawpointer())
|
|
else:
|
|
self.lu = qpms_scatsysw_build_modeproblem_matrix_irrep_packed_LU(
|
|
NULL, NULL, ssw.rawpointer(), iri)
|
|
|
|
def __dealloc__(self):
|
|
qpms_ss_LU_free(self.lu)
|
|
|
|
property iri:
|
|
def __get__(self):
|
|
return None if self.lu.full else self.lu.iri
|
|
|
|
def __call__(self, a_inc):
|
|
cdef size_t vlen
|
|
cdef qpms_iri_t iri = -1;
|
|
if self.lu.full:
|
|
vlen = self.lu.ssw[0].ss[0].fecv_size
|
|
if len(a_inc) != vlen:
|
|
raise ValueError("Length of a full coefficient vector has to be %d, not %d"
|
|
% (vlen, len(a_inc)))
|
|
else:
|
|
iri = self.lu.iri
|
|
vlen = self.lu.ssw[0].ss[0].saecv_sizes[iri]
|
|
if len(a_inc) != vlen:
|
|
raise ValueError("Length of a %d. irrep packed coefficient vector has to be %d, not %d"
|
|
% (iri, vlen, len(a_inc)))
|
|
a_inc = np.array(a_inc, dtype=complex, copy=False, order='C')
|
|
cdef const cdouble[::1] a_view = a_inc;
|
|
cdef np.ndarray f = np.empty((vlen,), dtype=complex, order='C')
|
|
cdef cdouble[::1] f_view = f
|
|
qpms_scatsys_scatter_solve(&f_view[0], &a_view[0], self.lu)
|
|
return f
|
|
|
|
def pitau(double theta, qpms_l_t lMax, double csphase = -1):
|
|
if(abs(csphase) != 1):
|
|
raise ValueError("csphase must be 1 or -1, is %g" % csphase)
|
|
cdef size_t nelem = qpms_lMax2nelem(lMax)
|
|
cdef np.ndarray[np.float_t, ndim=1] lega = np.empty((nelem,), dtype=float)
|
|
cdef np.ndarray[np.float_t, ndim=1] pia = np.empty((nelem,), dtype=float)
|
|
cdef np.ndarray[np.float_t, ndim=1] taua = np.empty((nelem,), dtype=float)
|
|
cdef double[::1] leg = lega
|
|
cdef double[::1] pi = pia
|
|
cdef double[::1] tau = taua
|
|
qpms_pitau_fill(&leg[0], &pi[0], &tau[0], theta, lMax, csphase)
|
|
return (lega, pia, taua)
|
|
|
|
def linton_gamma(cdouble x):
|
|
return clilgamma(x)
|
|
|
|
def linton_gamma_real(double x):
|
|
return lilgamma(x)
|
|
|
|
def gamma_inc(double a, cdouble x, int m = 0):
|
|
cdef qpms_csf_result res
|
|
with pgsl_ignore_error(15): #15 is underflow
|
|
complex_gamma_inc_e(a, x, m, &res)
|
|
return (res.val, res.err)
|
|
|
|
def gamma_inc_series(double a, cdouble x):
|
|
cdef qpms_csf_result res
|
|
with pgsl_ignore_error(15): #15 is underflow
|
|
cx_gamma_inc_series_e(a, x, &res)
|
|
return (res.val, res.err)
|
|
|
|
def gamma_inc_CF(double a, cdouble x):
|
|
cdef qpms_csf_result res
|
|
with pgsl_ignore_error(15): #15 is underflow
|
|
cx_gamma_inc_CF_e(a, x, &res)
|
|
return (res.val, res.err)
|
|
|
|
def lll_reduce(basis, double delta=0.75):
|
|
"""
|
|
Lattice basis reduction with the Lenstra-Lenstra-Lovász algorithm.
|
|
|
|
basis is array_like with dimensions (n, d), where
|
|
n is the size of the basis (dimensionality of the lattice)
|
|
and d is the dimensionality of the space into which the lattice
|
|
is embedded.
|
|
"""
|
|
basis = np.array(basis, copy=True, order='C', dtype=np.double)
|
|
if len(basis.shape) != 2:
|
|
raise ValueError("Expected two-dimensional array (got %d-dimensional)"
|
|
% len(basis.shape))
|
|
cdef size_t n, d
|
|
n, d = basis.shape
|
|
if n > d:
|
|
raise ValueError("Real space dimensionality (%d) cannot be smaller than"
|
|
"the dimensionality of the lattice (%d) embedded into it."
