"""Check that reading and writing .con files is consistent.""" from numpy import array import ase import ase.io # Error tolerance. TOL = 1e-6 # A correct .con file. CON_FILE = """\ 10000 RANDOM NUMBER SEED 0.0000 TIME 7.2200000000 10.8760700623 14.5090868079 84.7244899634 86.0479084995 85.7006486298 0 0 0 0 0 1 96 1.0 Cu Coordinates of Component 1 1.04833333333334 0.96500000000003 0.90250000000000 0 1 3.02000000000000 2.77000000000000 0.90250000000000 0 2 2.97833333333334 1.09000000000003 2.70750000000000 0 3 1.34000000000000 2.89500000000000 2.70750000000000 0 4 4.65833333333334 0.96500000000003 0.90250000000000 0 5 6.63000000000000 2.77000000000000 0.90250000000000 0 6 6.58833333333334 1.09000000000003 2.70750000000000 0 7 4.95000000000000 2.89500000000000 2.70750000000000 0 8 1.38166666666666 4.57499999999997 0.90250000000000 0 9 3.35333333333334 6.38000000000003 0.90250000000000 0 10 3.31166666666666 4.69999999999997 2.70750000000000 0 11 1.67333333333334 6.50500000000003 2.70750000000000 0 12 4.99166666666666 4.57499999999997 0.90250000000000 0 13 6.96333333333334 6.38000000000003 0.90250000000000 0 14 6.92166666666666 4.69999999999997 2.70750000000000 0 15 5.28333333333334 6.50500000000003 2.70750000000000 0 16 1.71500000000000 8.18500000000000 0.90250000000000 0 17 3.68666666666666 9.98999999999997 0.90250000000000 0 18 3.64500000000000 8.31000000000000 2.70750000000000 0 19 2.00666666666666 10.11499999999997 2.70750000000000 0 20 5.32500000000000 8.18500000000000 0.90250000000000 0 21 7.29666666666666 9.98999999999997 0.90250000000000 0 22 7.25500000000000 8.31000000000000 2.70750000000000 0 23 5.61666666666666 10.11499999999997 2.70750000000000 0 24 1.29833333333334 1.21500000000003 4.51250000000000 0 25 3.27000000000000 3.02000000000000 4.51250000000000 0 26 3.22833333333334 1.34000000000003 6.31750000000000 0 27 1.59000000000000 3.14500000000000 6.31750000000000 0 28 4.90833333333334 1.21500000000003 4.51250000000000 0 29 6.88000000000000 3.02000000000000 4.51250000000000 0 30 6.83833333333334 1.34000000000003 6.31750000000000 0 31 5.20000000000000 3.14500000000000 6.31750000000000 0 32 1.63166666666666 4.82499999999997 4.51250000000000 0 33 3.60333333333334 6.63000000000003 4.51250000000000 0 34 3.56166666666666 4.94999999999997 6.31750000000000 0 35 1.92333333333334 6.75500000000003 6.31750000000000 0 36 5.24166666666666 4.82499999999997 4.51250000000000 0 37 7.21333333333334 6.63000000000003 4.51250000000000 0 38 7.17166666666666 4.94999999999997 6.31750000000000 0 39 5.53333333333334 6.75500000000003 6.31750000000000 0 40 1.96500000000000 8.43500000000000 4.51250000000000 0 41 3.93666666666666 10.23999999999997 4.51250000000000 0 42 3.89500000000000 8.56000000000000 6.31750000000000 0 43 2.25666666666666 10.36499999999997 6.31750000000000 0 44 5.57500000000000 8.43500000000000 4.51250000000000 0 45 7.54666666666666 10.23999999999997 4.51250000000000 0 46 