From b730ab028e4d96b15a991401d91b84acd9a60e00 Mon Sep 17 00:00:00 2001 From: Niklas Siemer <70580458+niklassiemer@users.noreply.github.com> Date: Mon, 16 Oct 2023 16:45:29 +0200 Subject: [PATCH 1/4] Always use periodic_table.csv file embedded in the repo --- .../atomistics/structure/periodic_table.py | 33 ++---- setup.py | 2 +- tests/static/atomistics/periodic_table.csv | 109 ------------------ 3 files changed, 11 insertions(+), 133 deletions(-) delete mode 100644 tests/static/atomistics/periodic_table.csv diff --git a/pyiron_atomistics/atomistics/structure/periodic_table.py b/pyiron_atomistics/atomistics/structure/periodic_table.py index 05c908170..5c57bda71 100644 --- a/pyiron_atomistics/atomistics/structure/periodic_table.py +++ b/pyiron_atomistics/atomistics/structure/periodic_table.py @@ -5,10 +5,10 @@ from __future__ import print_function, unicode_literals import numpy as np import os -from pyiron_base import state import mendeleev import pandas from functools import lru_cache +import pyiron_atomistics __author__ = "Joerg Neugebauer, Sudarsan Surendralal, Martin Boeckmann" __copyright__ = ( @@ -204,7 +204,7 @@ def from_hdf(self, hdf): self.sub["tags"] = tag_dic -class PeriodicTable(object): +class PeriodicTable: """ An Object which stores an elementary table which can be modified for the current session """ @@ -396,27 +396,14 @@ def _get_periodic_table_df(file_name): """ if not file_name: - for resource_path in state.settings.resource_paths: - if os.path.exists(os.path.join(resource_path, "atomistics")): - resource_path = os.path.join(resource_path, "atomistics") - for path, folder_lst, file_lst in os.walk(resource_path): - for periodic_table_file_name in {"periodic_table.csv"}: - if ( - periodic_table_file_name in file_lst - and periodic_table_file_name.endswith(".csv") - ): - return pandas.read_csv( - os.path.join(path, periodic_table_file_name), - index_col=0, - ) - elif ( - periodic_table_file_name in file_lst - and periodic_table_file_name.endswith(".h5") - ): - return pandas.read_hdf( - os.path.join(path, periodic_table_file_name), mode="r" - ) - raise ValueError("Was not able to locate a periodic table. ") + return pandas.read_csv( + os.path.join( + os.path.dirname(pyiron_atomistics.__file__), + "_data", + "periodic_table.csv", + ), + index_col=0, + ) else: if file_name.endswith(".h5"): return pandas.read_hdf(file_name, mode="r") diff --git a/setup.py b/setup.py index 55f7ca2d7..9143af0e4 100644 --- a/setup.py +++ b/setup.py @@ -61,5 +61,5 @@ 'structuretoolkit==0.0.11' ], cmdclass=versioneer.get_cmdclass(), - + package_data={'': ['_data/*.csv']}, ) diff --git a/tests/static/atomistics/periodic_table.csv b/tests/static/atomistics/periodic_table.csv deleted file mode 100644 index ac382cbc0..000000000 --- a/tests/static/atomistics/periodic_table.csv +++ /dev/null @@ -1,109 +0,0 @@ -,AtomicNumber,AtomicRadius,AtomicMass,Color,CovalentRadius,CrystalStructure,Density,DiscoveryYear,ElectronAffinity,Electronegativity,Group,Name,Period,Phase,StandardName,VanDerWaalsRadius,MeltingPoint,Abbreviation -Ac,89,0.0,227.0,Silver,2.1500000953674316,FaceCenteredCubi,10070.0,1899,0.0,1.100000023841858,0,actinium,7,Solid,Actinium,0.0,1323,Ac -Ag,47,165.0,107.86820220947266,Silver,1.4500000476837158,FaceCenteredCubi,10490.0,62536,125.5999984741211,1.9299999475479126,11,silver,5,Solid,Silver,172.0,1234.93,Ag -Al,13,118.0,26.981538772583008,Silver,1.2100000381469727,FaceCenteredCubi,2700.0,1825,42.5,1.6100000143051147,13,aluminum,3,Solid,Aluminum,0.0,933.473,Al -Am,95,0.0,243.0,Silver,1.7999999523162842,SimpleHexagonal,13670.0,1944,0.0,1.2999999523162842,0,americium,7,Solid,Americium,0.0,1449,Am -Ar,18,71.0,39.948001861572266,Colorless,1.059999942779541,FaceCenteredCubi,1.784000039100647,1894,0.0,0.0,18,argon,3,Gas,Argon,188.0,83.81,Ar -As,33,114.0,74.92160034179688,Silver,1.190000057220459,SimpleTrigonal,5727.0,1250,78.0,2.180000066757202,15,arsenic,4,Solid,Arsenic,185.0,1090,As -At,85,127.0,210.0,Silver,1.5,,0.0,1940,270.1000061035156,2.200000047683716,17,astatine,6,Solid,Astatine,0.0,575,At -Au,79,174.0,196.96656799316406,Gold,1.3600000143051147,FaceCenteredCubi,19300.0,63036,222.8000030517578,2.5399999618530273,11,gold,6,Solid,Gold,166.0,1337.33,Au -B,5,87.0,10.810999870300293,Black,0.8399999737739563,SimpleTrigonal,2460.0,1808,26.700000762939453,2.0399999618530273,13,boron,2,Solid,Boron,0.0,2350,B -Ba,56,253.0,137.32699584960938,Silver,2.1500000953674316,BodyCenteredCubi,3510.0,1808,13.949999809265137,0.8899999856948853,2,barium,6,Solid,Barium,0.0,1000,Ba -Be,4,112.0,9.012182235717773,SlateGray,0.9599999785423279,SimpleHexagonal,1848.0,1797,0.0,1.5700000524520874,2,beryllium,2,Solid,Beryllium,0.0,1560,Be -Bh,107,0.0,272.0,,0.0,,0.0,1981,0.0,0.0,7,bohrium,7,,Bohrium,0.0,,Bh -Bi,83,143.0,208.9803924560547,Gray,1.4800000190734863,BaseCenteredMono,9780.0,1400,91.19999694824219,2.0199999809265137,15,bismuth,6,Solid,Bismuth,0.0,544.556,Bi -Bk,97,0.0,247.0,,0.0,SimpleHexagonal,14780.0,1949,0.0,1.2999999523162842,0,berkelium,7,Solid,Berkelium,0.0,1259,Bk -Br,35,94.0,79.90399932861328,Red,1.2000000476837158,BaseCenteredOrth,3120.0,1826,324.6000061035156,2.9600000381469727,17,bromine,4,Liquid,Bromine,185.0,265.95,Br -C,6,67.0,12.010700225830078,Black,0.7599999904632568,SimpleHexagonal,2260.0,0,153.89999389648438,2.549999952316284,14,carbon,2,Solid,Carbon,170.0,4713,C -Ca,20,194.0,40.077999114990234,Silver,1.7599999904632568,FaceCenteredCubi,1550.0,1808,2.369999885559082,1.0,2,calcium,4,Solid,Calcium,0.0,1115,Ca -Cd,48,161.0,112.41100311279297,Silver,1.440000057220459,SimpleHexagonal,8650.0,1817,0.0,1.690000057220459,12,cadmium,5,Solid,Cadmium,158.0,594.219,Cd -Ce,58,0.0,140.11599731445312,Silver,2.0399999618530273,SimpleHexagonal,6689.0,1803,50.0,1.1200000047683716,0,cerium,6,Solid,Cerium,0.0,1072,Ce -Cf,98,0.0,251.0,,0.0,SimpleHexagonal,15100.0,1950,0.0,1.2999999523162842,0,californium,7,Solid,Californium,0.0,1173,Cf -Cl,17,79.0,35.452999114990234,Yellow,1.0199999809265137,BaseCenteredOrth,3.2139999866485596,1774,349.0,3.1600000858306885,17,chlorine,3,Gas,Chlorine,175.0,171.65,Cl -Cm,96,0.0,247.0,Silver,1.690000057220459,SimpleHexagonal,13510.0,1944,0.0,1.2999999523162842,0,curium,7,Solid,Curium,0.0,1618,Cm -Co,27,152.0,58.93319320678711,Gray,1.2599999904632568,SimpleHexagonal,8900.0,1735,63.70000076293945,1.8799999952316284,9,cobalt,4,Solid,Cobalt,0.0,1768,Co -Cr,24,166.0,51.99610137939453,Silver,1.3899999856948853,BodyCenteredCubi,7140.0,1797,64.30000305175781,1.659999966621399,6,chromium,4,Solid,Chromium,0.0,2180,Cr -Cs,55,298.0,132.90545654296875,Silver,2.440000057220459,BodyCenteredCubi,1879.0,1860,45.5,0.7900000214576721,1,cesium,6,Solid,Cesium,0.0,301.65,Cs -Cu,29,145.0,63.54600143432617,Copper,1.3200000524520874,FaceCenteredCubi,8920.0,57536,118.4000015258789,1.899999976158142,11,copper,4,Solid,Copper,140.0,1357.77,Cu -Db,105,0.0,268.0,,0.0,,0.0,1967,0.0,0.0,5,dubnium,7,,Dubnium,0.0,,Db -Dy,66,228.0,162.5,Silver,1.9199999570846558,SimpleHexagonal,8551.0,1886,50.0,1.2200000286102295,0,dysprosium,6,Solid,Dysprosium,0.0,1685,Dy -Er,68,226.0,167.25900268554688,Silver,1.8899999856948853,SimpleHexagonal,9066.0,1842,50.0,1.2400000095367432,0,erbium,6,Solid,Erbium,0.0,1802,Er -Es,99,0.0,252.0,,0.0,,0.0,1952,0.0,1.2999999523162842,0,einsteinium,7,Solid,Einsteinium,0.0,1133,Es -Eu,63,231.0,151.96400451660156,Silver,1.9800000190734863,BodyCenteredCubi,5244.0,1901,50.0,0.0,0,europium,6,Solid,Europium,0.0,1095,Eu -F,9,42.0,18.998403549194336,Colorless,0.5699999928474426,BaseCenteredMono,1.6959999799728394,1886,328.0,3.9800000190734863,17,fluorine,2,Gas,Fluorine,147.0,53.48,F -Fe,26,156.0,55.845001220703125,Gray,1.3200000524520874,BodyCenteredCubi,7874.0,63536,15.699999809265137,1.8300000429153442,8,iron,4,Solid,Iron,0.0,1811,Fe -Fm,100,0.0,257.0,,0.0,,0.0,1952,0.0,1.2999999523162842,0,fermium,7,,Fermium,0.0,1800,Fm -Fr,87,0.0,223.0,Silver,2.5999999046325684,,0.0,1939,0.0,0.699999988079071,1,francium,7,Solid,Francium,0.0,294,Fr -Ga,31,136.0,69.7229995727539,Silver,1.2200000286102295,BaseCenteredOrth,5904.0,1875,28.899999618530273,1.809999942779541,13,gallium,4,Solid,Gallium,187.0,302.915,Ga -Gd,64,233.0,157.25,Silver,1.9600000381469727,SimpleHexagonal,7901.0,1880,50.0,1.2000000476837158,0,gadolinium,6,Solid,Gadolinium,0.0,1586,Gd -Ge,32,125.0,72.63999938964844,Gray,1.2000000476837158,FaceCenteredCubi,5323.0,1886,119.0,2.009999990463257,14,germanium,4,Solid,Germanium,0.0,1211.4,Ge -H,1,53.0,1.0079400539398193,Colorless,0.3100000023841858,SimpleHexagonal,0.08990000188350677,1766,72.80000305175781,2.200000047683716,1,hydrogen,1,Gas,Hydrogen,120.0,13.99,H -He,2,31.0,4.0026021003723145,Colorless,0.2800000011920929,FaceCenteredCubi,0.1784999966621399,1895,0.0,0.0,18,helium,1,Gas,Helium,140.0,xxxx,He -Hf,72,208.0,178.49000549316406,Gray,1.75,SimpleHexagonal,13310.0,1923,0.0,1.2999999523162842,4,hafnium,6,Solid,Hafnium,0.0,2506,Hf -Hg,80,171.0,200.58999633789062,Silver,1.3200000524520874,SimpleTrigonal,13534.0,64036,0.0,2.0,12,mercury,6,Liquid,Mercury,155.0,234.321,Hg -Ho,67,226.0,164.93031311035156,Silver,1.9199999570846558,SimpleHexagonal,8795.0,1878,50.0,1.2300000190734863,0,holmium,6,Solid,Holmium,0.0,1745,Ho -Hs,108,0.0,270.0,,0.0,,0.0,1984,0.0,0.0,8,hassium,7,,Hassium,0.0,,Hs -I,53,115.0,126.90447235107422,SlateGray,1.3899999856948853,BaseCenteredOrth,4940.0,1811,295.20001220703125,2.6600000858306885,17,iodine,5,Solid,Iodine,198.0,386.85,I -In,49,156.0,114.81800079345703,Silver,1.4199999570846558,CenteredTetragon,7310.0,1863,28.899999618530273,1.7799999713897705,13,indium,5,Solid,Indium,193.0,429.75,In -Ir,77,180.0,192.2169952392578,Silver,1.409999966621399,FaceCenteredCubi,22560.0,1803,151.0,2.200000047683716,9,iridium,6,Solid,Iridium,0.0,2719,Ir -K,19,243.0,39.09830093383789,Silver,2.0299999713897705,BodyCenteredCubi,856.0,1807,48.400001525878906,0.8199999928474426,1,potassium,4,Solid,Potassium,275.0,336.65,K -Kr,36,88.0,83.7979965209961,Colorless,1.159999966621399,FaceCenteredCubi,3.75,1898,0.0,3.0,18,krypton,4,Gas,Krypton,202.0,115.78,Kr -La,57,0.0,138.9054718017578,Silver,2.069999933242798,SimpleHexagonal,6146.0,1839,48.0,1.100000023841858,0,lanthanum,6,Solid,Lanthanum,0.0,1193,La -Li,3,167.0,6.940999984741211,Silver,1.2799999713897705,BodyCenteredCubi,535.0,1817,59.599998474121094,0.9800000190734863,1,lithium,2,Solid,Lithium,182.0,453.65,Li -Lr,103,0.0,262.0,,0.0,,0.0,1961,0.0,0.0,3,lawrencium,7,,Lawrencium,0.0,1900,Lr -Lu,71,217.0,174.966796875,Silver,1.8700000047683716,SimpleHexagonal,9841.0,1907,50.0,1.2699999809265137,3,lutetium,6,Solid,Lutetium,0.0,1936,Lu -Md,101,0.0,258.0,,0.0,,0.0,1955,0.0,1.2999999523162842,0,mendelevium,7,,Mendelevium,0.0,1100,Md -Mg,12,145.0,24.30500030517578,Silver,1.409999966621399,SimpleHexagonal,1738.0,1755,0.0,1.309999942779541,2,magnesium,3,Solid,Magnesium,173.0,923,Mg -Mn,25,161.0,54.938045501708984,Silver,1.3899999856948853,BodyCenteredCubi,7470.0,1774,0.0,1.5499999523162842,7,manganese,4,Solid,Manganese,0.0,1519,Mn -Mo,42,190.0,95.95999908447266,Gray,1.5399999618530273,BodyCenteredCubi,10280.0,1781,71.9000015258789,2.1600000858306885,6,molybdenum,5,Solid,Molybdenum,0.0,2895,Mo -N,7,56.0,14.006699562072754,Colorless,0.7099999785423279,SimpleHexagonal,1.2510000467300415,1772,7.0,3.0399999618530273,15,nitrogen,2,Gas,Nitrogen,155.0,63,N -Na,11,190.0,22.989768981933594,Silver,1.659999966621399,BodyCenteredCubi,968.0,1807,52.79999923706055,0.9300000071525574,1,sodium,3,Solid,Sodium,227.0,370.944,Na -Nb,41,198.0,92.90637969970703,Gray,1.6399999856948853,BodyCenteredCubi,8570.0,1801,86.0999984741211,1.600000023841858,5,niobium,5,Solid,Niobium,0.0,2750,Nb -Nd,60,206.0,144.24200439453125,Silver,2.009999990463257,SimpleHexagonal,7010.0,1885,50.0,1.1399999856948853,0,neodymium,6,Solid,Neodymium,0.0,1289,Nd -Ne,10,38.0,20.179100036621094,Colorless,0.5799999833106995,FaceCenteredCubi,0.8999999761581421,1898,0.0,0.0,18,neon,2,Gas,Neon,154.0,24.56,Ne -Ni,28,149.0,58.69340133666992,Gray,1.2400000095367432,FaceCenteredCubi,8908.0,1751,112.0,1.909999966621399,10,nickel,4,Solid,Nickel,163.0,1728,Ni -No,102,0.0,259.0,,0.0,,0.0,1958,0.0,1.2999999523162842,0,nobelium,7,,Nobelium,0.0,1100,No -Np,93,0.0,237.0,Silver,1.899999976158142,SimpleOrthorhomb,20450.0,1940,0.0,1.3600000143051147,0,neptunium,7,Solid,Neptunium,0.0,917,Np -O,8,48.0,15.99940013885498,Colorless,0.6600000262260437,BaseCenteredMono,1.4290000200271606,1774,141.0,3.440000057220459,16,oxygen,2,Gas,Oxygen,152.0,54.36,O -Os,76,185.0,190.22999572753906,SlateGray,1.440000057220459,SimpleHexagonal,22590.0,1803,106.0999984741211,2.200000047683716,8,osmium,6,Solid,Osmium,0.0,3306,Os -P,15,98.0,30.97376251220703,Colorless,1.0700000524520874,SimpleTriclinic,1823.0,1669,72.0,2.190000057220459,15,phosphorus,3,Solid,Phosphorus,180.0,852.35,P -Pa,91,0.0,231.03585815429688,Silver,2.0,CenteredTetragon,15370.0,1913,0.0,1.5,0,protactinium,7,Solid,Protactinium,0.0,1845,Pa -Pb,82,154.0,207.1999969482422,SlateGray,1.4600000381469727,FaceCenteredCubi,11340.0,61536,35.099998474121094,2.3299999237060547,14,lead,6,Solid,Lead,202.0,600.612,Pb -Pd,46,169.0,106.41999816894531,Silver,1.3899999856948853,FaceCenteredCubi,12023.0,1803,53.70000076293945,2.200000047683716,10,palladium,5,Solid,Palladium,163.0,1827.95,Pd -Pm,61,205.0,145.0,Silver,1.9900000095367432,,7264.0,1945,50.0,0.0,0,promethium,6,Solid,Promethium,0.0,1315,Pm -Po,84,135.0,209.0,Silver,1.399999976158142,SimpleCubic,9196.0,1898,183.3000030517578,2.0,16,polonium,6,Solid,Polonium,0.0,527,Po -Pr,59,247.0,140.90765380859375,Silver,2.0299999713897705,SimpleHexagonal,6640.0,1885,50.0,1.1299999952316284,0,praseodymium,6,Solid,Praseodymium,0.0,1204,Pr -Pt,78,177.0,195.08399963378906,Gray,1.3600000143051147,FaceCenteredCubi,21090.0,1735,205.3000030517578,2.2799999713897705,10,platinum,6,Solid,Platinum,175.0,2041.35,Pt -Pu,94,0.0,244.0,Silver,1.8700000047683716,SimpleMonoclinic,19816.0,1940,0.0,1.2799999713897705,0,plutonium,7,Solid,Plutonium,0.0,913,Pu -Ra,88,0.0,226.0,Silver,2.2100000381469727,BodyCenteredCubi,5000.0,1898,0.0,0.8999999761581421,2,radium,7,Solid,Radium,0.0,969,Ra -Rb,37,265.0,85.4677963256836,Silver,2.200000047683716,BodyCenteredCubi,1532.0,1861,46.900001525878906,0.8199999928474426,1,rubidium,5,Solid,Rubidium,0.0,312.45,Rb -Re,75,188.0,186.20700073242188,Gray,1.5099999904632568,SimpleHexagonal,21020.0,1925,14.5,1.899999976158142,7,rhenium,6,Solid,Rhenium,0.0,3458,Re -Rf,104,0.0,265.0,,0.0,,0.0,1964,0.0,0.0,4,rutherfordium,7,,Rutherfordium,0.0,,Rf -Rh,45,173.0,102.90550231933594,Silver,1.4199999570846558,FaceCenteredCubi,12450.0,1803,109.69999694824219,2.2799999713897705,9,rhodium,5,Solid,Rhodium,0.0,2236,Rh -Rn,86,120.0,222.0,Colorless,1.5,,9.729999542236328,1900,0.0,0.0,18,radon,6,Gas,Radon,0.0,202,Rn -Ru,44,178.0,101.06999969482422,Silver,1.4600000381469727,SimpleHexagonal,12370.0,1844,101.30000305175781,2.200000047683716,8,ruthenium,5,Solid,Ruthenium,0.0,2606,Ru -S,16,88.0,32.064998626708984,Yellow,1.0499999523162842,FaceCenteredOrth,1960.0,65036,200.0,2.5799999237060547,16,sulfur,3,Solid,Sulfur,180.0,388.36,S -Sb,51,133.0,121.76000213623047,Silver,1.3899999856948853,SimpleTrigonal,6697.0,62536,103.19999694824219,2.049999952316284,15,antimony,5,Solid,Antimony,0.0,903.778,Sb -Sc,21,184.0,44.95591354370117,Silver,1.7000000476837158,SimpleHexagonal,2985.0,1879,18.100000381469727,1.3600000143051147,3,scandium,4,Solid,Scandium,0.0,1814,Sc -Se,34,103.0,78.95999908447266,Gray,1.2000000476837158,SimpleMonoclinic,4819.0,1817,195.0,2.549999952316284,16,selenium,4,Solid,Selenium,190.0,493.95,Se -Sg,106,0.0,271.0,,0.0,,0.0,1974,0.0,0.0,6,seaborgium,7,,Seaborgium,0.0,,Sg -Si,14,111.0,28.085500717163086,Gray,1.1100000143051147,TetrahedralPacki,2330.0,1824,133.60000610351562,1.899999976158142,14,silicon,3,Solid,Silicon,210.0,1687,Si -Sm,62,238.0,150.36000061035156,Silver,1.9800000190734863,SimpleTrigonal,7353.0,1879,50.0,1.1699999570846558,0,samarium,6,Solid,Samarium,0.0,1345,Sm -Sn,50,145.0,118.70999908447266,Silver,1.3899999856948853,CenteredTetragon,7310.0,62536,107.30000305175781,1.9600000381469727,14,tin,5,Solid,Tin,217.0,505.078,Sn -Sr,38,219.0,87.62000274658203,Silver,1.9500000476837158,FaceCenteredCubi,2630.0,1790,5.03000020980835,0.949999988079071,2,strontium,5,Solid,Strontium,0.0,1050,Sr -Ta,73,200.0,180.9478759765625,Gray,1.7000000476837158,BodyCenteredCubi,16650.0,1802,31.0,1.5,5,tantalum,6,Solid,Tantalum,0.0,3290,Ta -Tb,65,225.0,158.92535400390625,Silver,1.940000057220459,SimpleHexagonal,8219.0,1843,50.0,0.0,0,terbium,6,Solid,Terbium,0.0,1632,Tb -Tc,43,183.0,98.0,Silver,1.4700000286102295,SimpleHexagonal,11500.0,1937,53.0,1.899999976158142,7,technetium,5,Solid,Technetium,0.0,2430,Tc -Te,52,123.0,127.5999984741211,Silver,1.3799999952316284,SimpleTrigonal,6240.0,1783,190.1999969482422,2.0999999046325684,16,tellurium,5,Solid,Tellurium,206.0,722.66,Te -Th,90,0.0,232.03805541992188,Silver,2.059999942779541,FaceCenteredCubi,11724.0,1829,0.0,1.2999999523162842,0,thorium,7,Solid,Thorium,0.0,2023,Th -Ti,22,176.0,47.867000579833984,Silver,1.600000023841858,SimpleHexagonal,4507.0,1791,7.599999904632568,1.5399999618530273,4,titanium,4,Solid,Titanium,0.0,1943,Ti -Tl,81,156.0,204.38330078125,Silver,1.4500000476837158,SimpleHexagonal,11850.0,1861,19.200000762939453,1.6200000047683716,13,thallium,6,Solid,Thallium,196.0,577,Tl -Tm,69,222.0,168.9342041015625,Silver,1.899999976158142,SimpleHexagonal,9321.0,1879,50.0,1.25,0,thulium,6,Solid,Thulium,0.0,1818,Tm -U,92,0.0,238.02891540527344,Silver,1.9600000381469727,BaseCenteredOrth,19050.0,1789,0.0,1.3799999952316284,0,uranium,7,Solid,Uranium,186.0,1408,U -V,23,171.0,50.94150161743164,Silver,1.5299999713897705,BodyCenteredCubi,6110.0,1801,50.599998474121094,1.6299999952316284,5,vanadium,4,Solid,Vanadium,0.0,2183,V -W,74,193.0,183.83999633789062,Gray,1.6200000047683716,BodyCenteredCubi,19250.0,1783,78.5999984741211,2.359999895095825,6,tungsten,6,Solid,Tungsten,0.0,3687,W -Xe,54,108.0,131.29299926757812,Colorless,1.399999976158142,FaceCenteredCubi,5.900000095367432,1898,0.0,2.5999999046325684,18,xenon,5,Gas,Xenon,216.0,161.4,Xe -Y,39,212.0,88.90585327148438,Silver,1.899999976158142,SimpleHexagonal,4472.0,1794,29.600000381469727,1.2200000286102295,3,yttrium,5,Solid,Yttrium,0.0,1795,Y -Yb,70,222.0,173.0540008544922,Silver,1.8700000047683716,FaceCenteredCubi,6570.0,1878,50.0,0.0,0,ytterbium,6,Solid,Ytterbium,0.0,1097,Yb -Zn,30,142.0,65.37999725341797,SlateGray,1.2200000286102295,SimpleHexagonal,7140.0,1500,0.0,1.649999976158142,12,zinc,4,Solid,Zinc,139.0,692.677,Zn -Zr,40,206.0,91.2239990234375,Silver,1.75,SimpleHexagonal,6511.0,1789,41.099998474121094,1.3300000429153442,4,zirconium,5,Solid,Zirconium,0.0,2127,Zr From 660de11a428ff41d09f4c57bd852fc674120ac4b Mon Sep 17 00:00:00 2001 From: Niklas Siemer <70580458+niklassiemer@users.noreply.github.com> Date: Mon, 16 Oct 2023 16:59:04 +0200 Subject: [PATCH 2/4] Actually add the periodic_table.csv file --- pyiron_atomistics/_data/periodic_table.csv | 109 +++++++++++++++++++++ 