|
|
% (d, n))
|
|
cdef double [:,:] basis_view = basis
|
|
if 0 != qpms_reduce_lattice_basis(&basis_view[0,0], n, d, delta):
|
|
raise RuntimeError("Something weird happened")
|
|
return basis
|
|
|
|
|
|
cdef PGen get_PGen_direct(direct_basis, bint include_origin=False, double layers=30):
|
|
dba = np.array(direct_basis)
|
|
if not (dba.shape == (2,2)):
|
|
raise NotImplementedError
|
|
cdef cart2_t b1, b2
|
|
b1.x = dba[0,0]
|
|
b1.y = dba[0,1]
|
|
b2.x = dba[1,0]
|
|
b2.y = dba[0,1]
|
|
cdef double maxR = layers*max(cart2norm(b1), cart2norm(b2))
|
|
return PGen_xyWeb_new(b1, b2, BASIS_RTOL, CART2_ZERO, 0, include_origin, maxR, False)
|
|
|
|
cdef double get_unitcell_volume(direct_basis):
|
|
dba = np.array(direct_basis)
|
|
if not (dba.shape == (2,2)):
|
|
raise NotImplementedError
|
|
cdef cart2_t b1, b2
|
|
b1.x = dba[0,0]
|
|
b1.y = dba[0,1]
|
|
b2.x = dba[1,0]
|
|
b2.y = dba[0,1]
|
|
return l2d_unitcell_area(b1, b2)
|
|
|
|
cdef PGen get_PGen_reciprocal2pi(direct_basis, double layers = 30):
|
|
dba = np.array(direct_basis)
|
|
if not (dba.shape == (2,2)):
|
|
raise NotImplementedError
|
|
cdef cart2_t b1, b2, rb1, rb2
|
|
b1.x = dba[0,0]
|
|
b1.y = dba[0,1]
|
|
b2.x = dba[1,0]
|
|
b2.y = dba[0,1]
|
|
if(l2d_reciprocalBasis2pi(b1, b2, &rb1, &rb2) != 0):
|
|
raise RuntimeError
|
|
cdef double maxK = layers*max(cart2norm(rb1), cart2norm(rb2))
|
|
return PGen_xyWeb_new(rb1, rb2, BASIS_RTOL, CART2_ZERO,
|
|
0, True, maxK, False)
|
|
|
|
cdef class Ewald3Calculator:
|
|
'''Wrapper class over qpms_ewald3_constants_t.
|
|
|
|
Mainly for testing low-level scalar Ewald summation functionality.'''
|
|
cdef qpms_ewald3_constants_t *c
|
|
|
|
def __cinit__(self, qpms_l_t lMax, int csphase = -1):
|
|
if (csphase != -1 and csphase != 1):
|
|
raise ValueError("csphase must be +1 or -1, not %d" % csphase)
|
|
self.c = qpms_ewald3_constants_init(lMax, csphase)
|
|
|
|
def __dealloc__(self):
|
|
qpms_ewald3_constants_free(self.c)
|
|
|
|
def sigma0(self, double eta, cdouble wavenumber, do_err = False):
|
|
cdef int retval
|
|
cdef double err
|
|
cdef cdouble result
|
|
retval = ewald3_sigma0(&result, &err, self.c, eta, wavenumber)
|
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if retval:
|
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raise RuntimeError("ewald3_sigma0 returned non-zero value (%d)" % retval)
|
|
if do_err:
|
|
return (result, err)
|
|
else:
|
|
return result
|
|
|
|
def sigma_short(self, double eta, cdouble wavenumber, direct_basis, wavevector, particle_shift, do_err=False):
|
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# FIXME now only 2d XY lattice in 3D is implemented here, we don't even do proper dimensionality checks.
|
|
cdef cart3_t beta, pshift
|
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beta.x = wavevector[0]
|
|
beta.y = wavevector[1]
|
|
beta.z = 0
|
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pshift.x = particle_shift[0]
|
|
pshift.y = particle_shift[1]
|
|
pshift.z = 0
|
|
cdef qpms_l_t n = self.c[0].nelem_sc
|
|
cdef np.ndarray[complex, ndim=1] result = np.empty((n,), dtype=complex)
|
|
cdef cdouble[::1] result_v = result
|
|
cdef np.ndarray[double, ndim=1] err
|
|
cdef double[::1] err_v
|
|
if do_err:
|
|
err = np.empty((n,), dtype=np.double)
|
|
err_v = err
|
|
cdef bint include_origin = not (particle_shift[0] == 0 and particle_shift[1] == 0)
|
|
cdef PGen rgen = get_PGen_direct(direct_basis, include_origin)
|
|
cdef int retval = ewald3_sigma_short(&result_v[0], &err_v[0] if do_err else NULL,
|
|
self.c, eta, wavenumber, LAT_2D_IN_3D_XYONLY, &rgen, False, beta, pshift)
|
|
if rgen.stateData: PGen_destroy(&rgen)
|
|
if retval: raise RuntimeError("ewald3_sigma_short returned %d" % retval)
|
|
if do_err:
|
|
return (result, err)
|
|
else:
|
|
return result
|
|
|
|
def sigma_long(self, double eta, cdouble wavenumber, direct_basis, wavevector, particle_shift, do_err=False):
|
|
# FIXME now only 2d XY lattice in 3D is implemented here, we don't even do proper dimensionality checks.
|
|
cdef cart3_t beta, pshift
|
|
beta.x = wavevector[0]
|
|
beta.y = wavevector[1]
|
|
beta.z = 0
|
|
pshift.x = particle_shift[0]
|
|
pshift.y = particle_shift[1]
|
|
pshift.z = 0
|
|
cdef qpms_l_t n = self.c[0].nelem_sc
|
|
cdef np.ndarray[complex, ndim=1] result = np.empty((n,), dtype=complex)
|
|
cdef cdouble[::1] result_v = result
|
|
cdef np.ndarray[double, ndim=1] err
|
|
cdef double[::1] err_v
|
|
if do_err:
|
|
err = np.empty((n,), dtype=np.double)
|
|
err_v = err
|
|
cdef PGen kgen = get_PGen_reciprocal2pi(direct_basis)
|
|
cdef double unitcell_volume = get_unitcell_volume(direct_basis)
|
|
cdef int retval = ewald3_sigma_long(&result_v[0], &err_v[0] if do_err else NULL,
|
|
self.c, eta, wavenumber, unitcell_volume, LAT_2D_IN_3D_XYONLY, &kgen, False, beta, pshift)
|
|
|
|
if kgen.stateData: PGen_destroy(&kgen)
|
|
if retval: raise RuntimeError("ewald3_sigma_long returned %d" % retval)
|
|
if do_err:
|
|
return (result, err)
|
|
else:
|
|
return result
|
|
|
|
|
|
|
|
|