def step_v(n, mn, mx):
step = ()
box = ()
for a, b in zip(mn, mx):
box += tuple([b - a])
step += tuple([(b - a) / rint(n)])
v = rint(n * n * n) / (box[0] * box[1] * box[2])
return step, v
def step_v(n, mn, mx):
step = ()
box = ()
for a,b in zip(mn,mx):
box += tuple( [b-a] )
step += tuple( [(b-a)/rint(n)] )
v = rint( n*n*n ) / (box[0]*box[1]*box[2])
return step, v
def number_from_string(s):
flds = s.split("/")
if (len(flds) == 2):
from boost.rational import int as rint
return rint(int(flds[0]), int(flds[1]))
return (eval(s) + 0) * 1
def compare(spgr, n=NSteps, verbose=False):
if verbose:
print cout.getvalue()
cout.truncate(0)
grp = space_group_info(spgr)
print >> cout, "Comparing asus for group: ", spgr, " n-steps= ", n
asuo = grp.direct_space_asu()
print >> cout, "=== Original python asu ==="
asuo.show_comprehensive_summary(cout)
print >> cout, ":: raw facets"
as_raw_asu(asuo, cout)
mxo = tuple(asuo.box_max())
mno = tuple(asuo.box_min())
print >> cout, "box min= ", mno, " max= ", mxo
### NEW C++ ASU
asun = new_asu.direct_space_asu(grp.type())
print >> cout, "=== New C++ asu ==="
asun.show_comprehensive_summary(cout)
mnn = asun.box_min()
mxn = asun.box_max()
print >> cout, "box min= ", mnn, " max= ", mxn
assert mnn == mno
assert mxn == mxo
old_vertices = asuo.shape_vertices()
new_vertices = asun.shape_vertices() # C++ sorted list
assert len(old_vertices) == len(new_vertices)
# TODO: the following seems to use the same ordering operation
# as mine in C++
old_vertices = sorted(old_vertices)
for a, b in zip(old_vertices, new_vertices):
print >> cout, a, " == ", b
assert a == b, str(a) + " != " + str(b)
ins, v = loop_grid(asun, n, mnn, mxn, asuo)
print >>cout, "N inside = ", ins, " volume = ", v, \
" expected volume = ", rint(1,grp.group().order_z())
### SHAPE ONLY
asun.shape_only()
asuo = asuo.shape_only()
mxo2 = tuple(asuo.box_max())
mno2 = tuple(asuo.box_min())
mnn2 = asun.box_min()
mxn2 = asun.box_max()
assert mxo2 == mxo
assert mno2 == mno
assert mxn2 == mxn
assert mnn2 == mnn
loop_grid(asun, n, mnn, mxn, asuo)
unit_cell = grp.any_compatible_unit_cell(volume=5000.0)
fasun = asun.as_float_asu(unit_cell, 1.0E-6)
fasuo = cctbx.crystal.direct_space_asu_float_asu(
unit_cell=unit_cell,
cuts=[cut.as_float_cut_plane() for cut in asuo.cuts],
is_inside_epsilon=1.e-6)
# python sucks big: still (in 2.5) there is no float.epsilon/max/tiny/etc
assert approx_equal(fasun.is_inside_epsilon(), fasuo.is_inside_epsilon(),
1.0E-100)
assert len(fasun.cuts()) == len(fasuo.cuts()), \
"%d != %d"%(len(fasuo.cuts()),len(fasun.cuts()))
assert ((len(fasun.cuts()) < 200) & (len(fasun.cuts()) > 3)), \
len(fasun.cuts())
if verbose:
print cout.getvalue()
cout.truncate(0)
def loop_grid(asu, n, mn, mx, asu2=None):
assert (asu2 is None) or isinstance(asu, new_asu.direct_space_asu)
first_is_new = False
step, vv = step_v(n, mn, mx)
grid = ()
for s in step:
g = rint(1) / s
g = g.numerator() // g.denominator() + 1
assert g > 0, "Step = " + str(step)
grid += tuple([g])
mna = list(mn)
mxa = list(mx)
for i in xrange(3):
mna[i] -= 5 * step[i]
mna[i] *= grid[i]
mna[i] = mna[i].numerator() // mna[i].denominator() - 1
mxa[i] += 5 * step[i]
mxa[i] *= grid[i]
mxa[i] = mxa[i].numerator() // mxa[i].denominator() + 1
print >>cout, "grid test step= ", step, " min= ", mna, " max= ", mxa, \
" grid=", grid
if isinstance(asu, new_asu.direct_space_asu):
import copy
# TODO: implement
# asu_opt = copy.copy(asu)
# asu_opt.optimize_for_grid(grid)
# assert asu_opt.is_optimized() and (not asu.is_optimized())
first_is_new = True
# max_p = asu_opt.get_optimized_grid_limits()
# print >>cout, "grid limits: ", max_p
result = 0
i = mna[0]
while i <= mxa[0]:
ii = rint(i, grid[0])
j = mna[1]
while j <= mxa[1]:
jj = rint(j, grid[1])
k = mna[2]
while k <= mxa[2]:
kk = rint(k, grid[2])
b = asu.is_inside((ii, jj, kk)) # rational test
if b:
result += 1
if first_is_new:
num = (i, j, k)
den = grid
where = asu.where_is(num, den) # integer test
#TODO: implement? assert b == asu.is_inside(num,den)
assert (b and
(where == 1 or where == -1)) or ((not b)
and where == 0)
#TODO: implemnt where_opt = asu_opt.where_is( num ) # optimized test
