def test_abinit_cmdline():
from ase.test import cli
cli(
"""
ase build -x fcc -a 4.04 Al |
ase -T run abinit -p xc=PBE,kpts=3.0,ecut=340,toldfe=1e-5,chksymbreak=0""",
'abinit')
def test_elk_cmdline():
from ase.test import cli, require
# warning! parameters are not converged - only an illustration!
require('elk')
cli("""ase build -x fcc -a 4.04 Al | \
ase run elk -p \
"tasks=0,kpts=1.5,rgkmax=5.0,tforce=True,smearing=(fermi-dirac,0.05)" """)
def test_aims_cmdline():
from ase.test import cli, require
require('aims')
# warning! parameters are not converged - only an illustration!
cli("""ase build -x bcc -a 3.6 Li | \
ase run aims -s 0.3 -p \
kpts=1.5,xc=LDA,sc_accuracy_rho=5.e-2,relativistic=none,compute_analytical_stress=True,sc_accuracy_forces=5.e-1"""
)
def test_ag():
from ase import Atoms
from ase.io import write
from ase.test import cli
write('x.json', Atoms('X'))
# Make sure ASE's gui can run in terminal mode without $DISPLAY and tkinter:
cli('ase -T gui --terminal -n "id=1" x.json')
def test_cmdline():
require('nwchem')
cli("""\
ase build O O.traj &&
ase run nwchem O.traj -o nwchem_cmdline.json &&
ase build O2 O2.traj &&
ase run nwchem O2.traj -o nwchem_cmdline.json""")
c = connect('nwchem_cmdline.json')
dct = read_json('nwchem_cmdline.json')
for name in ['O2', 'O']:
d = c.get([('formula', '=', name)])
id = d.id
e1 = d.energy
e2 = c.get_atoms(id).get_potential_energy()
e3 = read('{name}.nwo'.format(name=name)).get_potential_energy()
e4 = dct[id]['energy']
assert e1 == e2 == e3 == e4
print(e1)
ae = 2 * c.get('formula=O').energy - c.get('formula=O2').energy
assert_allclose(ae, 6.599194233179787, atol=1e-4, rtol=1e-4)
def test_gaussian_cmdline():
from ase.test import cli, require
from ase.db import connect
from ase.io import read
from ase.io.jsonio import read_json
require('gaussian')
cli("""\
ase build O O.xyz && ase run gaussian O.xyz -o gaussian_cmdline.json &&
ase build O2 O2.xyz && ase run gaussian O2.xyz -o gaussian_cmdline.json""")
c = connect('gaussian_cmdline.json')
dct = read_json('gaussian_cmdline.json')
for index, name in enumerate(['O', 'O2']):
d = c.get(index + 1)
id = d.id
e1 = d.energy
e2 = c.get_atoms(id).get_potential_energy()
e3 = read(name + '.log').get_potential_energy()
e4 = dct[id]['energy']
assert e1 == e2 == e3 == e4
print(e1)
ae = 2 * c.get(1).energy - c.get(2).energy
assert abs(ae - 0.65376) < 1e-3
from ase.test import cli, require
from ase.db import connect
from ase.io.jsonio import read_json
from ase.calculators.nwchem import NWChem
require('nwchem')
cli("""\
ase build O O.traj &&
ase run nwchem O.traj -o nwchem_cmdline.json &&
ase build O2 O2.traj &&
ase run nwchem O2.traj -o nwchem_cmdline.json""")
c = connect('nwchem_cmdline.json')
dct = read_json('nwchem_cmdline.json')
for name in ['O2', 'O']:
d = c.get([('formula', '=', name)])
id = d.id
e1 = d.energy
e2 = c.get_atoms(id).get_potential_energy()
e3 = NWChem.read_atoms(name).get_potential_energy()
e4 = dct[id]['energy']
assert e1 == e2 == e3 == e4
print(e1)
ae = 2 * c.get('formula=O').energy - c.get('formula=O2').energy
assert abs(ae - 6.6053) < 1e-4
from ase.test import cli, require
require('aims')
# warning! parameters are not converged - only an illustration!
cli("""ase-build -x bcc -a 3.6 Li | \
ase-run aims -s 0.3 -p \
kpts=1.5,xc=LDA,sc_accuracy_rho=5.e-2,relativistic=none,compute_analytical_stress=True,sc_accuracy_forces=5.e-1""")
from ase.test import cli, require
from ase.db import connect
from ase.io.jsonio import read_json
from ase.calculators.nwchem import NWChem
require('nwchem')
cli("""ase build O | ase run nwchem -d nwchem_cmdline.json &&
ase build O2 | ase run nwchem -d nwchem_cmdline.json""")
c = connect('nwchem_cmdline.json')
dct = read_json('nwchem_cmdline.json')
for name in ['O2', 'O']:
d = c.get([('name', '=', name)])
id = d.id
e1 = d.energy
e2 = c.get_atoms(id).get_potential_energy()
e3 = NWChem.read_atoms(name).get_potential_energy()
e4 = dct[id]['energy']
assert e1 == e2 == e3 == e4
print(e1)
