diff --git a/package/CHANGELOG b/package/CHANGELOG index 5e252f2b1af..879bff4a616 100644 --- a/package/CHANGELOG +++ b/package/CHANGELOG @@ -20,6 +20,10 @@ The rules for this file: * 1.0.1 Fixes + * Due to issues with the reliability/accuracy of `nsgrid`, this method is + currently not recommended for use. It has also been removed as an option + from lib.capped_distance and lib.self_capped_distance. Please use PKDTree + instead (Issue #2930) * Development status changed from beta to mature (Issue #2773) * pip installation only requests Python 2.7-compatible packages (#2736) * Testsuite does not use any more matplotlib.use('agg') (#2191) diff --git a/package/MDAnalysis/lib/distances.py b/package/MDAnalysis/lib/distances.py index c0d994862c2..5fc9724bec2 100644 --- a/package/MDAnalysis/lib/distances.py +++ b/package/MDAnalysis/lib/distances.py @@ -336,7 +336,7 @@ def capped_distance(reference, configuration, max_cutoff, min_cutoff=None, An automatic guessing of the optimal method to calculate the distances is included in the function. An optional keyword for the method is also provided. Users can enforce a particular method with this functionality. - Currently brute force, grid search, and periodic KDtree methods are + Currently brute force and periodic KDtree methods are implemented. Parameters @@ -354,7 +354,7 @@ def capped_distance(reference, configuration, max_cutoff, min_cutoff=None, triclinic and must be provided in the same format as returned by :attr:`MDAnalysis.coordinates.base.Timestep.dimensions`:\n ``[lx, ly, lz, alpha, beta, gamma]``. - method : {'bruteforce', 'nsgrid', 'pkdtree'}, optional + method : {'bruteforce', 'pkdtree'}, optional Keyword to override the automatic guessing of the employed search method. return_distances : bool, optional @@ -387,14 +387,19 @@ def capped_distance(reference, configuration, max_cutoff, min_cutoff=None, Note ----- - Currently supports brute force, grid-based, and periodic KDtree search + Currently supports brute force, and periodic KDtree search methods. See Also -------- distance_array MDAnalysis.lib.pkdtree.PeriodicKDTree.search - MDAnalysis.lib.nsgrid.FastNS.search + + + .. versionchanged:: 1.0.1 + nsgrid was temporarily removed and replaced with pkdtree due to issues + relating to its reliability and accuracy (Issues #2919, #2229, #2345, + #2670, #2930) """ if box is not None: box = np.asarray(box, dtype=np.float32) @@ -430,7 +435,7 @@ def _determine_method(reference, configuration, max_cutoff, min_cutoff=None, triclinic and must be provided in the same format as returned by :attr:`MDAnalysis.coordinates.base.Timestep.dimensions`:\n ``[lx, ly, lz, alpha, beta, gamma]``. - method : {'bruteforce', 'nsgrid', 'pkdtree'}, optional + method : {'bruteforce', 'pkdtree'}, optional Keyword to override the automatic guessing of the employed search method. @@ -438,10 +443,16 @@ def _determine_method(reference, configuration, max_cutoff, min_cutoff=None, ------- function : callable The function implementing the guessed (or deliberatly chosen) method. + + + .. versionchanged:: 1.0.1 + nsgrid was temporarily removed and replaced with pkdtree due to issues + relating to its reliability and accuracy (Issues #2919, #2229, #2345, + #2670, #2930) """ + # TODO: add 'nsgrid': _nsgrid_capped back once fixed methods = {'bruteforce': _bruteforce_capped, - 'pkdtree': _pkdtree_capped, - 'nsgrid': _nsgrid_capped} + 'pkdtree': _pkdtree_capped} if method is not None: return methods[method.lower()] @@ -451,7 +462,8 @@ def _determine_method(reference, configuration, max_cutoff, min_cutoff=None, elif len(reference) * len(configuration) >= 1e8: # CAUTION : for large datasets, shouldnt go into 'bruteforce' # in any case. Arbitrary number, but can be characterized - return methods['nsgrid'] + # Temporarily replace nsgrid with pkdtree Issue #2930 + return methods['pkdtree'] else: if box is None: min_dim = np.array([reference.min(axis=0), @@ -467,7 +479,8 @@ def _determine_method(reference, configuration, max_cutoff, min_cutoff=None, if np.any(max_cutoff > 0.3*size): return methods['bruteforce'] else: - return methods['nsgrid'] + # Temporarily replace nsgrid with pkdtree Issue #2930 + return methods['pkdtree'] @check_coords('reference', 'configuration', enforce_copy=False, @@ -741,7 +754,7 @@ def self_capped_distance(reference, max_cutoff, min_cutoff=None, box=None, An automatic guessing of the optimal method to calculate the distances is included in the function. An optional keyword for the method is also provided. Users can enforce a particular method with this functionality. - Currently brute force, grid search, and periodic KDtree methods are + Currently brute force, and periodic KDtree methods are implemented. Parameters @@ -757,7 +770,7 @@ def self_capped_distance(reference, max_cutoff, min_cutoff=None, box=None, triclinic and must be provided in the same format as returned by :attr:`MDAnalysis.coordinates.base.Timestep.dimensions`:\n ``[lx, ly, lz, alpha, beta, gamma]``. - method : {'bruteforce', 'nsgrid', 'pkdtree'}, optional + method : {'bruteforce', 'pkdtree'}, optional Keyword to override the automatic guessing of the employed search method. return_distances : bool, optional @@ -789,17 +802,21 @@ def self_capped_distance(reference, max_cutoff, min_cutoff=None, box=None, Note ----- - Currently supports brute force, grid-based, and periodic KDtree search + Currently supports brute force, and periodic KDtree search methods. See Also -------- self_distance_array MDAnalysis.lib.pkdtree.PeriodicKDTree.search - MDAnalysis.lib.nsgrid.FastNS.self_search + .. versionchanged:: 0.20.0 Added `return_distances` keyword. + .. versionchanged:: 1.0.1 + nsgrid was temporarily removed and replaced with pkdtree due to issues + relating to its reliability and accuracy (Issues #2919, #2229, #2345, + #2670, #2930) """ if box is not None: box = np.asarray(box, dtype=np.float32) @@ -833,7 +850,7 @@ def _determine_method_self(reference, max_cutoff, min_cutoff=None, box=None, triclinic and must be provided in the same format as returned by :attr:`MDAnalysis.coordinates.base.Timestep.dimensions`:\n ``[lx, ly, lz, alpha, beta, gamma]``. - method : {'bruteforce', 'nsgrid', 'pkdtree'}, optional + method : {'bruteforce', 'pkdtree'}, optional Keyword to override the automatic guessing of the employed search method. @@ -841,10 +858,16 @@ def _determine_method_self(reference, max_cutoff, min_cutoff=None, box=None, ------- function : callable The function implementing the guessed (or deliberatly chosen) method. + + + .. versionchanged:: 1.0.1 + nsgrid was temporarily removed and replaced with pkdtree due to issues + relating to its reliability and accuracy (Issues #2919, #2229, #2345, + #2670, #2930) """ + # TODO: add 'nsgrid': _nsgrid_capped back once fixed methods = {'bruteforce': _bruteforce_capped_self, - 'pkdtree': _pkdtree_capped_self, - 'nsgrid': _nsgrid_capped_self} + 'pkdtree': _pkdtree_capped_self} if method is not None: return methods[method.lower()] @@ -865,7 +888,8 @@ def _determine_method_self(reference, max_cutoff, min_cutoff=None, box=None, if max_cutoff < 0.03*size.min(): return methods['pkdtree'] else: - return methods['nsgrid'] + # Replaced nsgrid with pkdtree temporarily #2930 + return methods['pkdtree'] @check_coords('reference', enforce_copy=False, reduce_result_if_single=False) diff --git a/package/MDAnalysis/lib/nsgrid.cpp b/package/MDAnalysis/lib/nsgrid.cpp index 850162df588..4af66771d31 100644 --- a/package/MDAnalysis/lib/nsgrid.cpp +++ b/package/MDAnalysis/lib/nsgrid.cpp @@ -1,11 +1,11 @@ -/* Generated by Cython 0.29.19 */ +/* Generated by Cython 0.29.21 */ /* BEGIN: Cython Metadata { "distutils": { "depends": [ - "/home/richard/miniconda3/envs/mda/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h", - "/home/richard/miniconda3/envs/mda/lib/python3.6/site-packages/numpy/core/include/numpy/ufuncobject.h" + "/home/mdauser/software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h", + "/home/mdauser/software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/numpy/core/include/numpy/ufuncobject.h" ], "extra_compile_args": [ "-ffast-math", @@ -15,12 +15,12 @@ "-std=c++11" ], "include_dirs": [ - "/home/richard/miniconda3/envs/mda/lib/python3.6/site-packages/numpy/core/include" + "/home/mdauser/software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/numpy/core/include" ], "language": "c++", "name": "MDAnalysis.lib.nsgrid", "sources": [ - "MDAnalysis/lib/nsgrid.pyx" + "/home/mdauser/github/mdanalysis/package/MDAnalysis/lib/nsgrid.pyx" ] }, "module_name": "MDAnalysis.lib.nsgrid" @@ -34,8 +34,8 @@ END: Cython Metadata */ #elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03030000) #error Cython requires Python 2.6+ or Python 3.3+. #else -#define CYTHON_ABI "0_29_19" -#define CYTHON_HEX_VERSION 0x001D13F0 +#define CYTHON_ABI "0_29_21" +#define CYTHON_HEX_VERSION 0x001D15F0 #define CYTHON_FUTURE_DIVISION 0 #include #ifndef offsetof @@ -476,7 +476,11 @@ static CYTHON_INLINE void * PyThread_tss_get(Py_tss_t *key) { #define __Pyx_PyUnicode_DATA(u) PyUnicode_DATA(u) #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i) #define __Pyx_PyUnicode_WRITE(k, d, i, ch) PyUnicode_WRITE(k, d, i, ch) + #if defined(PyUnicode_IS_READY) && defined(PyUnicode_GET_SIZE) #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) + #else + #define __Pyx_PyUnicode_IS_TRUE(u) (0 != PyUnicode_GET_LENGTH(u)) + #endif #else #define CYTHON_PEP393_ENABLED 0 #define PyUnicode_1BYTE_KIND 1 @@ -539,6 +543,13 @@ static CYTHON_INLINE void * PyThread_tss_get(Py_tss_t *key) { #ifndef PySet_CheckExact #define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type) #endif +#if PY_VERSION_HEX >= 0x030900A4 + #define __Pyx_SET_REFCNT(obj, refcnt) Py_SET_REFCNT(obj, refcnt) + #define __Pyx_SET_SIZE(obj, size) Py_SET_SIZE(obj, size) +#else + #define __Pyx_SET_REFCNT(obj, refcnt) Py_REFCNT(obj) = (refcnt) + #define __Pyx_SET_SIZE(obj, size) Py_SIZE(obj) = (size) +#endif #if CYTHON_ASSUME_SAFE_MACROS #define __Pyx_PySequence_SIZE(seq) Py_SIZE(seq) #else @@ -578,7 +589,7 @@ static CYTHON_INLINE void * PyThread_tss_get(Py_tss_t *key) { #define __Pyx_PyInt_AsHash_t PyInt_AsSsize_t #endif #if PY_MAJOR_VERSION >= 3 - #define __Pyx_PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : (Py_INCREF(func), func)) + #define __Pyx_PyMethod_New(func, self, klass) ((self) ? ((void)(klass), PyMethod_New(func, self)) : __Pyx_NewRef(func)) #else #define __Pyx_PyMethod_New(func, self, klass) PyMethod_New(func, self, klass) #endif @@ -992,7 +1003,7 @@ typedef struct { } __Pyx_BufFmt_Context; -/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":775 +/* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":775 * # in Cython to enable them only on the right systems. * * ctypedef npy_int8 int8_t # <<<<<<<<<<<<<< @@ -1001,7 +1012,7 @@ typedef struct { */ typedef npy_int8 __pyx_t_5numpy_int8_t; -/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":776 +/* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":776 * * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t # <<<<<<<<<<<<<< @@ -1010,7 +1021,7 @@ typedef npy_int8 __pyx_t_5numpy_int8_t; */ typedef npy_int16 __pyx_t_5numpy_int16_t; -/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":777 +/* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":777 * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t # <<<<<<<<<<<<<< @@ -1019,7 +1030,7 @@ typedef npy_int16 __pyx_t_5numpy_int16_t; */ typedef npy_int32 __pyx_t_5numpy_int32_t; -/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":778 +/* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":778 * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t * ctypedef npy_int64 int64_t # <<<<<<<<<<<<<< @@ -1028,7 +1039,7 @@ typedef npy_int32 __pyx_t_5numpy_int32_t; */ typedef npy_int64 __pyx_t_5numpy_int64_t; -/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":782 +/* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":782 * #ctypedef npy_int128 int128_t * * ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<< @@ -1037,7 +1048,7 @@ typedef npy_int64 __pyx_t_5numpy_int64_t; */ typedef npy_uint8 __pyx_t_5numpy_uint8_t; -/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":783 +/* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":783 * * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<< @@ -1046,7 +1057,7 @@ typedef npy_uint8 __pyx_t_5numpy_uint8_t; */ typedef npy_uint16 __pyx_t_5numpy_uint16_t; -/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":784 +/* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":784 * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<< @@ -1055,7 +1066,7 @@ typedef npy_uint16 __pyx_t_5numpy_uint16_t; */ typedef npy_uint32 __pyx_t_5numpy_uint32_t; -/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":785 +/* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":785 * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t * ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<< @@ -1064,7 +1075,7 @@ typedef npy_uint32 __pyx_t_5numpy_uint32_t; */ typedef npy_uint64 __pyx_t_5numpy_uint64_t; -/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":789 +/* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":789 * #ctypedef npy_uint128 uint128_t * * ctypedef npy_float32 float32_t # <<<<<<<<<<<<<< @@ -1073,7 +1084,7 @@ typedef npy_uint64 __pyx_t_5numpy_uint64_t; */ typedef npy_float32 __pyx_t_5numpy_float32_t; -/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":790 +/* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":790 * * ctypedef npy_float32 float32_t * ctypedef npy_float64 float64_t # <<<<<<<<<<<<<< @@ -1082,7 +1093,7 @@ typedef npy_float32 __pyx_t_5numpy_float32_t; */ typedef npy_float64 __pyx_t_5numpy_float64_t; -/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":799 +/* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":799 * # The int types are mapped a bit surprising -- * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t # <<<<<<<<<<<<<< @@ -1091,7 +1102,7 @@ typedef npy_float64 __pyx_t_5numpy_float64_t; */ typedef npy_long __pyx_t_5numpy_int_t; -/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":800 +/* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":800 * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t * ctypedef npy_longlong long_t # <<<<<<<<<<<<<< @@ -1100,7 +1111,7 @@ typedef npy_long __pyx_t_5numpy_int_t; */ typedef npy_longlong __pyx_t_5numpy_long_t; -/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":801 +/* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":801 * ctypedef npy_long int_t * ctypedef npy_longlong long_t * ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<< @@ -1109,7 +1120,7 @@ typedef npy_longlong __pyx_t_5numpy_long_t; */ typedef npy_longlong __pyx_t_5numpy_longlong_t; -/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":803 +/* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":803 * ctypedef npy_longlong longlong_t * * ctypedef npy_ulong uint_t # <<<<<<<<<<<<<< @@ -1118,7 +1129,7 @@ typedef npy_longlong __pyx_t_5numpy_longlong_t; */ typedef npy_ulong __pyx_t_5numpy_uint_t; -/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":804 +/* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":804 * * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<< @@ -1127,7 +1138,7 @@ typedef npy_ulong __pyx_t_5numpy_uint_t; */ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; -/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":805 +/* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":805 * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t * ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<< @@ -1136,7 +1147,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; */ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; -/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":807 +/* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":807 * ctypedef npy_ulonglong ulonglong_t * * ctypedef npy_intp intp_t # <<<<<<<<<<<<<< @@ -1145,7 +1156,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; */ typedef npy_intp __pyx_t_5numpy_intp_t; -/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":808 +/* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":808 * * ctypedef npy_intp intp_t * ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<< @@ -1154,7 +1165,7 @@ typedef npy_intp __pyx_t_5numpy_intp_t; */ typedef npy_uintp __pyx_t_5numpy_uintp_t; -/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":810 +/* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":810 * ctypedef npy_uintp uintp_t * * ctypedef npy_double float_t # <<<<<<<<<<<<<< @@ -1163,7 +1174,7 @@ typedef npy_uintp __pyx_t_5numpy_uintp_t; */ typedef npy_double __pyx_t_5numpy_float_t; -/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":811 +/* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":811 * * ctypedef npy_double float_t * ctypedef npy_double double_t # <<<<<<<<<<<<<< @@ -1172,7 +1183,7 @@ typedef npy_double __pyx_t_5numpy_float_t; */ typedef npy_double __pyx_t_5numpy_double_t; -/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":812 +/* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":812 * ctypedef npy_double float_t * ctypedef npy_double double_t * ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<< @@ -1181,7 +1192,7 @@ typedef npy_double __pyx_t_5numpy_double_t; */ typedef npy_longdouble __pyx_t_5numpy_longdouble_t; -/* "MDAnalysis/lib/nsgrid.pyx":91 +/* "MDAnalysis/lib/nsgrid.pyx":100 * DEF EPSILON = 1e-5 * * ctypedef np.int_t ns_int # <<<<<<<<<<<<<< @@ -1190,7 +1201,7 @@ typedef npy_longdouble __pyx_t_5numpy_longdouble_t; */ typedef __pyx_t_5numpy_int_t __pyx_t_10MDAnalysis_3lib_6nsgrid_ns_int; -/* "MDAnalysis/lib/nsgrid.pyx":92 +/* "MDAnalysis/lib/nsgrid.pyx":101 * * ctypedef np.int_t ns_int * ctypedef np.float32_t real # <<<<<<<<<<<<<< @@ -1199,7 +1210,7 @@ typedef __pyx_t_5numpy_int_t __pyx_t_10MDAnalysis_3lib_6nsgrid_ns_int; */ typedef __pyx_t_5numpy_float32_t __pyx_t_10MDAnalysis_3lib_6nsgrid_real; -/* "MDAnalysis/lib/nsgrid.pyx":93 +/* "MDAnalysis/lib/nsgrid.pyx":102 * ctypedef np.int_t ns_int * ctypedef np.float32_t real * ctypedef np.float64_t dreal # <<<<<<<<<<<<<< @@ -1242,7 +1253,7 @@ struct __pyx_MemviewEnum_obj; struct __pyx_memoryview_obj; struct __pyx_memoryviewslice_obj; -/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":814 +/* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":814 * ctypedef npy_longdouble longdouble_t * * ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<< @@ -1251,7 +1262,7 @@ struct __pyx_memoryviewslice_obj; */ typedef npy_cfloat __pyx_t_5numpy_cfloat_t; -/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":815 +/* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":815 * * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<< @@ -1260,7 +1271,7 @@ typedef npy_cfloat __pyx_t_5numpy_cfloat_t; */ typedef npy_cdouble __pyx_t_5numpy_cdouble_t; -/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":816 +/* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":816 * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t * ctypedef npy_clongdouble clongdouble_t # <<<<<<<<<<<<<< @@ -1269,7 +1280,7 @@ typedef npy_cdouble __pyx_t_5numpy_cdouble_t; */ typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t; -/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":818 +/* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":818 * ctypedef npy_clongdouble clongdouble_t * * ctypedef npy_cdouble complex_t # <<<<<<<<<<<<<< @@ -1279,7 +1290,7 @@ typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t; typedef npy_cdouble __pyx_t_5numpy_complex_t; struct __pyx_t_10MDAnalysis_3lib_6nsgrid_cPBCBox_t; -/* "MDAnalysis/lib/nsgrid.pyx":94 +/* "MDAnalysis/lib/nsgrid.pyx":103 * ctypedef np.float32_t real * ctypedef np.float64_t dreal * ctypedef real rvec[DIM] # <<<<<<<<<<<<<< @@ -1288,7 +1299,7 @@ struct __pyx_t_10MDAnalysis_3lib_6nsgrid_cPBCBox_t; */ typedef __pyx_t_10MDAnalysis_3lib_6nsgrid_real __pyx_t_10MDAnalysis_3lib_6nsgrid_rvec[3]; -/* "MDAnalysis/lib/nsgrid.pyx":95 +/* "MDAnalysis/lib/nsgrid.pyx":104 * ctypedef np.float64_t dreal * ctypedef real rvec[DIM] * ctypedef dreal drvec[DIM] # <<<<<<<<<<<<<< @@ -1297,7 +1308,7 @@ typedef __pyx_t_10MDAnalysis_3lib_6nsgrid_real __pyx_t_10MDAnalysis_3lib_6nsgrid */ typedef __pyx_t_10MDAnalysis_3lib_6nsgrid_dreal __pyx_t_10MDAnalysis_3lib_6nsgrid_drvec[3]; -/* "MDAnalysis/lib/nsgrid.pyx":96 +/* "MDAnalysis/lib/nsgrid.pyx":105 * ctypedef real rvec[DIM] * ctypedef dreal drvec[DIM] * ctypedef ns_int ivec[DIM] # <<<<<<<<<<<<<< @@ -1306,7 +1317,7 @@ typedef __pyx_t_10MDAnalysis_3lib_6nsgrid_dreal __pyx_t_10MDAnalysis_3lib_6nsgri */ typedef __pyx_t_10MDAnalysis_3lib_6nsgrid_ns_int __pyx_t_10MDAnalysis_3lib_6nsgrid_ivec[3]; -/* "MDAnalysis/lib/nsgrid.pyx":97 +/* "MDAnalysis/lib/nsgrid.pyx":106 * ctypedef dreal drvec[DIM] * ctypedef ns_int ivec[DIM] * ctypedef real matrix[DIM][DIM] # <<<<<<<<<<<<<< @@ -1315,7 +1326,7 @@ typedef __pyx_t_10MDAnalysis_3lib_6nsgrid_ns_int __pyx_t_10MDAnalysis_3lib_6nsgr */ typedef __pyx_t_10MDAnalysis_3lib_6nsgrid_real __pyx_t_10MDAnalysis_3lib_6nsgrid_matrix[3][3]; -/* "MDAnalysis/lib/nsgrid.pyx":99 +/* "MDAnalysis/lib/nsgrid.pyx":108 * ctypedef real matrix[DIM][DIM] * * ctypedef vector[ns_int] intvec # <<<<<<<<<<<<<< @@ -1324,7 +1335,7 @@ typedef __pyx_t_10MDAnalysis_3lib_6nsgrid_real __pyx_t_10MDAnalysis_3lib_6nsgrid */ typedef std::vector<__pyx_t_10MDAnalysis_3lib_6nsgrid_ns_int> __pyx_t_10MDAnalysis_3lib_6nsgrid_intvec; -/* "MDAnalysis/lib/nsgrid.pyx":100 +/* "MDAnalysis/lib/nsgrid.pyx":109 * * ctypedef vector[ns_int] intvec * ctypedef vector[real] realvec # <<<<<<<<<<<<<< @@ -1333,7 +1344,7 @@ typedef std::vector<__pyx_t_10MDAnalysis_3lib_6nsgrid_ns_int> __pyx_t_10MDAnaly */ typedef std::vector<__pyx_t_10MDAnalysis_3lib_6nsgrid_real> __pyx_t_10MDAnalysis_3lib_6nsgrid_realvec; -/* "MDAnalysis/lib/nsgrid.pyx":101 +/* "MDAnalysis/lib/nsgrid.pyx":110 * ctypedef vector[ns_int] intvec * ctypedef vector[real] realvec * ctypedef vector[dreal] drealvec # <<<<<<<<<<<<<< @@ -1342,7 +1353,7 @@ typedef std::vector<__pyx_t_10MDAnalysis_3lib_6nsgrid_real> __pyx_t_10MDAnalysi */ typedef std::vector<__pyx_t_10MDAnalysis_3lib_6nsgrid_dreal> __pyx_t_10MDAnalysis_3lib_6nsgrid_drealvec; -/* "MDAnalysis/lib/nsgrid.pyx":113 +/* "MDAnalysis/lib/nsgrid.pyx":122 * # Utility class to handle PBC # * ############################### * cdef struct cPBCBox_t: # <<<<<<<<<<<<<< @@ -1357,7 +1368,7 @@ struct __pyx_t_10MDAnalysis_3lib_6nsgrid_cPBCBox_t { __pyx_t_10MDAnalysis_3lib_6nsgrid_dreal max_cutoff2; }; -/* "MDAnalysis/lib/nsgrid.pyx":122 +/* "MDAnalysis/lib/nsgrid.pyx":131 * * # Class to handle PBC calculations * cdef class _PBCBox(object): # <<<<<<<<<<<<<< @@ -1373,7 +1384,7 @@ struct __pyx_obj_10MDAnalysis_3lib_6nsgrid__PBCBox { }; -/* "MDAnalysis/lib/nsgrid.pyx":316 +/* "MDAnalysis/lib/nsgrid.pyx":325 * ######################### * * cdef class NSResults(object): # <<<<<<<<<<<<<< @@ -1395,7 +1406,7 @@ struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_NSResults { }; -/* "MDAnalysis/lib/nsgrid.pyx":511 +/* "MDAnalysis/lib/nsgrid.pyx":520 * * * cdef class _NSGrid(object): # <<<<<<<<<<<<<< @@ -1419,7 +1430,7 @@ struct __pyx_obj_10MDAnalysis_3lib_6nsgrid__NSGrid { }; -/* "MDAnalysis/lib/nsgrid.pyx":698 +/* "MDAnalysis/lib/nsgrid.pyx":707 * * * cdef class FastNS(object): # <<<<<<<<<<<<<< @@ -1516,7 +1527,7 @@ struct __pyx_memoryviewslice_obj { -/* "MDAnalysis/lib/nsgrid.pyx":122 +/* "MDAnalysis/lib/nsgrid.pyx":131 * * # Class to handle PBC calculations * cdef class _PBCBox(object): # <<<<<<<<<<<<<< @@ -1533,7 +1544,7 @@ struct __pyx_vtabstruct_10MDAnalysis_3lib_6nsgrid__PBCBox { static struct __pyx_vtabstruct_10MDAnalysis_3lib_6nsgrid__PBCBox *__pyx_vtabptr_10MDAnalysis_3lib_6nsgrid__PBCBox; -/* "MDAnalysis/lib/nsgrid.pyx":316 +/* "MDAnalysis/lib/nsgrid.pyx":325 * ######################### * * cdef