def main():
if len(sys.argv) < 2:
print >> sys.stderr, "scriptfile not specified."
sys.exit(2)
elif not os.path.isfile(sys.argv[1]):
print >> sys.stderr, "Cannot read %r" % sys.argv[1]
sys.exit(2)
scriptfile = sys.argv[1]
scriptbase = os.path.basename(scriptfile)
del sys.argv[1]
box = PdfFitSandbox()
try:
box.loadscript(scriptfile)
except:
exc_type, exc_value, exc_tb = sys.exc_info()
import traceback
for filename, lineno, fnc, line in traceback.extract_tb(exc_tb):
if os.path.basename(filename) != scriptbase:
continue
print >> sys.stderr, "%s:%i:%s" % (scriptfile, lineno, line)
print >> sys.stderr, exc_value
sys.exit(1)
# make sure reading from stderr will not hang, see
# http://www.python.org/doc/current/lib/popen2-flow-control.html
os.close(sys.stderr.fileno())
# all is ready, dump it
sys.stdout.write(safeCPickleDumps(box.allfits()))
return
def main():
if len(sys.argv) < 2:
print >> sys.stderr, "scriptfile not specified."
sys.exit(2)
elif not os.path.isfile(sys.argv[1]):
print >> sys.stderr, "Cannot read %r" % sys.argv[1]
sys.exit(2)
scriptfile = sys.argv[1]
scriptbase = os.path.basename(scriptfile)
del sys.argv[1]
box = PdfFitSandbox()
try:
box.loadscript(scriptfile)
except:
exc_type, exc_value, exc_tb = sys.exc_info()
import traceback
for filename, lineno, fnc, line in traceback.extract_tb(exc_tb):
if os.path.basename(filename) != scriptbase:
continue
print >> sys.stderr, "%s:%i:%s" % (scriptfile, lineno, line)
print >> sys.stderr, exc_value
sys.exit(1)
# make sure reading from stderr will not hang, see
# http://www.python.org/doc/current/lib/popen2-flow-control.html
os.close(sys.stderr.fileno())
# all is ready, dump it
sys.stdout.write( safeCPickleDumps(box.allfits()) )
return
def setUp(self):
from diffpy.pdfgui.control.pdffitsandbox import PdfFitSandbox
self.box = PdfFitSandbox()
return
class TestPdfFitSandbox(unittest.TestCase):
"""test methods of PdfFitSandbox"""
def setUp(self):
from diffpy.pdfgui.control.pdffitsandbox import PdfFitSandbox
self.box = PdfFitSandbox()
return
def tearDown(self):
import cPickle
cPickle.dumps(self.box)
return
def test___init__(self):
"""check PdfFitSandbox.__init__()
"""
# check if the first fit gets defined
self.assertEqual(1, len(self.box._fits))
f0 = self.box._fits[0]
self.assertEqual('0', f0.name)
# check string aliases
sandbox = self.box.sandbox()
self.assertEqual('X', eval("X", sandbox))
self.assertEqual('ALL', eval("ALL", sandbox))
self.assertEqual(None, self.box._curdataset)
self.assertEqual(None, self.box._curphase)
return
def test_allfits(self):
"""check PdfFitSandbox.allfits()
"""
self.assertEqual(0, len(self.box.allfits()))
fNi_stru = datafile('Ni.stru')
self.box.read_struct(fNi_stru)
self.assertEqual(0, len(self.box.allfits()))
self.box.refine()
self.assertEqual(1, len(self.box.allfits()))
return
def test_read_struct(self):
"""check PdfFitSandbox.read_struct()
"""
fNi_stru = datafile('Ni.stru')
f300K_stru = datafile('300K.stru')
self.box.read_struct(fNi_stru)
self.box.read_struct(f300K_stru)
self.assertEqual(2, len(self.box._fits[-1].strucs))
self.assertEqual(1, self.box._curphase)
p0 = self.box._fits[-1].strucs[0]
p1 = self.box._fits[-1].strucs[1]
self.assertEqual(4, len(p0))
self.assertEqual('Ni', p0.name)
self.assertEqual(20, len(p1))
self.assertEqual('300K', p1.name)
self.assertEqual(None, self.box._curdataset)
return
def test_read_struct_string(self):
"""check PdfFitSandbox.read_struct_string()
"""
fNi_stru = datafile('Ni.stru')
f300K_stru = datafile('300K.stru')
sNi = open(fNi_stru).read()
s300K = open(f300K_stru).read()
self.box.read_struct_string(sNi)
self.box.read_struct_string(s300K, 'LaMnO3 at 300K')
self.assertEqual(2, len(self.box._fits[-1].strucs))
self.assertEqual(1, self.box._curphase)
p0 = self.box._fits[-1].strucs[0]
p1 = self.box._fits[-1].strucs[1]
self.assertEqual(4, len(p0))
self.assertEqual('', p0.name)
self.assertEqual(20, len(p1))
self.assertEqual('LaMnO3 at 300K', p1.name)
self.assertEqual(None, self.box._curdataset)
return
def test_read_data(self):
"""check PdfFitSandbox.read_data()
"""
fNi_data = datafile("Ni_2-8.chi.gr")
f300K_data = datafile("300K.gr")
sandbox = self.box.sandbox()
sandbox.update({"fNi_data": fNi_data, "f300K_data": f300K_data})
exec "read_data(fNi_data, X, 40.1, 0.05)" in sandbox
exec "read_data(f300K_data, N, 32.1, 0.05)" in sandbox
self.assertEqual(2, len(self.box._fits[-1].datasets))
self.assertEqual(1, self.box._curdataset)
d0 = self.box._fits[-1].datasets[0]
self.assertEqual('Ni_2-8.chi', d0.name)
self.assertEqual('X', d0.stype)
self.assertAlmostEqual(40.1, d0.qmax, 8)
self.assertAlmostEqual(0.05, d0.qdamp, 8)
self.assertEqual(2000, len(d0.robs))
d1 = self.box._fits[-1].datasets[1]
self.assertEqual('300K', d1.name)
self.assertEqual('N', d1.stype)
self.assertAlmostEqual(32.1, d1.qmax, 8)
self.assertAlmostEqual(0.05, d1.qdamp, 8)
self.assertEqual(2000, len(d1.robs))
self.assertEqual(None, self.box._curphase)
return
def test_read_data_string(self):
"""check PdfFitSandbox.read_data_string()
"""
fNi_data = datafile("Ni_2-8.chi.gr")
f300K_data = datafile("300K.gr")
sNi = open(fNi_data).read()
s300K = open(f300K_data).read()
sandbox = self.box.sandbox()
sandbox.update({"sNi": sNi, "s300K": s300K})
exec "read_data_string(sNi, X, 40.1, 0.05)" in sandbox
exec "read_data_string(s300K, N, 32.1, 0.05, 'LaMnO3')" in sandbox
self.assertEqual(2, len(self.box._fits[-1].datasets))
self.assertEqual(1, self.box._curdataset)
d0 = self.box._fits[-1].datasets[0]
self.assertEqual('', d0.name)
self.assertEqual('X', d0.stype)
self.assertAlmostEqual(40.1, d0.qmax, 8)
self.assertAlmostEqual(0.05, d0.qdamp, 8)
self.assertEqual(2000, len(d0.robs))
d1 = self.box._fits[-1].datasets[1]
self.assertEqual('LaMnO3', d1.name)
self.assertEqual('N', d1.stype)
self.assertAlmostEqual(32.1, d1.qmax, 8)
self.assertAlmostEqual(0.05, d1.qdamp, 8)
self.assertEqual(2000, len(d1.robs))
self.assertEqual(None, self.box._curphase)
return
def test_read_data_lists(self):
"""check PdfFitSandbox.read_data_lists()
"""
self.assertRaises(NotImplementedError, self.box.read_data_lists, 'X',
40.1, 0.05, [], [])
return
def test_pdfrange(self):
"""check PdfFitSandbox.pdfrange()
"""
fNi_data = datafile("Ni_2-8.chi.gr")
f300K_data = datafile("300K.gr")
self.box.read_data(fNi_data, 'X', 40.1, 0.05)
self.box.read_data(f300K_data, 'N', 32.1, 0.05)
sandbox = self.box.sandbox()
exec "pdfrange(1, 2.3, 11.13)" in sandbox
exec "pdfrange(2, 5.7, 17.19)" in sandbox
self.assertEqual(2, len(self.box._fits[-1].datasets))
d0 = self.box._fits[-1].datasets[0]
d1 = self.box._fits[-1].datasets[1]
