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from ase.build import fcc100, add_adsorbate
from ase.constraints import FixAtoms, FixedPlane
from ase.calculators.emt import EMT
from ase.optimize import QuasiNewton
import re
import pytest
from ase.cli.template import prec_round, slice_split, \
MapFormatter, sym2num, \
Table, TableFormat
from ase.io import read
@pytest.fixture(scope="module")
def traj(tmp_path_factory):
slab = fcc100('Al', size=(2, 2, 3))
add_adsorbate(slab, 'Au', 1.7, 'hollow')
slab.center(axis=2, vacuum=4.0)
mask = [atom.tag > 1 for atom in slab]
fixlayers = FixAtoms(mask=mask)
plane = FixedPlane(-1, (1, 0, 0))
slab.set_constraint([fixlayers, plane])
slab.calc = EMT()
temp_path = tmp_path_factory.mktemp("data")
trajectory = temp_path / 'AlAu.traj'
with QuasiNewton(slab, trajectory=str(trajectory)) as qn:
qn.run(fmax=0.02)
return str(trajectory)
def test_singleFile_falseCalc_multipleImages(cli, traj):
stdout = cli.ase('diff', '--as-csv', traj)
r = c = -1
for rowcount, row in enumerate(stdout.split('\n')):
for colcount, col in enumerate(row.split(',')):
if col == 'Δx':
r = rowcount + 2
c = colcount
if (rowcount == r) & (colcount == c):
val = col
break
assert float(val) == 0.
def test_singleFile_trueCalc_multipleImages(cli, traj):
cli.ase('diff', traj, '-c')
def test_twoFiles_falseCalc_singleImage(cli, traj):
cli.ase('diff', f'{traj}@:1', f'{traj}@1:2')
def test_twoFiles_trueCalc_singleImage(cli, traj):
cli.ase('diff', f'{traj}@:1', f'{traj}@1:2', '-c')
def test_twoFiles_falseCalc_multipleImages(cli, traj):
cli.ase('diff', f'{traj}@:2', f'{traj}@2:4')
def test_twoFiles_trueCalc_multipleImages(cli, traj):
stdout = cli.ase('diff', f'{traj}@:2', f'{traj}@2:4', '-c',
'--rank-order', 'dfx', '--as-csv')
stdout = [row.split(',') for row in stdout.split('\n')]
stdout = [row for row in stdout if len(row) > 4]
header = stdout[0]
body = stdout[1:len(stdout) // 2 - 1] # note tables are appended in stdout
for c in range(len(header)):
if header[c] == 'Δfx':
break
dfx_ordered = [float(row[c]) for row in body]
for i in range(len(dfx_ordered) - 2):
assert dfx_ordered[i] <= dfx_ordered[i+1]
def test_cli_opt(cli, traj):
# template command line options
stdout = cli.ase('diff', f'{traj}@:1', f'{traj}@:2', '-c',
'--template', 'p1x,p2x,dx,f1x,f2x,dfx')
stdout = stdout.split('\n')
for counter, row in enumerate(stdout):
if '=' in row: # default toprule
header = stdout[counter + 1]
break
header = re.sub(r'\s+', ',', header).split(',')[1:-1]
assert header == ['p1x', 'p2x', 'Δx', 'f1x', 'f2x', 'Δfx']
cli.ase('diff', traj, '-c', '--template',
'p1x,f1x,p1y,f1y:0:-1,p1z,f1z,p1,f1',
'--max-lines', '6', '--summary-functions', 'rmsd')
def test_template_functions():
"""Test functions used in the template module."""
num = 1.55749
rnum = [prec_round(num, i) for i in range(1, 6)]
assert rnum == [1.6, 1.56, 1.557, 1.5575, 1.55749]
assert slice_split('a@1:3:1') == ('a', slice(1, 3, 1))
sym = 'H'
num = sym2num[sym]
mf = MapFormatter().format
sym2 = mf('{:h}', num)
assert sym == sym2
def test_template_classes(traj):
prec = 4
tableformat = TableFormat(precision=prec, representation='f', midrule='|')
table = Table(field_specs=('dx', 'dy', 'dz'), tableformat=tableformat)
images = read(traj, ':')
table_out = table.make(images[0], images[1]).split('\n')
for counter, row in enumerate(table_out):
if '|' in row:
break
row = table_out[counter + 2]
assert 'E' not in table_out[counter + 2]
row = re.sub(r'\s+', ',', table_out[counter + 2]).split(',')[1:-1]
assert len(row[0]) >= prec
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