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Fast grid-based neighbor search implementation. #1996

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seb-buch wants to merge 35 commits into from
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Fast grid-based neighbor search implementation. #1996

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1cdf993
First commit for gridded method
ayushsuhane Jun 26, 2018
b8fea35
removed the parallel handler to remove hard dependency on omp.h, can …
ayushsuhane Jun 26, 2018
30ff05c
added the license header
ayushsuhane Jun 30, 2018
b152ae7
Added MDAnalysis header file to c_gridsearch.pyx
seb-buch Jul 1, 2018
919bdba
Corrected C (de)allocation in c_gridsearch.pyx. Should fix memory leak
seb-buch Jul 1, 2018
11f50d2
Added Tests for grid search. Added grid in MDAnalysis.lib.__init__
seb-buch Jul 1, 2018
9b8cacd
Removed pointer to nsgrid structure to avoid need to free it
seb-buch Jul 4, 2018
1bc126c
Removed abort() from c_gridsearch.pyx
seb-buch Jul 4, 2018
0a7843c
grid allocation moved to FastNS method
seb-buch Jul 7, 2018
e07d64f
NSResults object added to store results from NS. Started documentation
seb-buch Jul 8, 2018
1293aaf
Merge remote-tracking branch 'origin/develop' into feature-grid
seb-buch Jul 8, 2018
6e0ceda
Corrected Memory Leak
seb-buch Jul 8, 2018
fe780bc
Added MDAnalysis/lib/c_search.pyx for Grid NS search
ayushsuhane Jun 26, 2018
f894970
removed the parallel handler to remove hard dependency on omp.h, can …
ayushsuhane Jun 26, 2018
2f0b0fb
Added MDAnalysis header file to c_gridsearch.pyx
seb-buch Jul 1, 2018
1bb569b
Corrected C (de)allocation in c_gridsearch.pyx. Should fix memory leak
seb-buch Jul 1, 2018
0884555
Removed pointer to nsgrid structure to avoid need to free it
seb-buch Jul 1, 2018
8913e21
Removed abort() from c_gridsearch.pyx and grid allocation moved to Fa…
seb-buch Jul 4, 2018
1bbf176
NSResults object added to store results from NS. Started documentation
seb-buch Jul 8, 2018
fda157e
Memory allocation changed to PyMem to enhance speed in c_gridsearch.pyx
seb-buch Jul 8, 2018
089eb09
Unneeded code removed from c_gridsearch.pyx
seb-buch Jul 16, 2018
da8db15
Module MDAnalysis/lib/c_gridsearch.pyx renamed to nsgrid.pyx
seb-buch Jul 18, 2018
66e2151
Tests written for FastNS
seb-buch Jul 18, 2018
b510849
Merge branch 'feature-grid' of github.com:seb-buch/mdanalysis into fe…
seb-buch Jul 18, 2018
4503462
Removed MDAnalysis/lib/c_gridsearch.pyx
seb-buch Jul 18, 2018
63b6f63
Removed all references to c_gridsearch.pyx/grid module that reappeare…
seb-buch Jul 18, 2018
9e47943
remove unused code
kain88-de Jul 21, 2018
ced71af
make init_callable twice
kain88-de Jul 21, 2018
c8bac83
use OK and ERROR as return codes
kain88-de Jul 21, 2018
0cc8b5c
remove dead code
kain88-de Jul 21, 2018
17ad023
remove possible memory leak
kain88-de Jul 21, 2018
fbb8364
Merge remote-tracking branch 'origin/develop' into feature-grid
seb-buch Jul 23, 2018
8b9bd62
Merge pull request #1 from kain88-de/feature-grid
seb-buch Jul 23, 2018
106a1f6
Merge branch 'feature-grid' of github.com:seb-buch/mdanalysis into fe…
seb-buch Jul 23, 2018
607aadf
started documentation for FastNS
seb-buch Aug 2, 2018
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4 changes: 3 additions & 1 deletion package/MDAnalysis/lib/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,7 @@
from __future__ import absolute_import

__all__ = ['log', 'transformations', 'util', 'mdamath', 'distances',
'NeighborSearch', 'formats', 'pkdtree']
'NeighborSearch', 'formats', 'pkdtree', 'nsgrid']

from . import log
from . import transformations
Expand All @@ -39,3 +39,5 @@
from . import NeighborSearch
from . import formats
from . import pkdtree
from . import nsgrid

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