self.assertAlmostEqual(2.3, d0.fitrmin, 8)
self.assertAlmostEqual(11.13, d0.fitrmax, 8)
self.assertAlmostEqual(5.7, d1.fitrmin, 8)
self.assertAlmostEqual(17.19, d1.fitrmax, 8)
# exceptions for invalid ranges
self.assertRaises(ControlRuntimeError, self.box.pdfrange, 1, 10, 1)
self.assertRaises(ControlRuntimeError, self.box.pdfrange, 1, 0, 10)
self.assertRaises(ControlRuntimeError, self.box.pdfrange, 1, 1, 1000)
exec "pdfrange(ALL, 1.0, 7.0)" in sandbox
self.assertEqual(1.0, d0.fitrmin)
self.assertEqual(7.0, d0.fitrmax)
self.assertEqual(1.0, d1.fitrmin)
self.assertEqual(7.0, d1.fitrmax)
exec "pdfrange('ALL', 2.0, 9.0)" in sandbox
self.assertEqual(2.0, d0.fitrmin)
self.assertEqual(9.0, d0.fitrmax)
self.assertEqual(2.0, d1.fitrmin)
self.assertEqual(9.0, d1.fitrmax)
return
def test_reset(self):
"""check PdfFitSandbox.reset()
"""
fNi_stru = datafile('Ni.stru')
fNi_data = datafile("Ni_2-8.chi.gr")
sandbox = self.box.sandbox()
sandbox.update({"fNi_stru": fNi_stru, "fNi_data": fNi_data})
exec "read_data(fNi_data, X, 40.1, 0.05)" in sandbox
exec "read_struct(fNi_stru)" in sandbox
self.assertEqual(1, len(self.box._fits))
self.assertEqual(1, len(self.box._fits[-1].strucs))
self.assertEqual(1, len(self.box._fits[-1].datasets))
self.assertEqual(0, self.box._curdataset)
self.assertEqual(0, self.box._curphase)
exec "reset()" in sandbox
self.assertEqual(1, len(self.box._fits))
self.assertEqual(0, len(self.box._fits[-1].strucs))
self.assertEqual(0, len(self.box._fits[-1].datasets))
self.assertEqual(None, self.box._curdataset)
self.assertEqual(None, self.box._curphase)
return
def test_alloc(self):
"""check PdfFitSandbox.alloc()
"""
from diffpy.pdfgui.control.calculation import Calculation
from diffpy.pdfgui.control.fitting import Fitting
fNi_stru = datafile('Ni.stru')
sandbox = self.box.sandbox()
sandbox.update({"fNi_stru": fNi_stru})
exec "read_struct(fNi_stru)" in sandbox
self.assertEqual(1, len(self.box._fits))
self.assertEqual(1, len(self.box._fits[-1].strucs))
self.assertEqual(0, len(self.box._fits[-1].datasets))
self.assertTrue(isinstance(self.box._fits[-1], Fitting))
exec "alloc(N, 37.0, 0.07, 0.01, 10.0, 1000)" in sandbox
self.assertEqual(1, len(self.box._fits))
self.assertEqual(1, len(self.box._fits[-1].strucs))
self.assertTrue(isinstance(self.box._fits[-1], Calculation))
c = self.box._fits[-1]
self.assertEqual(37.0, c.qmax)
self.assertEqual(0.07, c.qdamp)
self.assertEqual(0.01, c.rmin)
self.assertAlmostEqual(0.01, c.rstep, 8)
self.assertAlmostEqual(10.0, c.rmax, 8)
self.assertEqual(1000, c.rlen)
return
def test_calc(self):
"""check PdfFitSandbox.calc()
"""
from diffpy.pdfgui.control.calculation import Calculation
fNi_stru = datafile('Ni.stru')
sandbox = self.box.sandbox()
sandbox.update({"fNi_stru": fNi_stru})
exec "read_struct(fNi_stru)" in sandbox
self.assertRaises(ControlRuntimeError, self.box.calc)
exec "alloc(N, 37.0, 0.07, 0.01, 10.0, 1000)" in sandbox
self.assertEqual(1, len(self.box._fits))
exec "calc()" in sandbox
self.assertTrue(isinstance(self.box._fits[0], Calculation))
self.assertEqual(2, len(self.box._fits))
self.assertEqual(0, len(self.box._fits[-1].datasets))
self.assertEqual(0, len(self.box._fits[-1].strucs))
self.assertEqual(None, self.box._curdataset)
self.assertEqual(None, self.box._curphase)
return
def test_refine(self):
"""check PdfFitSandbox.refine()
"""
fNi_stru = datafile('Ni.stru')
fNi_data = datafile("Ni_2-8.chi.gr")
sandbox = self.box.sandbox()
sandbox.update({"fNi_stru": fNi_stru, "fNi_data": fNi_data})
exec "read_data(fNi_data, X, 40.1, 0.05)" in sandbox
exec "read_struct(fNi_stru)" in sandbox
exec "refine()" in sandbox
self.assertEqual(2, len(self.box._fits))
self.assertEqual(1, len(self.box._fits[0].strucs))
self.assertEqual(1, len(self.box._fits[0].datasets))
self.assertEqual(1, len(self.box._fits[1].strucs))
self.assertEqual(1, len(self.box._fits[1].datasets))
# check fit linking:
self.box._fits[-1].parameters[1] = Parameter(1, 0.05)
exec "refine(0.01)" in sandbox
self.assertEqual(3, len(self.box._fits))
names = [f.name for f in self.box._fits]
self.assertEqual('0', names[0])
self.assertEqual('1', names[1])
self.assertEqual('2', names[2])
self.assertEqual(0, self.box._curdataset)
self.assertEqual(0, self.box._curphase)
s = self.box._fits[-1].parameters[1].initialStr()
self.assertEqual("=1:1", s)
return
def test_refine_step(self):
"""check PdfFitSandbox.refine_step()
"""
self.assertRaises(NotImplementedError, self.box.refine_step)
self.assertRaises(NotImplementedError, self.box.refine_step, 0.01)
return
def test_save_pdf(self):
"""check PdfFitSandbox.save_pdf()
"""
sandbox = self.box.sandbox()
exec 'save_pdf(1, "filename.fgr")' in sandbox
return
def test_save_pdf_string(self):
"""check PdfFitSandbox.save_pdf_string()
"""
self.assertRaises(NotImplementedError, self.box.save_pdf_string, 1)
return
def test_save_dif(self):
"""check PdfFitSandbox.save_dif()
"""
sandbox = self.box.sandbox()
exec 'save_dif(1, "filename.diff")' in sandbox
return
def test_save_dif_string(self):
"""check PdfFitSandbox.save_dif_string()
"""
self.assertRaises(NotImplementedError, self.box.save_dif_string, 1)
return
def test_save_res(self):
"""check PdfFitSandbox.save_res()
"""
sandbox = self.box.sandbox()
exec 'save_res("filename.res")' in sandbox
return
def test_save_res_string(self):
"""check PdfFitSandbox.save_res_string()
"""
self.assertRaises(NotImplementedError, self.box.save_res_string)
return
def test_save_struct(self):
"""check PdfFitSandbox.save_struct()
"""
sandbox = self.box.sandbox()
exec 'save_struct(1, "filename.rstr")' in sandbox
return
def test_save_struct_string(self):
"""check PdfFitSandbox.save_struct_string()
"""
self.assertRaises(NotImplementedError, self.box.save_struct_string, 1)
return
def test_show_struct(self):
"""check PdfFitSandbox.show_struct()
"""
sandbox = self.box.sandbox()
exec 'show_struct(1)' in sandbox
return
def test_constrain(self):
"""check PdfFitSandbox.constrain()
"""
sandbox = self.box.sandbox()
self.assertRaises(ControlKeyError, self.box.constrain, 'delta', 1)
fNi_stru = datafile('Ni.stru')
self.box.read_struct(fNi_stru)
exec 'constrain(delta, 1)' in sandbox
self.assertRaises(ControlKeyError, self.box.constrain, 'qdamp', 10)
fNi_data = datafile("Ni_2-8.chi.gr")
self.box.read_data(fNi_data, "X", 40.1, 0.05)
exec 'constrain(qdamp, 10)' in sandbox
exec 'constrain(dscale, 2)' in sandbox
exec 'constrain(lat(1), 3)' in sandbox
exec 'constrain(lat(2), 3)' in sandbox
exec 'constrain(lat(3), "@3")' in sandbox
exec 'constrain(occ(1), 4)' in sandbox
