From 4bbafa239ec1cd64152ec1850bdae0dd7ca09eb3 Mon Sep 17 00:00:00 2001 From: "Oleg E. Peil" Date: Mon, 10 Aug 2015 13:52:29 +0200 Subject: [PATCH] Added documentation on the output file formats A description of the output file formats is added to the documentation. In particular, the outline of JSON headers for projector-group (*.plog) and control (*.ctrl) files are given. --- .../converters/vasp/doc/source/plotools.rst | 55 +- python/converters/vasp/python/plotools.py | 5 + .../vasp/test/{inpconf => }/.gitignore | 0 python/converters/vasp/test/adv_example.cfg | 20 - .../converters/vasp/test/inpconf/arraytest.py | 27 - .../converters/vasp/test/inpconf/example.cfg | 29 - .../vasp/test/inpconf/example_nogroup.cfg | 7 - .../vasp/test/inpconf/input_test_1.cfg | 10 - .../vasp/test/inpconf/input_test_2.cfg | 3 - .../vasp/test/inpconf/input_test_3.cfg | 25 - .../vasp/test/inpconf/input_test_4.cfg | 24 - .../vasp/test/inpconf/parse_groups_1.cfg | 13 - .../vasp/test/inpconf/parse_shells_1.cfg | 4 - .../vasp/test/inpconf/parse_shells_2.cfg | 5 - .../vasp/test/inpconf/parse_shells_3.cfg | 7 - .../vasp/test/inpconf/parse_shells_4.cfg | 17 - .../converters/vasp/test/inpconf/runtest.sh | 1 - python/converters/vasp/test/inpconf/test1.cfg | 12 - .../vasp/test/inpconf/test_groups.py | 44 - .../vasp/test/inpconf/test_inpconf.py | 9 - .../vasp/test/inpconf/test_input.py | 107 - .../vasp/test/inpconf/test_parameter_set.py | 48 - .../vasp/test/inpconf/test_shells.py | 76 - .../vasp/test/inpconf/test_special_parsers.py | 149 - .../converters/vasp/test/plocar_io/.gitignore | 2 - .../vasp/test/plocar_io/PLOCAR.example | Bin 18276 -> 0 bytes .../vasp/test/plocar_io/PLOCAR.example.out | 2401 ----------------- .../vasp/test/plocar_io/PLOCAR.noprec | 259 -- .../vasp/test/plocar_io/PLOCAR.prec8 | Bin 4136 -> 0 bytes .../vasp/test/plocar_io/PLOCAR.prec8.out | 272 -- .../vasp/test/plocar_io/PLOCAR.trunc | Bin 9 -> 0 bytes .../converters/vasp/test/plocar_io/mytest.py | 56 - .../converters/vasp/test/plocar_io/runtest.sh | 1 - .../vasp/test/plocar_io/test_fileio.py | 93 - .../vasp/test/plocar_io/test_plocar_io.py | 10 - .../converters/vasp/test/plotools/.gitignore | 2 - python/converters/vasp/test/plotools/DOSCAR | 609 ----- python/converters/vasp/test/plotools/EIGENVAL | 50 - python/converters/vasp/test/plotools/IBZKPT | 7 - python/converters/vasp/test/plotools/OUTCAR | 1835 ------------- python/converters/vasp/test/plotools/PLOCAR | Bin 2768 -> 0 bytes python/converters/vasp/test/plotools/POSCAR | 10 - .../converters/vasp/test/plotools/densmat.out | 10 - .../converters/vasp/test/plotools/example.cfg | 8 - .../converters/vasp/test/plotools/mytest.py | 56 - .../vasp/test/plotools/projgroups.out | 115 - .../vasp/test/plotools/projortho.out | 115 - .../vasp/test/plotools/projshells.out | 115 - .../converters/vasp/test/plotools/runtest.sh | 1 - .../vasp/test/plotools/test_consistency.py | 34 - .../vasp/test/plotools/test_plotools.py | 10 - .../vasp/test/plotools/test_projgroups.py | 79 - .../vasp/test/plotools/test_projshells.py | 86 - .../vasp/test/plotools/test_select_bands.py | 73 - python/converters/vasp/test/vaspio/.gitignore | 2 - .../vasp/test/vaspio/DOSCAR.example | 609 ----- .../vasp/test/vaspio/EIGENVAL.example | 50 - .../vasp/test/vaspio/EIGENVAL.example.out | 52 - .../vasp/test/vaspio/IBZKPT.example | 122 - .../vasp/test/vaspio/IBZKPT.example.out | 122 - .../converters/vasp/test/vaspio/IBZKPT.notet | 7 - .../vasp/test/vaspio/IBZKPT.notet.out | 6 - .../vasp/test/vaspio/POSCAR.example | 10 - .../vasp/test/vaspio/POSCAR.example.out | 10 - python/converters/vasp/test/vaspio/mytest.py | 56 - python/converters/vasp/test/vaspio/runtest.sh | 1 - .../vasp/test/vaspio/test_doscar.py | 32 - .../vasp/test/vaspio/test_eigenval.py | 45 - .../vasp/test/vaspio/test_kpoints.py | 57 - .../vasp/test/vaspio/test_poscar.py | 43 - .../vasp/test/vaspio/test_vaspio.py | 11 - 71 files changed, 58 insertions(+), 8183 deletions(-) rename python/converters/vasp/test/{inpconf => }/.gitignore (100%) delete mode 100644 python/converters/vasp/test/adv_example.cfg delete mode 100644 python/converters/vasp/test/inpconf/arraytest.py delete mode 100644 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python/converters/vasp/test/vaspio/IBZKPT.notet.out delete mode 100644 python/converters/vasp/test/vaspio/POSCAR.example delete mode 100644 python/converters/vasp/test/vaspio/POSCAR.example.out delete mode 100644 python/converters/vasp/test/vaspio/mytest.py delete mode 100755 python/converters/vasp/test/vaspio/runtest.sh delete mode 100644 python/converters/vasp/test/vaspio/test_doscar.py delete mode 100644 python/converters/vasp/test/vaspio/test_eigenval.py delete mode 100644 python/converters/vasp/test/vaspio/test_kpoints.py delete mode 100644 python/converters/vasp/test/vaspio/test_poscar.py delete mode 100644 python/converters/vasp/test/vaspio/test_vaspio.py diff --git a/python/converters/vasp/doc/source/plotools.rst b/python/converters/vasp/doc/source/plotools.rst index 874e71b9..41b21da0 100644 --- a/python/converters/vasp/doc/source/plotools.rst +++ b/python/converters/vasp/doc/source/plotools.rst @@ -72,7 +72,7 @@ Consistency with parameters Selecting projector subsets ---------------------------- +=========================== The first step of PLO processing is to select subsets of projectors corresponding to PLO groups. Each group contains a set of shells. @@ -117,7 +117,7 @@ The class is using a helper function `select_bands()` for selecting a subset of .. _ortho: Orthogonalization -================= +----------------- At the second stage the selected projectors are orthogonalized (orthonormalized). Orthogonalization can be performed in different ways if projection is made @@ -138,3 +138,54 @@ The way the normalization of a PLO group is done is controlled by two group para (False by default) +Storing generated projectors +**************************** + +After the PLOs are generated they are stored to text files which can be subsequently +converted to TRIQS h5-files (using the converter). The general format of the file +is a JSON-header containing all necessary parameters followed by a set of arrays. +There is always one (control) file containing general information (`k`-kpoints, lattice vectors etc.) +and `at least` one file containing correlated groups (one file for each group). + +Control file format +=================== + +Filename '.ctrl'. Contains the data shared between all shells. +The JSON-header consists of the following elements: + + * *nk*: number of `k`-points + + * *ns*: number of spin channels + + * *nc_flag*: collinear/noncollinear case (False/True) + + * *ng*: number of projector groups + + * Symmetry information (list of symmetry operations) + + * *efermi*: Fermi level (optional) + + * Lattice information + +Projector-group file format +=========================== + +Projector-group files have names '.plog'. +They essentially contain serialized objects of class 'ProjectorGroup'. +The JSON-header has, thus, the following elements: + + * *shells*: list of shells + + * each shell is a dictionary: + + - *lshell*: orbital number `l` + + - *nion*: number of ions + + - *ndim*: number of orbitals/ion + + - *nbmax*: maxmimum number of bands (needed for array allocations) + + * *emin*, *emax*: energy window + + diff --git a/python/converters/vasp/python/plotools.py b/python/converters/vasp/python/plotools.py index 7d69c79c..6b9f9622 100644 --- a/python/converters/vasp/python/plotools.py +++ b/python/converters/vasp/python/plotools.py @@ -2,6 +2,9 @@ import itertools as it import numpy as np +# 'simplejson' is supposed to be faster than 'json' in stdlib. +import simplejson as json + class Projector: """ Class describing a local-orbital projector. @@ -394,11 +397,13 @@ def plo_output(conf_pars, pshells, pgroups): # Projected shells Nshells # Shells: + # Shell <1> Shell 1 ndim # complex arrays: plo(ns, nion, ndim, nb) ... # Shells: + # Shell <2> Shell 2 ... diff --git a/python/converters/vasp/test/inpconf/.gitignore b/python/converters/vasp/test/.gitignore similarity index 100% rename from python/converters/vasp/test/inpconf/.gitignore rename to python/converters/vasp/test/.gitignore diff --git a/python/converters/vasp/test/adv_example.cfg b/python/converters/vasp/test/adv_example.cfg deleted file mode 100644 index a02179c1..00000000 --- a/python/converters/vasp/test/adv_example.cfg +++ /dev/null @@ -1,20 +0,0 @@ -[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/arraytest.py b/python/converters/vasp/test/inpconf/arraytest.py deleted file mode 100644 index 77f04d29..00000000 --- a/python/converters/vasp/test/inpconf/arraytest.py +++ /dev/null @@ -1,27 +0,0 @@ -r""" -Module defining a custom TestCase with extra functionality. -""" - -import unittest -import numpy as np - -class ArrayTestCase(unittest.TestCase): - """ - Custom TestCase class supporting array equality. - """ - def __init__(self, *args, **kwargs): - """ - Initializes a custom equality function for comparing numpy arrays. - """ - super(ArrayTestCase, 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) - - diff --git a/python/converters/vasp/test/inpconf/example.cfg b/python/converters/vasp/test/inpconf/example.cfg deleted file mode 100644 index 4b03d4e0..00000000 --- a/python/converters/vasp/test/inpconf/example.cfg +++ /dev/null @@ -1,29 +0,0 @@ -[General] - -[Group 1] -SHELLS = 1 2 -EMIN = -7.6 -EMAX = 3.0 - -[Group 2] -SHELLS = 3 -EMIN = -1.6 -EMAX = 2.0 - -[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 - -[Shell 3] -LSHELL = 3 -IONS = 1..4 - - diff --git a/python/converters/vasp/test/inpconf/example_nogroup.cfg b/python/converters/vasp/test/inpconf/example_nogroup.cfg deleted file mode 100644 index fa4905c5..00000000 --- a/python/converters/vasp/test/inpconf/example_nogroup.cfg +++ /dev/null @@ -1,7 +0,0 @@ -[Shell 1] -LSHELL = 2 -IONS = 5..8 -EMIN = -7.6 -EMAX = 3.0 - - diff --git a/python/converters/vasp/test/inpconf/input_test_1.cfg b/python/converters/vasp/test/inpconf/input_test_1.cfg deleted file mode 100644 index 4fff1843..00000000 --- a/python/converters/vasp/test/inpconf/input_test_1.cfg +++ /dev/null @@ -1,10 +0,0 @@ -[General] -EFERMI = 0.7 - -[Shell 1] -LSHELL = 2 -IONS = 5..8 - -[Shell 2] -IONS = 9..20 -LSHELL = 1 diff --git a/python/converters/vasp/test/inpconf/input_test_2.cfg b/python/converters/vasp/test/inpconf/input_test_2.cfg deleted file mode 100644 index 3d153421..00000000 --- a/python/converters/vasp/test/inpconf/input_test_2.cfg +++ /dev/null @@ -1,3 +0,0 @@ -[Shell 1] -LSHELL = 2 -IONS = 1..4 diff --git a/python/converters/vasp/test/inpconf/input_test_3.cfg b/python/converters/vasp/test/inpconf/input_test_3.cfg deleted file mode 100644 index d2883160..00000000 --- a/python/converters/vasp/test/inpconf/input_test_3.cfg +++ /dev/null @@ -1,25 +0,0 @@ -[General] - -[Group 1] -SHELLS = 1 2 -EMIN = -7.6 -EMAX = 3.0 - -[Group 2] -SHELLS = 3 -EMIN = -1.6 -EMAX = 2.0 - -[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/input_test_4.cfg b/python/converters/vasp/test/inpconf/input_test_4.cfg deleted file mode 100644 index f8ae6295..00000000 --- a/python/converters/vasp/test/inpconf/input_test_4.cfg +++ /dev/null @@ -1,24 +0,0 @@ -[General] - -[Group 1] -SHELLS = 1 2 -EMIN = -7.6 -EMAX = 3.0 - -[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 - -[Shell 3] -LSHELL = 3 -IONS = 1..4 - - diff --git a/python/converters/vasp/test/inpconf/parse_groups_1.cfg b/python/converters/vasp/test/inpconf/parse_groups_1.cfg deleted file mode 100644 index 91aa306a..00000000 --- a/python/converters/vasp/test/inpconf/parse_groups_1.cfg +++ /dev/null @@ -1,13 +0,0 @@ -[General] - -[Group 1] -SHELLS = 1 2 - -[Shell 1] -LSHELL = 2 -IONS = 5..8 - -[Shell 2] -LSHELL = 1 -IONS = 1..4 - diff --git a/python/converters/vasp/test/inpconf/parse_shells_1.cfg b/python/converters/vasp/test/inpconf/parse_shells_1.cfg deleted file mode 100644 index 6e0ff671..00000000 --- a/python/converters/vasp/test/inpconf/parse_shells_1.cfg +++ /dev/null @@ -1,4 +0,0 @@ -[General] - -[Group 1] - diff --git a/python/converters/vasp/test/inpconf/parse_shells_2.cfg b/python/converters/vasp/test/inpconf/parse_shells_2.cfg deleted file mode 100644 index 17a54e8b..00000000 --- a/python/converters/vasp/test/inpconf/parse_shells_2.cfg +++ /dev/null @@ -1,5 +0,0 @@ -[General] - -[Group 1] - -[Shell x] diff --git a/python/converters/vasp/test/inpconf/parse_shells_3.cfg b/python/converters/vasp/test/inpconf/parse_shells_3.cfg deleted file mode 100644 index ac479733..00000000 --- a/python/converters/vasp/test/inpconf/parse_shells_3.cfg +++ /dev/null @@ -1,7 +0,0 @@ -[General] - -[Group 1] - -[Shell 1] -LSHELL = 2 - diff --git a/python/converters/vasp/test/inpconf/parse_shells_4.cfg b/python/converters/vasp/test/inpconf/parse_shells_4.cfg deleted file mode 100644 index d8d32970..00000000 --- a/python/converters/vasp/test/inpconf/parse_shells_4.cfg +++ /dev/null @@ -1,17 +0,0 @@ -[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/runtest.sh b/python/converters/vasp/test/inpconf/runtest.sh deleted file mode 100755 index 9b7bd8ca..00000000 --- a/python/converters/vasp/test/inpconf/runtest.sh +++ /dev/null @@ -1 +0,0 @@ -PYTHONPATH=../../python:../../c:$PYTHONPATH python $1 diff --git a/python/converters/vasp/test/inpconf/test1.cfg b/python/converters/vasp/test/inpconf/test1.cfg deleted file mode 100644 index dec4cc4a..00000000 --- a/python/converters/vasp/test/inpconf/test1.cfg +++ /dev/null @@ -1,12 +0,0 @@ -[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/test_groups.py b/python/converters/vasp/test/inpconf/test_groups.py deleted file mode 100644 index ed3f209d..00000000 --- a/python/converters/vasp/test/inpconf/test_groups.py +++ /dev/null @@ -1,44 +0,0 @@ -r""" -Tests of 'parse_groups()' defined in ConfigParameters class -""" -import arraytest -import numpy as np -from inpconf import ConfigParameters - -################################################################################ -# -# TestParseGroups -# -################################################################################ -class TestParseGroups(arraytest.ArrayTestCase): - """ - Function: - - def parse_groups(self) - - Scenarios: - - - **if** a [Group] section does not contain all required parameters - **raise** Exception - - **if** a correct group section is defined **return** a list of dictionaries - """ -# Scenario 1 - def test_gr_required(self): - conf_pars = ConfigParameters('parse_groups_1.cfg') - err_mess = "Required parameter" - with self.assertRaisesRegexp(Exception, err_mess): - conf_pars.parse_groups() - -# Scenario 2 - def test_example(self): - conf_pars = ConfigParameters('example.cfg') - conf_pars.parse_groups() - res = conf_pars.groups - expected = [{'index': 1, 'shells': [1, 2], 'emin': -7.6, 'emax': 3.0, - 'normalize': True, 'normion': False}, - {'index': 2, 'shells': [3], 'emin': -1.6, 'emax': 2.0, - 'normalize': True, 'normion': False}] - self.assertListEqual(res, expected) - - - diff --git a/python/converters/vasp/test/inpconf/test_inpconf.py b/python/converters/vasp/test/inpconf/test_inpconf.py deleted file mode 100644 index 9700a765..00000000 --- a/python/converters/vasp/test/inpconf/test_inpconf.py +++ /dev/null @@ -1,9 +0,0 @@ -r""" -Test suite for module `inpconf.py`. -""" -import unittest - -if __name__ == '__main__': - suite = unittest.TestLoader().discover('./') - unittest.TextTestRunner(verbosity=2, buffer=True).run(suite) - diff --git a/python/converters/vasp/test/inpconf/test_input.py b/python/converters/vasp/test/inpconf/test_input.py deleted file mode 100644 index 365b96f2..00000000 --- a/python/converters/vasp/test/inpconf/test_input.py +++ /dev/null @@ -1,107 +0,0 @@ -r""" -Tests of 'parse_input()' defined in ConfigParameters class -""" -import arraytest -import numpy as np -from inpconf import ConfigParameters - -################################################################################ -# -# TestParseInput -# -################################################################################ -class TestParseInput(arraytest.ArrayTestCase): - """ - Function: - - def parse_input(self) - - Scenarios: - - - **if** no [Group] section exists and more than one [Shell] section - is given **raise** AssertionError - - **if** no [Group] section exists but the single [Shell] section - does not contain required group information **raise** KeyError - - **if** a shell referenced in a group does not exist - **raise** Exception - - **if** not all defined shells are referenced in the groups - **raise** Exception - - **if** all sections are parsed error-free check that the output - is correct - - correct example with a single shell and no explicit groups - """ -# Scenario 1 - def test_no_group(self): - conf_pars = ConfigParameters('input_test_1.cfg') - err_mess = "At least one group" - with self.assertRaisesRegexp(AssertionError, err_mess): - conf_pars.parse_input() - -# Scenario 2 - def test_gr_required(self): - conf_pars = ConfigParameters('input_test_2.cfg') - err_mess = "One \[Shell\] section is" - with self.assertRaisesRegexp(KeyError, err_mess): - conf_pars.parse_input() - -# Scenario 3 - def test_no_shell(self): - conf_pars = ConfigParameters('input_test_3.cfg') - err_mess = "Shell 3 referenced in" - with self.assertRaisesRegexp(Exception, err_mess): - conf_pars.parse_input() - -# Scenario 4 - def test_shell_outside_groups(self): - conf_pars = ConfigParameters('input_test_4.cfg') - err_mess = "Some shells are not inside" - with self.assertRaisesRegexp(AssertionError, err_mess): - conf_pars.parse_input() - -# Scenario 5 - def test_example(self): - conf_pars = ConfigParameters('example.cfg') - conf_pars.parse_input() -# with open('parse_input.output.test', 'wt') as f: -# f.write("Shells:\n") -# f.write(conf_pars.shells.__repr__() + '\n\n') -# f.write("Groups:\n") -# f.write(conf_pars.groups.__repr__() + '\n') - res = "Shells:\n" - res += conf_pars.shells.__repr__() + '\n\n' - res += "Groups:\n" - res += conf_pars.groups.__repr__() - - expected = r"""Shells: -[{'ion_list': array([4, 5, 6, 7]), 'user_index': 1, 'lshell': 2}, {'tmatrix': array([[ 0., 1., 0.], - [ 1., 0., 0.], - [ 0., 0., 1.]]), 'ion_list': array([0, 1, 2, 3]), 'user_index': 2, 'lshell': 1}, {'ion_list': array([0, 1, 2, 3]), 'user_index': 3, 'lshell': 3}] - -Groups: -[{'normalize': True, 'index': 1, 'shells': [0, 1], 'normion': False, 'emax': 3.0, 'emin': -7.6}, {'normalize': True, 'index': 2, 'shells': [2], 'normion': False, 'emax': 2.0, 'emin': -1.6}]""" - - self.assertEqual(res, expected) - -# Scenario 6 - def test_example_no_groups(self): - conf_pars = ConfigParameters('example_nogroup.cfg') - conf_pars.parse_input() -# with open('parse_input.output.test', 'wt') as f: -# f.write("Shells:\n") -# f.write(conf_pars.shells.__repr__() + '\n\n') -# f.write("Groups:\n") -# f.write(conf_pars.groups.__repr__() + '\n') - res = "Shells:\n" - res += conf_pars.shells.__repr__() + '\n\n' - res += "Groups:\n" - res += conf_pars.groups.__repr__() - - expected = r"""Shells: -[{'ion_list': array([4, 5, 6, 7]), 'user_index': 1, 'lshell': 2}] - -Groups: -[{'normalize': True, 'index': '1', 'emin': -7.6, 'emax': 3.0, 'normion': False, 'shells': [0]}]""" - - self.assertEqual(res, expected) - - diff --git a/python/converters/vasp/test/inpconf/test_parameter_set.py b/python/converters/vasp/test/inpconf/test_parameter_set.py deleted file mode 100644 index fb5bc988..00000000 --- a/python/converters/vasp/test/inpconf/test_parameter_set.py +++ /dev/null @@ -1,48 +0,0 @@ -r""" -Tests of 'parse_parameter_set()' defined in ConfigParameters class -""" -import arraytest -import numpy as np -from inpconf import ConfigParameters - -################################################################################ -# -# TestParseParameterSet -# -################################################################################ -class TestParseParameterSet(arraytest.ArrayTestCase): - """ - 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 - """ - def setUp(self): - """ - """ -# Dummy ConfigParameters object - self.cpars = ConfigParameters('test1.cfg') - -# Scenario 1 - def test_sh_required(self): - param_set = self.cpars.sh_required # contains 'lshell' and 'ions' - res = self.cpars.parse_parameter_set('Shell 1', param_set) - expected = {'lshell': 2} - self.assertDictEqual(res, expected) - -# Scenario 2 - def test_sh_required_exception(self): - section = 'Shell 1' - param_set = self.cpars.sh_required # contains 'lshell' and 'ions' - err_mess = "Required parameter" # .* in section [%s]"%(section) - with self.assertRaisesRegexp(Exception, err_mess): - self.cpars.parse_parameter_set(section, param_set, exception=True) - diff --git a/python/converters/vasp/test/inpconf/test_shells.py b/python/converters/vasp/test/inpconf/test_shells.py deleted file mode 100644 index 24f73981..00000000 --- a/python/converters/vasp/test/inpconf/test_shells.py +++ /dev/null @@ -1,76 +0,0 @@ -r""" -Tests of 'parse_shells()' defined in ConfigParameters class -""" -import arraytest -import numpy as np -from inpconf import ConfigParameters - -################################################################################ -# -# TestParseShells -# -################################################################################ -class TestParseShells(arraytest.ArrayTestCase): - """ - 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 - def test_no_shell(self): - conf_pars = ConfigParameters('parse_shells_1.cfg') - err_mess = "No projected shells" - with self.assertRaisesRegexp(AssertionError, err_mess): - conf_pars.parse_shells() - -# Scenario 2 - def test_bad_indices(self): - conf_pars = ConfigParameters('parse_shells_2.cfg') - err_mess = "Failed to extract shell indices" - with self.assertRaisesRegexp(ValueError, err_mess): - conf_pars.parse_shells() - -# Scenario 3 - def test_sh_required(self): - conf_pars = ConfigParameters('parse_shells_3.cfg') - err_mess = "Required parameter" - with self.assertRaisesRegexp(Exception, err_mess): - conf_pars.parse_shells() - -# Scenario 4 - def test_two_shells(self): - conf_pars = ConfigParameters('parse_shells_4.cfg') - conf_pars.parse_shells() - res = conf_pars.shells - expected = [{'user_index': 1, 'lshell': 2, 'ion_list': np.array([4, 5, 6, 7])}, - {'user_index': 2, 'lshell': 1, 'ion_list': np.array([0, 1, 2, 3]), - 'tmatrix': np.array([[ 0., 1., 0.], [ 1., 0., 0.], [ 0., 0., 1.]])}] -# ...lousy way to test equality of two dictionaries containing numpy arrays - self.assertEqual(len(res), len(expected)) - - arr = res[0].pop('ion_list') - arr_exp = expected[0].pop('ion_list') - self.assertEqual(arr, arr_exp) - - arr = res[1].pop('ion_list') - arr_exp = expected[1].pop('ion_list') - self.assertEqual(arr, arr_exp) - - arr = res[1].pop('tmatrix') - arr_exp = expected[1].pop('tmatrix') - self.assertEqual(arr, arr_exp) - - self.assertListEqual(res, expected) - - diff --git a/python/converters/vasp/test/inpconf/test_special_parsers.py b/python/converters/vasp/test/inpconf/test_special_parsers.py deleted file mode 100644 index 233c44a0..00000000 --- a/python/converters/vasp/test/inpconf/test_special_parsers.py +++ /dev/null @@ -1,149 +0,0 @@ -r""" -Tests of special parseres defined in ConfigParameters class -""" -import arraytest -import numpy as np -from inpconf import ConfigParameters - -################################################################################ -# -# TestParseStringLogical -# -################################################################################ -class TestParseStringLogical(arraytest.ArrayTestCase): - """ - 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 - """ - def setUp(self): - """ - """ -# Dummy ConfigParameters object - self.cpars = ConfigParameters('test1.cfg') - -# Scenario 1 - def test_true(self): - res = self.cpars.parse_string_logical('True') - self.assertEqual(res, True) - -# Scenario 2 - def test_false(self): - res = self.cpars.parse_string_logical('False') - self.assertEqual(res, False) - -# Scenario 3 - def test_incorrect(self): - with self.assertRaises(AssertionError): - self.cpars.parse_string_logical('0') - -################################################################################ -# -# TestParseStringIonList -# -################################################################################ -class TestParseStringIonList(arraytest.ArrayTestCase): - """ - 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 - """ - def setUp(self): - """ - """ -# Dummy ConfigParameters object - self.cpars = ConfigParameters('test1.cfg') - -# Scenario 1 - def test_simple_list(self): - expected = np.array([4, 5, 6, 7]) - res = self.cpars.parse_string_ion_list('5 6 7 8') - self.assertEqual(res, expected) - -# Scenario 2 - def test_atomic_symbol(self): - with self.assertRaises(NotImplementedError): - self.cpars.parse_string_ion_list('Ni') - -# Scenario 3 - def test_out_of_bounds(self): - err_mess = "Lowest ion index is" - with self.assertRaisesRegexp(AssertionError, err_mess): - self.cpars.parse_string_ion_list('0 1') - -# Scenario 4 - def test_list_range(self): - expected = np.array([4, 5, 6, 7]) - res = self.cpars.parse_string_ion_list('5..8') - self.assertEqual(res, expected) - -# Scenario 5 - def test_range_wrong_order(self): - err_mess = "First index of the range" - with self.assertRaisesRegexp(AssertionError, err_mess): - self.cpars.parse_string_ion_list('8..5') - - -################################################################################ -# -# TestParseStringTmatrix -# -################################################################################ -class TestParseStringTmatrix(arraytest.ArrayTestCase): - """ - 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 - - """ - def setUp(self): - """ - """ -# Dummy ConfigParameters object - self.cpars = ConfigParameters('test1.cfg') - -# Scenario 1 - def test_number_of_columns(self): - par_str = "1.0 0.0\n1.0" - err_mess = "Number of columns" - with self.assertRaisesRegexp(AssertionError, err_mess): - self.cpars.parse_string_tmatrix(par_str, real=True) - -# Scenario 2 - def test_complex_matrix_odd(self): - 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): - self.cpars.parse_string_tmatrix(par_str, real=False) - -# Scenario 3 - def test_complex_matrix(self): - par_str = "1.0 0.0 2.0 -3.0\n0.0 1.0 -1.0 1.0" - res = self.cpars.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) - - diff --git a/python/converters/vasp/test/plocar_io/.gitignore b/python/converters/vasp/test/plocar_io/.gitignore deleted file mode 100644 index 1ed2bd4a..00000000 --- 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b/python/converters/vasp/test/plocar_io/PLOCAR.trunc deleted file mode 100644 index c45ed08a22f3a1f375efeed9f0525e1edb5702dd..