# flake8: noqa """Check that reading multi image .con files is consistent.""" import os from numpy import array import ase import ase.io # Error tolerance. TOL = 1e-6 # A correct .con file. CON_FILE = """\ 0 Random Number Seed 0 Time 8.123222 5.744000 9.747867 90.000000 90.000000 90.000000 0 0 0 0 0 1 17 51.996100 Cr Coordinates of Component 1 1.01540277999999962 0.71799999999999997 1.01540277999999984 1 0 3.04620834000000063 2.15399999999999991 1.01540277999999984 1 1 3.04620834000000063 0.71799999999999997 3.04620834000000196 1 2 1.01540277999999962 2.15399999999999991 3.04620834000000196 1 3 1.01540277999999962 3.58999999999999986 1.01540277999999984 1 4 3.04620834000000063 5.02599999999999980 1.01540277999999984 1 5 3.04620834000000063 3.58999999999999986 3.04620834000000196 1 6 1.01540277999999962 5.02599999999999980 3.04620834000000196 1 7 5.07701389999999986 0.71799999999999997 1.01540277999999984 1 8 7.10781945999998488 2.15399999999999991 1.01540277999999984 1 9 7.10781945999998488 0.71799999999999997 3.04620834000000196 1 10 5.07701389999999986 2.15399999999999991 3.04620834000000196 1 11 5.07701389999999986 3.58999999999999986 1.01540277999999984 1 12 7.10781945999998488 5.02599999999999980 1.01540277999999984 1 13 7.10781945999998488 3.58999999999999986 3.04620834000000196 1 14 5.07701389999999986 5.02599999999999980 3.04620834000000196 1 15 3.04618285858587523 2.15398224021542450 4.60622193000079427 0 16 0 Random Number Seed 0 Time 8.123222 5.744000 9.747867 90.000000 90.000000 90.000000 0 0 0 0 0 1 17 51.996100 Cr Coordinates of Component 1 1.01540277999999962 0.71799999999999997 1.01540277999999984 1 0 3.04620834000000063 2.15399999999999991 1.01540277999999984 1 1 3.04620834000000063 0.71799999999999997 3.04620834000000196 1 2 1.01540277999999962 2.15399999999999991 3.04620834000000196 1 3 1.01540277999999962 3.58999999999999986 1.01540277999999984 1 4 3.04620834000000063 5.02599999999999980 1.01540277999999984 1 5 3.04620834000000063 3.58999999999999986 3.04620834000000196 1 6 1.01540277999999962 5.02599999999999980 3.04620834000000196 1 7 5.07701389999999986 0.71799999999999997 1.01540277999999984 1 8 7.10781945999998488 2.15399999999999991 1.01540277999999984 1 9 7.10781945999998488 0.71799999999999997 3.04620834000000196 1 10 5.07701389999999986 2.15399999999999991 3.04620834000000196 1 11 5.07701389999999986 3.58999999999999986 1.01540277999999984 1 12 7.10781945999998488 5.02599999999999980 1.01540277999999984 1 13 7.10781945999998488 3.58999999999999986 3.04620834000000196 1 14 5.07701389999999986 5.02599999999999980 3.04620834000000196 1 15 3.36369427985916092 2.20887986058760699 4.61557342394151693 0 16 0 Random Number Seed 0 Time 8.123222 5.744000 9.747867 90.000000 90.000000 90.000000 0 0 0 0 0 1 17 51.996100 Cr Coordinates of Component 1 1.01540277999999962 0.71799999999999997 1.01540277999999984 1 0 3.04620834000000063 2.15399999999999991 1.01540277999999984 1 1 3.04620834000000063 0.71799999999999997 3.04620834000000196 1 2 1.01540277999999962 2.15399999999999991 3.04620834000000196 1 3 1.01540277999999962 3.58999999999999986 1.01540277999999984 1 4 3.04620834000000063 5.02599999999999980 1.01540277999999984 1 5 3.04620834000000063 3.58999999999999986 3.04620834000000196 1 6 1.01540277999999962 5.02599999999999980 3.04620834000000196 1 7 5.07701389999999986 0.71799999999999997 