# assert where_opt == where
#TODO: implement? assert b == asu_opt.is_inside(num)
if asu2 is not None:
assert b == asu2.is_inside((ii, jj, kk)) # rational test
k += 1
j += 1
i += 1
shape = result / vv
return (result, shape)
def number_from_string(s):
flds = s.split("/")
if (len(flds) == 2):
from boost.rational import int as rint
return rint(int(flds[0]), int(flds[1]))
return (eval(s)+0)*1
def compare(spgr, n=NSteps, verbose=False):
if verbose:
print cout.getvalue()
cout.truncate(0)
grp = space_group_info(spgr)
print >>cout, "Comparing asus for group: ", spgr, " n-steps= ", n
asuo = grp.direct_space_asu()
print >>cout, "=== Original python asu ==="
asuo.show_comprehensive_summary(cout)
print >>cout, ":: raw facets"
as_raw_asu(asuo, cout)
mxo = tuple( asuo.box_max() )
mno = tuple( asuo.box_min() )
print >>cout, "box min= ", mno, " max= ", mxo
### NEW C++ ASU
asun = new_asu.direct_space_asu(grp.type())
print >>cout, "=== New C++ asu ==="
asun.show_comprehensive_summary(cout)
mnn = asun.box_min()
mxn = asun.box_max()
print >>cout, "box min= ", mnn, " max= ", mxn
assert mnn == mno
assert mxn == mxo
old_vertices = asuo.shape_vertices()
new_vertices = asun.shape_vertices() # C++ sorted list
assert len(old_vertices) == len(new_vertices)
# TODO: the following seems to use the same ordering operation
# as mine in C++
old_vertices = sorted(old_vertices)
for a,b in zip(old_vertices,new_vertices):
print >>cout, a, " == ", b
assert a == b, str(a)+" != "+str(b)
ins,v = loop_grid(asun, n, mnn, mxn, asuo)
print >>cout, "N inside = ", ins, " volume = ", v, \
" expected volume = ", rint(1,grp.group().order_z())
### SHAPE ONLY
asun.shape_only()
asuo = asuo.shape_only()
mxo2 = tuple( asuo.box_max() )
mno2 = tuple( asuo.box_min() )
mnn2 = asun.box_min()
mxn2 = asun.box_max()
assert mxo2 == mxo
assert mno2 == mno
assert mxn2 == mxn
assert mnn2 == mnn
loop_grid(asun, n, mnn, mxn, asuo)
unit_cell = grp.any_compatible_unit_cell(volume=5000.0)
fasun = asun.as_float_asu( unit_cell, 1.0E-6);
fasuo = cctbx.crystal.direct_space_asu_float_asu(
unit_cell=unit_cell,
cuts=[cut.as_float_cut_plane() for cut in asuo.cuts],
is_inside_epsilon=1.e-6)
# python sucks big: still (in 2.5) there is no float.epsilon/max/tiny/etc
assert approx_equal(fasun.is_inside_epsilon(), fasuo.is_inside_epsilon(),
1.0E-100)
assert len(fasun.cuts()) == len(fasuo.cuts()), \
"%d != %d"%(len(fasuo.cuts()),len(fasun.cuts()))
assert ((len(fasun.cuts()) < 200) & (len(fasun.cuts()) > 3)), \
len(fasun.cuts())
if verbose:
print cout.getvalue()
cout.truncate(0)
def loop_grid(asu, n, mn, mx, asu2=None):
assert (asu2 is None) or isinstance(asu, new_asu.direct_space_asu)
first_is_new = False
step, vv = step_v(n, mn, mx)
grid = ()
for s in step:
g = rint(1) / s
g = g.numerator()//g.denominator() + 1
assert g > 0, "Step = "+str(step)
grid += tuple([g])
mna = list(mn)
mxa = list(mx)
for i in xrange(3):
mna[i] -= 5*step[i]
mna[i] *= grid[i]
mna[i] = mna[i].numerator()//mna[i].denominator()-1
mxa[i] += 5*step[i]
mxa[i] *= grid[i]
mxa[i] = mxa[i].numerator()//mxa[i].denominator()+1
print >>cout, "grid test step= ", step, " min= ", mna, " max= ", mxa, \
" grid=", grid
if isinstance(asu, new_asu.direct_space_asu):
import copy
# TODO: implement
# asu_opt = copy.copy(asu)
# asu_opt.optimize_for_grid(grid)
# assert asu_opt.is_optimized() and (not asu.is_optimized())
first_is_new = True
# max_p = asu_opt.get_optimized_grid_limits()
# print >>cout, "grid limits: ", max_p
result = 0
i = mna[0]
while i <= mxa[0] :
ii = rint(i,grid[0])
j = mna[1]
while j <= mxa[1] :
jj = rint(j,grid[1])
k = mna[2]
while k <= mxa[2] :
kk = rint(k,grid[2])
b = asu.is_inside((ii,jj,kk)) # rational test
if b :
result += 1
if first_is_new:
num = (i, j, k)
den = grid
where = asu.where_is(num,den) # integer test
#TODO: implement? assert b == asu.is_inside(num,den)
assert ( b and (where==1 or where==-1)) or ( (not b) and where==0 )
#TODO: implemnt where_opt = asu_opt.where_is( num ) # optimized test
# assert where_opt == where
#TODO: implement? assert b == asu_opt.is_inside(num)
if asu2 is not None :
assert b == asu2.is_inside( (ii,jj,kk) ) # rational test
k += 1
j += 1
i += 1
shape = result / vv
return (result,shape)