Allow ions instead of atoms in CIF files

[DorianDepriester]

Is your feature request related to a problem? Please describe.
In some CIF files, atoms are given by their ionic names (e.g. Fe2+ instead of Fe). This is (sometimes) the case for generated files from The Materials Project. This actually results in failure of get_element_id_from_string().

Describe the solution you'd like
A simple regexp to automatically trim the atom names.

Describe alternatives you've considered
The user can edit the CIF file to remove the exponents.

[CSSFrancis]

@DorianDepriester I think ions result in slightly different atomic scattering factors.

I got fairly far on adding them but just never did. If this is something you are interested in I can prioritize this!

[DorianDepriester]

From my point of view, it would indeed be an interesting feature 😉

[CSSFrancis]

From my point of view, it would indeed be an interesting feature 😉

I'll see if I can make the PR later this week and we can think about making a new release!

[CSSFrancis]

@hakonanes @viljarjf

Any idea if there is anything to this other than adding to ionic scattering cross sections?

I think this is a pretty full list

import numpy as np

IONS = [
    "h1-",
    "li1+",
    "be2+",
    "o1-",
    "o2-",
    "f1-",
    "na1+",
    "mg2+",
    "al3+",
    "si4+",
    "cl1-",
    "k1+",
    "ca2+",
    "sc3+",
    "ti2+",
    "ti3+",
    "t14+",
    "v2+",
    "v3+",
    "v5+",
    "cr2+",
    "cr3+",
    "cr4+",
    "mn2+",
    "mn3+",
    "mn4+",
    "fe2+",
    "fe3+",
    "co2+",
    "co3+",
    "ni2+",
    "ni3+",
    "cu1+",
    "cu2+",
    "zn2+",
    "ga3+",
    "ge4+",
    "br1-",
    "br1+",
    "sr2+",
    "y3+",
    "zr4+",
    "nb3+",
    "nb5+",
    "mo3+",
    "mo5+",
    "mo6+",
    "ru3+",
    "ru4+",
    "rh3+",
    "rh4+",
    "pd2+",
    "pd4+",
    "ag1+",
    "ag2+",
    "cd2+",
    "in3+",
    "sn2+",
    "sn4+",
    "sb3+",
    "sb5+",
    "i1-",
    "cs1+",
    "ba2+",
    "la3+",
    "ce3+",
    "ce4+",
    "pr3+",
    "pr4+",
    "nd3+",
    "pm3+",
    "sm3+",
    "eu2+",
    "eu3+",
    "gd3+",
    "tb3+",
    "dy3+",
    "ho3+",
    "er3+",
    "tm3+",
    "yb2+",
    "yb3+",
    "lu3+",
    "hf4+",
    "ta5+",
    "w6+",
    "os4+",
    "ir3+",
    "ir4+",
    "pt2+",
    "pt4+",
    "au1+",
    "au3+",
    "hg1+",
    "hg2+",
    "tl1+",
    "tl3+",
    "pb2+",
    "pb4+",
    "bi3+",
    "bi5+",
    "ra2+",
    "ac3+",
    "u3+",
    "u4+",
    "u6+",
]