exec 'constrain(pfrac, 5)' in sandbox
exec 'constrain(u11(1), 6)' in sandbox
exec 'constrain(u22(1), 6)' in sandbox
exec 'constrain(u33(1), 6)' in sandbox
exec 'constrain(x(1), "@7+0.5")' in sandbox
cphase = self.box._fits[-1].strucs[self.box._curphase]
cdataset = self.box._fits[-1].datasets[self.box._curdataset]
self.assertEqual(10, len(cphase.constraints))
self.assertTrue('pscale' in cphase.constraints)
self.assertEqual('@6', cphase.constraints['u11(1)'].formula)
self.assertEqual('@7+0.5', cphase.constraints['x(1)'].formula)
self.assertEqual(2, len(cdataset.constraints))
self.assertEqual('@10', cdataset.constraints['qdamp'].formula)
exec 'constrain(x(2), 21, IDENT)' in sandbox
exec 'constrain(y(2), 22, FCOMP)' in sandbox
exec 'constrain(z(2), 23, FSQR)' in sandbox
self.assertEqual('@21', cphase.constraints['x(2)'].formula)
self.assertEqual('1.0-@22', cphase.constraints['y(2)'].formula)
self.assertEqual('@23*@23', cphase.constraints['z(2)'].formula)
return
def test_constrain_calculation(self):
"""check exceptions when attempting to constrain Calculation
"""
fNi_stru = datafile('Ni.stru')
sandbox = self.box.sandbox()
sandbox.update({"fNi_stru": fNi_stru})
exec "read_struct(fNi_stru)" in sandbox
exec "alloc(N, 37.0, 0.07, 0.01, 10.0, 1000)" in sandbox
self.assertRaises(ControlRuntimeError, self.box.constrain, 'delta', 1)
self.assertRaises(ControlRuntimeError, self.box.constrain, 'qdamp',
"@3*@3")
self.assertRaises(ControlRuntimeError, self.box.constrain, 'delta', 1,
'FCOMP')
return
def test_setpar(self):
"""check PdfFitSandbox.setpar()
"""
sandbox = self.box.sandbox()
curfit = self.box._fits[-1]
self.box.setpar(1, 5.0)
self.assertEqual(5.0, curfit.parameters[1].initialValue())
fNi_stru = datafile('Ni.stru')
fNi_data = datafile("Ni_2-8.chi.gr")
self.box.read_struct(fNi_stru)
self.box.read_data(fNi_data, "X", 40.1, 0.05)
exec 'constrain(dscale, 1)' in sandbox
exec 'constrain(lat(1), 3)' in sandbox
exec 'constrain(lat(2), 3)' in sandbox
exec 'constrain(lat(3), "@3")' in sandbox
exec 'setpar(1, 1.25)' in sandbox
exec 'setpar(3, 4.1)' in sandbox
self.assertEqual(1.25, curfit.parameters[1].initialValue())
self.assertEqual(4.1, curfit.parameters[3].initialValue())
exec 'setpar(1, dscale)' in sandbox
exec 'setpar(3, lat(1))' in sandbox
dscale = curfit.datasets[self.box._curdataset].dscale
a = curfit.strucs[self.box._curphase].lattice.a
self.assertEqual(dscale, curfit.parameters[1].initialValue())
self.assertEqual(a, curfit.parameters[3].initialValue())
return
def test_getpar(self):
"""check PdfFitSandbox.getpar()
"""
sandbox = self.box.sandbox()
curfit = self.box._fits[-1]
self.box.setpar(1, 5.0)
self.assertEqual(5.0, eval('getpar(1)', sandbox))
fNi_stru = datafile('Ni.stru')
fNi_data = datafile("Ni_2-8.chi.gr")
self.box.read_struct(fNi_stru)
self.box.read_data(fNi_data, "X", 40.1, 0.05)
exec 'setpar(1, dscale)' in sandbox
exec 'setpar(3, lat(1))' in sandbox
self.assertEqual(1.0, eval('getpar(1)', sandbox))
curphase = curfit.strucs[self.box._curphase]
a = curphase.lattice.a
self.assertEqual(a, eval('getpar(3)', sandbox))
return
def test_fixpar(self):
"""check PdfFitSandbox.fixpar()
"""
sandbox = self.box.sandbox()
curfit = self.box._fits[-1]
for i in range(1, 4):
curfit.parameters[i] = Parameter(i, 1.0 * i)
exec 'fixpar(1)' in sandbox
self.assertEqual(True, curfit.parameters[1].fixed)
self.assertEqual(False, curfit.parameters[2].fixed)
self.assertEqual(False, curfit.parameters[3].fixed)
exec 'fixpar(ALL)' in sandbox
self.assertEqual(True, curfit.parameters[1].fixed)
self.assertEqual(True, curfit.parameters[2].fixed)
self.assertEqual(True, curfit.parameters[3].fixed)
self.assertRaises(ControlKeyError, self.box.fixpar, 77)
return
def test_freepar(self):
"""check PdfFitSandbox.freepar()
"""
sandbox = self.box.sandbox()
curfit = self.box._fits[-1]
for i in range(1, 4):
curfit.parameters[i] = Parameter(i, 1.0 * i)
curfit.parameters[i].fixed = True
exec 'freepar(1)' in sandbox
self.assertEqual(False, curfit.parameters[1].fixed)
self.assertEqual(True, curfit.parameters[2].fixed)
self.assertEqual(True, curfit.parameters[3].fixed)
exec 'freepar(ALL)' in sandbox
self.assertEqual(False, curfit.parameters[1].fixed)
self.assertEqual(False, curfit.parameters[2].fixed)
self.assertEqual(False, curfit.parameters[3].fixed)
self.assertRaises(ControlKeyError, self.box.freepar, 77)
return
def test_setvar(self):
"""check PdfFitSandbox.setvar()
"""
sandbox = self.box.sandbox()
fNi_stru = datafile('Ni.stru')
fNi_data = datafile("Ni_2-8.chi.gr")
self.box.read_struct(fNi_stru)
self.box.read_data(fNi_data, "X", 40.1, 0.05)
curfit = self.box._fits[-1]
curdataset = curfit.datasets[self.box._curdataset]
curphase = curfit.strucs[self.box._curphase]
self.assertEqual(40.1, curdataset.qmax)
exec "setvar(qdamp, 0.007)" in sandbox
exec "setvar(lat(1), 3.75)" in sandbox
exec "setvar(x(4), 0.123)" in sandbox
exec "setvar(u13(1), 0.00123)" in sandbox
exec "setvar('pscale', 0.97)" in sandbox
self.assertEqual(0.007, curdataset.qdamp)
self.assertEqual(3.75, curphase.lattice.a)
self.assertEqual(0.123, curphase[3].xyz[0])
self.assertEqual(0.00123, curphase[0].U[0, 2])
self.assertEqual(0.00123, curphase[0].U[2, 0])
self.assertEqual(0.97, curphase.pdffit['scale'])
self.assertRaises(ControlKeyError, self.box.setvar, 'novar', 0.1)
return
def test_getvar(self):
"""check PdfFitSandbox.getvar()
"""
sandbox = self.box.sandbox()
f300K_stru = datafile('300K.stru')
f300K_data = datafile("300K.gr")
sandbox.update({"f300K_stru": f300K_stru, "f300K_data": f300K_data})
exec "read_data(f300K_data, 'N', 32.1, 0.05)" in sandbox
exec "read_struct(f300K_stru)" in sandbox
self.assertEqual(0.05, eval("getvar(qdamp)", sandbox))
self.assertEqual(1.0, eval("getvar('dscale')", sandbox))
self.assertEqual(1.0, eval("getvar(dscale)", sandbox))
self.assertAlmostEqual(0.95182216, eval("getvar(y(3))", sandbox), 8)
self.assertAlmostEqual(0.00475572, eval("getvar(u22(4))", sandbox), 8)
self.assertRaises(ControlKeyError, self.box.getvar, 'novar')
return
def test_getrw(self):
"""check PdfFitSandbox.getrw()
"""
self.assertRaises(NotImplementedError, self.box.getrw)
return
def test_getR(self):
"""check PdfFitSandbox.getR()
"""
self.assertRaises(NotImplementedError, self.box.getR)
return
def test_getpdf_fit(self):
"""check PdfFitSandbox.getpdf_fit()
"""
self.assertRaises(NotImplementedError, self.box.getpdf_fit)
return
def test_getpdf_obs(self):
"""check PdfFitSandbox.getpdf_obs()
"""
self.assertRaises(NotImplementedError, self.box.getpdf_obs)
return
def test_get_atoms(self):
"""check PdfFitSandbox.get_atoms()
