* Restructured the directory structure * Added some half-day long development including tests

python/converters/vasp/EIGENVAL

@@ -1,74 +0,0 @@
-    2    2    1    2
-  0.1333597E+02  0.2987800E-09  0.2987800E-09  0.2987800E-09  0.5000000E-15
-  1.000000000000000E-004
-  CAR 
- V                                       
-   22    4   15
- 
-  0.0000000E+00  0.0000000E+00  0.0000000E+00  0.3703704E-01
-   1      -31.708596    -31.708596
-   2      -31.708596    -31.708596
-   3      -31.708596    -31.708596
-   4      -31.061475    -31.061475
-   5      -31.061475    -31.061475
-   6      -31.061475    -31.061475
-   7       -0.811953     -0.811953
-   8        2.607665      2.607665
-   9        2.607665      2.607665
-  10        6.002735      6.002735
-  11        6.002735      6.002735
-  12        6.002735      6.002735
-  13        8.013630      8.013630
-  14        8.013630      8.013630
-  15        9.361252      9.361252
- 
-  0.3333333E+00  0.0000000E+00  0.0000000E+00  0.2222222E+00
-   1      -31.682851    -31.682851
-   2      -31.539793    -31.539793
-   3      -31.539793    -31.539793
-   4      -31.363786    -31.363786
-   5      -31.215960    -31.215960
-   6      -31.215960    -31.215960
-   7        1.216017      1.216017
-   8        3.394994      3.394994
-   9        3.771669      3.771669
-  10        6.050595      6.050595
-  11        6.050595      6.050595
-  12        6.457025      6.457025
-  13        6.771661      6.771661
-  14        7.383619      7.383619
-  15        7.383620      7.383620
- 
-  0.3333333E+00  0.3333333E+00  0.0000000E+00  0.4444444E+00
-   1      -31.935665    -31.935665
-   2      -31.782518    -31.782518
-   3      -31.447103    -31.447103
-   4      -31.284953    -31.284953
-   5      -31.234384    -31.234384
-   6      -31.067231    -31.067231
-   7        2.201004      2.201004
-   8        3.123182      3.123182
-   9        4.809697      4.809697
-  10        5.123957      5.123957
-  11        5.357025      5.357025
-  12        5.853431      5.853431
-  13        7.260017      7.260017
-  14        7.862532      7.862532
-  15        8.230907      8.230907
- 
-  0.3333333E+00  0.3333333E+00  0.3333333E+00  0.2962963E+00
-   1      -31.808727    -31.808727
-   2      -31.713049    -31.713049
-   3      -31.713049    -31.713049
-   4      -31.278227    -31.278227
-   5      -31.278227    -31.278227
-   6      -31.179331    -31.179331
-   7        3.831291      3.831291
-   8        3.998572      3.998572
-   9        4.466211      4.466211
-  10        4.466211      4.466211
-  11        4.724276      4.724276
-  12        4.724276      4.724276
-  13        8.230309      8.230309
-  14        8.253908      8.253831
-  15        8.292606      8.292606

python/converters/vasp/POSCAR

@@ -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
-Cartesian
-   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
-

python/converters/vasp/POSCAR.cart

@@ -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
-

python/converters/vasp/POSCAR.direct

@@ -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

python/converters/vasp/c/plocar_io/.gitignore

@@ -1,4 +1,5 @@
 makefile
+Makefile
 *.so
 *.o
 *.pyc

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 $@ ..
 

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
+

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
@@ -75,13 +82,25 @@ 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.
         """
+# 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
@@ -89,6 +108,9 @@ class ConfigParameters:
                 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'"
+        first_char = par_str[0].lower()
-        return par_str[0] == 't'
+        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]*)'
+        sh_patt1 = re.compile('shell +.*', re.IGNORECASE)
-        ismatch = lambda s: not re.match(sh_patt, s) is None
+        sec_shells = filter(sh_patt1.match, sections)
-        sec_shells = filter(ismatch, 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 <nshells>
@@ -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]*)'
+        gr_patt = re.compile('group *([0-9]*)')
-        ismatch = lambda s: not re.match(gr_patt, s) is None
+        sec_groups = filter(gr_patt.match, sections)
-        sec_groups = filter(ismatch, sections)
 
         self.ngroups = len(sec_groups)
 

python/converters/vasp/test.cfg

@@ -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
-

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

python/converters/vasp/test/inpconf/.gitignore

@@ -0,0 +1 @@
+*.pyc

python/converters/vasp/test/inpconf/runtest.sh

@@ -0,0 +1 @@
+PYTHONPATH=../../python:../../c:$PYTHONPATH python $1

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

python/converters/vasp/test/inpconf/test2.cfg

@@ -0,0 +1,4 @@
+[General]
+
+[Group 1]
+

python/converters/vasp/test/inpconf/test3.cfg

@@ -0,0 +1,5 @@
+[General]
+
+[Group 1]
+
+[Shell x]

python/converters/vasp/test/inpconf/test4.cfg

@@ -0,0 +1,7 @@
+[General]
+
+[Group 1]
+
+[Shell 1]
+LSHELL = 2
+

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
+

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)
+