From 4af8406b4c898ce52b48a804a492e08f08ed49e2 Mon Sep 17 00:00:00 2001 From: "Oleg E. Peil" Date: Wed, 18 Nov 2015 15:46:58 +0100 Subject: [PATCH] Fixed tests for ProjectorGroup The tests have been modified to conform to the recent input and code changes. --- python/vasp/test/_proj_group/example.cfg | 7 + python/vasp/test/_proj_group/mytest.py | 56 + python/vasp/test/_proj_group/one_site/DOSCAR | 507 ++ .../vasp/test/_proj_group/one_site/EIGENVAL | 924 ++++ python/vasp/test/_proj_group/one_site/IBZKPT | 194 + python/vasp/test/_proj_group/one_site/LOCPROJ | 4321 +++++++++++++++++ python/vasp/test/_proj_group/one_site/POSCAR | 13 + python/vasp/test/_proj_group/one_site/PROJCAR | 974 ++++ python/vasp/test/_proj_group/projgroups.out | 1903 +++++++- python/vasp/test/_proj_group/projortho.out | 125 +- python/vasp/test/_proj_group/simple.cfg | 7 + python/vasp/test/_proj_group/simple/DOSCAR | 507 ++ python/vasp/test/_proj_group/simple/EIGENVAL | 278 ++ python/vasp/test/_proj_group/simple/IBZKPT | 37 + python/vasp/test/_proj_group/simple/LOCPROJ | 1281 +++++ python/vasp/test/_proj_group/simple/POSCAR | 10 + python/vasp/test/_proj_group/simple/PROJCAR | 290 ++ python/vasp/test/_proj_group/test_one_site.py | 58 + .../vasp/test/_proj_group/test_projgroups.py | 80 - .../test/_proj_group/test_select_bands.py | 67 +- .../vasp/test/_proj_shell/test_projshells.py | 4 +- 21 files changed, 11296 insertions(+), 347 deletions(-) create mode 100644 python/vasp/test/_proj_group/example.cfg create mode 100644 python/vasp/test/_proj_group/mytest.py create mode 100644 python/vasp/test/_proj_group/one_site/DOSCAR create mode 100644 python/vasp/test/_proj_group/one_site/EIGENVAL create mode 100644 python/vasp/test/_proj_group/one_site/IBZKPT create mode 100644 python/vasp/test/_proj_group/one_site/LOCPROJ create mode 100644 python/vasp/test/_proj_group/one_site/POSCAR create mode 100644 python/vasp/test/_proj_group/one_site/PROJCAR create mode 100644 python/vasp/test/_proj_group/simple.cfg create mode 100644 python/vasp/test/_proj_group/simple/DOSCAR create mode 100644 python/vasp/test/_proj_group/simple/EIGENVAL create mode 100644 python/vasp/test/_proj_group/simple/IBZKPT create mode 100644 python/vasp/test/_proj_group/simple/LOCPROJ create mode 100644 python/vasp/test/_proj_group/simple/POSCAR create mode 100644 python/vasp/test/_proj_group/simple/PROJCAR create mode 100644 python/vasp/test/_proj_group/test_one_site.py delete mode 100644 python/vasp/test/_proj_group/test_projgroups.py diff --git a/python/vasp/test/_proj_group/example.cfg b/python/vasp/test/_proj_group/example.cfg new file mode 100644 index 00000000..c7da2ff6 --- /dev/null +++ b/python/vasp/test/_proj_group/example.cfg @@ -0,0 +1,7 @@ + +[Shell 1] +LSHELL = 2 +IONS = 2 +EWINDOW = -10.0 4.0 + + diff --git a/python/vasp/test/_proj_group/mytest.py b/python/vasp/test/_proj_group/mytest.py new file mode 100644 index 00000000..38f0689e --- /dev/null +++ b/python/vasp/test/_proj_group/mytest.py @@ -0,0 +1,56 @@ +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/vasp/test/_proj_group/one_site/DOSCAR b/python/vasp/test/_proj_group/one_site/DOSCAR new file mode 100644 index 00000000..a5fec189 --- /dev/null +++ b/python/vasp/test/_proj_group/one_site/DOSCAR @@ -0,0 +1,507 @@ + 5 5 0 1 + 0.1133347E+02 0.3841000E-09 0.3841000E-09 0.3841000E-09 0.4000000E-15 + 1.000000000000000E-004 + CAR + unknown system + 13.00000000 -2.00000000 501 5.60220911 1.00000000 + -2.000 0.0000E+00 0.2000E+02 + -1.970 0.0000E+00 0.2000E+02 + -1.940 0.0000E+00 0.2000E+02 + -1.910 0.0000E+00 0.2000E+02 + -1.880 0.0000E+00 0.2000E+02 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(-0.4167665-0.1944743j) + 3 (-0.000361-0.0001685j) + 4 (0.412118+0.1923052j) + 5 (0.0371652+0.0173423j) + 1 (0.4189292-0.3215328j) + 2 (-0.2059377+0.1580595j) + 3 (-0.0325343+0.0249704j) + 4 (-0.2129861+0.1634692j) + 5 (-0.000316+0.0002426j) diff --git a/python/vasp/test/_proj_group/projortho.out b/python/vasp/test/_proj_group/projortho.out index 622fe2b8..51bf747c 100644 --- a/python/vasp/test/_proj_group/projortho.out +++ b/python/vasp/test/_proj_group/projortho.out @@ -1,115 +1,10 @@ -pars: {'normalize': True, 'index': '1', 'emin': -15.0, 'emax': 5.0, 'normion': False, 'shells': [0]} -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 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(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) +density matrix: [[[[ 0.54239246 -0.00069108 0.00000947 -0.0006764 -0.00000019] + [-0.00069108 0.54295558 0.00000486 0.0008286 -0.00002492] + [ 0.00000947 0.00000486 0.57155761 0.00000454 0.00000002] + [-0.0006764 0.0008286 0.00000454 0.5466635 0.00002474] + [-0.00000019 -0.00002492 0.00000002 0.00002474 0.57284183]]]] +overlap matrix: [[[[ 1.00000008 -0. -0. -0. -0. ] + [-0. 1.00000008 0. 0. 0. ] + [-0. 0. 1.00000008 0. -0. ] + [-0. 0. 0. 1.00000008 -0. ] + [-0. 0. -0. -0. 1.00000008]]]] diff --git a/python/vasp/test/_proj_group/simple.cfg b/python/vasp/test/_proj_group/simple.cfg new file mode 100644 index 00000000..b86aeeec --- /dev/null +++ b/python/vasp/test/_proj_group/simple.cfg @@ -0,0 +1,7 @@ + +[Shell 1] +LSHELL = 2 +IONS = 1 +EWINDOW = -15.0 2.0 + + diff --git a/python/vasp/test/_proj_group/simple/DOSCAR b/python/vasp/test/_proj_group/simple/DOSCAR new file mode 100644 index 00000000..33b78e5d --- /dev/null +++ b/python/vasp/test/_proj_group/simple/DOSCAR @@ -0,0 +1,507 @@ + 1 1 0 1 + 0.1333597E+02 0.2587511E-09 0.2587511E-09 0.2587511E-09 0.4000000E-15 + 1.000000000000000E-004 + CAR + unknown system + 13.00000000 -2.00000000 501 7.60877984 1.00000000 + -2.000 0.0000E+00 0.6000E+01 + -1.970 0.0000E+00 0.6000E+01 + -1.940 0.0000E+00 0.6000E+01 + -1.910 0.0000E+00 0.6000E+01 + -1.880 0.0000E+00 0.6000E+01 + -1.850 0.0000E+00 0.6000E+01 + -1.820 0.0000E+00 0.6000E+01 + -1.790 0.0000E+00 0.6000E+01 + -1.760 0.0000E+00 0.6000E+01 + -1.730 0.0000E+00 0.6000E+01 + -1.700 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-0.0000000 + 31 0.0000000 -0.0000000 0.0000595 -0.0000227 -0.0000580 0.0000221 0.0002120 -0.0000808 0.0000004 -0.0000002 + 32 -0.0000108 0.0000041 -0.0001899 0.0000724 -0.0001903 0.0000726 0.0000008 -0.0000003 -0.0000909 0.0000347 + diff --git a/python/vasp/test/_proj_group/test_one_site.py b/python/vasp/test/_proj_group/test_one_site.py new file mode 100644 index 00000000..8e3416b1 --- /dev/null +++ b/python/vasp/test/_proj_group/test_one_site.py @@ -0,0 +1,58 @@ + +import os +import rpath +_rpath = os.path.dirname(rpath.__file__) + '/' + +import numpy as np +import vaspio +import elstruct +from inpconf import ConfigParameters +from proj_shell import ProjectorShell +from proj_group import ProjectorGroup +import mytest + +################################################################################ +# +# TestProjectorGroup +# +################################################################################ +class TestProjectorGroup(mytest.MyTestCase): + """ + Class: + + ProjectorGroup(sh_pars, proj_raw) + + Scenarios: + - **test** that orthogonalization is correct + """ + def setUp(self): + conf_file = _rpath + 'example.cfg' + self.pars = ConfigParameters(conf_file) + self.pars.parse_input() + vasp_data = vaspio.VaspData(_rpath + 'one_site/') + self.el_struct = elstruct.ElectronicStructure(vasp_data) + + efermi = vasp_data.doscar.efermi + self.eigvals = vasp_data.eigenval.eigs - efermi + ferw = vasp_data.eigenval.ferw + + self.proj_sh = ProjectorShell(self.pars.shells[0], vasp_data.plocar.plo, vasp_data.plocar.proj_params, 0) + self.proj_gr = ProjectorGroup(self.pars.groups[0], [self.proj_sh], self.eigvals, ferw) + +# Scenario 1 + def test_ortho(self): + self.proj_gr.orthogonalize() + + dens_mat, overl = self.proj_sh.density_matrix(self.el_struct) + + testout = _rpath + 'projortho.out.test' + with open(testout, 'wt') as f: + f.write("density matrix: %s\n"%(dens_mat)) + f.write("overlap matrix: %s\n"%(overl)) + + self.assertEqual(overl, np.eye(5)) + + expected_file = _rpath + 'projortho.out' + self.assertFileEqual(testout, expected_file) + + diff --git a/python/vasp/test/_proj_group/test_projgroups.py b/python/vasp/test/_proj_group/test_projgroups.py deleted file mode 100644 index 590f0f5c..00000000 --- a/python/vasp/test/_proj_group/test_projgroups.py +++ /dev/null @@ -1,80 +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 - ferw = self.vasp_data.plocar.ferw - - self.shells = [ProjectorShell(self.pars.shells[0], self.vasp_data.plocar.plo)] - self.proj_gr = ProjectorGroup(self.pars.groups[0], self.shells, eigvals, ferw) - -# 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/vasp/test/_proj_group/test_select_bands.py b/python/vasp/test/_proj_group/test_select_bands.py index 75dd399d..55a37d6c 100644 --- a/python/vasp/test/_proj_group/test_select_bands.py +++ b/python/vasp/test/_proj_group/test_select_bands.py @@ -1,8 +1,14 @@ +import os +import rpath +_rpath = os.path.dirname(rpath.__file__) + '/' + import numpy as np import vaspio +import elstruct from inpconf import ConfigParameters -from plotools import select_bands +from proj_shell import ProjectorShell +from proj_group import ProjectorGroup import mytest ################################################################################ @@ -14,29 +20,34 @@ class TestSelectBands(mytest.MyTestCase): """ Function: - def select_bands(eigvals, emin, emax) + def ProjectorGroup.select_bands(eigvals) 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('./') + def setUp(self): + conf_file = _rpath + 'simple.cfg' + self.pars = ConfigParameters(conf_file) + self.pars.parse_input() + vasp_data = vaspio.VaspData(_rpath + 'simple/') + self.el_struct = elstruct.ElectronicStructure(vasp_data) 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) + self.eigvals = vasp_data.eigenval.eigs - efermi + ferw = vasp_data.eigenval.ferw + + self.proj_sh = ProjectorShell(self.pars.shells[0], vasp_data.plocar.plo, vasp_data.plocar.proj_params, 0) + self.proj_gr = ProjectorGroup(self.pars.groups[0], [self.proj_sh], self.eigvals, ferw) + +# Scenario 1 + def test_correct(self): + ib_win, nb_min, nb_max = self.proj_gr.select_bands(self.eigvals) nb_min_exp = 3 - nb_max_exp = 8 - ib_win_exp = np.array([[[3, 8]], [[3, 8]], [[3, 7]], [[3, 7]]]) + nb_max_exp = 8 + ib_win_exp = np.array([[[3, 8]], [[3, 7]], [[3, 7]], [[3, 7]], [[3, 7]], [[3, 7]], [[3, 7]], [[3, 4]]]) self.assertEqual(nb_min, nb_min_exp) self.assertEqual(nb_max, nb_max_exp) @@ -44,30 +55,16 @@ class TestSelectBands(mytest.MyTestCase): # 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) + self.proj_gr.emin = 20.0 + self.proj_gr.emax = 25.0 + with self.assertRaisesRegexp(Exception, "No bands inside the window"): + ib_win, nb_min, nb_max = self.proj_gr.select_bands(self.eigvals) # 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 + self.proj_gr.emin = -50.0 + self.proj_gr.emax = -55.0 with self.assertRaisesRegexp(Exception, "Energy window does not overlap"): - ib_win, nb_min, nb_max = select_bands(eigvals, emin, emax) + ib_win, nb_min, nb_max = self.proj_gr.select_bands(self.eigvals) diff --git a/python/vasp/test/_proj_shell/test_projshells.py b/python/vasp/test/_proj_shell/test_projshells.py index d3e9a14c..2c665921 100644 --- a/python/vasp/test/_proj_shell/test_projshells.py +++ b/python/vasp/test/_proj_shell/test_projshells.py @@ -52,8 +52,8 @@ class TestProjectorShell(mytest.MyTestCase): 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] + ib1 = self.proj_sh.ib_win[ik, 0, 0] + ib2 = self.proj_sh.ib_win[ik, 0, 1] f.write("%i %i\n"%(ib1, ib2)) for ib in xrange(ib2 - ib1 + 1): for ilm in xrange(nlm):