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dev/script/__Lib/diffcalc/test/diffcalc/scenarios.py
Alexandre Gobbo 5db0f78aee Startup
2019-03-20 13:52:00 +01:00

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###
# Copyright 2008-2011 Diamond Light Source Ltd.
# This file is part of Diffcalc.
#
# Diffcalc is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# Diffcalc is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with Diffcalc. If not, see <http://www.gnu.org/licenses/>.
###
from datetime import datetime
from math import asin, sin, cos, atan2
from diffcalc.ub.reflections import _Reflection
from diffcalc.hkl.vlieg.geometry import VliegPosition
from diffcalc.hkl.you.geometry import YouPosition
from diffcalc.hkl.you.calc import sign
from diffcalc.util import TORAD, TODEG
class YouPositionScenario(YouPosition):
"""Convert six-circle Vlieg diffractometer angles into 4S+2D You geometry"""
def __init__(self, alpha=None, delta=None, gamma=None, omega=None,
chi=None, phi=None):
self.mu = alpha
self.eta = omega
self.chi = chi
self.phi = phi
self.unit = 'DEG'
asin_delta = asin(sin(delta*TORAD) * cos(gamma*TORAD))*TODEG # Eq.(83)
vals_delta = [asin_delta, 180. - asin_delta]
idx, _ = min([(i, abs(delta - d)) for i, d in enumerate(vals_delta)], key=lambda x: x[1])
self.delta = vals_delta[idx]
sgn = sign(cos(self.delta * TORAD))
self.nu = atan2(sgn*(cos(delta*TORAD)*cos(gamma*TORAD)*sin(alpha*TORAD) + cos(alpha*TORAD)*sin(gamma*TORAD)),
sgn*(cos(delta*TORAD)*cos(gamma*TORAD)*cos(alpha*TORAD) - sin(alpha*TORAD)*sin(gamma*TORAD)))*TODEG # Eq.(84)
class SessionScenario:
"""
A test scenario. The test case must have __name, lattice and bmatrix set
and if umatrix is set then so must ref 1 and ref 2. Matrices should be 3*3
python arrays of lists and ref1 and ref2 in the format (h, k, l, position,
energy, tag)."""
def __init__(self):
self.name = None
self.lattice = None
self.bmatrix = None
self.ref1 = None
self.ref2 = None
self.umatrix = None
self.calculations = [] # CalculationScenarios
def __str__(self):
toReturn = "\nTestScenario:"
toReturn += "\n name: " + self.name
toReturn += "\n lattice:" + str(self.lattice)
toReturn += "\n bmatrix:" + str(self.bmatrix)
toReturn += "\n ref1:" + str(self.ref1)
toReturn += "\n ref2:" + str(self.ref2)
toReturn += "\n umatrix:" + str(self.umatrix)
return toReturn
class CalculationScenario:
"""
Used as part of a test scenario. A UB matrix appropriate for this
calcaultion will have been calculated or loaded
"""
def __init__(self, tag, package, mode, energy, modeToTest, modeNumber):
self.tag = tag
self.package = package
self.mode = mode
self.energy = energy
self.wavelength = 12.39842 / energy
self.modeToTest = modeToTest
self.modeNumber = modeNumber
self.hklList = None # hkl triples
self.posList = []
self.paramList = []
def sessions(P=VliegPosition):
############################ SESSION0 ############################
# From the dif_init.mat next to dif_dos.exe on Vlieg'session2 cd
#session2 = SessionScenario()
#session2.name = 'latt1'
#session2.lattice = ([4.0004, 4.0004, 2.270000, 90, 90, 90])
#session2.bmatrix = (((1.570639, 0, 0) ,(0.0, 1.570639, 0) ,
# (0.0, 0.0, 2.767923)))
#self.scenarios.append(session2)
############################ SESSION1 ############################
# From b16 on 27June2008 (From Chris Nicklin)
session1 = SessionScenario()
session1.name = "b16_270608"
session1.time = datetime.now()
session1.lattice = ((3.8401, 3.8401, 5.43072, 90, 90, 90))
session1.bmatrix = (((1.636204, 0, 0), (0, 1.636204, 0), (0, 0, 1.156971)))
session1.ref1 = _Reflection(1, 0, 1.0628,
P(5.000, 22.790, 0.000, 1.552, 22.400, 14.255),
10, 'ref1', session1.time)
session1.ref2 = _Reflection(0, 1, 1.0628,
P(5.000, 22.790, 0.000, 4.575, 24.275, 101.320),
10, 'ref2', session1.time)
session1.umatrix = ((0.997161, -0.062217, 0.042420),
(0.062542, 0.998022, -0.006371),
(-0.041940, 0.009006, 0.999080))
session1.ref1calchkl = (1, 0, 1.0628) # Must match the guessed value!