ATOMIC_SCATTERING_PARAMETERS_PENG_IONS = np.array(
    [
        [
            1,
            0.140e0,
            0.649e0,
            0.137e1,
            0.337e0,
            0.787e0,
            0.984e0,
            0.867e1,
            0.389e2,
            0.111e3,
            0.166e3,
            0.046,
        ],
        [
            3,
            0.460e-2,
            0.165e-1,
            0.435e-1,
            0.649e-1,
            0.270e-1,
            0.358e-1,
            0.239e0,
            0.879e0,
            0.264e1,
            0.709e1,
            0.031,
        ],
        [
            4,
            0.340e-2,
            0.103e-1,
            0.233e-1,
            0.325e-1,
            0.120e-1,
            0.267e-1,
            0.162e0,
            0.531e0,
            0.148e1,
            0.388e1,
            0.022,
        ],
        [
            8,
            0.205e0,
            0.628e0,
            0.117e1,
            0.103e1,
            0.290e0,
            0.397e0,
            0.264e1,
            0.880e1,
            0.271e2,
            0.918e2,
            0.012,
        ],
        [
            8,
            0.421e-1,
            0.210e0,
            0.852e0,
            0.182e1,
            0.117e1,
            0.609e-1,
            0.559e0,
            0.296e1,
            0.115e2,
            0.377e2,
            0.037,
        ],
        [
            9,
            0.134e0,
            0.391e0,
            0.814e0,
            0.928e0,
            0.347e0,
            0.228e0,
            0.147e1,
            0.468e1,
            0.132e2,
            0.360e2,
            0.013,
        ],
        [
            11,
            0.256e-1,
            0.919e-1,
            0.297e0,
            0.514e0,
            0.199e0,
            0.397e-1,
            0.287e0,
            0.118e1,
            0.375e1,
            0.108e2,
            0.018,
        ],
        [
            12,
            0.210e-1,
            0.672e-1,
            0.198e0,
            0.368e0,
            0.174e0,
            0.331e-1,
            0.222e0,
            0.838e0,
            0.248e1,
            0.675e1,
            0.019,
        ],
        [
            13,
            0.192e-1,
            0.579e-1,
            0.163e0,
            0.284e0,
            0.114e0,
            0.306e-1,
            0.198e0,
            0.713e0,
            0.204e1,
            0.525e1,
            0.029,
        ],
        [
            14,
            0.192e0,
            0.289e0,
            0.100e0,
            -0.728e-1,
            0.120e-2,
            0.359e0,
            0.196e1,
            0.934e1,
            0.111e2,
            0.134e2,
            0.055,
        ],
        [
            17,
            0.265e0,
            0.596e0,
            0.160e1,
            0.269e1,
            0.123e1,
            0.252e0,
            0.156e1,
            0.621e1,
            0.178e2,
            0.478e2,
            0.010,
        ],
        [
            19,
            0.199e0,
            0.396e0,
            0.928e0,
            0.145e1,
            0.450e0,
            0.192e0,
            0.110e1,
            0.391e1,
            0.975e1,
            0.234e2,
            0.013,
        ],
        [
            20,
            0.164e0,
            0.327e0,
            0.743e0,
            0.116e1,
            0.307e0,
            0.157e0,
            0.894e0,
            0.315e1,
            0.767e1,
            0.177e2,
            0.013,
        ],
        [
            21,
            0.163e0,
            0.307e0,
            0.716e0,
            0.880e0,
            0.139e0,
            0.157e0,
            0.899e0,
            0.306e1,
            0.705e1,
            0.161e2,
            0.013,
        ],
        [
            22,
            0.399e0,
            0.104e1,
            0.121e1,
            -0.797e-1,
            0.352e0,
            0.376e0,
            0.274e1,
            0.810e1,
            0.142e2,
            0.232e2,
            0.009,
        ],
        [
            22,
            0.364e0,
            0.919e0,
            0.135e1,
            -0.933e0,
            0.589e0,
            0.364e0,
            0.267e1,
            0.818e1,
            0.118e2,
            0.149e2,
            0.013,
        ],
        [
            22,
            0.116e0,
            0.256e0,
            0.565e0,
            0.772e0,
            0.132e0,
            0.108e0,
            0.655e0,
            0.238e1,
            0.551e1,
            0.123e2,
            0.015,
        ],
        [
            23,
            0.317e0,
            0.939e0,
            0.149e1,
            -0.131e1,
            0.147e1,
            0.269e0,
            0.209e1,
            0.722e1,
            0.152e2,
            0.176e2,
            0.009,
        ],
        [
            23,
            0.341e0,
            0.805e0,
            0.942e0,
            0.783e-1,
            0.156e0,
            0.321e0,
            0.223e1,
            0.599e1,
            0.134e2,
            0.169e2,
            0.020,
        ],
        [
            23,
            0.367e-1,
            0.124e0,
            0.244e0,
            0.723e0,
            0.435e0,
            0.330e-1,
            0.222e0,
            0.824e0,
            0.280e1,
            0.670e1,
            0.017,
        ],
        [
            24,
            0.237e0,
            0.634e0,
            0.123e1,
            0.713e0,
            0.859e-1,
            0.177e0,
            0.135e1,
            0.430e1,
            0.122e2,
            0.390e2,
            0.011,
        ],
        [
            24,
            0.393e0,
            0.105e1,
            0.162e1,
            -0.115e1,
