def returncenters(guvfilename, molar, grcutoff):
'''Given distribution, returns placed atoms
Input: guvfilename and molarity
Returns: Placed centers as Atom objects
'''
conc = molar * 6.0221415E-4
shellindices = grid.readshellindices()
if guvfilename[-3:] == ".dx":
(distribution, origin, delta, gridcount) = \
grid.readdx(guvfilename)
elif guvfilename[-3:] == ".h5":
grids = grid.h5ToGrids(guvfilename)
print "Warning, assuming target molecule is 'O', please contact the developer for more info."
if 'guv' not in grids['O'].keys():
exit("Error, guv distribution not found in file")
gGrid = grids['O']['guv']
distribution = gGrid.distribution
origin = gGrid.origin
delta = gGrid.deltas
gridcount = gGrid.gridcount
else:
exit("Error, incompatible file type! -> {0}".format(guvfilename))
(popzero, totalpop, gridvolume) = converttopop(distribution,
delta, conc)
return doplacement(popzero, conc, gridvolume, origin, delta, shellindices,
grcutoff)
import os
testscriptdir = os.getcwd()
# Test reading/writing
print "Testing reading/writing dx files.."
dxfilename = os.path.join(testscriptdir, "data", "dxfiles",
"AlaDP_3DRISM_smallbuffer.dx.gz")
originalgrid = grid.dx2Grid(dxfilename)
maxvalue = originalgrid.distribution.max()
maxindices = tuple(np.argwhere(originalgrid.distribution == maxvalue)[0])
originalgrid.distribution[maxindices] = maxvalue * 2.0
originalgrid.writedx("modified.dx")
newgrid = grid.dx2Grid("modified.dx")
newmax = newgrid.distribution.max()
assert newmax == maxvalue * 2.0
#cleanup
os.remove("modified.dx")
# Test shells
print "Testing shell-related utilities.."
storedprecomputedshells = grid.readshellindices()
newshells = grid.precomputeshellindices(40)
for storedshell, newshell in zip(storedprecomputedshells, newshells):
for storedpoint, newpoint in zip(storedshell, newshell):
for storedindex, newindex in zip(storedpoint, newpoint):
assert storedindex == newindex
#matplotlib.pyplot.scatter(xset, rdfnearH, color="silver")
#matplotlib.pyplot.scatter(xset, rdfnearO, color="red")
#matplotlib.pyplot.scatter(xset, rdfnearH2, color="blue")
#matplotlib.pyplot.show()
#quit()
# Test reading/writing
print "Testing reading/writing dx files.."
originalgrid = grid.dx2Grid(dxfilename)
maxvalue = originalgrid.distribution.max()
maxindices = tuple(np.argwhere(originalgrid.distribution == maxvalue)[0])
originalgrid.distribution[maxindices] = maxvalue * 2.0
originalgrid.writedx("modified.dx")
newgrid = grid.dx2Grid("modified.dx")
newmax = newgrid.distribution.max()
assert newmax == maxvalue * 2.0
#cleanup
del originalgrid
del newgrid
os.remove("modified.dx")
# Test shells
print "Testing shell-related utilities.."
storedprecomputedshells = grid.readshellindices()
newshells = grid.precomputeshellindices(40)
for storedshell, newshell in zip(storedprecomputedshells, newshells):
for storedpoint, newpoint in zip(storedshell, newshell):
for storedindex, newindex in zip(storedpoint, newpoint):
assert storedindex == newindex
