def exercise_2(small=1.e-9):
m = [2, 1, 2, 0, 0, 0]
n = [2, 2, 1, 0, 0, 0]
m_dc = copy.deepcopy(m)
n_dc = copy.deepcopy(n)
qq = tools.common(n, m, small)
assert approx_equal(m, m_dc)
assert approx_equal(n, n_dc)
assert qq.t() == (2.0, 1.0, 1.0, 0.0, 0.0, 0.0)
def exercise_2(small = 1.e-9): m = [2,1,2,0,0,0] n = [2,2,1,0,0,0] m_dc = copy.deepcopy(m) n_dc = copy.deepcopy(n) qq = tools.common(n,m,small) assert approx_equal(m,m_dc) assert approx_equal(n,n_dc) assert qq.t() == (2.0, 1.0, 1.0, 0.0, 0.0, 0.0)
def exercise(small=1.e-9):
for symbol in ["P 1"]:
space_group_info = sgtbx.space_group_info(symbol=symbol)
random_xray_structure = random_structure.xray_structure(
space_group_info=space_group_info,
elements=["N"] * 10,
volume_per_atom=50.0,
random_u_iso=False,
u_iso=adptbx.b_as_u(20.0))
sg = random_xray_structure.space_group()
uc = random_xray_structure.unit_cell()
print(symbol, uc)
print()
sys.stdout.flush()
counter = 0
trials = 100000
i = 0
branch_0 = 0
branch_1 = 0
branch_1_1 = 0
branch_1_2 = 0
branch_1_2_1 = 0
branch_1_2_2 = 0
branch_1_2_3 = 0
branch_1_2_3_1 = 0
branch_1_2_3_2 = 0
while i < trials:
i += 1
counter += 1
r = random.random()
if (r < 0.333):
m = adptbx.random_u_cart(u_scale=20. * random.random(),
u_min=0)
n = adptbx.random_u_cart(u_scale=20. * random.random(),
u_min=0)
while 1:
for ind in range(6):
r = random.random()
m = flex.double(m)
if (r > 0.5):
m[ind] = n[ind]
m = list(m)
if (adptbx.is_positive_definite(m, 0)
and adptbx.is_positive_definite(n, 0)):
break
elif (r >= 0.333 and r < 0.66):
m, n = branch_3_mn()
else:
m, n = branch_2_mn(0)
m_dc = copy.deepcopy(m)
n_dc = copy.deepcopy(n)
m = factor(list(m), i)
n = factor(list(n), i)
qq = tools.common(n, m, small)
#assert approx_equal(m,m_dc)
#assert approx_equal(n,n_dc)
if (qq.branch_0()): branch_0 += 1
if (qq.branch_1()): branch_1 += 1
if (qq.branch_1_1()): branch_1_1 += 1
if (qq.branch_1_2()): branch_1_2 += 1
if (qq.branch_1_2_1()): branch_1_2_1 += 1
if (qq.branch_1_2_2()): branch_1_2_2 += 1
if (qq.branch_1_2_3()): branch_1_2_3 += 1
if (qq.branch_1_2_3_1()): branch_1_2_3_1 += 1
if (qq.branch_1_2_3_2()): branch_1_2_3_2 += 1
if (counter >= 10000):
counter = 0
print("." * 30, symbol)
print("i= ", i, "out of ", trials)
print("branch_0 = ", branch_0)
print("branch_1 = ", branch_1)
print("branch_1_1 = ", branch_1_1)
print("branch_1_2 = ", branch_1_2)
print("branch_1_2_1 = ", branch_1_2_1)
print("branch_1_2_2 = ", branch_1_2_2)
print("branch_1_2_3 = ", branch_1_2_3)
print("branch_1_2_3_1 = ", branch_1_2_3_1)
print("branch_1_2_3_2 = ", branch_1_2_3_2)
sys.stdout.flush()
def exercise_branch_2_1(small=1.e-9):
m = [2, 1, 2, 0, 0, 0]
n = [2, 1, 1, 0, 0, 0]
counter = 0
trials = 100000
i = 0
branch_0 = 0
branch_1 = 0
branch_1_1 = 0
branch_1_2 = 0
branch_1_2_1 = 0
branch_1_2_2 = 0
branch_1_2_3 = 0
branch_1_2_3_1 = 0
branch_1_2_3_2 = 0
while i < trials:
i += 1
m = [2, 1, 2, 0, 0, 0]
n = [2, 1, 1, 0, 0, 0]
counter += 1
c = scitbx.math.euler_angles_as_matrix(
[random.uniform(0, 360) for j in range(3)], deg=True).elems
r = random.random()
if (r < 0.25):
