Added capped function for grid search#2008

Merged

richardjgowers merged 48 commits intoMDAnalysis:developfrom

ayushsuhane:cappedgrid

Aug 7, 2018

Commits on Aug 6, 2018

First commit for gridded method
ayushsuhane
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removed the parallel handler to remove hard dependency on omp.h, can be added again for conditional compilation
ayushsuhane
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added the license header
ayushsuhane
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Added MDAnalysis header file to c_gridsearch.pyx

seb-buch
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ayushsuhane
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Corrected C (de)allocation in c_gridsearch.pyx. Should fix memory leak

seb-buch
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ayushsuhane
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Added Tests for grid search. Added grid in MDAnalysis.lib.__init__

seb-buch
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ayushsuhane
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Removed pointer to nsgrid structure to avoid need to free it

seb-buch
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ayushsuhane
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Removed abort() from c_gridsearch.pyx

seb-buch
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ayushsuhane
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grid allocation moved to FastNS method

seb-buch
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NSResults object added to store results from NS. Started documentation

seb-buch
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ayushsuhane
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Corrected Memory Leak

seb-buch
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ayushsuhane
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Added MDAnalysis/lib/c_search.pyx for Grid NS search
ayushsuhane
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removed the parallel handler to remove hard dependency on omp.h, can be added again for conditional compilation
ayushsuhane
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Added MDAnalysis header file to c_gridsearch.pyx

seb-buch
authored and
ayushsuhane
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Corrected C (de)allocation in c_gridsearch.pyx. Should fix memory leak

seb-buch
authored and
ayushsuhane
committed
Removed pointer to nsgrid structure to avoid need to free it

seb-buch
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ayushsuhane
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Removed abort() from c_gridsearch.pyx and grid allocation moved to FastNS method.

seb-buch
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ayushsuhane
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NSResults object added to store results from NS. Started documentation

seb-buch
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ayushsuhane
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Memory allocation changed to PyMem to enhance speed in c_gridsearch.pyx

seb-buch
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ayushsuhane
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Unneeded code removed from c_gridsearch.pyx

seb-buch
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ayushsuhane
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Module MDAnalysis/lib/c_gridsearch.pyx renamed to nsgrid.pyx

seb-buch
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Tests written for FastNS

seb-buch
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ayushsuhane
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Removed all references to c_gridsearch.pyx/grid module that reappeared after merge/rebase

seb-buch
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ayushsuhane
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remove unused code

kain88-de
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make init_callable twice

kain88-de
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ayushsuhane
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use OK and ERROR as return codes

kain88-de
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ayushsuhane
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remove dead code

kain88-de
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ayushsuhane
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remove possible memory leak

kain88-de
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ayushsuhane
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added the capped function, modified the nsgrid to use box, coordinates as input parameters, modified tests
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recovering accidently removed augment in setupd during rebase
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corrected name in documentation
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minor corrections to remove pylint error
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Used vectors in place of lists and dict, cleaned code and modified function to take coordinates as input, modified tests accordingly
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removed dict from buffers for speedup and modified tests
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mend
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reverted tests, removed sorting from get_indices, get_distances, modified compilation libs in setup
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minor changes for failing tests
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added hack to handle NoPBC, tests to follow
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conform tests a/c to modifications in API
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removed python functions, added no pbc handle using python min, max
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docs unchecked
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returning list for get_indices, checked Docs
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removed parallel libraries
ayushsuhane
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solved contiguous issue, fixed tests, and added checks in API
ayushsuhane
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Added self_capped for nsgrid, moved no pbc box handling outside nsgrid and modified tests
ayushsuhane
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Commits on Aug 7, 2018