def test_abc():
# Should get out params back
a = 9.5
b = 8.6
c = 5.2
alp = 90.000
bet = 106.239525
gam = 90.000
tmpcell = gs.cellABC2cellCART(a, b, c, alp, bet, gam)
a_out = np.linalg.norm(tmpcell[0])
b_out = np.linalg.norm(tmpcell[1])
c_out = np.linalg.norm(tmpcell[2])
alp_out = np.degrees(
np.arccos(
np.dot(tmpcell[1], tmpcell[2]) /
(np.linalg.norm(tmpcell[1]) * np.linalg.norm(tmpcell[2]))))
bet_out = np.degrees(
np.arccos(
np.dot(tmpcell[0], tmpcell[2]) /
(np.linalg.norm(tmpcell[0]) * np.linalg.norm(tmpcell[2]))))
gam_out = np.degrees(
np.arccos(
np.dot(tmpcell[0], tmpcell[1]) /
(np.linalg.norm(tmpcell[0]) * np.linalg.norm(tmpcell[1]))))
npt.assert_almost_equal(a_out, a)
npt.assert_almost_equal(b_out, b)
npt.assert_almost_equal(c_out, c)
npt.assert_almost_equal(alp_out, alp)
npt.assert_almost_equal(bet_out, bet)
npt.assert_almost_equal(gam_out, gam)
def test_abc(a, b, c, alp, bet, gam):
tmpcell = gs.cellABC2cellCART (a, b, c, alp, bet, gam)
a_out = np.linalg.norm(tmpcell[0])
b_out = np.linalg.norm(tmpcell[1])
c_out = np.linalg.norm(tmpcell[2])
alp_out = np.degrees(np.arccos(np.dot(tmpcell[1],tmpcell[2])/(np.linalg.norm(tmpcell[1])*np.linalg.norm(tmpcell[2]))))
bet_out = np.degrees(np.arccos(np.dot(tmpcell[0],tmpcell[2])/(np.linalg.norm(tmpcell[0])*np.linalg.norm(tmpcell[2]))))
gam_out = np.degrees(np.arccos(np.dot(tmpcell[0],tmpcell[1])/(np.linalg.norm(tmpcell[0])*np.linalg.norm(tmpcell[1]))))
npt.assert_almost_equal(a_out,a)
npt.assert_almost_equal(b_out,b)
npt.assert_almost_equal(c_out,c)
npt.assert_almost_equal(alp_out,alp)
npt.assert_almost_equal(bet_out,bet)
npt.assert_almost_equal(gam_out,gam)
def test_cell():
# Should not end up rotates
incell = [[9.1209595, 0., -2.65670807], [0., 8.6, 0.], [0., 0., 5.2]]
a, b, c, al, be, ga = gs.cellCART2cellABC(incell)
outcell = gs.cellABC2cellCART(a, b, c, al, be, ga)
npt.assert_almost_equal(incell, outcell)
def rot_cell(incell):
a, b, c, al, be, ga = gs.cellCART2cellABC(incell)
outcell = gs.cellABC2cellCART(a, b, c, al, be, ga)
return outcell
outVec = np.transpose(rotMat * np.transpose(np.matrix(inVec))) outVec = [outVec[0,0], outVec[0,1], outVec[0,2]] return outVec if __name__ == '__main__': import sys a = float(sys.argv[1]) b = float(sys.argv[2]) c = float(sys.argv[3]) al = float(sys.argv[4]) be = float(sys.argv[5]) ga = float(sys.argv[6]) inFile = file(sys.argv[7], 'r') Cij_in = np.loadtxt(inFile) # Get cart vectors for lattice (lat_a, lat_b, lat_c) = cellABC2cellCART(a, b, c, al, be, ga) print "initial lattice vectors:" print lat_a print lat_b print lat_c # rotate by 90 - gamma around z to put b on y axis angle = -1.0 * np.radians(90 - ga) lat_a = rotVec(lat_a, 2, angle) lat_b = rotVec(lat_b, 2, angle) lat_c = rotVec(lat_c, 2, angle) Cij = rotCij(Cij_in, 2, angle) print "after rotating around z:" print lat_a print lat_b print lat_c print Cij
def test_cell (incell):
a, b, c, al, be, ga = gs.cellCART2cellABC (incell)
outcell = gs.cellABC2cellCART (a, b, c, al, be, ga)
npt.assert_almost_equal(incell, outcell)
def rot_cell(incell):
a, b, c, al, be, ga = gs.cellCART2cellABC (incell)
outcell = gs.cellABC2cellCART (a, b, c, al, be, ga)
return outcell
outVec = [outVec[0, 0], outVec[0, 1], outVec[0, 2]]
return outVec
if __name__ == '__main__':
import sys
a = float(sys.argv[1])
b = float(sys.argv[2])
c = float(sys.argv[3])
al = float(sys.argv[4])
be = float(sys.argv[5])
ga = float(sys.argv[6])
inFile = file(sys.argv[7], 'r')
Cij_in = np.loadtxt(inFile)
# Get cart vectors for lattice
(lat_a, lat_b, lat_c) = cellABC2cellCART(a, b, c, al, be, ga)
print "initial lattice vectors:"
print lat_a
print lat_b
print lat_c
# rotate by 90 - gamma around z to put b on y axis
angle = -1.0 * np.radians(90 - ga)
lat_a = rotVec(lat_a, 2, angle)
lat_b = rotVec(lat_b, 2, angle)
lat_c = rotVec(lat_c, 2, angle)
Cij = rotCij(Cij_in, 2, angle)
print "after rotating around z:"
print lat_a
print lat_b
print lat_c
print Cij