TST: More updated to use absolute path for data files

tests/conftest.py

@@ -0,0 +1,8 @@
+import os.path
+
+import pytest
+
+@pytest.fixture
+def datafile_directory():
+    """Absolute path to the `tests` directory (which also contains the data files)"""
+    return os.path.dirname(__file__)

tests/test_bop.py

@@ -144,9 +144,9 @@ def test_crystal_elastic_constants(a0, par):
     TersoffBrenner(tersoff_brenner.Tersoff_PRB_39_5566_Si_C),
     StillingerWeber(stillinger_weber.Stillinger_Weber_PRB_31_5262_Si)
 ])
-def test_amorphous(par):
+def test_amorphous(par, datafile_directory):
     # Tests for amorphous Si
-    aSi = ase.io.read(f'{os.path.dirname(__file__)}/aSi_N8.xyz')
+    aSi = ase.io.read(f'{datafile_directory}/aSi_N8.xyz')
     aSi.calc = Manybody(**par)
     # Non-zero forces and Hessian
     compute_forces_and_hessian(aSi, par)

tests/test_eam_average_atom.py

@@ -42,12 +42,11 @@
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 # ======================================================================
 
+import os.path
 import unittest
 
 import numpy as np
 
-import os
-
 from matscipy.calculators.eam import io, average_atom
 
 import matscipytest
@@ -79,11 +78,11 @@ def test_average_atom_Ni_Al(self):
         input_table = "Mishin-Ni-Al-2009.eam.alloy"
         reference_table = "Mishin-Ni-Al-2009_reference_A-atom_Ni85Al15.eam.alloy"
         concentrations = np.array((0.85, 0.15))
-        source, parameters, F, f, rep = io.read_eam(input_table)
+        source, parameters, F, f, rep = io.read_eam(f'{os.path.dirname(__file__)}/{input_table}')
         (new_parameters, new_F, new_f, new_rep) = average_atom.average_potential(
             concentrations, parameters, F, f, rep
         )
-        ref_source, ref_parameters, ref_F, ref_f, ref_rep = io.read_eam(reference_table)
+        ref_source, ref_parameters, ref_F, ref_f, ref_rep = io.read_eam(f'{os.path.dirname(__file__)}/{reference_table}')
         diff_F = np.linalg.norm(ref_F - new_F)
         diff_f = np.linalg.norm(ref_f - new_f)
         diff_rep = np.linalg.norm(ref_rep - new_rep)
@@ -113,11 +112,11 @@ def test_average_atom_Fe_Cu_Ni(self):
         input_table = "FeCuNi.eam.alloy"
         reference_table = "FeCuNi_reference_A-atom_Fe33Cu33Ni33.eam.alloy"
         concentrations = np.array((1.0 / 3.0, 1.0 / 3.0, 1.0 / 3.0))
-        source, parameters, F, f, rep = io.read_eam(input_table)
+        source, parameters, F, f, rep = io.read_eam(f'{os.path.dirname(__file__)}/{input_table}')
         (new_parameters, new_F, new_f, new_rep) = average_atom.average_potential(
             concentrations, parameters, F, f, rep
         )
-        ref_source, ref_parameters, ref_F, ref_f, ref_rep = io.read_eam(reference_table)
+        ref_source, ref_parameters, ref_F, ref_f, ref_rep = io.read_eam(f'{os.path.dirname(__file__)}/{reference_table}')
         diff_F = np.linalg.norm(ref_F - new_F)
         diff_f = np.linalg.norm(ref_f - new_f)
         diff_rep = np.linalg.norm(ref_rep - new_rep)

tests/test_eam_calculator.py

@@ -23,7 +23,7 @@
 #
 
 import gzip
-import random
+import os.path
 import unittest
 
 import numpy as np
@@ -53,8 +53,8 @@ class TestEAMCalculator(matscipytest.MatSciPyTestCase):
     tol = 2e-6
 