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 9 OcmZQ!U|?VbVlDsxJOB^? diff --git a/python/converters/vasp/test/plocar_io/mytest.py b/python/converters/vasp/test/plocar_io/mytest.py deleted file mode 100644 index 1490b477..00000000 --- a/python/converters/vasp/test/plocar_io/mytest.py +++ /dev/null @@ -1,56 +0,0 @@ -r""" -Module defining a custom TestCase with extra functionality. -""" - -import unittest -import numpy as np -import difflib - -class MyTestCase(unittest.TestCase): - """ - Custom TestCase class supporting additional equality checks: - - numpy array equality - - file equality - """ - def __init__(self, *args, **kwargs): - """ - Initializes a custom equality function for comparing numpy arrays. - """ - super(MyTestCase, 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 assertFileEqual(self, file1, file2): - """ - Compares two files using difflib. - Empty lines are ignored. - Files are assumed to be relatively small, otherwise - the data is truncated. - """ - MAX_SIZE = 100000 - with open(file1, 'r') as f1: - str1 = f1.read(MAX_SIZE) - with open(file2, 'r') as f2: - str2 = f2.read(MAX_SIZE) -# -# Make a diff -# -# Remove empty lines - lstr1 = filter(lambda s: s.strip() != '', str1.splitlines(True)) - lstr2 = filter(lambda s: s.strip() != '', str2.splitlines(True)) -# diff - delta = difflib.unified_diff(lstr1, lstr2) -# combine delta's to a string - diff = ''.join(delta) -# if 'diff' is non-empty, files are different - if diff: - return self.fail("Files '%s' and '%s' differ"%(file1, file2)) - - diff --git a/python/converters/vasp/test/plocar_io/runtest.sh b/python/converters/vasp/test/plocar_io/runtest.sh deleted file mode 100755 index 9b7bd8ca..00000000 --- a/python/converters/vasp/test/plocar_io/runtest.sh +++ /dev/null @@ -1 +0,0 @@ -PYTHONPATH=../../python:../../c:$PYTHONPATH python $1 diff --git a/python/converters/vasp/test/plocar_io/test_fileio.py b/python/converters/vasp/test/plocar_io/test_fileio.py deleted file mode 100644 index 59e013af..00000000 --- a/python/converters/vasp/test/plocar_io/test_fileio.py +++ /dev/null @@ -1,93 +0,0 @@ -r""" -Tests of 'read_plocar()' from module 'plocar_io.c_plocar_io' -""" -import mytest -import numpy as np -from plocar_io.c_plocar_io import read_plocar - -################################################################################ -# -# TestFileIO -# -################################################################################ -class TestFileIO(mytest.MyTestCase): - """ - Function: - - def read_plocar(filename) - - Scenarios: - - - **if** file PLOCAR does not exist **raise** IOError - - **if** PLOCAR is truncated **raise** IOError - - **if** the precision flag is not 4 or 8 **raise** ValueError - - **if** PLOCAR with prec=8 is read **compare** the output - - **if** PLOCAR with prec=4 is read **compare** the output - """ -# Scenario 1 - def test_no_plocar(self): - err_mess = "Error opening xPLOCAR" - with self.assertRaisesRegexp(IOError, err_mess): - read_plocar('xPLOCAR') - -# Scenario 2 - def test_end_of_file(self): - err_mess = "End-of-file reading" - with self.assertRaisesRegexp(IOError, err_mess): - read_plocar('PLOCAR.trunc') - -# Scenario 3 - def test_wrong_prec(self): - err_mess = "only 'prec = 4, 8' are supported" - with self.assertRaisesRegexp(ValueError, err_mess): - read_plocar('PLOCAR.noprec') - -# Scenario 4 - def test_plocar_prec8(self): - pars, plo, ferw = read_plocar('PLOCAR.prec8') - nion, ns, nk, nb, nlm = plo.shape - - test_file = 'PLOCAR.prec8.out.test' - with open(test_file, 'wt') as f: - f.write(" nlm =%5i\n"%(nlm)) - ion = 1 - isp = 1 - for ik in xrange(nk): - for ib in xrange(nb): - f.write("%5i%5i%5i%5i%10.5f\n"%(ion, isp, ik+1, ib+1, ferw[0, 0, ik, ib])) - for ilm in xrange(nlm): - p = plo[0, 0, ik, ib, ilm] - f.write("%5i%15.7f%15.7f\n"%(ilm+1, p.real, p.imag)) - - expected_file = 'PLOCAR.prec8.out' - self.assertFileEqual(test_file, expected_file) - -# Scenario 5 - def test_plocar_example(self): - pars, plo, ferw = read_plocar('PLOCAR.example') - nion, ns, nk, nb, nlm = plo.shape - - self.assertEqual(pars['nion'], nion) - self.assertEqual(pars['ns'], ns) - self.assertEqual(pars['nk'], nk) - self.assertEqual(pars['nb'], nb) - - test_file = 'PLOCAR.example.out.test' - with open(test_file, 'wt') as f: - f.write("pars: %s\n"%(pars)) - for ion in xrange(nion): - for isp in xrange(ns): - for ik in xrange(nk): - for ib in xrange(nb): - f.write("%5i%5i%5i%5i %s\n"%(ion+1, isp+1, ik+1, ib+1, - ferw[ion, isp, ik, ib])) - for ilm in xrange(nlm): - p = plo[ion, isp, ik, ib, ilm] - f.write("%5i %s\n"%(ilm+1, p)) - - expected_file = 'PLOCAR.example.out' - self.assertFileEqual(test_file, expected_file) - - - - diff --git a/python/converters/vasp/test/plocar_io/test_plocar_io.py b/python/converters/vasp/test/plocar_io/test_plocar_io.py deleted file mode 100644 index 3bb77c5f..00000000 --- a/python/converters/vasp/test/plocar_io/test_plocar_io.py +++ /dev/null @@ -1,10 +0,0 @@ -r""" -Test suite for module `plocar_io`. -""" -import unittest - -if __name__ == '__main__': - suite = unittest.TestLoader().discover('./') - unittest.TextTestRunner(verbosity=2, buffer=True).run(suite) -# unittest.TextTestRunner(verbosity=2, buffer=False).run(suite) - diff --git a/python/converters/vasp/test/plotools/.gitignore b/python/converters/vasp/test/plotools/.gitignore deleted file mode 100644 index 1ed2bd4a..00000000 --- a/python/converters/vasp/test/plotools/.gitignore +++ /dev/null @@ -1,2 +0,0 @@ -*.pyc -*.test diff --git a/python/converters/vasp/test/plotools/DOSCAR 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1.000000000000000E-004 - CAR - V - 11 4 9 - - 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3703704E-01 - 1 -31.099965 - 2 -31.099965 - 3 -31.099965 - 4 -0.813470 - 5 5.974027 - 6 5.974027 - 7 5.974027 - 8 7.986328 - 9 7.986328 - - 0.3333333E+00 0.0000000E+00 0.0000000E+00 0.4444444E+00 - 1 -31.819277 - 2 -31.322999 - 3 -31.105684 - 4 2.193081 - 5 4.784864 - 6 5.839340 - 7 7.833446 - 8 8.202781 - 9 8.589551 - - 0.3333333E+00 0.3333333E+00 0.0000000E+00 0.2962963E+00 - 1 -31.750021 - 2 -31.750021 - 3 -31.217560 - 4 3.978315 - 5 4.708263 - 6 4.708263 - 7 8.262522 - 8 8.262522 - 9 14.771374 - - -0.3333333E+00 0.3333333E+00 0.3333333E+00 0.2222222E+00 - 1 -31.719893 - 2 -31.577292 - 3 -31.577292 - 4 3.383714 - 5 3.756320 - 6 7.355029 - 7 7.355029 - 8 8.411511 - 9 11.054129 diff --git a/python/converters/vasp/test/plotools/IBZKPT b/python/converters/vasp/test/plotools/IBZKPT deleted file mode 100644 index e724e052..00000000 --- a/python/converters/vasp/test/plotools/IBZKPT +++ /dev/null @@ -1,7 +0,0 @@ -Automatically generated mesh - 4 -Reciprocal lattice - 0.00000000000000 0.00000000000000 0.00000000000000 1 - 0.33333333333333 0.00000000000000 0.00000000000000 12 - 0.33333333333333 0.33333333333333 0.00000000000000 8 - -0.33333333333333 0.33333333333333 0.33333333333333 6 diff --git a/python/converters/vasp/test/plotools/OUTCAR b/python/converters/vasp/test/plotools/OUTCAR deleted file mode 100644 index 61b740df..00000000 --- a/python/converters/vasp/test/plotools/OUTCAR +++ /dev/null @@ -1,1835 +0,0 @@ - vasp.5.3.3 18Dez12 (build Jan 22 2015 14:01:41) complex - - executed on gfortran date 2015.02.19 13:40:40 - running on 1 total cores - distrk: each k-point on 1 cores, 1 groups - distr: one band on NCORES_PER_BAND= 1 cores, 1 groups - - --------------------------------------------------------------------------------------------------------- - - - INCAR: - POTCAR: PAW V_pv 07Sep2000 - POTCAR: PAW V_pv 07Sep2000 - VRHFIN =V: p6 d4 s1 - LEXCH = CA - EATOM = 1323.7742 eV, 97.2947 Ry - - TITEL = PAW V_pv 07Sep2000 - LULTRA = F use ultrasoft PP ? - IUNSCR = 1 unscreen: 0-lin 1-nonlin 2-no - RPACOR = 1.700 partial core radius - POMASS = 50.941; ZVAL = 11.000 mass and valenz - RCORE = 2.300 outmost cutoff radius - RWIGS = 2.300; RWIGS = 1.217 wigner-seitz radius (au A) - ENMAX = 263.722; ENMIN = 197.791 eV - RCLOC = 1.779 cutoff for local pot - LCOR = T correct aug charges - LPAW = T paw PP - EAUG = 598.473 - DEXC = 0.000 - RMAX = 2.359 core radius for proj-oper - RAUG = 1.300 factor for augmentation sphere - RDEP = 2.430 radius for radial grids - RDEPT = 1.700 core radius for aug-charge - - Atomic configuration - 8 entries - n l j E occ. - 1 0 0.50 -5334.6266 2.0000 - 2 0 0.50 -595.8619 2.0000 - 2 1 1.50 -498.2253 6.0000 - 3 0 0.50 -66.0397 2.0000 - 3 1 1.50 -40.3980 6.0000 - 3 2 2.50 -2.6339 4.0000 - 4 0 0.50 -4.0393 1.0000 - 4 3 2.50 -1.3606 0.0000 - Description - l E TYP RCUT TYP RCUT - 1 -40.3979618 23 2.000 - 1 5.4423304 23 2.000 - 2 -2.6338670 23 2.300 - 2 -1.2520253 23 2.300 - 0 -4.0392529 23 2.300 - 0 27.2116520 23 2.300 - local pseudopotential read in - partial core-charges read in - partial kinetic energy density read in - atomic valenz-charges read in - non local Contribution for L= 1 read in - real space projection operators read in - non local Contribution for L= 1 read in - real space projection operators read in - non local Contribution for L= 2 read in - real space projection operators read in - non local Contribution for L= 2 read in - real space projection operators read in - non local Contribution for L= 0 read in - real space projection operators read in - non local Contribution for L= 0 read in - real space projection operators read in - PAW grid and wavefunctions read in - - number of l-projection operators is LMAX = 6 - number of lm-projection operators is LMMAX = 18 - - PAW V_pv 07Sep2000 : - energy of atom 1 EATOM=-1323.7742 - kinetic energy error for atom= 0.0058 (will be added to EATOM!!) - - - POSCAR: V SF test - positions in direct lattice - velocities in cartesian coordinates - No initial velocities read in - exchange correlation table for LEXCH = 2 - RHO(1)= 0.500 N(1) = 2000 - RHO(2)= 100.500 N(2) = 4000 - - - --------------------------------------------------------------------------------------------------------- - - - ion position nearest neighbor table - 1 0.000 0.000 0.000- - - LATTYP: Found a body centered cubic cell. - ALAT = 2.9878000000 - - Lattice vectors: - - A1 = ( -1.4939000000, 1.4939000000, 1.4939000000) - A2 = ( 1.4939000000, -1.4939000000, 1.4939000000) - A3 = ( 1.4939000000, 1.4939000000, -1.4939000000) - - -Analysis of symmetry for initial positions (statically): -===================================================================== - Subroutine PRICEL returns: - Original cell was already a primitive cell. - - - Routine SETGRP: Setting up the symmetry group for a - body centered cubic supercell. - - - Subroutine GETGRP returns: Found 48 space group operations - (whereof 48 operations were pure point group operations) - out of a pool of 48 trial point group operations. - - -The static configuration has the point symmetry O_h . - - -Analysis of symmetry for dynamics (positions and initial velocities): -===================================================================== - Subroutine PRICEL returns: - Original cell was already a primitive cell. - - - Routine SETGRP: Setting up the symmetry group for a - body centered cubic supercell. - - - Subroutine GETGRP returns: Found 48 space group operations - (whereof 48 operations were pure point group operations) - out of a pool of 48 trial point group operations. - - -The dynamic configuration has the point symmetry O_h . - - - irot : 1 - -------------------------------------------------------------------- - isymop: 1 0 0 - 0 1 0 - 0 0 1 - - gtrans: 0.0000000 0.0000000 0.0000000 - - ptrans: 0.0000000 0.0000000 0.0000000 - rotmap: - ( 1-> 1) - - - irot : 2 - -------------------------------------------------------------------- - isymop: -1 0 0 - 0 -1 0 - 0 0 -1 - - gtrans: 0.0000000 0.0000000 0.0000000 - - ptrans: 0.0000000 0.0000000 0.0000000 - rotmap: - ( 1-> 1) - - - irot : 3 - -------------------------------------------------------------------- - isymop: 0 0 1 - 1 0 0 - 0 1 0 - - gtrans: 0.0000000 0.0000000 0.0000000 - - ptrans: 0.0000000 0.0000000 0.0000000 - rotmap: - ( 1-> 1) - - - irot : 4 - -------------------------------------------------------------------- - isymop: 0 0 -1 - -1 0 0 - 0 -1 0 - - gtrans: 0.0000000 0.0000000 0.0000000 - - ptrans: 0.0000000 0.0000000 0.0000000 - rotmap: - ( 1-> 1) - - - irot : 5 - -------------------------------------------------------------------- - isymop: 0 1 0 - 0 0 1 - 1 0 0 - - gtrans: 0.0000000 0.0000000 0.0000000 - - ptrans: 0.0000000 0.0000000 0.0000000 - rotmap: - ( 1-> 1) - - - irot : 6 - -------------------------------------------------------------------- - isymop: 0 -1 0 - 0 0 -1 - -1 0 0 - - gtrans: 0.0000000 0.0000000 0.0000000 - - ptrans: 0.0000000 0.0000000 0.0000000 - rotmap: - ( 1-> 1) - - - irot : 7 - -------------------------------------------------------------------- - isymop: 0 1 0 - 0 1 -1 - -1 1 0 - - gtrans: 0.0000000 0.0000000 0.0000000 - - ptrans: 0.0000000 0.0000000 0.0000000 - rotmap: - ( 1-> 1) - - - irot : 8 - -------------------------------------------------------------------- - isymop: 0 -1 0 - 0 -1 1 - 1 -1 0 - - gtrans: 0.0000000 0.0000000 0.0000000 - - ptrans: 0.0000000 0.0000000 0.0000000 - rotmap: - ( 1-> 1) - - - irot : 9 - -------------------------------------------------------------------- - isymop: 1 0 0 - 1 -1 0 - 1 0 -1 - - gtrans: 0.0000000 0.0000000 0.0000000 - - ptrans: 0.0000000 0.0000000 0.0000000 - rotmap: - ( 1-> 1) - - - irot : 10 - -------------------------------------------------------------------- - isymop: -1 0 0 - -1 1 0 - -1 0 1 - - gtrans: 0.0000000 0.0000000 0.0000000 - - ptrans: 0.0000000 0.0000000 0.0000000 - rotmap: - ( 1-> 1) - - - irot : 11 - -------------------------------------------------------------------- - isymop: 0 0 1 - -1 0 1 - 0 -1 1 - - gtrans: 0.0000000 0.0000000 0.0000000 - - ptrans: 0.0000000 0.0000000 0.0000000 - rotmap: - ( 1-> 1) - - - irot : 12 - -------------------------------------------------------------------- - isymop: 0 0 -1 - 1 0 -1 - 0 1 -1 - - gtrans: 0.0000000 0.0000000 0.0000000 - - ptrans: 0.0000000 0.0000000 0.0000000 - rotmap: - ( 1-> 1) - - - irot : 13 - -------------------------------------------------------------------- - isymop: 0 1 -1 - 1 0 -1 - 0 0 -1 - - gtrans: 0.0000000 0.0000000 0.0000000 - - ptrans: 0.0000000 0.0000000 0.0000000 - rotmap: - ( 1-> 1) - - - irot : 14 - -------------------------------------------------------------------- - isymop: 0 -1 1 - -1 0 1 - 0 0 1 - - gtrans: 0.0000000 0.0000000 0.0000000 - - ptrans: 0.0000000 0.0000000 0.0000000 - rotmap: - ( 1-> 1) - - - irot : 15 - -------------------------------------------------------------------- - isymop: 1 -1 0 - 0 -1 1 - 0 -1 0 - - gtrans: 0.0000000 0.0000000 0.0000000 - - ptrans: 0.0000000 0.0000000 0.0000000 - rotmap: - ( 1-> 1) - - - irot : 16 - -------------------------------------------------------------------- - isymop: -1 1 0 - 0 1 -1 - 0 1 0 - - gtrans: 0.0000000 0.0000000 0.0000000 - - ptrans: 0.0000000 0.0000000 0.0000000 - rotmap: - ( 1-> 1) - - - irot : 17 - -------------------------------------------------------------------- - isymop: -1 0 1 - -1 1 0 - -1 0 0 - - gtrans: 0.0000000 0.0000000 0.0000000 - - ptrans: 0.0000000 0.0000000 0.0000000 - rotmap: - ( 1-> 1) - - - irot : 18 - -------------------------------------------------------------------- - isymop: 1 0 -1 - 1 -1 0 - 1 0 0 - - gtrans: 0.0000000 0.0000000 0.0000000 - - ptrans: 0.0000000 0.0000000 0.0000000 - rotmap: - ( 1-> 1) - - - irot : 19 - -------------------------------------------------------------------- - isymop: 1 0 -1 - 1 0 0 - 1 -1 0 - - gtrans: 0.0000000 0.0000000 0.0000000 - - ptrans: 0.0000000 0.0000000 0.0000000 - rotmap: - ( 1-> 1) - - - irot : 20 - -------------------------------------------------------------------- - isymop: -1 0 1 - -1 0 0 - -1 1 