1.01540277999999984 1 8 7.10781945999998488 2.15399999999999991 1.01540277999999984 1 9 7.10781945999998488 0.71799999999999997 3.04620834000000196 1 10 5.07701389999999986 2.15399999999999991 3.04620834000000196 1 11 5.07701389999999986 3.58999999999999986 1.01540277999999984 1 12 7.10781945999998488 5.02599999999999980 1.01540277999999984 1 13 7.10781945999998488 3.58999999999999986 3.04620834000000196 1 14 5.07701389999999986 5.02599999999999980 3.04620834000000196 1 15 3.62116697589668135 2.40183843231018113 4.63674682635805180 0 16 0 Random Number Seed 0 Time 8.123222 5.744000 9.747867 90.000000 90.000000 90.000000 0 0 0 0 0 1 17 51.996100 Cr Coordinates of Component 1 1.01540277999999962 0.71799999999999997 1.01540277999999984 1 0 3.04620834000000063 2.15399999999999991 1.01540277999999984 1 1 3.04620834000000063 0.71799999999999997 3.04620834000000196 1 2 1.01540277999999962 2.15399999999999991 3.04620834000000196 1 3 1.01540277999999962 3.58999999999999986 1.01540277999999984 1 4 3.04620834000000063 5.02599999999999980 1.01540277999999984 1 5 3.04620834000000063 3.58999999999999986 3.04620834000000196 1 6 1.01540277999999962 5.02599999999999980 3.04620834000000196 1 7 5.07701389999999986 0.71799999999999997 1.01540277999999984 1 8 7.10781945999998488 2.15399999999999991 1.01540277999999984 1 9 7.10781945999998488 0.71799999999999997 3.04620834000000196 1 10 5.07701389999999986 2.15399999999999991 3.04620834000000196 1 11 5.07701389999999986 3.58999999999999986 1.01540277999999984 1 12 7.10781945999998488 5.02599999999999980 1.01540277999999984 1 13 7.10781945999998488 3.58999999999999986 3.04620834000000196 1 14 5.07701389999999986 5.02599999999999980 3.04620834000000196 1 15 3.83933949582109157 2.63825709178043821 4.65669727965894875 0 16 0 Random Number Seed 0 Time 8.123222 5.744000 9.747867 90.000000 90.000000 90.000000 0 0 0 0 0 1 17 51.996100 Cr Coordinates of Component 1 1.01540277999999962 0.71799999999999997 1.01540277999999984 1 0 3.04620834000000063 2.15399999999999991 1.01540277999999984 1 1 3.04620834000000063 0.71799999999999997 3.04620834000000196 1 2 1.01540277999999962 2.15399999999999991 3.04620834000000196 1 3 1.01540277999999962 3.58999999999999986 1.01540277999999984 1 4 3.04620834000000063 5.02599999999999980 1.01540277999999984 1 5 3.04620834000000063 3.58999999999999986 3.04620834000000196 1 6 1.01540277999999962 5.02599999999999980 3.04620834000000196 1 7 5.07701389999999986 0.71799999999999997 1.01540277999999984 1 8 7.10781945999998488 2.15399999999999991 1.01540277999999984 1 9 7.10781945999998488 0.71799999999999997 3.04620834000000196 1 10 5.07701389999999986 2.15399999999999991 3.04620834000000196 1 11 5.07701389999999986 3.58999999999999986 1.01540277999999984 1 12 7.10781945999998488 5.02599999999999980 1.01540277999999984 1 13 7.10781945999998488 3.58999999999999986 3.04620834000000196 1 14 5.07701389999999986 5.02599999999999980 3.04620834000000196 1 15 4.06162234392075128 2.87141228075409316 4.66819033729618926 0 16 0 Random Number Seed 0 Time 8.123222 5.744000 9.747867 90.000000 90.000000 90.000000 0 0 0 0 0 1 17 51.996100 Cr Coordinates of Component 1 1.01540277999999962 0.71799999999999997 1.01540277999999984 1 0 3.04620834000000063 2.15399999999999991 1.01540277999999984 1 1 3.04620834000000063 0.71799999999999997 3.04620834000000196 1 2 1.01540277999999962 