7.50500000000000 8.56000000000000 6.31750000000000 0 47 5.86666666666666 10.36499999999997 6.31750000000000 0 48 1.54833333333334 1.46500000000003 8.12250000000000 0 49 3.52000000000000 3.27000000000000 8.12250000000000 0 50 3.47833333333334 1.59000000000003 9.92750000000000 0 51 1.84000000000000 3.39500000000000 9.92750000000000 0 52 5.15833333333334 1.46500000000003 8.12250000000000 0 53 7.13000000000000 3.27000000000000 8.12250000000000 0 54 7.08833333333334 1.59000000000003 9.92750000000000 0 55 5.45000000000000 3.39500000000000 9.92750000000000 0 56 1.88166666666666 5.07499999999997 8.12250000000000 0 57 3.85333333333334 6.88000000000003 8.12250000000000 0 58 3.81166666666666 5.19999999999997 9.92750000000000 0 59 2.17333333333334 7.00500000000003 9.92750000000000 0 60 5.49166666666666 5.07499999999997 8.12250000000000 0 61 7.46333333333334 6.88000000000003 8.12250000000000 0 62 7.42166666666666 5.19999999999997 9.92750000000000 0 63 5.78333333333334 7.00500000000003 9.92750000000000 0 64 2.21500000000000 8.68500000000000 8.12250000000000 0 65 4.18666666666666 10.48999999999997 8.12250000000000 0 66 4.14500000000000 8.81000000000000 9.92750000000000 0 67 2.50666666666666 10.61499999999997 9.92750000000000 0 68 5.82500000000000 8.68500000000000 8.12250000000000 0 69 7.79666666666666 10.48999999999997 8.12250000000000 0 70 7.75500000000000 8.81000000000000 9.92750000000000 0 71 6.11666666666666 10.61499999999997 9.92750000000000 0 72 1.79833333333334 1.71500000000003 11.73250000000000 0 73 3.77000000000000 3.52000000000000 11.73250000000000 0 74 3.72833333333334 1.84000000000003 13.53750000000000 0 75 2.09000000000000 3.64500000000000 13.53750000000000 0 76 5.40833333333334 1.71500000000003 11.73250000000000 0 77 7.38000000000000 3.52000000000000 11.73250000000000 0 78 7.33833333333334 1.84000000000003 13.53750000000000 0 79 5.70000000000000 3.64500000000000 13.53750000000000 0 80 2.13166666666666 5.32499999999997 11.73250000000000 0 81 4.10333333333334 7.13000000000003 11.73250000000000 0 82 4.06166666666666 5.44999999999997 13.53750000000000 0 83 2.42333333333334 7.25500000000003 13.53750000000000 0 84 5.74166666666666 5.32499999999997 11.73250000000000 0 85 7.71333333333334 7.13000000000003 11.73250000000000 0 86 7.67166666666666 5.44999999999997 13.53750000000000 0 87 6.03333333333334 7.25500000000003 13.53750000000000 0 88 2.46500000000000 8.93500000000000 11.73250000000000 0 89 4.43666666666666 10.73999999999997 11.73250000000000 0 90 4.39500000000000 9.06000000000000 13.53750000000000 0 91 2.75666666666666 10.86499999999997 13.53750000000000 0 92 6.07500000000000 8.93500000000000 11.73250000000000 0 93 8.04666666666666 10.73999999999997 11.73250000000000 0 94 8.00500000000000 9.06000000000000 13.53750000000000 0 95 6.36666666666666 10.86499999999997 13.53750000000000 0 96 """ # The corresponding data as an ASE Atoms object. data = ase.Atoms('Cu96', cell=array([[7.22, 