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0.00000000 2.75445008 0.00000000 - 0.56002379 2.54896816 1.79539968 - 4.54678788 2.95993201 5.55978141 - 1.99338212 5.30341824 1.88219076 - 3.11342985 0.20548193 5.47298991 - 3.55122302 1.72814193 0.39644425 - 1.55558880 3.78075840 6.95873661 - 4.12568276 4.48259185 3.28114617 - 0.98112906 1.02630815 4.07403471 - 0.93260966 1.11059427 6.94181952 - 4.17420208 4.39830581 0.41336136 - 1.60410812 3.86504444 4.09095181 - 3.50270370 1.64385573 3.26422908 - diff --git a/python/converters/vasp/POSCAR.cart b/python/converters/vasp/POSCAR.cart deleted file mode 100644 index a9de6f86..00000000 --- a/python/converters/vasp/POSCAR.cart +++ /dev/null @@ -1,29 +0,0 @@ -LuNiO3, low-T, P2_1/n -1.0 - 5.1234998703 0.0000000000 0.0000000000 - 0.0000000000 5.5089001656 0.0000000000 - -0.0166880521 0.0000000000 7.3551808822 - Lu Ni O - 4 4 12 -Kartesian - 5.00246185 0.42418531 1.86086070 - 0.10434997 5.08471473 5.49431996 - 2.67444393 3.17863552 1.81672974 - 2.43236789 2.33026481 5.53845136 - 2.56174994 0.00000000 0.00000000 - -0.00834403 2.75445008 3.67759044 - 2.55340591 0.00000000 3.67759044 - 0.00000000 2.75445008 0.00000000 - 0.56002379 2.54896816 1.79539968 - 4.54678788 2.95993201 5.55978141 - 1.99338212 5.30341824 1.88219076 - 3.11342985 0.20548193 5.47298991 - 3.55122302 1.72814193 0.39644425 - 1.55558880 3.78075840 6.95873661 - 4.12568276 4.48259185 3.28114617 - 0.98112906 1.02630815 4.07403471 - 0.93260966 1.11059427 6.94181952 - 4.17420208 4.39830581 0.41336136 - 1.60410812 3.86504444 4.09095181 - 3.50270370 1.64385573 3.26422908 - diff --git a/python/converters/vasp/POSCAR.direct b/python/converters/vasp/POSCAR.direct deleted file mode 100644 index 0ed61cab..00000000 --- a/python/converters/vasp/POSCAR.direct +++ /dev/null @@ -1,28 +0,0 @@ -LuNiO3, low-T, P2_1/n -1.0 - 5.1234998703 0.0000000000 0.0000000000 - 0.0000000000 5.5089001656 0.0000000000 - -0.0166880521 0.0000000000 7.3551808822 - Lu Ni O - 4 4 12 -Direct - 0.977199972 0.077000000 0.252999991 - 0.022800028 0.922999978 0.746999979 - 0.522800028 0.577000022 0.247000009 - 0.477199972 0.423000008 0.753000021 - 0.500000000 0.000000000 0.000000000 - 0.000000000 0.500000000 0.500000000 - 0.500000000 0.000000000 0.500000000 - 0.000000000 0.500000000 0.000000000 - 0.110100001 0.462700009 0.244100004 - 0.889899969 0.537299991 0.755900025 - 0.389899999 0.962700009 0.255899996 - 0.610100031 0.037299991 0.744099975 - 0.693300009 0.313699991 0.053900000 - 0.306699991 0.686300039 0.946099997 - 0.806699991 0.813699961 0.446099997 - 0.193300009 0.186300009 0.553900003 - 0.185100004 0.201600000 0.943799973 - 0.814899981 0.798399985 0.056200027 - 0.314899981 0.701600015 0.556200027 - 0.685100019 0.298399985 0.443799973 diff --git a/python/converters/vasp/plocar_io/.gitignore b/python/converters/vasp/c/plocar_io/.gitignore similarity index 72% rename from python/converters/vasp/plocar_io/.gitignore rename to python/converters/vasp/c/plocar_io/.gitignore index f0ad8e09..675673c3 100644 --- a/python/converters/vasp/plocar_io/.gitignore +++ b/python/converters/vasp/c/plocar_io/.gitignore @@ -1,4 +1,5 @@ makefile +Makefile *.so *.o *.pyc diff --git a/python/converters/vasp/plocar_io/__init__.py b/python/converters/vasp/c/plocar_io/__init__.py similarity index 100% rename from python/converters/vasp/plocar_io/__init__.py