"""
self.assertRaises(NotImplementedError, self.box.get_atoms)
return
def test_setphase(self):
"""check PdfFitSandbox.setphase()
"""
sandbox = self.box.sandbox()
fNi_stru = datafile('Ni.stru')
f300K_stru = datafile('300K.stru')
self.assertEqual(None, self.box._curphase)
self.box.read_struct(fNi_stru)
self.assertEqual(0, self.box._curphase)
self.box.read_struct(f300K_stru)
self.assertEqual(1, self.box._curphase)
self.assertEqual(20, eval("num_atoms()", sandbox))
exec "setphase(1)" in sandbox
self.assertEqual(0, self.box._curphase)
self.assertEqual(4, eval("num_atoms()", sandbox))
exec "setphase(2)" in sandbox
self.assertEqual(1, self.box._curphase)
self.assertEqual(20, eval("num_atoms()", sandbox))
self.assertRaises(IndexError, self.box.setphase, 3)
return
def test_setdata(self):
"""check PdfFitSandbox.setdata()
"""
sandbox = self.box.sandbox()
fNi_data = datafile("Ni_2-8.chi.gr")
f300K_data = datafile("300K.gr")
self.assertEqual(None, self.box._curdataset)
self.box.read_data(fNi_data, "X", 40.1, 0.05)
self.assertEqual(0, self.box._curdataset)
self.box.read_data(f300K_data, 'N', 32.1, 0.07)
self.assertEqual(1, self.box._curdataset)
self.assertEqual(0.07, eval("getvar('qdamp')", sandbox))
exec "setdata(1)" in sandbox
self.assertEqual(0, self.box._curdataset)
self.assertEqual(0.05, eval("getvar('qdamp')", sandbox))
exec "setdata(2)" in sandbox
self.assertEqual(1, self.box._curdataset)
self.assertEqual(0.07, eval("getvar('qdamp')", sandbox))
self.assertRaises(IndexError, self.box.setdata, 3)
return
def test_psel(self):
"""check PdfFitSandbox.psel()
"""
self.assertRaises(NotImplementedError, self.box.psel, 1)
return
def test_pdesel(self):
"""check PdfFitSandbox.pdesel()
"""
self.assertRaises(NotImplementedError, self.box.pdesel, 1)
return
def test_isel(self):
"""check PdfFitSandbox.isel()
"""
self.assertRaises(NotImplementedError, self.box.isel, 1, 1)
return
def test_idesel(self):
"""check PdfFitSandbox.idesel()
"""
self.assertRaises(NotImplementedError, self.box.idesel, 1, 1)
return
def test_jsel(self):
"""check PdfFitSandbox.jsel()
"""
self.assertRaises(NotImplementedError, self.box.jsel, 1, 1)
return
def test_jdesel(self):
"""check PdfFitSandbox.jdesel()
"""
self.assertRaises(NotImplementedError, self.box.jdesel, 1, 1)
return
def test_bang(self):
"""check PdfFitSandbox.bang()
"""
self.assertRaises(NotImplementedError, self.box.bang, 1, 2, 3)
return
def test_blen(self):
"""check PdfFitSandbox.blen()
"""
sandbox = self.box.sandbox()
exec 'blen(1, 2)' in sandbox
exec 'blen(1, 1, 1.5, 5.0)' in sandbox
exec 'blen(1, 2, 1.5, 5.0)' in sandbox
return
def test_show_scat(self):
"""check PdfFitSandbox.show_scat()
"""
sandbox = self.box.sandbox()
exec 'show_scat("X")' in sandbox
return
def test_show_scat_string(self):
"""check PdfFitSandbox.show_scat_string()
"""
self.assertRaises(NotImplementedError, self.box.show_scat_string, 'X')
return
def test_get_scat(self):
"""check PdfFitSandbox.get_scat()
"""
self.assertRaises(NotImplementedError, self.box.get_scat)
return
def test_set_scat(self):
"""check PdfFitSandbox.set_scat()
"""
self.assertRaises(NotImplementedError, self.box.set_scat)
return
def test_reset_scat(self):
"""check PdfFitSandbox.reset_scat()
"""
self.assertRaises(NotImplementedError, self.box.reset_scat)
return
def test_num_atoms(self):
"""check PdfFitSandbox.num_atoms()
"""
self.assertRaises(ControlKeyError, self.box.num_atoms)
sandbox = self.box.sandbox()
fNi_stru = datafile('Ni.stru')
self.box.read_struct(fNi_stru)
self.assertEqual(4, eval('num_atoms()', sandbox))
return
def test_lat(self):
"""check PdfFitSandbox.lat()
"""
sandbox = self.box.sandbox()
self.assertEqual('lat(1)', eval('lat(1)', sandbox))
self.assertEqual('lat(2)', eval('lat(2)', sandbox))
self.assertEqual('lat(3)', eval('lat(3)', sandbox))
self.assertEqual('lat(4)', eval('lat(4)', sandbox))
self.assertEqual('lat(5)', eval('lat(5)', sandbox))
self.assertEqual('lat(6)', eval('lat(6)', sandbox))
self.box.lat(7)
return
def test_x(self):
"""check PdfFitSandbox.x()
"""
sandbox = self.box.sandbox()
self.assertEqual('x(1)', eval('x(1)', sandbox))
return
def test_y(self):
"""check PdfFitSandbox.y()
"""
sandbox = self.box.sandbox()
self.assertEqual('y(1)', eval('y(1)', sandbox))
return
def test_z(self):
"""check PdfFitSandbox.z()
"""
sandbox = self.box.sandbox()
self.assertEqual('z(1)', eval('z(1)', sandbox))
return
def test_u11(self):
"""check PdfFitSandbox.u11()
"""
sandbox = self.box.sandbox()
self.assertEqual('u11(1)', eval('u11(1)', sandbox))
return
def test_u22(self):
"""check PdfFitSandbox.u22()
"""
sandbox = self.box.sandbox()
self.assertEqual('u22(1)', eval('u22(1)', sandbox))
return
def test_u33(self):
"""check PdfFitSandbox.u33()
"""
sandbox = self.box.sandbox()
self.assertEqual('u33(1)', eval('u33(1)', sandbox))
return
def test_u12(self):
"""check PdfFitSandbox.u12()
"""
sandbox = self.box.sandbox()
self.assertEqual('u12(1)', eval('u12(1)', sandbox))
return
def test_u13(self):
"""check PdfFitSandbox.u13()
"""
sandbox = self.box.sandbox()
self.assertEqual('u13(1)', eval('u13(1)', sandbox))
return
def test_u23(self):
"""check PdfFitSandbox.u23()
"""
sandbox = self.box.sandbox()
self.assertEqual('u23(1)', eval('u23(1)', sandbox))
return
def test_occ(self):
"""check PdfFitSandbox.occ()
"""
sandbox = self.box.sandbox()
self.assertEqual('occ(1)', eval('occ(1)', sandbox))
return
def test_pscale(self):
"""check PdfFitSandbox.pscale()
"""
sandbox = self.box.sandbox()
self.assertEqual('pscale', eval('pscale()', sandbox))
return
def test_pfrac(self):
"""check PdfFitSandbox.pfrac()
"""
sandbox = self.box.sandbox()
self.assertEqual('pscale', eval('pfrac()', sandbox))
return
def test_spdiameter(self):
"""check PdfFitSandbox.spdiameter()
"""
sandbox = self.box.sandbox()
self.assertEqual('spdiameter', eval('spdiameter()', sandbox))
return
def test_stepcut(self):
"""check PdfFitSandbox.stepcut()
"""
sandbox = self.box.sandbox()
self.assertEqual('stepcut', eval('stepcut()', sandbox))
return
def test_sratio(self):
"""check PdfFitSandbox.sratio() and PdfFitSandbox.srat()
"""
sandbox = self.box.sandbox()
self.assertEqual('sratio', eval('sratio()', sandbox))
self.assertEqual('sratio', eval('srat()', sandbox))
return
def test_delta1(self):
"""check PdfFitSandbox.delta1() and PdfFitSandbox.gamma()
"""
sandbox = self.box.sandbox()
self.assertEqual('delta1', eval('delta1()', sandbox))
self.assertEqual('delta1', eval('gamma()', sandbox))
return
def test_delta2(self):
"""check PdfFitSandbox.delta2() and PdfFitSandbox.delta()
"""
sandbox = self.box.sandbox()
