def test_mirror_reflectivity():
rh1 = np.array([
0.97199571, 0.97748356, 0.95360848, 0.92357963, 0.93588329, 0.94249572,
0.94771043, 0.95137756, 0.95416567, 0.95693941, 0.95906606, 0.9606963,
0.96193867, 0.96298571, 0.9637671, 0.96434822, 0.96458685, 0.96443861,
0.963873, 0.96273628, 0.9607325, 0.95705164, 0.94578432, 0.69383757,
0.65937538, 0.57222587, 0.40829232, 0.26919575, 0.18904094, 0.14024917
])
r1 = mirror_reflectivity('Rh', 0.0025, np.arange(1000, 31000, 1000))
assert_allclose(rh1, r1, rtol=0.005)
assert_allclose(mirror_reflectivity('Pt', 0.001, 80000), 0.74, rtol=0.005)
def reflectdata(formula, rho, angle, rough, polar, e1, e2, de, fname):
"""mirror reflectivity data as file"""
en_array = energy_array(e1, e2, de)
angle = float(angle)
rho = float(rho)
rough = float(rough)
reflectivity = xraydb.mirror_reflectivity(formula,
0.001 * angle,
en_array,
rho,
roughness=rough,
polarization=polar)
_del, _bet, _ = xraydb.xray_delta_beta(formula, rho, en_array)
ang_crit = 1000 * (np.pi / 2 - np.arcsin(1 - _del - 1j * _bet)).real
header = (' X-ray reflectivity data from xrayweb %s ' % time.ctime(),
' Material.formula : %s ' % formula,
' Material.density : %.4f gr/cm^3 ' % rho,
' Material.angle : %.4f mrad ' % angle,
' Material.roughness : %.4f Ang ' % rough,
' Material.polarization: %s ' % polar, ' Column.1: energy (eV)',
' Column.2: reflectivity', ' Column.3: critical_angle (mrad)')
arr_names = ('energy ', 'reflectivity ', 'crit_angle ')
txt = make_asciifile(header, arr_names, (en_array, reflectivity, ang_crit))
return Response(txt, mimetype='text/plain')
def reflectdata(formula, rho, angle, rough, polar, e1, e2, estep):
"""mirror reflectivity data as file"""
en_array = np.arange(float(e1), float(e2), float(estep))
angle = float(angle)
rho = float(rho)
rough = float(rough)
reflectivity = xraydb.mirror_reflectivity(formula,
angle,
en_array,
rho,
roughness=rough,
polarization=polar)
header = (' X-ray reflectivity data from xrayweb %s ' % time.ctime(),
' Material.formula : %s ' % formula,
' Material.density : %.3f gr/cm^3 ' % rho,
' Material.angle : %.6f rad ' % angle,
' Material.roughness : %.3f Ang ' % rough,
' Material.polarization: %s ' % polar, ' Column.1: energy (eV)',
' Column.2: reflectivity')
arr_names = ('energy ', 'reflectivity ')
txt = make_asciifile(header, arr_names, (en_array, reflectivity))
fname = 'xrayweb_reflect_%s_%s.txt' % (formula,
time.strftime('%Y%h%d_%H%M%S'))
return Response(
txt,
mimetype='text/plain',
headers={"Content-Disposition": "attachment;filename=%s" % fname})
def reflectdata(formula, rho, angle, rough, polar, e1, e2, estep):
"""mirror reflectivity data as file"""
en_array = np.arange(float(e1), float(e2)+float(estep), float(estep))
angle = float(angle)
rho = float(rho)
rough = float(rough)
reflectivity = xraydb.mirror_reflectivity(formula, 0.001*angle, en_array, rho,
roughness=rough, polarization=polar)
_del, _bet, _ = xraydb.xray_delta_beta(formula, rho, en_array)
ang_crit = 1000*(np.pi/2 - np.arcsin(1 - _del - 1j*_bet)).real
header = (' X-ray reflectivity data from xrayweb %s ' % time.ctime(),
' Material.formula : %s ' % formula,
' Material.density : %.4f gr/cm^3 ' % rho,
' Material.angle : %.4f mrad ' % angle,
' Material.roughness : %.4f Ang ' % rough,
' Material.polarization: %s ' % polar,
' Column.1: energy (eV)',
' Column.2: reflectivity',
' Column.3: crit_angle (mrad)')
arr_names = ('energy ', 'reflectivity ', 'crit_angle ')
txt = make_asciifile(header, arr_names, (en_array, reflectivity, ang_crit))
fname = 'xrayweb_reflect_%s_%s.txt' % (formula,
time.strftime('%Y%h%d_%H%M%S'))
return Response(txt, mimetype='text/plain',
headers={"Content-Disposition":
"attachment;filename=%s" % fname})
import numpy as np
from xraydb import mirror_reflectivity
import matplotlib.pyplot as plt
energy = np.linspace(1000, 51000, 501)
r_si = mirror_reflectivity('Si', 0.002, energy)
r_ni = mirror_reflectivity('Ni', 0.002, energy)
r_rh = mirror_reflectivity('Rh', 0.002, energy)
r_pt = mirror_reflectivity('Pt', 0.002, energy)
plt.plot(energy, r_si, label='Si')
plt.plot(energy, r_ni, label='Ni')
plt.plot(energy, r_rh, label='Rh')
plt.plot(energy, r_pt, label='Pt')
plt.title('X-ray reflectivity at $\\theta=2 \mathrm{mrad}$')
plt.xlabel('Energy (eV)')
plt.ylabel('Reflectivity')
plt.legend()
plt.show()
def reflectivity(material=None):
message = []
ref_plot = angc_plot = {}
has_data = False
de = '50'
if request.method == 'POST':
formula1 = request.form.get('formula1', 'None')
density1 = request.form.get('density1', '')
angle1 = request.form.get('angle1', '0')
material1 = request.form.get('mats1', 'silicon')
e1 = request.form.get('e1', '1000')
e2 = request.form.get('e2', '50000')
de = request.form.get('de', '50')
mode = request.form.get('mode', 'Linear')
roughness = request.form.get('roughness')
polarization = request.form.get('polarization')
if not xraydb.validate_formula(formula1):
message.append("cannot interpret chemical formula")
try:
density = max(0, float(density1))
except:
message.append('Density must be a positive number.')
