Pytest suite (WIP)

setup.py

@@ -1,7 +1,9 @@
 import setuptools
 from numpy.distutils.core import setup, Extension
 
-mod = Extension(name='p2ptrans.fmodules', sources=['source/lap.f90', 'source/utils.f90', 'source/tiling.f90', 'source/potential.f90', 'source/transform.f90'], extra_f90_compile_args=["-fopenmp","-O3"], extra_link_args=['-lgomp'], f2py_options=["only:","munkres", "free_trans", "rot_mat", "center", "eye", "norm", "split", "det", "sort", "sphere", "circle", "distance", "derivative", "closest", "fixed_tmat", "fixed_tmat_int", "intoptimization", "fastoptimization", "optimize_vec", ":"])
+mod = Extension(name='p2ptrans.fmodules', sources=['source/lap.f90', 'source/utils.f90', 'source/tiling.f90', 'source/potential.f90', 'source/transform.f90'],\
+                extra_f90_compile_args=["-fopenmp","-O3"], extra_link_args=['-lgomp'],\
+                f2py_options=["only:","munkres", "free_trans", "rot_mat", "center", "eye", "norm", "split", "det", "sort", "sphere", "circle", "distance", "derivative", "closest", "fixed_tmat", "fixed_tmat_int", "intoptimization", "fastoptimization", "optimize_vec", ":"])
 
 setup(name='p2ptrans',
       version='2.0.2',
@@ -15,6 +17,7 @@
       python_requires='>=3',
       install_requires=[
           'numpy',
+          'pytest',
           'matplotlib',
           'spglib',
           'pylada @ git+https://github.com/pylada/pylada-light#egg=pylada',

tests/BCC_POSCAR

@@ -0,0 +1,9 @@
+BCC structure
+  2.87
+  0.5  0.5 -0.5
+  -0.5  0.5  0.5
+  0.5 -0.5  0.5
+  Fe
+  1
+Direct
+  0.0  0.0  0.0

tests/DC_C_POSCAR

@@ -0,0 +1,16 @@
+C8
+1.0
+3.573710 0.000000 0.000000
+0.000000 3.573710 0.000000
+0.000000 0.000000 3.573710
+C
+8
+direct
+0.250000 0.750000 0.250000 C
+0.000000 0.000000 0.500000 C
+0.250000 0.250000 0.750000 C
+0.000000 0.500000 0.000000 C
+0.750000 0.750000 0.750000 C
+0.500000 0.000000 0.000000 C
+0.750000 0.250000 0.250000 C
+0.500000 0.500000 0.500000 C

tests/DC_Si_POSCAR

@@ -0,0 +1,16 @@
+Si8
+1.0
+5.468728 0.000000 0.000000
+0.000000 5.468728 0.000000
+0.000000 0.000000 5.468728
+Si
+8
+direct
+0.250000 0.750000 0.250000 Si
+0.000000 0.000000 0.500000 Si
+0.250000 0.250000 0.750000 Si
+0.000000 0.500000 0.000000 Si
+0.750000 0.750000 0.750000 Si
+0.500000 0.000000 0.000000 Si
+0.750000 0.250000 0.250000 Si
+0.500000 0.500000 0.500000 Si

tests/FCC_POSCAR

@@ -0,0 +1,9 @@
+FCC structure
+  3.57
+  0.5  0.5  0.0
+  0.5  0.0  0.5
+  0.0  0.5  0.5
+  Fe
+  1
+Direct
+  0.0  0.0  0.0