0 - - gtrans: 0.0000000 0.0000000 0.0000000 - - ptrans: 0.0000000 0.0000000 0.0000000 - rotmap: - ( 1-> 1) - - - irot : 21 - -------------------------------------------------------------------- - isymop: 0 -1 1 - 0 0 1 - -1 0 1 - - gtrans: 0.0000000 0.0000000 0.0000000 - - ptrans: 0.0000000 0.0000000 0.0000000 - rotmap: - ( 1-> 1) - - - irot : 22 - -------------------------------------------------------------------- - isymop: 0 1 -1 - 0 0 -1 - 1 0 -1 - - gtrans: 0.0000000 0.0000000 0.0000000 - - ptrans: 0.0000000 0.0000000 0.0000000 - rotmap: - ( 1-> 1) - - - irot : 23 - -------------------------------------------------------------------- - isymop: -1 1 0 - 0 1 0 - 0 1 -1 - - gtrans: 0.0000000 0.0000000 0.0000000 - - ptrans: 0.0000000 0.0000000 0.0000000 - rotmap: - ( 1-> 1) - - - irot : 24 - -------------------------------------------------------------------- - isymop: 1 -1 0 - 0 -1 0 - 0 -1 1 - - gtrans: 0.0000000 0.0000000 0.0000000 - - ptrans: 0.0000000 0.0000000 0.0000000 - rotmap: - ( 1-> 1) - - - irot : 25 - -------------------------------------------------------------------- - isymop: 0 0 -1 - 0 1 -1 - 1 0 -1 - - gtrans: 0.0000000 0.0000000 0.0000000 - - ptrans: 0.0000000 0.0000000 0.0000000 - rotmap: - ( 1-> 1) - - - irot : 26 - -------------------------------------------------------------------- - isymop: 0 0 1 - 0 -1 1 - -1 0 1 - - gtrans: 0.0000000 0.0000000 0.0000000 - - ptrans: 0.0000000 0.0000000 0.0000000 - rotmap: - ( 1-> 1) - - - irot : 27 - -------------------------------------------------------------------- - isymop: 0 -1 0 - 1 -1 0 - 0 -1 1 - - gtrans: 0.0000000 0.0000000 0.0000000 - - ptrans: 0.0000000 0.0000000 0.0000000 - rotmap: - ( 1-> 1) - - - irot : 28 - -------------------------------------------------------------------- - isymop: 0 1 0 - -1 1 0 - 0 1 -1 - - gtrans: 0.0000000 0.0000000 0.0000000 - - ptrans: 0.0000000 0.0000000 0.0000000 - rotmap: - ( 1-> 1) - - - irot : 29 - -------------------------------------------------------------------- - isymop: -1 0 0 - -1 0 1 - -1 1 0 - - gtrans: 0.0000000 0.0000000 0.0000000 - - ptrans: 0.0000000 0.0000000 0.0000000 - rotmap: - ( 1-> 1) - - - irot : 30 - -------------------------------------------------------------------- - isymop: 1 0 0 - 1 0 -1 - 1 -1 0 - - gtrans: 0.0000000 0.0000000 0.0000000 - - ptrans: 0.0000000 0.0000000 0.0000000 - rotmap: - ( 1-> 1) - - - irot : 31 - -------------------------------------------------------------------- - isymop: 1 -1 0 - 1 0 -1 - 1 0 0 - - gtrans: 0.0000000 0.0000000 0.0000000 - - ptrans: 0.0000000 0.0000000 0.0000000 - rotmap: - ( 1-> 1) - - - irot : 32 - -------------------------------------------------------------------- - isymop: -1 1 0 - -1 0 1 - -1 0 0 - - gtrans: 0.0000000 0.0000000 0.0000000 - - ptrans: 0.0000000 0.0000000 0.0000000 - rotmap: - ( 1-> 1) - - - irot : 33 - -------------------------------------------------------------------- - isymop: -1 0 1 - 0 -1 1 - 0 0 1 - - gtrans: 0.0000000 0.0000000 0.0000000 - - ptrans: 0.0000000 0.0000000 0.0000000 - rotmap: - ( 1-> 1) - - - irot : 34 - -------------------------------------------------------------------- - isymop: 1 0 -1 - 0 1 -1 - 0 0 -1 - - gtrans: 0.0000000 0.0000000 0.0000000 - - ptrans: 0.0000000 0.0000000 0.0000000 - rotmap: - ( 1-> 1) - - - irot : 35 - -------------------------------------------------------------------- - isymop: 0 1 -1 - -1 1 0 - 0 1 0 - - gtrans: 0.0000000 0.0000000 0.0000000 - - ptrans: 0.0000000 0.0000000 0.0000000 - rotmap: - ( 1-> 1) - - - irot : 36 - -------------------------------------------------------------------- - isymop: 0 -1 1 - 1 -1 0 - 0 -1 0 - - gtrans: 0.0000000 0.0000000 0.0000000 - - ptrans: 0.0000000 0.0000000 0.0000000 - rotmap: - ( 1-> 1) - - - irot : 37 - -------------------------------------------------------------------- - isymop: 1 0 -1 - 0 0 -1 - 0 1 -1 - - gtrans: 0.0000000 0.0000000 0.0000000 - - ptrans: 0.0000000 0.0000000 0.0000000 - rotmap: - ( 1-> 1) - - - irot : 38 - -------------------------------------------------------------------- - isymop: -1 0 1 - 0 0 1 - 0 -1 1 - - gtrans: 0.0000000 0.0000000 0.0000000 - - ptrans: 0.0000000 0.0000000 0.0000000 - rotmap: - ( 1-> 1) - - - irot : 39 - -------------------------------------------------------------------- - isymop: 0 -1 1 - 0 -1 0 - 1 -1 0 - - gtrans: 0.0000000 0.0000000 0.0000000 - - ptrans: 0.0000000 0.0000000 0.0000000 - rotmap: - ( 1-> 1) - - - irot : 40 - -------------------------------------------------------------------- - isymop: 0 1 -1 - 0 1 0 - -1 1 0 - - gtrans: 0.0000000 0.0000000 0.0000000 - - ptrans: 0.0000000 0.0000000 0.0000000 - rotmap: - ( 1-> 1) - - - irot : 41 - -------------------------------------------------------------------- - isymop: -1 1 0 - -1 0 0 - -1 0 1 - - gtrans: 0.0000000 0.0000000 0.0000000 - - ptrans: 0.0000000 0.0000000 0.0000000 - rotmap: - ( 1-> 1) - - - irot : 42 - -------------------------------------------------------------------- - isymop: 1 -1 0 - 1 0 0 - 1 0 -1 - - gtrans: 0.0000000 0.0000000 0.0000000 - - ptrans: 0.0000000 0.0000000 0.0000000 - rotmap: - ( 1-> 1) - - - irot : 43 - -------------------------------------------------------------------- - isymop: -1 0 0 - 0 0 -1 - 0 -1 0 - - gtrans: 0.0000000 0.0000000 0.0000000 - - ptrans: 0.0000000 0.0000000 0.0000000 - rotmap: - ( 1-> 1) - - - irot : 44 - -------------------------------------------------------------------- - isymop: 1 0 0 - 0 0 1 - 0 1 0 - - gtrans: 0.0000000 0.0000000 0.0000000 - - ptrans: 0.0000000 0.0000000 0.0000000 - rotmap: - ( 1-> 1) - - - irot : 45 - -------------------------------------------------------------------- - isymop: 0 -1 0 - -1 0 0 - 0 0 -1 - - gtrans: 0.0000000 0.0000000 0.0000000 - - ptrans: 0.0000000 0.0000000 0.0000000 - rotmap: - ( 1-> 1) - - - irot : 46 - -------------------------------------------------------------------- - isymop: 0 1 0 - 1 0 0 - 0 0 1 - - gtrans: 0.0000000 0.0000000 0.0000000 - - ptrans: 0.0000000 0.0000000 0.0000000 - rotmap: - ( 1-> 1) - - - irot : 47 - -------------------------------------------------------------------- - isymop: 0 0 -1 - 0 -1 0 - -1 0 0 - - gtrans: 0.0000000 0.0000000 0.0000000 - - ptrans: 0.0000000 0.0000000 0.0000000 - rotmap: - ( 1-> 1) - - - irot : 48 - -------------------------------------------------------------------- - isymop: 0 0 1 - 0 1 0 - 1 0 0 - - gtrans: 0.0000000 0.0000000 0.0000000 - - ptrans: 0.0000000 0.0000000 0.0000000 - rotmap: - ( 1-> 1) - - - KPOINTS: k-points - -Automatic generation of k-mesh. -Space group operators: - irot det(A) alpha n_x n_y n_z tau_x tau_y tau_z - 1 1.000000 0.000001 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 - 2 -1.000000 0.000001 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 - 3 1.000000 120.000000 -0.577350 -0.577350 -0.577350 0.000000 0.000000 0.000000 - 4 -1.000000 120.000000 -0.577350 -0.577350 -0.577350 0.000000 0.000000 0.000000 - 5 1.000000 120.000000 0.577350 0.577350 0.577350 0.000000 0.000000 0.000000 - 6 -1.000000 120.000000 0.577350 0.577350 0.577350 0.000000 0.000000 0.000000 - 7 1.000000 90.000000 0.000000 0.000000 -1.000000 0.000000 0.000000 0.000000 - 8 -1.000000 90.000000 0.000000 0.000000 -1.000000 0.000000 0.000000 0.000000 - 9 1.000000 180.000000 0.000000 0.707107 0.707107 0.000000 0.000000 0.000000 - 10 -1.000000 180.000000 0.000000 0.707107 0.707107 0.000000 0.000000 0.000000 - 11 1.000000 90.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 - 12 -1.000000 90.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 - 13 1.000000 180.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 - 14 -1.000000 180.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 - 15 1.000000 120.000000 -0.577350 0.577350 0.577350 0.000000 0.000000 0.000000 - 16 -1.000000 120.000000 -0.577350 0.577350 0.577350 0.000000 0.000000 0.000000 - 17 1.000000 120.000000 -0.577350 0.577350 -0.577350 0.000000 0.000000 0.000000 - 18 -1.000000 120.000000 -0.577350 0.577350 -0.577350 0.000000 0.000000 0.000000 - 19 1.000000 90.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 - 20 -1.000000 90.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 - 21 1.000000 90.000000 -1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 - 22 -1.000000 90.000000 -1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 - 23 1.000000 180.000000 0.707107 0.000000 0.707107 0.000000 0.000000 0.000000 - 24 -1.000000 180.000000 0.707107 0.000000 0.707107 0.000000 0.000000 0.000000 - 25 1.000000 120.000000 0.577350 -0.577350 0.577350 0.000000 0.000000 0.000000 - 26 -1.000000 120.000000 0.577350 -0.577350 0.577350 0.000000 0.000000 0.000000 - 27 1.000000 120.000000 -0.577350 -0.577350 0.577350 0.000000 0.000000 0.000000 - 28 -1.000000 120.000000 -0.577350 -0.577350 0.577350 0.000000 0.000000 0.000000 - 29 1.000000 180.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 - 30 -1.000000 180.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 - 31 1.000000 90.000000 0.000000 -1.000000 0.000000 0.000000 0.000000 0.000000 - 32 -1.000000 90.000000 0.000000 -1.000000 0.000000 0.000000 0.000000 0.000000 - 33 1.000000 180.000000 0.707107 0.707107 0.000000 0.000000 0.000000 0.000000 - 34 -1.000000 180.000000 0.707107 0.707107 0.000000 0.000000 0.000000 0.000000 - 35 1.000000 90.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 - 36 -1.000000 90.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 - 37 1.000000 120.000000 0.577350 -0.577350 -0.577350 0.000000 0.000000 0.000000 - 38 -1.000000 120.000000 0.577350 -0.577350 -0.577350 0.000000 0.000000 0.000000 - 39 1.000000 180.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 - 40 -1.000000 180.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 - 41 1.000000 120.000000 0.577350 0.577350 -0.577350 0.000000 0.000000 0.000000 - 42 -1.000000 120.000000 0.577350 0.577350 -0.577350 0.000000 0.000000 0.000000 - 43 1.000000 180.000000 0.000000 -0.707107 0.707107 0.000000 0.000000 0.000000 - 44 -1.000000 180.000000 0.000000 -0.707107 0.707107 0.000000 0.000000 0.000000 - 45 1.000000 180.000000 0.707107 -0.707107 0.000000 0.000000 0.000000 0.000000 - 46 -1.000000 180.000000 0.707107 -0.707107 0.000000 0.000000 0.000000 0.000000 - 47 1.000000 180.000000 0.707107 0.000000 -0.707107 0.000000 0.000000 0.000000 - 48 -1.000000 180.000000 0.707107 0.000000 -0.707107 0.000000 0.000000 0.000000 - - Subroutine IBZKPT returns following result: - =========================================== - - Found 4 irreducible k-points: - - Following reciprocal coordinates: - Coordinates Weight - 0.000000 0.000000 0.000000 1.000000 - 0.333333 0.000000 0.000000 12.000000 - 0.333333 0.333333 0.000000 8.000000 - -0.333333 0.333333 0.333333 6.000000 - - Following cartesian coordinates: - Coordinates Weight - 0.000000 0.000000 0.000000 1.000000 - 0.000000 0.333333 0.333333 12.000000 - 0.333333 0.333333 0.666667 8.000000 - 0.666667 -0.000000 -0.000000 6.000000 - - - --------------------------------------------------------------------------------------------------------- - - - - - Dimension of arrays: - k-points NKPTS = 4 k-points in BZ NKDIM = 4 number of bands NBANDS= 9 - number of dos NEDOS = 301 number of ions NIONS = 1 - non local maximal LDIM = 6 non local SUM 2l+1 LMDIM = 18 - total plane-waves NPLWV = 8000 - max r-space proj IRMAX = 1 max aug-charges IRDMAX= 135207 - dimension x,y,z NGX = 20 NGY = 20 NGZ = 20 - dimension x,y,z NGXF= 40 NGYF= 40 NGZF= 40 - support grid NGXF= 80 NGYF= 80 NGZF= 80 - ions per type = 1 - NGX,Y,Z is equivalent to a cutoff of 12.85, 12.85, 12.85 a.u. - NGXF,Y,Z is equivalent to a cutoff of 25.70, 25.70, 25.70 a.u. - - - I would recommend the setting: - dimension x,y,z NGX = 19 NGY = 19 NGZ = 19 - SYSTEM = V - POSCAR = V SF test - - Startparameter for this run: - NWRITE = 2 write-flag & timer - PREC = accura normal or accurate (medium, high low for compatibility) - ISTART = 1 job : 0-new 1-cont 2-samecut - ICHARG = 1 charge: 1-file 2-atom 10-const - ISPIN = 1 spin polarized calculation? - LNONCOLLINEAR = F non collinear calculations - LSORBIT = F spin-orbit coupling - INIWAV = 1 electr: 0-lowe 1-rand 2-diag - LASPH = F aspherical Exc in radial PAW - METAGGA= F non-selfconsistent MetaGGA calc. - - Electronic Relaxation 1 - ENCUT = 500.0 eV 36.75 Ry 6.06 a.u. 4.72 4.72 4.72*2*pi/ulx,y,z - ENINI = 500.0 initial cutoff - ENAUG = 598.5 eV augmentation charge cutoff - NELM = 100; NELMIN= 5; NELMDL= -5 # of ELM steps - EDIFF = 0.1E-05 stopping-criterion for ELM - LREAL = F real-space projection - NLSPLINE = F spline interpolate recip. space projectors - LCOMPAT= F compatible to vasp.4.4 - GGA_COMPAT = T GGA compatible to vasp.4.4-vasp.4.6 - LMAXPAW = -100 max onsite density - LMAXMIX = 2 max onsite mixed and CHGCAR - VOSKOWN= 0 Vosko Wilk Nusair interpolation - ROPT = 0.00000 - Ionic relaxation - EDIFFG = 0.1E-04 stopping-criterion for IOM - NSW = 0 number of steps for IOM - NBLOCK = 1; KBLOCK = 1 inner block; outer block - IBRION = -1 ionic relax: 0-MD 1-quasi-New 2-CG - NFREE = 0 steps in history (QN), initial steepest desc. (CG) - ISIF = 2 stress and relaxation - IWAVPR = 10 prediction: 0-non 1-charg 2-wave 3-comb - ISYM = 2 0-nonsym 1-usesym 2-fastsym - LCORR = T Harris-Foulkes like correction to forces - - POTIM = 0.5000 time-step for ionic-motion - TEIN = 0.0 initial temperature - TEBEG = 0.0; TEEND = 0.0 temperature during run - SMASS = -3.00 Nose mass-parameter (am) - estimated Nose-frequenzy (Omega) = 0.10E-29 period in steps =****** mass= -0.153E-27a.u. - SCALEE = 1.0000 scale energy and forces - NPACO = 256; APACO = 16.0 distance and # of slots for P.C. - PSTRESS= 0.0 pullay stress - - Mass of Ions in am - POMASS = 50.94 - Ionic Valenz - ZVAL = 11.00 - Atomic Wigner-Seitz radii - RWIGS = -1.00 - virtual crystal weights - VCA = 1.00 - NELECT = 11.0000 total number of electrons - NUPDOWN= -1.0000 fix difference up-down - - DOS related values: - EMIN = 10.00; EMAX =-10.00 energy-range for DOS - EFERMI = 0.00 - ISMEAR = 2; SIGMA = 0.10 broadening in eV -4-tet -1-fermi 0-gaus - - Electronic relaxation 2 (details) - IALGO = 68 algorithm - LDIAG = T sub-space diagonalisation (order eigenvalues) - LSUBROT= T optimize rotation matrix (better conditioning) - TURBO = 0 0=normal 1=particle mesh - IRESTART = 0 0=no restart 2=restart with 2 vectors - NREBOOT = 0 no. of reboots - NMIN = 0 reboot dimension - EREF = 0.00 reference energy to select bands - IMIX = 4 mixing-type and parameters - AMIX = 0.40; BMIX = 1.00 - AMIX_MAG = 1.60; BMIX_MAG = 1.00 - AMIN = 0.10 - WC = 100.; INIMIX= 1; MIXPRE= 1; MAXMIX= -45 - - Intra band minimization: - WEIMIN = 0.0000 energy-eigenvalue tresh-hold - EBREAK = 0.28E-07 absolut break condition - DEPER = 0.30 relativ break condition - - TIME = 0.40 timestep for ELM - - volume/ion in A,a.u. = 13.34 90.00 - Fermi-wavevector in a.u.,A,eV,Ry = 1.535315 2.901325 32.071552 2.357193 - Thomas-Fermi vector in A = 2.642121 - - Write flags - LWAVE = T write WAVECAR - LCHARG = T write CHGCAR - LVTOT = F write LOCPOT, total local potential - LVHAR = F write LOCPOT, Hartree potential only - LELF = F write electronic localiz. function (ELF) - LORBIT = 10 0 simple, 1 ext, 2 COOP (PROOUT) - - - Dipole corrections - LMONO = F monopole corrections only (constant potential shift) - LDIPOL = F correct potential (dipole corrections) - IDIPOL = 0 1-x, 2-y, 3-z, 4-all directions - EPSILON= 1.0000000 bulk dielectric constant - - Exchange correlation treatment: - GGA = -- GGA type - LEXCH = 2 internal setting for exchange type - VOSKOWN= 0 Vosko Wilk Nusair interpolation - LHFCALC = F Hartree Fock is set to - LHFONE = F Hartree Fock one center treatment - AEXX = 0.0000 exact exchange contribution - - Linear response parameters - LEPSILON= F determine dielectric tensor - LRPA = F only Hartree local field effects (RPA) - LNABLA = F use nabla operator in PAW spheres - LVEL = F velocity operator in full k-point grid - LINTERFAST= F fast interpolation - KINTER = 0 interpolate to denser k-point grid - CSHIFT =0.1000 complex shift for real part using Kramers Kronig - OMEGAMAX= -1.0 maximum frequency - DEG_THRESHOLD= 0.2000000E-02 threshold for treating states as degnerate - RTIME = 0.100 relaxation time in fs - - Orbital magnetization related: - ORBITALMAG= F switch on orbital magnetization - LCHIMAG = F perturbation theory with respect to B field - DQ = 0.001000 dq finite difference perturbation B field - - - --------------------------------------------------------------------------------------------------------- - - - Static calculation - charge density and potential will be updated during run - non-spin polarized calculation - RMM-DIIS sequential band-by-band and - variant of blocked Davidson during initial phase - perform sub-space diagonalisation - before iterative eigenvector-optimisation - modified Broyden-mixing scheme, WC = 100.0 - initial mixing is a Kerker type mixing with AMIX = 0.4000 and BMIX = 1.0000 - Hartree-type preconditioning will be used - using additional bands 3 - reciprocal scheme for non local part - use partial core corrections - calculate Harris-corrections to forces - (improved forces if not selfconsistent) - use of overlap-Matrix (Vanderbilt PP) - Methfessel and Paxton Order N= 2 SIGMA = 0.10 - - --------------------------------------------------------------------------------------------------------- - - - energy-cutoff : 500.00 - volume of cell : 13.34 - direct lattice vectors reciprocal lattice vectors - -1.493900000 1.493900000 1.493900000 0.000000000 0.334694424 0.334694424 - 1.493900000 -1.493900000 1.493900000 0.334694424 0.000000000 0.334694424 - 1.493900000 1.493900000 -1.493900000 0.334694424 0.334694424 0.000000000 - - length of vectors - 2.587510701 2.587510701 2.587510701 0.473329394 0.473329394 0.473329394 - - - - old parameters found on file WAVECAR: - energy-cutoff : 500.00 - volume of cell : 13.34 - direct lattice vectors reciprocal lattice vectors - -1.493900000 1.493900000 1.493900000 0.000000000 0.334694424 0.334694424 - 1.493900000 -1.493900000 1.493900000 0.334694424 0.000000000 0.334694424 - 1.493900000 1.493900000 -1.493900000 0.334694424 0.334694424 0.000000000 - - length of vectors - - - k-points in units of 2pi/SCALE and weight: k-points - 0.00000000 0.00000000 0.00000000 0.037 - 0.00000000 0.33333333 0.33333333 0.444 - 0.33333333 0.33333333 0.66666667 0.296 - 0.66666667 -0.00000000 -0.00000000 0.222 - - k-points in reciprocal lattice and weights: k-points - 0.00000000 0.00000000 0.00000000 0.037 - 0.33333333 0.00000000 0.00000000 0.444 - 0.33333333 0.33333333 0.00000000 0.296 - -0.33333333 0.33333333 0.33333333 0.222 - - position of ions in fractional coordinates (direct lattice) - 0.00000000 0.00000000 0.00000000 - - position of ions in cartesian coordinates (Angst): - 0.00000000 0.00000000 0.00000000 - - - --------------------------------------------------------------------------------------------------------- - - - k-point 1 : 0.0000 0.0000 0.0000 plane waves: 321 - k-point 2 : 0.3333 0.0000 0.0000 plane waves: 350 - k-point 3 : 0.3333 0.3333 0.0000 plane waves: 333 - k-point 4 : -0.3333 0.3333 0.3333 plane waves: 334 - - maximum and minimum number of plane-waves per node : 350 321 - - maximum number of plane-waves: 350 - maximum index in each direction: - IXMAX= 5 IYMAX= 4 IZMAX= 4 - IXMIN= -5 IYMIN= -5 IZMIN= -5 - - WARNING: aliasing errors must be expected set NGX to 22 to avoid them - NGY is ok and might be reduce to 20 - NGZ is ok and might be reduce to 20 - aliasing errors are usually negligible using standard VASP settings - and one can safely disregard these warnings - - serial 3D FFT for wavefunctions - parallel 3D FFT for charge: - minimum data exchange during FFTs selected (reduces bandwidth) - - - total amount of memory used by VASP on root node 43541. kBytes -======================================================================== - - base : 30000. kBytes - nonl-proj : 207. kBytes - fftplans : 9608. kBytes - grid : 3500. kBytes - one-center: 15. kBytes - wavefun : 211. kBytes - - Broyden mixing: mesh for mixing (old mesh) - NGX = 9 NGY = 9 NGZ = 9 - (NGX = 40 NGY = 40 NGZ = 40) - gives a total of 729 points - - initial charge density was supplied: - number of electron 11.0000001 magnetization - keeping initial charge density in first step - - --------------------------------------------------------------------------------------------------------- - - - Maximum index for augmentation-charges 131019 (set IRDMAX) - - --------------------------------------------------------------------------------------------------------- - - - First call to EWALD: gamma= 0.747 - Maximum number of real-space cells 3x 3x 3 - Maximum number of reciprocal cells 3x 3x 3 - - FEWALD executed in parallel - FEWALD: cpu time 0.02: real time 0.00 - - ------------------------------------------ Iteration 1( 1) --------------------------------------- - - - POTLOK: cpu time 0.08: real time 0.01 - SETDIJ: cpu time 0.43: real time 0.05 - EDDAV: cpu time 0.28: real time 0.04 - DOS: cpu time 0.00: real time 0.00 - -------------------------------------------- - LOOP: cpu time 0.80: real time 0.10 - - eigenvalue-minimisations : 72 - total energy-change (2. order) :-0.3607050E+01 (-0.1329591E+03) - number of electron 11.0000001 magnetization - augmentation part 11.0000001 magnetization - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 101.92704955 - Ewald energy TEWEN = -1061.13304792 - -1/2 Hartree DENC = -255.69199547 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 28.52081228 - PAW double counting = 1565.45123275 -1547.56812874 - entropy T*S EENTRO = -0.00527157 - eigenvalues EBANDS = -158.87611961 - atomic energy EATOM = 1323.76841912 - --------------------------------------------------- - free energy TOTEN = -3.60704961 eV - - energy without entropy = -3.60177804 energy(sigma->0) = -3.60573172 - - --------------------------------------------------------------------------------------------------------- - - - - ------------------------------------------ Iteration 1( 2) --------------------------------------- - - - EDDAV: cpu time 0.28: real time 0.03 - DOS: cpu time 0.00: real time 0.00 - -------------------------------------------- - LOOP: cpu time 0.28: real time 0.04 - - eigenvalue-minimisations : 73 - total energy-change (2. order) :-0.6251543E+01 (-0.5022761E+01) - number of electron 11.0000001 magnetization - augmentation part 11.0000001 magnetization - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 101.92704955 - Ewald energy TEWEN = -1061.13304792 - -1/2 Hartree DENC = -255.69199547 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 28.52081228 - PAW double counting = 1565.45123275 -1547.56812874 - entropy T*S EENTRO = -0.00933688 - eigenvalues EBANDS = -165.12359716 - atomic energy EATOM = 1323.76841912 - --------------------------------------------------- - free energy TOTEN = -9.85859248 eV - - energy without entropy = -9.84925560 energy(sigma->0) = -9.85625826 - - --------------------------------------------------------------------------------------------------------- - - - - ------------------------------------------ Iteration 1( 3) --------------------------------------- - - - EDDAV: cpu time 0.24: real time 0.03 - DOS: cpu time 0.00: real time 0.00 - -------------------------------------------- - LOOP: cpu time 0.25: real time 0.03 - - eigenvalue-minimisations : 63 - total energy-change (2. order) :-0.1916239E+00 (-0.1867081E+00) - number of electron 11.0000001 magnetization - augmentation part 11.0000001 magnetization - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 101.92704955 - Ewald energy TEWEN = -1061.13304792 - -1/2 Hartree DENC = -255.69199547 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 28.52081228 - PAW double counting = 1565.45123275 -1547.56812874 - entropy T*S EENTRO = -0.00933676 - eigenvalues EBANDS = -165.31522114 - atomic energy EATOM = 1323.76841912 - --------------------------------------------------- - free energy TOTEN = -10.05021634 eV - - energy without entropy = -10.04087958 energy(sigma->0) = -10.04788215 - - --------------------------------------------------------------------------------------------------------- - - - - ------------------------------------------ Iteration 1( 4) --------------------------------------- - - - EDDAV: cpu time 0.22: real time 0.03 - DOS: cpu time 0.00: real time 0.00 - -------------------------------------------- - LOOP: cpu time 0.22: real time 0.03 - - eigenvalue-minimisations : 63 - total energy-change (2. order) :-0.6464665E-03 (-0.6462300E-03) - number of electron 11.0000001 magnetization - augmentation part 11.0000001 magnetization - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 101.92704955 - Ewald energy TEWEN = -1061.13304792 - -1/2 Hartree DENC = -255.69199547 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 28.52081228 - PAW double counting = 1565.45123275 -1547.56812874 - entropy T*S EENTRO = -0.00933676 - eigenvalues EBANDS = -165.31586761 - atomic energy EATOM = 1323.76841912 - --------------------------------------------------- - free energy TOTEN = -10.05086281 eV - - energy without entropy = -10.04152605 energy(sigma->0) = -10.04852862 - - --------------------------------------------------------------------------------------------------------- - - - - ------------------------------------------ Iteration 1( 5) --------------------------------------- - - - EDDAV: cpu time 0.19: real time 0.02 - DOS: cpu time 0.00: real time 0.00 - CHARGE: cpu time 0.33: real time 0.04 - MIXING: cpu time 0.01: real time 0.00 - -------------------------------------------- - LOOP: cpu time 0.54: real time 0.07 - - eigenvalue-minimisations : 62 - total energy-change (2. order) :-0.4900846E-05 (-0.4901315E-05) - number of electron 11.0000001 magnetization - augmentation part 4.5843479 magnetization - - Broyden mixing: - rms(total) = 0.38931E+00 rms(broyden)= 0.38713E+00 - rms(prec ) = 0.77935E+00 - weight for this iteration 100.00 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 101.92704955 - Ewald energy TEWEN = -1061.13304792 - -1/2 Hartree DENC = -255.69199547 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 28.52081228 - PAW double counting = 1565.45123275 -1547.56812874 - entropy T*S EENTRO = -0.00933676 - eigenvalues EBANDS = -165.31587251 - atomic energy EATOM = 1323.76841912 - --------------------------------------------------- - free energy TOTEN = -10.05086771 eV - - energy without entropy = -10.04153095 energy(sigma->0) = -10.04853352 - - --------------------------------------------------------------------------------------------------------- - - - - ------------------------------------------ Iteration 1( 6) --------------------------------------- - - - POTLOK: cpu time 0.06: real time 0.01 - SETDIJ: cpu time 0.30: real time 0.04 - EDDIAG: cpu time 0.06: real time 0.01 - RMM-DIIS: cpu time 0.25: real time 0.03 - ORTHCH: cpu time 0.00: real time 0.00 - DOS: cpu time 0.00: real time 0.00 - CHARGE: cpu time 0.32: real time 0.04 - MIXING: cpu time 0.01: real time 0.00 - -------------------------------------------- - LOOP: cpu time 1.00: real time 0.13 - - eigenvalue-minimisations : 72 - total energy-change (2. order) : 0.4542073E-01 (-0.1028885E-01) - number of electron 11.0000001 magnetization - augmentation part 4.6333393 magnetization - - Broyden mixing: - rms(total) = 0.32511E+00 rms(broyden)= 0.32500E+00 - rms(prec ) = 0.44839E+00 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.8427 - 1.8427 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 101.92704955 - Ewald energy TEWEN = -1061.13304792 - -1/2 Hartree DENC = -251.49903640 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 28.31112760 - PAW double counting = 1512.01533700 -1494.93514383 - entropy T*S EENTRO = -0.00953603 - eigenvalues EBANDS = -168.45061607 - atomic energy EATOM = 1323.76841912 - --------------------------------------------------- - free energy TOTEN = -10.00544698 eV - - energy without entropy = -9.99591095 energy(sigma->0) = -10.00306297 - - --------------------------------------------------------------------------------------------------------- - - - - ------------------------------------------ Iteration 1( 7) --------------------------------------- - - - POTLOK: cpu time 0.06: real time 0.01 - SETDIJ: cpu time 0.30: real time 0.04 - EDDIAG: cpu