def find_stable_Smat_poles(self):
cal = rk.get_asym_calc(cu.hartrees, [0, 0])
csmat = rw.get_Smat_fun(1.0, 2.0, 2.0, cal, 1.0)
dsmat = csmat.discretise(1., 8., 100)
rk.get_tool(rk.mcsmatfit, dsmat, archive_root=TEST_ROOT, silent=True)
rk.get_tool(rk.mcsmatfit, dsmat, archive_root=TEST_ROOT, silent=True)
dsmat.asymcalc.units = cu.rydbergs
self.assertRaises(Exception,
rk.get_tool,
rk.mcsmatfit,
dsmat,
archive_root=TEST_ROOT,
silent=True)
def runTest(self):
# Test that the three modes (mpmath, python with and without sympy
# nroots) all return different results.
dsmat = self.get_dsmat()
rk.use_python_types()
mcsmatfit = rk.get_tool(rk.mcsmatfit, dsmat, silent=True)
roots1 = self.get_roots(mcsmatfit)
mcsmatfit = rk.get_tool(
rk.mcsmatfit,
dsmat,
silent=True,
param_file_path="test_mcsmatfit_calc_modes.yaml")
roots2 = self.get_roots(mcsmatfit)
rk.use_mpmath_types(dps=100)
dsmat = self.get_dsmat()
mcsmatfit = rk.get_tool(rk.mcsmatfit, dsmat, silent=True)
roots3 = self.get_roots(mcsmatfit)
self.assertNotEqual(str(roots1), str(roots2))
self.assertNotEqual(str(roots1), str(roots3))
self.assertNotEqual(str(roots2), str(roots3))
def find_stable_Smat_poles(self):
cal = rk.get_asym_calc(cu.hartrees, [0,0])
csmat = rw.get_Smat_fun(1.0,2.0,2.0,cal,1.0)
dsmat = csmat.discretise(1.,8.,100)
mcsmatfit = rk.get_tool(rk.mcsmatfit, dsmat, archive_root=TEST_ROOT,
silent=True)
cfins = mcsmatfit.get_elastic_Fins(range(2,4,2))
mcsmatfit.find_stable_Smat_poles(cfins)
# Import again with same config and check no exception
rk.get_tool(rk.mcsmatfit, dsmat, archive_root=TEST_ROOT, silent=True)
testPath = fileDir+os.sep+"test_mcsmatfit_data1"+os.sep+"default.yaml"
self.assertRaises(Exception, rk.get_tool, rk.mcsmatfit, dsmat,
archive_root=TEST_ROOT, param_file_path=testPath,
silent=True)
testPath = fileDir+os.sep+"test_mcsmatfit_data2"+os.sep+"default.yaml"
self.assertRaises(Exception, rk.get_tool, rk.mcsmatfit, dsmat,
archive_root=TEST_ROOT, param_file_path=testPath,
silent=True)
def find_stable_Smat_poles(self):
cal = rk.get_asym_calc(cu.hartrees, [0,0])
csmat = rw.get_Smat_fun(1.0,2.0,2.0,cal,1.0)
dsmat = csmat.discretise(1.,8.,100)
mcsmatfit = rk.get_tool(rk.mcsmatfit, dsmat, archive_root=TEST_ROOT,
silent=True)
mcsmatfit.get_elastic_Smat(6)
cfins = mcsmatfit.get_elastic_Fins(range(2,10,2))
mcsmatfit.find_stable_Smat_poles(cfins)
self.assertFalse(mcsmatfit.all_coeffs_loaded)
self.assertFalse(mcsmatfit.all_roots_loaded)
cfins = mcsmatfit.get_elastic_Fins(range(2,10,2))
self.assertTrue(mcsmatfit.all_coeffs_loaded)
# False because we haven't called find_stable_Smat_poles yet
self.assertFalse(mcsmatfit.all_roots_loaded)
roots = mcsmatfit.find_Fin_roots(cfins)
mcsmatfit.find_stable_Smat_poles(roots)
self.assertTrue(mcsmatfit.all_roots_loaded)
desc_str)
else:
# System is a molecule
# Read in the K matrix data
# Get a calculator with units and channel angular momentum
calc = rk.get_asym_calc(rk.rydbergs, ang_mom)
kmatdict,_ = rmol.read_Kmats(input_data_file)
# Initialise the data into the required container
dmat = rk.get_dmat_from_discrete(rk.Kmat, kmatdict, calc, desc_str)
# Slice the data set
if sl is not None:
dmat = dmat[sl]
if sys.argv[2] in ("poles", "plotSmat", "plotXS"):
sfittool = rk.get_tool(rk.mcsmatfit, dmat, archive_path, param_path)
if sys.argv[2] == "poles":
if not Npts:
Npts = 40
# Perform the calculation of the poles and the quality indicators
cfins = sfittool.get_elastic_Fins(range(2,Npts+2,2))
sfittool.find_stable_Smat_poles(cfins)
elif sys.argv[2] in ("plotSmat", "plotXS"):
if not Npts:
Npts = 20
# Perform the calculation of the poles and the quality indicators
csmat = sfittool.get_elastic_Smat(Npts)
if sys.argv[2] == "plotSmat":
sfittool.plot_Smat_fit(csmat, num_plot_points=num_plot_points)
elif sys.argv[1] == "uracil":
sfittool.plot_XS_fit(csmat, num_plot_points=num_plot_points, logy=True)
if len(sys.argv) > 1 and sys.argv[1] == "mpmath":
cu.use_mpmath_types()
print "mpmath"
else:
print "python"
TEST_ROOT = "chart"
if os.path.isdir(TEST_ROOT):
shutil.rmtree(TEST_ROOT)
cal = cu.AsymCalc(cu.hartrees, [0, 0])
csmat = rw.get_Smat_fun(1.0, 2.0, 2.0, cal, 1.0)
print "Plot all data as S-matrix, direct from continuous data. No archive."