session1.ref2calchkl = (-0.0329, 1.0114, 1.04)
############################ SESSION2 ############################
# cubic crystal from bliss tutorial
session2 = SessionScenario()
session2.name = "cubic_from_bliss_tutorial"
session2.time = datetime.now()
session2.lattice = ((1.54, 1.54, 1.54, 90, 90, 90))
session2.ref1 = _Reflection(1, 0, 0, P(0, 60, 0, 30, 0, 0),
12.39842 / 1.54, 'ref1', session2.time)
session2.ref2 = _Reflection(0, 1, 0, P(0, 60, 0, 30, 0, -90),
12.39842 / 1.54, 'ref2', session2.time)
session2.bmatrix = (((4.07999, 0, 0), (0, 4.07999, 0), (0, 0, 4.07999)))
session2.umatrix = (((1, 0, 0), (0, -1, 0), (0, 0, -1)))
session2.ref1calchkl = (1, 0, 0) # Must match the guessed value!
session2.ref2calchkl = (0, 1, 0)
# sixc-0a : fixed omega = 0
c = CalculationScenario('sixc-0a', 'sixc', '0', 12.39842 / 1.54, '4cBeq', 1)
c.alpha = 0
c.gamma = 0
c.w = 0
#c.hklList=((0.7, 0.9, 1.3), (1,0,0), (0,1,0), (1, 1, 0))
c.hklList = ((0.7, 0.9, 1.3),)
c.posList.append(
P(0.000000, 119.669750, 0.000000, 59.834875, -48.747500, 307.874983651098))
#c.posList.append(P(0.000000, 60.000000, 0.000000, 30.000, 0.000000, 0.000000))
#c.posList.append(P(0.000000, 60.000000, 0.000000, 30.000, 0.000000, -90.0000))
#c.posList.append(P(0.000000, 90.000000, 0.000000, 45.000, 0.000000, -45.0000))
session2.calculations.append(c)
############################ SESSION3 ############################
# AngleCalc scenarios from SPEC sixc. using crystal and alignment
session3 = SessionScenario()
session3.name = "spec_sixc_b16_270608"
session3.time = datetime.now()
session3.lattice = ((3.8401, 3.8401, 5.43072, 90, 90, 90))
session3.bmatrix = (((1.636204, 0, 0), (0, 1.636204, 0), (0, 0, 1.156971)))
session3.umatrix = ((0.997161, -0.062217, 0.042420),
(0.062542, 0.998022, -0.006371),
(-0.041940, 0.009006, 0.999080))
session3.ref1 = _Reflection(1, 0, 1.0628,
P(5.000, 22.790, 0.000, 1.552, 22.400, 14.255),
12.39842 / 1.24, 'ref1', session3.time)
session3.ref2 = _Reflection(0, 1, 1.0628,
P(5.000, 22.790, 0.000, 4.575, 24.275, 101.320),
12.39842 / 1.24, 'ref2', session3.time)
session3.ref1calchkl = (1, 0, 1.0628)
session3.ref2calchkl = (-0.0329, 1.0114, 1.04)
# sixc-0a : fixed omega = 0
ac = CalculationScenario('sixc-0a', 'sixc', '0', 12.39842 / 1.24, '4cBeq', 1)
ac.alpha = 0
ac.gamma = 0
ac.w = 0
### with 'omega_low':-90, 'omega_high':270, 'phi_low':-180, 'phi_high':180
ac.hklList = []
ac.hklList.append((0.7, 0.9, 1.3))
ac.posList.append(P(0.0, 27.352179, 0.000000, 13.676090, 37.774500, 53.965500))
ac.paramList.append({'Bin': 8.3284, 'Bout': 8.3284, 'rho': 36.5258,
'eta': 0.1117, 'twotheta': 27.3557})
ac.hklList.append((1, 0, 0))
ac.posList.append(P(0., 18.580230, 0.000000, 9.290115, -2.403500, 3.589000))
ac.paramList.append({'Bin': -0.3880, 'Bout': -0.3880, 'rho': -2.3721,
'eta': -0.0089, 'twotheta': 18.5826})
ac.hklList.append((0, 1, 0))
ac.posList.append(P(0., 18.580230, 0.000000, 9.290115, 0.516000, 93.567000))
ac.paramList.append({'Bin': 0.0833, 'Bout': 0.0833, 'rho': 0.5092,
'eta': -0.0414, 'twotheta': 18.5826})
ac.hklList.append((1, 1, 0))
ac.posList.append(P(0., 26.394192, 0.000000, 13.197096, -1.334500, 48.602000))
ac.paramList.append({'Bin': -0.3047, 'Bout': -0.3047, 'rho': -1.2992,
'eta': -0.0351, 'twotheta': 26.3976})
session3.calculations.append(ac)
############################ SESSION4 ############################
# test crystal
session4 = SessionScenario()
session4.name = "test_orth"
session4.time = datetime.now()
session4.lattice = ((1.41421, 1.41421, 1.00000, 90, 90, 90))
session4.system = 'Orthorhombic'
session4.bmatrix = (((4.44288, 0, 0), (0, 4.44288, 0), (0, 0, 6.28319)))
session4.ref1 = _Reflection(0, 1, 2,
P(0.0000, 122.4938, 0.0000, 80.7181, 90.0000, -45.0000),
15., 'ref1', session4.time)
session4.ref2 = _Reflection(1, 0, 2,
P(0.0000, 122.4938, 0.000, 61.2469, 70.5288, -45.0000),
15, 'ref2', session4.time)
session4.ref3 = _Reflection(1, 0, 1,
P(0.0000, 60.8172, 0.000, 30.4086, 54.7356, -45.0000),
15, 'ref3', session4.time)
session4.ref4 = _Reflection(1, 1, 2,
P(0.0000, 135.0736, 0.000, 67.5368, 63.4349, 0.0000),
15, 'ref4', session4.time)
session4.reflist = (session4.ref1,
session4.ref2,
session4.ref3,
session4.ref4)
session4.umatrix = ((0.70711, 0.70711, 0.00),
(-0.70711, 0.70711, 0.00),
(0.00, 0.00, 1.00))
session4.ref1calchkl = (0, 1, 2) # Must match the guessed value!