rename to python/converters/vasp/c/plocar_io/__init__.py diff --git a/python/converters/vasp/plocar_io/c_plocar_io.c b/python/converters/vasp/c/plocar_io/c_plocar_io.c similarity index 100% rename from python/converters/vasp/plocar_io/c_plocar_io.c rename to python/converters/vasp/c/plocar_io/c_plocar_io.c diff --git a/python/converters/vasp/plocar_io/makefile.darwin b/python/converters/vasp/c/plocar_io/makefile.darwin similarity index 97% rename from python/converters/vasp/plocar_io/makefile.darwin rename to python/converters/vasp/c/plocar_io/makefile.darwin index 10491743..b2d8a5e5 100644 --- a/python/converters/vasp/plocar_io/makefile.darwin +++ b/python/converters/vasp/c/plocar_io/makefile.darwin @@ -5,5 +5,4 @@ LIB_FLAGS=-L/opt/local/Library/Frameworks/Python.framework/Versions/Current/lib/ c_plocar_io.so: c_plocar_io.c $(CC) $< -fPIC -shared -o $@ $(INC_FLAGS) $(LIB_FLAGS) -lpython2.7 - cp $@ .. diff --git a/python/converters/vasp/c/plocar_io/makefile.linux b/python/converters/vasp/c/plocar_io/makefile.linux new file mode 100644 index 00000000..c4450516 --- /dev/null +++ b/python/converters/vasp/c/plocar_io/makefile.linux @@ -0,0 +1,8 @@ + +CC=gcc +INC_FLAGS=-I/usr/include/python2.7 -I/usr/lib/python2.7/dist-packages/numpy/core/include/numpy +LIB_FLAGS=-L/usr/lib/python2.7 + +c_plocar_io.so: c_plocar_io.c + $(CC) $< -fPIC -shared -o $@ $(INC_FLAGS) $(LIB_FLAGS) -lpython2.7 + diff --git a/python/converters/vasp/.gitignore b/python/converters/vasp/python/.gitignore similarity index 100% rename from python/converters/vasp/.gitignore rename to python/converters/vasp/python/.gitignore diff --git a/python/converters/vasp/pyconf.py b/python/converters/vasp/python/inpconf.py similarity index 73% rename from python/converters/vasp/pyconf.py rename to python/converters/vasp/python/inpconf.py index 0dc2fe7e..42e8ba62 100644 --- a/python/converters/vasp/pyconf.py +++ b/python/converters/vasp/python/inpconf.py @@ -1,8 +1,12 @@ +r""" + Module for parsing and checking an input config-file. +""" import ConfigParser import numpy as np import re import sys +import itertools as it import vaspio def issue_warning(message): @@ -12,6 +16,7 @@ def issue_warning(message): print print " !!! WARNING !!!: " + message print + ################################################################################ ################################################################################ # @@ -34,23 +39,6 @@ class ConfigParameters: 1. internal name of a parameter 2. function used to convert an input string into data for a given parameter """ - self.sh_required = { - 'ions': ('ion_list', self.parse_ion_list), - 'lshell': ('lshell', int)} - - self.sh_optional = { - 'rtransform': ('tmatrix', lambda s: self.parse_tmatrix(s, real=True)), - 'ctransform': ('tmatrix', lambda s: self.parse_tmatrix(s, real=False))} - - self.gr_required = { - 'emin': ('emin', float), - 'emax': ('emax', float)} - - self.gr_optional = { - 'normalize' : ('normalize', self.parse_logical), - 'normion' : ('normion', self.parse_logical)} - - ################################################################################ # # __init__() @@ -58,10 +46,29 @@ class ConfigParameters: ################################################################################ def __init__(self, input_filename, verbosity=1): self.verbosity = verbosity - self.cp = ConfigParser.ConfigParser() + self.cp = ConfigParser.SafeConfigParser() self.cp.readfp(open(input_filename, 'r')) - self.conf_pars = {} + self.parameters = {} + + self.sh_required = { + 'ions': ('ion_list', self.parse_string_ion_list), + 'lshell': ('lshell', int)} + + self.sh_optional = { + 'rtransform': ('tmatrix', lambda s: self.parse_string_tmatrix(s, real=True)), + 'ctransform': ('tmatrix', lambda s: self.parse_string_tmatrix(s, real=False))} + + self.gr_required = { + 'shells': ('shells', lambda s: map(int, s.split())), + 'emin': ('emin', float), + 'emax': ('emax', float)} + + self.gr_optional = { + 'normalize' : ('normalize', self.parse_string_logical), + 'normion' : ('normion', self.parse_string_logical)} + + # # Special parsers @@ -75,19 +82,34 @@ class ConfigParameters: """ The ion list accepts two formats: 1). A list of ion indices according to POSCAR. + The list can be defined as a range '9..20'. 2). An element name, in which case all ions with this name are included. The second option requires an input from POSCAR file. """ - try: - l_tmp = map(int, par_str.split()) +# First check if a range is given + patt = '([0-9]+)\.\.([0-9]+)' + match = re.match(patt, par_str) + if match: + i1, i2 = tuple(map(int, match.groups()[:2])) + mess = "First index of the range must be smaller or equal to the second" + assert i1 <= i2, mess + ion_list = np.array(range(i1 - 1, i2)) + else: +# Check if a set of indices is given + try: + l_tmp = map(int, par_str.split()) + l_tmp.sort() # Subtract 1 so that VASP indices (starting with 1) are converted # to Python indices (starting with 0) - ion_list = np.array(l_tmp) - 1 - except ValueError: - err_msg = "Only an option with a list of ion indices is implemented" - raise NotImplementedError(err_msg) + ion_list = np.array(l_tmp) - 1 + except ValueError: + err_msg = "Only an option with a list of ion indices is implemented" + raise NotImplementedError(err_msg) + + err_mess = "Lowest ion index is smaller than 1 in '%s'"%(par_str) + assert np.all(ion_list >= 0), err_mess return ion_list @@ -102,8 +124,44 @@ class ConfigParameters: (case does not matter). In fact, only the first symbol matters so that one can write 'T' or 'F'. """ - assert par_str[0] in 'tf', "Logical parameters should be given by either 'True' or 'False'" - return par_str[0] == 't' + first_char = par_str[0].lower() + assert first_char in 'tf', "Logical parameters should be given by either 'True' or 'False'" + return first_char == 't' + +################################################################################ +# +# parse_string_tmatrix() +# +################################################################################ + def parse_string_tmatrix(self, par_str, real): + """ + Transformation matrix is defined as a set of rows separated + by a new line symbol. + """ + str_rows = par_str.split('\n') + try: + rows = [map(float, s.split()) for s in str_rows] + except ValueError: + err_mess = "Cannot parse a matrix string:\n%s"%(par_str) + raise ValueError(err_mess) + + nr = len(rows) + nm = len(rows[0]) + + err_mess = "Number of columns must be the same:\n%s"%(par_str) + for row in rows: + assert len(row) == nm, err_mess + + if real: + mat = np.array(rows) + else: + err_mess = "Complex matrix must contain 2*M values:\n%s"%(par_str) + assert 2 * (nm / 2) == nm, err_mess + + tmp = np.array(rows, dtype=np.complex128) + mat = tmp[:, 0::2] + 1.0j * tmp[:, 1::2] + + return mat ################################################################################ # @@ -122,7 +180,7 @@ class ConfigParameters: except ConfigParser.NoOptionError: if exception: message = "Required parameter '%s' not found in section [%s]"%(par, section) - raise ConfigParser.NoOptionError(message) + raise Exception(message) else: continue @@ -149,9 +207,8 @@ class ConfigParameters: # (note that ConfigParser transforms all names to lower case) sections = self.cp.sections() - sh_patt = 'shell *([0-9]*)' - ismatch = lambda s: not re.match(sh_patt, s) is None - sec_shells = filter(ismatch, sections) + sh_patt1 = re.compile('shell +.*', re.IGNORECASE) + sec_shells = filter(sh_patt1.match, sections) self.nshells = len(sec_shells) assert self.nshells > 0, "No projected shells found in the input file" @@ -164,15 +221,17 @@ class ConfigParameters: print " Found 1 projected shell" # Get shell indices - get_ind = lambda s: int(re.match(sh_patt, s).groups()[0]) + sh_patt2 = re.compile('shell +([0-9]*)$', re.IGNORECASE) try: + get_ind = lambda s: int(sh_patt2.match(s).groups()[0]) sh_inds = map(get_ind, sec_shells) - except ValueError: + except (ValueError, AttributeError): raise ValueError("Failed to extract shell indices from a list: %s"%(sec_shells)) - self.sh_sections = {ind: sec for ind, sec in sh_inds, sec_shells} + self.sh_sections = {ind: sec for ind, sec in it.izip(sh_inds, sec_shells)} # Check that all indices are unique +# In principle redundant because the list of sections will contain only unique names assert len(sh_inds) == len(set(sh_inds)), "There must be no shell with the same index!" # Ideally, indices should run from 1 to @@ -180,7 +239,7 @@ class ConfigParameters: sh_inds.sort() if sh_inds != range(1, len(sh_inds) + 1): issue_warning("Shell indices are not uniform or not starting from 1. " - "This might be an indication of a incorrect setup." + "This might be an indication of a incorrect setup.") # Parse shell parameters self.shells = {} @@ -230,9 +289,8 @@ class ConfigParameters: # Find group sections sections = self.cp.sections() - gr_patt = 'group *([0-9]*)' - ismatch = lambda s: not re.match(gr_patt, s) is None - sec_groups = filter(ismatch, sections) + gr_patt = re.compile('group *([0-9]*)') + sec_groups = filter(gr_patt.match, sections) self.ngroups = len(sec_groups) diff --git a/python/converters/vasp/plotools.py b/python/converters/vasp/python/plotools.py similarity index 100% rename from python/converters/vasp/plotools.py rename to python/converters/vasp/python/plotools.py diff --git a/python/converters/vasp/vaspio.py b/python/converters/vasp/python/vaspio.py similarity index 100% rename from python/converters/vasp/vaspio.py rename to python/converters/vasp/python/vaspio.py diff --git a/python/converters/vasp/test.cfg b/python/converters/vasp/test.cfg deleted file mode 100644 index 7640037e..00000000 --- a/python/converters/vasp/test.cfg +++ /dev/null @@ -1,13 +0,0 @@ -[General] - -[PLO Group 1] - -IONS = 5 6 7 8 -#IONS = Ni -EMIN = -0.6 -EMAX = 2.7 -LSHELL = 2 -RTRANSFORM = - 0.0 0.0 0.0 0.0 1.0 - 0.0 0.0 1.0 0.0 0.0 - diff --git a/python/converters/vasp/test/adv_example.cfg b/python/converters/vasp/test/adv_example.cfg new file mode 100644 index 00000000..a02179c1 --- /dev/null +++ b/python/converters/vasp/test/adv_example.cfg @@ -0,0 +1,20 @@ +[General] +EFERMI = -0.6 + +[Group 1] +SHELLS = 1 2 +EMIN = -7.6 +EMAX = 2.7 + +[Shell 1] +# Ni shell +IONS = 5 6 7 8 +LSHELL = 2 +RTRANSFORM = + 0.0 0.0 0.0 0.0 1.0 + 0.0 0.0 1.0 0.0 0.0 + +[Shell 2] +# Oxygen shell +IONS = 9..20 +LSHELL = 1 diff --git a/python/converters/vasp/test/inpconf/.gitignore b/python/converters/vasp/test/inpconf/.gitignore new file mode 100644 index 00000000..0d20b648 --- /dev/null +++ b/python/converters/vasp/test/inpconf/.gitignore @@ -0,0 +1 @@ +*.pyc diff --git a/python/converters/vasp/test/inpconf/runtest.sh b/python/converters/vasp/test/inpconf/runtest.sh new file mode 100644 index 00000000..9b7bd8ca --- /dev/null +++ b/python/converters/vasp/test/inpconf/runtest.sh @@ -0,0 +1 @@ +PYTHONPATH=../../python:../../c:$PYTHONPATH python $1 diff --git a/python/converters/vasp/test/inpconf/test1.cfg b/python/converters/vasp/test/inpconf/test1.cfg new file mode 100644 index 00000000..dec4cc4a --- /dev/null +++ b/python/converters/vasp/test/inpconf/test1.cfg @@ -0,0 +1,12 @@ +[General] +EFERMI = 0.7 + +[Group 1] +SHELLS = 1 + +[Shell 1] +LSHELL = 2 + +[Shell 2] +IONS = 9..20 +LSHELL = 1 diff --git a/python/converters/vasp/test/inpconf/test2.cfg b/python/converters/vasp/test/inpconf/test2.cfg new file mode 100644 index 00000000..6e0ff671 --- /dev/null +++ b/python/converters/vasp/test/inpconf/test2.cfg @@ -0,0 +1,4 @@ +[General] + +[Group 1] + diff --git a/python/converters/vasp/test/inpconf/test3.cfg b/python/converters/vasp/test/inpconf/test3.cfg new file mode 100644 index 00000000..17a54e8b --- /dev/null +++ b/python/converters/vasp/test/inpconf/test3.cfg @@ -0,0 +1,5 @@ +[General] + +[Group 1] + +[Shell x] diff --git a/python/converters/vasp/test/inpconf/test4.cfg b/python/converters/vasp/test/inpconf/test4.cfg new file mode 100644 index 00000000..ac479733 --- /dev/null +++ b/python/converters/vasp/test/inpconf/test4.cfg @@ -0,0 +1,7 @@ +[General] + +[Group 1] + +[Shell 1] +LSHELL = 2 + diff --git a/python/converters/vasp/test/inpconf/test5.cfg b/python/converters/vasp/test/inpconf/test5.cfg new file mode 100644 index 00000000..d8d32970 --- /dev/null +++ b/python/converters/vasp/test/inpconf/test5.cfg @@ -0,0 +1,17 @@ +[General] + +[Group 1] +SHELLS = 1 2 + +[Shell 1] +LSHELL = 2 +IONS = 5..8 + +[Shell 2] +LSHELL = 1 +IONS = 1..4 + +RTRANSFORM = 0.0 1.0 0.0 + 1.0 0.0 0.0 + 0.0 0.0 1.0 + diff --git a/python/converters/vasp/test/inpconf/test_inpconf.py b/python/converters/vasp/test/inpconf/test_inpconf.py new file mode 100644 index 00000000..58af01a9 --- /dev/null +++ b/python/converters/vasp/test/inpconf/test_inpconf.py @@ -0,0 +1,252 @@ +r""" +Test suite for module `inpconf.py`. +""" + +import unittest +import numpy as np +from inpconf import ConfigParameters +import ConfigParser + +class TestSpecialParsers(unittest.TestCase): + """ + Tests of special parsers. + """ + def __init__(self, *args, **kwargs): + """ + Initializes a custom equality function for comparing numpy arrays. + """ + super(TestSpecialParsers, self).