2.15399999999999991 3.04620834000000196 1 3 1.01540277999999962 3.58999999999999986 1.01540277999999984 1 4 3.04620834000000063 5.02599999999999980 1.01540277999999984 1 5 3.04620834000000063 3.58999999999999986 3.04620834000000196 1 6 1.01540277999999962 5.02599999999999980 3.04620834000000196 1 7 5.07701389999999986 0.71799999999999997 1.01540277999999984 1 8 7.10781945999998488 2.15399999999999991 1.01540277999999984 1 9 7.10781945999998488 0.71799999999999997 3.04620834000000196 1 10 5.07701389999999986 2.15399999999999991 3.04620834000000196 1 11 5.07701389999999986 3.58999999999999986 1.01540277999999984 1 12 7.10781945999998488 5.02599999999999980 1.01540277999999984 1 13 7.10781945999998488 3.58999999999999986 3.04620834000000196 1 14 5.07701389999999986 5.02599999999999980 3.04620834000000196 1 15 4.28380999862949441 3.10482201783771883 4.65660558580467221 0 16 0 Random Number Seed 0 Time 8.123222 5.744000 9.747867 90.000000 90.000000 90.000000 0 0 0 0 0 1 17 51.996100 Cr Coordinates of Component 1 1.01540277999999962 0.71799999999999997 1.01540277999999984 1 0 3.04620834000000063 2.15399999999999991 1.01540277999999984 1 1 3.04620834000000063 0.71799999999999997 3.04620834000000196 1 2 1.01540277999999962 2.15399999999999991 3.04620834000000196 1 3 1.01540277999999962 3.58999999999999986 1.01540277999999984 1 4 3.04620834000000063 5.02599999999999980 1.01540277999999984 1 5 3.04620834000000063 3.58999999999999986 3.04620834000000196 1 6 1.01540277999999962 5.02599999999999980 3.04620834000000196 1 7 5.07701389999999986 0.71799999999999997 1.01540277999999984 1 8 7.10781945999998488 2.15399999999999991 1.01540277999999984 1 9 7.10781945999998488 0.71799999999999997 3.04620834000000196 1 10 5.07701389999999986 2.15399999999999991 3.04620834000000196 1 11 5.07701389999999986 3.58999999999999986 1.01540277999999984 1 12 7.10781945999998488 5.02599999999999980 1.01540277999999984 1 13 7.10781945999998488 3.58999999999999986 3.04620834000000196 1 14 5.07701389999999986 5.02599999999999980 3.04620834000000196 1 15 4.50188452903429326 3.34154720502221236 4.63664894132718874 0 16 0 Random Number Seed 0 Time 8.123222 5.744000 9.747867 90.000000 90.000000 90.000000 0 0 0 0 0 1 17 51.996100 Cr Coordinates of Component 1 1.01540277999999962 0.71799999999999997 1.01540277999999984 1 0 3.04620834000000063 2.15399999999999991 1.01540277999999984 1 1 3.04620834000000063 0.71799999999999997 3.04620834000000196 1 2 1.01540277999999962 2.15399999999999991 3.04620834000000196 1 3 1.01540277999999962 3.58999999999999986 1.01540277999999984 1 4 3.04620834000000063 5.02599999999999980 1.01540277999999984 1 5 3.04620834000000063 3.58999999999999986 3.04620834000000196 1 6 1.01540277999999962 5.02599999999999980 3.04620834000000196 1 7 5.07701389999999986 0.71799999999999997 1.01540277999999984 1 8 7.10781945999998488 2.15399999999999991 1.01540277999999984 1 9 7.10781945999998488 0.71799999999999997 3.04620834000000196 1 10 5.07701389999999986 2.15399999999999991 3.04620834000000196 1 11 5.07701389999999986 3.58999999999999986 1.01540277999999984 1 12 7.10781945999998488 5.02599999999999980 1.01540277999999984 1 13 7.10781945999998488 3.58999999999999986 3.04620834000000196 1 14 5.07701389999999986 5.02599999999999980 3.04620834000000196 1 15 4.75928919917819293 3.53496190773495211 4.61566200013953409 0 16 0 Random Number