     def test_forces(self):
-        for calc in [EAM('Au-Grochola-JCP05.eam.alloy')]:
-            a = io.read('Au_923.xyz')
+        for calc in [EAM(f'{os.path.dirname(__file__)}/Au-Grochola-JCP05.eam.alloy')]:
+            a = io.read(f'{os.path.dirname(__file__)}/Au_923.xyz')
             a.center(vacuum=10.0)
             a.calc = calc
             f = a.get_forces()
@@ -67,7 +67,7 @@ def test_forces(self):
 
     def test_stress(self):
         a = FaceCenteredCubic('Au', size=[2,2,2])
-        calc = EAM('Au-Grochola-JCP05.eam.alloy')
+        calc = EAM(f'{os.path.dirname(__file__)}/Au-Grochola-JCP05.eam.alloy')
         a.calc = calc
         self.assertArrayAlmostEqual(a.get_stress(), numerical_stress(a), tol=self.tol)
 
@@ -80,7 +80,7 @@ def test_stress(self):
 
     def test_Grochola(self):
         a = FaceCenteredCubic('Au', size=[2,2,2])
-        calc = EAM('Au-Grochola-JCP05.eam.alloy')
+        calc = EAM(f'{os.path.dirname(__file__)}/Au-Grochola-JCP05.eam.alloy')
         a.calc = calc
         FIRE(StrainFilter(a, mask=[1,1,1,0,0,0]), logfile=None).run(fmax=0.001)
         a0 = a.cell.diagonal().mean()/2
@@ -94,17 +94,17 @@ def test_Grochola(self):
     def test_direct_evaluation(self):
         a = FaceCenteredCubic('Au', size=[2,2,2])
         a.rattle(0.1)
-        calc = EAM('Au-Grochola-JCP05.eam.alloy')
+        calc = EAM(f'{os.path.dirname(__file__)}/Au-Grochola-JCP05.eam.alloy')
         a.calc = calc
         f = a.get_forces()
 
-        calc2 = EAM('Au-Grochola-JCP05.eam.alloy')
+        calc2 = EAM(f'{os.path.dirname(__file__)}/Au-Grochola-JCP05.eam.alloy')
         i_n, j_n, dr_nc, abs_dr_n = neighbour_list('ijDd', a, cutoff=calc2.cutoff)
         epot, virial, f2 = calc2.energy_virial_and_forces(a.numbers, i_n, j_n, dr_nc, abs_dr_n)
         self.assertArrayAlmostEqual(f, f2)
 