class NSResults(object): # <<<<<<<<<<<<<< @@ -1548,7 +1559,7 @@ struct __pyx_vtabstruct_10MDAnalysis_3lib_6nsgrid_NSResults { static struct __pyx_vtabstruct_10MDAnalysis_3lib_6nsgrid_NSResults *__pyx_vtabptr_10MDAnalysis_3lib_6nsgrid_NSResults; -/* "MDAnalysis/lib/nsgrid.pyx":511 +/* "MDAnalysis/lib/nsgrid.pyx":520 * * * cdef class _NSGrid(object): # <<<<<<<<<<<<<< @@ -1882,6 +1893,63 @@ static CYTHON_INLINE PyObject *__Pyx_GetAttr3(PyObject *, PyObject *, PyObject * __Pyx__ArgTypeTest(obj, type, name, exact)) static int __Pyx__ArgTypeTest(PyObject *obj, PyTypeObject *type, const char *name, int exact); +/* PyObjectCallNoArg.proto */ +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func); +#else +#define __Pyx_PyObject_CallNoArg(func) __Pyx_PyObject_Call(func, __pyx_empty_tuple, NULL) +#endif + +/* PyObjectLookupSpecial.proto */ +#if CYTHON_USE_PYTYPE_LOOKUP && CYTHON_USE_TYPE_SLOTS +static CYTHON_INLINE PyObject* __Pyx_PyObject_LookupSpecial(PyObject* obj, PyObject* attr_name) { + PyObject *res; + PyTypeObject *tp = Py_TYPE(obj); +#if PY_MAJOR_VERSION < 3 + if (unlikely(PyInstance_Check(obj))) + return __Pyx_PyObject_GetAttrStr(obj, attr_name); +#endif + res = _PyType_Lookup(tp, attr_name); + if (likely(res)) { + descrgetfunc f = Py_TYPE(res)->tp_descr_get; + if (!f) { + Py_INCREF(res); + } else { + res = f(res, obj, (PyObject *)tp); + } + } else { + PyErr_SetObject(PyExc_AttributeError, attr_name); + } + return res; +} +#else +#define __Pyx_PyObject_LookupSpecial(o,n) __Pyx_PyObject_GetAttrStr(o,n) +#endif + +/* GetTopmostException.proto */ +#if CYTHON_USE_EXC_INFO_STACK +static _PyErr_StackItem * __Pyx_PyErr_GetTopmostException(PyThreadState *tstate); +#endif + +/* SaveResetException.proto */ +#if CYTHON_FAST_THREAD_STATE +#define __Pyx_ExceptionSave(type, value, tb) __Pyx__ExceptionSave(__pyx_tstate, type, value, tb) +static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); +#define __Pyx_ExceptionReset(type, value, tb) __Pyx__ExceptionReset(__pyx_tstate, type, value, tb) +static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb); +#else +#define __Pyx_ExceptionSave(type, value, tb) PyErr_GetExcInfo(type, value, tb) +#define __Pyx_ExceptionReset(type, value, tb) PyErr_SetExcInfo(type, value, tb) +#endif + +/* GetException.proto */ +#if CYTHON_FAST_THREAD_STATE +#define __Pyx_GetException(type, value, tb) __Pyx__GetException(__pyx_tstate, type, value, tb) +static int __Pyx__GetException(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); +#else +static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); +#endif + /* Import.proto */ static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); @@ -1945,30 +2013,6 @@ static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index); /* RaiseNoneIterError.proto */ static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void); -/* GetTopmostException.proto */ -#if CYTHON_USE_EXC_INFO_STACK -static _PyErr_StackItem * __Pyx_PyErr_GetTopmostException(PyThreadState *tstate); -#endif - -/* SaveResetException.proto */ -#if CYTHON_FAST_THREAD_STATE -#define __Pyx_ExceptionSave(type, value, tb) __Pyx__ExceptionSave(__pyx_tstate, type, value, tb) -static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); -#define __Pyx_ExceptionReset(type, value, tb) __Pyx__ExceptionReset(__pyx_tstate, type, value, tb) -static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb); -#else -#define __Pyx_ExceptionSave(type, value, tb) PyErr_GetExcInfo(type, value, tb) -#define __Pyx_ExceptionReset(type, value, tb) PyErr_SetExcInfo(type, value, tb) -#endif - -/* GetException.proto */ -#if CYTHON_FAST_THREAD_STATE -#define __Pyx_GetException(type, value, tb) __Pyx__GetException(__pyx_tstate, type, value, tb) -static int __Pyx__GetException(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); -#else -static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); -#endif - /* ListCompAppend.proto */ #if CYTHON_USE_PYLIST_INTERNALS && CYTHON_ASSUME_SAFE_MACROS static CYTHON_INLINE int __Pyx_ListComp_Append(PyObject* list, PyObject* x) { @@ -1977,7 +2021,7 @@ static CYTHON_INLINE int __Pyx_ListComp_Append(PyObject* list, PyObject* x) { if (likely(L->allocated > len)) { Py_INCREF(x); PyList_SET_ITEM(list, len, x); - Py_SIZE(list) = len+1; + __Pyx_SET_SIZE(list, len + 1); return 0; } return PyList_Append(list, x); @@ -2086,7 +2130,7 @@ static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) { if (likely(L->allocated > len) & likely(len > (L->allocated >> 1))) { Py_INCREF(x); PyList_SET_ITEM(list, len, x); - Py_SIZE(list) = len+1; + __Pyx_SET_SIZE(list, len + 1); return 0; } return PyList_Append(list, x); @@ -2545,6 +2589,7 @@ static PyObject *__pyx_builtin_range; static PyObject *__pyx_builtin_ValueError; static PyObject *__pyx_builtin_TypeError; static PyObject *__pyx_builtin_MemoryError; +static PyObject *__pyx_builtin_UserWarning; static PyObject *__pyx_builtin_RuntimeError; static PyObject *__pyx_builtin_ImportError; static PyObject *__pyx_builtin_enumerate; @@ -2564,6 +2609,7 @@ static const char __pyx_k_pbc[] = "pbc"; static const char __pyx_k_base[] = "base"; static const char __pyx_k_copy[] = "copy"; static const char __pyx_k_dict[] = "__dict__"; +static const char __pyx_k_exit[] = "__exit__"; static const char __pyx_k_intp[] = "intp"; static const char __pyx_k_main[] = "__main__"; static const char __pyx_k_mode[] = "mode"; @@ -2575,10 +2621,12 @@ static const char __pyx_k_sqrt[] = "sqrt"; static const char __pyx_k_step[] = "step"; static const char __pyx_k_stop[] = "stop"; static const char __pyx_k_test[] = "__test__"; +static const char __pyx_k_warn[] = "warn"; static const char __pyx_k_ASCII[] = "ASCII"; static const char __pyx_k_class[] = "__class__"; static const char __pyx_k_dtype[] = "dtype"; static const char __pyx_k_empty[] = "empty"; +static const char __pyx_k_enter[] = "__enter__"; static const char __pyx_k_error[] = "error"; static const char __pyx_k_flags[] = "flags"; static const char __pyx_k_force[] = "force"; @@ -2590,6 +2638,7 @@ static const char __pyx_k_start[] = "start"; static const char __pyx_k_FastNS[] = "FastNS"; static const char __pyx_k_NSGrid[] = "_NSGrid"; static const char __pyx_k_PBCBox[] = "_PBCBox"; +static const char __pyx_k_always[] = "always"; static const char __pyx_k_astype[] = "astype"; static const char __pyx_k_coords[] = "coords"; static const char __pyx_k_cutoff[] = "cutoff"; @@ -2616,6 +2665,7 @@ static const char __pyx_k_max_size[] = "max_size"; static const char __pyx_k_periodic[] = "periodic"; static const char __pyx_k_pyx_type[] = "__pyx_type"; static const char __pyx_k_setstate[] = "__setstate__"; +static const char __pyx_k_warnings[] = "warnings"; static const char __pyx_k_NSResults[] = "NSResults"; static const char __pyx_k_TypeError[] = "TypeError"; static const char __pyx_k_enumerate[] = "enumerate"; @@ -2628,13 +2678,16 @@ static const char __pyx_k_pyx_vtable[] = "__pyx_vtable__"; static const char __pyx_k_ImportError[] = "ImportError"; static const char __pyx_k_MemoryError[] = "MemoryError"; static const char __pyx_k_PickleError[] = "PickleError"; +static const char __pyx_k_UserWarning[] = "UserWarning"; static const char __pyx_k_RuntimeError[] = "RuntimeError"; static const char __pyx_k_max_gridsize[] = "max_gridsize"; static const char __pyx_k_pyx_checksum[] = "__pyx_checksum"; static const char __pyx_k_searchcoords[] = "searchcoords"; +static const char __pyx_k_simplefilter[] = "simplefilter"; static const char __pyx_k_stringsource[] = "stringsource"; static const char __pyx_k_pyx_getbuffer[] = "__pyx_getbuffer"; static const char __pyx_k_reduce_cython[] = "__reduce_cython__"; +static const char __pyx_k_catch_warnings[] = "catch_warnings"; static const char __pyx_k_View_MemoryView[] = "View.MemoryView"; static const char __pyx_k_allocate_buffer[] = "allocate_buffer"; static const char __pyx_k_dtype_is_object[] = "dtype_is_object"; @@ -2662,7 +2715,7 @@ static const char __pyx_k_Box_must_be_a_x_matrix_Got_x[] = "Box must be a {} x { static const char __pyx_k_unable_to_allocate_array_data[] = "unable to allocate array data."; static const char __pyx_k_Could_not_allocate_memory_from[] = "Could not allocate memory from _NSGrid.nbeads ({} bits requested)"; static const char __pyx_k_strided_and_direct_or_indirect[] = ""; -static const char __pyx_k_Neighbor_search_library_mod_MDA[] = "\nNeighbor search library --- :mod:`MDAnalysis.lib.nsgrid`\n========================================================\n\n\nAbout the code\n--------------\n\nThis Neighbor search library is a serialized Cython version greatly\ninspired by the NS grid search implemented in\n`GROMACS `_ .\n\nGROMACS 4.x code (more precisely\n`nsgrid.c `_\nand `ns.c `_ )\nwas used as reference to write this file.\n\nGROMACS 4.x code is released under the GNU Public Licence v2.\n\nAbout the algorithm\n-------------------\n\nThe neighbor search implemented here is based on\n`cell lists `_ which allow\ncomputation of pairs [#]_ with a cost of :math:`O(N)`, instead\nof :math:`O(N^2)`. The basic algorithm is described in\nAppendix F, Page 552 of\n``Understanding Molecular Dynamics: From Algorithm to Applications`` by Frenkel and Smit.\n\nIn brief, the algorithm divides the domain into smaller subdomains called `cells`\nand distributes every particle to these cells based on their positions. Subsequently,\nany distance based query first identifies the corresponding cell position in the\ndomain followed by distance evaluations within the identified cell and\nneighboring cells only. Care must be taken to ensure that `cellsize` is\ngreater than the desired search distance, otherwise all of the neighbours might\nnot reflect in the results.\n\n.. [#] a pair correspond to two particles that are considered as neighbors .\n\n.. versionadded:: 0.19.0\n\nClasses\n-------\n"; +static const char __pyx_k_Neighbor_search_library_mod_MDA[] = "\nNeighbor search library --- :mod:`MDAnalysis.lib.nsgrid`\n========================================================\n\n\n.. warning::\n The current nsgrid code can return incorrect values. Do not use it for\n production use. We instead recommend the use of\n :mod:`MDAnalysis.lib.pkdtree`. See issue\n `#2930 `_ for further\n information.\n\n\nAbout the code\n--------------\n\nThis Neighbor search library is a serialized Cython version greatly\ninspired by the NS grid search implemented in\n`GROMACS `_ .\n\nGROMACS 4.x code (more precisely\n`nsgrid.c `_\nand `ns.c `_ )\nwas used as reference to write this file.\n\nGROMACS 4.x code is released under the GNU Public Licence v2.\n\nAbout the algorithm\n-------------------\n\nThe neighbor search implemented here is based on\n`cell lists `_ which allow\ncomputation of pairs [#]_ with a cost of :math:`O(N)`, instead\nof :math:`O(N^2)`. The basic algorithm is described in\nAppendix F, Page 552 of\n``Understanding Molecular Dynamics: From Algorithm to Applications`` by Frenkel and Smit.\n\nIn brief, the algorithm divides the domain into smaller subdomains called `cells`\nand distributes every particle to these cells based on their positions. Subsequently,\nany distance based query first identifies the corresponding cell position in the\ndomain followed by distance evaluations within the identified cell and\nneighboring cells only. Care must be taken to ensure that `cellsize` is\ngreater than the desired search distance, otherwise all of the neighbours might\nnot reflect in the results.\n\n.. [#] a pair correspond to two particles that are considered as neighbors .\n\n.. versionadded:: 0.19.0\n\nClasses\n-------\n"; static const char __pyx_k_Pickling_of_struct_members_such[] = "Pickling of struct members such as self.c_pbcbox must be explicitly requested with @auto_pickle(True)"; static const char __pyx_k_coords_must_have_a_shape_of_n_3[] = "coords must have a shape of (n, 3), got {}."; static const char __pyx_k_numpy_core_multiarray_failed_to[] = "numpy.core.multiarray failed to import"; @@ -2686,6 +2739,7 @@ static const char __pyx_k_Indirect_dimensions_not_supporte[] = "Indirect dimensi static const char __pyx_k_Invalid_mode_expected_c_or_fortr[] = "Invalid mode, expected 'c' or 'fortran', got %s"; static const char __pyx_k_Non_native_byte_order_not_suppor[] = "Non-native byte order not supported"; static const char __pyx_k_Out_of_bounds_on_buffer_access_a[] = "Out of bounds on buffer access (axis %d)"; +static const char __pyx_k_The_current_nsgrid_code_can_retu[] = "The current nsgrid code can return incorrect values and should not be used for production work. We instead recommend the use of MDAnalysis.lib.pkdtree. See issue #2930 for more details."; static const char __pyx_k_Unable_to_convert_item_to_object[] = "Unable to convert item to object"; static const char __pyx_k_got_differing_extents_in_dimensi[] = "got differing extents in dimension %d (got %d and %d)"; static const char __pyx_k_ndarray_is_not_Fortran_contiguou[] = "ndarray is not Fortran contiguous"; @@ -2736,18 +2790,22 @@ static PyObject *__pyx_n_s_PBCBox; static PyObject *__pyx_n_s_PickleError; static PyObject *__pyx_kp_s_Pickling_of_struct_members_such; static PyObject *__pyx_n_s_RuntimeError; +static PyObject *__pyx_kp_s_The_current_nsgrid_code_can_retu; static PyObject *__pyx_n_s_TypeError; static PyObject *__pyx_kp_s_Unable_to_convert_item_to_object; +static PyObject *__pyx_n_s_UserWarning; static PyObject *__pyx_n_s_ValueError; static PyObject *__pyx_n_s_View_MemoryView; static PyObject *__pyx_n_s_allclose; static PyObject *__pyx_n_s_allocate_buffer; +static PyObject *__pyx_n_s_always; static PyObject *__pyx_n_s_asarray; static PyObject *__pyx_n_s_astype; static PyObject *__pyx_n_s_base; static PyObject *__pyx_n_s_box; static PyObject *__pyx_n_s_c; static PyObject *__pyx_n_u_c; +static PyObject *__pyx_n_s_catch_warnings; static PyObject *__pyx_n_s_class; static PyObject *__pyx_n_s_cline_in_traceback; static PyObject *__pyx_kp_s_contiguous_and_direct; @@ -2761,8 +2819,10 @@ static PyObject *__pyx_n_s_dtype; static PyObject *__pyx_n_s_dtype_is_object; static PyObject *__pyx_n_s_empty; static PyObject *__pyx_n_s_encode; +static PyObject *__pyx_n_s_enter; static PyObject *__pyx_n_s_enumerate; static PyObject *__pyx_n_s_error; +static PyObject *__pyx_n_s_exit; static PyObject *__pyx_n_s_flags; static PyObject *__pyx_n_s_float32; static PyObject *__pyx_n_s_force; @@ -2821,6 +2881,7 @@ static PyObject *__pyx_kp_s_self_beadids_self_cellids_self_n; static PyObject *__pyx_n_s_setstate; static PyObject *__pyx_n_s_setstate_cython; static PyObject *__pyx_n_s_shape; +static PyObject *__pyx_n_s_simplefilter; static PyObject *__pyx_n_s_size; static PyObject *__pyx_n_s_sqrt; static PyObject *__pyx_n_s_start; @@ -2838,6 +2899,8 @@ static PyObject *__pyx_kp_s_unable_to_allocate_shape_and_str; static PyObject *__pyx_kp_u_unknown_dtype_code_in_numpy_pxd; static PyObject *__pyx_n_s_unpack; static PyObject *__pyx_n_s_update; +static PyObject *__pyx_n_s_warn; +static PyObject *__pyx_n_s_warnings; static int __pyx_pf_10MDAnalysis_3lib_6nsgrid_7_PBCBox___init__(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid__PBCBox *__pyx_v_self, __Pyx_memviewslice __pyx_v_box, int __pyx_v_periodic); /* proto */ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_7_PBCBox_2update(struct __pyx_obj_10MDAnalysis_3lib_6nsgrid__PBCBox *__pyx_v_self, __Pyx_memviewslice __pyx_v_box); /* proto */ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_7_PBCBox_4__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_10MDAnalysis_3lib_6nsgrid__PBCBox *__pyx_v_self); /* proto */ @@ -2927,15 +2990,15 @@ static PyObject *__pyx_int_184977713; static PyObject *__pyx_int_221827040; static PyObject *__pyx_int_neg_1; static PyObject *__pyx_tuple_; -static PyObject *__pyx_slice__6; +static PyObject *__pyx_slice__8; static PyObject *__pyx_tuple__2; static PyObject *__pyx_tuple__3; static PyObject *__pyx_tuple__4; static PyObject *__pyx_tuple__5; +static PyObject *__pyx_tuple__6; static PyObject *__pyx_tuple__7; -static PyObject *__pyx_tuple__8; static PyObject *__pyx_tuple__9; -static PyObject *__pyx_slice__32; +static PyObject *__pyx_slice__34; static PyObject *__pyx_tuple__10; static PyObject *__pyx_tuple__11; static PyObject *__pyx_tuple__12; @@ -2958,23 +3021,25 @@ static PyObject *__pyx_tuple__28; static PyObject *__pyx_tuple__29; static PyObject *__pyx_tuple__30; static PyObject *__pyx_tuple__31; +static PyObject *__pyx_tuple__32; static PyObject *__pyx_tuple__33; -static PyObject *__pyx_tuple__34; static PyObject *__pyx_tuple__35; static PyObject *__pyx_tuple__36; +static PyObject *__pyx_tuple__37; static PyObject *__pyx_tuple__38; static PyObject *__pyx_tuple__40; -static PyObject *__pyx_tuple__41; static PyObject *__pyx_tuple__42; static PyObject *__pyx_tuple__43; static PyObject *__pyx_tuple__44; static PyObject *__pyx_tuple__45; -static PyObject *__pyx_codeobj__37; +static PyObject *__pyx_tuple__46; +static PyObject *__pyx_tuple__47; static PyObject *__pyx_codeobj__39; -static PyObject *__pyx_codeobj__46; +static PyObject *__pyx_codeobj__41; +static PyObject *__pyx_codeobj__48; /* Late includes */ -/* "MDAnalysis/lib/nsgrid.pyx":104 +/* "MDAnalysis/lib/nsgrid.pyx":113 * * # Useful Functions * cdef real rvec_norm2(const rvec a) nogil: # <<<<<<<<<<<<<< @@ -2985,7 +3050,7 @@ static PyObject *__pyx_codeobj__46; static __pyx_t_10MDAnalysis_3lib_6nsgrid_real __pyx_f_10MDAnalysis_3lib_6nsgrid_rvec_norm2(__pyx_t_10MDAnalysis_3lib_6nsgrid_real *__pyx_v_a) { __pyx_t_10MDAnalysis_3lib_6nsgrid_real __pyx_r; - /* "MDAnalysis/lib/nsgrid.pyx":105 + /* "MDAnalysis/lib/nsgrid.pyx":114 * # Useful Functions * cdef real rvec_norm2(const rvec a) nogil: * return a[XX]*a[XX] + a[YY]*a[YY] + a[ZZ]*a[ZZ] # <<<<<<<<<<<<<< @@ -2995,7 +3060,7 @@ static __pyx_t_10MDAnalysis_3lib_6nsgrid_real __pyx_f_10MDAnalysis_3lib_6nsgrid_ __pyx_r = ((((__pyx_v_a[0]) * (__pyx_v_a[0])) + ((__pyx_v_a[1]) * (__pyx_v_a[1]))) + ((__pyx_v_a[2]) * (__pyx_v_a[2]))); goto __pyx_L0; - /* "MDAnalysis/lib/nsgrid.pyx":104 + /* "MDAnalysis/lib/nsgrid.pyx":113 * * # Useful Functions * cdef real rvec_norm2(const rvec a) nogil: # <<<<<<<<<<<<<< @@ -3008,7 +3073,7 @@ static __pyx_t_10MDAnalysis_3lib_6nsgrid_real __pyx_f_10MDAnalysis_3lib_6nsgrid_ return __pyx_r; } -/* "MDAnalysis/lib/nsgrid.pyx":107 +/* "MDAnalysis/lib/nsgrid.pyx":116 * return a[XX]*a[XX] + a[YY]*a[YY] + a[ZZ]*a[ZZ] * * cdef dreal drvec_norm2(const drvec a) nogil: # <<<<<<<<<<<<<< @@ -3019,7 +3084,7 @@ static __pyx_t_10MDAnalysis_3lib_6nsgrid_real __pyx_f_10MDAnalysis_3lib_6nsgrid_ static __pyx_t_10MDAnalysis_3lib_6nsgrid_dreal __pyx_f_10MDAnalysis_3lib_6nsgrid_drvec_norm2(__pyx_t_10MDAnalysis_3lib_6nsgrid_dreal *__pyx_v_a) { __pyx_t_10MDAnalysis_3lib_6nsgrid_dreal __pyx_r; - /* "MDAnalysis/lib/nsgrid.pyx":108 + /* "MDAnalysis/lib/nsgrid.pyx":117 * * cdef dreal drvec_norm2(const drvec a) nogil: * return a[XX]*a[XX] + a[YY]*a[YY] + a[ZZ]*a[ZZ] # <<<<<<<<<<<<<< @@ -3029,7 +3094,7 @@ static __pyx_t_10MDAnalysis_3lib_6nsgrid_dreal __pyx_f_10MDAnalysis_3lib_6nsgrid __pyx_r = ((((__pyx_v_a[0]) * (__pyx_v_a[0])) + ((__pyx_v_a[1]) * (__pyx_v_a[1]))) + ((__pyx_v_a[2]) * (__pyx_v_a[2]))); goto __pyx_L0; - /* "MDAnalysis/lib/nsgrid.pyx":107 + /* "MDAnalysis/lib/nsgrid.pyx":116 * return a[XX]*a[XX] + a[YY]*a[YY] + a[ZZ]*a[ZZ] * * cdef dreal drvec_norm2(const drvec a) nogil: # <<<<<<<<<<<<<< @@ -3042,7 +3107,7 @@ static __pyx_t_10MDAnalysis_3lib_6nsgrid_dreal __pyx_f_10MDAnalysis_3lib_6nsgrid return __pyx_r; } -/* "MDAnalysis/lib/nsgrid.pyx":146 +/* "MDAnalysis/lib/nsgrid.pyx":155 * cdef bint periodic * * def __init__(self, real[:, ::1] box, bint periodic): # <<<<<<<<<<<<<< @@ -3088,11 +3153,11 @@ static int __pyx_pw_10MDAnalysis_3lib_6nsgrid_7_PBCBox_1__init__(PyObject *__pyx case 1: if (likely((values[1] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_periodic)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("__init__", 1, 2, 2, 1); __PYX_ERR(0, 146, __pyx_L3_error) + __Pyx_RaiseArgtupleInvalid("__init__", 1, 2, 2, 1); __PYX_ERR(0, 155, __pyx_L3_error) } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) __PYX_ERR(0, 146, __pyx_L3_error) + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) __PYX_ERR(0, 155, __pyx_L3_error) } } else if (PyTuple_GET_SIZE(__pyx_args) != 2) { goto __pyx_L5_argtuple_error; @@ -3100,12 +3165,12 @@ static int __pyx_pw_10MDAnalysis_3lib_6nsgrid_7_PBCBox_1__init__(PyObject *__pyx values[0] = PyTuple_GET_ITEM(__pyx_args, 0); values[1] = PyTuple_GET_ITEM(__pyx_args, 1); } - __pyx_v_box = __Pyx_PyObject_to_MemoryviewSlice_d_dc_nn___pyx_t_10MDAnalysis_3lib_6nsgrid_real(values[0], PyBUF_WRITABLE); if (unlikely(!__pyx_v_box.memview)) __PYX_ERR(0, 146, __pyx_L3_error) - __pyx_v_periodic = __Pyx_PyObject_IsTrue(values[1]); if (unlikely((__pyx_v_periodic == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 146, __pyx_L3_error) + __pyx_v_box = __Pyx_PyObject_to_MemoryviewSlice_d_dc_nn___pyx_t_10MDAnalysis_3lib_6nsgrid_real(values[0], PyBUF_WRITABLE); if (unlikely(!__pyx_v_box.memview)) __PYX_ERR(0, 155, __pyx_L3_error) + __pyx_v_periodic = __Pyx_PyObject_IsTrue(values[1]); if (unlikely((__pyx_v_periodic == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 155, __pyx_L3_error) } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("__init__", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(0, 146, __pyx_L3_error) + __Pyx_RaiseArgtupleInvalid("__init__", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(0, 155, __pyx_L3_error) __pyx_L3_error:; __Pyx_AddTraceback("MDAnalysis.lib.nsgrid._PBCBox.