tests/conftest.py

@@ -0,0 +1,112 @@
+from pylada.crystal import Structure
+from p2ptrans import read
+import os, glob, shutil
+import numpy as np
+import pytest
+
+BCC_filename = './BCC_POSCAR'
+FCC_filename = './FCC_POSCAR'
+testmat_filename = './testmat.txt'
+testmat_map_filename = './testmat_map.txt'
+
+_bcc = Structure([[0.5,-0.5, 0.5],
+                  [ 0.5, 0.5,-0.5],
+                  [-0.5, 0.5, 0.5]], scale=2.87, name='BCC structure')\
+           .add_atom(0., 0., 0., 'Fe')
+
+_fcc = Structure([[0.5, 0.5, 0.0],
+                  [ 0.5, 0.0, 0.5],
+                  [ 0.0, 0.5, 0.5]], scale=3.57, name='FCC structure')\
+           .add_atom(0., 0., 0., 'Fe')
+
+@pytest.fixture(scope="session")
+def bcc_fcc_s():
+    '''Fixture that returns the test fcc and bcc structures (session scope)'''
+    return _bcc, _fcc
+
+@pytest.fixture()
+def bcc_fcc():
+    '''Fixture that returns the test fcc and bcc structures'''
+    return _bcc, _fcc
+
+@pytest.fixture()
+def bcc_fcc_filenames():
+    '''Fixture that returns the fcc and bcc filenames'''
+    return BCC_filename, FCC_filename
+
+@pytest.fixture(scope='session')
+def bcc_fcc_filenames_s():
+    '''Fixture that returns the fcc and bcc filenames (session scope)'''
+    return BCC_filename, FCC_filename
+
+
+
+@pytest.fixture(scope="session")
+def p2p_default_options_s():
+    '''Fixture that returns the defualt options from readOptions in the runner'''
+    # (fileA, fileB, ncell, filename, interactive, savedisplay, outdir,
+    # use, switch, prim, anim, vol, minimize, test, crystfile, n_steps,
+    # showversion, map_ncell)
+    return ('./POSCAR_A', './POSCAR_B', 300, './p2p.in', False, False, '.',
+        False, False, True, False, False, False, False, './cryst.in', 60,
+        False, None)
+
+def p2p_int_default_options():
+    '''Fixture that returns the defualt p2pint options'''
+    # (fileA, fileB, planeA, planeB,
+    # ruleA, ruleB, ncell, n_iter, filename,
+    # interactive, savedisplay, outdir, use, minimize, test, n_iter, sym,
+    # vacuum, layers, surface, max_thickness, showversion)
+    return [['./POSCAR_A'], ['./POSCAR_B'], [0, 0, 1], [1, 1, 0],
+            {'1': {'Si'}}, {'1': {'Si'}}, 100, 1000, './p2p.in',
+            False, False, '.', False, False, False, 1000, 1,
+            10, 1, False, None, False]
+
+
+@pytest.fixture()
+def lap_test_matrix():
+    return np.loadtxt(testmat_filename)
+
+@pytest.fixture()
+def lap_test_map():
+    return np.loadtxt(testmat_map_filename)
+
+
+
+def assert_structs_approx_eq(A, B, tol=0.001):
+    '''Assert that the two structures have the same cell, scales, and atoms of the same type in the same positions'''
+    assert len(A) == len(B)
+    np.testing.assert_allclose(A.cell, B.cell, tol)
+    assert A.scale == pytest.approx(B.scale)
+    for aAtom, bAtom in zip(A, B):
+        assert aAtom.type == bAtom.type
+        assert aAtom.pos == pytest.approx(bAtom.pos, tol)
+
+
+def cleanup():
+    '''Removes dat files, the progress file, and tranPOSCARS from the current directory'''
+    for dat in glob.iglob('*dat'):
+        os.remove(dat)
+    if os.path.exists('progress.txt'):
+        os.remove('progress.txt')
+    if os.path.exists('out.txt'):
+        os.remove('out.txt')
+    if os.path.exists('TransPOSCARS'):
+        shutil.rmtree('TransPOSCARS')
+    if os.path.exists('DC_C_POSCAR-DC_Si_POSCAR'):
+        shutil.rmtree('DC_C_POSCAR-DC_Si_POSCAR')
+
+
+@pytest.fixture()
+def double_cleanup():
+    '''Fixture that cleans up both before and after'''
+    cleanup()
+    yield
+    cleanup()
+
+@pytest.fixture(scope="session")
+def double_cleanup_s():
+    '''Fixture that cleans up both before and after (session scope)'''
+    cleanup()
+    yield
+    cleanup()

tests/cryst_test_file

@@ -0,0 +1,5 @@
+# test comment
+ccell1 = [[1., 2., 3.],[4., 5., 6.],[7., 8., 9.]]
+ccell2 = [[9., 8., 7.],[6., 5., 4.],[3., 2., 1.]]
+planehkl = [1, 2, 3]
+diruvw = [3, 2, 1]