time 0.06: real time 0.01 - RMM-DIIS: cpu time 0.20: real time 0.03 - ORTHCH: cpu time 0.00: real time 0.00 - DOS: cpu time 0.00: real time 0.00 - CHARGE: cpu time 0.32: real time 0.04 - MIXING: cpu time 0.01: real time 0.00 - -------------------------------------------- - LOOP: cpu time 0.96: real time 0.12 - - eigenvalue-minimisations : 73 - total energy-change (2. order) : 0.7787893E-02 (-0.2217404E-02) - number of electron 11.0000001 magnetization - augmentation part 4.6454380 magnetization - - Broyden mixing: - rms(total) = 0.13806E+00 rms(broyden)= 0.13805E+00 - rms(prec ) = 0.17948E+00 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.7677 - 1.1386 2.3968 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 101.92704955 - Ewald energy TEWEN = -1061.13304792 - -1/2 Hartree DENC = -250.12922671 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 28.24893659 - PAW double counting = 1442.02679998 -1425.54475140 - entropy T*S EENTRO = -0.00854256 - eigenvalues EBANDS = -169.15329574 - atomic energy EATOM = 1323.76841912 - --------------------------------------------------- - free energy TOTEN = -9.99765908 eV - - energy without entropy = -9.98911652 energy(sigma->0) = -9.99552344 - - --------------------------------------------------------------------------------------------------------- - - - - ------------------------------------------ Iteration 1( 8) --------------------------------------- - - - POTLOK: cpu time 0.06: real time 0.01 - SETDIJ: cpu time 0.30: real time 0.04 - EDDIAG: cpu time 0.06: real time 0.01 - RMM-DIIS: cpu time 0.20: real time 0.03 - ORTHCH: cpu time 0.00: real time 0.00 - DOS: cpu time 0.00: real time 0.00 - CHARGE: cpu time 0.32: real time 0.04 - MIXING: cpu time 0.01: real time 0.00 - -------------------------------------------- - LOOP: cpu time 0.96: real time 0.12 - - eigenvalue-minimisations : 72 - total energy-change (2. order) : 0.1892672E-02 (-0.1258810E-03) - number of electron 11.0000001 magnetization - augmentation part 4.6417685 magnetization - - Broyden mixing: - rms(total) = 0.59290E-02 rms(broyden)= 0.59288E-02 - rms(prec ) = 0.11437E-01 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.5800 - 2.4981 1.1209 1.1209 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 101.92704955 - Ewald energy TEWEN = -1061.13304792 - -1/2 Hartree DENC = -250.12072559 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 28.25453040 - PAW double counting = 1402.39780367 -1386.19164756 - entropy T*S EENTRO = -0.00851326 - eigenvalues EBANDS = -168.88963481 - atomic energy EATOM = 1323.76841912 - --------------------------------------------------- - free energy TOTEN = -9.99576641 eV - - energy without entropy = -9.98725315 energy(sigma->0) = -9.99363810 - - --------------------------------------------------------------------------------------------------------- - - - - ------------------------------------------ Iteration 1( 9) --------------------------------------- - - - POTLOK: cpu time 0.06: real time 0.01 - SETDIJ: cpu time 0.30: real time 0.04 - EDDIAG: cpu time 0.06: real time 0.01 - RMM-DIIS: cpu time 0.22: real time 0.03 - ORTHCH: cpu time 0.00: real time 0.00 - DOS: cpu time 0.00: real time 0.00 - CHARGE: cpu time 0.32: real time 0.04 - MIXING: cpu time 0.01: real time 0.00 - -------------------------------------------- - LOOP: cpu time 0.97: real time 0.12 - - eigenvalue-minimisations : 77 - total energy-change (2. order) : 0.6248862E-05 (-0.4989408E-05) - number of electron 11.0000001 magnetization - augmentation part 4.6422488 magnetization - - Broyden mixing: - rms(total) = 0.20071E-02 rms(broyden)= 0.20069E-02 - rms(prec ) = 0.30073E-02 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.8246 - 1.0381 1.1221 2.5086 2.6297 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 101.92704955 - Ewald energy TEWEN = -1061.13304792 - -1/2 Hartree DENC = -250.07203143 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 28.25270327 - PAW double counting = 1400.68328469 -1384.48861981 - entropy T*S EENTRO = -0.00844601 - eigenvalues EBANDS = -168.92507162 - atomic energy EATOM = 1323.76841912 - --------------------------------------------------- - free energy TOTEN = -9.99576016 eV - - energy without entropy = -9.98731415 energy(sigma->0) = -9.99364866 - - --------------------------------------------------------------------------------------------------------- - - - - ------------------------------------------ Iteration 1( 10) --------------------------------------- - - - POTLOK: cpu time 0.06: real time 0.01 - SETDIJ: cpu time 0.30: real time 0.04 - EDDIAG: cpu time 0.06: real time 0.01 - RMM-DIIS: cpu time 0.16: real time 0.02 - ORTHCH: cpu time 0.00: real time 0.00 - DOS: cpu time 0.00: real time 0.00 - CHARGE: cpu time 0.32: real time 0.04 - MIXING: cpu time 0.01: real time 0.00 - -------------------------------------------- - LOOP: cpu time 0.91: real time 0.11 - - eigenvalue-minimisations : 55 - total energy-change (2. order) :-0.2638173E-05 (-0.5987658E-06) - number of electron 11.0000001 magnetization - augmentation part 4.6424864 magnetization - - Broyden mixing: - rms(total) = 0.97890E-03 rms(broyden)= 0.97843E-03 - rms(prec ) = 0.15974E-02 - weight for this iteration 100.00 - - eigenvalues of (default mixing * dielectric matrix) - average eigenvalue GAMMA= 1.6894 - 2.6464 2.5149 0.9584 1.1635 1.1635 - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 101.92704955 - Ewald energy TEWEN = -1061.13304792 - -1/2 Hartree DENC = -250.08760088 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 28.25330069 - PAW double counting = 1402.75339521 -1386.53753650 - entropy T*S EENTRO = -0.00844322 - eigenvalues EBANDS = -168.93129885 - atomic energy EATOM = 1323.76841912 - --------------------------------------------------- - free energy TOTEN = -9.99576280 eV - - energy without entropy = -9.98731958 energy(sigma->0) = -9.99365200 - - --------------------------------------------------------------------------------------------------------- - - - - ------------------------------------------ Iteration 1( 11) --------------------------------------- - - - POTLOK: cpu time 0.06: real time 0.01 - SETDIJ: cpu time 0.30: real time 0.04 - EDDIAG: cpu time 0.06: real time 0.01 - RMM-DIIS: cpu time 0.12: real time 0.01 - ORTHCH: cpu time 0.00: real time 0.00 - DOS: cpu time 0.00: real time 0.00 - -------------------------------------------- - LOOP: cpu time 0.54: real time 0.07 - - eigenvalue-minimisations : 38 - total energy-change (2. order) : 0.3651744E-06 (-0.1644459E-06) - number of electron 11.0000001 magnetization - augmentation part 4.6424864 magnetization - - Free energy of the ion-electron system (eV) - --------------------------------------------------- - alpha Z PSCENC = 101.92704955 - Ewald energy TEWEN = -1061.13304792 - -1/2 Hartree DENC = -250.10153291 - -exchange EXHF = 0.00000000 - -V(xc)+E(xc) XCENC = 28.25398425 - PAW double counting = 1402.64345375 -1386.42726146 - entropy T*S EENTRO = -0.00845882 - eigenvalues EBANDS = -168.91836799 - atomic energy EATOM = 1323.76841912 - --------------------------------------------------- - free energy TOTEN = -9.99576244 eV - - energy without entropy = -9.98730362 energy(sigma->0) = -9.99364773 - - --------------------------------------------------------------------------------------------------------- - - - - - average (electrostatic) potential at core - the test charge radii are 0.9339 - (the norm of the test charge is 1.0000) - 1 -46.7799 - - - - E-fermi : 5.8440 XC(G=0): -13.1912 alpha+bet :-14.7286 - 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V SF test - 2.9878 - -0.5 0.5 0.5 - 0.5 -0.5 0.5 - 0.5 0.5 -0.5 - V - 1 -Direct - 0.0 0.0 0.0 - diff --git a/python/converters/vasp/test/plotools/densmat.out b/python/converters/vasp/test/plotools/densmat.out deleted file mode 100644 index fddea444..00000000 --- a/python/converters/vasp/test/plotools/densmat.out +++ /dev/null @@ -1,10 +0,0 @@ -density matrix: [[[[ 2.71066432e-01 -1.07856040e-02 9.07814858e-03 -2.60324510e-01 - -2.14321077e-09] - [ -1.07856040e-02 2.97099774e-01 9.52322235e-02 -1.38848431e-02 - -1.97357976e-01] - [ 9.07814858e-03 9.52322235e-02 1.42730494e-01 4.53909162e-03 - -4.31946315e-02] - [ -2.60324510e-01 -1.38848431e-02 4.53909162e-03 2.95736883e-01 - 4.02728377e-02] - [ -2.14321077e-09 -1.97357976e-01 -4.31946315e-02 4.02728377e-02 - 2.35328545e-01]]]] diff --git a/python/converters/vasp/test/plotools/example.cfg b/python/converters/vasp/test/plotools/example.cfg deleted file mode 100644 index 6158ea30..00000000 --- a/python/converters/vasp/test/plotools/example.cfg +++ /dev/null @@ -1,8 +0,0 @@ - -[Shell 1] -LSHELL = 2 -IONS = 1 -EMIN = -15.0 -EMAX = 5.0 - - diff --git a/python/converters/vasp/test/plotools/mytest.py b/python/converters/vasp/test/plotools/mytest.py deleted file mode 100644 index 38f0689e..00000000 --- a/python/converters/vasp/test/plotools/mytest.py +++ /dev/null @@ -1,56 +0,0 @@ -r""" -Module defining a custom TestCase with extra functionality. -""" - -import unittest -import numpy as np -import difflib - -class MyTestCase(unittest.TestCase): - """ - Custom TestCase class supporting additional equality checks: - - numpy array equality - - file equality - """ - def __init__(self, *args, **kwargs): - """ - Initializes a custom equality function for comparing numpy arrays. - """ - super(MyTestCase, 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 assertFileEqual(self, file1, file2): - """ - Compares two files using difflib. - Empty lines are ignored. - Files are assumed to be relatively small; - the data is truncated for files larger than MAX_SIZE bytes. - """ - MAX_SIZE = 100000 - with open(file1, 'r') as f1: - str1 = f1.read(MAX_SIZE) - with open(file2, 'r') as f2: - str2 = f2.read(MAX_SIZE) -# -# Make a diff -# -# Remove empty lines - lstr1 = filter(lambda s: s.strip() != '', str1.splitlines(True)) - lstr2 = filter(lambda s: s.strip() != '', str2.splitlines(True)) -# diff - delta = difflib.unified_diff(lstr1, lstr2) -# combine delta's to a string - diff = ''.join(delta) -# if 'diff' is non-empty, files are different - if diff: - return self.fail("Files '%s' and '%s' differ"%(file1, file2)) - - diff --git a/python/converters/vasp/test/plotools/projgroups.out b/python/converters/vasp/test/plotools/projgroups.out deleted file mode 100644 index 622fe2b8..00000000 --- a/python/converters/vasp/test/plotools/projgroups.out +++ /dev/null @@ -1,115 +0,0 @@ -pars: {'normalize': True, 'index': '1', 'emin': -15.0, 'emax': 5.0, 'normion': False, 'shells': [0]} -3 8 - 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1 (2.5198055198e-08+0j) - 2 (2.51956215891e-08+0j) - 3 (-1.39707700703e-12+0j) - 4 (2.51956464581e-08+0j) - 5 (-9.58669992349e-14+0j) - 1 (0.423249542713+0j) - 2 (0.441459685564+0j) - 3 (5.45383349593e-10+0j) - 4 (0.441459536552+0j) - 5 (-5.07696386694e-15+0j) - 1 (-0.624317586422+0j) - 2 (0.299283236265+0j) - 3 (3.00651912255e-08+0j) - 4 (0.299281418324+0j) - 5 (-5.44629513472e-14+0j) - 1 (-2.9753928743e-07+0j) - 2 (-0.495364636183+0j) - 3 (1.61749496311e-14+0j) - 4 (0.495365083218+0j) - 5 (2.86656725024e-08+0j) - 1 (2.31630860326e-12+0j) - 2 (-2.07712407274e-08+0j) - 3 (6.79555596435e-05+0j) - 4 (2.07689296872e-08+0j) - 5 (-0.686951518059+0j) - 1 (-2.55608547661e-08+0j) - 2 (1.27339729872e-08+0j) - 3 (-0.749936163425+0j) - 4 (1.27377095538e-08+0j) - 5 (-6.18639533059e-05+0j) -3 8 - 1 (-7.42354511196e-10+0j) - 2 (-0.407458901405+0j) - 3 (-0.132825627923+0j) - 4 (-1.12258624618e-09+0j) - 5 (0.230060741305+0j) - 1 (-0.529840826988+0j) - 2 (1.02242869726e-09+0j) - 3 (1.47169805231e-08+0j) - 4 (0.529840826988+0j) - 5 (8.58095106082e-09+0j) - 1 (-5.59593660299e-09+0j) - 2 (-0.46026712656+0j) - 3 (-0.189698129892+0j) - 4 (-3.64733043767e-09+0j) - 5 (0.328566819429+0j) - 1 (-5.92653073284e-08+0j) - 2 (-0.511403858662+0j) - 3 (0.342116594315+0j) - 4 (-5.81566510505e-08+0j) - 5 (-0.592563331127+0j) - 1 (9.17969966707e-09+0j) - 2 (3.7528921637e-10+0j) - 3 (0.743389487267+0j) - 4 (-7.80711495452e-09+0j) - 5 (0.429196119308+0j) - 1 (-0.60352396965+0j) - 2 (5.06060757743e-07+0j) - 3 (1.02901012156e-07+0j) - 4 (-0.60352396965+0j) - 5 (-1.76288821763e-07+0j) -3 7 - 1 (-0.157831609249+0j) - 2 (0.157831639051+0j) - 3 (1.93573299612e-08+0j) - 4 (0.157831639051+0j) - 5 (5.40782289825e-14+0j) - 1 (-1.07380124348e-07+0j) - 2 (-0.227066069841+0j) - 3 (-1.22580686934e-07+0j) - 4 (0.227065965533+0j) - 5 (0.299297988415+0j) - 1 (0.115845791996+0j) - 2 (0.057922616601+0j) - 3 (0.13223952055+0j) - 4 (0.0579231306911+0j) - 5 (3.36705625159e-07+0j) - 1 (0.159106343985+0j) - 2 (0.0795532241464+0j) - 3 (-0.240490317345+0j) - 4 (0.0795530825853+0j) - 5 (1.18692518924e-07+0j) - 1 (3.98122104173e-08+0j) - 2 (-0.241537705064+0j) - 3 (-6.01558127755e-08+0j) - 4 (0.241537734866+0j) - 5 (-0.421558618546+0j) -3 7 - 1 (7.91286647317e-10+0j) - 2 (3.03037844818e-10+0j) - 3 (0.204362645745+0j) - 4 (4.89190632447e-10+0j) - 5 (-0.353966474533+0j) - 1 (9.13699960137e-09+0j) - 2 (1.0438577086e-10+0j) - 3 (-0.42577791214+0j) - 4 (-6.95880419954e-09+0j) - 5 (-0.245822981+0j) - 1 (0.368288576603+0j) - 2 (1.67113629601e-08+0j) - 3 (-1.44080747333e-10+0j) - 4 (0.365979760885+0j) - 5 (1.25375620996e-09+0j) - 1 (0.365983724594+0j) - 2 (-2.74820233237e-09+0j) - 3 (1.77222470032e-09+0j) - 4 (-0.368292748928+0j) - 5 (7.90098320103e-10+0j) - 1 (-3.99936368467e-08+0j) - 2 (0.546248733997+0j) - 3 (-2.91795543284e-09+0j) - 4 (-2.16134438347e-07+0j) - 5 (1.55786352707e-08+0j) diff --git a/python/converters/vasp/test/plotools/projshells.out b/python/converters/vasp/test/plotools/projshells.out deleted file mode 100644 index 1368195d..00000000 --- a/python/converters/vasp/test/plotools/projshells.out +++ /dev/null @@ -1,115 +0,0 @@ -pars: {'ion_list': array([0]), 'user_index': 1, 'lshell': 2} -3 8 - 1 (2.5198055198e-08+0j) - 2 (2.51956215891e-08+0j) - 3 (-1.39707700703e-12+0j) - 4 (2.51956464581e-08+0j) - 5 (-9.58669992349e-14+0j) - 1 (0.423249542713+0j) - 2 (0.441459685564+0j) - 3 (5.45383349593e-10+0j) - 4 (0.441459536552+0j) - 5 (-5.07696386694e-15+0j) - 1 (-0.624317586422+0j) - 2 (0.299283236265+0j) - 3 (3.00651912255e-08+0j) - 