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); @@ -3130,7 +3195,7 @@ static int __pyx_pf_10MDAnalysis_3lib_6nsgrid_7_PBCBox___init__(struct __pyx_obj int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__init__", 0); - /* "MDAnalysis/lib/nsgrid.pyx":159 + /* "MDAnalysis/lib/nsgrid.pyx":168 * """ * * self.periodic = periodic # <<<<<<<<<<<<<< @@ -3139,16 +3204,16 @@ static int __pyx_pf_10MDAnalysis_3lib_6nsgrid_7_PBCBox___init__(struct __pyx_obj */ __pyx_v_self->periodic = __pyx_v_periodic; - /* "MDAnalysis/lib/nsgrid.pyx":160 + /* "MDAnalysis/lib/nsgrid.pyx":169 * * self.periodic = periodic * self.update(box) # <<<<<<<<<<<<<< * * cdef void fast_update(self, real[:, ::1] box) nogil: */ - __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_update); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 160, __pyx_L1_error) + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_update); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 169, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_2); - __pyx_t_3 = __pyx_memoryview_fromslice(__pyx_v_box, 2, (PyObject *(*)(char *)) __pyx_memview_get_nn___pyx_t_10MDAnalysis_3lib_6nsgrid_real, (int (*)(char *, PyObject *)) __pyx_memview_set_nn___pyx_t_10MDAnalysis_3lib_6nsgrid_real, 0);; if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 160, __pyx_L1_error) + __pyx_t_3 = __pyx_memoryview_fromslice(__pyx_v_box, 2, (PyObject *(*)(char *)) __pyx_memview_get_nn___pyx_t_10MDAnalysis_3lib_6nsgrid_real, (int (*)(char *, PyObject *)) __pyx_memview_set_nn___pyx_t_10MDAnalysis_3lib_6nsgrid_real, 0);; if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 169, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); __pyx_t_4 = NULL; if (CYTHON_UNPACK_METHODS && likely(PyMethod_Check(__pyx_t_2))) { @@ -3163,12 +3228,12 @@ static int __pyx_pf_10MDAnalysis_3lib_6nsgrid_7_PBCBox___init__(struct __pyx_obj __pyx_t_1 = (__pyx_t_4) ? __Pyx_PyObject_Call2Args(__pyx_t_2, __pyx_t_4, __pyx_t_3) : __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_3); __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0; __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 160, __pyx_L1_error) + if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 169, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "MDAnalysis/lib/nsgrid.pyx":146 + /* "MDAnalysis/lib/nsgrid.pyx":155 * cdef bint periodic * * def __init__(self, real[:, ::1] box, bint periodic): # <<<<<<<<<<<<<< @@ -3192,7 +3257,7 @@ static int __pyx_pf_10MDAnalysis_3lib_6nsgrid_7_PBCBox___init__(struct __pyx_obj return __pyx_r; } -/* "MDAnalysis/lib/nsgrid.pyx":162 +/* "MDAnalysis/lib/nsgrid.pyx":171 * self.update(box) * * cdef void fast_update(self, real[:, ::1] box) nogil: # <<<<<<<<<<<<<< @@ -3219,7 +3284,7 @@ static void __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_update(struct __pyx_ __pyx_t_10MDAnalysis_3lib_6nsgrid_real __pyx_t_11; __pyx_t_10MDAnalysis_3lib_6nsgrid_dreal __pyx_t_12; - /* "MDAnalysis/lib/nsgrid.pyx":174 + /* "MDAnalysis/lib/nsgrid.pyx":183 * * # Update matrix * self.is_triclinic = False # <<<<<<<<<<<<<< @@ -3228,7 +3293,7 @@ static void __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_update(struct __pyx_ */ __pyx_v_self->is_triclinic = 0; - /* "MDAnalysis/lib/nsgrid.pyx":175 + /* "MDAnalysis/lib/nsgrid.pyx":184 * # Update matrix * self.is_triclinic = False * for i in range(DIM): # <<<<<<<<<<<<<< @@ -3238,7 +3303,7 @@ static void __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_update(struct __pyx_ for (__pyx_t_1 = 0; __pyx_t_1 < 3; __pyx_t_1+=1) { __pyx_v_i = __pyx_t_1; - /* "MDAnalysis/lib/nsgrid.pyx":176 + /* "MDAnalysis/lib/nsgrid.pyx":185 * self.is_triclinic = False * for i in range(DIM): * for j in range(DIM): # <<<<<<<<<<<<<< @@ -3248,7 +3313,7 @@ static void __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_update(struct __pyx_ for (__pyx_t_2 = 0; __pyx_t_2 < 3; __pyx_t_2+=1) { __pyx_v_j = __pyx_t_2; - /* "MDAnalysis/lib/nsgrid.pyx":177 + /* "MDAnalysis/lib/nsgrid.pyx":186 * for i in range(DIM): * for j in range(DIM): * self.c_pbcbox.box[i][j] = box[i, j] # <<<<<<<<<<<<<< @@ -3261,7 +3326,7 @@ static void __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_update(struct __pyx_ if (__pyx_t_4 < 0) __pyx_t_4 += __pyx_v_box.shape[1]; ((__pyx_v_self->c_pbcbox.box[__pyx_v_i])[__pyx_v_j]) = (*((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=1 */ ((char *) (((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=0 */ (__pyx_v_box.data + __pyx_t_3 * __pyx_v_box.strides[0]) )) + __pyx_t_4)) ))); - /* "MDAnalysis/lib/nsgrid.pyx":179 + /* "MDAnalysis/lib/nsgrid.pyx":188 * self.c_pbcbox.box[i][j] = box[i, j] * * if i != j: # <<<<<<<<<<<<<< @@ -3271,7 +3336,7 @@ static void __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_update(struct __pyx_ __pyx_t_5 = ((__pyx_v_i != __pyx_v_j) != 0); if (__pyx_t_5) { - /* "MDAnalysis/lib/nsgrid.pyx":183 + /* "MDAnalysis/lib/nsgrid.pyx":192 * # elements to zero if the box is orthogonal, so we can * # safely check floating point values for equality here * if box[i, j] != 0.0: # <<<<<<<<<<<<<< @@ -3285,7 +3350,7 @@ static void __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_update(struct __pyx_ __pyx_t_5 = (((*((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=1 */ ((char *) (((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=0 */ (__pyx_v_box.data + __pyx_t_4 * __pyx_v_box.strides[0]) )) + __pyx_t_3)) ))) != 0.0) != 0); if (__pyx_t_5) { - /* "MDAnalysis/lib/nsgrid.pyx":184 + /* "MDAnalysis/lib/nsgrid.pyx":193 * # safely check floating point values for equality here * if box[i, j] != 0.0: * self.is_triclinic = True # <<<<<<<<<<<<<< @@ -3294,7 +3359,7 @@ static void __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_update(struct __pyx_ */ __pyx_v_self->is_triclinic = 1; - /* "MDAnalysis/lib/nsgrid.pyx":183 + /* "MDAnalysis/lib/nsgrid.pyx":192 * # elements to zero if the box is orthogonal, so we can * # safely check floating point values for equality here * if box[i, j] != 0.0: # <<<<<<<<<<<<<< @@ -3303,7 +3368,7 @@ static void __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_update(struct __pyx_ */ } - /* "MDAnalysis/lib/nsgrid.pyx":179 + /* "MDAnalysis/lib/nsgrid.pyx":188 * self.c_pbcbox.box[i][j] = box[i, j] * * if i != j: # <<<<<<<<<<<<<< @@ -3314,7 +3379,7 @@ static void __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_update(struct __pyx_ } } - /* "MDAnalysis/lib/nsgrid.pyx":187 + /* "MDAnalysis/lib/nsgrid.pyx":196 * * # Update diagonals * for i in range(DIM): # <<<<<<<<<<<<<< @@ -3324,7 +3389,7 @@ static void __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_update(struct __pyx_ for (__pyx_t_1 = 0; __pyx_t_1 < 3; __pyx_t_1+=1) { __pyx_v_i = __pyx_t_1; - /* "MDAnalysis/lib/nsgrid.pyx":188 + /* "MDAnalysis/lib/nsgrid.pyx":197 * # Update diagonals * for i in range(DIM): * self.c_pbcbox.fbox_diag[i] = box[i, i] # <<<<<<<<<<<<<< @@ -3337,7 +3402,7 @@ static void __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_update(struct __pyx_ if (__pyx_t_4 < 0) __pyx_t_4 += __pyx_v_box.shape[1]; (__pyx_v_self->c_pbcbox.fbox_diag[__pyx_v_i]) = (*((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=1 */ ((char *) (((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=0 */ (__pyx_v_box.data + __pyx_t_3 * __pyx_v_box.strides[0]) )) + __pyx_t_4)) ))); - /* "MDAnalysis/lib/nsgrid.pyx":189 + /* "MDAnalysis/lib/nsgrid.pyx":198 * for i in range(DIM): * self.c_pbcbox.fbox_diag[i] = box[i, i] * self.c_pbcbox.hbox_diag[i] = self.c_pbcbox.fbox_diag[i] * 0.5 # <<<<<<<<<<<<<< @@ -3346,7 +3411,7 @@ static void __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_update(struct __pyx_ */ (__pyx_v_self->c_pbcbox.hbox_diag[__pyx_v_i]) = ((__pyx_v_self->c_pbcbox.fbox_diag[__pyx_v_i]) * 0.5); - /* "MDAnalysis/lib/nsgrid.pyx":190 + /* "MDAnalysis/lib/nsgrid.pyx":199 * self.c_pbcbox.fbox_diag[i] = box[i, i] * self.c_pbcbox.hbox_diag[i] = self.c_pbcbox.fbox_diag[i] * 0.5 * self.c_pbcbox.mhbox_diag[i] = - self.c_pbcbox.hbox_diag[i] # <<<<<<<<<<<<<< @@ -3356,7 +3421,7 @@ static void __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_update(struct __pyx_ (__pyx_v_self->c_pbcbox.mhbox_diag[__pyx_v_i]) = (-(__pyx_v_self->c_pbcbox.hbox_diag[__pyx_v_i])); } - /* "MDAnalysis/lib/nsgrid.pyx":196 + /* "MDAnalysis/lib/nsgrid.pyx":205 * # Physical limitation of the cut-off * # by half the length of the shortest box vector. * min_hv2 = min(0.25 * rvec_norm2(&box[XX, XX]), 0.25 * rvec_norm2(&box[YY, XX])) # <<<<<<<<<<<<<< @@ -3380,7 +3445,7 @@ static void __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_update(struct __pyx_ } __pyx_v_min_hv2 = __pyx_t_8; - /* "MDAnalysis/lib/nsgrid.pyx":197 + /* "MDAnalysis/lib/nsgrid.pyx":206 * # by half the length of the shortest box vector. * min_hv2 = min(0.25 * rvec_norm2(&box[XX, XX]), 0.25 * rvec_norm2(&box[YY, XX])) * min_hv2 = min(min_hv2, 0.25 * rvec_norm2(&box[ZZ, XX])) # <<<<<<<<<<<<<< @@ -3400,7 +3465,7 @@ static void __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_update(struct __pyx_ } __pyx_v_min_hv2 = __pyx_t_10; - /* "MDAnalysis/lib/nsgrid.pyx":203 + /* "MDAnalysis/lib/nsgrid.pyx":212 * # in the grid search and pbc_dx is a lot faster * # than checking all possible combinations. * tmp = box[YY, YY] # <<<<<<<<<<<<<< @@ -3413,7 +3478,7 @@ static void __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_update(struct __pyx_ if (__pyx_t_4 < 0) __pyx_t_4 += __pyx_v_box.shape[1]; __pyx_v_tmp = (*((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=1 */ ((char *) (((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=0 */ (__pyx_v_box.data + __pyx_t_3 * __pyx_v_box.strides[0]) )) + __pyx_t_4)) ))); - /* "MDAnalysis/lib/nsgrid.pyx":204 + /* "MDAnalysis/lib/nsgrid.pyx":213 * # than checking all possible combinations. * tmp = box[YY, YY] * if box[ZZ, YY] < 0: # <<<<<<<<<<<<<< @@ -3427,7 +3492,7 @@ static void __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_update(struct __pyx_ __pyx_t_5 = (((*((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=1 */ ((char *) (((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=0 */ (__pyx_v_box.data + __pyx_t_4 * __pyx_v_box.strides[0]) )) + __pyx_t_3)) ))) < 0.0) != 0); if (__pyx_t_5) { - /* "MDAnalysis/lib/nsgrid.pyx":205 + /* "MDAnalysis/lib/nsgrid.pyx":214 * tmp = box[YY, YY] * if box[ZZ, YY] < 0: * tmp -= box[ZZ, YY] # <<<<<<<<<<<<<< @@ -3440,7 +3505,7 @@ static void __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_update(struct __pyx_ if (__pyx_t_4 < 0) __pyx_t_4 += __pyx_v_box.shape[1]; __pyx_v_tmp = (__pyx_v_tmp - (*((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=1 */ ((char *) (((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=0 */ (__pyx_v_box.data + __pyx_t_3 * __pyx_v_box.strides[0]) )) + __pyx_t_4)) )))); - /* "MDAnalysis/lib/nsgrid.pyx":204 + /* "MDAnalysis/lib/nsgrid.pyx":213 * # than checking all possible combinations. * tmp = box[YY, YY] * if box[ZZ, YY] < 0: # <<<<<<<<<<<<<< @@ -3450,7 +3515,7 @@ static void __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_update(struct __pyx_ goto __pyx_L11; } - /* "MDAnalysis/lib/nsgrid.pyx":207 + /* "MDAnalysis/lib/nsgrid.pyx":216 * tmp -= box[ZZ, YY] * else: * tmp += box[ZZ, YY] # <<<<<<<<<<<<<< @@ -3466,7 +3531,7 @@ static void __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_update(struct __pyx_ } __pyx_L11:; 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Got: {} x {})".format( # <<<<<<<<<<<<<< * DIM, DIM, box.shape[0], box.shape[1])) * if (box[XX, XX] == 0) or (box[YY, YY] == 0) or (box[ZZ, ZZ] == 0): */ - __pyx_t_4 = __Pyx_PyObject_CallOneArg(__pyx_builtin_ValueError, __pyx_t_3); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 231, __pyx_L1_error) + __pyx_t_4 = __Pyx_PyObject_CallOneArg(__pyx_builtin_ValueError, __pyx_t_3); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 240, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_Raise(__pyx_t_4, 0, 0, 0); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - __PYX_ERR(0, 231, __pyx_L1_error) + __PYX_ERR(0, 240, __pyx_L1_error) - /* "MDAnalysis/lib/nsgrid.pyx":230 + /* "MDAnalysis/lib/nsgrid.pyx":239 * """ * * if box.shape[0] != DIM or box.shape[1] != DIM: # <<<<<<<<<<<<<< @@ -3696,7 +3761,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_7_PBCBox_2update(struct __py */ } - /* "MDAnalysis/lib/nsgrid.pyx":233 + /* "MDAnalysis/lib/nsgrid.pyx":242 * raise ValueError("Box must be a {} x {} matrix. Got: {} x {})".format( * DIM, DIM, box.shape[0], box.shape[1])) * if (box[XX, XX] == 0) or (box[YY, YY] == 0) or (box[ZZ, ZZ] == 0): # <<<<<<<<<<<<<< @@ -3732,20 +3797,20 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_7_PBCBox_2update(struct __py __pyx_L7_bool_binop_done:; if (unlikely(__pyx_t_1)) { - /* "MDAnalysis/lib/nsgrid.pyx":234 + /* "MDAnalysis/lib/nsgrid.pyx":243 * DIM, DIM, box.shape[0], box.shape[1])) * if (box[XX, XX] == 0) or (box[YY, YY] == 0) or (box[ZZ, ZZ] == 0): * raise ValueError("Box does not correspond to PBC=xyz") # <<<<<<<<<<<<<< * self.fast_update(box) * */ - __pyx_t_4 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple_, NULL); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 234, __pyx_L1_error) + __pyx_t_4 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple_, NULL); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 243, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_4); __Pyx_Raise(__pyx_t_4, 0, 0, 0); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - __PYX_ERR(0, 234, __pyx_L1_error) + __PYX_ERR(0, 243, __pyx_L1_error) - /* "MDAnalysis/lib/nsgrid.pyx":233 + /* "MDAnalysis/lib/nsgrid.pyx":242 * raise ValueError("Box must be a {} x {} matrix. 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} -/* "MDAnalysis/lib/nsgrid.pyx":237 +/* "MDAnalysis/lib/nsgrid.pyx":246 * self.fast_update(box) * * cdef void fast_pbc_dx(self, rvec ref, rvec other, drvec dx) nogil: # <<<<<<<<<<<<<< @@ -3806,7 +3871,7 @@ static void __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_pbc_dx(struct __pyx_ __pyx_t_10MDAnalysis_3lib_6nsgrid_ns_int __pyx_t_3; __pyx_t_10MDAnalysis_3lib_6nsgrid_ns_int __pyx_t_4; - /* "MDAnalysis/lib/nsgrid.pyx":250 + /* "MDAnalysis/lib/nsgrid.pyx":259 * cdef ns_int i, j * * for i in range(DIM): # <<<<<<<<<<<<<< @@ -3816,7 +3881,7 @@ static void __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_pbc_dx(struct __pyx_ for (__pyx_t_1 = 0; __pyx_t_1 < 3; __pyx_t_1+=1) { __pyx_v_i = __pyx_t_1; - /* "MDAnalysis/lib/nsgrid.pyx":251 + /* "MDAnalysis/lib/nsgrid.pyx":260 * * for i in range(DIM): * dx[i] = other[i] - ref[i] # <<<<<<<<<<<<<< @@ -3826,7 +3891,7 @@ static void __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_pbc_dx(struct __pyx_ (__pyx_v_dx[__pyx_v_i]) = ((__pyx_v_other[__pyx_v_i]) - (__pyx_v_ref[__pyx_v_i])); } - /* "MDAnalysis/lib/nsgrid.pyx":253 + /* "MDAnalysis/lib/nsgrid.pyx":262 * dx[i] = other[i] - ref[i] * * if self.periodic: # <<<<<<<<<<<<<< @@ -3836,7 +3901,7 @@ static void __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_pbc_dx(struct __pyx_ __pyx_t_2 = (__pyx_v_self->periodic != 0); if (__pyx_t_2) { - /* "MDAnalysis/lib/nsgrid.pyx":254 + /* "MDAnalysis/lib/nsgrid.pyx":263 * * if self.periodic: * for i in range(DIM-1, -1, -1): # <<<<<<<<<<<<<< @@ -3846,7 +3911,7 @@ static void __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_pbc_dx(struct __pyx_ for (__pyx_t_1 = 2; __pyx_t_1 > -1L; __pyx_t_1-=1) { __pyx_v_i = __pyx_t_1; - /* "MDAnalysis/lib/nsgrid.pyx":255 + /* "MDAnalysis/lib/nsgrid.pyx":264 * if self.periodic: * for i in range(DIM-1, -1, -1): * while dx[i] > self.c_pbcbox.hbox_diag[i]: # <<<<<<<<<<<<<< @@ -3857,7 +3922,7 @@ static void __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_pbc_dx(struct __pyx_ __pyx_t_2 = (((__pyx_v_dx[__pyx_v_i]) > (__pyx_v_self->c_pbcbox.hbox_diag[__pyx_v_i])) != 0); if (!__pyx_t_2) break; - /* "MDAnalysis/lib/nsgrid.pyx":256 + /* "MDAnalysis/lib/nsgrid.pyx":265 * for i in range(DIM-1, -1, -1): * while dx[i] > self.c_pbcbox.hbox_diag[i]: * for j in range(i, -1, -1): # <<<<<<<<<<<<<< @@ -3867,7 +3932,7 @@ static void __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_pbc_dx(struct __pyx_ for (__pyx_t_3 = __pyx_v_i; __pyx_t_3 > -1L; __pyx_t_3-=1) { __pyx_v_j = __pyx_t_3; - /* "MDAnalysis/lib/nsgrid.pyx":257 + /* "MDAnalysis/lib/nsgrid.pyx":266 * while dx[i] > self.c_pbcbox.hbox_diag[i]: * for j in range(i, -1, -1): * dx[j] -= self.c_pbcbox.box[i][j] # <<<<<<<<<<<<<< @@ -3879,7 +3944,7 @@ static void __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_pbc_dx(struct __pyx_ } } - /* "MDAnalysis/lib/nsgrid.pyx":259 + /* "MDAnalysis/lib/nsgrid.pyx":268 * dx[j] -= self.c_pbcbox.box[i][j] * * while dx[i] <= self.c_pbcbox.mhbox_diag[i]: # <<<<<<<<<<<<<< @@ -3890,7 +3955,7 @@ static void __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_pbc_dx(struct __pyx_ __pyx_t_2 = (((__pyx_v_dx[__pyx_v_i]) <= (__pyx_v_self->c_pbcbox.mhbox_diag[__pyx_v_i])) != 0); if (!__pyx_t_2) break; - /* "MDAnalysis/lib/nsgrid.pyx":260 + /* "MDAnalysis/lib/nsgrid.pyx":269 * * while dx[i] <= self.c_pbcbox.mhbox_diag[i]: * for j in range(i, -1, -1): # <<<<<<<<<<<<<< @@ -3900,7 +3965,7 @@ static void __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_pbc_dx(struct __pyx_ for (__pyx_t_3 = __pyx_v_i; __pyx_t_3 > -1L; __pyx_t_3-=1) { __pyx_v_j = __pyx_t_3; - /* "MDAnalysis/lib/nsgrid.pyx":261 + /* "MDAnalysis/lib/nsgrid.pyx":270 * while dx[i] <= self.c_pbcbox.mhbox_diag[i]: * for j in range(i, -1, -1): * dx[j] += self.c_pbcbox.box[i][j] # <<<<<<<<<<<<<< @@ -3913,7 +3978,7 @@ static void __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_pbc_dx(struct __pyx_ } } - /* "MDAnalysis/lib/nsgrid.pyx":253 + /* "MDAnalysis/lib/nsgrid.pyx":262 * dx[i] = other[i] - ref[i] * * if self.periodic: # <<<<<<<<<<<<<< @@ -3922,7 +3987,7 @@ static void __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_pbc_dx(struct __pyx_ */ } - /* "MDAnalysis/lib/nsgrid.pyx":237 + /* "MDAnalysis/lib/nsgrid.pyx":246 * self.fast_update(box) * * cdef void fast_pbc_dx(self, rvec ref, rvec other, drvec dx) nogil: # <<<<<<<<<<<<<< @@ -3933,7 +3998,7 @@ static void __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_pbc_dx(struct __pyx_ /* function exit code */ } -/* "MDAnalysis/lib/nsgrid.pyx":263 +/* "MDAnalysis/lib/nsgrid.pyx":272 * dx[j] += self.c_pbcbox.box[i][j] * * cdef dreal fast_distance2(self, rvec a, rvec b) nogil: # <<<<<<<<<<<<<< @@ -3945,7 +4010,7 @@ static __pyx_t_10MDAnalysis_3lib_6nsgrid_dreal __pyx_f_10MDAnalysis_3lib_6nsgrid __pyx_t_10MDAnalysis_3lib_6nsgrid_drvec __pyx_v_dx; __pyx_t_10MDAnalysis_3lib_6nsgrid_dreal __pyx_r; - /* "MDAnalysis/lib/nsgrid.pyx":273 + /* "MDAnalysis/lib/nsgrid.pyx":282 * * cdef drvec dx * self.fast_pbc_dx(a, b, dx) # <<<<<<<<<<<<<< @@ -3954,7 +4019,7 @@ static __pyx_t_10MDAnalysis_3lib_6nsgrid_dreal __pyx_f_10MDAnalysis_3lib_6nsgrid */ ((struct __pyx_vtabstruct_10MDAnalysis_3lib_6nsgrid__PBCBox *)__pyx_v_self->__pyx_vtab)->fast_pbc_dx(__pyx_v_self, __pyx_v_a, __pyx_v_b, __pyx_v_dx); - /* "MDAnalysis/lib/nsgrid.pyx":274 + /* "MDAnalysis/lib/nsgrid.pyx":283 * cdef drvec dx * self.fast_pbc_dx(a, b, dx) * return drvec_norm2(dx) # <<<<<<<<<<<<<< @@ -3964,7 +4029,7 @@ static __pyx_t_10MDAnalysis_3lib_6nsgrid_dreal __pyx_f_10MDAnalysis_3lib_6nsgrid __pyx_r = __pyx_f_10MDAnalysis_3lib_6nsgrid_drvec_norm2(__pyx_v_dx); goto __pyx_L0; - /* "MDAnalysis/lib/nsgrid.pyx":263 + /* "MDAnalysis/lib/nsgrid.pyx":272 * dx[j] += self.c_pbcbox.box[i][j] * * cdef dreal fast_distance2(self, rvec a, rvec b) nogil: # <<<<<<<<<<<<<< @@ -3977,7 +4042,7 @@ static __pyx_t_10MDAnalysis_3lib_6nsgrid_dreal __pyx_f_10MDAnalysis_3lib_6nsgrid return __pyx_r; } -/* "MDAnalysis/lib/nsgrid.pyx":276 +/* "MDAnalysis/lib/nsgrid.pyx":285 * return drvec_norm2(dx) * * cdef real[:, ::1] fast_put_atoms_in_bbox(self, real[:, ::1] coords) nogil: # <<<<<<<<<<<<<< @@ -4004,12 +4069,6 @@ static __Pyx_memviewslice __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_put_at __pyx_t_10MDAnalysis_3lib_6nsgrid_ns_int __pyx_t_9; __pyx_t_10MDAnalysis_3lib_6nsgrid_ns_int __pyx_t_10; __pyx_t_10MDAnalysis_3lib_6nsgrid_ns_int __pyx_t_11; - Py_ssize_t __pyx_t_12; - Py_ssize_t __pyx_t_13; - Py_ssize_t __pyx_t_14; - Py_ssize_t __pyx_t_15; - Py_ssize_t __pyx_t_16; - Py_ssize_t __pyx_t_17; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; @@ -4021,7 +4080,7 @@ static __Pyx_memviewslice __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_put_at __Pyx_PyGILState_Release(__pyx_gilstate_save); #endif - /* "MDAnalysis/lib/nsgrid.pyx":277 + /* "MDAnalysis/lib/nsgrid.pyx":286 * * cdef real[:, ::1] fast_put_atoms_in_bbox(self, real[:, ::1] coords) nogil: * """Shifts all ``coords`` to an orthogonal brick shaped box # <<<<<<<<<<<<<< @@ -4030,7 +4089,7 @@ static __Pyx_memviewslice __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_put_at */ /*try:*/ { - /* "MDAnalysis/lib/nsgrid.pyx":288 + /* "MDAnalysis/lib/nsgrid.pyx":297 * cdef real[:, ::1] bbox_coords * * natoms = coords.shape[0] # <<<<<<<<<<<<<< @@ -4039,7 +4098,7 @@ static __Pyx_memviewslice __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_put_at */ __pyx_v_natoms = (__pyx_v_coords.shape[0]); - /* "MDAnalysis/lib/nsgrid.pyx":289 + /* "MDAnalysis/lib/nsgrid.pyx":298 * * natoms = coords.shape[0] * with gil: # <<<<<<<<<<<<<< @@ -4052,20 +4111,20 @@ static __Pyx_memviewslice __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_put_at #endif /*try:*/ { - /* "MDAnalysis/lib/nsgrid.pyx":290 + /* "MDAnalysis/lib/nsgrid.pyx":299 * natoms = coords.shape[0] * with gil: * bbox_coords = coords.copy() # <<<<<<<<<<<<<< * * if self.periodic: */ - __pyx_t_1 = __pyx_memoryview_copy_slice_d_dc_nn___pyx_t_10MDAnalysis_3lib_6nsgrid_real_c(__pyx_v_coords); if (unlikely(!__pyx_t_1.memview)) __PYX_ERR(0, 290, __pyx_L7_error) + __pyx_t_1 = __pyx_memoryview_copy_slice_d_dc_nn___pyx_t_10MDAnalysis_3lib_6nsgrid_real_c(__pyx_v_coords); if (unlikely(!__pyx_t_1.memview)) __PYX_ERR(0, 299, __pyx_L7_error) __pyx_v_bbox_coords = __pyx_t_1; __pyx_t_1.memview = NULL; __pyx_t_1.data = NULL; } - /* "MDAnalysis/lib/nsgrid.pyx":289 + /* "MDAnalysis/lib/nsgrid.pyx":298 * * natoms = coords.shape[0] * with gil: # <<<<<<<<<<<<<< @@ -4089,7 +4148,7 @@ static __Pyx_memviewslice __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_put_at } } - /* "MDAnalysis/lib/nsgrid.pyx":292 + /* "MDAnalysis/lib/nsgrid.pyx":301 * bbox_coords = coords.copy() * * if self.periodic: # <<<<<<<<<<<<<< @@ -4099,7 +4158,7 @@ static __Pyx_memviewslice __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_put_at __pyx_t_2 = (__pyx_v_self->periodic != 0); if (__pyx_t_2) { - /* "MDAnalysis/lib/nsgrid.pyx":293 + /* "MDAnalysis/lib/nsgrid.pyx":302 * * if self.periodic: * if self.is_triclinic: # <<<<<<<<<<<<<< @@ -4109,7 +4168,7 @@ static __Pyx_memviewslice __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_put_at __pyx_t_2 = (__pyx_v_self->is_triclinic != 0); if (__pyx_t_2) { - /* "MDAnalysis/lib/nsgrid.pyx":294 + /* "MDAnalysis/lib/nsgrid.pyx":303 * if self.periodic: * if self.is_triclinic: * for i in range(natoms): # <<<<<<<<<<<<<< @@ -4121,7 +4180,7 @@ static __Pyx_memviewslice __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_put_at for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { __pyx_v_i = __pyx_t_5; - /* "MDAnalysis/lib/nsgrid.pyx":295 + /* "MDAnalysis/lib/nsgrid.pyx":304 * if self.is_triclinic: * for i in range(natoms): * for m in range(DIM - 1, -1, -1): # <<<<<<<<<<<<<< @@ -4131,7 +4190,7 @@ static __Pyx_memviewslice __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_put_at for (__pyx_t_6 = 2; __pyx_t_6 > -1L; __pyx_t_6-=1) { __pyx_v_m = __pyx_t_6; - /* "MDAnalysis/lib/nsgrid.pyx":296 + /* "MDAnalysis/lib/nsgrid.pyx":305 * for i in range(natoms): * for m in range(DIM - 1, -1, -1): * while bbox_coords[i, m] < 0: # <<<<<<<<<<<<<< @@ -4146,7 +4205,7 @@ static __Pyx_memviewslice __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_put_at __pyx_t_2 = (((*((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=1 */ ((char *) (((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=0 */ (__pyx_v_bbox_coords.data + __pyx_t_7 * __pyx_v_bbox_coords.strides[0]) )) + __pyx_t_8)) ))) < 0.0) != 0); if (!__pyx_t_2) break; - /* "MDAnalysis/lib/nsgrid.pyx":297 + /* "MDAnalysis/lib/nsgrid.pyx":306 * for m in range(DIM - 1, -1, -1): * while bbox_coords[i, m] < 0: * for d in range(m+1): # <<<<<<<<<<<<<< @@ -4158,7 +4217,7 @@ static __Pyx_memviewslice __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_put_at for (__pyx_t_11 = 0; __pyx_t_11 < __pyx_t_10; __pyx_t_11+=1) { __pyx_v_d = __pyx_t_11; - /* "MDAnalysis/lib/nsgrid.pyx":298 + /* "MDAnalysis/lib/nsgrid.pyx":307 * while bbox_coords[i, m] < 0: * for d in range(m+1): * bbox_coords[i, d] += self.c_pbcbox.box[m][d] # <<<<<<<<<<<<<< @@ -4173,7 +4232,7 @@ static __Pyx_memviewslice __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_put_at } } - /* "MDAnalysis/lib/nsgrid.pyx":299 + /* "MDAnalysis/lib/nsgrid.pyx":308 * for d in range(m+1): * bbox_coords[i, d] += self.c_pbcbox.box[m][d] * while bbox_coords[i, m] >= self.c_pbcbox.box[m][m]: # <<<<<<<<<<<<<< @@ -4181,14 +4240,14 @@ static __Pyx_memviewslice __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_put_at * bbox_coords[i, d] -= self.c_pbcbox.box[m][d] */ while (1) { - __pyx_t_12 = __pyx_v_i; - __pyx_t_13 = __pyx_v_m; - if (__pyx_t_12 < 0) __pyx_t_12 += __pyx_v_bbox_coords.shape[0]; - if (__pyx_t_13 < 0) __pyx_t_13 += __pyx_v_bbox_coords.shape[1]; - __pyx_t_2 = (((*((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=1 */ ((char *) (((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=0 */ (__pyx_v_bbox_coords.data + __pyx_t_12 * __pyx_v_bbox_coords.strides[0]) )) + __pyx_t_13)) ))) >= ((__pyx_v_self->c_pbcbox.box[__pyx_v_m])[__pyx_v_m])) != 0); + __pyx_t_7 = __pyx_v_i; + __pyx_t_8 = __pyx_v_m; + if (__pyx_t_7 < 0) __pyx_t_7 += __pyx_v_bbox_coords.shape[0]; + if (__pyx_t_8 < 0) __pyx_t_8 += __pyx_v_bbox_coords.shape[1]; + __pyx_t_2 = (((*((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=1 */ ((char *) (((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=0 */ (__pyx_v_bbox_coords.data + __pyx_t_7 * __pyx_v_bbox_coords.strides[0]) )) + __pyx_t_8)) ))) >= ((__pyx_v_self->c_pbcbox.box[__pyx_v_m])[__pyx_v_m])) != 0); if (!