tests/interface_test.py

@@ -0,0 +1,95 @@
+from p2ptrans.interfaces import findMatchingInterfaces
+from conftest import assert_structs_approx_eq
+from pylada.crystal import Structure
+import numpy as np
+import pytest
+import os
+
+
+@pytest.fixture(scope="module")
+def find_matching_interface(double_cleanup_s):
+    (A, B, ncell, n_iter, sym, filename, interactive,
+    savedisplay, term_outdir, minimize, test, A3D, B3D) = (\
+    Structure(np.array([[3.57371   , 0.        , 0.        ],
+                        [0.        , 2.52699457, 0.        ],
+                        [0.        , 0.        , 2.52699457]]), name='C8 (1 1 0) 0')\
+    .add_atom(0.0, 0.0, 0.0, '1', site=0)\
+    .add_atom(2.6802824999999992, 1.2634972874970873, 6.661338147750939e-16, '1', site=1),
+    Structure(np.array([[ 3.86697465, -6.89049062e-16,  0.        ],
+                        [ 0.,          3.86697465e+00,  0.        ],
+                        [ 0.,          0.,              5.46872800]]), name='Si8 (0 0 1) 0')\
+    .add_atom(0.0, 0.0, 0.0, '1', site=0),
+    100, 1000, 1, './p2p.in', False, False, './DC_C_POSCAR-DC_Si_POSCAR/term_000-000', False, False,
+    np.array([[ 0., -0.70710678,  0.70710678],
+            [ 0.,  0.70710678,  0.70710678],
+            [-1.,  0.,          0.,       ]]),
+    np.array([[-0.70710678,  0.70710678,  0.],
+            [-0.70710678, -0.70710678,  0.],
+            [ 0.,          0.,          1.]]))
+
+    ttrans, dispStruc, vec_classes, dmin = findMatchingInterfaces(A, B, ncell, 5000,
+                                sym=sym, filename=filename,
+                                interactive=interactive,
+                                savedisplay=savedisplay,
+                                outdir=term_outdir,
+                                minimize=minimize, test=test,
+                                A3D=A3D, B3D=B3D)
+    return (ttrans, dispStruc, vec_classes, dmin)
+
+def test_interface_ttrans(find_matching_interface):
+    '''Test that the left 3x3 of the ttrans matrix is similar'''
+    #[[[ 0.924162, -0.23104 ,  0.      , -0.893427], another possiblity...
+    #  [ 0.326741,  0.980222,  0.      ,  1.895085],
+    #  [ 0.      ,  0.      ,  1.      ,  2.247815]]]
+    #[[[ 0.92416173, -0.23104043, 0., -0.89342744],
+    #  [ 0.32674051, 0.98022154,  0.,  1.89508484],
+    #  [ 0.,         0.,          1.,  2.24781482]]]
+    # [[[ 0.23104043 -0.92416173  0.         -3.57370943]
+    #   [ 0.98022154  0.32674051  0.          0.63191172]
+    #   [ 0.          0.          1.          2.2478148 ]]]
+    ttrans, dispStruc, vec_classes, dmin = find_matching_interface  
+    test_ttrans = np.array([[[ 0.92416173, -0.23104043,  0., -0.89342701],
+                             [ 0.32674051,  0.98022154,  0.,  1.89508287],
+                             [ 0.,          0.,          1.,  2.2478148 ]]])
+
+    np.testing.assert_allclose(np.sort(abs(ttrans[0, 0:2,0:2]), axis=None),
+                                [0.23104 ,  0.326741,  0.924162,  0.980222], 0.001)
+    np.testing.assert_allclose(ttrans[0, 2, :3], [0, 0, 1], 0.001)
+    np.testing.assert_allclose(ttrans[0, :4, 2], [0, 0, 1], 0.001)
+    # ignores last column
+
+
+@pytest.mark.skip(reason="Too inconsistant...")
+def test_interface_dispStruct(find_matching_interface):
+    #TODO: need to fix cell negetives
+    ttrans, dispStruc, vec_classes, dmin = find_matching_interface
+    test_dispStruc = Structure(np.array([[ -7.14742   ,   3.57371   ,   0.        ],
+                                        [ -2.52699457, -15.16196742,   0.        ],
+                                        [   0.       ,  -0.        ,   7.99572257]]))\
+    .add_atom(-3.5737104474246926, -17.6888747705878, 2.247814822377832, '0', atom='1', site=0)\
+    .add_atom(-0.893427947424688, -12.6348856305878, 2.247814822377832, '1', atom='1', site=1)\
+    .add_atom(-4.467137947424693, -13.898382915587801, 2.247814822377832, '2', atom='1', site=2)\
+    .add_atom(-4.474246906305268e-07, -16.4253774855878, 2.247814822377832, '3', atom='1', site=3)\
+    .add_atom(-6.253992947424691, -6.317399205587799, 2.247814822377832, '0', atom='1', site=4)\
+    .add_atom(-5.360565447424691, -10.107891060587797, 2.247814822377832, '2', atom='1', site=5)\
+    .add_atom(-2.680282947424688, -5.0539019205878, 2.247814822377832, '3', atom='1', site=6)\
+    .add_atom(-1.78685544742469, -8.844393775587802, 2.247814822377832, '1', atom='1', site=7)
+    assert_structs_approx_eq(dispStruc[0], test_dispStruc)
+
+def test_interface_vec_classes(find_matching_interface):
+    '''Test that four vec classes are found, and that they are all similar to expected'''
+    ttrans, dispStruc, vec_classes, dmin = find_matching_interface
+    vec_classes = np.array(vec_classes[0])
+    #sorted_vec_classes = vec_classes[np.lexsort(np.transpose(np.round(vec_classes, 2)))]
+    assert len(vec_classes == 4)
+    for vec_class in vec_classes:
+        np.testing.assert_allclose(abs(vec_class), [ 0.893501,  0.631446, 2.247841], 0.001)
+
+def test_interface_dmin(find_matching_interface):
+    #TODO: what is the reasonable tolerance on this?  
+    ttrans, dispStruc, vec_classes, dmin = find_matching_interface
+    test_dmin = -44.17527158660921
+    assert -50 <= dmin <= -40
+
+
+