         a = FaceCenteredCubic('Cu', size=[2,2,2])
-        calc = EAM('CuAg.eam.alloy')
+        calc = EAM(f'{os.path.dirname(__file__)}/CuAg.eam.alloy')
         a.calc = calc
         FIRE(StrainFilter(a, mask=[1,1,1,0,0,0]), logfile=None).run(fmax=0.001)
         e_Cu = a.get_potential_energy()/len(a)
@@ -151,7 +151,7 @@ def test_CuZr(self):
         # This is a test for the potential published in:
         # Mendelev, Sordelet, Kramer, J. Appl. Phys. 102, 043501 (2007)
         a = FaceCenteredCubic('Cu', size=[2,2,2])
-        calc = EAM('CuZr_mm.eam.fs', kind='eam/fs')
+        calc = EAM(f'{os.path.dirname(__file__)}/CuZr_mm.eam.fs', kind='eam/fs')
         a.calc = calc
         FIRE(StrainFilter(a, mask=[1,1,1,0,0,0]), logfile=None).run(fmax=0.001)
         a_Cu = a.cell.diagonal().mean()/2
@@ -215,20 +215,20 @@ def test_forces_CuZr_glass(self):
                 modify sort id format float "%.14g"
         """
         format = "lammps-dump" if "lammps-dump" in io.formats.all_formats.keys() else "lammps-dump-text"
-        atoms = io.read("CuZr_glass_460_atoms_forces.lammps.dump.gz", format=format)
+        atoms = io.read(f"{os.path.dirname(__file__)}/CuZr_glass_460_atoms_forces.lammps.dump.gz", format=format)
         old_atomic_numbers = atoms.get_atomic_numbers()
         sel, = np.where(old_atomic_numbers == 1)
         new_atomic_numbers = np.zeros_like(old_atomic_numbers)
         new_atomic_numbers[sel] = 40 # Zr
         sel, = np.where(old_atomic_numbers == 2)
         new_atomic_numbers[sel] = 29 # Cu
         atoms.set_atomic_numbers(new_atomic_numbers)
-        calculator = EAM('ZrCu.onecolumn.eam.alloy')
+        calculator = EAM(f'{os.path.dirname(__file__)}/ZrCu.onecolumn.eam.alloy')
         atoms.calc = calculator
         atoms.pbc = [True, True, True]
         forces = atoms.get_forces()
         # Read tabulated forces and compare
-        with gzip.open("CuZr_glass_460_atoms_forces.lammps.dump.gz") as file:
+        with gzip.open(f"{os.path.dirname(__file__)}/CuZr_glass_460_atoms_forces.lammps.dump.gz") as file:
             for line in file:
                 if line.startswith(b"ITEM: ATOMS "): # ignore header
                     break
@@ -275,7 +275,7 @@ def test_funcfl(self):
         for i in range(1, 202):
             latticeconstant = amin + i * da
             atoms = FaceCenteredCubic(symbol='Au', size=[5,5,5], pbc=(1,1,1), latticeconstant=latticeconstant)
-            calc = EAM('Au-Grochola-JCP05.eam.alloy')
+            calc = EAM(f'{os.path.dirname(__file__)}/Au-Grochola-JCP05.eam.alloy')
             atoms.calc = calc
             energy = atoms.get_potential_energy()
             print(energy)

tests/test_eam_calculator_forces_and_hessian.py

@@ -41,6 +41,7 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 # ======================================================================
 
+import os.path
 import unittest
 
 import gzip
@@ -94,20 +95,20 @@ def test_forces_CuZr_glass(self):
                 modify sort id format float "%.14g"
         """
         format = "lammps-dump" if "lammps-dump" in io.formats.all_formats.keys() else "lammps-dump-text"
-        atoms = io.read("CuZr_glass_460_atoms_forces.lammps.dump.gz", format=format)
+        atoms = io.read(f"{os.path.dirname(__file__)}/CuZr_glass_460_atoms_forces.lammps.dump.gz", format=format)
         old_atomic_numbers = atoms.get_atomic_numbers()
         sel, = np.where(old_atomic_numbers == 1)
         new_atomic_numbers = np.zeros_like(old_atomic_numbers)
         new_atomic_numbers[sel] = 40 # Zr
         sel, = np.where(old_atomic_numbers == 2)
         new_atomic_numbers[sel] = 29 # Cu
         atoms.set_atomic_numbers(new_atomic_numbers)
-        calculator = EAM('ZrCu.onecolumn.eam.alloy')
+        calculator = EAM(f'{os.path.dirname(__file__)}/ZrCu.onecolumn.eam.alloy')
         atoms.set_calculator(calculator)
         atoms.pbc = [True, True, True]
         forces = atoms.get_forces()
         # Read tabulated forces and compare
-        with gzip.open("CuZr_glass_460_atoms_forces.lammps.dump.gz") as file:
+        with gzip.open(f"{os.path.dirname(__file__)}/CuZr_glass_460_atoms_forces.lammps.dump.gz") as file:
             for line in file:
                 if line.startswith(b"ITEM: ATOMS "): # ignore header
                     break
@@ -123,7 +124,7 @@ def test_hessian_monoatomic(self):
         """
         def _test_for_size(size):
             atoms = FaceCenteredCubic('Cu', size=size)
-            calculator = EAM('CuAg.eam.alloy')
+            calculator = EAM(f'{os.path.dirname(__file__)}/CuAg.eam.alloy')
             self._test_hessian(atoms, calculator)
         _test_for_size(size=[1, 1, 1])
         _test_for_size(size=[2, 2, 2])
@@ -143,7 +144,7 @@ def test_hessian_monoatomic_with_duplicate_pairs(self):
         Hessian from ASE
         """
         atoms = FaceCenteredCubic('Cu', size=[2, 2, 2])
-        calculator = EAM('CuAg.eam.alloy')
+        calculator = EAM(f'{os.path.dirname(__file__)}/CuAg.eam.alloy')
         self._test_hessian(atoms, calculator)
 