__pyx_t_2) break; - /* "MDAnalysis/lib/nsgrid.pyx":300 + /* "MDAnalysis/lib/nsgrid.pyx":309 * bbox_coords[i, d] += self.c_pbcbox.box[m][d] * while bbox_coords[i, m] >= self.c_pbcbox.box[m][m]: * for d in range(m+1): # <<<<<<<<<<<<<< @@ -4200,24 +4259,24 @@ static __Pyx_memviewslice __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_put_at for (__pyx_t_11 = 0; __pyx_t_11 < __pyx_t_10; __pyx_t_11+=1) { __pyx_v_d = __pyx_t_11; - /* "MDAnalysis/lib/nsgrid.pyx":301 + /* "MDAnalysis/lib/nsgrid.pyx":310 * while bbox_coords[i, m] >= self.c_pbcbox.box[m][m]: * for d in range(m+1): * bbox_coords[i, d] -= self.c_pbcbox.box[m][d] # <<<<<<<<<<<<<< * else: * for i in range(natoms): */ - __pyx_t_13 = __pyx_v_i; - __pyx_t_12 = __pyx_v_d; - if (__pyx_t_13 < 0) __pyx_t_13 += __pyx_v_bbox_coords.shape[0]; - if (__pyx_t_12 < 0) __pyx_t_12 += __pyx_v_bbox_coords.shape[1]; - *((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=1 */ ((char *) (((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=0 */ (__pyx_v_bbox_coords.data + __pyx_t_13 * __pyx_v_bbox_coords.strides[0]) )) + __pyx_t_12)) )) -= ((__pyx_v_self->c_pbcbox.box[__pyx_v_m])[__pyx_v_d]); + __pyx_t_8 = __pyx_v_i; + __pyx_t_7 = __pyx_v_d; + if (__pyx_t_8 < 0) __pyx_t_8 += __pyx_v_bbox_coords.shape[0]; + if (__pyx_t_7 < 0) __pyx_t_7 += __pyx_v_bbox_coords.shape[1]; + *((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=1 */ ((char *) (((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=0 */ (__pyx_v_bbox_coords.data + __pyx_t_8 * __pyx_v_bbox_coords.strides[0]) )) + __pyx_t_7)) )) -= ((__pyx_v_self->c_pbcbox.box[__pyx_v_m])[__pyx_v_d]); } } } } - /* "MDAnalysis/lib/nsgrid.pyx":293 + /* "MDAnalysis/lib/nsgrid.pyx":302 * * if self.periodic: * if self.is_triclinic: # <<<<<<<<<<<<<< @@ -4227,7 +4286,7 @@ static __Pyx_memviewslice __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_put_at goto __pyx_L10; } - /* "MDAnalysis/lib/nsgrid.pyx":303 + /* "MDAnalysis/lib/nsgrid.pyx":312 * bbox_coords[i, d] -= self.c_pbcbox.box[m][d] * else: * for i in range(natoms): # <<<<<<<<<<<<<< @@ -4240,7 +4299,7 @@ static __Pyx_memviewslice __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_put_at for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { __pyx_v_i = __pyx_t_5; - /* "MDAnalysis/lib/nsgrid.pyx":304 + /* "MDAnalysis/lib/nsgrid.pyx":313 * else: * for i in range(natoms): * for m in range(DIM): # <<<<<<<<<<<<<< @@ -4250,7 +4309,7 @@ static __Pyx_memviewslice __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_put_at for (__pyx_t_6 = 0; __pyx_t_6 < 3; __pyx_t_6+=1) { __pyx_v_m = __pyx_t_6; - /* "MDAnalysis/lib/nsgrid.pyx":305 + /* "MDAnalysis/lib/nsgrid.pyx":314 * for i in range(natoms): * for m in range(DIM): * while bbox_coords[i, m] < 0: # <<<<<<<<<<<<<< @@ -4258,28 +4317,28 @@ static __Pyx_memviewslice __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_put_at * while bbox_coords[i, m] >= self.c_pbcbox.box[m][m]: */ while (1) { - __pyx_t_14 = __pyx_v_i; - __pyx_t_15 = __pyx_v_m; - if (__pyx_t_14 < 0) __pyx_t_14 += __pyx_v_bbox_coords.shape[0]; - if (__pyx_t_15 < 0) __pyx_t_15 += __pyx_v_bbox_coords.shape[1]; - __pyx_t_2 = (((*((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=1 */ ((char *) (((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=0 */ (__pyx_v_bbox_coords.data + __pyx_t_14 * __pyx_v_bbox_coords.strides[0]) )) + __pyx_t_15)) ))) < 0.0) != 0); + __pyx_t_7 = __pyx_v_i; + __pyx_t_8 = __pyx_v_m; + if (__pyx_t_7 < 0) __pyx_t_7 += __pyx_v_bbox_coords.shape[0]; + if (__pyx_t_8 < 0) __pyx_t_8 += __pyx_v_bbox_coords.shape[1]; + __pyx_t_2 = (((*((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=1 */ ((char *) (((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=0 */ (__pyx_v_bbox_coords.data + __pyx_t_7 * __pyx_v_bbox_coords.strides[0]) )) + __pyx_t_8)) ))) < 0.0) != 0); if (!__pyx_t_2) break; - /* "MDAnalysis/lib/nsgrid.pyx":306 + /* "MDAnalysis/lib/nsgrid.pyx":315 * for m in range(DIM): * while bbox_coords[i, m] < 0: * bbox_coords[i, m] += self.c_pbcbox.box[m][m] # <<<<<<<<<<<<<< * while bbox_coords[i, m] >= self.c_pbcbox.box[m][m]: * bbox_coords[i, m] -= self.c_pbcbox.box[m][m] */ - __pyx_t_15 = __pyx_v_i; - __pyx_t_14 = __pyx_v_m; - if (__pyx_t_15 < 0) __pyx_t_15 += __pyx_v_bbox_coords.shape[0]; - if (__pyx_t_14 < 0) __pyx_t_14 += __pyx_v_bbox_coords.shape[1]; - *((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=1 */ ((char *) (((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=0 */ (__pyx_v_bbox_coords.data + __pyx_t_15 * __pyx_v_bbox_coords.strides[0]) )) + __pyx_t_14)) )) += ((__pyx_v_self->c_pbcbox.box[__pyx_v_m])[__pyx_v_m]); + __pyx_t_8 = __pyx_v_i; + __pyx_t_7 = __pyx_v_m; + if (__pyx_t_8 < 0) __pyx_t_8 += __pyx_v_bbox_coords.shape[0]; + if (__pyx_t_7 < 0) __pyx_t_7 += __pyx_v_bbox_coords.shape[1]; + *((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=1 */ ((char *) (((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=0 */ (__pyx_v_bbox_coords.data + __pyx_t_8 * __pyx_v_bbox_coords.strides[0]) )) + __pyx_t_7)) )) += ((__pyx_v_self->c_pbcbox.box[__pyx_v_m])[__pyx_v_m]); } - /* "MDAnalysis/lib/nsgrid.pyx":307 + /* "MDAnalysis/lib/nsgrid.pyx":316 * while bbox_coords[i, m] < 0: * bbox_coords[i, m] += self.c_pbcbox.box[m][m] * while bbox_coords[i, m] >= self.c_pbcbox.box[m][m]: # <<<<<<<<<<<<<< @@ -4287,32 +4346,32 @@ static __Pyx_memviewslice __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_put_at * */ while (1) { - __pyx_t_16 = __pyx_v_i; - __pyx_t_17 = __pyx_v_m; - if (__pyx_t_16 < 0) __pyx_t_16 += __pyx_v_bbox_coords.shape[0]; - if (__pyx_t_17 < 0) __pyx_t_17 += __pyx_v_bbox_coords.shape[1]; - __pyx_t_2 = (((*((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=1 */ ((char *) (((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=0 */ (__pyx_v_bbox_coords.data + __pyx_t_16 * __pyx_v_bbox_coords.strides[0]) )) + __pyx_t_17)) ))) >= ((__pyx_v_self->c_pbcbox.box[__pyx_v_m])[__pyx_v_m])) != 0); + __pyx_t_7 = __pyx_v_i; + __pyx_t_8 = __pyx_v_m; + if (__pyx_t_7 < 0) __pyx_t_7 += __pyx_v_bbox_coords.shape[0]; + if (__pyx_t_8 < 0) __pyx_t_8 += __pyx_v_bbox_coords.shape[1]; + __pyx_t_2 = (((*((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=1 */ ((char *) (((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=0 */ (__pyx_v_bbox_coords.data + __pyx_t_7 * __pyx_v_bbox_coords.strides[0]) )) + __pyx_t_8)) ))) >= ((__pyx_v_self->c_pbcbox.box[__pyx_v_m])[__pyx_v_m])) != 0); if (!__pyx_t_2) break; - /* "MDAnalysis/lib/nsgrid.pyx":308 + /* "MDAnalysis/lib/nsgrid.pyx":317 * bbox_coords[i, m] += self.c_pbcbox.box[m][m] * while bbox_coords[i, m] >= self.c_pbcbox.box[m][m]: * bbox_coords[i, m] -= self.c_pbcbox.box[m][m] # <<<<<<<<<<<<<< * * return bbox_coords */ - __pyx_t_17 = __pyx_v_i; - __pyx_t_16 = __pyx_v_m; - if (__pyx_t_17 < 0) __pyx_t_17 += __pyx_v_bbox_coords.shape[0]; - if (__pyx_t_16 < 0) __pyx_t_16 += __pyx_v_bbox_coords.shape[1]; - *((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=1 */ ((char *) (((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=0 */ (__pyx_v_bbox_coords.data + __pyx_t_17 * __pyx_v_bbox_coords.strides[0]) )) + __pyx_t_16)) )) -= ((__pyx_v_self->c_pbcbox.box[__pyx_v_m])[__pyx_v_m]); + __pyx_t_8 = __pyx_v_i; + __pyx_t_7 = __pyx_v_m; + if (__pyx_t_8 < 0) __pyx_t_8 += __pyx_v_bbox_coords.shape[0]; + if (__pyx_t_7 < 0) __pyx_t_7 += __pyx_v_bbox_coords.shape[1]; + *((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=1 */ ((char *) (((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=0 */ (__pyx_v_bbox_coords.data + __pyx_t_8 * __pyx_v_bbox_coords.strides[0]) )) + __pyx_t_7)) )) -= ((__pyx_v_self->c_pbcbox.box[__pyx_v_m])[__pyx_v_m]); } } } } __pyx_L10:; - /* "MDAnalysis/lib/nsgrid.pyx":292 + /* "MDAnalysis/lib/nsgrid.pyx":301 * bbox_coords = coords.copy() * * if self.periodic: # <<<<<<<<<<<<<< @@ -4321,7 +4380,7 @@ static __Pyx_memviewslice __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_put_at */ } - /* "MDAnalysis/lib/nsgrid.pyx":310 + /* "MDAnalysis/lib/nsgrid.pyx":319 * bbox_coords[i, m] -= self.c_pbcbox.box[m][m] * * return bbox_coords # <<<<<<<<<<<<<< @@ -4333,7 +4392,7 @@ static __Pyx_memviewslice __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_put_at goto __pyx_L3_return; } - /* "MDAnalysis/lib/nsgrid.pyx":277 + /* "MDAnalysis/lib/nsgrid.pyx":286 * * cdef real[:, ::1] fast_put_atoms_in_bbox(self, real[:, ::1] coords) nogil: * """Shifts all ``coords`` to an orthogonal brick shaped box # <<<<<<<<<<<<<< @@ -4355,7 +4414,7 @@ static __Pyx_memviewslice __pyx_f_10MDAnalysis_3lib_6nsgrid_7_PBCBox_fast_put_at } } - /* "MDAnalysis/lib/nsgrid.pyx":276 + /* "MDAnalysis/lib/nsgrid.pyx":285 * return drvec_norm2(dx) * * cdef real[:, ::1] fast_put_atoms_in_bbox(self, real[:, ::1] coords) nogil: # <<<<<<<<<<<<<< @@ -4499,7 +4558,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_7_PBCBox_6__setstate_cython_ return __pyx_r; } -/* "MDAnalysis/lib/nsgrid.pyx":336 +/* "MDAnalysis/lib/nsgrid.pyx":345 * cdef vector[dreal] pair_distances2_buffer * * def __init__(self, dreal cutoff, real[:, ::1]coords, real[:, ::1]searchcoords): # <<<<<<<<<<<<<< @@ -4548,17 +4607,17 @@ static int __pyx_pw_10MDAnalysis_3lib_6nsgrid_9NSResults_1__init__(PyObject *__p case 1: if (likely((values[1] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_coords)) != 0)) kw_args--; 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} -/* "MDAnalysis/lib/nsgrid.pyx":538 +/* "MDAnalysis/lib/nsgrid.pyx":547 * """ * * cdef readonly dreal used_cutoff # cutoff used for cell creation # <<<<<<<<<<<<<< @@ -7096,7 +7154,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_7_NSGrid_11used_cutoff___get int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__get__", 0); __Pyx_XDECREF(__pyx_r); - __pyx_t_1 = PyFloat_FromDouble(__pyx_v_self->used_cutoff); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 538, __pyx_L1_error) + __pyx_t_1 = PyFloat_FromDouble(__pyx_v_self->used_cutoff); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 547, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; @@ -7228,7 +7286,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_7_NSGrid_6__setstate_cython_ return __pyx_r; } -/* "MDAnalysis/lib/nsgrid.pyx":717 +/* "MDAnalysis/lib/nsgrid.pyx":732 * cdef bint periodic * * def __init__(self, cutoff, coords, box, max_gridsize=5000, pbc=True): # <<<<<<<<<<<<<< @@ -7285,13 +7343,13 @@ static int __pyx_pw_10MDAnalysis_3lib_6nsgrid_6FastNS_1__init__(PyObject *__pyx_ case 1: if (likely((values[1] = __Pyx_PyDict_GetItemStr(__pyx_kwds, __pyx_n_s_coords)) != 0)) kw_args--; 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if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 870, __pyx_L1_error) + __pyx_t_3 = __Pyx_PyDict_NewPresized(1); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 893, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); - if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_force, Py_True) < 0) __PYX_ERR(0, 870, __pyx_L1_error) - __pyx_t_5 = __Pyx_PyObject_Call(((PyObject *)__pyx_ptype_10MDAnalysis_3lib_6nsgrid__NSGrid), __pyx_t_2, __pyx_t_3); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 870, __pyx_L1_error) + if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_force, Py_True) < 0) __PYX_ERR(0, 893, __pyx_L1_error) + __pyx_t_5 = __Pyx_PyObject_Call(((PyObject *)__pyx_ptype_10MDAnalysis_3lib_6nsgrid__NSGrid), __pyx_t_2, __pyx_t_3); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 893, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_v_searchgrid = ((struct __pyx_obj_10MDAnalysis_3lib_6nsgrid__NSGrid *)__pyx_t_5); __pyx_t_5 = 0; - /* "MDAnalysis/lib/nsgrid.pyx":872 + /* "MDAnalysis/lib/nsgrid.pyx":895 * searchgrid = _NSGrid(searchcoords_bbox.shape[0], self.grid.used_cutoff, self.box, self.max_gridsize, force=True) * * size_search = searchcoords.shape[0] # <<<<<<<<<<<<<< @@ -8126,20 +8387,20 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_2search(struct __pyx */ __pyx_v_size_search = (__pyx_v_searchcoords.shape[0]); - /* "MDAnalysis/lib/nsgrid.pyx":874 + /* "MDAnalysis/lib/nsgrid.pyx":897 * size_search = searchcoords.shape[0] * * results = NSResults(self.cutoff, self.coords, searchcoords) # <<<<<<<<<<<<<< * * with nogil: */ - __pyx_t_5 = PyFloat_FromDouble(__pyx_v_self->cutoff); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 874, __pyx_L1_error) + __pyx_t_5 = PyFloat_FromDouble(__pyx_v_self->cutoff); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 897, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_5); - __pyx_t_3 = __pyx_memoryview_fromslice(__pyx_v_self->coords, 2, (PyObject *(*)(char *)) __pyx_memview_get_nn___pyx_t_10MDAnalysis_3lib_6nsgrid_real, (int (*)(char *, PyObject *)) __pyx_memview_set_nn___pyx_t_10MDAnalysis_3lib_6nsgrid_real, 0);; if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 874, __pyx_L1_error) + __pyx_t_3 = __pyx_memoryview_fromslice(__pyx_v_self->coords, 2, (PyObject *(*)(char *)) __pyx_memview_get_nn___pyx_t_10MDAnalysis_3lib_6nsgrid_real, (int (*)(char *, PyObject *)) __pyx_memview_set_nn___pyx_t_10MDAnalysis_3lib_6nsgrid_real, 0);; if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 897, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); - __pyx_t_2 = __pyx_memoryview_fromslice(__pyx_v_searchcoords, 2, (PyObject *(*)(char *)) __pyx_memview_get_nn___pyx_t_10MDAnalysis_3lib_6nsgrid_real, (int (*)(char *, PyObject *)) __pyx_memview_set_nn___pyx_t_10MDAnalysis_3lib_6nsgrid_real, 0);; if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 874, __pyx_L1_error) + __pyx_t_2 = __pyx_memoryview_fromslice(__pyx_v_searchcoords, 2, (PyObject *(*)(char *)) __pyx_memview_get_nn___pyx_t_10MDAnalysis_3lib_6nsgrid_real, (int (*)(char *, PyObject *)) __pyx_memview_set_nn___pyx_t_10MDAnalysis_3lib_6nsgrid_real, 0);; if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 897, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_2); - __pyx_t_6 = PyTuple_New(3); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 874, __pyx_L1_error) + __pyx_t_6 = PyTuple_New(3); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 897, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_6); __Pyx_GIVEREF(__pyx_t_5); PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_5); @@ -8150,13 +8411,13 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_2search(struct __pyx __pyx_t_5 = 0; __pyx_t_3 = 0; __pyx_t_2 = 0; - __pyx_t_2 = __Pyx_PyObject_Call(((PyObject *)__pyx_ptype_10MDAnalysis_3lib_6nsgrid_NSResults), __pyx_t_6, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 874, __pyx_L1_error) + __pyx_t_2 = __Pyx_PyObject_Call(((PyObject *)__pyx_ptype_10MDAnalysis_3lib_6nsgrid_NSResults), __pyx_t_6, NULL); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 897, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __pyx_v_results = ((struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_NSResults *)__pyx_t_2); __pyx_t_2 = 0; - /* "MDAnalysis/lib/nsgrid.pyx":876 + /* "MDAnalysis/lib/nsgrid.pyx":899 * results = NSResults(self.cutoff, self.coords, searchcoords) * * with nogil: # <<<<<<<<<<<<<< @@ -8171,7 +8432,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_2search(struct __pyx #endif /*try:*/ { - /* "MDAnalysis/lib/nsgrid.pyx":877 + /* "MDAnalysis/lib/nsgrid.pyx":900 * * with nogil: * for i in range(size_search): # <<<<<<<<<<<<<< @@ -8183,7 +8444,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_2search(struct __pyx for (__pyx_t_10 = 0; __pyx_t_10 < __pyx_t_9; __pyx_t_10+=1) { __pyx_v_i = __pyx_t_10; - /* "MDAnalysis/lib/nsgrid.pyx":879 + /* "MDAnalysis/lib/nsgrid.pyx":902 * for i in range(size_search): * # Start with first search coordinate * current_beadid = i # <<<<<<<<<<<<<< @@ -8192,7 +8453,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_2search(struct __pyx */ __pyx_v_current_beadid = __pyx_v_i; - /* "MDAnalysis/lib/nsgrid.pyx":881 + /* "MDAnalysis/lib/nsgrid.pyx":904 * current_beadid = i * # find the cellindex of the coordinate * cellindex = searchgrid.cellids[current_beadid] # <<<<<<<<<<<<<< @@ -8201,7 +8462,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_2search(struct __pyx */ __pyx_v_cellindex = (__pyx_v_searchgrid->cellids[__pyx_v_current_beadid]); - /* "MDAnalysis/lib/nsgrid.pyx":882 + /* "MDAnalysis/lib/nsgrid.pyx":905 * # find the cellindex of the coordinate * cellindex = searchgrid.cellids[current_beadid] * for xi in range(DIM): # <<<<<<<<<<<<<< @@ -8211,7 +8472,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_2search(struct __pyx for (__pyx_t_11 = 0; __pyx_t_11 < 3; __pyx_t_11+=1) { __pyx_v_xi = __pyx_t_11; - /* "MDAnalysis/lib/nsgrid.pyx":883 + /* "MDAnalysis/lib/nsgrid.pyx":906 * cellindex = searchgrid.cellids[current_beadid] * for xi in range(DIM): * for yi in range(DIM): # <<<<<<<<<<<<<< @@ -8221,7 +8482,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_2search(struct __pyx for (__pyx_t_12 = 0; __pyx_t_12 < 3; __pyx_t_12+=1) { __pyx_v_yi = __pyx_t_12; - /* "MDAnalysis/lib/nsgrid.pyx":884 + /* "MDAnalysis/lib/nsgrid.pyx":907 * for xi in range(DIM): * for yi in range(DIM): * for zi in range(DIM): # <<<<<<<<<<<<<< @@ -8231,7 +8492,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_2search(struct __pyx for (__pyx_t_13 = 0; __pyx_t_13 < 3; __pyx_t_13+=1) { __pyx_v_zi = __pyx_t_13; - /* "MDAnalysis/lib/nsgrid.pyx":885 + /* "MDAnalysis/lib/nsgrid.pyx":908 * for yi in range(DIM): * for zi in range(DIM): * check = True # <<<<<<<<<<<<<< @@ -8240,7 +8501,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_2search(struct __pyx */ __pyx_v_check = 1; - /* "MDAnalysis/lib/nsgrid.pyx":887 + /* "MDAnalysis/lib/nsgrid.pyx":910 * check = True * #Probe the search coordinates in a brick shaped box * probe[XX] = searchcoords_bbox[current_beadid, XX] + (xi - 1) * searchgrid.cellsize[XX] # <<<<<<<<<<<<<< @@ -8253,7 +8514,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_2search(struct __pyx if (__pyx_t_15 < 0) __pyx_t_15 += __pyx_v_searchcoords_bbox.shape[1]; (__pyx_v_probe[0]) = ((*((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=1 */ ((char *) (((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=0 */ (__pyx_v_searchcoords_bbox.data + __pyx_t_14 * __pyx_v_searchcoords_bbox.strides[0]) )) + __pyx_t_15)) ))) + ((__pyx_v_xi - 1) * (__pyx_v_searchgrid->cellsize[0]))); - /* "MDAnalysis/lib/nsgrid.pyx":888 + /* "MDAnalysis/lib/nsgrid.pyx":911 * #Probe the search coordinates in a brick shaped box * probe[XX] = searchcoords_bbox[current_beadid, XX] + (xi - 1) * searchgrid.cellsize[XX] * probe[YY] = searchcoords_bbox[current_beadid, YY] + (yi - 1) * searchgrid.cellsize[YY] # <<<<<<<<<<<<<< @@ -8266,7 +8527,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_2search(struct __pyx if (__pyx_t_14 < 0) __pyx_t_14 += __pyx_v_searchcoords_bbox.shape[1]; (__pyx_v_probe[1]) = ((*((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=1 */ ((char *) (((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=0 */ (__pyx_v_searchcoords_bbox.data + __pyx_t_15 * __pyx_v_searchcoords_bbox.strides[0]) )) + __pyx_t_14)) ))) + ((__pyx_v_yi - 1) * (__pyx_v_searchgrid->cellsize[1]))); - /* "MDAnalysis/lib/nsgrid.pyx":889 + /* "MDAnalysis/lib/nsgrid.pyx":912 * probe[XX] = searchcoords_bbox[current_beadid, XX] + (xi - 1) * searchgrid.cellsize[XX] * probe[YY] = searchcoords_bbox[current_beadid, YY] + (yi - 1) * searchgrid.cellsize[YY] * probe[ZZ] = searchcoords_bbox[current_beadid, ZZ] + (zi - 1) * searchgrid.cellsize[ZZ] # <<<<<<<<<<<<<< @@ -8279,7 +8540,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_2search(struct __pyx if (__pyx_t_15 < 0) __pyx_t_15 += __pyx_v_searchcoords_bbox.shape[1]; (__pyx_v_probe[2]) = ((*((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=1 */ ((char *) (((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=0 */ (__pyx_v_searchcoords_bbox.data + __pyx_t_14 * __pyx_v_searchcoords_bbox.strides[0]) )) + __pyx_t_15)) ))) + ((__pyx_v_zi - 1) * (__pyx_v_searchgrid->cellsize[2]))); - /* "MDAnalysis/lib/nsgrid.pyx":891 + /* "MDAnalysis/lib/nsgrid.pyx":914 * probe[ZZ] = searchcoords_bbox[current_beadid, ZZ] + (zi - 1) * searchgrid.cellsize[ZZ] * # Make sure the probe coordinates is inside the brick-shaped box * if self.periodic: # <<<<<<<<<<<<<< @@ -8289,7 +8550,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_2search(struct __pyx __pyx_t_1 = (__pyx_v_self->periodic != 0); if (__pyx_t_1) { - /* "MDAnalysis/lib/nsgrid.pyx":892 + /* "MDAnalysis/lib/nsgrid.pyx":915 * # Make sure the probe coordinates is inside the brick-shaped box * if self.periodic: * for m in range(DIM - 1, -1, -1): # <<<<<<<<<<<<<< @@ -8299,7 +8560,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_2search(struct __pyx for (__pyx_t_16 = 2; __pyx_t_16 > -1L; __pyx_t_16-=1) { __pyx_v_m = __pyx_t_16; - /* "MDAnalysis/lib/nsgrid.pyx":893 + /* "MDAnalysis/lib/nsgrid.pyx":916 * if self.periodic: * for m in range(DIM - 1, -1, -1): * while probe[m] < 0: # <<<<<<<<<<<<<< @@ -8310,7 +8571,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_2search(struct __pyx __pyx_t_1 = (((__pyx_v_probe[__pyx_v_m]) < 0.0) != 0); if (!__pyx_t_1) break; - /* "MDAnalysis/lib/nsgrid.pyx":894 + /* "MDAnalysis/lib/nsgrid.pyx":917 * for m in range(DIM - 1, -1, -1): * while probe[m] < 0: * for d in range(m+1): # <<<<<<<<<<<<<< @@ -8322,7 +8583,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_2search(struct __pyx for (__pyx_t_19 = 0; __pyx_t_19 < __pyx_t_18; __pyx_t_19+=1) { __pyx_v_d = __pyx_t_19; - /* "MDAnalysis/lib/nsgrid.pyx":895 + /* "MDAnalysis/lib/nsgrid.pyx":918 * while probe[m] < 0: * for d in range(m+1): * probe[d] += self.box.c_pbcbox.box[m][d] # <<<<<<<<<<<<<< @@ -8334,7 +8595,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_2search(struct __pyx } } - /* "MDAnalysis/lib/nsgrid.pyx":896 + /* "MDAnalysis/lib/nsgrid.pyx":919 * for d in range(m+1): * probe[d] += self.box.c_pbcbox.box[m][d] * while probe[m] >= self.box.c_pbcbox.box[m][m]: # <<<<<<<<<<<<<< @@ -8345,7 +8606,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_2search(struct __pyx __pyx_t_1 = (((__pyx_v_probe[__pyx_v_m]) >= ((__pyx_v_self->box->c_pbcbox.box[__pyx_v_m])[__pyx_v_m])) != 0); if (!