m = adptbx.c_u_c_transpose(c, m)
n = adptbx.c_u_c_transpose(c, n)
elif (r >= 0.25 and r < 0.5):
m = adptbx.c_u_c_transpose(c, m)
elif (r >= 0.5 and r < 0.75):
n = adptbx.c_u_c_transpose(c, n)
else:
r = random.random()
run_away = 1000
while run_away > 0:
run_away -= 1
r = random.random()
if (r < 0.33):
m = adptbx.c_u_c_transpose(c, m)
n = adptbx.c_u_c_transpose(c, n)
elif (r >= 0.33 and r < 0.66):
m = adptbx.c_u_c_transpose(c, m)
else:
n = adptbx.c_u_c_transpose(c, n)
m = adptbx.c_u_c_transpose(c, m)
n = adptbx.c_u_c_transpose(c, n)
m = [
m[0], m[1], m[2], m[3] * random.choice((0, 1)),
m[4] * random.choice((0, 1)), m[5] * random.choice((0, 1))
]
n = [
n[0], n[1], n[2], n[3] * random.choice((0, 1)),
n[4] * random.choice((0, 1)), n[5] * random.choice((0, 1))
]
m = factor(list(m), i)
n = factor(list(n), i)
if (adptbx.is_positive_definite(m, small)
and adptbx.is_positive_definite(n, small)):
break
m_dc = copy.deepcopy(m)
n_dc = copy.deepcopy(n)
qq = tools.common(n, m, small)
#assert approx_equal(m,m_dc)
#assert approx_equal(n,n_dc)
if (qq.branch_0()): branch_0 += 1
if (qq.branch_1()): branch_1 += 1
if (qq.branch_1_1()): branch_1_1 += 1
if (qq.branch_1_2()): branch_1_2 += 1
if (qq.branch_1_2_1()): branch_1_2_1 += 1
if (qq.branch_1_2_2()): branch_1_2_2 += 1
if (qq.branch_1_2_3()): branch_1_2_3 += 1
if (qq.branch_1_2_3_1()): branch_1_2_3_1 += 1
if (qq.branch_1_2_3_2()): branch_1_2_3_2 += 1
if (counter >= 10000):
counter = 0
print("." * 30)
print("i= ", i, "out of ", trials)
print("branch_0 = ", branch_0)
print("branch_1 = ", branch_1)
print("branch_1_1 = ", branch_1_1)
print("branch_1_2 = ", branch_1_2)
print("branch_1_2_1 = ", branch_1_2_1)
print("branch_1_2_2 = ", branch_1_2_2)
print("branch_1_2_3 = ", branch_1_2_3)
print("branch_1_2_3_1 = ", branch_1_2_3_1)
print("branch_1_2_3_2 = ", branch_1_2_3_2)
sys.stdout.flush()
def exercise(small = 1.e-9):
for symbol in ["P 1"]:
space_group_info = sgtbx.space_group_info(symbol = symbol)
random_xray_structure = random_structure.xray_structure(
space_group_info = space_group_info,
elements = ["N"]*10,
volume_per_atom = 50.0,
random_u_iso = False,
u_iso = adptbx.b_as_u(20.0))
sg = random_xray_structure.space_group()
uc = random_xray_structure.unit_cell()
print symbol, uc
print
sys.stdout.flush()
counter = 0
trials = 100000
i = 0
branch_0 = 0
branch_1 = 0
branch_1_1 = 0
branch_1_2 = 0
branch_1_2_1 = 0
branch_1_2_2 = 0
branch_1_2_3 = 0
branch_1_2_3_1 = 0
branch_1_2_3_2 = 0
while i < trials:
i += 1
counter += 1
r = random.random()
if(r < 0.333):
m = adptbx.random_u_cart(u_scale=20.*random.random(), u_min=0)
n = adptbx.random_u_cart(u_scale=20.*random.random(), u_min=0)
while 1:
for ind in xrange(6):
r = random.random()
m = flex.double(m)
if(r > 0.5):
m[ind] = n[ind]
m = list(m)
if(adptbx.is_positive_definite(m,0) and
adptbx.is_positive_definite(n,0)): break
elif(r>=0.333 and r<0.66):
m,n = branch_3_mn()
else:
m,n = branch_2_mn(0)
m_dc = copy.deepcopy(m)
n_dc = copy.deepcopy(n)
m = factor(list(m), i)
n = factor(list(n), i)
qq = tools.common(n,m,small)
#assert approx_equal(m,m_dc)