Seed 0 Time 8.123222 5.744000 9.747867 90.000000 90.000000 90.000000 0 0 0 0 0 1 17 51.996100 Cr Coordinates of Component 1 1.01540277999999962 0.71799999999999997 1.01540277999999984 1 0 3.04620834000000063 2.15399999999999991 1.01540277999999984 1 1 3.04620834000000063 0.71799999999999997 3.04620834000000196 1 2 1.01540277999999962 2.15399999999999991 3.04620834000000196 1 3 1.01540277999999962 3.58999999999999986 1.01540277999999984 1 4 3.04620834000000063 5.02599999999999980 1.01540277999999984 1 5 3.04620834000000063 3.58999999999999986 3.04620834000000196 1 6 1.01540277999999962 5.02599999999999980 3.04620834000000196 1 7 5.07701389999999986 0.71799999999999997 1.01540277999999984 1 8 7.10781945999998488 2.15399999999999991 1.01540277999999984 1 9 7.10781945999998488 0.71799999999999997 3.04620834000000196 1 10 5.07701389999999986 2.15399999999999991 3.04620834000000196 1 11 5.07701389999999986 3.58999999999999986 1.01540277999999984 1 12 7.10781945999998488 5.02599999999999980 1.01540277999999984 1 13 7.10781945999998488 3.58999999999999986 3.04620834000000196 1 14 5.07701389999999986 5.02599999999999980 3.04620834000000196 1 15 5.07701160164306042 3.58998956883621734 4.60626159988447537 0 16 """ # The corresponding data for the second to last image as an ASE Atoms object. data = ase.Atoms('Cr17',cell = array([[8.123222, 0, 0], [0, 5.744000, 0], [0, 0, 9.747867]]), positions = array([ [1.01540277999999962, 0.71799999999999997, 1.01540277999999984], [3.04620834000000063, 2.15399999999999991, 1.01540277999999984], [3.04620834000000063, 0.71799999999999997, 3.04620834000000196], [1.01540277999999962, 2.15399999999999991, 3.04620834000000196], [1.01540277999999962, 3.58999999999999986, 1.01540277999999984], [3.04620834000000063, 5.02599999999999980, 1.01540277999999984], [3.04620834000000063, 3.58999999999999986, 3.04620834000000196], [1.01540277999999962, 5.02599999999999980, 3.04620834000000196], [5.07701389999999986, 0.71799999999999997, 1.01540277999999984], [7.10781945999998488, 2.15399999999999991, 1.01540277999999984], [7.10781945999998488, 0.71799999999999997, 3.04620834000000196], [5.07701389999999986, 2.15399999999999991, 3.04620834000000196], [5.07701389999999986, 3.58999999999999986, 1.01540277999999984], [7.10781945999998488, 5.02599999999999980, 1.01540277999999984], [7.10781945999998488, 3.58999999999999986, 3.04620834000000196], [5.07701389999999986, 5.02599999999999980, 3.04620834000000196], [4.75928919917819293, 3.53496190773495211, 4.61566200013953409]]), pbc=(True, True, True)) def test_eon(): # First, write a correct .con file and try to read it. con_file = 'neb.con' with open(con_file, 'w') as f: f.write(CON_FILE) images = ase.io.read(con_file, format='eon', index =':') box = images[-2] # Check cell vectors. assert (abs(box.cell - data.cell)).sum() < TOL # read: cell vector check # Check atom positions. # read: position check assert (abs(box.positions - data.positions)).sum() < TOL # Now that we know that reading a .con file works, we will write # one and read it back in. out_file = 'out.con' ase.io.write(out_file, data, format='eon') data2 = ase.io.read(out_file, format='eon') # Check cell vectors. # write: cell vector check assert (abs(data2.cell - data.cell)).sum() < TOL # Check atom positions. # write: position check assert (abs(data2.positions - data.positions)).sum() < TOL