def runTest(self):
fp = lambda e: mpmath.matrix([[e, e], [e, e]])
rk.use_mpmath_types()
cal = rk.get_asym_calc(cu.rydbergs, [0, 0])
dmat = rk.get_dmat_from_continuous(rk.Smat, fp, cal, 1., 5., 10,
"dum4")
self.assertEqual(nw.mode, nw.mode_mpmath)
self.assertEqual(nw.dps, nw.dps_default_mpmath)
for mat in dmat.values():
nw.shape(mat) # Will get an exception if types are wrong.
def runTest(self):
data = {}
data[1.] = mpmath.matrix([[1., 1.], [1., 1.]])
data[2.] = mpmath.matrix([[2., 2.], [2., 2.]])
rk.use_mpmath_types()
cal = rk.get_asym_calc(cu.rydbergs, [0, 0])
dmat = rk.get_dmat_from_discrete(rk.Smat, data, cal, "dum2")
self.assertEqual(nw.mode, nw.mode_mpmath)
self.assertEqual(nw.dps, nw.dps_default_mpmath)
for mat in dmat.values():
nw.shape(mat) # Will get an exception if types are wrong.
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 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)
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)
param_path = "test_configuration_3.yaml"
elif desc_str == "pbq":
input_data_file = "kmatrix_input_pbq.txt"
ang_mom = [1,3,3]
sl = slice(0,624)
num_plot_points = 312
param_path = "test_configuration_2.yaml"
else:
raise Exception(exceptStr)
rk.use_mpmath_types(dps=100)
if input_data_file is None:
# System is a radial well
# Get a calculator with units and channel angular momentum
calc = rk.get_asym_calc(rk.hartrees, ang_mom)
# Get a function pointer for the S matrix
csmat = tcrw.get_Smat_fun(1.0, 2.0, 2.0, calc, 1.0)
# Initialise the data into the required container
dmat = rk.get_dmat_from_continuous(rk.Smat, csmat, calc, 1., 8., 1200,
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
use_pyrazine = True
if sys.argv[1] == "mpmath":
rk.use_mpmath_types()
print "mpmath"
else:
print "python"
TEST_ROOT = "chart"
if os.path.isdir(TEST_ROOT):
shutil.rmtree(TEST_ROOT)
if sys.argv[2] == "radwell":
calc = rk.get_asym_calc(rk.hartrees, [0,0])
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")
def get_dsmat(self):
cal = rk.get_asym_calc(cu.hartrees, [0, 0])
csmat = rw.get_Smat_fun(1.0, 2.0, 2.0, cal, 1.0)
return csmat.discretise(1., 8., 100)
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()