4 (0.299281418324+0j) - 5 (-5.44629513472e-14+0j) - 1 (-2.9753928743e-07+0j) - 2 (-0.495364636183+0j) - 3 (1.61749496311e-14+0j) - 4 (0.495365083218+0j) - 5 (2.86656725024e-08+0j) - 1 (2.31630860326e-12+0j) - 2 (-2.07712407274e-08+0j) - 3 (6.79555596435e-05+0j) - 4 (2.07689296872e-08+0j) - 5 (-0.686951518059+0j) - 1 (-2.55608547661e-08+0j) - 2 (1.27339729872e-08+0j) - 3 (-0.749936163425+0j) - 4 (1.27377095538e-08+0j) - 5 (-6.18639533059e-05+0j) -3 8 - 1 (-7.42354511196e-10+0j) - 2 (-0.407458901405+0j) - 3 (-0.132825627923+0j) - 4 (-1.12258624618e-09+0j) - 5 (0.230060741305+0j) - 1 (-0.529840826988+0j) - 2 (1.02242869726e-09+0j) - 3 (1.47169805231e-08+0j) - 4 (0.529840826988+0j) - 5 (8.58095106082e-09+0j) - 1 (-5.59593660299e-09+0j) - 2 (-0.46026712656+0j) - 3 (-0.189698129892+0j) - 4 (-3.64733043767e-09+0j) - 5 (0.328566819429+0j) - 1 (-5.92653073284e-08+0j) - 2 (-0.511403858662+0j) - 3 (0.342116594315+0j) - 4 (-5.81566510505e-08+0j) - 5 (-0.592563331127+0j) - 1 (9.17969966707e-09+0j) - 2 (3.7528921637e-10+0j) - 3 (0.743389487267+0j) - 4 (-7.80711495452e-09+0j) - 5 (0.429196119308+0j) - 1 (-0.60352396965+0j) - 2 (5.06060757743e-07+0j) - 3 (1.02901012156e-07+0j) - 4 (-0.60352396965+0j) - 5 (-1.76288821763e-07+0j) -3 7 - 1 (-0.157831609249+0j) - 2 (0.157831639051+0j) - 3 (1.93573299612e-08+0j) - 4 (0.157831639051+0j) - 5 (5.40782289825e-14+0j) - 1 (-1.07380124348e-07+0j) - 2 (-0.227066069841+0j) - 3 (-1.22580686934e-07+0j) - 4 (0.227065965533+0j) - 5 (0.299297988415+0j) - 1 (0.115845791996+0j) - 2 (0.057922616601+0j) - 3 (0.13223952055+0j) - 4 (0.0579231306911+0j) - 5 (3.36705625159e-07+0j) - 1 (0.159106343985+0j) - 2 (0.0795532241464+0j) - 3 (-0.240490317345+0j) - 4 (0.0795530825853+0j) - 5 (1.18692518924e-07+0j) - 1 (3.98122104173e-08+0j) - 2 (-0.241537705064+0j) - 3 (-6.01558127755e-08+0j) - 4 (0.241537734866+0j) - 5 (-0.421558618546+0j) -3 7 - 1 (7.91286647317e-10+0j) - 2 (3.03037844818e-10+0j) - 3 (0.204362645745+0j) - 4 (4.89190632447e-10+0j) - 5 (-0.353966474533+0j) - 1 (9.13699960137e-09+0j) - 2 (1.0438577086e-10+0j) - 3 (-0.42577791214+0j) - 4 (-6.95880419954e-09+0j) - 5 (-0.245822981+0j) - 1 (0.368288576603+0j) - 2 (1.67113629601e-08+0j) - 3 (-1.44080747333e-10+0j) - 4 (0.365979760885+0j) - 5 (1.25375620996e-09+0j) - 1 (0.365983724594+0j) - 2 (-2.74820233237e-09+0j) - 3 (1.77222470032e-09+0j) - 4 (-0.368292748928+0j) - 5 (7.90098320103e-10+0j) - 1 (-3.99936368467e-08+0j) - 2 (0.546248733997+0j) - 3 (-2.91795543284e-09+0j) - 4 (-2.16134438347e-07+0j) - 5 (1.55786352707e-08+0j) diff --git a/python/converters/vasp/test/plotools/runtest.sh b/python/converters/vasp/test/plotools/runtest.sh deleted file mode 100755 index 9b7bd8ca..00000000 --- a/python/converters/vasp/test/plotools/runtest.sh +++ /dev/null @@ -1 +0,0 @@ -PYTHONPATH=../../python:../../c:$PYTHONPATH python $1 diff --git a/python/converters/vasp/test/plotools/test_consistency.py b/python/converters/vasp/test/plotools/test_consistency.py deleted file mode 100644 index eeac9961..00000000 --- a/python/converters/vasp/test/plotools/test_consistency.py +++ /dev/null @@ -1,34 +0,0 @@ - -import vaspio -from inpconf import ConfigParameters -import mytest - -################################################################################ -# -# TestDataConsistency -# -################################################################################ -class TestDataConsistency(mytest.MyTestCase): - """ - Function: - - def read_plocar(filename) - - Scenarios: - - - **if** file PLOCAR does not exist **raise** IOError - - **if** PLOCAR is truncated **raise** IOError - - **if** the precision flag is not 4 or 8 **raise** ValueError - - **if** PLOCAR with prec=8 is read **compare** the output - - **if** PLOCAR with prec=4 is read **compare** the output - """ -# Scenario 1 - def test_example(self): - conf_file = 'example.cfg' - pars = ConfigParameters(conf_file) - pars.parse_input() - vasp_data = vaspio.VaspData('./') - - print pars.shells - print pars.groups - diff --git a/python/converters/vasp/test/plotools/test_plotools.py b/python/converters/vasp/test/plotools/test_plotools.py deleted file mode 100644 index c26da112..00000000 --- a/python/converters/vasp/test/plotools/test_plotools.py +++ /dev/null @@ -1,10 +0,0 @@ -r""" -Test suite for module `plotools`. -""" -import unittest - -if __name__ == '__main__': - suite = unittest.TestLoader().discover('./') -# unittest.TextTestRunner(verbosity=2, buffer=True).run(suite) - unittest.TextTestRunner(verbosity=2, buffer=False).run(suite) - diff --git a/python/converters/vasp/test/plotools/test_projgroups.py b/python/converters/vasp/test/plotools/test_projgroups.py deleted file mode 100644 index de238537..00000000 --- a/python/converters/vasp/test/plotools/test_projgroups.py +++ /dev/null @@ -1,79 +0,0 @@ - -import numpy as np -import vaspio -from inpconf import ConfigParameters -from plotools import ProjectorShell, ProjectorGroup -import mytest - -################################################################################ -# -# TestProjectorGroup -# -################################################################################ -class TestProjectorGroup(mytest.MyTestCase): - """ - Class: - - ProjectorGroup(sh_pars, proj_raw) - - Scenarios: - - test output for a correct input - - test the output of 'orthogonalization()' (sanity check) - """ - def setUp(self): - conf_file = 'example.cfg' - self.pars = ConfigParameters(conf_file) - self.pars.parse_input() - self.vasp_data = vaspio.VaspData('./') - - efermi = self.vasp_data.doscar.efermi - eigvals = self.vasp_data.eigenval.eigs - efermi - - self.shells = [ProjectorShell(self.pars.shells[0], self.vasp_data.plocar.plo)] - self.proj_gr = ProjectorGroup(self.pars.groups[0], self.shells, eigvals) - -# Scenario 1 - def test_example(self): -# proj_sh.select_projectors(ib_win, nb_min, nb_max) -# - testout = 'projgroups.out.test' - nion, ns, nk, nlm, nbtot = self.proj_gr.shells[0].proj_win.shape - with open(testout, 'wt') as f: - f.write("pars: %s\n"%(self.pars.groups[0])) - for ion in xrange(nion): - for isp in xrange(ns): - for ik in xrange(nk): - ib1 = self.proj_gr.ib_win[ik, 0, 0] - ib2 = self.proj_gr.ib_win[ik, 0, 1] - f.write("%i %i\n"%(ib1, ib2)) - ib1w = ib1 - self.proj_gr.nb_min - ib2w = ib2 - self.proj_gr.nb_min + 1 - for ib in xrange(ib1w, ib2w): - for ilm in xrange(nlm): - p = self.proj_gr.shells[0].proj_win[ion, isp, ik, ilm, ib] - f.write("%5i %s\n"%(ilm+1, p)) - -# Scenario 2 - def test_ortho(self): - self.proj_gr.orthogonalize() - - testout = 'projortho.out.test' - nion, ns, nk, nlm, nbtot = self.proj_gr.shells[0].proj_win.shape - with open(testout, 'wt') as f: - f.write("pars: %s\n"%(self.pars.groups[0])) - for ion in xrange(nion): - for isp in xrange(ns): - for ik in xrange(nk): - ib1 = self.proj_gr.ib_win[ik, 0, 0] - ib2 = self.proj_gr.ib_win[ik, 0, 1] - f.write("%i %i\n"%(ib1, ib2)) - ib1w = ib1 - self.proj_gr.nb_min - ib2w = ib2 - self.proj_gr.nb_min + 1 - for ib in xrange(ib1w, ib2w): - for ilm in xrange(nlm): - p = self.proj_gr.shells[0].proj_win[ion, isp, ik, ilm, ib] - f.write("%5i %s\n"%(ilm+1, p)) - - expected_file = 'projortho.out' - self.assertFileEqual(testout, expected_file) - diff --git a/python/converters/vasp/test/plotools/test_projshells.py b/python/converters/vasp/test/plotools/test_projshells.py deleted file mode 100644 index c78bd7f5..00000000 --- a/python/converters/vasp/test/plotools/test_projshells.py +++ /dev/null @@ -1,86 +0,0 @@ - -import numpy as np -import vaspio -import elstruct -from inpconf import ConfigParameters -from plotools import select_bands, ProjectorShell -import mytest - -################################################################################ -# -# TestProjectorShell -# -################################################################################ -class TestProjectorShell(mytest.MyTestCase): - """ - Class: - - ProjectorShell(sh_pars, proj_raw) - - Scenarios: - - compare output for a correct input - - test density matrix - """ -# Scenario 1 - def test_example(self): - conf_file = 'example.cfg' - pars = ConfigParameters(conf_file) - pars.parse_input() - vasp_data = vaspio.VaspData('./') - - efermi = vasp_data.doscar.efermi - eigvals = vasp_data.eigenval.eigs - efermi - emin = pars.groups[0]['emin'] - emax = pars.groups[0]['emax'] - ib_win, nb_min, nb_max = select_bands(eigvals, emin, emax) - - proj_sh = ProjectorShell(pars.shells[0], vasp_data.plocar.plo) - - proj_sh.select_projectors(ib_win, nb_min, nb_max) - - testout = 'projshells.out.test' - nion, ns, nk, nlm, nbtot = proj_sh.proj_win.shape - with open(testout, 'wt') as f: - f.write("pars: %s\n"%(pars.shells[0])) - for ion in xrange(nion): - for isp in xrange(ns): - for ik in xrange(nk): - ib1 = ib_win[ik, 0, 0] - ib2 = ib_win[ik, 0, 1] - f.write("%i %i\n"%(ib1, ib2)) - for ib in xrange(ib2 - nb_min + 1): - for ilm in xrange(nlm): - p = proj_sh.proj_win[ion, isp, ik, ilm, ib] - f.write("%5i %s\n"%(ilm+1, p)) - - expected_file = 'projshells.out' - self.assertFileEqual(testout, expected_file) - -# Scenario 2 - def test_dens_mat(self): - conf_file = 'example.cfg' - pars = ConfigParameters(conf_file) - pars.parse_input() - vasp_data = vaspio.VaspData('./') - el_struct = elstruct.ElectronicStructure(vasp_data) - - efermi = el_struct.efermi - eigvals = el_struct.eigvals - efermi - emin = pars.groups[0]['emin'] - emax = pars.groups[0]['emax'] - ib_win, nb_min, nb_max = select_bands(eigvals, emin, emax) - - proj_sh = ProjectorShell(pars.shells[0], vasp_data.plocar.plo) - - proj_sh.select_projectors(ib_win, nb_min, nb_max) - - dens_mat = proj_sh.density_matrix(el_struct) - print dens_mat - - testout = 'densmat.out.test' - with open(testout, 'wt') as f: - f.write("density matrix: %s\n"%(dens_mat)) - - expected_file = 'densmat.out' - self.assertFileEqual(testout, expected_file) - diff --git a/python/converters/vasp/test/plotools/test_select_bands.py b/python/converters/vasp/test/plotools/test_select_bands.py deleted file mode 100644 index 75dd399d..00000000 --- a/python/converters/vasp/test/plotools/test_select_bands.py +++ /dev/null @@ -1,73 +0,0 @@ - -import numpy as np -import vaspio -from inpconf import ConfigParameters -from plotools import select_bands -import mytest - -################################################################################ -# -# TestSelectBands -# -################################################################################ -class TestSelectBands(mytest.MyTestCase): - """ - Function: - - def select_bands(eigvals, emin, emax) - - Scenarios: - - compare output for a correct input - - **if** emin > max(eigvals) **raise** Exception - - **if** emax > min(eigvals) **raise** Exception - """ -# Scenario 1 - def test_example(self): - conf_file = 'example.cfg' - pars = ConfigParameters(conf_file) - pars.parse_input() - vasp_data = vaspio.VaspData('./') - - efermi = vasp_data.doscar.efermi - eigvals = vasp_data.eigenval.eigs - efermi - emin = pars.groups[0]['emin'] - emax = pars.groups[0]['emax'] - ib_win, nb_min, nb_max = select_bands(eigvals, emin, emax) - - nb_min_exp = 3 - nb_max_exp = 8 - ib_win_exp = np.array([[[3, 8]], [[3, 8]], [[3, 7]], [[3, 7]]]) - - self.assertEqual(nb_min, nb_min_exp) - self.assertEqual(nb_max, nb_max_exp) - self.assertEqual(ib_win, ib_win_exp) - -# Scenario 2 - def test_emin_too_large(self): - conf_file = 'example.cfg' - pars = ConfigParameters(conf_file) - pars.parse_input() - vasp_data = vaspio.VaspData('./') - - efermi = vasp_data.doscar.efermi - eigvals = vasp_data.eigenval.eigs - efermi - emin = 20.0 - emax = 25.0 - with self.assertRaisesRegexp(Exception, "Energy window does not overlap"): - ib_win, nb_min, nb_max = select_bands(eigvals, emin, emax) - -# Scenario 3 - def test_emax_too_small(self): - conf_file = 'example.cfg' - pars = ConfigParameters(conf_file) - pars.parse_input() - vasp_data = vaspio.VaspData('./') - - efermi = vasp_data.doscar.efermi - eigvals = vasp_data.eigenval.eigs - efermi - emin = -50.0 - emax = -55.0 - with self.assertRaisesRegexp(Exception, "Energy window does not overlap"): - ib_win, nb_min, nb_max = select_bands(eigvals, emin, emax) - - diff --git a/python/converters/vasp/test/vaspio/.gitignore b/python/converters/vasp/test/vaspio/.gitignore deleted file mode 100644 index 1ed2bd4a..00000000 --- a/python/converters/vasp/test/vaspio/.gitignore +++ /dev/null @@ -1,2 +0,0 @@ -*.pyc -*.test diff --git a/python/converters/vasp/test/vaspio/DOSCAR.example b/python/converters/vasp/test/vaspio/DOSCAR.example deleted file mode 100644 index 94594e73..00000000 --- a/python/converters/vasp/test/vaspio/DOSCAR.example +++ /dev/null @@ -1,609 +0,0 @@ - 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1 1 1 1 - 0.1333597E+02 0.2587511E-09 0.2587511E-09 0.2587511E-09 0.5000000E-15 - 1.000000000000000E-004 - CAR - V - 11 4 9 - - 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3703704E-01 - 1 -31.099965 - 2 -31.099965 - 3 -31.099965 - 4 -0.813470 - 5 5.974027 - 6 5.974027 - 7 5.974027 - 8 7.986328 - 9 7.986328 - - 0.3333333E+00 0.0000000E+00 0.0000000E+00 0.4444444E+00 - 1 -31.819277 - 2 -31.322999 - 3 -31.105684 - 4 2.193081 - 5 4.784864 - 6 5.839340 - 7 7.833446 - 8 8.202781 - 9 8.589551 - - 0.3333333E+00 0.3333333E+00 0.0000000E+00 0.2962963E+00 - 1 -31.750021 - 2 -31.750021 - 3 -31.217560 - 4 3.978315 - 5 4.708263 - 6 4.708263 - 7 8.262522 - 8 8.262522 - 9 14.771374 - - -0.3333333E+00 0.3333333E+00 0.3333333E+00 0.2222222E+00 - 1 -31.719893 - 2 -31.577292 - 3 -31.577292 - 4 3.383714 - 5 3.756320 - 6 7.355029 - 7 7.355029 - 8 8.411511 - 9 11.054129 diff --git a/python/converters/vasp/test/vaspio/EIGENVAL.example.out b/python/converters/vasp/test/vaspio/EIGENVAL.example.out deleted file mode 100644 index a59166b4..00000000 --- a/python/converters/vasp/test/vaspio/EIGENVAL.example.out +++ /dev/null @@ -1,52 +0,0 @@ -nq = 1 -ispin = 1 -nelect = 11 -nktot = 4 -nband = 9 -kpts: -[[ 0. 0. 0. ] - [ 0.3333333 0. 