ae = 2 * c.get('name=O').energy - c.get('name=O2').energy
assert abs(ae - 6.6053) < 1e-4
from ase.test import cli, require
# warning! parameters are not converged - only an illustration!
require('elk')
cli("""ase build -x fcc -a 4.04 Al | \
ase run elk -p \
"tasks=0,kpts=1.5,rgkmax=5.0,tforce=True,smearing=(fermi-dirac,0.05)" """)
from ase.test import cli, require
from ase.db import connect
from ase.db.jsondb import read_json
from ase.calculators.nwchem import NWChem
require('nwchem')
cli("""ase-build O | ase-run nwchem -d nwchem_cmdline.json &&
ase-build O2 | ase-run nwchem -d nwchem_cmdline.json""")
c = connect('nwchem_cmdline.json')
dct = read_json('nwchem_cmdline.json')
for name in ['O2', 'O']:
d = c.get([('name', '=', name)])
id = d.id
e1 = d.energy
e2 = c.get_atoms(id).get_potential_energy()
e3 = NWChem.read_atoms(name).get_potential_energy()
e4 = dct[id]['energy']
assert e1 == e2 == e3 == e4
print(e1)
ae = 2 * c.get('name=O').energy - c.get('name=O2').energy
assert abs(ae - 6.6053) < 1e-4
from ase.test import cli, require
require('aims')
# warning! parameters are not converged - only an illustration!
cli("""ase-build -x bcc -a 3.6 Li | \
ase-run aims -s 0.3 -p \
kpts=1.5,xc=LDA,sc_accuracy_rho=5.e-2,relativistic=none,compute_analytical_stress=True,sc_accuracy_forces=5.e-1"""
)
def test_fleur_cmdline():
from ase.test import cli, require
require('fleur')
cli('ase build -x fcc -a 4.04 Al | ase run fleur -p kpts=3.0,xc=PBE')
import sys
from ase import Atoms
from ase.io import write
from ase.test import cli
write('x.json', Atoms('X'))
# Make sure ASE's gui can run in terminal mode without $DISPLAY and tkinter:
cli('ase -T gui --terminal x.json@id=1')
assert 'tkinter' not in sys.modules
assert 'Tkinter' not in sys.modules # legacy Python
def test_db(name):
def count(n, *args, **kwargs):
m = len(list(con.select(columns=['id'], *args, **kwargs)))
assert m == n, (m, n)
if name == 'postgresql':
pytest.importorskip('psycopg2')
if os.environ.get('POSTGRES_DB'): # gitlab-ci
name = 'postgresql://*****:*****@postgres:5432/testase'
else:
name = os.environ.get('ASE_TEST_POSTGRES_URL')
if name is None:
return
elif name == 'mysql':
pytest.importorskip('pymysql')
if os.environ.get('CI_PROJECT_DIR'): # gitlab-ci
name = 'mysql://*****:*****@mysql:3306/testase_mysql'
else:
name = os.environ.get('MYSQL_DB_URL')
if name is None:
return
elif name == 'mariadb':
pytest.importorskip('pymysql')
if os.environ.get('CI_PROJECT_DIR'): # gitlab-ci
name = 'mariadb://*****:*****@mariadb:3306/testase_mysql'
else:
name = os.environ.get('MYSQL_DB_URL')
if name is None:
return
con = connect(name)
if 'postgres' in name or 'mysql' in name or 'mariadb' in name:
con.delete([row.id for row in con.select()])
cli(cmd.replace('testase.json', name))
assert con.get_atoms(H=1)[0].magmom == 1
count(5)
count(3, 'hydro')
count(0, 'foo')
count(3, abc=42)
count(3, 'abc')
count(0, 'abc,foo')
count(3, 'abc,hydro')
count(0, foo='bar')
count(1, formula='H2')
count(1, formula='H2O')
count(3, 'fmax<0.1')
count(1, '0.5<mass<1.5')
count(5, 'energy')
id = con.reserve(abc=7)
assert con[id].abc == 7
for key in ['calculator', 'energy', 'abc', 'name', 'fmax']:
count(6, sort=key)
count(6, sort='-' + key)
cli('ase -T gui --terminal -n 3 {}'.format(name))
con.delete([id])
from ase.test import cli, require
require('fleur')
cli('ase build -x fcc -a 4.04 Al | ase run fleur -p kpts=3.0,xc=PBE')
from ase.test import cli, require
from ase.db import connect
require('gaussian')
cli("""\
ase-build O | ase-run gaussian -d oxygen.json &&
ase-build O2 | ase-run gaussian -d oxygen.json""")
conn = connect('oxygen.json')
e1 = conn['O'].get_potential_energy()
e2 = conn['O2'].get_potential_energy()
ae = 2 * e1 - e2
print(ae)
assert abs(ae - 5.664) < 1e-3
from ase.test import cli
from ase.db import connect
cmd = """
ase-build H | ase-run emt -d y.json &&
ase-build H2O | ase-run emt -d y.json &&