__pyx_t_1) break; - /* "MDAnalysis/lib/nsgrid.pyx":897 + /* "MDAnalysis/lib/nsgrid.pyx":920 * probe[d] += self.box.c_pbcbox.box[m][d] * while probe[m] >= self.box.c_pbcbox.box[m][m]: * for d in range(m+1): # <<<<<<<<<<<<<< @@ -8357,7 +8618,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_2search(struct __pyx for (__pyx_t_19 = 0; __pyx_t_19 < __pyx_t_18; __pyx_t_19+=1) { __pyx_v_d = __pyx_t_19; - /* "MDAnalysis/lib/nsgrid.pyx":898 + /* "MDAnalysis/lib/nsgrid.pyx":921 * while probe[m] >= self.box.c_pbcbox.box[m][m]: * for d in range(m+1): * probe[d] -= self.box.c_pbcbox.box[m][d] # <<<<<<<<<<<<<< @@ -8370,7 +8631,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_2search(struct __pyx } } - /* "MDAnalysis/lib/nsgrid.pyx":891 + /* "MDAnalysis/lib/nsgrid.pyx":914 * probe[ZZ] = searchcoords_bbox[current_beadid, ZZ] + (zi - 1) * searchgrid.cellsize[ZZ] * # Make sure the probe coordinates is inside the brick-shaped box * if self.periodic: # <<<<<<<<<<<<<< @@ -8380,7 +8641,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_2search(struct __pyx goto __pyx_L17; } - /* "MDAnalysis/lib/nsgrid.pyx":900 + /* "MDAnalysis/lib/nsgrid.pyx":923 * probe[d] -= self.box.c_pbcbox.box[m][d] * else: * for m in range(DIM -1, -1, -1): # <<<<<<<<<<<<<< @@ -8391,7 +8652,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_2search(struct __pyx for (__pyx_t_16 = 2; __pyx_t_16 > -1L; __pyx_t_16-=1) { __pyx_v_m = __pyx_t_16; - /* "MDAnalysis/lib/nsgrid.pyx":901 + /* "MDAnalysis/lib/nsgrid.pyx":924 * else: * for m in range(DIM -1, -1, -1): * if probe[m] < 0: # <<<<<<<<<<<<<< @@ -8401,7 +8662,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_2search(struct __pyx __pyx_t_1 = (((__pyx_v_probe[__pyx_v_m]) < 0.0) != 0); if (__pyx_t_1) { - /* "MDAnalysis/lib/nsgrid.pyx":902 + /* "MDAnalysis/lib/nsgrid.pyx":925 * for m in range(DIM -1, -1, -1): * if probe[m] < 0: * check = False # <<<<<<<<<<<<<< @@ -8410,7 +8671,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_2search(struct __pyx */ __pyx_v_check = 0; - /* "MDAnalysis/lib/nsgrid.pyx":903 + /* "MDAnalysis/lib/nsgrid.pyx":926 * if probe[m] < 0: * check = False * break # <<<<<<<<<<<<<< @@ -8419,7 +8680,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_2search(struct __pyx */ goto __pyx_L29_break; - /* "MDAnalysis/lib/nsgrid.pyx":901 + /* "MDAnalysis/lib/nsgrid.pyx":924 * else: * for m in range(DIM -1, -1, -1): * if probe[m] < 0: # <<<<<<<<<<<<<< @@ -8428,7 +8689,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_2search(struct __pyx */ } - /* "MDAnalysis/lib/nsgrid.pyx":904 + /* "MDAnalysis/lib/nsgrid.pyx":927 * check = False * break * if probe[m] > self.box.c_pbcbox.box[m][m]: # <<<<<<<<<<<<<< @@ -8438,7 +8699,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_2search(struct __pyx __pyx_t_1 = (((__pyx_v_probe[__pyx_v_m]) > ((__pyx_v_self->box->c_pbcbox.box[__pyx_v_m])[__pyx_v_m])) != 0); if (__pyx_t_1) { - /* "MDAnalysis/lib/nsgrid.pyx":905 + /* "MDAnalysis/lib/nsgrid.pyx":928 * break * if probe[m] > self.box.c_pbcbox.box[m][m]: * check = False # <<<<<<<<<<<<<< @@ -8447,7 +8708,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_2search(struct __pyx */ __pyx_v_check = 0; - /* "MDAnalysis/lib/nsgrid.pyx":906 + /* "MDAnalysis/lib/nsgrid.pyx":929 * if probe[m] > self.box.c_pbcbox.box[m][m]: * check = False * break # <<<<<<<<<<<<<< @@ -8456,7 +8717,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_2search(struct __pyx */ goto __pyx_L29_break; - /* "MDAnalysis/lib/nsgrid.pyx":904 + /* "MDAnalysis/lib/nsgrid.pyx":927 * check = False * break * if probe[m] > self.box.c_pbcbox.box[m][m]: # <<<<<<<<<<<<<< @@ -8469,7 +8730,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_2search(struct __pyx } __pyx_L17:; - /* "MDAnalysis/lib/nsgrid.pyx":907 + /* "MDAnalysis/lib/nsgrid.pyx":930 * check = False * break * if not check: # <<<<<<<<<<<<<< @@ -8479,7 +8740,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_2search(struct __pyx __pyx_t_1 = ((!(__pyx_v_check != 0)) != 0); if (__pyx_t_1) { - /* "MDAnalysis/lib/nsgrid.pyx":908 + /* "MDAnalysis/lib/nsgrid.pyx":931 * break * if not check: * continue # <<<<<<<<<<<<<< @@ -8488,7 +8749,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_2search(struct __pyx */ goto __pyx_L15_continue; - /* "MDAnalysis/lib/nsgrid.pyx":907 + /* "MDAnalysis/lib/nsgrid.pyx":930 * check = False * break * if not check: # <<<<<<<<<<<<<< @@ -8497,7 +8758,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_2search(struct __pyx */ } - /* "MDAnalysis/lib/nsgrid.pyx":910 + /* "MDAnalysis/lib/nsgrid.pyx":933 * continue * # Get the cell index corresponding to the probe * cellindex_probe = self.grid.coord2cellid(probe) # <<<<<<<<<<<<<< @@ -8506,7 +8767,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_2search(struct __pyx */ __pyx_v_cellindex_probe = ((struct __pyx_vtabstruct_10MDAnalysis_3lib_6nsgrid__NSGrid *)__pyx_v_self->grid->__pyx_vtab)->coord2cellid(__pyx_v_self->grid, __pyx_v_probe); - /* "MDAnalysis/lib/nsgrid.pyx":912 + /* "MDAnalysis/lib/nsgrid.pyx":935 * cellindex_probe = self.grid.coord2cellid(probe) * # for this cellindex search in grid * for j in range(self.grid.nbeads[cellindex_probe]): # <<<<<<<<<<<<<< @@ -8518,7 +8779,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_2search(struct __pyx for (__pyx_t_18 = 0; __pyx_t_18 < __pyx_t_17; __pyx_t_18+=1) { __pyx_v_j = __pyx_t_18; - /* "MDAnalysis/lib/nsgrid.pyx":913 + /* "MDAnalysis/lib/nsgrid.pyx":936 * # for this cellindex search in grid * for j in range(self.grid.nbeads[cellindex_probe]): * bid = self.grid.beadids[cellindex_probe * self.grid.nbeads_per_cell + j] # <<<<<<<<<<<<<< @@ -8527,7 +8788,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_2search(struct __pyx */ __pyx_v_bid = (__pyx_v_self->grid->beadids[((__pyx_v_cellindex_probe * __pyx_v_self->grid->nbeads_per_cell) + __pyx_v_j)]); - /* "MDAnalysis/lib/nsgrid.pyx":915 + /* "MDAnalysis/lib/nsgrid.pyx":938 * bid = self.grid.beadids[cellindex_probe * self.grid.nbeads_per_cell + j] * # find distance between search coords[i] and coords[bid] * d2 = self.box.fast_distance2(&searchcoords_bbox[current_beadid, XX], &self.coords_bbox[bid, XX]) # <<<<<<<<<<<<<< @@ -8544,7 +8805,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_2search(struct __pyx if (__pyx_t_22 < 0) __pyx_t_22 += __pyx_v_self->coords_bbox.shape[1]; __pyx_v_d2 = ((struct __pyx_vtabstruct_10MDAnalysis_3lib_6nsgrid__PBCBox *)__pyx_v_self->box->__pyx_vtab)->fast_distance2(__pyx_v_self->box, (&(*((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=1 */ ((char *) (((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=0 */ (__pyx_v_searchcoords_bbox.data + __pyx_t_15 * __pyx_v_searchcoords_bbox.strides[0]) )) + __pyx_t_14)) )))), (&(*((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=1 */ ((char *) (((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=0 */ (__pyx_v_self->coords_bbox.data + __pyx_t_21 * __pyx_v_self->coords_bbox.strides[0]) )) + __pyx_t_22)) ))))); - /* "MDAnalysis/lib/nsgrid.pyx":916 + /* "MDAnalysis/lib/nsgrid.pyx":939 * # find distance between search coords[i] and coords[bid] * d2 = self.box.fast_distance2(&searchcoords_bbox[current_beadid, XX], &self.coords_bbox[bid, XX]) * if d2 <= cutoff2: # <<<<<<<<<<<<<< @@ -8554,7 +8815,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_2search(struct __pyx __pyx_t_1 = ((__pyx_v_d2 <= __pyx_v_cutoff2) != 0); if (__pyx_t_1) { - /* "MDAnalysis/lib/nsgrid.pyx":917 + /* "MDAnalysis/lib/nsgrid.pyx":940 * d2 = self.box.fast_distance2(&searchcoords_bbox[current_beadid, XX], &self.coords_bbox[bid, XX]) * if d2 <= cutoff2: * results.add_neighbors(current_beadid, bid, d2) # <<<<<<<<<<<<<< @@ -8563,7 +8824,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_2search(struct __pyx */ ((struct __pyx_vtabstruct_10MDAnalysis_3lib_6nsgrid_NSResults *)__pyx_v_results->__pyx_vtab)->add_neighbors(__pyx_v_results, __pyx_v_current_beadid, __pyx_v_bid, __pyx_v_d2); - /* "MDAnalysis/lib/nsgrid.pyx":918 + /* "MDAnalysis/lib/nsgrid.pyx":941 * if d2 <= cutoff2: * results.add_neighbors(current_beadid, bid, d2) * npairs += 1 # <<<<<<<<<<<<<< @@ -8572,7 +8833,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_2search(struct __pyx */ __pyx_v_npairs = (__pyx_v_npairs + 1); - /* "MDAnalysis/lib/nsgrid.pyx":916 + /* "MDAnalysis/lib/nsgrid.pyx":939 * # find distance between search coords[i] and coords[bid] * d2 = self.box.fast_distance2(&searchcoords_bbox[current_beadid, XX], &self.coords_bbox[bid, XX]) * if d2 <= cutoff2: # <<<<<<<<<<<<<< @@ -8588,7 +8849,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_2search(struct __pyx } } - /* "MDAnalysis/lib/nsgrid.pyx":876 + /* "MDAnalysis/lib/nsgrid.pyx":899 * results = NSResults(self.cutoff, self.coords, searchcoords) * * with nogil: # <<<<<<<<<<<<<< @@ -8607,7 +8868,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_2search(struct __pyx } } - /* "MDAnalysis/lib/nsgrid.pyx":919 + /* "MDAnalysis/lib/nsgrid.pyx":942 * results.add_neighbors(current_beadid, bid, d2) * npairs += 1 * return results # <<<<<<<<<<<<<< @@ -8619,7 +8880,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_2search(struct __pyx __pyx_r = ((PyObject *)__pyx_v_results); goto __pyx_L0; - /* "MDAnalysis/lib/nsgrid.pyx":811 + /* "MDAnalysis/lib/nsgrid.pyx":834 * self.grid.fill_grid(self.coords_bbox) * * def search(self, search_coords): # <<<<<<<<<<<<<< @@ -8646,7 +8907,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_2search(struct __pyx return __pyx_r; } -/* "MDAnalysis/lib/nsgrid.pyx":921 +/* "MDAnalysis/lib/nsgrid.pyx":944 * return results * * def self_search(self): # <<<<<<<<<<<<<< @@ -8715,7 +8976,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct int __pyx_clineno = 0; __Pyx_RefNannySetupContext("self_search", 0); - /* "MDAnalysis/lib/nsgrid.pyx":948 + /* "MDAnalysis/lib/nsgrid.pyx":971 * cdef rvec probe * * cdef dreal cutoff2 = self.cutoff * self.cutoff # <<<<<<<<<<<<<< @@ -8724,7 +8985,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct */ __pyx_v_cutoff2 = (__pyx_v_self->cutoff * __pyx_v_self->cutoff); - /* "MDAnalysis/lib/nsgrid.pyx":949 + /* "MDAnalysis/lib/nsgrid.pyx":972 * * cdef dreal cutoff2 = self.cutoff * self.cutoff * cdef ns_int npairs = 0 # <<<<<<<<<<<<<< @@ -8733,7 +8994,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct */ __pyx_v_npairs = 0; - /* "MDAnalysis/lib/nsgrid.pyx":952 + /* "MDAnalysis/lib/nsgrid.pyx":975 * cdef bint check * * size_search = self.coords.shape[0] # <<<<<<<<<<<<<< @@ -8742,20 +9003,20 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct */ __pyx_v_size_search = (__pyx_v_self->coords.shape[0]); - /* "MDAnalysis/lib/nsgrid.pyx":954 + /* "MDAnalysis/lib/nsgrid.pyx":977 * size_search = self.coords.shape[0] * * results = NSResults(self.cutoff, self.coords, self.coords) # <<<<<<<<<<<<<< * * with nogil: */ - __pyx_t_1 = PyFloat_FromDouble(__pyx_v_self->cutoff); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 954, __pyx_L1_error) + __pyx_t_1 = PyFloat_FromDouble(__pyx_v_self->cutoff); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 977, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); - __pyx_t_2 = __pyx_memoryview_fromslice(__pyx_v_self->coords, 2, (PyObject *(*)(char *)) __pyx_memview_get_nn___pyx_t_10MDAnalysis_3lib_6nsgrid_real, (int (*)(char *, PyObject *)) __pyx_memview_set_nn___pyx_t_10MDAnalysis_3lib_6nsgrid_real, 0);; if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 954, __pyx_L1_error) + __pyx_t_2 = __pyx_memoryview_fromslice(__pyx_v_self->coords, 2, (PyObject *(*)(char *)) __pyx_memview_get_nn___pyx_t_10MDAnalysis_3lib_6nsgrid_real, (int (*)(char *, PyObject *)) __pyx_memview_set_nn___pyx_t_10MDAnalysis_3lib_6nsgrid_real, 0);; if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 977, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_2); - __pyx_t_3 = __pyx_memoryview_fromslice(__pyx_v_self->coords, 2, (PyObject *(*)(char *)) __pyx_memview_get_nn___pyx_t_10MDAnalysis_3lib_6nsgrid_real, (int (*)(char *, PyObject *)) __pyx_memview_set_nn___pyx_t_10MDAnalysis_3lib_6nsgrid_real, 0);; if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 954, __pyx_L1_error) + __pyx_t_3 = __pyx_memoryview_fromslice(__pyx_v_self->coords, 2, (PyObject *(*)(char *)) __pyx_memview_get_nn___pyx_t_10MDAnalysis_3lib_6nsgrid_real, (int (*)(char *, PyObject *)) __pyx_memview_set_nn___pyx_t_10MDAnalysis_3lib_6nsgrid_real, 0);; if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 977, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); - __pyx_t_4 = PyTuple_New(3); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 954, __pyx_L1_error) + __pyx_t_4 = PyTuple_New(3); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 977, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_4); __Pyx_GIVEREF(__pyx_t_1); PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_1); @@ -8766,13 +9027,13 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct __pyx_t_1 = 0; __pyx_t_2 = 0; __pyx_t_3 = 0; - __pyx_t_3 = __Pyx_PyObject_Call(((PyObject *)__pyx_ptype_10MDAnalysis_3lib_6nsgrid_NSResults), __pyx_t_4, NULL); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 954, __pyx_L1_error) + __pyx_t_3 = __Pyx_PyObject_Call(((PyObject *)__pyx_ptype_10MDAnalysis_3lib_6nsgrid_NSResults), __pyx_t_4, NULL); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 977, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __pyx_v_results = ((struct __pyx_obj_10MDAnalysis_3lib_6nsgrid_NSResults *)__pyx_t_3); __pyx_t_3 = 0; - /* "MDAnalysis/lib/nsgrid.pyx":956 + /* "MDAnalysis/lib/nsgrid.pyx":979 * results = NSResults(self.cutoff, self.coords, self.coords) * * with nogil: # <<<<<<<<<<<<<< @@ -8787,7 +9048,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct #endif /*try:*/ { - /* "MDAnalysis/lib/nsgrid.pyx":957 + /* "MDAnalysis/lib/nsgrid.pyx":980 * * with nogil: * for i in range(size_search): # <<<<<<<<<<<<<< @@ -8799,7 +9060,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct for (__pyx_t_7 = 0; __pyx_t_7 < __pyx_t_6; __pyx_t_7+=1) { __pyx_v_i = __pyx_t_7; - /* "MDAnalysis/lib/nsgrid.pyx":959 + /* "MDAnalysis/lib/nsgrid.pyx":982 * for i in range(size_search): * # Start with first search coordinate * current_beadid = i # <<<<<<<<<<<<<< @@ -8808,7 +9069,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct */ __pyx_v_current_beadid = __pyx_v_i; - /* "MDAnalysis/lib/nsgrid.pyx":961 + /* "MDAnalysis/lib/nsgrid.pyx":984 * current_beadid = i * # find the cellindex of the coordinate * cellindex = self.grid.cellids[current_beadid] # <<<<<<<<<<<<<< @@ -8817,7 +9078,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct */ __pyx_v_cellindex = (__pyx_v_self->grid->cellids[__pyx_v_current_beadid]); - /* "MDAnalysis/lib/nsgrid.pyx":962 + /* "MDAnalysis/lib/nsgrid.pyx":985 * # find the cellindex of the coordinate * cellindex = self.grid.cellids[current_beadid] * for xi in range(DIM): # <<<<<<<<<<<<<< @@ -8827,7 +9088,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct for (__pyx_t_8 = 0; __pyx_t_8 < 3; __pyx_t_8+=1) { __pyx_v_xi = __pyx_t_8; - /* "MDAnalysis/lib/nsgrid.pyx":963 + /* "MDAnalysis/lib/nsgrid.pyx":986 * cellindex = self.grid.cellids[current_beadid] * for xi in range(DIM): * for yi in range(DIM): # <<<<<<<<<<<<<< @@ -8837,7 +9098,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct for (__pyx_t_9 = 0; __pyx_t_9 < 3; __pyx_t_9+=1) { __pyx_v_yi = __pyx_t_9; - /* "MDAnalysis/lib/nsgrid.pyx":964 + /* "MDAnalysis/lib/nsgrid.pyx":987 * for xi in range(DIM): * for yi in range(DIM): * for zi in range(DIM): # <<<<<<<<<<<<<< @@ -8847,7 +9108,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct for (__pyx_t_10 = 0; __pyx_t_10 < 3; __pyx_t_10+=1) { __pyx_v_zi = __pyx_t_10; - /* "MDAnalysis/lib/nsgrid.pyx":965 + /* "MDAnalysis/lib/nsgrid.pyx":988 * for yi in range(DIM): * for zi in range(DIM): * check = True # <<<<<<<<<<<<<< @@ -8856,7 +9117,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct */ __pyx_v_check = 1; - /* "MDAnalysis/lib/nsgrid.pyx":968 + /* "MDAnalysis/lib/nsgrid.pyx":991 * # Calculate and/or reinitialize shifted coordinates * # Probe the search coordinates in a brick shaped box * probe[XX] = self.coords_bbox[current_beadid, XX] + (xi - 1) * self.grid.cellsize[XX] # <<<<<<<<<<<<<< @@ -8869,7 +9130,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct if (__pyx_t_12 < 0) __pyx_t_12 += __pyx_v_self->coords_bbox.shape[1]; (__pyx_v_probe[0]) = ((*((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=1 */ ((char *) (((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=0 */ (__pyx_v_self->coords_bbox.data + __pyx_t_11 * __pyx_v_self->coords_bbox.strides[0]) )) + __pyx_t_12)) ))) + ((__pyx_v_xi - 1) * (__pyx_v_self->grid->cellsize[0]))); - /* "MDAnalysis/lib/nsgrid.pyx":969 + /* "MDAnalysis/lib/nsgrid.pyx":992 * # Probe the search coordinates in a brick shaped box * probe[XX] = self.coords_bbox[current_beadid, XX] + (xi - 1) * self.grid.cellsize[XX] * probe[YY] = self.coords_bbox[current_beadid, YY] + (yi - 1) * self.grid.cellsize[YY] # <<<<<<<<<<<<<< @@ -8882,7 +9143,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct if (__pyx_t_11 < 0) __pyx_t_11 += __pyx_v_self->coords_bbox.shape[1]; (__pyx_v_probe[1]) = ((*((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=1 */ ((char *) (((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=0 */ (__pyx_v_self->coords_bbox.data + __pyx_t_12 * __pyx_v_self->coords_bbox.strides[0]) )) + __pyx_t_11)) ))) + ((__pyx_v_yi - 1) * (__pyx_v_self->grid->cellsize[1]))); - /* "MDAnalysis/lib/nsgrid.pyx":970 + /* "MDAnalysis/lib/nsgrid.pyx":993 * probe[XX] = self.coords_bbox[current_beadid, XX] + (xi - 1) * self.grid.cellsize[XX] * probe[YY] = self.coords_bbox[current_beadid, YY] + (yi - 1) * self.grid.cellsize[YY] * probe[ZZ] = self.coords_bbox[current_beadid, ZZ] + (zi - 1) * self.grid.cellsize[ZZ] # <<<<<<<<<<<<<< @@ -8895,7 +9156,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct if (__pyx_t_12 < 0) __pyx_t_12 += __pyx_v_self->coords_bbox.shape[1]; (__pyx_v_probe[2]) = ((*((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=1 */ ((char *) (((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=0 */ (__pyx_v_self->coords_bbox.data + __pyx_t_11 * __pyx_v_self->coords_bbox.strides[0]) )) + __pyx_t_12)) ))) + ((__pyx_v_zi - 1) * (__pyx_v_self->grid->cellsize[2]))); - /* "MDAnalysis/lib/nsgrid.pyx":972 + /* "MDAnalysis/lib/nsgrid.pyx":995 * probe[ZZ] = self.coords_bbox[current_beadid, ZZ] + (zi - 1) * self.grid.cellsize[ZZ] * # Make sure the shifted coordinates is inside the brick-shaped box * if self.periodic: # <<<<<<<<<<<<<< @@ -8905,7 +9166,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct __pyx_t_13 = (__pyx_v_self->periodic != 0); if (__pyx_t_13) { - /* "MDAnalysis/lib/nsgrid.pyx":973 + /* "MDAnalysis/lib/nsgrid.pyx":996 * # Make sure the shifted coordinates is inside the brick-shaped box * if self.periodic: * for m in range(DIM - 1, -1, -1): # <<<<<<<<<<<<<< @@ -8915,7 +9176,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct for (__pyx_t_14 = 2; __pyx_t_14 > -1L; __pyx_t_14-=1) { __pyx_v_m = __pyx_t_14; - /* "MDAnalysis/lib/nsgrid.pyx":974 + /* "MDAnalysis/lib/nsgrid.pyx":997 * if self.periodic: * for m in range(DIM - 1, -1, -1): * while probe[m] < 0: # <<<<<<<<<<<<<< @@ -8926,7 +9187,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct __pyx_t_13 = (((__pyx_v_probe[__pyx_v_m]) < 0.0) != 0); if (!__pyx_t_13) break; - /* "MDAnalysis/lib/nsgrid.pyx":975 + /* "MDAnalysis/lib/nsgrid.pyx":998 * for m in range(DIM - 1, -1, -1): * while probe[m] < 0: * for d in range(m+1): # <<<<<<<<<<<<<< @@ -8938,7 +9199,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct for (__pyx_t_17 = 0; __pyx_t_17 < __pyx_t_16; __pyx_t_17+=1) { __pyx_v_d = __pyx_t_17; - /* "MDAnalysis/lib/nsgrid.pyx":976 + /* "MDAnalysis/lib/nsgrid.pyx":999 * while probe[m] < 0: * for d in range(m+1): * probe[d] += self.box.c_pbcbox.box[m][d] # <<<<<<<<<<<<<< @@ -8950,7 +9211,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct } } - /* "MDAnalysis/lib/nsgrid.pyx":977 + /* "MDAnalysis/lib/nsgrid.pyx":1000 * for d in range(m+1): * probe[d] += self.box.c_pbcbox.box[m][d] * while probe[m] >= self.box.c_pbcbox.box[m][m]: # <<<<<<<<<<<<<< @@ -8961,7 +9222,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct __pyx_t_13 = (((__pyx_v_probe[__pyx_v_m]) >= ((__pyx_v_self->box->c_pbcbox.box[__pyx_v_m])[__pyx_v_m])) != 0); if (!__pyx_t_13) break; - /* "MDAnalysis/lib/nsgrid.pyx":978 + /* "MDAnalysis/lib/nsgrid.pyx":1001 * probe[d] += self.box.c_pbcbox.box[m][d] * while probe[m] >= self.box.c_pbcbox.box[m][m]: * for d in range(m+1): # <<<<<<<<<<<<<< @@ -8973,7 +9234,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct for (__pyx_t_17 = 0; __pyx_t_17 < __pyx_t_16; __pyx_t_17+=1) { __pyx_v_d = __pyx_t_17; - /* "MDAnalysis/lib/nsgrid.pyx":979 + /* "MDAnalysis/lib/nsgrid.pyx":1002 * while probe[m] >= self.box.c_pbcbox.box[m][m]: * for d in range(m+1): * probe[d] -= self.box.c_pbcbox.box[m][d] # <<<<<<<<<<<<<< @@ -8986,7 +9247,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct } } - /* "MDAnalysis/lib/nsgrid.pyx":972 + /* "MDAnalysis/lib/nsgrid.pyx":995 * probe[ZZ] = self.coords_bbox[current_beadid, ZZ] + (zi - 1) * self.grid.cellsize[ZZ] * # Make sure the shifted coordinates is inside the brick-shaped box * if self.periodic: # <<<<<<<<<<<<<< @@ -8996,7 +9257,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct goto __pyx_L14; } - /* "MDAnalysis/lib/nsgrid.pyx":981 + /* "MDAnalysis/lib/nsgrid.pyx":1004 * probe[d] -= self.box.c_pbcbox.box[m][d] * else: * for m in range(DIM -1, -1, -1): # <<<<<<<<<<<<<< @@ -9007,7 +9268,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct for (__pyx_t_14 = 2; __pyx_t_14 > -1L; __pyx_t_14-=1) { __pyx_v_m = __pyx_t_14; - /* "MDAnalysis/lib/nsgrid.pyx":982 + /* "MDAnalysis/lib/nsgrid.pyx":1005 * else: * for m in range(DIM -1, -1, -1): * if probe[m] < 0: # <<<<<<<<<<<<<< @@ -9017,7 +9278,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct __pyx_t_13 = (((__pyx_v_probe[__pyx_v_m]) < 0.0) != 0); if (__pyx_t_13) { - /* "MDAnalysis/lib/nsgrid.pyx":983 + /* "MDAnalysis/lib/nsgrid.pyx":1006 * for m in range(DIM -1, -1, -1): * if probe[m] < 0: * check = False # <<<<<<<<<<<<<< @@ -9026,7 +9287,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct */ __pyx_v_check = 0; - /* "MDAnalysis/lib/nsgrid.pyx":984 + /* "MDAnalysis/lib/nsgrid.pyx":1007 * if probe[m] < 0: * check = False * break # <<<<<<<<<<<<<< @@ -9035,7 +9296,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct */ goto __pyx_L26_break; - /* "MDAnalysis/lib/nsgrid.pyx":982 + /* "MDAnalysis/lib/nsgrid.pyx":1005 * else: * for m in range(DIM -1, -1, -1): * if probe[m] < 0: # <<<<<<<<<<<<<< @@ -9044,7 +9305,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct */ } - /* "MDAnalysis/lib/nsgrid.pyx":985 + /* "MDAnalysis/lib/nsgrid.pyx":1008 * check = False * break * elif probe[m] > self.box.c_pbcbox.box[m][m]: # <<<<<<<<<<<<<< @@ -9054,7 +9315,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct __pyx_t_13 = (((__pyx_v_probe[__pyx_v_m]) > ((__pyx_v_self->box->c_pbcbox.box[__pyx_v_m])[__pyx_v_m])) != 0); if (__pyx_t_13) { - /* "MDAnalysis/lib/nsgrid.pyx":986 + /* "MDAnalysis/lib/nsgrid.pyx":1009 * break * elif probe[m] > self.box.c_pbcbox.box[m][m]: * check = False # <<<<<<<<<<<<<< @@ -9063,7 +9324,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct */ __pyx_v_check = 0; - /* "MDAnalysis/lib/nsgrid.pyx":987 + /* "MDAnalysis/lib/nsgrid.pyx":1010 * elif probe[m] > self.box.c_pbcbox.box[m][m]: * check = False * break # <<<<<<<<<<<<<< @@ -9072,7 +9333,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct */ goto __pyx_L26_break; - /* "MDAnalysis/lib/nsgrid.pyx":985 + /* "MDAnalysis/lib/nsgrid.pyx":1008 * check = False * break * elif probe[m] > self.box.c_pbcbox.box[m][m]: # <<<<<<<<<<<<<< @@ -9085,7 +9346,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct } __pyx_L14:; - /* "MDAnalysis/lib/nsgrid.pyx":988 + /* "MDAnalysis/lib/nsgrid.pyx":1011 * check = False * break * if not check: # <<<<<<<<<<<<<< @@ -9095,7 +9356,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct __pyx_t_13 = ((!