def requirevtk(code=0, parallel=False):
from ase.test import NotAvailable
if not hasvtk:
# VTK required but not installed, force termination
# with exit status determined by the code argument.
raise NotAvailable('VTK is not installed.', code)
if parallel and not hasmpi:
# VTK MPI required but not installed, force termination
# with exit status determined by the code argument.
raise NotAvailable('VTK is not MPI compatible.', code)
def installed():
import os
from ase.test import NotAvailable
dcmd = os.getenv('DFTB_COMMAND')
dpre = os.getenv('DFTB_PREFIX')
if dcmd == None:
raise NotAvailable('DFTB_COMMAND not defined')
if dpre == None:
raise NotAvailable('DFTB_PREFIX not defined (for slater koster files)')
return True
def main():
if "ASE_CP2K_COMMAND" not in os.environ:
raise NotAvailable('$ASE_CP2K_COMMAND not defined')
# Basically, the entire CP2K input is passed in explicitly.
# Disable ASE's input generation by setting everything to None.
# ASE should only add the CELL and the COORD section.
calc = CP2K(basis_set=None,
basis_set_file=None,
max_scf=None,
cutoff=None,
force_eval_method=None,
potential_file=None,
poisson_solver=None,
pseudo_potential=None,
stress_tensor=False,
xc=None,
label='test_H2_inp',
inp=inp)
h2 = molecule('H2', calculator=calc)
h2.center(vacuum=2.0)
energy = h2.get_potential_energy()
energy_ref = -30.6989595886
diff = abs((energy - energy_ref) / energy_ref)
assert diff < 1e-10
print('passed test "H2_None"')
def installed():
import os
from ase.test import NotAvailable
vcmd = os.getenv('VASP_COMMAND')
vscr = os.getenv('VASP_SCRIPT')
if vcmd == None and vscr == None:
raise NotAvailable('Neither VASP_COMMAND nor VASP_SCRIPT defined')
return True
def main():
if sys.version_info < (2, 7):
raise NotAvailable('read_xml requires Python version 2.7 or greater')
assert installed()
# simple test calculation of CO molecule
d = 1.14
co = Atoms('CO', positions=[(0, 0, 0), (0, 0, d)],
pbc=True)
co.center(vacuum=5.)
calc = Vasp(xc='LDA',
prec='Low',
algo='Fast',
ismear=0,
sigma=1.,
nbands=12,
istart=0,
nelm=3,
lwave=False,
lcharg=False,
ldipol=True)
co.set_calculator(calc)
energy = co.get_potential_energy()
forces = co.get_forces()
dipole_moment = co.get_dipole_moment()
# check that parsing of vasprun.xml file works
conf = read('vasprun.xml')
assert conf.calc.parameters['kpoints_generation']
assert conf.calc.parameters['sigma'] == 1.0
assert conf.calc.parameters['ialgo'] == 68
assert energy - conf.get_potential_energy() == 0.0
# Check some arrays
assert np.allclose(conf.get_forces(), forces)
assert np.allclose(conf.get_dipole_moment(), dipole_moment, atol=1e-6)
# Check k-point-dependent properties
assert len(conf.calc.get_eigenvalues(spin=0)) >= 12
assert conf.calc.get_occupation_numbers()[2] == 2
assert conf.calc.get_eigenvalues(spin=1) is None
kpt = conf.calc.get_kpt(0)
assert kpt.weight == 1.
# Perform a spin-polarised calculation
co.calc.set(ispin=2, ibrion=-1)
co.get_potential_energy()
conf = read('vasprun.xml')
assert len(conf.calc.get_eigenvalues(spin=1)) >= 12
assert conf.calc.get_occupation_numbers(spin=1)[0] == 1.
