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# 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()
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