ase-build O2 | ase-run emt -d y.json &&
ase-build H2 | ase-run emt -f 0.02 -d y.json &&
ase-build O2 | ase-run emt -f 0.02 -d y.json &&
ase-build -x fcc Cu | ase-run emt -E 5 -d y.json &&
ase-db y.json natoms=1,H=1 --delete --yes &&
ase-db y.json "H>0" -k hydro"""
for name in ['y.json', 'y.db']: #, 'postgres://localhost']:
cli(cmd.replace('y.json', name))
con = connect(name)
assert len(list(con.select())) == 5
assert len(list(con.select('hydro'))) == 2
import sys
from ase import Atoms
from ase.io import write
from ase.test import cli
write('x.json', Atoms('X'))
# Make sure ASE's gui can run in terminal mode without $DISPLAY and tkinter:
cli('ase gui --terminal x.json@id=1')
assert 'tkinter' not in sys.modules
assert 'Tkinter' not in sys.modules # legacy Python
from ase.test import cli, require
from ase.db import connect
from ase.io.jsonio import read_json
from ase.calculators.gaussian import Gaussian
require('gaussian')
cli("""\
ase-build O | ase-run gaussian -d gaussian_cmdline.json &&
ase-build O2 | ase-run gaussian -d gaussian_cmdline.json""")
c = connect('gaussian_cmdline.json')
dct = read_json('gaussian_cmdline.json')
for name in ['O2', 'O']:
d = c.get([('name', '=', name)])
id = d.id
e1 = d.energy
e2 = c.get_atoms(id).get_potential_energy()
e3 = Gaussian.read_atoms(name).get_potential_energy()
e4 = dct[id]['energy']
assert e1 == e2 == e3 == e4
print(e1)
ae = 2 * c.get('name=O').energy - c.get('name=O2').energy
assert abs(ae - 1.060) < 1e-3
from ase.test import cli
cli("""
ase build -x fcc -a 4.04 Al |
ase run abinit -p xc=PBE,kpts=3.0,ecut=340,toldfe=1e-5,chksymbreak=0""",
'abinit')
from ase.test import cli
cli(
"""
ase-build -x fcc -a 4.04 Al |
ase-run abinit -p xc=PBE,kpts=3.0,ecut=340,toldfe=1e-5,chksymbreak=0""",
'abinit')
ase build O2 | ase run emt -d y.json &&
ase build H2 | ase run emt -f 0.02 -d y.json &&
ase build O2 | ase run emt -f 0.02 -d y.json &&
ase build -x fcc Cu | ase run emt -E 5,1 -d y.json &&
ase db -v y.json natoms=1,Cu=1 --delete --yes &&
ase db -v y.json "H>0" -k hydro=1,abc=42,foo=bar &&
ase db -v y.json "H>0" --delete-keys foo"""
def count(n, *args, **kwargs):
m = len(list(con.select(*args, **kwargs)))
assert m == n, (m, n)
for name in ['y.json', 'y.db']:
cli(cmd.replace('y.json', name))
con = connect(name)
assert con.get_atoms(H=1)[0].magmom == 1
count(5)
count(3, 'hydro')
count(0, 'foo')
count(3, abc=42)
count(3, 'abc')
count(0, 'abc,foo')
count(3, 'abc,hydro')
count(0, foo='bar')
count(1, formula='H2')
count(1, formula='H2O')
count(3, 'fmax<0.1')
count(1, '0.5<mass<1.5')
count(5, 'energy')
t0 = time.time()
for name in ['testase.json', 'testase.db', 'postgresql']:
if name == 'postgresql':
if os.environ.get('POSTGRES_DB'): # gitlab-ci
name = 'postgresql://*****:*****@postgres:5432/testase'
else:
name = os.environ.get('ASE_TEST_POSTGRES_URL')
if name is None:
continue
con = connect(name)
t1 = time.time()
if 'postgres' in name:
con.delete([row.id for row in con.select()])
cli(cmd.replace('testase.json', name))
assert con.get_atoms(H=1)[0].magmom == 1
count(5)
count(3, 'hydro')
count(0, 'foo')
count(3, abc=42)
count(3, 'abc')
count(0, 'abc,foo')
count(3, 'abc,hydro')
count(0, foo='bar')
count(1, formula='H2')
count(1, formula='H2O')
count(3, 'fmax<0.1')
count(1, '0.5<mass<1.5')
count(5, 'energy')
from ase.test import cli, require
from ase.db import connect
from ase.db.json import read_json
from ase.calculators.nwchem import NWChem
require('nwchem')
cli("""ase-build O | ase-run nwchem -d oxygen.json &&
ase-build O2 | ase-run nwchem -d oxygen.json""")
conn = connect('oxygen.json')
dct = read_json('oxygen.json')
for name in ['O2', 'O']:
e1 = conn[name].get_potential_energy()
e2 = NWChem.read_atoms(name).get_potential_energy()
e3 = dct[name]['results']['energy']
assert e1 == e2 == e3
print(e1)
ae = 2 * dct['O']['results']['energy'] - dct['O2']['results']['energy']
assert abs(ae - 6.6053) < 1e-4