0, 0], [1, 10.83, 0], [1, 1, 14.44]]), positions=array([[1.04833333, 0.965, 0.9025], [3.02, 2.77, 0.9025], [2.97833333, 1.09, 2.7075], [1.34, 2.895, 2.7075], [4.65833333, 0.965, 0.9025], [6.63, 2.77, 0.9025], [6.58833333, 1.09, 2.7075], [4.95, 2.895, 2.7075], [1.38166667, 4.575, 0.9025], [3.35333333, 6.38, 0.9025], [3.31166667, 4.7, 2.7075], [1.67333333, 6.505, 2.7075], [4.99166667, 4.575, 0.9025], [6.96333333, 6.38, 0.9025], [6.92166667, 4.7, 2.7075], [5.28333333, 6.505, 2.7075], [1.715, 8.185, 0.9025], [3.68666667, 9.99, 0.9025], [3.645, 8.31, 2.7075], [2.00666667, 10.115, 2.7075], [5.325, 8.185, 0.9025], [7.29666667, 9.99, 0.9025], [7.255, 8.31, 2.7075], [5.61666667, 10.115, 2.7075], [1.29833333, 1.215, 4.5125], [3.27, 3.02, 4.5125], [3.22833333, 1.34, 6.3175], [1.59, 3.145, 6.3175], [4.90833333, 1.215, 4.5125], [6.88, 3.02, 4.5125], [6.83833333, 1.34, 6.3175], [5.2, 3.145, 6.3175], [1.63166667, 4.825, 4.5125], [3.60333333, 6.63, 4.5125], [3.56166667, 4.95, 6.3175], [1.92333333, 6.755, 6.3175], [5.24166667, 4.825, 4.5125], [7.21333333, 6.63, 4.5125], [7.17166667, 4.95, 6.3175], [5.53333333, 6.755, 6.3175], [1.965, 8.435, 4.5125], [3.93666667, 10.24, 4.5125], [3.895, 8.56, 6.3175], [2.25666667, 10.365, 6.3175], [5.575, 8.435, 4.5125], [7.54666667, 10.24, 4.5125], [7.505, 8.56, 6.3175], [5.86666667, 10.365, 6.3175], [1.54833333, 1.465, 8.1225], [3.52, 3.27, 8.1225], [3.47833333, 1.59, 9.9275], [1.84, 3.395, 9.9275], [5.15833333, 1.465, 8.1225], [7.13, 3.27, 8.1225], [7.08833333, 1.59, 9.9275], [5.45, 3.395, 9.9275], [1.88166667, 5.075, 8.1225], [3.85333333, 6.88, 8.1225], [3.81166667, 5.2, 9.9275], [2.17333333, 7.005, 9.9275], [5.49166667, 5.075, 8.1225], [7.46333333, 6.88, 8.1225], [7.42166667, 5.2, 9.9275], [5.78333333, 7.005, 9.9275], [2.215, 8.685, 8.1225], [4.18666667, 10.49, 8.1225], [4.145, 8.81, 9.9275], [2.50666667, 10.615, 9.9275], [5.825, 8.685, 8.1225], [7.79666667, 10.49, 8.1225], [7.755, 8.81, 9.9275], [6.11666667, 10.615, 9.9275], [1.79833333, 1.715, 11.7325], [3.77, 3.52, 11.7325], [3.72833333, 1.84, 13.5375], [2.09, 3.645, 13.5375], [5.40833333, 1.715, 11.7325], [7.38, 3.52, 11.7325], [7.33833333, 1.84, 13.5375], [5.7, 3.645, 13.5375], [2.13166667, 5.325, 11.7325], [4.10333333, 7.13, 11.7325], [4.06166667, 5.45, 13.5375], [2.42333333, 7.255, 13.5375], [5.74166667, 5.325, 11.7325], [7.71333333, 7.13, 11.7325], [7.67166667, 5.45, 13.5375], [6.03333333, 7.255, 13.5375], [2.465, 8.935, 11.7325], [4.43666667, 10.74, 11.7325], [4.395, 9.06, 13.5375], [2.75666667, 10.865, 13.5375], [6.075, 8.935, 11.7325], [8.04666667, 10.74, 11.7325], [8.005, 9.06, 13.5375], [6.36666667, 10.865, 13.5375]]), pbc=(True, True, True)) def test_eon_readwrite(): # First, write a correct .con file and try to read it. con_file = 'pos.con' with open(con_file, 'w') as f: f.write(CON_FILE) box = ase.io.read(con_file, format='eon') # 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