chart = rk.get_tool(rk.chart, csmat)
chart.plot_Smatrix()
print "Use discretised data."
dsmat = csmat.discretise(1., 8., 100)
chart = rk.get_tool(rk.chart, dsmat)
print "Plot all data as S-matrix. No archive. Row."
chart.plot_Smatrix(i=0)
print "Archive created"
chart = rk.get_tool(rk.chart, dsmat, TEST_ROOT)
print "Plot all data as S-matrix. Column."
chart.plot_Smatrix(j=1)
csmat = rw.get_Smat_fun(1.0,2.0,2.0,calc,1.0)
dmat = rk.get_dmat_from_continuous(rk.Smat, csmat, calc, 1., 8., 200,
"radwell")
else:
# This data is only available in the distribution package.
if sys.argv[2] == "pyrazine":
input_data_file = "../../../../examples/kmatrix_input_pyrazine.txt"
calc = rk.get_asym_calc(rk.rydbergs, [3,5,5])
else:
input_data_file = "../../../../examples/kmatrix_input_pbq.txt"
calc = rk.get_asym_calc(rk.rydbergs, [1,3,3])
kmatdict,_ = rmol.read_Kmats(input_data_file)
dmat = rk.get_dmat_from_discrete(rk.Kmat, kmatdict, calc, "PBQ")
sfittool = rk.get_tool(rk.mcsmatfit, dmat, TEST_ROOT)
csmat = sfittool.get_elastic_Smat(10)
print "S matrix"
print "All elements. Default number of points"
sfittool.plot_Smat_fit(csmat)
print "All elements"
sfittool.plot_Smat_fit(csmat, 100)
print "Row eVs"
sfittool.plot_Smat_fit(csmat, 100, units=rk.eVs, i=1)
print "Column hartrees imaginary"
sfittool.plot_Smat_fit(csmat, 100, units=rk.hartrees, j=0, imag=True)
print "Element"
sfittool.plot_Smat_fit(csmat, 100, i=1, j=0)
print "Element logx"
import os
import sys
import shutil
fileDir = os.path.dirname(os.path.realpath(__file__))
rkPath = fileDir + '/../../../..'
sys.path.insert(0, rkPath)
import reskit as rk
import channelutil as cu
import twochanradialwell as tcrw
TEST_ROOT = "chart-Smat-fin-fit"
if os.path.isdir(TEST_ROOT):
shutil.rmtree(TEST_ROOT)
calc = rk.get_asym_calc(rk.hartrees, [0, 0])
csmat = tcrw.get_Smat_fun(1.0, 2.0, 2.0, calc, 1.0)
dmat = rk.get_dmat_from_continuous(rk.Smat, csmat, calc, 1., 8., 1200,
"radwell")
sfittool = rk.get_tool(rk.mcsmatfit, dmat, TEST_ROOT)
cfin = sfittool.get_elastic_Fin(10)
chart = rk.get_tool(rk.chart, cfin, TEST_ROOT)
chart.plot_raw()
import os
import sys
fileDir = os.path.dirname(os.path.realpath(__file__))
rkPath = fileDir + '/../../../..'
sys.path.insert(0, rkPath)
import reskit as rk
POLE_DATA_FOLDER = "create_formatted_QI_tables"
smatfit = rk.get_tool(rk.mcsmatfit, None)
typs = ["latex", "html", "raw"]
quants = ["E", "k"]
truns = [True, False]
sig_digits = [None, 4, 10]
def _create_table(typ, quant, trun, sig_digit):
smatfit.create_formatted_QI_tables(typ + quant,
trun,
sig_digit,
spec_path=POLE_DATA_FOLDER)
for typ in typs:
for quant in quants:
for trun in truns:
for sig_digit in sig_digits:
_create_table(typ, quant, trun, sig_digit)