1 file changed, 109 insertions(+) create mode 100644 pyiron_atomistics/_data/periodic_table.csv diff --git a/pyiron_atomistics/_data/periodic_table.csv b/pyiron_atomistics/_data/periodic_table.csv new file mode 100644 index 000000000..ac382cbc0 --- /dev/null +++ b/pyiron_atomistics/_data/periodic_table.csv @@ -0,0 +1,109 @@ +,AtomicNumber,AtomicRadius,AtomicMass,Color,CovalentRadius,CrystalStructure,Density,DiscoveryYear,ElectronAffinity,Electronegativity,Group,Name,Period,Phase,StandardName,VanDerWaalsRadius,MeltingPoint,Abbreviation +Ac,89,0.0,227.0,Silver,2.1500000953674316,FaceCenteredCubi,10070.0,1899,0.0,1.100000023841858,0,actinium,7,Solid,Actinium,0.0,1323,Ac +Ag,47,165.0,107.86820220947266,Silver,1.4500000476837158,FaceCenteredCubi,10490.0,62536,125.5999984741211,1.9299999475479126,11,silver,5,Solid,Silver,172.0,1234.93,Ag +Al,13,118.0,26.981538772583008,Silver,1.2100000381469727,FaceCenteredCubi,2700.0,1825,42.5,1.6100000143051147,13,aluminum,3,Solid,Aluminum,0.0,933.473,Al +Am,95,0.0,243.0,Silver,1.7999999523162842,SimpleHexagonal,13670.0,1944,0.0,1.2999999523162842,0,americium,7,Solid,Americium,0.0,1449,Am +Ar,18,71.0,39.948001861572266,Colorless,1.059999942779541,FaceCenteredCubi,1.784000039100647,1894,0.0,0.0,18,argon,3,Gas,Argon,188.0,83.81,Ar +As,33,114.0,74.92160034179688,Silver,1.190000057220459,SimpleTrigonal,5727.0,1250,78.0,2.180000066757202,15,arsenic,4,Solid,Arsenic,185.0,1090,As +At,85,127.0,210.0,Silver,1.5,,0.0,1940,270.1000061035156,2.200000047683716,17,astatine,6,Solid,Astatine,0.0,575,At +Au,79,174.0,196.96656799316406,Gold,1.3600000143051147,FaceCenteredCubi,19300.0,63036,222.8000030517578,2.5399999618530273,11,gold,6,Solid,Gold,166.0,1337.33,Au +B,5,87.0,10.810999870300293,Black,0.8399999737739563,SimpleTrigonal,2460.0,1808,26.700000762939453,2.0399999618530273,13,boron,2,Solid,Boron,0.0,2350,B +Ba,56,253.0,137.32699584960938,Silver,2.1500000953674316,BodyCenteredCubi,3510.0,1808,13.949999809265137,0.8899999856948853,2,barium,6,Solid,Barium,0.0,1000,Ba +Be,4,112.0,9.012182235717773,SlateGray,0.9599999785423279,SimpleHexagonal,1848.0,1797,0.0,1.5700000524520874,2,beryllium,2,Solid,Beryllium,0.0,1560,Be +Bh,107,0.0,272.0,,0.0,,0.0,1981,0.0,0.0,7,bohrium,7,,Bohrium,0.0,,Bh +Bi,83,143.0,208.9803924560547,Gray,1.4800000190734863,BaseCenteredMono,9780.0,1400,91.19999694824219,2.0199999809265137,15,bismuth,6,Solid,Bismuth,0.0,544.556,Bi +Bk,97,0.0,247.0,,0.0,SimpleHexagonal,14780.0,1949,0.0,1.2999999523162842,0,berkelium,7,Solid,Berkelium,0.0,1259,Bk +Br,35,94.0,79.90399932861328,Red,1.2000000476837158,BaseCenteredOrth,3120.0,1826,324.6000061035156,2.9600000381469727,17,bromine,4,Liquid,Bromine,185.0,265.95,Br +C,6,67.0,12.010700225830078,Black,0.7599999904632568,SimpleHexagonal,2260.0,0,153.89999389648438,2.549999952316284,14,carbon,2,Solid,Carbon,170.0,4713,C +Ca,20,194.0,40.077999114990234,Silver,1.7599999904632568,FaceCenteredCubi,1550.0,1808,2.369999885559082,1.0,2,calcium,4,Solid,Calcium,0.0,1115,Ca +Cd,48,161.0,112.41100311279297,Silver,1.440000057220459,SimpleHexagonal,8650.0,1817,0.0,1.690000057220459,12,cadmium,5,Solid,Cadmium,158.0,594.219,Cd +Ce,58,0.0,140.11599731445312,Silver,2.0399999618530273,SimpleHexagonal,6689.0,1803,50.0,1.1200000047683716,0,cerium,6,Solid,Cerium,0.0,1072,Ce +Cf,98,0.0,251.0,,0.0,SimpleHexagonal,15100.0,1950,0.0,1.2999999523162842,0,californium,7,Solid,Californium,0.0,1173,Cf +Cl,17,79.0,35.452999114990234,Yellow,1.0199999809265137,BaseCenteredOrth,3.2139999866485596,1774,349.0,3.1600000858306885,17,chlorine,3,Gas,Chlorine,175.0,171.65,Cl +Cm,96,0.0,247.0,Silver,1.690000057220459,SimpleHexagonal,13510.0,1944,0.0,1.2999999523162842,0,curium,7,Solid,Curium,0.0,1618,Cm +Co,27,152.0,58.93319320678711,Gray,1.2599999904632568,SimpleHexagonal,8900.0,1735,63.70000076293945,1.8799999952316284,9,cobalt,4,Solid,Cobalt,0.0,1768,Co +Cr,24,166.0,51.99610137939453,Silver,1.3899999856948853,BodyCenteredCubi,7140.0,1797,64.30000305175781,1.659999966621399,6,chromium,4,Solid,Chromium,0.0,2180,Cr +Cs,55,298.0,132.90545654296875,Silver,2.440000057220459,BodyCenteredCubi,1879.0,1860,45.5,0.7900000214576721,1,cesium,6,Solid,Cesium,0.0,301.65,Cs +Cu,29,145.0,63.54600143432617,Copper,1.3200000524520874,FaceCenteredCubi,8920.0,57536,118.4000015258789,1.899999976158142,11,copper,4,Solid,Copper,140.0,1357.77,Cu +Db,105,0.0,268.0,,0.0,,0.0,1967,0.0,0.0,5,dubnium,7,,Dubnium,0.0,,Db +Dy,66,228.0,162.5,Silver,1.9199999570846558,SimpleHexagonal,8551.0,1886,50.0,1.2200000286102295,0,dysprosium,6,Solid,Dysprosium,0.0,1685,Dy +Er,68,226.0,167.25900268554688,Silver,1.8899999856948853,SimpleHexagonal,9066.0,1842,50.0,1.2400000095367432,0,erbium,6,Solid,Erbium,0.0,1802,Er +Es,99,0.0,252.0,,0.0,,0.0,1952,0.0,1.2999999523162842,0,einsteinium,7,Solid,Einsteinium,0.0,1133,Es +Eu,63,231.0,151.96400451660156,Silver,1.9800000190734863,BodyCenteredCubi,5244.0,1901,50.0,0.0,0,europium,6,Solid,Europium,0.0,1095,Eu +F,9,42.0,18.998403549194336,Colorless,0.5699999928474426,BaseCenteredMono,1.6959999799728394,1886,328.0,3.9800000190734863,17,fluorine,2,Gas,Fluorine,147.0,53.48,F +Fe,26,156.0,55.845001220703125,Gray,1.3200000524520874,BodyCenteredCubi,7874.0,63536,15.699999809265137,1.8300000429153442,8,iron,4,Solid,Iron,0.0,1811,Fe +Fm,100,0.0,257.0,,0.0,,0.0,1952,0.0,1.2999999523162842,0,fermium,7,,Fermium,0.0,1800,Fm +Fr,87,0.0,223.0,Silver,2.5999999046325684,,0.0,1939,0.0,0.699999988079071,1,francium,7,Solid,Francium,0.0,294,Fr +Ga,31,136.0,69.7229995727539,Silver,1.2200000286102295,BaseCenteredOrth,5904.0,1875,28.899999618530273,1.809999942779541,13,gallium,4,Solid,Gallium,187.0,302.915,Ga +Gd,64,233.0,157.25,Silver,1.9600000381469727,SimpleHexagonal,7901.0,1880,50.0,1.2000000476837158,0,gadolinium,6,Solid,Gadolinium,0.0,1586,Gd +Ge,32,125.0,72.63999938964844,Gray,1.2000000476837158,FaceCenteredCubi,5323.0,1886,119.0,2.009999990463257,14,germanium,4,Solid,Germanium,0.0,1211.4,Ge +H,1,53.0,1.0079400539398193,Colorless,0.3100000023841858,SimpleHexagonal,0.08990000188350677,1766,72.80000305175781,2.200000047683716,1,hydrogen,1,Gas,Hydrogen,120.0,13.99,H +He,2,31.0,4.0026021003723145,Colorless,0.2800000011920929,FaceCenteredCubi,0.1784999966621399,1895,0.0,0.0,18,helium,1,Gas,Helium,140.0,xxxx,He +Hf,72,208.0,178.49000549316406,Gray,1.75,SimpleHexagonal,13310.0,1923,0.0,1.2999999523162842,4,hafnium,6,Solid,Hafnium,0.0,2506,Hf +Hg,80,171.0,200.58999633789062,Silver,1.3200000524520874,SimpleTrigonal,13534.0,64036,0.0,2.0,12,mercury,6,Liquid,Mercury,155.0,234.321,Hg +Ho,67,226.0,164.93031311035156,Silver,1.9199999570846558,SimpleHexagonal,8795.0,1878,50.0,1.2300000190734863,0,holmium,6,Solid,Holmium,0.0,1745,Ho +Hs,108,0.0,270.0,,0.0,,0.0,1984,0.0,0.0,8,hassium,7,,Hassium,0.0,,Hs +I,53,115.0,126.90447235107422,SlateGray,1.3899999856948853,BaseCenteredOrth,4940.0,1811,295.20001220703125,2.6600000858306885,17,iodine,5,Solid,Iodine,198.0,386.85,I +In,49,156.0,114.81800079345703,Silver,1.4199999570846558,CenteredTetragon,7310.0,1863,28.899999618530273,1.7799999713897705,13,indium,5,Solid,Indium,193.0,429.75,In +Ir,77,180.0,192.2169952392578,Silver,1.409999966621399,FaceCenteredCubi,22560.0,1803,151.0,2.200000047683716,9,iridium,6,Solid,Iridium,0.0,2719,Ir +K,19,243.0,39.09830093383789,Silver,2.0299999713897705,BodyCenteredCubi,856.0,1807,48.400001525878906,0.8199999928474426,1,potassium,4,Solid,Potassium,275.0,336.65,K +Kr,36,88.0,83.7979965209961,Colorless,1.159999966621399,FaceCenteredCubi,3.75,1898,0.0,3.0,18,krypton,4,Gas,Krypton,202.0,115.78,Kr +La,57,0.0,138.9054718017578,Silver,2.069999933242798,SimpleHexagonal,6146.0,1839,48.0,1.100000023841858,0,lanthanum,6,Solid,Lanthanum,0.0,1193,La +Li,3,167.0,6.940999984741211,Silver,1.2799999713897705,BodyCenteredCubi,535.0,1817,59.599998474121094,0.9800000190734863,1,lithium,2,Solid,Lithium,182.0,453.65,Li +Lr,103,0.0,262.0,,0.0,,0.0,1961,0.0,0.0,3,lawrencium,7,,Lawrencium,0.0,1900,Lr +Lu,71,217.0,174.966796875,Silver,1.8700000047683716,SimpleHexagonal,9841.0,1907,50.0,1.2699999809265137,3,lutetium,6,Solid,Lutetium,0.0,1936,Lu +Md,101,0.0,258.0,,0.0,,0.0,1955,0.0,1.2999999523162842,0,mendelevium,7,,Mendelevium,0.0,1100,Md +Mg,12,145.0,24.30500030517578,Silver,1.409999966621399,SimpleHexagonal,1738.0,1755,0.0,1.309999942779541,2,magnesium,3,Solid,Magnesium,173.0,923,Mg +Mn,25,161.0,54.938045501708984,Silver,1.3899999856948853,BodyCenteredCubi,7470.0,1774,0.0,1.5499999523162842,7,manganese,4,Solid,Manganese,0.0,1519,Mn +Mo,42,190.0,95.95999908447266,Gray,1.5399999618530273,BodyCenteredCubi,10280.0,1781,71.9000015258789,2.1600000858306885,6,molybdenum,5,Solid,Molybdenum,0.0,2895,Mo +N,7,56.0,14.006699562072754,Colorless,0.7099999785423279,SimpleHexagonal,1.2510000467300415,1772,7.0,3.0399999618530273,15,nitrogen,2,Gas,Nitrogen,155.0,63,N +Na,11,190.0,22.989768981933594,Silver,1.659999966621399,BodyCenteredCubi,968.0,1807,52.79999923706055,0.9300000071525574,1,sodium,3,Solid,Sodium,227.0,370.944,Na +Nb,41,198.0,92.90637969970703,Gray,1.6399999856948853,BodyCenteredCubi,8570.0,1801,86.0999984741211,1.600000023841858,5,niobium,5,Solid,Niobium,0.0,2750,Nb +Nd,60,206.0,144.24200439453125,Silver,2.009999990463257,SimpleHexagonal,7010.0,1885,50.0,1.1399999856948853,0,neodymium,6,Solid,Neodymium,0.0,1289,Nd +Ne,10,38.0,20.179100036621094,Colorless,0.5799999833106995,FaceCenteredCubi,0.8999999761581421,1898,0.0,0.0,18,neon,2,Gas,Neon,154.0,24.56,Ne +Ni,28,149.0,58.69340133666992,Gray,1.2400000095367432,FaceCenteredCubi,8908.0,1751,112.0,1.909999966621399,10,nickel,4,Solid,Nickel,163.0,1728,Ni +No,102,0.0,259.0,,0.0,,0.0,1958,0.0,1.2999999523162842,0,nobelium,7,,Nobelium,0.0,1100,No +Np,93,0.0,237.0,Silver,1.899999976158142,SimpleOrthorhomb,20450.0,1940,0.0,1.3600000143051147,0,neptunium,7,Solid,Neptunium,0.0,917,Np +O,8,48.0,15.99940013885498,Colorless,0.6600000262260437,BaseCenteredMono,1.4290000200271606,1774,141.0,3.440000057220459,16,oxygen,2,Gas,Oxygen,152.0,54.36,O +Os,76,185.0,190.22999572753906,SlateGray,1.440000057220459,SimpleHexagonal,22590.0,1803,106.0999984741211,2.200000047683716,8,osmium,6,Solid,Osmium,0.0,3306,Os +P,15,98.0,30.97376251220703,Colorless,1.0700000524520874,SimpleTriclinic,1823.0,1669,72.0,2.190000057220459,15,phosphorus,3,Solid,Phosphorus,180.0,852.35,P +Pa,91,0.0,231.03585815429688,Silver,2.0,CenteredTetragon,15370.0,1913,0.0,1.5,0,protactinium,7,Solid,Protactinium,0.0,1845,Pa +Pb,82,154.0,207.1999969482422,SlateGray,1.4600000381469727,FaceCenteredCubi,11340.0,61536,35.099998474121094,2.3299999237060547,14,lead,6,Solid,Lead,202.0,600.612,Pb +Pd,46,169.0,106.41999816894531,Silver,1.3899999856948853,FaceCenteredCubi,12023.0,1803,53.70000076293945,2.200000047683716,10,palladium,5,Solid,Palladium,163.0,1827.95,Pd +Pm,61,205.0,145.0,Silver,1.9900000095367432,,7264.0,1945,50.0,0.0,0,promethium,6,Solid,Promethium,0.0,1315,Pm +Po,84,135.0,209.0,Silver,1.399999976158142,SimpleCubic,9196.0,1898,183.3000030517578,2.0,16,polonium,6,Solid,Polonium,0.0,527,Po +Pr,59,247.0,140.90765380859375,Silver,2.0299999713897705,SimpleHexagonal,6640.0,1885,50.0,1.1299999952316284,0,praseodymium,6,Solid,Praseodymium,0.0,1204,Pr +Pt,78,177.0,195.08399963378906,Gray,1.3600000143051147,FaceCenteredCubi,21090.0,1735,205.3000030517578,2.2799999713897705,10,platinum,6,Solid,Platinum,175.0,2041.35,Pt +Pu,94,0.0,244.0,Silver,1.8700000047683716,SimpleMonoclinic,19816.0,1940,0.0,1.2799999713897705,0,plutonium,7,Solid,Plutonium,0.0,913,Pu +Ra,88,0.0,226.0,Silver,2.2100000381469727,BodyCenteredCubi,5000.0,1898,0.0,0.8999999761581421,2,radium,7,Solid,Radium,0.0,969,Ra +Rb,37,265.0,85.4677963256836,Silver,2.200000047683716,BodyCenteredCubi,1532.0,1861,46.900001525878906,0.8199999928474426,1,rubidium,5,Solid,Rubidium,0.0,312.45,Rb +Re,75,188.0,186.20700073242188,Gray,1.5099999904632568,SimpleHexagonal,21020.0,1925,14.5,1.899999976158142,7,rhenium,6,Solid,Rhenium,0.0,3458,Re +Rf,104,0.0,265.0,,0.0,,0.0,1964,0.0,0.0,4,rutherfordium,7,,Rutherfordium,0.0,,Rf +Rh,45,173.0,102.90550231933594,Silver,1.4199999570846558,FaceCenteredCubi,12450.0,1803,109.69999694824219,2.2799999713897705,9,rhodium,5,Solid,Rhodium,0.0,2236,Rh +Rn,86,120.0,222.0,Colorless,1.5,,9.729999542236328,1900,0.0,0.0,18,radon,6,Gas,Radon,0.0,202,Rn +Ru,44,178.0,101.06999969482422,Silver,1.4600000381469727,SimpleHexagonal,12370.0,1844,101.30000305175781,2.200000047683716,8,ruthenium,5,Solid,Ruthenium,0.0,2606,Ru +S,16,88.0,32.064998626708984,Yellow,1.0499999523162842,FaceCenteredOrth,1960.0,65036,200.0,2.5799999237060547,16,sulfur,3,Solid,Sulfur,180.0,388.36,S +Sb,51,133.0,121.76000213623047,Silver,1.3899999856948853,SimpleTrigonal,6697.0,62536,103.19999694824219,2.049999952316284,15,antimony,5,Solid,Antimony,0.0,903.778,Sb +Sc,21,184.0,44.95591354370117,Silver,1.7000000476837158,SimpleHexagonal,2985.0,1879,18.100000381469727,1.3600000143051147,3,scandium,4,Solid,Scandium,0.0,1814,Sc +Se,34,103.0,78.95999908447266,Gray,1.2000000476837158,SimpleMonoclinic,4819.0,1817,195.0,2.549999952316284,16,selenium,4,Solid,Selenium,190.0,493.95,Se +Sg,106,0.0,271.0,,0.0,,0.0,1974,0.0,0.0,6,seaborgium,7,,Seaborgium,0.0,,Sg +Si,14,111.0,28.085500717163086,Gray,1.1100000143051147,TetrahedralPacki,2330.0,1824,133.60000610351562,1.899999976158142,14,silicon,3,Solid,Silicon,210.0,1687,Si +Sm,62,238.0,150.36000061035156,Silver,1.9800000190734863,SimpleTrigonal,7353.0,1879,50.0,1.1699999570846558,0,samarium,6,Solid,Samarium,0.0,1345,Sm +Sn,50,145.0,118.70999908447266,Silver,1.3899999856948853,CenteredTetragon,7310.0,62536,107.30000305175781,1.9600000381469727,14,tin,5,Solid,Tin,217.0,505.078,Sn +Sr,38,219.0,87.62000274658203,Silver,1.9500000476837158,FaceCenteredCubi,2630.0,1790,5.03000020980835,0.949999988079071,2,strontium,5,Solid,Strontium,0.0,1050,Sr +Ta,73,200.0,180.9478759765625,Gray,1.7000000476837158,BodyCenteredCubi,16650.0,1802,31.0,1.5,5,tantalum,6,Solid,Tantalum,0.0,3290,Ta +Tb,65,225.0,158.92535400390625,Silver,1.940000057220459,SimpleHexagonal,8219.0,1843,50.0,0.0,0,terbium,6,Solid,Terbium,0.0,1632,Tb +Tc,43,183.0,98.0,Silver,1.4700000286102295,SimpleHexagonal,11500.0,1937,53.0,1.899999976158142,7,technetium,5,Solid,Technetium,0.0,2430,Tc +Te,52,123.0,127.5999984741211,Silver,1.3799999952316284,SimpleTrigonal,6240.0,1783,190.1999969482422,2.0999999046325684,16,tellurium,5,Solid,Tellurium,206.0,722.66,Te +Th,90,0.0,232.03805541992188,Silver,2.059999942779541,FaceCenteredCubi,11724.0,1829,0.0,1.2999999523162842,0,thorium,7,Solid,Thorium,0.0,2023,Th +Ti,22,176.0,47.867000579833984,Silver,1.600000023841858,SimpleHexagonal,4507.0,1791,7.599999904632568,1.5399999618530273,4,titanium,4,Solid,Titanium,0.0,1943,Ti +Tl,81,156.0,204.38330078125,Silver,1.4500000476837158,SimpleHexagonal,11850.0,1861,19.200000762939453,1.6200000047683716,13,thallium,6,Solid,Thallium,196.0,577,Tl +Tm,69,222.0,168.9342041015625,Silver,1.899999976158142,SimpleHexagonal,9321.0,1879,50.0,1.25,0,thulium,6,Solid,Thulium,0.0,1818,Tm +U,92,0.0,238.02891540527344,Silver,1.9600000381469727,BaseCenteredOrth,19050.0,1789,0.0,1.3799999952316284,0,uranium,7,Solid,Uranium,186.0,1408,U +V,23,171.0,50.94150161743164,Silver,1.5299999713897705,BodyCenteredCubi,6110.0,1801,50.599998474121094,1.6299999952316284,5,vanadium,4,Solid,Vanadium,0.0,2183,V +W,74,193.0,183.83999633789062,Gray,1.6200000047683716,BodyCenteredCubi,19250.0,1783,78.5999984741211,2.359999895095825,6,tungsten,6,Solid,Tungsten,0.0,3687,W +Xe,54,108.0,131.29299926757812,Colorless,1.399999976158142,FaceCenteredCubi,5.900000095367432,1898,0.0,2.5999999046325684,18,xenon,5,Gas,Xenon,216.0,161.4,Xe +Y,39,212.0,88.90585327148438,Silver,1.899999976158142,SimpleHexagonal,4472.0,1794,29.600000381469727,1.2200000286102295,3,yttrium,5,Solid,Yttrium,0.0,1795,Y +Yb,70,222.0,173.0540008544922,Silver,1.8700000047683716,FaceCenteredCubi,6570.0,1878,50.0,0.0,0,ytterbium,6,Solid,Ytterbium,0.0,1097,Yb +Zn,30,142.0,65.37999725341797,SlateGray,1.2200000286102295,SimpleHexagonal,7140.0,1500,0.0,1.649999976158142,12,zinc,4,Solid,Zinc,139.0,692.677,Zn +Zr,40,206.0,91.2239990234375,Silver,1.75,SimpleHexagonal,6511.0,1789,41.099998474121094,1.3300000429153442,4,zirconium,5,Solid,Zirconium,0.0,2127,Zr From 8612dabb58cfd6677d41fc72dafb5ae9f6d71af1 Mon Sep 17 00:00:00 2001 From: Niklas Siemer <70580458+niklassiemer@users.noreply.github.com> Date: Tue, 17 Oct 2023 08:31:53 +0200 Subject: [PATCH 3/4] Use pkgutil.get_data instead of __file__ --- .../atomistics/structure/periodic_table.py | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/pyiron_atomistics/atomistics/structure/periodic_table.py b/pyiron_atomistics/atomistics/structure/periodic_table.py index 5c57bda71..84690c589 100644 --- a/pyiron_atomistics/atomistics/structure/periodic_table.py +++ b/pyiron_atomistics/atomistics/structure/periodic_table.py @@ -3,12 +3,12 @@ # Distributed under the terms of "New BSD License", see the LICENSE file. from __future__ import print_function, unicode_literals +import pkgutil +import io import numpy as np -import os import mendeleev import pandas from functools import lru_cache -import pyiron_atomistics __author__ = "Joerg Neugebauer, Sudarsan Surendralal, Martin Boeckmann" __copyright__ = ( @@ -397,10 +397,8 @@ def _get_periodic_table_df(file_name): """ if not file_name: return pandas.read_csv( - os.path.join( - os.path.dirname(pyiron_atomistics.__file__), - "_data", - "periodic_table.csv", + io.BytesIO( + pkgutil.get_data("pyiron_atomistics", "_data/periodic_table.csv") ), index_col=0, ) From fe2152ab40e62b2a2b3810890c059ed9875e7240 Mon Sep 17 00:00:00 2001 From: Niklas Siemer <70580458+niklassiemer@users.noreply.github.com> Date: Tue, 24 Oct 2023 10:37:25 +0200 Subject: [PATCH 4/4] Rename _data to data --- pyiron_atomistics/atomistics/structure/periodic_table.py | 2 +- pyiron_atomistics/{_data => data}/periodic_table.csv | 0 setup.py | 2 +- 3 files changed, 2 insertions(+), 2 deletions(-) rename pyiron_atomistics/{_data => data}/periodic_table.csv (100%) diff --git a/pyiron_atomistics/atomistics/structure/periodic_table.py b/pyiron_atomistics/atomistics/structure/periodic_table.py index 84690c589..7c2529e23 100644 --- a/pyiron_atomistics/atomistics/structure/periodic_table.py +++ b/pyiron_atomistics/atomistics/structure/periodic_table.py @@ -398,7 +398,7 @@ def _get_periodic_table_df(file_name): if not file_name: return pandas.read_csv( io.BytesIO( - pkgutil.get_data("pyiron_atomistics", "_data/periodic_table.csv") + pkgutil.get_data("pyiron_atomistics", "data/periodic_table.csv") ), index_col=0, ) diff --git a/pyiron_atomistics/_data/periodic_table.csv b/pyiron_atomistics/data/periodic_table.csv similarity index 100% rename from pyiron_atomistics/_data/periodic_table.csv rename to pyiron_atomistics/data/periodic_table.csv diff --git a/setup.py b/setup.py index 9143af0e4..e730f775e 100644 --- a/setup.py +++ b/setup.py @@ -61,5 +61,5 @@ 'structuretoolkit==0.0.11' ], cmdclass=versioneer.get_cmdclass(), - package_data={'': ['_data/*.csv']}, + package_data={'': ['data/*.csv']}, )