(__pyx_v_check != 0)) != 0); if (__pyx_t_13) { - /* "MDAnalysis/lib/nsgrid.pyx":989 + /* "MDAnalysis/lib/nsgrid.pyx":1012 * break * if not check: * continue # <<<<<<<<<<<<<< @@ -9104,7 +9365,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct */ goto __pyx_L12_continue; - /* "MDAnalysis/lib/nsgrid.pyx":988 + /* "MDAnalysis/lib/nsgrid.pyx":1011 * check = False * break * if not check: # <<<<<<<<<<<<<< @@ -9113,7 +9374,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct */ } - /* "MDAnalysis/lib/nsgrid.pyx":991 + /* "MDAnalysis/lib/nsgrid.pyx":1014 * continue * # Get the cell index corresponding to the probe * cellindex_probe = self.grid.coord2cellid(probe) # <<<<<<<<<<<<<< @@ -9122,7 +9383,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct */ __pyx_v_cellindex_probe = ((struct __pyx_vtabstruct_10MDAnalysis_3lib_6nsgrid__NSGrid *)__pyx_v_self->grid->__pyx_vtab)->coord2cellid(__pyx_v_self->grid, __pyx_v_probe); - /* "MDAnalysis/lib/nsgrid.pyx":993 + /* "MDAnalysis/lib/nsgrid.pyx":1016 * cellindex_probe = self.grid.coord2cellid(probe) * # for this cellindex search in grid * for j in range(self.grid.nbeads[cellindex_probe]): # <<<<<<<<<<<<<< @@ -9134,7 +9395,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct for (__pyx_t_16 = 0; __pyx_t_16 < __pyx_t_15; __pyx_t_16+=1) { __pyx_v_j = __pyx_t_16; - /* "MDAnalysis/lib/nsgrid.pyx":994 + /* "MDAnalysis/lib/nsgrid.pyx":1017 * # for this cellindex search in grid * for j in range(self.grid.nbeads[cellindex_probe]): * bid = self.grid.beadids[cellindex_probe * self.grid.nbeads_per_cell + j] # <<<<<<<<<<<<<< @@ -9143,7 +9404,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct */ __pyx_v_bid = (__pyx_v_self->grid->beadids[((__pyx_v_cellindex_probe * __pyx_v_self->grid->nbeads_per_cell) + __pyx_v_j)]); - /* "MDAnalysis/lib/nsgrid.pyx":995 + /* "MDAnalysis/lib/nsgrid.pyx":1018 * for j in range(self.grid.nbeads[cellindex_probe]): * bid = self.grid.beadids[cellindex_probe * self.grid.nbeads_per_cell + j] * if bid < current_beadid: # <<<<<<<<<<<<<< @@ -9153,7 +9414,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct __pyx_t_13 = ((__pyx_v_bid < __pyx_v_current_beadid) != 0); if (__pyx_t_13) { - /* "MDAnalysis/lib/nsgrid.pyx":996 + /* "MDAnalysis/lib/nsgrid.pyx":1019 * bid = self.grid.beadids[cellindex_probe * self.grid.nbeads_per_cell + j] * if bid < current_beadid: * continue # <<<<<<<<<<<<<< @@ -9162,7 +9423,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct */ goto __pyx_L29_continue; - /* "MDAnalysis/lib/nsgrid.pyx":995 + /* "MDAnalysis/lib/nsgrid.pyx":1018 * for j in range(self.grid.nbeads[cellindex_probe]): * bid = self.grid.beadids[cellindex_probe * self.grid.nbeads_per_cell + j] * if bid < current_beadid: # <<<<<<<<<<<<<< @@ -9171,7 +9432,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct */ } - /* "MDAnalysis/lib/nsgrid.pyx":998 + /* "MDAnalysis/lib/nsgrid.pyx":1021 * continue * # find distance between search coords[i] and coords[bid] * d2 = self.box.fast_distance2(&self.coords_bbox[current_beadid, XX], &self.coords_bbox[bid, XX]) # <<<<<<<<<<<<<< @@ -9188,7 +9449,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct if (__pyx_t_20 < 0) __pyx_t_20 += __pyx_v_self->coords_bbox.shape[1]; __pyx_v_d2 = ((struct __pyx_vtabstruct_10MDAnalysis_3lib_6nsgrid__PBCBox *)__pyx_v_self->box->__pyx_vtab)->fast_distance2(__pyx_v_self->box, (&(*((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=1 */ ((char *) (((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=0 */ (__pyx_v_self->coords_bbox.data + __pyx_t_12 * __pyx_v_self->coords_bbox.strides[0]) )) + __pyx_t_11)) )))), (&(*((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=1 */ ((char *) (((__pyx_t_10MDAnalysis_3lib_6nsgrid_real *) ( /* dim=0 */ (__pyx_v_self->coords_bbox.data + __pyx_t_19 * __pyx_v_self->coords_bbox.strides[0]) )) + __pyx_t_20)) ))))); - /* "MDAnalysis/lib/nsgrid.pyx":999 + /* "MDAnalysis/lib/nsgrid.pyx":1022 * # find distance between search coords[i] and coords[bid] * d2 = self.box.fast_distance2(&self.coords_bbox[current_beadid, XX], &self.coords_bbox[bid, XX]) * if d2 <= cutoff2 and d2 > EPSILON: # <<<<<<<<<<<<<< @@ -9206,7 +9467,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct __pyx_L33_bool_binop_done:; if (__pyx_t_13) { - /* "MDAnalysis/lib/nsgrid.pyx":1000 + /* "MDAnalysis/lib/nsgrid.pyx":1023 * d2 = self.box.fast_distance2(&self.coords_bbox[current_beadid, XX], &self.coords_bbox[bid, XX]) * if d2 <= cutoff2 and d2 > EPSILON: * results.add_neighbors(current_beadid, bid, d2) # <<<<<<<<<<<<<< @@ -9215,7 +9476,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct */ ((struct __pyx_vtabstruct_10MDAnalysis_3lib_6nsgrid_NSResults *)__pyx_v_results->__pyx_vtab)->add_neighbors(__pyx_v_results, __pyx_v_current_beadid, __pyx_v_bid, __pyx_v_d2); - /* "MDAnalysis/lib/nsgrid.pyx":1001 + /* "MDAnalysis/lib/nsgrid.pyx":1024 * if d2 <= cutoff2 and d2 > EPSILON: * results.add_neighbors(current_beadid, bid, d2) * results.add_neighbors(bid, current_beadid, d2) # <<<<<<<<<<<<<< @@ -9224,7 +9485,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct */ ((struct __pyx_vtabstruct_10MDAnalysis_3lib_6nsgrid_NSResults *)__pyx_v_results->__pyx_vtab)->add_neighbors(__pyx_v_results, __pyx_v_bid, __pyx_v_current_beadid, __pyx_v_d2); - /* "MDAnalysis/lib/nsgrid.pyx":1002 + /* "MDAnalysis/lib/nsgrid.pyx":1025 * results.add_neighbors(current_beadid, bid, d2) * results.add_neighbors(bid, current_beadid, d2) * npairs += 2 # <<<<<<<<<<<<<< @@ -9232,7 +9493,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct */ __pyx_v_npairs = (__pyx_v_npairs + 2); - /* "MDAnalysis/lib/nsgrid.pyx":999 + /* "MDAnalysis/lib/nsgrid.pyx":1022 * # find distance between search coords[i] and coords[bid] * d2 = self.box.fast_distance2(&self.coords_bbox[current_beadid, XX], &self.coords_bbox[bid, XX]) * if d2 <= cutoff2 and d2 > EPSILON: # <<<<<<<<<<<<<< @@ -9249,7 +9510,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct } } - /* "MDAnalysis/lib/nsgrid.pyx":956 + /* "MDAnalysis/lib/nsgrid.pyx":979 * results = NSResults(self.cutoff, self.coords, self.coords) * * with nogil: # <<<<<<<<<<<<<< @@ -9268,7 +9529,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct } } - /* "MDAnalysis/lib/nsgrid.pyx":1003 + /* "MDAnalysis/lib/nsgrid.pyx":1026 * results.add_neighbors(bid, current_beadid, d2) * npairs += 2 * return results # <<<<<<<<<<<<<< @@ -9278,7 +9539,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct __pyx_r = ((PyObject *)__pyx_v_results); goto __pyx_L0; - /* "MDAnalysis/lib/nsgrid.pyx":921 + /* "MDAnalysis/lib/nsgrid.pyx":944 * return results * * def self_search(self): # <<<<<<<<<<<<<< @@ -9301,7 +9562,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_4self_search(struct return __pyx_r; } -/* "MDAnalysis/lib/nsgrid.pyx":711 +/* "MDAnalysis/lib/nsgrid.pyx":726 * cdef real[:, ::1] coords * cdef real[:, ::1] coords_bbox * cdef readonly dreal cutoff # <<<<<<<<<<<<<< @@ -9331,7 +9592,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6nsgrid_6FastNS_6cutoff___get__(stru int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__get__", 0); __Pyx_XDECREF(__pyx_r); - __pyx_t_1 = PyFloat_FromDouble(__pyx_v_self->cutoff); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 711, __pyx_L1_error) + __pyx_t_1 = PyFloat_FromDouble(__pyx_v_self->cutoff); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 726, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; @@ -10584,7 +10845,7 @@ static PyObject *__pyx_f_10MDAnalysis_3lib_6nsgrid___pyx_unpickle_FastNS__set_st return __pyx_r; } -/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":258 +/* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":258 * # experimental exception made for __getbuffer__ and __releasebuffer__ * # -- the details of this may change. * def __getbuffer__(ndarray self, Py_buffer* info, int flags): # <<<<<<<<<<<<<< @@ -10636,7 +10897,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_info->obj = Py_None; __Pyx_INCREF(Py_None); __Pyx_GIVEREF(__pyx_v_info->obj); - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":265 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":265 * * cdef int i, ndim * cdef int endian_detector = 1 # <<<<<<<<<<<<<< @@ -10645,7 +10906,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_endian_detector = 1; - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":266 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":266 * cdef int i, ndim * cdef int endian_detector = 1 * cdef bint little_endian = ((&endian_detector)[0] != 0) # <<<<<<<<<<<<<< @@ -10654,7 +10915,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_little_endian = ((((char *)(&__pyx_v_endian_detector))[0]) != 0); - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":268 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":268 * cdef bint little_endian = ((&endian_detector)[0] != 0) * * ndim = PyArray_NDIM(self) # <<<<<<<<<<<<<< @@ -10663,7 +10924,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_ndim = PyArray_NDIM(__pyx_v_self); - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":270 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":270 * ndim = PyArray_NDIM(self) * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -10677,7 +10938,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L4_bool_binop_done; } - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":271 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":271 * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_ARRAY_C_CONTIGUOUS)): # <<<<<<<<<<<<<< @@ -10688,7 +10949,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = __pyx_t_2; __pyx_L4_bool_binop_done:; - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":270 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":270 * ndim = PyArray_NDIM(self) * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -10697,20 +10958,20 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ if (unlikely(__pyx_t_1)) { - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":272 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":272 * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_ARRAY_C_CONTIGUOUS)): * raise ValueError(u"ndarray is not C contiguous") # <<<<<<<<<<<<<< * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) */ - __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__11, NULL); if (unlikely(!__pyx_t_3)) __PYX_ERR(2, 272, __pyx_L1_error) + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__13, NULL); if (unlikely(!__pyx_t_3)) __PYX_ERR(2, 272, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); __Pyx_Raise(__pyx_t_3, 0, 0, 0); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __PYX_ERR(2, 272, __pyx_L1_error) - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":270 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":270 * ndim = PyArray_NDIM(self) * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -10719,7 +10980,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":274 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":274 * raise ValueError(u"ndarray is not C contiguous") * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -10733,7 +10994,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L7_bool_binop_done; } - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":275 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":275 * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_ARRAY_F_CONTIGUOUS)): # <<<<<<<<<<<<<< @@ -10744,7 +11005,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = __pyx_t_2; __pyx_L7_bool_binop_done:; - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":274 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":274 * raise ValueError(u"ndarray is not C contiguous") * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -10753,20 +11014,20 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ if (unlikely(__pyx_t_1)) { - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":276 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":276 * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_ARRAY_F_CONTIGUOUS)): * raise ValueError(u"ndarray is not Fortran contiguous") # <<<<<<<<<<<<<< * * info.buf = PyArray_DATA(self) */ - __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__12, NULL); if (unlikely(!__pyx_t_3)) __PYX_ERR(2, 276, __pyx_L1_error) + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__14, NULL); if (unlikely(!__pyx_t_3)) __PYX_ERR(2, 276, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); __Pyx_Raise(__pyx_t_3, 0, 0, 0); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __PYX_ERR(2, 276, __pyx_L1_error) - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":274 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":274 * raise ValueError(u"ndarray is not C contiguous") * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -10775,7 +11036,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":278 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":278 * raise ValueError(u"ndarray is not Fortran contiguous") * * info.buf = PyArray_DATA(self) # <<<<<<<<<<<<<< @@ -10784,7 +11045,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->buf = PyArray_DATA(__pyx_v_self); - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":279 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":279 * * info.buf = PyArray_DATA(self) * info.ndim = ndim # <<<<<<<<<<<<<< @@ -10793,7 +11054,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->ndim = __pyx_v_ndim; - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":280 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":280 * info.buf = PyArray_DATA(self) * info.ndim = ndim * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -10803,7 +11064,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = (((sizeof(npy_intp)) != (sizeof(Py_ssize_t))) != 0); if (__pyx_t_1) { - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":283 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":283 * # Allocate new buffer for strides and shape info. * # This is allocated as one block, strides first. * info.strides = PyObject_Malloc(sizeof(Py_ssize_t) * 2 * ndim) # <<<<<<<<<<<<<< @@ -10812,7 +11073,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->strides = ((Py_ssize_t *)PyObject_Malloc((((sizeof(Py_ssize_t)) * 2) * ((size_t)__pyx_v_ndim)))); - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":284 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":284 * # This is allocated as one block, strides first. * info.strides = PyObject_Malloc(sizeof(Py_ssize_t) * 2 * ndim) * info.shape = info.strides + ndim # <<<<<<<<<<<<<< @@ -10821,7 +11082,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->shape = (__pyx_v_info->strides + __pyx_v_ndim); - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":285 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":285 * info.strides = PyObject_Malloc(sizeof(Py_ssize_t) * 2 * ndim) * info.shape = info.strides + ndim * for i in range(ndim): # <<<<<<<<<<<<<< @@ -10833,7 +11094,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { __pyx_v_i = __pyx_t_6; - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":286 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":286 * info.shape = info.strides + ndim * for i in range(ndim): * info.strides[i] = PyArray_STRIDES(self)[i] # <<<<<<<<<<<<<< @@ -10842,7 +11103,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ (__pyx_v_info->strides[__pyx_v_i]) = (PyArray_STRIDES(__pyx_v_self)[__pyx_v_i]); - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":287 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":287 * for i in range(ndim): * info.strides[i] = PyArray_STRIDES(self)[i] * info.shape[i] = PyArray_DIMS(self)[i] # <<<<<<<<<<<<<< @@ -10852,7 +11113,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P (__pyx_v_info->shape[__pyx_v_i]) = (PyArray_DIMS(__pyx_v_self)[__pyx_v_i]); } - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":280 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":280 * info.buf = PyArray_DATA(self) * info.ndim = ndim * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -10862,7 +11123,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L9; } - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":289 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":289 * info.shape[i] = PyArray_DIMS(self)[i] * else: * info.strides = PyArray_STRIDES(self) # <<<<<<<<<<<<<< @@ -10872,7 +11133,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P /*else*/ { __pyx_v_info->strides = ((Py_ssize_t *)PyArray_STRIDES(__pyx_v_self)); - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":290 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":290 * else: * info.strides = PyArray_STRIDES(self) * info.shape = PyArray_DIMS(self) # <<<<<<<<<<<<<< @@ -10883,7 +11144,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } __pyx_L9:; - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":291 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":291 * info.strides = PyArray_STRIDES(self) * info.shape = PyArray_DIMS(self) * info.suboffsets = NULL # <<<<<<<<<<<<<< @@ -10892,7 +11153,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->suboffsets = NULL; - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":292 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":292 * info.shape = PyArray_DIMS(self) * info.suboffsets = NULL * info.itemsize = PyArray_ITEMSIZE(self) # <<<<<<<<<<<<<< @@ -10901,7 +11162,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->itemsize = PyArray_ITEMSIZE(__pyx_v_self); - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":293 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":293 * info.suboffsets = NULL * info.itemsize = PyArray_ITEMSIZE(self) * info.readonly = not PyArray_ISWRITEABLE(self) # <<<<<<<<<<<<<< @@ -10910,7 +11171,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->readonly = (!(PyArray_ISWRITEABLE(__pyx_v_self) != 0)); - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":296 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":296 * * cdef int t * cdef char* f = NULL # <<<<<<<<<<<<<< @@ -10919,7 +11180,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_f = NULL; - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":297 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":297 * cdef int t * cdef char* f = NULL * cdef dtype descr = PyArray_DESCR(self) # <<<<<<<<<<<<<< @@ -10932,7 +11193,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_descr = ((PyArray_Descr *)__pyx_t_3); __pyx_t_3 = 0; - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":300 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":300 * cdef int offset * * info.obj = self # <<<<<<<<<<<<<< @@ -10945,7 +11206,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_DECREF(__pyx_v_info->obj); __pyx_v_info->obj = ((PyObject *)__pyx_v_self); - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":302 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":302 * info.obj = self * * if not PyDataType_HASFIELDS(descr): # <<<<<<<<<<<<<< @@ -10955,7 +11216,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = ((!(PyDataType_HASFIELDS(__pyx_v_descr) != 0)) != 0); if (__pyx_t_1) { - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":303 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":303 * * if not PyDataType_HASFIELDS(descr): * t = descr.type_num # <<<<<<<<<<<<<< @@ -10965,7 +11226,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_4 = __pyx_v_descr->type_num; __pyx_v_t = __pyx_t_4; - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":304 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":304 * if not PyDataType_HASFIELDS(descr): * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -10985,7 +11246,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } __pyx_L15_next_or:; - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":305 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":305 * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or * (descr.byteorder == c'<' and not little_endian)): # <<<<<<<<<<<<<< @@ -11002,7 +11263,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = __pyx_t_2; __pyx_L14_bool_binop_done:; - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":304 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":304 * if not PyDataType_HASFIELDS(descr): * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -11011,20 +11272,20 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ if (unlikely(__pyx_t_1)) { - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":306 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":306 * if ((descr.byteorder == c'>' and little_endian) or * (descr.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" */ - __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__13, NULL); if (unlikely(!__pyx_t_3)) __PYX_ERR(2, 306, __pyx_L1_error) + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__15, NULL); if (unlikely(!__pyx_t_3)) __PYX_ERR(2, 306, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); __Pyx_Raise(__pyx_t_3, 0, 0, 0); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __PYX_ERR(2, 306, __pyx_L1_error) - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":304 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":304 * if not PyDataType_HASFIELDS(descr): * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -11033,7 +11294,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":307 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":307 * (descr.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") * if t == NPY_BYTE: f = "b" # <<<<<<<<<<<<<< @@ -11046,7 +11307,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; case NPY_UBYTE: - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":308 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":308 * raise ValueError(u"Non-native byte order not supported") * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" # <<<<<<<<<<<<<< @@ -11057,7 +11318,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; case NPY_SHORT: - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":309 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":309 * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" * elif t == NPY_SHORT: f = "h" # <<<<<<<<<<<<<< @@ -11068,7 +11329,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; case NPY_USHORT: - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":310 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":310 * elif t == NPY_UBYTE: f = "B" * elif t == NPY_SHORT: f = "h" * elif t == NPY_USHORT: f = "H" # <<<<<<<<<<<<<< @@ -11079,7 +11340,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; case NPY_INT: - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":311 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":311 * elif t == NPY_SHORT: f = "h" * elif t == NPY_USHORT: f = "H" * elif t == NPY_INT: f = "i" # <<<<<<<<<<<<<< @@ -11090,7 +11351,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; case NPY_UINT: - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":312 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":312 * elif t == NPY_USHORT: f = "H" * elif t == NPY_INT: f = "i" * elif t == NPY_UINT: f = "I" # <<<<<<<<<<<<<< @@ -11101,7 +11362,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; case NPY_LONG: - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":313 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":313 * elif t == NPY_INT: f = "i" * elif t == NPY_UINT: f = "I" * elif t == NPY_LONG: f = "l" # <<<<<<<<<<<<<< @@ -11112,7 +11373,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; case NPY_ULONG: - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":314 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":314 * elif t == NPY_UINT: f = "I" * elif t == NPY_LONG: f = "l" * elif t == NPY_ULONG: f = "L" # <<<<<<<<<<<<<< @@ -11123,7 +11384,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; case NPY_LONGLONG: - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":315 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":315 * elif t == NPY_LONG: f = "l" * elif t == NPY_ULONG: f = "L" * elif t == NPY_LONGLONG: f = "q" # <<<<<<<<<<<<<< @@ -11134,7 +11395,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; case NPY_ULONGLONG: - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":316 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":316 * elif t == NPY_ULONG: f = "L" * elif t == NPY_LONGLONG: f = "q" * elif t == NPY_ULONGLONG: f = "Q" # <<<<<<<<<<<<<< @@ -11145,7 +11406,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; case NPY_FLOAT: - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":317 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":317 * elif t == NPY_LONGLONG: f = "q" * elif t == NPY_ULONGLONG: f = "Q" * elif t == NPY_FLOAT: f = "f" # <<<<<<<<<<<<<< @@ -11156,7 +11417,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; case NPY_DOUBLE: - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":318 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":318 * elif t == NPY_ULONGLONG: f = "Q" * elif t == NPY_FLOAT: f = "f" * elif t == NPY_DOUBLE: f = "d" # <<<<<<<<<<<<<< @@ -11167,7 +11428,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; case NPY_LONGDOUBLE: - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":319 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":319 * elif t == NPY_FLOAT: f = "f" * elif t == NPY_DOUBLE: f = "d" * elif t == NPY_LONGDOUBLE: f = "g" # <<<<<<<<<<<<<< @@ -11178,7 +11439,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; case NPY_CFLOAT: - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":320 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":320 * elif t == NPY_DOUBLE: f = "d" * elif t == NPY_LONGDOUBLE: f = "g" * elif t == NPY_CFLOAT: f = "Zf" # <<<<<<<<<<<<<< @@ -11189,7 +11450,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; case NPY_CDOUBLE: - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":321 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":321 * elif t == NPY_LONGDOUBLE: f = "g" * elif t == NPY_CFLOAT: f = "Zf" * elif t == NPY_CDOUBLE: f = "Zd" # <<<<<<<<<<<<<< @@ -11200,7 +11461,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; case NPY_CLONGDOUBLE: - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":322 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":322 * elif t == NPY_CFLOAT: f = "Zf" * elif t == NPY_CDOUBLE: f = "Zd" * elif t == NPY_CLONGDOUBLE: f = "Zg" # <<<<<<<<<<<<<< @@ -11211,7 +11472,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; case NPY_OBJECT: - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":323 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":323 * elif t == NPY_CDOUBLE: f = "Zd" * elif t == NPY_CLONGDOUBLE: f = "Zg" * elif t == NPY_OBJECT: f = "O" # <<<<<<<<<<<<<< @@ -11222,7 +11483,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; default: - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":325 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":325 * elif t == NPY_OBJECT: f = "O" * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) # <<<<<<<<<<<<<< @@ -11243,7 +11504,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; } - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":326 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":326 * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) * info.format = f # <<<<<<<<<<<<<< @@ -11252,7 +11513,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->format = __pyx_v_f; - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":327 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":327 * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) * info.format = f * return # <<<<<<<<<<<<<< @@ -11262,7 +11523,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_r = 0; goto __pyx_L0; - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":302 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":302 * info.obj = self * * if not PyDataType_HASFIELDS(descr): # <<<<<<<<<<<<<< @@ -11271,7 +11532,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":329 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":329 * return * else: * info.format = PyObject_Malloc(_buffer_format_string_len) # <<<<<<<<<<<<<< @@ -11281,7 +11542,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P /*else*/ { __pyx_v_info->format = ((char *)PyObject_Malloc(0xFF)); - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":330 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":330 * else: * info.format = PyObject_Malloc(_buffer_format_string_len) * info.format[0] = c'^' # Native data types, manual alignment # <<<<<<<<<<<<<< @@ -11290,7 +11551,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ (__pyx_v_info->format[0]) = '^'; - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":331 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":331 * info.format = PyObject_Malloc(_buffer_format_string_len) * info.format[0] = c'^' # Native data types, manual alignment * offset = 0 # <<<<<<<<<<<<<< @@ -11299,7 +11560,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_offset = 0; - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":332 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":332 * info.format[0] = c'^' # Native data types, manual alignment * offset = 0 * f = _util_dtypestring(descr, info.format + 1, # <<<<<<<<<<<<<< @@ -11309,7 +11570,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_9 = __pyx_f_5numpy__util_dtypestring(__pyx_v_descr, (__pyx_v_info->format + 1), (__pyx_v_info->format + 0xFF), (&__pyx_v_offset)); if (unlikely(__pyx_t_9 == ((char *)NULL))) __PYX_ERR(2, 332, __pyx_L1_error) __pyx_v_f = __pyx_t_9; - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":335 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":335 * info.format + _buffer_format_string_len, * &offset) * f[0] = c'\0' # Terminate format string # <<<<<<<<<<<<<< @@ -11319,7 +11580,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P (__pyx_v_f[0]) = '\x00'; 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__pyx_t_4 = 0; - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":854 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":854 * child, new_offset = fields * * if (end - f) - (new_offset - offset[0]) < 15: # <<<<<<<<<<<<<< @@ -11909,20 +12170,20 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = ((((__pyx_v_end - __pyx_v_f) - ((int)__pyx_t_5)) < 15) != 0); if (unlikely(__pyx_t_6)) { - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":855 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":855 * * if (end - f) - (new_offset - offset[0]) < 15: * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") # <<<<<<<<<<<<<< * * if ((child.byteorder == c'>' and little_endian) or */ - __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_tuple__14, NULL); if (unlikely(!__pyx_t_3)) __PYX_ERR(2, 855, __pyx_L1_error) + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_tuple__16, NULL); if (unlikely(!__pyx_t_3)) __PYX_ERR(2, 855, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); __Pyx_Raise(__pyx_t_3, 0, 0, 0); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __PYX_ERR(2, 855, __pyx_L1_error) - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":854 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":854 * child, new_offset = fields * * if (end - f) - (new_offset - offset[0]) < 15: # <<<<<<<<<<<<<< @@ -11931,7 +12192,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ } - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":857 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":857 * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") * * if ((child.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -11951,7 +12212,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __pyx_L8_next_or:; - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":858 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":858 * * if ((child.byteorder == c'>' and little_endian) or * (child.byteorder == c'<' and not little_endian)): # <<<<<<<<<<<<<< @@ -11968,7 +12229,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = __pyx_t_7; __pyx_L7_bool_binop_done:; - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":857 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":857 * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") * * if ((child.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -11977,20 +12238,20 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ if (unlikely(__pyx_t_6)) { - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":859 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":859 * if ((child.byteorder == c'>' and little_endian) or * (child.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< * # One could encode it in the format string and have Cython * # complain instead, BUT: < and > in format strings also imply */ - __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__13, NULL); if (unlikely(!__pyx_t_3)) __PYX_ERR(2, 859, __pyx_L1_error) + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__15, NULL); if (unlikely(!__pyx_t_3)) __PYX_ERR(2, 859, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); __Pyx_Raise(__pyx_t_3, 0, 0, 0); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __PYX_ERR(2, 859, __pyx_L1_error) - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":857 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":857 * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") * * if ((child.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -11999,7 +12260,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ } - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":869 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":869 * * # Output padding bytes * while offset[0] < new_offset: # <<<<<<<<<<<<<< @@ -12015,7 +12276,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; if (!__pyx_t_6) break; - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":870 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":870 * # Output padding bytes * while offset[0] < new_offset: * f[0] = 120 # "x"; pad byte # <<<<<<<<<<<<<< @@ -12024,7 +12285,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ (__pyx_v_f[0]) = 0x78; - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":871 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":871 * while offset[0] < new_offset: * f[0] = 120 # "x"; pad byte * f += 1 # <<<<<<<<<<<<<< @@ -12033,7 +12294,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ __pyx_v_f = (__pyx_v_f + 1); - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":872 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":872 * f[0] = 120 # "x"; pad byte * f += 1 * offset[0] += 1 # <<<<<<<<<<<<<< @@ -12044,7 +12305,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx (__pyx_v_offset[__pyx_t_8]) = ((__pyx_v_offset[__pyx_t_8]) + 1); } - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":874 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":874 * offset[0] += 1 * * offset[0] += child.itemsize # <<<<<<<<<<<<<< @@ -12054,7 +12315,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_8 = 0; (__pyx_v_offset[__pyx_t_8]) = ((__pyx_v_offset[__pyx_t_8]) + __pyx_v_child->elsize); - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":876 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":876 * offset[0] += child.itemsize * * if not PyDataType_HASFIELDS(child): # <<<<<<<<<<<<<< @@ -12064,7 +12325,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = ((!(PyDataType_HASFIELDS(__pyx_v_child) != 0)) != 0); if (__pyx_t_6) { - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":877 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":877 * * if not PyDataType_HASFIELDS(child): * t = child.type_num # <<<<<<<<<<<<<< @@ -12076,7 +12337,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_XDECREF_SET(__pyx_v_t, __pyx_t_4); __pyx_t_4 = 0; - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":878 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":878 * if not PyDataType_HASFIELDS(child): * t = child.type_num * if end - f < 5: # <<<<<<<<<<<<<< @@ -12086,20 +12347,20 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = (((__pyx_v_end - __pyx_v_f) < 5) != 0); if (unlikely(__pyx_t_6)) { - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":879 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":879 * t = child.type_num * if end - f < 5: * raise RuntimeError(u"Format string allocated too short.") # <<<<<<<<<<<<<< * * # Until ticket #99 is fixed, use integers to avoid warnings */ - __pyx_t_4 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_tuple__15, NULL); if (unlikely(!__pyx_t_4)) __PYX_ERR(2, 879, __pyx_L1_error) + __pyx_t_4 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_tuple__17, NULL); if (unlikely(!__pyx_t_4)) __PYX_ERR(2, 879, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_4); __Pyx_Raise(__pyx_t_4, 0, 0, 0); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __PYX_ERR(2, 879, __pyx_L1_error) - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":878 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":878 * if not PyDataType_HASFIELDS(child): * t = child.type_num * if end - f < 5: # <<<<<<<<<<<<<< @@ -12108,7 +12369,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ } - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":882 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":882 * * # Until ticket #99 is fixed, use integers to avoid warnings * if t == NPY_BYTE: f[0] = 98 #"b" # <<<<<<<<<<<<<< @@ -12126,7 +12387,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":883 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":883 * # Until ticket #99 is fixed, use integers to avoid warnings * if t == NPY_BYTE: f[0] = 98 #"b" * elif t == NPY_UBYTE: f[0] = 66 #"B" # <<<<<<<<<<<<<< @@ -12144,7 +12405,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":884 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":884 * if t == NPY_BYTE: f[0] = 98 #"b" * elif t == NPY_UBYTE: f[0] = 66 #"B" * elif t == NPY_SHORT: f[0] = 104 #"h" # <<<<<<<<<<<<<< @@ -12162,7 +12423,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":885 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":885 * elif t == NPY_UBYTE: f[0] = 66 #"B" * elif t == NPY_SHORT: f[0] = 104 #"h" * elif t == NPY_USHORT: f[0] = 72 #"H" # <<<<<<<<<<<<<< @@ -12180,7 +12441,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":886 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":886 * elif t == NPY_SHORT: f[0] = 104 #"h" * elif t == NPY_USHORT: f[0] = 72 #"H" * elif t == NPY_INT: f[0] = 105 #"i" # <<<<<<<<<<<<<< @@ -12198,7 +12459,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":887 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":887 * elif t == NPY_USHORT: f[0] = 72 #"H" * elif t == NPY_INT: f[0] = 105 #"i" * elif t == NPY_UINT: f[0] = 73 #"I" # <<<<<<<<<<<<<< @@ -12216,7 +12477,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":888 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":888 * elif t == NPY_INT: f[0] = 105 #"i" * elif t == NPY_UINT: f[0] = 73 #"I" * elif t == NPY_LONG: f[0] = 108 #"l" # <<<<<<<<<<<<<< @@ -12234,7 +12495,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":889 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":889 * elif t == NPY_UINT: f[0] = 73 #"I" * elif t == NPY_LONG: f[0] = 108 #"l" * elif t == NPY_ULONG: f[0] = 76 #"L" # <<<<<<<<<<<<<< @@ -12252,7 +12513,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":890 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":890 * elif t == NPY_LONG: f[0] = 108 #"l" * elif t == NPY_ULONG: f[0] = 76 #"L" * elif t == NPY_LONGLONG: f[0] = 113 #"q" # <<<<<<<<<<<<<< @@ -12270,7 +12531,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":891 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":891 * elif t == NPY_ULONG: f[0] = 76 #"L" * elif t == NPY_LONGLONG: f[0] = 113 #"q" * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" # <<<<<<<<<<<<<< @@ -12288,7 +12549,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":892 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":892 * elif t == NPY_LONGLONG: f[0] = 113 #"q" * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" * elif t == NPY_FLOAT: f[0] = 102 #"f" # <<<<<<<<<<<<<< @@ -12306,7 +12567,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":893 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":893 * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" * elif t == NPY_FLOAT: f[0] = 102 #"f" * elif t == NPY_DOUBLE: f[0] = 100 #"d" # <<<<<<<<<<<<<< @@ -12324,7 +12585,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":894 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":894 * elif t == NPY_FLOAT: f[0] = 102 #"f" * elif t == NPY_DOUBLE: f[0] = 100 #"d" * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" # <<<<<<<<<<<<<< @@ -12342,7 +12603,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":895 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":895 * elif t == NPY_DOUBLE: f[0] = 100 #"d" * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf # <<<<<<<<<<<<<< @@ -12362,7 +12623,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":896 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":896 * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd # <<<<<<<<<<<<<< @@ -12382,7 +12643,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":897 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":897 * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd * elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg # <<<<<<<<<<<<<< @@ -12402,7 +12663,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":898 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":898 * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd * elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg * elif t == NPY_OBJECT: f[0] = 79 #"O" # <<<<<<<<<<<<<< @@ -12420,7 +12681,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":900 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":900 * elif t == NPY_OBJECT: f[0] = 79 #"O" * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) # <<<<<<<<<<<<<< @@ -12439,7 +12700,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __pyx_L15:; - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":901 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":901 * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) * f += 1 # <<<<<<<<<<<<<< @@ -12448,7 +12709,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ __pyx_v_f = (__pyx_v_f + 1); - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":876 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":876 * offset[0] += child.itemsize * * if not PyDataType_HASFIELDS(child): # <<<<<<<<<<<<<< @@ -12458,7 +12719,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L13; } - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":905 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":905 * # Cython ignores struct boundary information ("T{...}"), * # so don't output it * f = _util_dtypestring(child, f, end, offset) # <<<<<<<<<<<<<< @@ -12471,7 +12732,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __pyx_L13:; - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":850 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":850 * cdef tuple fields * * for childname in descr.names: # <<<<<<<<<<<<<< @@ -12481,7 +12742,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":906 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":906 * # so don't output it * f = _util_dtypestring(child, f, end, offset) * return f # <<<<<<<<<<<<<< @@ -12491,7 +12752,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_r = __pyx_v_f; goto __pyx_L0; - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":841 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":841 * return () * * cdef inline char* _util_dtypestring(dtype descr, char* f, char* end, int* offset) except NULL: # <<<<<<<<<<<<<< @@ -12516,7 +12777,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx return __pyx_r; } -/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1021 +/* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":1021 * int _import_umath() except -1 * * cdef inline void set_array_base(ndarray arr, object base): # <<<<<<<<<<<<<< @@ -12528,7 +12789,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("set_array_base", 0); - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1022 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":1022 * * cdef inline void set_array_base(ndarray arr, object base): * Py_INCREF(base) # important to do this before stealing the reference below! # <<<<<<<<<<<<<< @@ -12537,7 +12798,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a */ Py_INCREF(__pyx_v_base); - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1023 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":1023 * cdef inline void set_array_base(ndarray arr, object base): * Py_INCREF(base) # important to do this before stealing the reference below! * PyArray_SetBaseObject(arr, base) # <<<<<<<<<<<<<< @@ -12546,7 +12807,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a */ (void)(PyArray_SetBaseObject(__pyx_v_arr, __pyx_v_base)); - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1021 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":1021 * int _import_umath() except -1 * * cdef inline void set_array_base(ndarray arr, object base): # <<<<<<<<<<<<<< @@ -12558,7 +12819,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a __Pyx_RefNannyFinishContext(); } -/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1025 +/* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":1025 * PyArray_SetBaseObject(arr, base) * * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<< @@ -12573,7 +12834,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py int __pyx_t_1; __Pyx_RefNannySetupContext("get_array_base", 0); - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1026 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":1026 * * cdef inline object get_array_base(ndarray arr): * base = PyArray_BASE(arr) # <<<<<<<<<<<<<< @@ -12582,7 +12843,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py */ __pyx_v_base = PyArray_BASE(__pyx_v_arr); - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1027 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":1027 * cdef inline object get_array_base(ndarray arr): * base = PyArray_BASE(arr) * if base is NULL: # <<<<<<<<<<<<<< @@ -12592,7 +12853,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py __pyx_t_1 = ((__pyx_v_base == NULL) != 0); if (__pyx_t_1) { - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1028 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":1028 * base = PyArray_BASE(arr) * if base is NULL: * return None # <<<<<<<<<<<<<< @@ -12603,7 +12864,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1027 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":1027 * cdef inline object get_array_base(ndarray arr): * base = PyArray_BASE(arr) * if base is NULL: # <<<<<<<<<<<<<< @@ -12612,7 +12873,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py */ } - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1029 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":1029 * if base is NULL: * return None * return base # <<<<<<<<<<<<<< @@ -12624,7 +12885,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py __pyx_r = ((PyObject *)__pyx_v_base); goto __pyx_L0; - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1025 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":1025 * PyArray_SetBaseObject(arr, base) * * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<< @@ -12639,7 +12900,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py return __pyx_r; } -/* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1033 +/* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":1033 * # Versions of the import_* functions which are more suitable for * # Cython code. * cdef inline int import_array() except -1: # <<<<<<<<<<<<<< @@ -12663,7 +12924,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { int __pyx_clineno = 0; __Pyx_RefNannySetupContext("import_array", 0); - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1034 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":1034 * # Cython code. * cdef inline int import_array() except -1: * try: # <<<<<<<<<<<<<< @@ -12679,7 +12940,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { __Pyx_XGOTREF(__pyx_t_3); /*try:*/ { - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1035 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":1035 * cdef inline int import_array() except -1: * try: * _import_array() # <<<<<<<<<<<<<< @@ -12688,7 +12949,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { */ __pyx_t_4 = _import_array(); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(2, 1035, __pyx_L3_error) - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1034 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":1034 * # Cython code. * cdef inline int import_array() except -1: * try: # <<<<<<<<<<<<<< @@ -12702,7 +12963,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { goto __pyx_L8_try_end; __pyx_L3_error:; - /* "../../../miniconda3/envs/mda/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":1036 + /* "../../../software/anaconda/install/envs/mda-dev/lib/python3.8/site-packages/Cython/Includes/numpy/__init__.pxd":1036 * try: * _import_array() * except Exception: # <<<<<<<<<<<<<< @@ -12717,14 +12978,14 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { __Pyx_GOTREF(__pyx_t_6); 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PyErr_Fetch(&etype, &eval, &etb); - ++Py_REFCNT(o); + __Pyx_SET_REFCNT(o, Py_REFCNT(o) + 1); __pyx_pw_10MDAnalysis_3lib_6nsgrid_7_NSGrid_3__dealloc__(o); - --Py_REFCNT(o); + __Pyx_SET_REFCNT(o, Py_REFCNT(o) - 1); PyErr_Restore(etype, eval, etb); } (*Py_TYPE(o)->tp_free)(o); @@ -27217,7 +27478,7 @@ static PyTypeObject __pyx_type_10MDAnalysis_3lib_6nsgrid_FastNS = { 0, /*tp_setattro*/ 0, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ - "FastNS(cutoff, coords, box, max_gridsize=5000, pbc=True)\nGrid based search between two group of atoms\n\n Instantiates a class object which uses :class:`_PBCBox` and\n :class:`_NSGrid` to construct a cuboidal\n grid in an orthogonal brick shaped box.