session4.ref2calchkl = (1, 0, 2)
############################ SESSION5 ############################
# test crystal
session5 = SessionScenario()
session5.name = "Dalyite"
session5.time = datetime.now()
session5.lattice = ((7.51, 7.73, 7.00, 106.0, 113.5, 99.5))
session5.system = 'Triclinic'
session5.bmatrix = (((0.96021, 0.27759, 0.49527), (0, 0.84559, 0.25738), (0, 0, 0.89760)))
session5.ref1 = _Reflection(0, 1, 2,
P(0.0000, 23.7405, 0.0000, 11.8703, 46.3100, 43.1304),
12.3984, 'ref1', session5.time)
session5.ref2 = _Reflection(1, 0, 3,
P(0.0000, 34.4282, 0.000, 17.2141, 46.4799, 12.7852),
12.3984, 'ref2', session5.time)
session5.ref3 = _Reflection(2, 2, 6,
P(0.0000, 82.8618, 0.000, 41.4309, 41.5154, 26.9317),
12.3984, 'ref3', session5.time)
session5.ref4 = _Reflection(4, 1, 4,
P(0.0000, 71.2763, 0.000, 35.6382, 29.5042, 14.5490),
12.3984, 'ref4', session5.time)
session5.ref5 = _Reflection(8, 3, 1,
P(0.0000, 97.8850, 0.000, 48.9425, 5.6693, 16.7929),
12.3984, 'ref5', session5.time)
session5.ref6 = _Reflection(6, 4, 5,
P(0.0000, 129.6412, 0.000, 64.8206, 24.1442, 24.6058),
12.3984, 'ref6', session5.time)
session5.ref7 = _Reflection(3, 5, 7,
P(0.0000, 135.9159, 0.000, 67.9579, 34.3696, 35.1816),
12.3984, 'ref7', session5.time)
session5.reflist = (session5.ref1,
session5.ref2,
session5.ref3,
session5.ref4,
session5.ref5,
session5.ref6,
session5.ref7
)
session5.umatrix = (( 0.99982, 0.00073, 0.01903),
( 0.00073, 0.99710, -0.07612),
(-0.01903, 0.07612, 0.99692))
session5.ref1calchkl = (0, 1, 2) # Must match the guessed value!
session5.ref2calchkl = (1, 0, 3)
############################ SESSION6 ############################
# test crystal
session6 = SessionScenario()
session6.name = "Acanthite"
session6.time = datetime.now()
session6.lattice = ((4.229, 6.931, 7.862, 90, 99.61, 90))
session6.system = 'Monoclinic'
session6.bmatrix = ((1.50688, 0.00000, 0.13532),
(0.00000, 0.90653, 0.00000),
(0.00000, 0.00000, 0.79918))
session6.ref1 = _Reflection(0, 1, 2,
P(0.0000, 21.1188, 0.0000, 10.5594, 59.6447, 61.8432),
10., 'ref1', session6.time)
session6.ref2 = _Reflection(1, 0, 3,
P(0.0000, 35.2291, 0.000, 62.4207, 87.1516, -90.0452),
10., 'ref2', session6.time)
session6.ref3 = _Reflection(1, 1, 6,
P(0.0000, 64.4264, 0.000, 63.9009, 97.7940, -88.8808),
10., 'ref3', session6.time)
session6.ref4 = _Reflection(1, 2, 2,
P(0.0000, 34.4369, 0.000, 72.4159, 60.1129, -29.0329),
10., 'ref4', session6.time)
session6.ref5 = _Reflection(2, 2, 1,
P(0.0000, 43.0718, 0.000, 21.5359, 8.3873, 29.0230),
10., 'ref5', session6.time)
session6.reflist = (session6.ref1,
session6.ref2,
session6.ref3,
session6.ref4,
session6.ref5,
)
session6.umatrix = (( 0.99411, 0.00079, 0.10835),
( 0.00460, 0.99876, -0.04949),
(-0.10825, 0.04969, 0.99288))
session6.ref1calchkl = (0, 1, 2) # Must match the guessed value!
session6.ref2calchkl = (1, 0, 3)
########################################################################
return (session1, session2, session3, session4, session5, session6)
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