How to use the matscipy.calculators.eam.io.read_eam function in matscipy

was created with an independent implementation. This is not
        a very strong test, but should capture some regressions.

        References
        ----------
        [1] G. Bonny, R.C. Pasianot, N. Castin, and L. Malerba (2009), 
            "Ternary Fe-Cu-Ni many-body potential to model reactor 
            pressure vessel steels: First validation by simulated 
            thermal annealing", Philosophical Magazine, 89(34-36), 
            3531-3546. DOI: 10.1080/14786430903299824.
        [2] https://www.ctcms.nist.gov/potentials/Download/2009--Bonny-G-Pasianot-R-C-Castin-N-Malerba-L--Fe-Cu-Ni/1/FeCuNi.eam.alloy
        """
        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)
        (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)
        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)
        print(diff_F, diff_f, diff_rep)
        self.assertTrue(diff_F < self.tol)
        self.assertTrue(diff_f < self.tol)
        self.assertTrue(diff_rep < self.tol)

References
        ----------
        [1] G.P. Purja Pun, and Y. Mishin (2009), "Development of an
            interatomic potential for the Ni-Al system", Philosophical
            Magazine, 89(34-36), 3245-3267. DOI: 10.1080/14786430903258184.
        [2] https://www.ctcms.nist.gov/potentials/Download/2009--Purja-Pun-G-P-Mishin-Y--Ni-Al/2/Mishin-Ni-Al-2009.eam.alloy
        """
        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)
        (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)
        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)
        print(diff_F, diff_f, diff_rep)
        self.assertTrue(diff_F < self.tol)
        self.assertTrue(diff_f < self.tol)
        self.assertTrue(diff_rep < self.tol)

the NIST database [2]_. The generated The generated A-atom
        potential is compared to a reference A-atom potential, which
        was created with an independent implementation. This is not
        a very strong test, but should capture some regressions.

        References
        ----------
        [1] G.P. Purja Pun, and Y. Mishin (2009), "Development of an
            interatomic potential for the Ni-Al system", Philosophical
            Magazine, 89(34-36), 3245-3267. DOI: 10.1080/14786430903258184.
        [2] https://www.ctcms.nist.gov/potentials/Download/2009--Purja-Pun-G-P-Mishin-Y--Ni-Al/2/Mishin-Ni-Al-2009.eam.alloy
        """
        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)
        (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)
        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)
        print(diff_F, diff_f, diff_rep)
        self.assertTrue(diff_F < self.tol)
        self.assertTrue(diff_f < self.tol)
        self.assertTrue(diff_rep < self.tol)

----------
        [1] G. Bonny, R.C. Pasianot, N. Castin, and L. Malerba (2009), 
            "Ternary Fe-Cu-Ni many-body potential to model reactor 
            pressure vessel steels: First validation by simulated 
            thermal annealing", Philosophical Magazine, 89(34-36), 
            3531-3546. DOI: 10.1080/14786430903299824.
        [2] https://www.ctcms.nist.gov/potentials/Download/2009--Bonny-G-Pasianot-R-C-Castin-N-Malerba-L--Fe-Cu-Ni/1/FeCuNi.eam.alloy
        """
        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)
        (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)
        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)
        print(diff_F, diff_f, diff_rep)
        self.assertTrue(diff_F < self.tol)
        self.assertTrue(diff_f < self.tol)
        self.assertTrue(diff_rep < self.tol)

def test_eam_read_write(self):
        source,parameters,F,f,rep = read_eam("Au_u3.eam")
        write_eam(source,parameters,F,f,rep,"Au_u3_copy.eam")
        source1,parameters1,F1,f1,rep1 = read_eam("Au_u3_copy.eam")
        os.remove("Au_u3_copy.eam")
        for i,p in enumerate(parameters):
            try:
                diff = p - parameters1[i]
            except:
                diff = None
            if diff is None:
                self.assertTrue(p == parameters1[i])
            else:
                self.assertTrue(diff < self.tol)
        self.assertTrue((F == F1).all())
        self.assertTrue((f == f1).all())
        self.assertTrue((rep == rep1).all())

def test_eam_read_write(self):
        source,parameters,F,f,rep = read_eam("Au_u3.eam")
        write_eam(source,parameters,F,f,rep,"Au_u3_copy.eam")
        source1,parameters1,F1,f1,rep1 = read_eam("Au_u3_copy.eam")
        os.remove("Au_u3_copy.eam")
        for i,p in enumerate(parameters):
            try:
                diff = p - parameters1[i]
            except:
                diff = None
            if diff is None:
                self.assertTrue(p == parameters1[i])
            else:
                self.assertTrue(diff < self.tol)
        self.assertTrue((F == F1).all())
        self.assertTrue((f == f1).all())
        self.assertTrue((rep == rep1).all())

def __init__(self, fn=None, atomic_numbers=None, F=None, f=None, rep=None,
                 cutoff=None, kind='eam/alloy'):
        Calculator.__init__(self)
        if fn is not None:
            source, parameters, F, f, rep = read_eam(fn, kind=kind)
            self._db_atomic_numbers = parameters.atomic_numbers
            self._db_cutoff = parameters.cutoff
            dr = parameters.distance_grid_spacing
            dF = parameters.density_grid_spacing

            # Create spline interpolation
            self.F = _make_splines(dF, F)
            self.f = _make_splines(dr, f)
            self.rep = _make_splines(dr, rep)
        else:
            self._db_atomic_numbers = atomic_numbers
            self.F = F
            self.f = f
            self.rep = rep
            self._db_cutoff = cutoff