tests/test_units.py

@@ -0,0 +1,78 @@
+from p2ptrans import read, analysis, core, format_spglib
+from p2ptrans.fmodules import hungarian as lap
+from conftest import assert_structs_approx_eq
+from spglib import get_spacegroup
+import numpy as np
+import pytest
+
+
+def test_read_poscars(bcc_fcc, bcc_fcc_filenames):
+    '''Test that pylada reads test files correctly'''
+    bcc, fcc = bcc_fcc
+    bcc_file, fcc_file = bcc_fcc_filenames
+    read_bcc = read.poscar(bcc_file)
+    read_fcc = read.poscar(fcc_file)
+
+    assert_structs_approx_eq(read_bcc, bcc)
+    assert_structs_approx_eq(read_fcc, fcc)
+
+def test_spacegroup(bcc_fcc):
+    '''Tests that spglib reports the correct spacegroups'''
+    bcc, fcc = bcc_fcc
+    assert get_spacegroup(format_spglib.to_spglib(bcc), symprec=0.3, angle_tolerance=3.0) == 'Im-3m (229)'
+    assert get_spacegroup(format_spglib.to_spglib(fcc), symprec=0.3, angle_tolerance=3.0) == 'Fm-3m (225)'
+
+def test_read_cryst_defaults():
+    '''Test that the cryst param defaults are the unit matrix'''
+    ccell1, ccell2, planehkl, diruvw = analysis.readCrystParam('./FILE_DNE')
+    assert (ccell1 == [[1., 0., 0.],
+                       [0., 1., 0.],
+                       [0., 0., 1.]]).all
+    assert (ccell2 == [[1., 0., 0.],
+                       [0., 1., 0.],
+                       [0., 0., 1.]]).all
+    assert planehkl == [1, 0, 0]
+    assert diruvw == [0, 1, 0]
+
+def test_read_cryst():
+    '''Tests that the cryst param file is read correctly'''
+    ccell1, ccell2, planehkl, diruvw = analysis.readCrystParam('./cryst_test_file')
+    assert ccell1 == [[1., 2., 3.],[4., 5., 6.],[7., 8., 9.]]
+    assert ccell2 == [[9., 8., 7.],[6., 5., 4.],[3., 2., 1.]]
+    assert planehkl == [1, 2, 3]
+    assert diruvw == [3, 2, 1]
+
+#def test_p2pint_extra_params(): #TODO:this
+#    assert False
+
+@pytest.mark.skip(reason="Replaced with smaller and larger tests...")
+def test_optimize(double_cleanup, bcc_fcc):
+    BCC, FCC = bcc_fcc
+    BCC_cell = BCC.cell * 2.87
+    FCC_cell = FCC.cell * 3.57
+    # optimization(A, Acell, mulA, B, Bcell, mulB, ncell, filename, outdir, max_cell_size)
+    result = core.optimization(BCC, BCC_cell, 1, FCC, FCC_cell, 1, 300, './p2p.in', '.', 1000)
+    Apos, Apos_map, Bpos, Bposst, n_map, natA, class_list, tmat, dmin, atoms, atom_types, foundcell, vec = result
+    print(Apos, Apos_map, Bpos, Bposst, n_map, natA, class_list, tmat, dmin, atoms, atom_types, foundcell, vec)
+
+
+def test_LAP(lap_test_matrix, lap_test_map):
+    test_mat = lap_test_matrix
+    test_map = lap_test_map
+    dist, mapping = lap.munkres(test_mat, )
+    assert dist == pytest.approx(94.08380269604208, 0.0001)
+    np.testing.assert_allclose(mapping, test_map)
+
+'''!ASHHH ! way to print given matrix
+    integer :: L
+
+    Print *, "start Matrix"
+    DO i = 1, N        ! print row-by-row
+      DO j = 1, N
+        print *, C(i, j)
+      END DO
+      !WRITE(*,*) (C(i,j), j=1, L)
+    END DO
+    print *, "end Matrix"
+    stop
+    !END ASHHHH'''

tests/testinglist

@@ -0,0 +1,7 @@
+
+- resuses results
+- runs from continue.dat
+
+- individual bits of p2ptrans work
+
+- does interfaces