#assert approx_equal(n,n_dc)
if(qq.branch_0() ): branch_0 += 1
if(qq.branch_1() ): branch_1 += 1
if(qq.branch_1_1() ): branch_1_1 += 1
if(qq.branch_1_2() ): branch_1_2 += 1
if(qq.branch_1_2_1() ): branch_1_2_1 += 1
if(qq.branch_1_2_2() ): branch_1_2_2 += 1
if(qq.branch_1_2_3() ): branch_1_2_3 += 1
if(qq.branch_1_2_3_1()): branch_1_2_3_1 += 1
if(qq.branch_1_2_3_2()): branch_1_2_3_2 += 1
if (counter >= 10000):
counter = 0
print "."*30, symbol
print "i= ", i, "out of ", trials
print "branch_0 = ", branch_0
print "branch_1 = ", branch_1
print "branch_1_1 = ", branch_1_1
print "branch_1_2 = ", branch_1_2
print "branch_1_2_1 = ", branch_1_2_1
print "branch_1_2_2 = ", branch_1_2_2
print "branch_1_2_3 = ", branch_1_2_3
print "branch_1_2_3_1 = ", branch_1_2_3_1
print "branch_1_2_3_2 = ", branch_1_2_3_2
sys.stdout.flush()
def exercise_branch_2_1(small = 1.e-9):
m = [2,1,2,0,0,0]
n = [2,1,1,0,0,0]
counter = 0
trials = 100000
i = 0
branch_0 = 0
branch_1 = 0
branch_1_1 = 0
branch_1_2 = 0
branch_1_2_1 = 0
branch_1_2_2 = 0
branch_1_2_3 = 0
branch_1_2_3_1 = 0
branch_1_2_3_2 = 0
while i < trials:
i += 1
m = [2,1,2,0,0,0]
n = [2,1,1,0,0,0]
counter += 1
c = scitbx.math.euler_angles_as_matrix(
[random.uniform(0,360) for j in xrange(3)], deg=True).elems
r = random.random()
if(r<0.25):
m = adptbx.c_u_c_transpose(c, m)
n = adptbx.c_u_c_transpose(c, n)
elif(r>=0.25 and r < 0.5):
m = adptbx.c_u_c_transpose(c, m)
elif(r>=0.5 and r < 0.75):
n = adptbx.c_u_c_transpose(c, n)
else:
r = random.random()
run_away = 1000
while run_away > 0:
run_away -= 1
r = random.random()
if(r<0.33):
m = adptbx.c_u_c_transpose(c, m)
n = adptbx.c_u_c_transpose(c, n)
elif(r>=0.33 and r < 0.66):
m = adptbx.c_u_c_transpose(c, m)
else:
n = adptbx.c_u_c_transpose(c, n)
m = adptbx.c_u_c_transpose(c, m)
n = adptbx.c_u_c_transpose(c, n)
m = [m[0],m[1],m[2],m[3]*random.choice((0,1)),m[4]*random.choice((0,1)),m[5]*random.choice((0,1))]
n = [n[0],n[1],n[2],n[3]*random.choice((0,1)),n[4]*random.choice((0,1)),n[5]*random.choice((0,1))]
m = factor(list(m), i)
n = factor(list(n), i)
if(adptbx.is_positive_definite(m,small) and
adptbx.is_positive_definite(n,small)): break
m_dc = copy.deepcopy(m)
n_dc = copy.deepcopy(n)
qq = tools.common(n,m,small)
#assert approx_equal(m,m_dc)
#assert approx_equal(n,n_dc)
if(qq.branch_0() ): branch_0 += 1
if(qq.branch_1() ): branch_1 += 1
if(qq.branch_1_1() ): branch_1_1 += 1
if(qq.branch_1_2() ): branch_1_2 += 1
if(qq.branch_1_2_1() ): branch_1_2_1 += 1
if(qq.branch_1_2_2() ): branch_1_2_2 += 1
if(qq.branch_1_2_3() ): branch_1_2_3 += 1
if(qq.branch_1_2_3_1()): branch_1_2_3_1 += 1
if(qq.branch_1_2_3_2()): branch_1_2_3_2 += 1
if (counter >= 10000):
counter = 0
print "."*30
print "i= ", i, "out of ", trials
print "branch_0 = ", branch_0
print "branch_1 = ", branch_1
print "branch_1_1 = ", branch_1_1
print "branch_1_2 = ", branch_1_2
print "branch_1_2_1 = ", branch_1_2_1
print "branch_1_2_2 = ", branch_1_2_2
print "branch_1_2_3 = ", branch_1_2_3
print "branch_1_2_3_1 = ", branch_1_2_3_1
print "branch_1_2_3_2 = ", branch_1_2_3_2
sys.stdout.flush()