if len(message) == 0:
has_data = True
en_array = energy_array(e1, e2, de)
use_log = mode.lower() == 'log'
ref_array = xraydb.mirror_reflectivity(formula1,
0.001 * float(angle1),
en_array,
density,
roughness=float(roughness),
polarization=polarization)
title = "%s, %s mrad" % (formula1, angle1)
ref_plot = make_plot(en_array,
ref_array,
title,
formula1,
yformat='.3f',
ytitle='Reflectivity',
ylog_scale=use_log)
title = "%s Reflectivity, %s mrad" % (formula1, angle1)
ref_plot = make_plot(en_array,
ref_array,
title,
formula1,
yformat='.3f',
ytitle='Reflectivity',
ylog_scale=use_log)
_del, _bet, _ = xraydb.xray_delta_beta(formula1, density, en_array)
ang_crit = 1000 * np.arccos(1 - _del - 1j * _bet).real
title = "%s, Critical Angle" % (formula1)
angc_plot = make_plot(en_array,
ang_crit,
title,
formula1,
ytitle='Critical Angle (mrad)',
ylog_scale=use_log)
else:
request.form = {
'mats1': 'silicon',
'formula1': materials_['silicon'].formula,
'density1': materials_['silicon'].density,
'angle1': 2.5,
'mats2': 'None',
'formula2': '',
'density2': '',
'angle2': 2.5,
'e1': 1000,
'e2': 50000,
'de': de,
'polarization': 's',
'roughness': '0',
'mode': 'Linear'
}
return render_template('reflectivity.html',
message=message,
errors=len(message),
ref_plot=ref_plot,
angc_plot=angc_plot,
has_data=has_data,
matlist=mirror_mat,
de=int(de),
materials_dict=materials_dict)
def reflectivity(material=None):
message = ['']
ref_plot = output = {}
energies = reflectivities = []
num = errors = 0
df = ef = ef2 = sf = af = rf = 0
isLog = True
if request.method == 'POST':
#obtain form input and verify
formula = request.form.get('formula')
density = request.form.get('density')
angle = request.form.get('angle')
roughness = request.form.get('roughness')
polarization = request.form.get('polarization')
energy1 = request.form.get('energy1')
energy2 = request.form.get('energy2')
step = request.form.get('step')
mode = request.form.get('mode')
output = validate_input(formula,
density,
step,
energy1,
energy2,
mode,
material,
angle,
roughness,
page='reflectivity')
message = output['message']
else:
request.form = {
'formula': materials_dict['silicon'].formula,
'density': materials_dict['silicon'].density,
'energy1': '1000',
'energy2': '50000',
'step': '100',
'angle': '0.001',
'roughness': '0'
}
#if verification passes, calculate output and pass to render_template
if message[0] == 'Input is valid':
df = output['df']
ef = output['ef']
ef2 = output['ef2']
sf = output['sf']
isLog = output['isLog']
af = output['af']
rf = output['rf']
while ef2 < (
ef + (sf * 2)
): #this ensures that there are always at least 3 energy values for a meaningful plot
ef2 += sf
ef2 += sf #this includes energy2 in the plot, normally np.arrage excludes the upper bound
en_array = np.arange(ef, ef2, sf)
num = en_array.size
ref_array = xraydb.mirror_reflectivity(formula, af, en_array, df, rf,
polarization)
ref_plot = make_plot(en_array,
ref_array,
material,
formula,
ytitle='Reflectivity',
ylog_scale=isLog)
energies = [nformat(x) for x in en_array]
reflectivities = [nformat(x) for x in ref_array]
message = []
else:
errors = len(message)
return render_template('reflectivity.html',
message=message,
errors=errors,
ref_plot=ref_plot,
energies=energies,
reflectivities=reflectivities,
num=num,
matlist=mirror_list,
materials_dict=materials_dict_j)