self.assertEqual('delta2', eval('delta2()', sandbox))
self.assertEqual('delta2', eval('delta()', sandbox))
return
def test_dscale(self):
"""check PdfFitSandbox.dscale()
"""
sandbox = self.box.sandbox()
self.assertEqual('dscale', eval('dscale()', sandbox))
return
def test_qdamp(self):
"""check PdfFitSandbox.qdamp() and PdfFitSandbox.qsig()
"""
sandbox = self.box.sandbox()
self.assertEqual('qdamp', eval('qdamp()', sandbox))
self.assertEqual('qdamp', eval('qsig()', sandbox))
return
def test_qbroad(self):
"""check PdfFitSandbox.qbroad() and PdfFitSandbox.qalp()
"""
sandbox = self.box.sandbox()
self.assertEqual('qbroad', eval('qbroad()', sandbox))
self.assertEqual('qbroad', eval('qalp()', sandbox))
return
def test_rcut(self):
"""check PdfFitSandbox.rcut()
"""
sandbox = self.box.sandbox()
self.assertEqual('rcut', eval('rcut()', sandbox))
return
def setUp(self):
from diffpy.pdfgui.control.pdffitsandbox import PdfFitSandbox
self.box = PdfFitSandbox()
return
class TestPdfFitSandbox(unittest.TestCase):
"""test methods of PdfFitSandbox"""
def setUp(self):
from diffpy.pdfgui.control.pdffitsandbox import PdfFitSandbox
self.box = PdfFitSandbox()
return
def tearDown(self):
import cPickle
cPickle.dumps(self.box)
return
def test___init__(self):
"""check PdfFitSandbox.__init__()
"""
# check if the first fit gets defined
self.assertEqual(1, len(self.box._fits))
f0 = self.box._fits[0]
self.assertEqual('0', f0.name)
# check string aliases
sandbox = self.box.sandbox()
self.assertEqual('X', eval("X", sandbox))
self.assertEqual('ALL', eval("ALL", sandbox))
self.assertEqual(None, self.box._curdataset)
self.assertEqual(None, self.box._curphase)
return
def test_allfits(self):
"""check PdfFitSandbox.allfits()
"""
self.assertEqual(0, len(self.box.allfits()))
fNi_stru = datafile('Ni.stru')
self.box.read_struct(fNi_stru)
self.assertEqual(0, len(self.box.allfits()))
self.box.refine()
self.assertEqual(1, len(self.box.allfits()))
return
def test_read_struct(self):
"""check PdfFitSandbox.read_struct()
"""
fNi_stru = datafile('Ni.stru')
f300K_stru = datafile('300K.stru')
self.box.read_struct(fNi_stru)
self.box.read_struct(f300K_stru)
self.assertEqual(2, len(self.box._fits[-1].strucs))
self.assertEqual(1, self.box._curphase)
p0 = self.box._fits[-1].strucs[0]
p1 = self.box._fits[-1].strucs[1]
self.assertEqual(4, len(p0))
self.assertEqual('Ni', p0.name)
self.assertEqual(20, len(p1))
self.assertEqual('300K', p1.name)
self.assertEqual(None, self.box._curdataset)
return
def test_read_struct_string(self):
"""check PdfFitSandbox.read_struct_string()
"""
fNi_stru = datafile('Ni.stru')
f300K_stru = datafile('300K.stru')
sNi = open(fNi_stru).read()
s300K = open(f300K_stru).read()
self.box.read_struct_string(sNi)
self.box.read_struct_string(s300K, 'LaMnO3 at 300K')
self.assertEqual(2, len(self.box._fits[-1].strucs))
self.assertEqual(1, self.box._curphase)
p0 = self.box._fits[-1].strucs[0]
p1 = self.box._fits[-1].strucs[1]
self.assertEqual(4, len(p0))
self.assertEqual('', p0.name)
self.assertEqual(20, len(p1))
self.assertEqual('LaMnO3 at 300K', p1.name)
self.assertEqual(None, self.box._curdataset)
return
def test_read_data(self):
"""check PdfFitSandbox.read_data()
"""
fNi_data = datafile("Ni_2-8.chi.gr")
f300K_data = datafile("300K.gr")
sandbox = self.box.sandbox()
sandbox.update({ "fNi_data" : fNi_data, "f300K_data" : f300K_data })
exec "read_data(fNi_data, X, 40.1, 0.05)" in sandbox
exec "read_data(f300K_data, N, 32.1, 0.05)" in sandbox
self.assertEqual(2, len(self.box._fits[-1].datasets))
self.assertEqual(1, self.box._curdataset)
d0 = self.box._fits[-1].datasets[0]
self.assertEqual('Ni_2-8.chi', d0.name)
self.assertEqual('X', d0.stype)
self.assertAlmostEqual(40.1, d0.qmax, 8)
self.assertAlmostEqual(0.05, d0.qdamp, 8)
self.assertEqual(2000, len(d0.robs))
d1 = self.box._fits[-1].datasets[1]
self.assertEqual('300K', d1.name)
self.assertEqual('N', d1.stype)
self.assertAlmostEqual(32.1, d1.qmax, 8)
self.assertAlmostEqual(0.05, d1.qdamp, 8)
self.assertEqual(2000, len(d1.robs))
self.assertEqual(None, self.box._curphase)
return
def test_read_data_string(self):
"""check PdfFitSandbox.read_data_string()
"""
fNi_data = datafile("Ni_2-8.chi.gr")
f300K_data = datafile("300K.gr")
sNi = open(fNi_data).read()
s300K = open(f300K_data).read()
sandbox = self.box.sandbox()
sandbox.update({ "sNi" : sNi, "s300K" : s300K })
exec "read_data_string(sNi, X, 40.1, 0.05)" in sandbox
exec "read_data_string(s300K, N, 32.1, 0.05, 'LaMnO3')" in sandbox
self.assertEqual(2, len(self.box._fits[-1].datasets))
self.assertEqual(1, self.box._curdataset)
d0 = self.box._fits[-1].datasets[0]
self.assertEqual('', d0.name)
self.assertEqual('X', d0.stype)
self.assertAlmostEqual(40.1, d0.qmax, 8)
self.assertAlmostEqual(0.05, d0.qdamp, 8)
self.assertEqual(2000, len(d0.robs))
d1 = self.box._fits[-1].datasets[1]
self.assertEqual('LaMnO3', d1.name)
self.assertEqual('N', d1.stype)
self.assertAlmostEqual(32.1, d1.qmax, 8)
self.assertAlmostEqual(0.05, d1.qdamp, 8)
self.assertEqual(2000, len(d1.robs))
self.assertEqual(None, self.box._curphase)
return
def test_read_data_lists(self):
"""check PdfFitSandbox.read_data_lists()
"""
self.assertRaises(NotImplementedError, self.box.read_data_lists,
'X', 40.1, 0.05, [], [] )
return
def test_pdfrange(self):
"""check PdfFitSandbox.pdfrange()
"""
fNi_data = datafile("Ni_2-8.chi.gr")
f300K_data = datafile("300K.gr")
self.box.read_data(fNi_data, 'X', 40.1, 0.05)
self.box.read_data(f300K_data, 'N', 32.1, 0.05)
sandbox = self.box.sandbox()
exec "pdfrange(1, 2.3, 11.13)" in sandbox
exec "pdfrange(2, 5.7, 17.19)" in sandbox
self.assertEqual(2, len(self.box._fits[-1].datasets))
d0 = self.box._fits[-1].datasets[0]
d1 = self.box._fits[-1].datasets[1]
self.assertAlmostEqual(2.3, d0.fitrmin, 8)
self.assertAlmostEqual(11.13, d0.fitrmax, 8)
self.assertAlmostEqual(5.7, d1.fitrmin, 8)
self.assertAlmostEqual(17.19, d1.fitrmax, 8)
# exceptions for invalid ranges
self.assertRaises(ControlRuntimeError, self.box.pdfrange, 1, 10, 1)
self.assertRaises(ControlRuntimeError, self.box.pdfrange, 1, 0, 10)
self.assertRaises(ControlRuntimeError, self.box.pdfrange, 1, 1, 1000)
exec "pdfrange(ALL, 1.0, 7.0)" in sandbox
self.assertEqual(1.0, d0.fitrmin)
self.assertEqual(7.0, d0.fitrmax)
self.assertEqual(1.0, d1.fitrmin)
self.assertEqual(7.0, d1.fitrmax)
exec "pdfrange('ALL', 2.0, 9.0)" in sandbox
self.assertEqual(2.0, d0.fitrmin)
self.assertEqual(9.0, d0.fitrmax)
self.assertEqual(2.0, d1.fitrmin)
self.assertEqual(9.0, d1.fitrmax)
return
def test_reset(self):
"""check PdfFitSandbox.reset()
"""