__init__(*args, **kwargs) + self.addTypeEqualityFunc(np.ndarray, self.is_arrays_equal) + + def is_arrays_equal(self, arr1, arr2, msg=None): + """ + Raises self.failureException is arrays arr1 and arr2 + are not equal. + """ + if not np.allclose(arr1, arr2): + raise self.failureException(msg) + + def setUp(self): + """ + """ + pass + +################################################################################ +# +# test_parse_string_logical() +# +################################################################################ + def test_parse_string_logical(self): + """ + Function: + + def parse_string_logical(self, par_str) + + Scenarios: + + - **if** par_str == 'True' **return** True + - **if** par_str == 'False' **return** False + - **if** par_str == '0' **raise** assertion + """ + conf_pars = ConfigParameters('test1.cfg') + +# Scenario 1 + res = conf_pars.parse_string_logical('True') + self.assertEqual(res, True) + +# Scenario 2 + res = conf_pars.parse_string_logical('False') + self.assertEqual(res, False) + +# Scenario 3 + with self.assertRaises(AssertionError): + conf_pars.parse_string_logical('0') + +################################################################################ +# +# test_parse_string_ion_list() +# +################################################################################ + def test_parse_string_ion_list(self): + """ + Function: + + def parse_string_ion_list(self, par_str) + + Scenarios: + + - **if** par_str == '5 6 7 8' **return** array([4, 5, 6, 7]) + - **if** par_str == 'Ni' **raise** NotImplementedError + - **if** par_str == '0 1' **raise** AssertionError + - **if** par_str == '5..8' **return** array([4, 5, 6, 7]) + - **if** par_str == '8..5' **raise** AssertionError + """ + conf_pars = ConfigParameters('test1.cfg') + +# Scenario 1 + expected = np.array([4, 5, 6, 7]) + res = conf_pars.parse_string_ion_list('5 6 7 8') + self.assertEqual(res, expected) + +# Scenario 2 + with self.assertRaises(NotImplementedError): + conf_pars.parse_string_ion_list('Ni') + +# Scenario 3 + with self.assertRaises(AssertionError): + conf_pars.parse_string_ion_list('0 1') + +# Scenario 4 + res = conf_pars.parse_string_ion_list('5..8') + self.assertEqual(res, expected) + +# Scenario 5 + err_mess = "First index of the range" + with self.assertRaisesRegexp(AssertionError, err_mess): + conf_pars.parse_string_ion_list('8..5') + + +################################################################################ +# +# test_parse_string_tmatrix() +# +################################################################################ + def test_parse_string_tmatrix(self): + """ + Function: + + def parse_string_tmatrix(self, par_str) + + Parses a matrix defined as a set of rows in the conf-file. + + Scenarios: + + - **if** number of columns is not the same **raise** AssertionError + - **if** complex matrix is read and the number of columns is odd + **raise** AssertionError + - **if** a correct matrix is given **return** an array + + """ + conf_pars = ConfigParameters('test1.cfg') +# Scenario 1 + par_str = "1.0 0.0\n1.0" + err_mess = "Number of columns" + with self.assertRaisesRegexp(AssertionError, err_mess): + conf_pars.parse_string_tmatrix(par_str, real=True) + +# Scenario 2 + par_str = "1.0 0.0 2.0 1.0 0.0\n0.0 1.0 2.0 3.0 -1.0" + err_mess = "Complex matrix must" + with self.assertRaisesRegexp(AssertionError, err_mess): + conf_pars.parse_string_tmatrix(par_str, real=False) + +# Scenario 3 + par_str = "1.0 0.0 2.0 -3.0\n0.0 1.0 -1.0 1.0" + res = conf_pars.parse_string_tmatrix(par_str, real=False) + expected = np.array([[1.0, 2.0 - 3.0j], [1.0j, -1.0 + 1.0j]]) + self.assertEqual(res, expected) + + +################################################################################ +# +# test_parse_parameter_set() +# +################################################################################ + def test_parse_parameter_set(self): + """ + Function: + + def parse_parameter_set(self, section, param_set, excpetion=False) + + Scenarios: + + - **if** config-file section [Shell 1] contains 'LSHELL = 2' **and** + 'lshell' and 'ions' are in `param_set` **return** a dictionary {'lshell': 2} + + - **if** config-file section [Shell 1] contains 'LSHELL = 2' **and** + 'lshell' and 'ions' are in `param_set` and + exception=True **raise** Exception + """ + conf_pars = ConfigParameters('test1.cfg') + param_set = conf_pars.sh_required # contains 'lshell' and 'ions' + +# Scenario 1 + res = conf_pars.parse_parameter_set('Shell 1', param_set) + expected = {'lshell': 2} + self.assertDictEqual(res, expected) + +# Scenario 2 + section = 'Shell 1' + err_mess = "Required parameter" # .* in section [%s]"%(section) + with self.assertRaisesRegexp(Exception, err_mess): + conf_pars.parse_parameter_set(section, param_set, exception=True) + +################################################################################ +# +# test_parse_shells() +# +################################################################################ + def test_parse_shells(self): + """ + Function: + + def parse_shells(self) + + Scenarios: + + - **if** config-file does not contain a valid [Shell] section + **raise** AssertionError + - **if** a [Shell] section does not contain a valid index + **raise** ValueError + - **if** a [Shell] section does not contain all required parameters + **raise** Exception + - **if** two correct [Shell] sections are defined + **return** a dictionary of shell parameters + """ +# Scenario 1 + conf_pars = ConfigParameters('test2.cfg') + err_mess = "No projected shells" + with self.assertRaisesRegexp(AssertionError, err_mess): + conf_pars.parse_shells() + +# Scenario 2 + conf_pars = ConfigParameters('test3.cfg') + err_mess = "Failed to extract shell indices" + with self.assertRaisesRegexp(ValueError, err_mess): + conf_pars.parse_shells() + +# Scenario 3 + conf_pars = ConfigParameters('test4.cfg') + err_mess = "Required parameter" + with self.assertRaisesRegexp(Exception, err_mess): + conf_pars.parse_shells() + +# Scenario 4 + conf_pars = ConfigParameters('test5.cfg') + conf_pars.parse_shells() + res = conf_pars.shells + expected = {1: {'lshell': 2, 'ion_list': np.array([4, 5, 6, 7])}, + 2: {'lshell': 1, 'ion_list': np.array([0, 1, 2, 3]), + 'tmatrix': np.array([[ 0., 1., 0.], [ 1., 0., 0.], [ 0., 0., 1.]])}} + self.assertSetEqual(set(res.keys()), set(expected.keys())) + + arr = res[1].pop('ion_list') + arr_exp = expected[1].pop('ion_list') + self.assertEqual(arr, arr_exp) + + arr = res[2].pop('ion_list') + arr_exp = expected[2].pop('ion_list') + self.assertEqual(arr, arr_exp) + + arr = res[2].pop('tmatrix') + arr_exp = expected[2].pop('tmatrix') + self.assertEqual(arr, arr_exp) + + self.assertDictEqual(res, expected) + + +if __name__ == '__main__': + suite = unittest.TestLoader().loadTestsFromTestCase(TestSpecialParsers) +# unittest.TextTestRunner(verbosity=2, buffer=False).run(suite) + unittest.TextTestRunner(verbosity=2, buffer=True).run(suite) +