0. ] - [ 0.3333333 0.3333333 0. ] - [-0.3333333 0.3333333 0.3333333]] -kwghts: -[ 0.03703704 0.4444444 0.2962963 0.2222222 ] -eigs: -[[[-31.099965] - [-31.099965] - [-31.099965] - [ -0.81347 ] - [ 5.974027] - [ 5.974027] - [ 5.974027] - [ 7.986328] - [ 7.986328]] - - [[-31.819277] - [-31.322999] - [-31.105684] - [ 2.193081] - [ 4.784864] - [ 5.83934 ] - [ 7.833446] - [ 8.202781] - [ 8.589551]] - - [[-31.750021] - [-31.750021] - [-31.21756 ] - [ 3.978315] - [ 4.708263] - [ 4.708263] - [ 8.262522] - [ 8.262522] - [ 14.771374]] - - [[-31.719893] - [-31.577292] - [-31.577292] - [ 3.383714] - [ 3.75632 ] - [ 7.355029] - [ 7.355029] - [ 8.411511] - [ 11.054129]]] diff --git a/python/converters/vasp/test/vaspio/IBZKPT.example b/python/converters/vasp/test/vaspio/IBZKPT.example deleted file mode 100644 index f460c3c6..00000000 --- a/python/converters/vasp/test/vaspio/IBZKPT.example +++ /dev/null @@ -1,122 +0,0 @@ -Automatically generated mesh - 10 -Reciprocal lattice - 0.00000000000000 0.00000000000000 0.00000000000000 1 - 0.20000000000000 0.00000000000000 0.00000000000000 12 - 0.40000000000000 0.00000000000000 0.00000000000000 12 - 0.20000000000000 0.20000000000000 0.00000000000000 24 - 0.40000000000000 0.20000000000000 -0.00000000000000 24 - 0.20000000000000 0.20000000000000 0.20000000000000 8 - -0.20000000000000 0.20000000000000 0.20000000000000 6 - -0.40000000000000 0.40000000000000 0.20000000000000 24 - -0.40000000000000 -0.40000000000000 0.20000000000000 8 - -0.40000000000000 0.40000000000000 0.40000000000000 6 -Tetrahedra - 107 0.00133333333333 - 4 1 2 2 4 - 12 2 2 4 4 - 4 2 4 4 6 - 4 2 3 4 5 - 4 2 4 4 5 - 12 4 4 5 6 - 16 3 4 5 5 - 28 4 5 5 6 - 8 4 5 6 6 - 4 3 3 4 5 - 12 3 4 4 5 - 4 4 4 4 5 - 4 2 2 3 4 - 12 2 3 4 4 - 8 2 4 4 4 - 8 2 2 2 4 - 12 2 2 4 7 - 12 2 4 4 7 - 8 1 2 2 2 - 4 2 2 2 2 - 4 2 2 2 7 - 16 5 5 6 6 - 12 3 4 5 6 - 8 3 5 5 6 - 8 3 4 4 6 - 4 3 4 6 8 - 4 3 5 6 8 - 4 3 4 4 4 - 4 3 4 4 8 - 8 4 4 7 8 - 4 4 4 8 8 - 4 2 2 3 7 - 16 2 3 4 7 - 12 3 4 7 8 - 4 3 4 5 7 - 4 3 5 7 8 - 4 3 5 5 5 - 12 3 5 5 8 - 16 5 5 8 9 - 24 3 4 5 8 - 8 4 5 8 8 - 4 5 8 8 8 - 16 5 8 8 9 - 4 3 3 4 8 - 12 3 5 8 8 - 12 3 3 5 8 - 4 3 4 8 8 - 8 4 5 5 9 - 12 4 5 8 9 - 4 4 7 8 9 - 4 2 3 5 8 - 4 2 4 5 8 - 8 2 4 7 8 - 12 2 3 4 8 - 4 2 2 4 8 - 4 2 2 7 8 - 4 1 2 4 7 - 8 1 2 2 7 - 4 2 3 4 6 - 4 3 5 6 6 - 8 5 6 6 6 - 8 5 5 5 6 - 4 4 4 5 5 - 16 4 5 5 8 - 4 3 4 4 7 - 4 3 7 8 8 - 8 4 4 5 8 - 4 5 5 6 9 - 4 4 5 6 8 - 4 5 5 6 8 - 8 5 8 8 10 - 8 5 8 9 10 - 4 4 7 8 8 - 4 4 8 8 8 - 8 8 8 8 10 - 4 7 8 8 8 - 4 8 8 8 9 - 20 8 8 9 10 - 4 4 5 7 8 - 4 5 7 8 8 - 4 5 5 5 8 - 4 5 8 9 9 - 8 8 9 9 10 - 6 9 9 10 10 - 12 8 9 10 10 - 4 8 8 10 10 - 8 4 8 8 9 - 4 3 4 5 9 - 4 3 4 8 9 - 4 7 8 9 10 - 4 7 8 8 10 - 4 4 7 8 10 - 4 2 4 8 8 - 4 2 7 8 8 - 4 2 4 4 8 - 4 3 3 5 6 - 4 4 5 5 5 - 4 3 5 8 9 - 4 3 8 8 9 - 6 5 5 8 8 - 2 3 3 5 5 - 4 4 5 6 9 - 4 4 8 9 10 - 4 8 10 10 10 - 6 8 8 9 9 - 4 9 10 10 10 - 2 10 10 10 10 diff --git a/python/converters/vasp/test/vaspio/IBZKPT.example.out b/python/converters/vasp/test/vaspio/IBZKPT.example.out deleted file mode 100644 index 2752e039..00000000 --- a/python/converters/vasp/test/vaspio/IBZKPT.example.out +++ /dev/null @@ -1,122 +0,0 @@ -nktot = 10 -ntet = 107 -volt = 0.00133333333333 -kpts: -[[ 0. 0. 0. ] - [ 0.2 0. 0. ] - [ 0.4 0. 0. ] - [ 0.2 0.2 0. ] - [ 0.4 0.2 -0. ] - [ 0.2 0.2 0.2] - [-0.2 0.2 0.2] - [-0.4 0.4 0.2] - [-0.4 -0.4 0.2] - [-0.4 0.4 0.4]] -tets: -[[ 4 1 2 2 4] - [12 2 2 4 4] - [ 4 2 4 4 6] - [ 4 2 3 4 5] - [ 4 2 4 4 5] - [12 4 4 5 6] - [16 3 4 5 5] - [28 4 5 5 6] - [ 8 4 5 6 6] - [ 4 3 3 4 5] - [12 3 4 4 5] - [ 4 4 4 4 5] - [ 4 2 2 3 4] - [12 2 3 4 4] - [ 8 2 4 4 4] - [ 8 2 2 2 4] - [12 2 2 4 7] - [12 2 4 4 7] - [ 8 1 2 2 2] - [ 4 2 2 2 2] - [ 4 2 2 2 7] - [16 5 5 6 6] - [12 3 4 5 6] - [ 8 3 5 5 6] - [ 8 3 4 4 6] - [ 4 3 4 6 8] - [ 4 3 5 6 8] - [ 4 3 4 4 4] - [ 4 3 4 4 8] - [ 8 4 4 7 8] - [ 4 4 4 8 8] - [ 4 2 2 3 7] - [16 2 3 4 7] - [12 3 4 7 8] - [ 4 3 4 5 7] - [ 4 3 5 7 8] - [ 4 3 5 5 5] - [12 3 5 5 8] - [16 5 5 8 9] - [24 3 4 5 8] - [ 8 4 5 8 8] - [ 4 5 8 8 8] - [16 5 8 8 9] - [ 4 3 3 4 8] - [12 3 5 8 8] - [12 3 3 5 8] - [ 4 3 4 8 8] - [ 8 4 5 5 9] - [12 4 5 8 9] - [ 4 4 7 8 9] - [ 4 2 3 5 8] - [ 4 2 4 5 8] - [ 8 2 4 7 8] - [12 2 3 4 8] - [ 4 2 2 4 8] - [ 4 2 2 7 8] - [ 4 1 2 4 7] - [ 8 1 2 2 7] - [ 4 2 3 4 6] - [ 4 3 5 6 6] - [ 8 5 6 6 6] - [ 8 5 5 5 6] - [ 4 4 4 5 5] - [16 4 5 5 8] - [ 4 3 4 4 7] - [ 4 3 7 8 8] - [ 8 4 4 5 8] - [ 4 5 5 6 9] - [ 4 4 5 6 8] - [ 4 5 5 6 8] - [ 8 5 8 8 10] - [ 8 5 8 9 10] - [ 4 4 7 8 8] - [ 4 4 8 8 8] - [ 8 8 8 8 10] - [ 4 7 8 8 8] - [ 4 8 8 8 9] - [20 8 8 9 10] - [ 4 4 5 7 8] - [ 4 5 7 8 8] - [ 4 5 5 5 8] - [ 4 5 8 9 9] - [ 8 8 9 9 10] - [ 6 9 9 10 10] - [12 8 9 10 10] - [ 4 8 8 10 10] - [ 8 4 8 8 9] - [ 4 3 4 5 9] - [ 4 3 4 8 9] - [ 4 7 8 9 10] - [ 4 7 8 8 10] - [ 4 4 7 8 10] - [ 4 2 4 8 8] - [ 4 2 7 8 8] - [ 4 2 4 4 8] - [ 4 3 3 5 6] - [ 4 4 5 5 5] - [ 4 3 5 8 9] - [ 4 3 8 8 9] - [ 6 5 5 8 8] - [ 2 3 3 5 5] - [ 4 4 5 6 9] - [ 4 4 8 9 10] - [ 4 8 10 10 10] - [ 6 8 8 9 9] - [ 4 9 10 10 10] - [ 2 10 10 10 10]] diff --git a/python/converters/vasp/test/vaspio/IBZKPT.notet b/python/converters/vasp/test/vaspio/IBZKPT.notet deleted file mode 100644 index e724e052..00000000 --- a/python/converters/vasp/test/vaspio/IBZKPT.notet +++ /dev/null @@ -1,7 +0,0 @@ -Automatically generated mesh - 4 -Reciprocal lattice - 0.00000000000000 0.00000000000000 0.00000000000000 1 - 0.33333333333333 0.00000000000000 0.00000000000000 12 - 0.33333333333333 0.33333333333333 0.00000000000000 8 - -0.33333333333333 0.33333333333333 0.33333333333333 6 diff --git a/python/converters/vasp/test/vaspio/IBZKPT.notet.out b/python/converters/vasp/test/vaspio/IBZKPT.notet.out deleted file mode 100644 index b40b8387..00000000 --- a/python/converters/vasp/test/vaspio/IBZKPT.notet.out +++ /dev/null @@ -1,6 +0,0 @@ -nktot = 4 -kpts: -[[ 0. 0. 0. ] - [ 0.33333333 0. 0. ] - [ 0.33333333 0.33333333 0. ] - [-0.33333333 0.33333333 0.33333333]] diff --git a/python/converters/vasp/test/vaspio/POSCAR.example b/python/converters/vasp/test/vaspio/POSCAR.example deleted file mode 100644 index 89a0ebcb..00000000 --- a/python/converters/vasp/test/vaspio/POSCAR.example +++ /dev/null @@ -1,10 +0,0 @@ - V SF test - 2.9878 - -0.5 0.5 0.5 - 0.5 -0.5 0.5 - 0.5 0.5 -0.5 - V - 1 -Direct - 0.0 0.0 0.0 - diff --git a/python/converters/vasp/test/vaspio/POSCAR.example.out b/python/converters/vasp/test/vaspio/POSCAR.example.out deleted file mode 100644 index b0d1a9d7..00000000 --- a/python/converters/vasp/test/vaspio/POSCAR.example.out +++ /dev/null @@ -1,10 +0,0 @@ -nq = 1 -ntypes = 1 -nions = [1] -el_names = ['V'] -a_brav: -[[-1. 1. 1.] - [ 1. -1. 1.] - [ 1. 1. -1.]] -q_types: -[array([[ 0., 0., 0.]])] diff --git a/python/converters/vasp/test/vaspio/mytest.py b/python/converters/vasp/test/vaspio/mytest.py deleted file mode 100644 index 38f0689e..00000000 --- a/python/converters/vasp/test/vaspio/mytest.py +++ /dev/null @@ -1,56 +0,0 @@ -r""" -Module defining a custom TestCase with extra functionality. -""" - -import unittest -import numpy as np -import difflib - -class MyTestCase(unittest.TestCase): - """ - Custom TestCase class supporting additional equality checks: - - numpy array equality - - file equality - """ - def __init__(self, *args, **kwargs): - """ - Initializes a custom equality function for comparing numpy arrays. - """ - super(MyTestCase, 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 assertFileEqual(self, file1, file2): - """ - Compares two files using difflib. - Empty lines are ignored. - Files are assumed to be relatively small; - the data is truncated for files larger than MAX_SIZE bytes. - """ - MAX_SIZE = 100000 - with open(file1, 'r') as f1: - str1 = f1.read(MAX_SIZE) - with open(file2, 'r') as f2: - str2 = f2.read(MAX_SIZE) -# -# Make a diff -# -# Remove empty lines - lstr1 = filter(lambda s: s.strip() != '', str1.splitlines(True)) - lstr2 = filter(lambda s: s.strip() != '', str2.splitlines(True)) -# diff - delta = difflib.unified_diff(lstr1, lstr2) -# combine delta's to a string - diff = ''.join(delta) -# if 'diff' is non-empty, files are different - if diff: - return self.fail("Files '%s' and '%s' differ"%(file1, file2)) - - diff --git a/python/converters/vasp/test/vaspio/runtest.sh b/python/converters/vasp/test/vaspio/runtest.sh deleted file mode 100755 index 9b7bd8ca..00000000 --- a/python/converters/vasp/test/vaspio/runtest.sh +++ /dev/null @@ -1 +0,0 @@ -PYTHONPATH=../../python:../../c:$PYTHONPATH python $1 diff --git a/python/converters/vasp/test/vaspio/test_doscar.py b/python/converters/vasp/test/vaspio/test_doscar.py deleted file mode 100644 index 721c6be9..00000000 --- a/python/converters/vasp/test/vaspio/test_doscar.py +++ /dev/null @@ -1,32 +0,0 @@ -r""" -Tests for class 'Doscar' from module 'vaspio' -""" -import mytest -import numpy as np -from vaspio import Doscar - -################################################################################ -# -# TestDoscar -# -################################################################################ -class TestDoscar(mytest.MyTestCase): - """ - Function: - - def Doscar.from_file(vasp_dir, dos_filename) - - Scenarios: - - correct DOSCAR file - - """ -# Scenario 1 - def test_example(self): - filename = 'DOSCAR.example' - doscar = Doscar() - doscar.from_file(vasp_dir='./', dos_filename=filename) - - test_efermi = doscar.efermi - expected = 5.84395237 - self.assertAlmostEqual(test_efermi, expected) - diff --git a/python/converters/vasp/test/vaspio/test_eigenval.py b/python/converters/vasp/test/vaspio/test_eigenval.py deleted file mode 100644 index 612eccdc..00000000 --- a/python/converters/vasp/test/vaspio/test_eigenval.py +++ /dev/null @@ -1,45 +0,0 @@ -r""" -Tests for class 'Eigneval' from module 'vaspio' -""" -import mytest -import numpy as np -from vaspio import Eigenval - -################################################################################ -# -# TestEigenval -# -################################################################################ -class TestEigenval(mytest.MyTestCase): - """ - Function: - - def Eigenval.from_file(vasp_dir, eig_filename) - - Scenarios: - - correct EIGENVAL file - - """ -# Scenario 1 - def test_example(self): - filename = 'EIGENVAL.example' - eigenval = Eigenval() - eigenval.from_file(vasp_dir='./', eig_filename=filename) - - testout = 'EIGENVAL.example.out.test' - with open(testout, 'w') as f: - writeline = lambda s: f.write(s + '\n') - writeprop = lambda pname: writeline("%s = %s"%(pname, eigenval.__dict__[pname])) - - writeprop('nq') - writeprop('ispin') - writeprop('nelect') - writeprop('nktot') - writeprop('nband') - writeline("kpts:\n%s"%(eigenval.kpts)) - writeline("kwghts:\n%s"%(eigenval.kwghts)) - writeline("eigs:\n%s"%(eigenval.eigs)) - - expected = 'EIGENVAL.example.out' - self.assertFileEqual(testout, expected) - diff --git a/python/converters/vasp/test/vaspio/test_kpoints.py b/python/converters/vasp/test/vaspio/test_kpoints.py deleted file mode 100644 index 6b4849de..00000000 --- a/python/converters/vasp/test/vaspio/test_kpoints.py +++ /dev/null @@ -1,57 +0,0 @@ -r""" -Tests for class 'Ibzkpt' from module 'vaspio' -""" -import mytest -import numpy as np -from vaspio import Kpoints - -################################################################################ -# -# TestIbzkpt -# -################################################################################ -class TestIbzkpt(mytest.MyTestCase): - """ - Function: - - def read_plocar(filename) - - Scenarios: - - full IBZKPT file with tetrahedra - - partial IBZKPT file with k-points only - - """ -# Scenario 1 - def test_example(self): - ibz_file = 'IBZKPT.example' - kpoints = Kpoints() - kpoints.from_file(vasp_dir='./', ibz_filename=ibz_file) - - testout = 'IBZKPT.example.out.test' - with open(testout, 'w') as f: - writeline = lambda s: f.write(s + '\n') - writeline("nktot = %s"%(kpoints.nktot)) - writeline("ntet = %s"%(kpoints.ntet)) - writeline("volt = %s"%(kpoints.volt)) - writeline("kpts:\n%s"%(kpoints.kpts)) - writeline("tets:\n%s"%(kpoints.itet)) - - expected = 'IBZKPT.example.out' - self.assertFileEqual(testout, expected) - -# Scenario 2 - def test_notet(self): - ibz_file = 'IBZKPT.notet' - kpoints = Kpoints() - kpoints.from_file(vasp_dir='./', ibz_filename=ibz_file) - - testout = 'IBZKPT.notet.out.test' - with open(testout, 'w') as f: - writeline = lambda s: f.write(s + '\n') - writeline("nktot = %s"%(kpoints.nktot)) - writeline("kpts:\n%s"%(kpoints.kpts)) - - expected = 'IBZKPT.notet.out' - self.assertFileEqual(testout, expected) - - diff --git a/python/converters/vasp/test/vaspio/test_poscar.py b/python/converters/vasp/test/vaspio/test_poscar.py deleted file mode 100644 index bfe4420c..00000000 --- a/python/converters/vasp/test/vaspio/test_poscar.py +++ /dev/null @@ -1,43 +0,0 @@ -r""" -Tests for class 'Poscar' from module 'vaspio' -""" -import mytest -import numpy as np -from vaspio import Poscar - -################################################################################ -# -# TestPoscar -# -################################################################################ -class TestPoscar(mytest.MyTestCase): - """ - Function: - - def Poscar.from_file(vasp_dir, poscar_filename) - - Scenarios: - - correct POSCAR file - - """ -# Scenario 1 - def test_example(self): - filename = 'POSCAR.example' - poscar = Poscar() - poscar.from_file(vasp_dir='./', poscar_filename=filename) - - testout = 'POSCAR.example.out.test' - with open(testout, 'w') as f: - writeline = lambda s: f.write(s + '\n') - writeprop = lambda pname: writeline("%s = %s"%(pname, poscar.__dict__[pname])) - - writeprop('nq') - writeprop('ntypes') - writeprop('nions') - writeprop('el_names') - writeline("a_brav:\n%s"%(poscar.a_brav)) - writeline("q_types:\n%s"%(poscar.q_types)) - - expected = 'POSCAR.example.out' - self.assertFileEqual(testout, expected) - diff --git a/python/converters/vasp/test/vaspio/test_vaspio.py b/python/converters/vasp/test/vaspio/test_vaspio.py deleted file mode 100644 index 6683d67a..00000000 --- a/python/converters/vasp/test/vaspio/test_vaspio.py +++ /dev/null @@ -1,11 +0,0 @@ - -r""" -Test suite for module `vaspio`. -""" -import unittest - -if __name__ == '__main__': - suite = unittest.TestLoader().discover('./') - unittest.TextTestRunner(verbosity=2, buffer=True).run(suite) -# unittest.TextTestRunner(verbosity=2, buffer=False).run(suite) -