fNi_stru = datafile('Ni.stru')
fNi_data = datafile("Ni_2-8.chi.gr")
sandbox = self.box.sandbox()
sandbox.update({ "fNi_stru" : fNi_stru, "fNi_data" : fNi_data })
exec "read_data(fNi_data, X, 40.1, 0.05)" in sandbox
exec "read_struct(fNi_stru)" in sandbox
self.assertEqual(1, len(self.box._fits))
self.assertEqual(1, len(self.box._fits[-1].strucs))
self.assertEqual(1, len(self.box._fits[-1].datasets))
self.assertEqual(0, self.box._curdataset)
self.assertEqual(0, self.box._curphase)
exec "reset()" in sandbox
self.assertEqual(1, len(self.box._fits))
self.assertEqual(0, len(self.box._fits[-1].strucs))
self.assertEqual(0, len(self.box._fits[-1].datasets))
self.assertEqual(None, self.box._curdataset)
self.assertEqual(None, self.box._curphase)
return
def test_alloc(self):
"""check PdfFitSandbox.alloc()
"""
from diffpy.pdfgui.control.calculation import Calculation
from diffpy.pdfgui.control.fitting import Fitting
fNi_stru = datafile('Ni.stru')
sandbox = self.box.sandbox()
sandbox.update({ "fNi_stru" : fNi_stru })
exec "read_struct(fNi_stru)" in sandbox
self.assertEqual(1, len(self.box._fits))
self.assertEqual(1, len(self.box._fits[-1].strucs))
self.assertEqual(0, len(self.box._fits[-1].datasets))
self.failUnless(isinstance(self.box._fits[-1], Fitting))
exec "alloc(N, 37.0, 0.07, 0.01, 10.0, 1000)" in sandbox
self.assertEqual(1, len(self.box._fits))
self.assertEqual(1, len(self.box._fits[-1].strucs))
self.failUnless(isinstance(self.box._fits[-1], Calculation))
c = self.box._fits[-1]
self.assertEqual(37.0, c.qmax)
self.assertEqual(0.07, c.qdamp)
self.assertEqual(0.01, c.rmin)
self.assertAlmostEqual(0.01, c.rstep, 8)
self.assertAlmostEqual(10.0, c.rmax, 8)
self.assertEqual(1000, c.rlen)
return
def test_calc(self):
"""check PdfFitSandbox.calc()
"""
from diffpy.pdfgui.control.calculation import Calculation
fNi_stru = datafile('Ni.stru')
sandbox = self.box.sandbox()
sandbox.update({ "fNi_stru" : fNi_stru })
exec "read_struct(fNi_stru)" in sandbox
self.assertRaises(ControlRuntimeError, self.box.calc)
exec "alloc(N, 37.0, 0.07, 0.01, 10.0, 1000)" in sandbox
self.assertEqual(1, len(self.box._fits))
exec "calc()" in sandbox
self.failUnless(isinstance(self.box._fits[0], Calculation))
self.assertEqual(2, len(self.box._fits))
self.assertEqual(0, len(self.box._fits[-1].datasets))
self.assertEqual(0, len(self.box._fits[-1].strucs))
self.assertEqual(None, self.box._curdataset)
self.assertEqual(None, self.box._curphase)
return
def test_refine(self):
"""check PdfFitSandbox.refine()
"""
fNi_stru = datafile('Ni.stru')
fNi_data = datafile("Ni_2-8.chi.gr")
sandbox = self.box.sandbox()
sandbox.update({ "fNi_stru" : fNi_stru, "fNi_data" : fNi_data })
exec "read_data(fNi_data, X, 40.1, 0.05)" in sandbox
exec "read_struct(fNi_stru)" in sandbox
exec "refine()" in sandbox
self.assertEqual(2, len(self.box._fits))
self.assertEqual(1, len(self.box._fits[0].strucs))
self.assertEqual(1, len(self.box._fits[0].datasets))
self.assertEqual(1, len(self.box._fits[1].strucs))
self.assertEqual(1, len(self.box._fits[1].datasets))
# check fit linking:
self.box._fits[-1].parameters[1] = Parameter(1, 0.05)
exec "refine(0.01)" in sandbox
self.assertEqual(3, len(self.box._fits))
names = [ f.name for f in self.box._fits ]
self.assertEqual('0', names[0])
self.assertEqual('1', names[1])
self.assertEqual('2', names[2])
self.assertEqual(0, self.box._curdataset)
self.assertEqual(0, self.box._curphase)
s = self.box._fits[-1].parameters[1].initialStr()
self.assertEqual("=1:1", s)
return
def test_refine_step(self):
"""check PdfFitSandbox.refine_step()
"""
self.assertRaises(NotImplementedError, self.box.refine_step)
self.assertRaises(NotImplementedError, self.box.refine_step, 0.01)
return
def test_save_pdf(self):
"""check PdfFitSandbox.save_pdf()
"""
sandbox = self.box.sandbox()
exec 'save_pdf(1, "filename.fgr")' in sandbox
return
def test_save_pdf_string(self):
"""check PdfFitSandbox.save_pdf_string()
"""
self.assertRaises(NotImplementedError, self.box.save_pdf_string, 1)
return
def test_save_dif(self):
"""check PdfFitSandbox.save_dif()
"""
sandbox = self.box.sandbox()
exec 'save_dif(1, "filename.diff")' in sandbox
return
def test_save_dif_string(self):
"""check PdfFitSandbox.save_dif_string()
"""
self.assertRaises(NotImplementedError, self.box.save_dif_string, 1)
return
def test_save_res(self):
"""check PdfFitSandbox.save_res()
"""
sandbox = self.box.sandbox()
exec 'save_res("filename.res")' in sandbox
return
def test_save_res_string(self):
"""check PdfFitSandbox.save_res_string()
"""
self.assertRaises(NotImplementedError, self.box.save_res_string)
return
def test_save_struct(self):
"""check PdfFitSandbox.save_struct()
"""
sandbox = self.box.sandbox()
exec 'save_struct(1, "filename.rstr")' in sandbox
return
def test_save_struct_string(self):
"""check PdfFitSandbox.save_struct_string()
"""
self.assertRaises(NotImplementedError, self.box.save_struct_string, 1)
return
def test_show_struct(self):
"""check PdfFitSandbox.show_struct()
"""
sandbox = self.box.sandbox()
exec 'show_struct(1)' in sandbox
return
def test_constrain(self):
"""check PdfFitSandbox.constrain()
"""
sandbox = self.box.sandbox()
self.assertRaises(ControlKeyError, self.box.constrain, 'delta', 1)
fNi_stru = datafile('Ni.stru')
self.box.read_struct(fNi_stru)
exec 'constrain(delta, 1)' in sandbox
self.assertRaises(ControlKeyError, self.box.constrain, 'qdamp', 10)
fNi_data = datafile("Ni_2-8.chi.gr")
self.box.read_data(fNi_data, "X", 40.1, 0.05)
exec 'constrain(qdamp, 10)' in sandbox
exec 'constrain(dscale, 2)' in sandbox
exec 'constrain(lat(1), 3)' in sandbox
exec 'constrain(lat(2), 3)' in sandbox
exec 'constrain(lat(3), "@3")' in sandbox
exec 'constrain(occ(1), 4)' in sandbox
exec 'constrain(pfrac, 5)' in sandbox
exec 'constrain(u11(1), 6)' in sandbox
exec 'constrain(u22(1), 6)' in sandbox
exec 'constrain(u33(1), 6)' in sandbox
exec 'constrain(x(1), "@7+0.5")' in sandbox
cphase = self.box._fits[-1].strucs[self.box._curphase]
cdataset = self.box._fits[-1].datasets[self.box._curdataset]
self.assertEqual(10, len(cphase.constraints))
self.failUnless('pscale' in cphase.constraints)
self.assertEqual('@6', cphase.constraints['u11(1)'].formula)
self.assertEqual('@7+0.5', cphase.constraints['x(1)'].formula)
self.assertEqual(2, len(cdataset.constraints))
self.assertEqual('@10', cdataset.constraints['qdamp'].formula)
exec 'constrain(x(2), 21, IDENT)' in sandbox
exec 'constrain(y(2), 22, FCOMP)' in sandbox
exec 'constrain(z(2), 23, FSQR)' in sandbox
self.assertEqual('@21', cphase.constraints['x(2)'].formula)