            0.407e0,
            0.359e0,
            0.257e1,
            0.868e1,
            0.110e2,
            0.158e2,
            0.011,
        ],
        [
            24,
            0.132e0,
            0.292e0,
            0.703e0,
            0.692e0,
            0.959e-1,
            0.109e0,
            0.695e0,
            0.239e1,
            0.565e1,
            0.147e2,
            0.013,
        ],
        [
            25,
            0.576e-1,
            0.210e0,
            0.604e0,
            0.132e1,
            0.659e0,
            0.398e-1,
            0.284e0,
            0.129e1,
            0.423e1,
            0.145e2,
            0.034,
        ],
        [
            25,
            0.116e0,
            0.523e0,
            0.881e0,
            0.589e0,
            0.214e0,
            0.117e-1,
            0.876e0,
            0.306e1,
            0.644e1,
            0.143e2,
            0.009,
        ],
        [
            25,
            0.381e0,
            0.183e1,
            -0.133e1,
            0.995e0,
            0.618e-1,
            0.354e0,
            0.272e1,
            0.347e1,
            0.547e1,
            0.161e2,
            0.017,
        ],
        [
            26,
            0.307e0,
            0.838e0,
            0.111e1,
            0.280e0,
            0.277e0,
            0.230e0,
            0.162e1,
            0.487e1,
            0.107e2,
            0.192e2,
            0.016,
        ],
        [
            26,
            0.198e0,
            0.387e0,
            0.889e0,
            0.709e0,
            0.117e0,
            0.154e0,
            0.893e0,
            0.262e1,
            0.665e1,
            0.180e2,
            0.012,
        ],
        [
            27,
            0.213e0,
            0.488e0,
            0.998e0,
            0.828e0,
            0.230e0,
            0.148e0,
            0.939e0,
            0.278e1,
            0.731e1,
            0.207e2,
            0.016,
        ],
        [
            27,
            0.331e0,
            0.487e0,
            0.729e0,
            0.608e0,
            0.131e0,
            0.267e0,
            0.141e1,
            0.289e1,
            0.645e1,
            0.158e2,
            0.010,
        ],
        [
            28,
            0.338e0,
            0.982e0,
            0.132 + 1,
            -0.356e1,
            0.362e1,
            0.237e0,
            0.167e1,
            0.573e1,
            0.114e2,
            0.121e2,
            0.018,
        ],
        [
            28,
            0.347e0,
            0.877e0,
            0.790e0,
            0.538e-1,
            0.192e0,
            0.260e0,
            0.171e1,
            0.475e1,
            0.751e1,
            0.130e2,
            0.011,
        ],
        [
            29,
            0.312e0,
            0.812e0,
            0.111e1,
            0.794e0,
            0.257e0,
            0.201e0,
            0.131e1,
            0.380e1,
            0.105e2,
            0.282e2,
            0.003,
        ],
        [
            29,
            0.224e0,
            0.544e0,
            0.970e0,
            0.727e0,
            0.182e0,
            0.145e0,
            0.933e0,
            0.269e1,
            0.711e1,
            0.194e2,
            0.013,
        ],
        [
            30,
            0.252e0,
            0.600e0,
            0.917e0,
            0.663e0,
            0.161e0,
            0.161e0,
            0.101e1,
            0.276e1,
            0.708e1,
            0.190e2,
            0.013,
        ],
        [
            31,
            0.391e0,
            0.947e0,
            0.690e0,
            0.709e-1,
            0.653e-1,
            0.264e0,
            0.165e1,
            0.482e1,
            0.107e2,
            0.152e2,
            0.014,
        ],
        [
            32,
            0.346e0,
            0.830e0,
            0.599e0,
            0.949e-1,
            -0.217e-1,
            0.232e0,
            0.145e1,
            0.408e1,
            0.132e2,
            0.295e2,
            0.016,
        ],
        [
            35,
            0.125e0,
            0.563e0,
            0.143e1,
            0.352e1,
            0.322e1,
            0.530e-1,
            0.469e0,
            0.215e1,
            0.111e2,
            0.389e2,
            0.057,
        ],
        [
            37,
            0.368e0,
            0.884e0,
            0.114e1,
            0.226e1,
            0.881e0,
            0.187e0,
            0.112e1,
            0.398e1,
            0.109e2,
            0.266e2,
            0.012,
        ],
        [
            38,
            0.346e0,
            0.804e0,
            0.988e0,
            0.189e1,
            0.609e0,
            0.176e0,
            0.104e1,
            0.359e1,
            0.932e1,
            0.214e2,
            0.012,
        ],
        [
            39,
            0.465e0,
            0.923e0,
            0.241e1,
            -0.231e1,
            0.248e1,
            0.240e0,
            0.143e1,
            0.645e1,
            0.997e1,
            0.122e2,
            0.018,
        ],
        [
            40,
            0.234e0,
            0.642e0,
            0.747e0,
            0.147e1,
            0.377e0,
            0.113e0,
            0.736e0,
            0.254e1,
            0.672e1,
            0.147e2,
            0.014,
        ],
        [
            41,
            0.377e0,
            0.749e0,
            0.129e1,
            0.161e1,
            0.481e0,
            0.184e0,
            0.102e1,
            0.380e1,
            0.944e1,
            0.257e2,
            0.008,
        ],
        [
            41,