     def test_hessian_crystalline_alloy(self):
@@ -152,7 +153,7 @@ def test_hessian_crystalline_alloy(self):
         Reference: finite difference approximation of 
         Hessian from ASE
         """
-        calculator = EAM('ZrCu.onecolumn.eam.alloy')
+        calculator = EAM(f'{os.path.dirname(__file__)}/ZrCu.onecolumn.eam.alloy')
         lattice_size = [4, 4, 4]
         # The lattice parameters are not correct, but that should be irrelevant
         # CuZr3
@@ -171,9 +172,9 @@ def test_hessian_amorphous_alloy(self):
         Reference: finite difference approximation of 
         Hessian from ASE
         """
-        atoms = io.read('CuZr_glass_460_atoms.gz')
+        atoms = io.read(f'{os.path.dirname(__file__)}/CuZr_glass_460_atoms.gz')
         atoms.pbc = [True, True, True]
-        calculator = EAM('ZrCu.onecolumn.eam.alloy')
+        calculator = EAM(f'{os.path.dirname(__file__)}/ZrCu.onecolumn.eam.alloy')
         self._test_hessian(atoms, calculator)
 
     def test_dynamical_matrix(self):
@@ -184,9 +185,9 @@ def test_dynamical_matrix(self):
         first form the complete Hessian and then divide by masses.
         The former method is implemented.
         """
-        atoms = io.read('CuZr_glass_460_atoms.gz')
+        atoms = io.read(f'{os.path.dirname(__file__)}/CuZr_glass_460_atoms.gz')
         atoms.pbc = [True, True, True]
-        calculator = EAM('ZrCu.onecolumn.eam.alloy')
+        calculator = EAM(f'{os.path.dirname(__file__)}/ZrCu.onecolumn.eam.alloy')
         dynamical_matrix = calculator.calculate_hessian_matrix(
             atoms, divide_by_masses=True
         )

tests/test_hessian_precon.py

@@ -1,3 +1,4 @@
+import os.path
 import unittest
 
 import numpy as np
@@ -23,7 +24,7 @@ def setUp(self):
         del self.atoms[0]
         np.random.seed(0)
         self.atoms.rattle(1e-2)
-        self.eam = EAM('Mishin-Ni-Al-2009.eam.alloy')
+        self.eam = EAM(f'{os.path.dirname(__file__)}/Mishin-Ni-Al-2009.eam.alloy')
         self.tol = 1e-6
 
     def test_newton_opt(self):

tests/test_mcfm.py

@@ -19,6 +19,9 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
+
+import os.path
+
 import numpy as np
 
 import ase.io
@@ -233,7 +236,7 @@ def create_mcfm_potential(atoms,
 class TestMCFM(matscipytest.MatSciPyTestCase):
 
     def prepare_data(self):
-        self.atoms = load_atoms("carbon_chain.xyz")
+        self.atoms = load_atoms(f"{os.path.dirname(__file__)}/carbon_chain.xyz")
         self.morse1 = MorsePotentialPerAtom(r0=2, epsilon=2, rho0=6)
         self.morse2 = MorsePotentialPerAtom(r0=2, epsilon=4, rho0=6)
         self.mcfm_pot = create_mcfm_potential(self.atoms,