self.assertEqual('1.0-@22', cphase.constraints['y(2)'].formula)
self.assertEqual('@23*@23', cphase.constraints['z(2)'].formula)
return
def test_constrain_calculation(self):
"""check exceptions when attempting to constrain Calculation
"""
fNi_stru = datafile('Ni.stru')
sandbox = self.box.sandbox()
sandbox.update({ "fNi_stru" : fNi_stru })
exec "read_struct(fNi_stru)" in sandbox
exec "alloc(N, 37.0, 0.07, 0.01, 10.0, 1000)" in sandbox
self.assertRaises(ControlRuntimeError,
self.box.constrain, 'delta', 1)
self.assertRaises(ControlRuntimeError,
self.box.constrain, 'qdamp', "@3*@3")
self.assertRaises(ControlRuntimeError,
self.box.constrain, 'delta', 1, 'FCOMP')
return
def test_setpar(self):
"""check PdfFitSandbox.setpar()
"""
sandbox = self.box.sandbox()
curfit = self.box._fits[-1]
self.box.setpar(1, 5.0)
self.assertEqual(5.0, curfit.parameters[1].initialValue())
fNi_stru = datafile('Ni.stru')
fNi_data = datafile("Ni_2-8.chi.gr")
self.box.read_struct(fNi_stru)
self.box.read_data(fNi_data, "X", 40.1, 0.05)
exec 'constrain(dscale, 1)' in sandbox
exec 'constrain(lat(1), 3)' in sandbox
exec 'constrain(lat(2), 3)' in sandbox
exec 'constrain(lat(3), "@3")' in sandbox
exec 'setpar(1, 1.25)' in sandbox
exec 'setpar(3, 4.1)' in sandbox
self.assertEqual(1.25, curfit.parameters[1].initialValue())
self.assertEqual(4.1, curfit.parameters[3].initialValue())
exec 'setpar(1, dscale)' in sandbox
exec 'setpar(3, lat(1))' in sandbox
dscale = curfit.datasets[self.box._curdataset].dscale
a = curfit.strucs[self.box._curphase].lattice.a
self.assertEqual(dscale, curfit.parameters[1].initialValue())
self.assertEqual(a, curfit.parameters[3].initialValue())
return
def test_getpar(self):
"""check PdfFitSandbox.getpar()
"""
sandbox = self.box.sandbox()
curfit = self.box._fits[-1]
self.box.setpar(1, 5.0)
self.assertEqual(5.0, eval('getpar(1)', sandbox))
fNi_stru = datafile('Ni.stru')
fNi_data = datafile("Ni_2-8.chi.gr")
self.box.read_struct(fNi_stru)
self.box.read_data(fNi_data, "X", 40.1, 0.05)
exec 'setpar(1, dscale)' in sandbox
exec 'setpar(3, lat(1))' in sandbox
self.assertEqual(1.0, eval('getpar(1)', sandbox))
curphase = curfit.strucs[self.box._curphase]
a = curphase.lattice.a
self.assertEqual(a, eval('getpar(3)', sandbox))
return
def test_fixpar(self):
"""check PdfFitSandbox.fixpar()
"""
sandbox = self.box.sandbox()
curfit = self.box._fits[-1]
for i in range(1, 4):
curfit.parameters[i] = Parameter(i, 1.0*i)
exec 'fixpar(1)' in sandbox
self.assertEqual(True, curfit.parameters[1].fixed)
self.assertEqual(False, curfit.parameters[2].fixed)
self.assertEqual(False, curfit.parameters[3].fixed)
exec 'fixpar(ALL)' in sandbox
self.assertEqual(True, curfit.parameters[1].fixed)
self.assertEqual(True, curfit.parameters[2].fixed)
self.assertEqual(True, curfit.parameters[3].fixed)
self.assertRaises(ControlKeyError, self.box.fixpar, 77)
return
def test_freepar(self):
"""check PdfFitSandbox.freepar()
"""
sandbox = self.box.sandbox()
curfit = self.box._fits[-1]
for i in range(1, 4):
curfit.parameters[i] = Parameter(i, 1.0*i)
curfit.parameters[i].fixed = True
exec 'freepar(1)' in sandbox
self.assertEqual(False, curfit.parameters[1].fixed)
self.assertEqual(True, curfit.parameters[2].fixed)
self.assertEqual(True, curfit.parameters[3].fixed)
exec 'freepar(ALL)' in sandbox
self.assertEqual(False, curfit.parameters[1].fixed)
self.assertEqual(False, curfit.parameters[2].fixed)
self.assertEqual(False, curfit.parameters[3].fixed)
self.assertRaises(ControlKeyError, self.box.freepar, 77)
return
def test_setvar(self):
"""check PdfFitSandbox.setvar()
"""
sandbox = self.box.sandbox()
fNi_stru = datafile('Ni.stru')
fNi_data = datafile("Ni_2-8.chi.gr")
self.box.read_struct(fNi_stru)
self.box.read_data(fNi_data, "X", 40.1, 0.05)
curfit = self.box._fits[-1]
curdataset = curfit.datasets[self.box._curdataset]
curphase = curfit.strucs[self.box._curphase]
self.assertEqual(40.1, curdataset.qmax)
exec "setvar(qdamp, 0.007)" in sandbox
exec "setvar(lat(1), 3.75)" in sandbox
exec "setvar(x(4), 0.123)" in sandbox
exec "setvar(u13(1), 0.00123)" in sandbox
exec "setvar('pscale', 0.97)" in sandbox
self.assertEqual(0.007, curdataset.qdamp)
self.assertEqual(3.75, curphase.lattice.a)
self.assertEqual(0.123, curphase[3].xyz[0])
self.assertEqual(0.00123, curphase[0].U[0,2])
self.assertEqual(0.00123, curphase[0].U[2,0])
self.assertEqual(0.97, curphase.pdffit['scale'])
self.assertRaises(ControlKeyError, self.box.setvar, 'novar', 0.1)
return
def test_getvar(self):
"""check PdfFitSandbox.getvar()
"""
sandbox = self.box.sandbox()
f300K_stru = datafile('300K.stru')
f300K_data = datafile("300K.gr")
sandbox.update({"f300K_stru" : f300K_stru, "f300K_data" : f300K_data})
exec "read_data(f300K_data, 'N', 32.1, 0.05)" in sandbox
exec "read_struct(f300K_stru)" in sandbox
self.assertEqual(0.05, eval("getvar(qdamp)", sandbox))
self.assertEqual(1.0, eval("getvar('dscale')", sandbox))
self.assertEqual(1.0, eval("getvar(dscale)", sandbox))
self.assertAlmostEqual(0.95182216, eval("getvar(y(3))", sandbox), 8)
self.assertAlmostEqual(0.00475572, eval("getvar(u22(4))", sandbox), 8)
self.assertRaises(ControlKeyError, self.box.getvar, 'novar')
return
def test_getrw(self):
"""check PdfFitSandbox.getrw()
"""
self.assertRaises(NotImplementedError, self.box.getrw)
return
def test_getR(self):
"""check PdfFitSandbox.getR()
"""
self.assertRaises(NotImplementedError, self.box.getR)
return
def test_getpdf_fit(self):
"""check PdfFitSandbox.getpdf_fit()
"""
self.assertRaises(NotImplementedError, self.box.getpdf_fit)
return
def test_getpdf_obs(self):
"""check PdfFitSandbox.getpdf_obs()
"""
self.assertRaises(NotImplementedError, self.box.getpdf_obs)
return
def test_get_atoms(self):
"""check PdfFitSandbox.get_atoms()
"""
self.assertRaises(NotImplementedError, self.box.get_atoms)
return
def test_setphase(self):
"""check PdfFitSandbox.setphase()
"""
sandbox = self.box.sandbox()
fNi_stru = datafile('Ni.stru')
f300K_stru = datafile('300K.stru')
self.assertEqual(None, self.box._curphase)
self.box.read_struct(fNi_stru)
self.assertEqual(0, self.box._curphase)
self.box.read_struct(f300K_stru)
self.assertEqual(1, self.box._curphase)
self.assertEqual(20, eval("num_atoms()", sandbox))
exec "setphase(1)" in sandbox
self.assertEqual(0, self.box._curphase)
self.assertEqual(4, eval("num_atoms()", sandbox))
exec "setphase(2)" in sandbox
self.assertEqual(1, self.box._curphase)
self.assertEqual(20, eval("num_atoms()", sandbox))
self.assertRaises(IndexError, self.box.setphase, 3)
return
def test_setdata(self):
"""check PdfFitSandbox.setdata()
"""
sandbox = self.box.sandbox()