            0.828e-1,
            0.271e0,
            0.654e0,
            0.124e1,
            0.829e0,
            0.369e-1,
            0.261e0,
            0.957e0,
            0.394e1,
            0.944e1,
            0.017,
        ],
        [
            42,
            0.401e0,
            0.756e0,
            0.138e1,
            0.158e1,
            0.497e0,
            0.191e0,
            0.106e1,
            0.384e1,
            0.938e1,
            0.246e2,
            0.007,
        ],
        [
            42,
            0.479e0,
            0.846e0,
            0.156e2,
            -0.152e2,
            0.160e1,
            0.241e0,
            0.146e1,
            0.679e1,
            0.713e1,
            0.104e2,
            0.011,
        ],
        [
            42,
            0.203e0,
            0.567e0,
            0.646e0,
            0.116e1,
            0.171e0,
            0.971e-1,
            0.647e0,
            0.228e1,
            0.561e1,
            0.124e2,
            0.013,
        ],
        [
            44,
            0.428e0,
            0.773e0,
            0.155e1,
            0.146e1,
            0.486e0,
            0.191e0,
            0.109e1,
            0.382e1,
            0.908e1,
            0.217e2,
            0.006,
        ],
        [
            44,
            0.282e0,
            0.653e0,
            0.114e1,
            0.153e1,
            0.418e0,
            0.125e0,
            0.753e0,
            0.285e1,
            0.701e1,
            0.175e2,
            0.006,
        ],
        [
            45,
            0.352e0,
            0.723e0,
            0.150e1,
            0.163e1,
            0.499e0,
            0.151e0,
            0.878e0,
            0.328e1,
            0.816e1,
            0.207e2,
            0.006,
        ],
        [
            45,
            0.397e0,
            0.725e0,
            0.151e1,
            0.119e1,
            0.251e0,
            0.177e0,
            0.101e1,
            0.362e1,
            0.856e1,
            0.189e2,
            0.008,
        ],
        [
            46,
            0.935e0,
            0.311e1,
            0.246e2,
            -0.436e2,
            0.211e2,
            0.393e0,
            0.406e1,
            0.431e2,
            0.540e2,
            0.698e2,
            0.263,
        ],
        [
            46,
            0.348e0,
            0.640e0,
            0.122e1,
            0.145e1,
            0.427e0,
            0.151e0,
            0.832e0,
            0.285e1,
            0.659e1,
            0.156e2,
            0.012,
        ],
        [
            47,
            0.503e0,
            0.940e0,
            0.217e1,
            0.199e1,
            0.726e0,
            0.199e0,
            0.119e1,
            0.405e1,
            0.113e2,
            0.324e2,
            0.007,
        ],
        [
            47,
            0.431e0,
            0.756e0,
            0.172e1,
            0.178e1,
            0.526e0,
            0.175e0,
            0.979e0,
            0.330e1,
            0.824e1,
            0.214e2,
            0.014,
        ],
        [
            48,
            0.425e0,
            0.745e0,
            0.173e1,
            0.174e1,
            0.487e0,
            0.168e0,
            0.944e0,
            0.314e1,
            0.784e1,
            0.204e2,
            0.014,
        ],
        [
            49,
            0.417e0,
            0.755e0,
            0.159e1,
            0.136e1,
            0.451e0,
            0.164e0,
            0.960e0,
            0.308e1,
            0.703e1,
            0.161e2,
            0.007,
        ],
        [
            50,
            0.797e0,
            0.213e1,
            0.215e1,
            -0.164e1,
            0.272e1,
            0.317e0,
            0.251e1,
            0.904e1,
            0.242e2,
            0.264e2,
            0.006,
        ],
        [
            50,
            0.261e0,
            0.642e0,
            0.153e1,
            0.136e1,
            0.177e0,
            0.957e-1,
            0.625e0,
            0.251e1,
            0.631e1,
            0.159e2,
            0.009,
        ],
        [
            51,
            0.552e0,
            0.114e1,
            0.187e1,
            0.136e1,
            0.414e0,
            0.212e4,
            0.142e1,
            0.421e1,
            0.125e2,
            0.290e2,
            0.009,
        ],
        [
            51,
            0.377e0,
            0.588e0,
            0.122e1,
            0.118e1,
            0.244e0,
            0.151e0,
            0.812e0,
            0.240e1,
            0.527e1,
            0.119e2,
            0.009,
        ],
        [
            53,
            0.901e0,
            0.280e1,
            0.561e1,
            -0.869e1,
            0.126e2,
            0.312e0,
            0.259e1,
            0.141e2,
            0.344e2,
            0.395e2,
            0.060,
        ],
        [
            55,
            0.587e0,
            0.140e1,
            0.187e1,
            0.348e1,
            0.167e1,
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        [
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        [
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        ],
    ]
)

IONS_DICT = dict()
for ion, row in zip(IONS, ATOMIC_SCATTERING_PARAMETERS_PENG_IONS):
    c = -1 if ion[-1] == "-" else 1
    charge = int(ion[-2]) * c
    IONS_DICT[ion] = dict(z=row[0], a=list(row[1:6]), b=list(row[6:11]), charge=charge)

[hakonanes]

@CSSFrancis, I think this should be good. Can you give a complete reference to the values?

[CSSFrancis]

@hakonanes I'll try to make a PR with a reference later this week!