# tests of the dlpoly I/O from ase import io as aseIO from ase.io.dlp4 import iread_dlp_history from io import StringIO import numpy as np #Test HISTORY reading with no frames count fd = StringIO(""" tes 2 3 2 timestep 1 2 2 3 0.000500 23.01 -0.3943E-01 0.4612E-01 -0.9486E-01 22.98 0.4551 0.6568 0.7694 19.21 o1 1 16.000000 -0.730000 7.9029E+00 -3.7677E+00 4.1862E+00 -6.6695E-01 1.4565E+00 -1.0286E+01 -2.9693E+04 4.8692E+04 -3.2588E+05 Ni+ 2 16.000000 -0.730000 7.7028E+00 -3.4396E+00 1.9907E+00 6.6695E-01 -1.4565E+00 1.0286E+01 2.9693E+04 -4.8692E+04 3.2588E+05 timestep 2 2 2 3 0.000500 22.90 -0.3925E-01 0.4591E-01 -0.9443E-01 22.88 0.4531 0.6538 0.7660 19.12 o1 1 16.000000 -0.730000 7.9019E+00 -3.7659E+00 4.1735E+00 -1.5895E+00 2.9698E+00 -2.0415E+01 -2.9065E+04 4.7608E+04 -3.1855E+05 Ni+ 2 16.000000 -0.730000 7.7038E+00 -3.4414E+00 2.0034E+00 1.5895E+00 -2.9698E+00 2.0415E+01 2.9065E+04 -4.7608E+04 3.1855E+05 timestep 3 2 2 3 0.000500 22.73 -0.3896E-01 0.4557E-01 -0.9374E-01 22.71 0.4497 0.6490 0.7603 18.98 o1 1 16.000000 -0.730000 7.9001E+00 -3.7628E+00 4.1528E+00 -2.4898E+00 4.4453E+00 -3.0289E+01 -2.8009E+04 4.5827E+04 -3.0655E+05 Ni+ 2 16.000000 -0.730000 7.7056E+00 -3.4445E+00 2.0241E+00 2.4898E+00 -4.4453E+00 3.0289E+01 2.8009E+04 -4.5827E+04 3.0655E+05 """) def test_dlp(): cells = [] cells.append(np.array([[23.01, -0.3943E-01, 0.4612E-01], [-0.9486E-01, 22.98, 0.4551], [0.6568, 0.7694, 19.21]])) cells.append(np.array([[22.90, -0.3925E-01, 0.4591E-01], [-0.9443E-01, 22.88, 0.4531], [0.6538, 0.7660, 19.12]])) cells.append(np.array([[22.73, -0.3896E-01, 0.4557E-01], [-0.9374E-01, 22.71, 0.4497], [0.6490, 0.7603, 18.98]])) traj = aseIO.read(fd, format='dlp-history', index=slice(0,None)) assert len(traj) == 3 traj = aseIO.iread(fd, format='dlp-history', index=slice(0,None)) for i, frame in enumerate(traj): assert len(frame) == 2 assert all(frame.symbols == 'ONi') assert np.isclose(frame.get_cell(),cells[i]).all() symbols = frame.get_chemical_symbols() traj = iread_dlp_history(fd, symbols) for i, frame in enumerate(traj): assert len(frame) == 2 assert all(frame.symbols == 'ONi') assert np.isclose(frame.get_cell(),cells[i]).all() #Test HISTORY reading with frames count fd3 = StringIO("""CONFIG generated by ASE 1 3 4 3 50 timestep 20 4 1 3 0.000001 0.000020 23.9999973028 0.0000000000 0.0000000000 0.0000000000 23.9999973028 0.0000000000 0.0000000000 0.0000000000 23.9999973028 O 1 15.999000 0.000000 0.000006 8.959496879 -1.661839486 1.126248332 0.2667319780E-01 -0.2231196511 1.080148616 H 2 1.007840 0.524220 0.000090 8.032217062 -1.727260411 0.8982923098 -8.811024033 0.1970595032 -26.41823023 H 3 1.007840 0.524220 0.000122 9.342483347 -1.135343745 0.4245589951 2.878496975 4.344743208 0.1239887959 X 4 0.000000 -1.048440 0.000306 8.890036278 -1.602994794 1.007366857 55.52293578 -10.07719146 92.19090576 timestep 25 4 1 3 0.000001 0.000025 23.9999947494 0.0000000000 0.0000000000 0.0000000000 23.9999947494 0.0000000000 0.0000000000 