\n\n Minimum image convention is used for distance evaluations\n if pbc is set to ``True``.\n ", /*tp_doc*/ + "FastNS(cutoff, coords, box, max_gridsize=5000, pbc=True)\nGrid based search between two group of atoms\n\n Instantiates a class object which uses :class:`_PBCBox` and\n :class:`_NSGrid` to construct a cuboidal\n grid in an orthogonal brick shaped box.\n\n Minimum image convention is used for distance evaluations\n if pbc is set to ``True``.\n\n\n .. warning::\n The nsgrid code can return incorrect values and should not be used for\n production work. We instead recommend the use of\n :mod:`MDAnalysis.lib.pkdtree`.\n ", /*tp_doc*/ __pyx_tp_traverse_10MDAnalysis_3lib_6nsgrid_FastNS, /*tp_traverse*/ __pyx_tp_clear_10MDAnalysis_3lib_6nsgrid_FastNS, /*tp_clear*/ 0, /*tp_richcompare*/ @@ -27286,9 +27547,9 @@ static void __pyx_tp_dealloc_array(PyObject *o) { { PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); - ++Py_REFCNT(o); + __Pyx_SET_REFCNT(o, Py_REFCNT(o) + 1); __pyx_array___dealloc__(o); - --Py_REFCNT(o); + __Pyx_SET_REFCNT(o, Py_REFCNT(o) - 1); PyErr_Restore(etype, eval, etb); } Py_CLEAR(p->mode); @@ -27597,9 +27858,9 @@ static void __pyx_tp_dealloc_memoryview(PyObject *o) { { PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); - ++Py_REFCNT(o); + __Pyx_SET_REFCNT(o, Py_REFCNT(o) + 1); __pyx_memoryview___dealloc__(o); - --Py_REFCNT(o); + __Pyx_SET_REFCNT(o, Py_REFCNT(o) - 1); PyErr_Restore(etype, eval, etb); } Py_CLEAR(p->obj); @@ -27847,9 +28108,9 @@ static void __pyx_tp_dealloc__memoryviewslice(PyObject *o) { { PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); - ++Py_REFCNT(o); + __Pyx_SET_REFCNT(o, Py_REFCNT(o) + 1); __pyx_memoryviewslice___dealloc__(o); - --Py_REFCNT(o); + __Pyx_SET_REFCNT(o, Py_REFCNT(o) - 1); PyErr_Restore(etype, eval, etb); } Py_CLEAR(p->from_object); @@ -28058,18 +28319,22 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_PickleError, __pyx_k_PickleError, sizeof(__pyx_k_PickleError), 0, 0, 1, 1}, {&__pyx_kp_s_Pickling_of_struct_members_such, __pyx_k_Pickling_of_struct_members_such, sizeof(__pyx_k_Pickling_of_struct_members_such), 0, 0, 1, 0}, {&__pyx_n_s_RuntimeError, __pyx_k_RuntimeError, sizeof(__pyx_k_RuntimeError), 0, 0, 1, 1}, + {&__pyx_kp_s_The_current_nsgrid_code_can_retu, __pyx_k_The_current_nsgrid_code_can_retu, sizeof(__pyx_k_The_current_nsgrid_code_can_retu), 0, 0, 1, 0}, {&__pyx_n_s_TypeError, __pyx_k_TypeError, sizeof(__pyx_k_TypeError), 0, 0, 1, 1}, {&__pyx_kp_s_Unable_to_convert_item_to_object, __pyx_k_Unable_to_convert_item_to_object, sizeof(__pyx_k_Unable_to_convert_item_to_object), 0, 0, 1, 0}, + {&__pyx_n_s_UserWarning, __pyx_k_UserWarning, sizeof(__pyx_k_UserWarning), 0, 0, 1, 1}, {&__pyx_n_s_ValueError, __pyx_k_ValueError, sizeof(__pyx_k_ValueError), 0, 0, 1, 1}, {&__pyx_n_s_View_MemoryView, __pyx_k_View_MemoryView, sizeof(__pyx_k_View_MemoryView), 0, 0, 1, 1}, {&__pyx_n_s_allclose, __pyx_k_allclose, sizeof(__pyx_k_allclose), 0, 0, 1, 1}, {&__pyx_n_s_allocate_buffer, __pyx_k_allocate_buffer, sizeof(__pyx_k_allocate_buffer), 0, 0, 1, 1}, + {&__pyx_n_s_always, __pyx_k_always, sizeof(__pyx_k_always), 0, 0, 1, 1}, {&__pyx_n_s_asarray, __pyx_k_asarray, sizeof(__pyx_k_asarray), 0, 0, 1, 1}, {&__pyx_n_s_astype, __pyx_k_astype, sizeof(__pyx_k_astype), 0, 0, 1, 1}, {&__pyx_n_s_base, __pyx_k_base, sizeof(__pyx_k_base), 0, 0, 1, 1}, {&__pyx_n_s_box, __pyx_k_box, sizeof(__pyx_k_box), 0, 0, 1, 1}, {&__pyx_n_s_c, __pyx_k_c, sizeof(__pyx_k_c), 0, 0, 1, 1}, {&__pyx_n_u_c, __pyx_k_c, sizeof(__pyx_k_c), 0, 1, 0, 1}, + {&__pyx_n_s_catch_warnings, __pyx_k_catch_warnings, sizeof(__pyx_k_catch_warnings), 0, 0, 1, 1}, {&__pyx_n_s_class, __pyx_k_class, sizeof(__pyx_k_class), 0, 0, 1, 1}, {&__pyx_n_s_cline_in_traceback, __pyx_k_cline_in_traceback, sizeof(__pyx_k_cline_in_traceback), 0, 0, 1, 1}, {&__pyx_kp_s_contiguous_and_direct, __pyx_k_contiguous_and_direct, sizeof(__pyx_k_contiguous_and_direct), 0, 0, 1, 0}, @@ -28083,8 +28348,10 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_dtype_is_object, __pyx_k_dtype_is_object, sizeof(__pyx_k_dtype_is_object), 0, 0, 1, 1}, {&__pyx_n_s_empty, __pyx_k_empty, sizeof(__pyx_k_empty), 0, 0, 1, 1}, {&__pyx_n_s_encode, __pyx_k_encode, sizeof(__pyx_k_encode), 0, 0, 1, 1}, + {&__pyx_n_s_enter, __pyx_k_enter, sizeof(__pyx_k_enter), 0, 0, 1, 1}, {&__pyx_n_s_enumerate, __pyx_k_enumerate, sizeof(__pyx_k_enumerate), 0, 0, 1, 1}, {&__pyx_n_s_error, __pyx_k_error, sizeof(__pyx_k_error), 0, 0, 1, 1}, + {&__pyx_n_s_exit, __pyx_k_exit, sizeof(__pyx_k_exit), 0, 0, 1, 1}, {&__pyx_n_s_flags, __pyx_k_flags, sizeof(__pyx_k_flags), 0, 0, 1, 1}, {&__pyx_n_s_float32, __pyx_k_float32, sizeof(__pyx_k_float32), 0, 0, 1, 1}, {&__pyx_n_s_force, __pyx_k_force, sizeof(__pyx_k_force), 0, 0, 1, 1}, @@ -28143,6 +28410,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_setstate, __pyx_k_setstate, sizeof(__pyx_k_setstate), 0, 0, 1, 1}, {&__pyx_n_s_setstate_cython, __pyx_k_setstate_cython, sizeof(__pyx_k_setstate_cython), 0, 0, 1, 1}, {&__pyx_n_s_shape, __pyx_k_shape, sizeof(__pyx_k_shape), 0, 0, 1, 1}, + {&__pyx_n_s_simplefilter, __pyx_k_simplefilter, sizeof(__pyx_k_simplefilter), 0, 0, 1, 1}, {&__pyx_n_s_size, __pyx_k_size, sizeof(__pyx_k_size), 0, 0, 1, 1}, {&__pyx_n_s_sqrt, __pyx_k_sqrt, sizeof(__pyx_k_sqrt), 0, 0, 1, 1}, {&__pyx_n_s_start, __pyx_k_start, sizeof(__pyx_k_start), 0, 0, 1, 1}, @@ -28160,13 +28428,16 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_kp_u_unknown_dtype_code_in_numpy_pxd, __pyx_k_unknown_dtype_code_in_numpy_pxd, sizeof(__pyx_k_unknown_dtype_code_in_numpy_pxd), 0, 1, 0, 0}, {&__pyx_n_s_unpack, __pyx_k_unpack, sizeof(__pyx_k_unpack), 0, 0, 1, 1}, {&__pyx_n_s_update, __pyx_k_update, sizeof(__pyx_k_update), 0, 0, 1, 1}, + {&__pyx_n_s_warn, __pyx_k_warn, sizeof(__pyx_k_warn), 0, 0, 1, 1}, + {&__pyx_n_s_warnings, __pyx_k_warnings, sizeof(__pyx_k_warnings), 0, 0, 1, 1}, {0, 0, 0, 0, 0, 0, 0} }; 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if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 286, __pyx_L1_error) + __pyx_t_1 = __Pyx_PyObject_Call(((PyObject *)__pyx_MemviewEnum_type), __pyx_tuple__42, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 286, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __Pyx_XGOTREF(generic); __Pyx_DECREF_SET(generic, __pyx_t_1); @@ -29192,7 +29497,7 @@ if (!__Pyx_RefNanny) { * cdef indirect = Enum("") * */ - __pyx_t_1 = __Pyx_PyObject_Call(((PyObject *)__pyx_MemviewEnum_type), __pyx_tuple__41, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 287, __pyx_L1_error) + __pyx_t_1 = __Pyx_PyObject_Call(((PyObject *)__pyx_MemviewEnum_type), __pyx_tuple__43, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 287, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __Pyx_XGOTREF(strided); __Pyx_DECREF_SET(strided, __pyx_t_1); @@ -29206,7 +29511,7 @@ if (!__Pyx_RefNanny) { * * */ - __pyx_t_1 = __Pyx_PyObject_Call(((PyObject *)__pyx_MemviewEnum_type), __pyx_tuple__42, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 288, __pyx_L1_error) + __pyx_t_1 = __Pyx_PyObject_Call(((PyObject *)__pyx_MemviewEnum_type), __pyx_tuple__44, NULL); 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__Pyx_XGOTREF(indirect_contiguous); __Pyx_DECREF_SET(indirect_contiguous, __pyx_t_1); @@ -30266,6 +30571,158 @@ static int __Pyx__ArgTypeTest(PyObject *obj, PyTypeObject *type, const char *nam return 0; } +/* PyObjectCallNoArg */ +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func) { +#if CYTHON_FAST_PYCALL + if (PyFunction_Check(func)) { + return __Pyx_PyFunction_FastCall(func, NULL, 0); + } +#endif +#ifdef __Pyx_CyFunction_USED + if (likely(PyCFunction_Check(func) || __Pyx_CyFunction_Check(func))) +#else + if (likely(PyCFunction_Check(func))) +#endif + { + if (likely(PyCFunction_GET_FLAGS(func) & METH_NOARGS)) { + return __Pyx_PyObject_CallMethO(func, NULL); + } + } + return __Pyx_PyObject_Call(func, __pyx_empty_tuple, NULL); +} +#endif + +/* GetTopmostException */ +#if CYTHON_USE_EXC_INFO_STACK +static _PyErr_StackItem * +__Pyx_PyErr_GetTopmostException(PyThreadState *tstate) +{ + _PyErr_StackItem *exc_info = tstate->exc_info; + while ((exc_info->exc_type == NULL || exc_info->exc_type == Py_None) && + exc_info->previous_item != NULL) + { + exc_info = exc_info->previous_item; + } + return exc_info; +} +#endif + +/* SaveResetException */ +#if CYTHON_FAST_THREAD_STATE +static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { + #if CYTHON_USE_EXC_INFO_STACK + _PyErr_StackItem *exc_info = __Pyx_PyErr_GetTopmostException(tstate); + *type = exc_info->exc_type; + *value = exc_info->exc_value; + *tb = exc_info->exc_traceback; + #else + *type = tstate->exc_type; + *value = tstate->exc_value; + *tb = tstate->exc_traceback; + #endif + Py_XINCREF(*type); + Py_XINCREF(*value); + Py_XINCREF(*tb); +} +static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) { + PyObject *tmp_type, *tmp_value, *tmp_tb; + #if CYTHON_USE_EXC_INFO_STACK + _PyErr_StackItem *exc_info = tstate->exc_info; + tmp_type = exc_info->exc_type; + tmp_value = exc_info->exc_value; + tmp_tb = exc_info->exc_traceback; + exc_info->exc_type = type; + exc_info->exc_value = value; + exc_info->exc_traceback = tb; + #else + tmp_type = tstate->exc_type; + tmp_value = tstate->exc_value; + tmp_tb = tstate->exc_traceback; + tstate->exc_type = type; + tstate->exc_value = value; + tstate->exc_traceback = tb; + #endif + Py_XDECREF(tmp_type); + Py_XDECREF(tmp_value); + Py_XDECREF(tmp_tb); +} +#endif + +/* GetException */ +#if CYTHON_FAST_THREAD_STATE +static int __Pyx__GetException(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) +#else +static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) +#endif +{ + PyObject *local_type, *local_value, *local_tb; +#if CYTHON_FAST_THREAD_STATE + PyObject *tmp_type, *tmp_value, *tmp_tb; + local_type = tstate->curexc_type; + local_value = tstate->curexc_value; + local_tb = tstate->curexc_traceback; + tstate->curexc_type = 0; + tstate->curexc_value = 0; + tstate->curexc_traceback = 0; +#else + PyErr_Fetch(&local_type, &local_value, &local_tb); +#endif + PyErr_NormalizeException(&local_type, &local_value, &local_tb); +#if CYTHON_FAST_THREAD_STATE + if (unlikely(tstate->curexc_type)) +#else + if (unlikely(PyErr_Occurred())) +#endif + goto bad; + #if PY_MAJOR_VERSION >= 3 + if (local_tb) { + if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0)) + goto bad; + } + #endif + Py_XINCREF(local_tb); + Py_XINCREF(local_type); + Py_XINCREF(local_value); + *type = local_type; + *value = local_value; + *tb = local_tb; +#if CYTHON_FAST_THREAD_STATE + #if CYTHON_USE_EXC_INFO_STACK + { + _PyErr_StackItem *exc_info = tstate->exc_info; + tmp_type = exc_info->exc_type; + tmp_value = exc_info->exc_value; + tmp_tb = exc_info->exc_traceback; + exc_info->exc_type = local_type; + exc_info->exc_value = local_value; + exc_info->exc_traceback = local_tb; + } + #else + tmp_type = tstate->exc_type; + tmp_value = tstate->exc_value; + tmp_tb = tstate->exc_traceback; + tstate->exc_type = local_type; + tstate->exc_value = local_value; + tstate->exc_traceback = local_tb; + #endif + Py_XDECREF(tmp_type); + Py_XDECREF(tmp_value); + Py_XDECREF(tmp_tb); +#else + PyErr_SetExcInfo(local_type, local_value, local_tb); +#endif + return 0; +bad: + *type = 0; + *value = 0; + *tb = 0; + Py_XDECREF(local_type); + Py_XDECREF(local_value); + Py_XDECREF(local_tb); + return -1; +} + /* Import */ static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) { PyObject *empty_list = 0; @@ -30669,136 +31126,6 @@ static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) { PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); } -/* GetTopmostException */ -#if CYTHON_USE_EXC_INFO_STACK -static _PyErr_StackItem * -__Pyx_PyErr_GetTopmostException(PyThreadState *tstate) -{ - _PyErr_StackItem *exc_info = tstate->exc_info; - while ((exc_info->exc_type == NULL || exc_info->exc_type == Py_None) && - exc_info->previous_item != NULL) - { - exc_info = exc_info->previous_item; - } - return exc_info; -} -#endif - -/* SaveResetException */ -#if CYTHON_FAST_THREAD_STATE -static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { - #if CYTHON_USE_EXC_INFO_STACK - _PyErr_StackItem *exc_info = __Pyx_PyErr_GetTopmostException(tstate); - *type = exc_info->exc_type; - *value = exc_info->exc_value; - *tb = exc_info->exc_traceback; - #else - *type = tstate->exc_type; - *value = tstate->exc_value; - *tb = tstate->exc_traceback; - #endif - Py_XINCREF(*type); - Py_XINCREF(*value); - Py_XINCREF(*tb); -} -static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) { - PyObject *tmp_type, *tmp_value, *tmp_tb; - #if CYTHON_USE_EXC_INFO_STACK - _PyErr_StackItem *exc_info = tstate->exc_info; - tmp_type = exc_info->exc_type; - tmp_value = exc_info->exc_value; - tmp_tb = exc_info->exc_traceback; - exc_info->exc_type = type; - exc_info->exc_value = value; - exc_info->exc_traceback = tb; - #else - tmp_type = tstate->exc_type; - tmp_value = tstate->exc_value; - tmp_tb = tstate->exc_traceback; - tstate->exc_type = type; - tstate->exc_value = value; - tstate->exc_traceback = tb; - #endif - Py_XDECREF(tmp_type); - Py_XDECREF(tmp_value); - Py_XDECREF(tmp_tb); -} -#endif - -/* GetException */ -#if CYTHON_FAST_THREAD_STATE -static int __Pyx__GetException(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) -#else -static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) -#endif -{ - PyObject *local_type, *local_value, *local_tb; -#if CYTHON_FAST_THREAD_STATE - PyObject *tmp_type, *tmp_value, *tmp_tb; - local_type = tstate->curexc_type; - local_value = tstate->curexc_value; - local_tb = tstate->curexc_traceback; - tstate->curexc_type = 0; - tstate->curexc_value = 0; - tstate->curexc_traceback = 0; -#else - PyErr_Fetch(&local_type, &local_value, &local_tb); -#endif - PyErr_NormalizeException(&local_type, &local_value, &local_tb); -#if CYTHON_FAST_THREAD_STATE - if (unlikely(tstate->curexc_type)) -#else - if (unlikely(PyErr_Occurred())) -#endif - goto bad; - #if PY_MAJOR_VERSION >= 3 - if (local_tb) { - if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0)) - goto bad; - } - #endif - Py_XINCREF(local_tb); - Py_XINCREF(local_type); - Py_XINCREF(local_value); - *type = local_type; - *value = local_value; - *tb = local_tb; -#if CYTHON_FAST_THREAD_STATE - #if CYTHON_USE_EXC_INFO_STACK - { - _PyErr_StackItem *exc_info = tstate->exc_info; - tmp_type = exc_info->exc_type; - tmp_value = exc_info->exc_value; - tmp_tb = exc_info->exc_traceback; - exc_info->exc_type = local_type; - exc_info->exc_value = local_value; - exc_info->exc_traceback = local_tb; - } - #else - tmp_type = tstate->exc_type; - tmp_value = tstate->exc_value; - tmp_tb = tstate->exc_traceback; - tstate->exc_type = local_type; - tstate->exc_value = local_value; - tstate->exc_traceback = local_tb; - #endif - Py_XDECREF(tmp_type); - Py_XDECREF(tmp_value); - Py_XDECREF(tmp_tb); -#else - PyErr_SetExcInfo(local_type, local_value, local_tb); -#endif - return 0; -bad: - *type = 0; - *value = 0; - *tb = 0; - Py_XDECREF(local_type); - Py_XDECREF(local_value); - Py_XDECREF(local_tb); - return -1; -} - /* BytesEquals */ static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) { #if CYTHON_COMPILING_IN_PYPY @@ -31000,7 +31327,7 @@ static CYTHON_INLINE PyObject* __Pyx_decode_c_string( stop += length; } if (unlikely(stop <= start)) - return PyUnicode_FromUnicode(NULL, 0); + return __Pyx_NewRef(__pyx_empty_unicode); length = stop - start; cstring += start; if (decode_func) { @@ -32533,15 +32860,17 @@ static int __Pyx_ValidateAndInit_memviewslice( (dtype->size > 1) ? "s" : ""); goto fail; } - for (i = 0; i < ndim; i++) { - spec = axes_specs[i]; - if (unlikely(!__pyx_check_strides(buf, i, ndim, spec))) - goto fail; - if (unlikely(!__pyx_check_suboffsets(buf, i, ndim, spec))) + if (buf->len > 0) { + for (i = 0; i < ndim; i++) { + spec = axes_specs[i]; + if (unlikely(!__pyx_check_strides(buf, i, ndim, spec))) + goto fail; + if (unlikely(!__pyx_check_suboffsets(buf, i, ndim, spec))) + goto fail; + } + if (unlikely(buf->strides && !__pyx_verify_contig(buf, ndim, c_or_f_flag))) goto fail; } - if (unlikely(buf->strides && !__pyx_verify_contig(buf, ndim, c_or_f_flag))) - goto fail; if (unlikely(__Pyx_init_memviewslice(memview, ndim, memviewslice, new_memview != NULL) == -1)) { goto fail; diff --git a/package/MDAnalysis/lib/nsgrid.pyx b/package/MDAnalysis/lib/nsgrid.pyx index eadd8edf6ef..4391c427eca 100644 --- a/package/MDAnalysis/lib/nsgrid.pyx +++ b/package/MDAnalysis/lib/nsgrid.pyx @@ -34,6 +34,14 @@ Neighbor search library --- :mod:`MDAnalysis.lib.nsgrid` ======================================================== +.. warning:: + The current nsgrid code can return incorrect values. Do not use it for + production use. We instead recommend the use of + :mod:`MDAnalysis.lib.pkdtree`. See issue + `#2930 `_ for further + information. + + About the code -------------- @@ -78,6 +86,7 @@ Classes from cpython.mem cimport PyMem_Malloc, PyMem_Realloc, PyMem_Free from libc.math cimport sqrt import numpy as np +import warnings from libcpp.vector cimport vector cimport numpy as np @@ -704,6 +713,12 @@ cdef class FastNS(object): Minimum image convention is used for distance evaluations if pbc is set to ``True``. + + + .. warning:: + The nsgrid code can return incorrect values and should not be used for + production work. We instead recommend the use of + :mod:`MDAnalysis.lib.pkdtree`. """ cdef _PBCBox box cdef real[:, ::1] coords @@ -776,6 +791,14 @@ cdef class FastNS(object): """ + with warnings.catch_warnings(): + warnings.simplefilter('always', UserWarning) + wmsg = ('The current nsgrid code can return incorrect values ' + 'and should not be used for production work. We ' + 'instead recommend the use of MDAnalysis.lib.pkdtree. ' + 'See issue #2930 for more details.') + warnings.warn(wmsg) + from MDAnalysis.lib.mdamath import triclinic_vectors if (coords.ndim != 2 or coords.shape[1] != 3): diff --git a/testsuite/MDAnalysisTests/lib/test_distances.py b/testsuite/MDAnalysisTests/lib/test_distances.py index cb02dbd8cf2..c691b7c5e8c 100644 --- a/testsuite/MDAnalysisTests/lib/test_distances.py +++ b/testsuite/MDAnalysisTests/lib/test_distances.py @@ -96,7 +96,7 @@ def test_capped_distance_noresults(): np.array([[0.1, 0.1, 0.1], [0.2, 0.1, 0.1]], dtype=np.float32)) -method_1 = ('bruteforce', 'pkdtree', 'nsgrid') +method_1 = ('bruteforce', 'pkdtree') # add nsgrid back min_cutoff_1 = (None, 0.1) @@ -220,7 +220,7 @@ def test_self_capped_distance(npoints, box, method, min_cutoff, ret_dist): [(1, 0.02, '_bruteforce_capped_self'), (1, 0.2, '_bruteforce_capped_self'), (600, 0.02, '_pkdtree_capped_self'), - (600, 0.2, '_nsgrid_capped_self')]) + (600, 0.2, '_pkdtree_capped_self')]) # tmp switch to pkdtree def test_method_selfselection(box, npoints, cutoff, meth): np.random.seed(90003) points = (np.random.uniform(low=0, high=1.0, @@ -235,9 +235,9 @@ def test_method_selfselection(box, npoints, cutoff, meth): @pytest.mark.parametrize('npoints,cutoff,meth', [(1, 0.02, '_bruteforce_capped'), (1, 0.2, '_bruteforce_capped'), - (200, 0.02, '_nsgrid_capped'), + (200, 0.02, '_pkdtree_capped'), # tmp switch to pkdtree (200, 0.35, '_bruteforce_capped'), - (10000, 0.35, '_nsgrid_capped')]) + (10000, 0.35, '_pkdtree_capped')]) # tmp switch to pkdtree def test_method_selection(box, npoints, cutoff, meth): np.random.seed(90003) points = (np.random.uniform(low=0, high=1.0, @@ -991,7 +991,7 @@ def test_input_unchanged_self_distance_array(self, coords, box, backend): assert_equal(crd, ref) @pytest.mark.parametrize('box', boxes) - @pytest.mark.parametrize('met', ["bruteforce", "pkdtree", "nsgrid", None]) + @pytest.mark.parametrize('met', ["bruteforce", "pkdtree", None]) # add nsgrid back def test_input_unchanged_capped_distance(self, coords, box, met): crds = coords[:2] refs = [crd.copy() for crd in crds] @@ -1000,7 +1000,7 @@ def test_input_unchanged_capped_distance(self, coords, box, met): assert_equal(crds, refs) @pytest.mark.parametrize('box', boxes) - @pytest.mark.parametrize('met', ["bruteforce", "pkdtree", "nsgrid", None]) + @pytest.mark.parametrize('met', ["bruteforce", "pkdtree", None]) # add nsgrid back def test_input_unchanged_self_capped_distance(self, coords, box, met): crd = coords[0] ref = crd.copy() @@ -1101,7 +1101,7 @@ def test_empty_input_self_distance_array(self, empty_coord, box, backend): @pytest.mark.parametrize('box', boxes) @pytest.mark.parametrize('min_cut', [min_cut, None]) @pytest.mark.parametrize('ret_dist', [False, True]) - @pytest.mark.parametrize('met', ["bruteforce", "pkdtree", "nsgrid", None]) + @pytest.mark.parametrize('met', ["bruteforce", "pkdtree", None]) # add nsgrid back def test_empty_input_capped_distance(self, empty_coord, min_cut, box, met, ret_dist): res = distances.capped_distance(empty_coord, empty_coord, @@ -1117,7 +1117,7 @@ def test_empty_input_capped_distance(self, empty_coord, min_cut, box, met, @pytest.mark.parametrize('box', boxes) @pytest.mark.parametrize('min_cut', [min_cut, None]) @pytest.mark.parametrize('ret_dist', [False, True]) - @pytest.mark.parametrize('met', ["bruteforce", "pkdtree", "nsgrid", None]) + @pytest.mark.parametrize('met', ["bruteforce", "pkdtree", None]) # add nsgrid back def test_empty_input_self_capped_distance(self, empty_coord, min_cut, box, met, ret_dist): res = distances.self_capped_distance(empty_coord, @@ -1234,7 +1234,7 @@ def test_output_type_self_distance_array(self, incoords, box, backend): @pytest.mark.parametrize('min_cut', [min_cut, None]) @pytest.mark.parametrize('ret_dist', [False, True]) @pytest.mark.parametrize('incoords', list(comb(coords, 2))) - @pytest.mark.parametrize('met', ["bruteforce", "pkdtree", "nsgrid", None]) + @pytest.mark.parametrize('met', ["bruteforce", "pkdtree", None]) # add nsgrid back def test_output_type_capped_distance(self, incoords, min_cut, box, met, ret_dist): res = distances.capped_distance(*incoords, max_cutoff=self.max_cut, @@ -1257,7 +1257,7 @@ def test_output_type_capped_distance(self, incoords, min_cut, box, met, @pytest.mark.parametrize('min_cut', [min_cut, None]) @pytest.mark.parametrize('ret_dist', [False, True]) @pytest.mark.parametrize('incoords', coords) - @pytest.mark.parametrize('met', ["bruteforce", "pkdtree", "nsgrid", None]) + @pytest.mark.parametrize('met', ["bruteforce", "pkdtree", None]) # add nsgrid back def test_output_type_self_capped_distance(self, incoords, min_cut, box, met, ret_dist): res = distances.self_capped_distance(incoords, diff --git a/testsuite/MDAnalysisTests/lib/test_nsgrid.py b/testsuite/MDAnalysisTests/lib/test_nsgrid.py index fb0035a5442..eb56bb33fdb 100644 --- a/testsuite/MDAnalysisTests/lib/test_nsgrid.py +++ b/testsuite/MDAnalysisTests/lib/test_nsgrid.py @@ -274,3 +274,15 @@ def test_around_overlapping(): # box=u.dimensions) # assert np.count_nonzero(np.any(dist <= 0.0, axis=0)) == 48 assert u.select_atoms('around 0.0 index 0:11').n_atoms == 48 + + +def test_fastns_warning(universe): + """ + Tests for warning on the use of FastNS. + TODO: remove when nsgrid is fixed. + """ + wmsg = ("The current nsgrid code can return incorrect values and should " + "not be used for production work.") + with pytest.warns(UserWarning, match=wmsg): + searcher = nsgrid.FastNS(3, universe.atoms.positions, + universe.dimensions)