fNi_data = datafile("Ni_2-8.chi.gr")
f300K_data = datafile("300K.gr")
self.assertEqual(None, self.box._curdataset)
self.box.read_data(fNi_data, "X", 40.1, 0.05)
self.assertEqual(0, self.box._curdataset)
self.box.read_data(f300K_data, 'N', 32.1, 0.07)
self.assertEqual(1, self.box._curdataset)
self.assertEqual(0.07, eval("getvar('qdamp')", sandbox))
exec "setdata(1)" in sandbox
self.assertEqual(0, self.box._curdataset)
self.assertEqual(0.05, eval("getvar('qdamp')", sandbox))
exec "setdata(2)" in sandbox
self.assertEqual(1, self.box._curdataset)
self.assertEqual(0.07, eval("getvar('qdamp')", sandbox))
self.assertRaises(IndexError, self.box.setdata, 3)
return
def test_psel(self):
"""check PdfFitSandbox.psel()
"""
self.assertRaises(NotImplementedError, self.box.psel, 1)
return
def test_pdesel(self):
"""check PdfFitSandbox.pdesel()
"""
self.assertRaises(NotImplementedError, self.box.pdesel, 1)
return
def test_isel(self):
"""check PdfFitSandbox.isel()
"""
self.assertRaises(NotImplementedError, self.box.isel, 1, 1)
return
def test_idesel(self):
"""check PdfFitSandbox.idesel()
"""
self.assertRaises(NotImplementedError, self.box.idesel, 1, 1)
return
def test_jsel(self):
"""check PdfFitSandbox.jsel()
"""
self.assertRaises(NotImplementedError, self.box.jsel, 1, 1)
return
def test_jdesel(self):
"""check PdfFitSandbox.jdesel()
"""
self.assertRaises(NotImplementedError, self.box.jdesel, 1, 1)
return
def test_bang(self):
"""check PdfFitSandbox.bang()
"""
self.assertRaises(NotImplementedError, self.box.bang, 1, 2, 3)
return
def test_blen(self):
"""check PdfFitSandbox.blen()
"""
sandbox = self.box.sandbox()
exec 'blen(1, 2)' in sandbox
exec 'blen(1, 1, 1.5, 5.0)' in sandbox
exec 'blen(1, 2, 1.5, 5.0)' in sandbox
return
def test_show_scat(self):
"""check PdfFitSandbox.show_scat()
"""
sandbox = self.box.sandbox()
exec 'show_scat("X")' in sandbox
return
def test_show_scat_string(self):
"""check PdfFitSandbox.show_scat_string()
"""
self.assertRaises(NotImplementedError, self.box.show_scat_string, 'X')
return
def test_get_scat(self):
"""check PdfFitSandbox.get_scat()
"""
self.assertRaises(NotImplementedError, self.box.get_scat)
return
def test_set_scat(self):
"""check PdfFitSandbox.set_scat()
"""
self.assertRaises(NotImplementedError, self.box.set_scat)
return
def test_reset_scat(self):
"""check PdfFitSandbox.reset_scat()
"""
self.assertRaises(NotImplementedError, self.box.reset_scat)
return
def test_num_atoms(self):
"""check PdfFitSandbox.num_atoms()
"""
self.assertRaises(ControlKeyError, self.box.num_atoms)
sandbox = self.box.sandbox()
fNi_stru = datafile('Ni.stru')
self.box.read_struct(fNi_stru)
self.assertEqual(4, eval('num_atoms()', sandbox))
return
def test_lat(self):
"""check PdfFitSandbox.lat()
"""
sandbox = self.box.sandbox()
self.assertEqual('lat(1)', eval('lat(1)', sandbox))
self.assertEqual('lat(2)', eval('lat(2)', sandbox))
self.assertEqual('lat(3)', eval('lat(3)', sandbox))
self.assertEqual('lat(4)', eval('lat(4)', sandbox))
self.assertEqual('lat(5)', eval('lat(5)', sandbox))
self.assertEqual('lat(6)', eval('lat(6)', sandbox))
self.box.lat(7)
return
def test_x(self):
"""check PdfFitSandbox.x()
"""
sandbox = self.box.sandbox()
self.assertEqual('x(1)', eval('x(1)', sandbox))
return
def test_y(self):
"""check PdfFitSandbox.y()
"""
sandbox = self.box.sandbox()
self.assertEqual('y(1)', eval('y(1)', sandbox))
return
def test_z(self):
"""check PdfFitSandbox.z()
"""
sandbox = self.box.sandbox()
self.assertEqual('z(1)', eval('z(1)', sandbox))
return
def test_u11(self):
"""check PdfFitSandbox.u11()
"""
sandbox = self.box.sandbox()
self.assertEqual('u11(1)', eval('u11(1)', sandbox))
return
def test_u22(self):
"""check PdfFitSandbox.u22()
"""
sandbox = self.box.sandbox()
self.assertEqual('u22(1)', eval('u22(1)', sandbox))
return
def test_u33(self):
"""check PdfFitSandbox.u33()
"""
sandbox = self.box.sandbox()
self.assertEqual('u33(1)', eval('u33(1)', sandbox))
return
def test_u12(self):
"""check PdfFitSandbox.u12()
"""
sandbox = self.box.sandbox()
self.assertEqual('u12(1)', eval('u12(1)', sandbox))
return
def test_u13(self):
"""check PdfFitSandbox.u13()
"""
sandbox = self.box.sandbox()
self.assertEqual('u13(1)', eval('u13(1)', sandbox))
return
def test_u23(self):
"""check PdfFitSandbox.u23()
"""
sandbox = self.box.sandbox()
self.assertEqual('u23(1)', eval('u23(1)', sandbox))
return
def test_occ(self):
"""check PdfFitSandbox.occ()
"""
sandbox = self.box.sandbox()
self.assertEqual('occ(1)', eval('occ(1)', sandbox))
return
def test_pscale(self):
"""check PdfFitSandbox.pscale()
"""
sandbox = self.box.sandbox()
self.assertEqual('pscale', eval('pscale()', sandbox))
return
def test_pfrac(self):
"""check PdfFitSandbox.pfrac()
"""
sandbox = self.box.sandbox()
self.assertEqual('pscale', eval('pfrac()', sandbox))
return
def test_spdiameter(self):
"""check PdfFitSandbox.spdiameter()
"""
sandbox = self.box.sandbox()
self.assertEqual('spdiameter', eval('spdiameter()', sandbox))
return
def test_stepcut(self):
"""check PdfFitSandbox.stepcut()
"""
sandbox = self.box.sandbox()
self.assertEqual('stepcut', eval('stepcut()', sandbox))
return
def test_sratio(self):
"""check PdfFitSandbox.sratio() and PdfFitSandbox.srat()
"""
sandbox = self.box.sandbox()
self.assertEqual('sratio', eval('sratio()', sandbox))
self.assertEqual('sratio', eval('srat()', sandbox))
return
def test_delta1(self):
"""check PdfFitSandbox.delta1() and PdfFitSandbox.gamma()
"""
sandbox = self.box.sandbox()
self.assertEqual('delta1', eval('delta1()', sandbox))
self.assertEqual('delta1', eval('gamma()', sandbox))
return
def test_delta2(self):
"""check PdfFitSandbox.delta2() and PdfFitSandbox.delta()
"""
sandbox = self.box.sandbox()
self.assertEqual('delta2', eval('delta2()', sandbox))
self.assertEqual('delta2', eval('delta()', sandbox))
return
def test_dscale(self):
"""check PdfFitSandbox.dscale()
"""
sandbox = self.box.sandbox()
self.assertEqual('dscale', eval('dscale()', sandbox))
return
def test_qdamp(self):
"""check PdfFitSandbox.qdamp() and PdfFitSandbox.qsig()
"""
sandbox = self.box.sandbox()
self.assertEqual('qdamp', eval('qdamp()', sandbox))
self.assertEqual('qdamp', eval('qsig()', sandbox))
return
def test_qbroad(self):
"""check PdfFitSandbox.qbroad() and PdfFitSandbox.qalp()
"""
sandbox = self.box.sandbox()
self.assertEqual('qbroad', eval('qbroad()', sandbox))
self.assertEqual('qbroad', eval('qalp()', sandbox))
return
def test_rcut(self):
"""check PdfFitSandbox.rcut()
"""
sandbox = self.box.sandbox()
self.assertEqual('rcut', eval('rcut()', sandbox))
return
