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created cuda branch with void kernel #37

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created cuda branch with void kernel #37

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3d8ea3c
created cuda branch with void kernel
rodenki Mar 31, 2017
87543b2
Delete .travis.yml
maxscheurer Mar 31, 2017
c2bfe54
renamed relevant cuda files
rodenki Mar 31, 2017
e49c0d7
working empty Kernel
rodenki Mar 31, 2017
5d7b063
using appropriate parameters in cy_sasa_cuda.py (setup.py broken)
rodenki Apr 4, 2017
301bb29
fixed setup.py
rodenki Apr 4, 2017
d533f89
preparing cuda calculation without restriction or contact area
rodenki Apr 4, 2017
9c9aebf
- cudamemcpy working
rodenki Apr 4, 2017
8427cb3
working sasa computation (large error)
rodenki Apr 4, 2017
e370e90
fixing setup.py
maxscheurer Apr 4, 2017
0fb05b7
fixing absolute file path
maxscheurer Apr 4, 2017
9d8b4f2
fixing SASA code both on GPU and CPU
maxscheurer Apr 6, 2017
8dc3226
shared memory optimization
maxscheurer Apr 6, 2017
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44 changes: 0 additions & 44 deletions .travis.yml
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7 changes: 5 additions & 2 deletions PyContact/cy_modules/cy_gridsearch.pyx
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,9 @@ from cython.view cimport array as cvarray
import numpy as np

cdef extern from "src/gridsearch.C":
double sasa_grid(const float *pos,int natoms, float pairdist, int allow_double_counting, int maxpairs, const float *radius,const int npts, double srad, int pointstyle, int restricted, const int* restrictedList)
double sasa_grid(const float *pos, int natoms, float pairdist, int allow_double_counting, int maxpairs,
const float *radius, const int npts, double srad, int pointstyle,
int restricted, const int* restrictedList)

cdef extern from "src/gridsearch.C":
int* find_within(const float *xyz, int *flgs, int *others, int num, float r)
Expand All @@ -13,7 +15,8 @@ def cy_sasa(npcoords, natoms, pairdist, allow_double_counting, maxsize, nprad,
cdef int [::1] cy_restrictedList = restrictedList
cdef float [::1] cy_radius = nprad
cdef float [::1] c_coords = npcoords[0]
cdef float sasa = sasa_grid(&c_coords[0], natoms, pairdist, 0, -1, &cy_radius[0] ,surfacePoints, probeRadius, pointstyle, restricted, &cy_restrictedList[0])
cdef float sasa = sasa_grid(&c_coords[0], natoms, pairdist, 0, -1, &cy_radius[0], surfacePoints, probeRadius,
pointstyle, restricted, &cy_restrictedList[0])
return sasa

def cy_find_within(xyz, flgs, others, num, r):
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