0.0000000000 23.9999947494 O 1 15.999000 0.000000 0.000009 8.959496057 -1.661840415 1.126253614 0.2654602737E-01 -0.2183166171 1.081886602 H 2 1.007840 0.524220 0.000118 8.032173027 -1.727259262 0.8981602672 -8.411427448 0.2001414576 -26.32335141 H 3 1.007840 0.524220 0.000109 9.342496294 -1.135322518 0.4245603266 2.696729507 4.061912168 0.3982827447 X 4 0.000000 -1.048440 0.000783 8.890307677 -1.603039909 1.007817534 53.34791281 -8.026205690 88.19217461 timestep 30 4 1 3 0.000001 0.000030 23.9999911871 0.0000000000 0.0000000000 0.0000000000 23.9999911871 0.0000000000 0.0000000000 0.0000000000 23.9999911871 O 1 15.999000 0.000000 0.000014 8.959494848 -1.661841259 1.126258859 0.2405131707E-01 -0.2181324108 1.081956510 H 2 1.007840 0.524220 0.000241 8.032130776 -1.727257880 0.8980287209 -7.954693535 0.2745105780 -26.22606481 H 3 1.007840 0.524220 0.000100 9.342508077 -1.135302770 0.4245629245 2.523105947 3.799828794 0.6859162402 X 4 0.000000 -1.048440 0.001277 8.890566873 -1.603074821 1.008248758 50.89374213 -6.163817531 84.30161133 """) def test_dlp3(): cells = [] cells.append(np.array([[23.9999973028, 0.0, 0.0], [0.0, 23.9999973028, 0.0], [0.0, 0.0, 23.9999973028]])) cells.append(np.array([[23.9999947494, 0.0, 0.0], [0.0, 23.9999947494, 0.0], [0.0, 0.0, 23.9999947494]])) cells.append(np.array([[23.9999911871, 0.0, 0.0], [0.0, 23.9999911871, 0.0], [0.0, 0.0, 23.9999911871]])) traj = aseIO.read(fd3, format='dlp-history', index=slice(0,None)) assert len(traj) == 3 traj = aseIO.iread(fd3, format='dlp-history', index=slice(0,None)) for i, frame in enumerate(traj): assert len(frame) == 4 assert all(frame.symbols == 'OHHX') assert np.isclose(frame.get_cell(),cells[i]).all() symbols = frame.get_chemical_symbols() traj = iread_dlp_history(fd3, symbols) for i, frame in enumerate(traj): assert len(frame) == 4 assert all(frame.symbols == 'OHHX') assert np.isclose(frame.get_cell(),cells[i]).all() assert frame.has('initial_charges') #Test REVCON reading fd2 = StringIO(""" ch3cl 2 0 5 103.350212873 c1 1 0.1843387826E-03 0.9416060951E-04 1.246412527 -0.458762453613E-03 0.115950998393E-02 0.398056206380E-02 -0.474964352912E-01 0.182081702320 0.229243689875 cl 2 -0.2059439421E-03 0.1412072888E-04 -0.5580793078 -0.940840256180E-04 0.395951857541E-04 -0.239995080203E-02 -0.111106651883 0.751717008835E-01 -1.80980665091 hc 3 -0.5196456534 -0.9003296761 1.595983262 -0.172904226091E-03 -0.532458921776E-03 0.870577192032E-03 -0.946235115819E-01 -0.277617843971 0.570439906153 hc 4 1.040017099 0.7706891154E-04 1.595602116 0.842082010780E-03 -0.190324565710E-03 0.148901125710E-02 0.309680778021 -0.636899601725E-01 0.690354198940 h1 5 -0.5195887524 0.9005809880 1.595908521 -0.630491688097E-03 0.709696007109E-03 0.401075989715E-02 -0.564541792647E-01 0.840544009392E-01 0.319768855941 """) def test_dlp2(): mol = aseIO.read(fd2, format='dlp4', symbols=['C', 'Cl', 'H', 'H', 'H']) assert (mol.get_array('dlp4_labels') == np.array(['1', '', '', '', '1'])).all()