# Cleanup
calc.clean()
def installed2():
# Check if env variables exist for Vasp2
import os
from ase.test import NotAvailable
vcmd = os.getenv('VASP_COMMAND')
vscr = os.getenv('VASP_SCRIPT')
vase = os.getenv('ASE_VASP_COMMAND')
if vcmd is None and vscr is None and vase is None:
raise NotAvailable(
'Neither ASE_VASP_COMMAND, VASP_COMMAND nor VASP_SCRIPT defined')
return True
def main():
if "ASE_CP2K_COMMAND" not in os.environ:
raise NotAvailable('$ASE_CP2K_COMMAND not defined')
calc = CP2K(label='test_H2_LDA')
h2 = molecule('H2', calculator=calc)
h2.center(vacuum=2.0)
energy = h2.get_potential_energy()
energy_ref = -30.6989595886
diff = abs((energy - energy_ref) / energy_ref)
assert diff < 1e-10
print('passed test "H2_LDA"')
def main():
if "ASE_CP2K_COMMAND" not in os.environ:
raise NotAvailable('$ASE_CP2K_COMMAND not defined')
calc = CP2K()
h2 = molecule('H2', calculator=calc)
h2.center(vacuum=2.0)
h2.get_potential_energy()
calc.write('test_restart') # write a restart
calc2 = CP2K(restart='test_restart') # load a restart
assert not calc2.calculation_required(h2, ['energy'])
print('passed test "restart"')
def main():
if "ASE_CP2K_COMMAND" not in os.environ:
raise NotAvailable('$ASE_CP2K_COMMAND not defined')
calc = CP2K(label='test_O2', uks=True, cutoff=150 * units.Rydberg,
basis_set="SZV-MOLOPT-SR-GTH")
o2 = molecule('O2', calculator=calc)
o2.center(vacuum=2.0)
energy = o2.get_potential_energy()
energy_ref = -861.057011375
diff = abs((energy - energy_ref) / energy_ref)
assert diff < 1e-10
print('passed test "O2"')
def main():
if "ASE_CP2K_COMMAND" not in os.environ:
raise NotAvailable('$ASE_CP2K_COMMAND not defined')
calc = CP2K(xc='XC_GGA_X_PBE XC_GGA_C_PBE',
pseudo_potential="GTH-PBE",
label='test_H2_libxc')
h2 = molecule('H2', calculator=calc)
h2.center(vacuum=2.0)
energy = h2.get_potential_energy()
energy_ref = -31.591716529642
diff = abs((energy - energy_ref) / energy_ref)
assert diff < 1e-10
print('passed test "H2_libxc"')
def plot(self, name=''):
"""Plot the individual curves"""
try:
import matplotlib.pyplot as plt
except ImportError:
raise NotAvailable('This needs matplotlib module.')
if self.form == 'eam' or self.form == 'alloy':
nrow = 2
elif self.form == 'adp':
nrow = 3
else:
raise RuntimeError('Unknown form of potential: %s' % self.form)
if hasattr(self, 'r'):
r = self.r
else:
r = np.linspace(0, self.cutoff, 50)
if hasattr(self, 'rho'):
rho = self.rho
else:
rho = np.linspace(0, 10.0, 50)
plt.subplot(nrow, 2, 1)
self.elem_subplot(rho, self.embedded_energy, r'$\rho$',
r'Embedding Energy $F(\bar\rho)$', name, plt)
plt.subplot(nrow, 2, 2)
self.elem_subplot(r, self.electron_density, r'$r$',
r'Electron Density $\rho(r)$', name, plt)
plt.subplot(nrow, 2, 3)
self.multielem_subplot(r, self.phi, r'$r$',
r'Pair Potential $\phi(r)$', name, plt)
plt.ylim(-1.0, 1.0) # need reasonable values
if self.form == 'adp':
plt.subplot(nrow, 2, 5)
self.multielem_subplot(r, self.d, r'$r$', r'Dipole Energy', name,
plt)
plt.subplot(nrow, 2, 6)
self.multielem_subplot(r, self.q, r'$r$', r'Quadrupole Energy',
name, plt)
plt.plot()
def installed():
import os
from ase.test import NotAvailable
# check if CASTEP_COMMAND is set a environment variable
if not os.environ.has_key('CASTEP_COMMAND'):
print("WARNING: Environment variable CASTEP_COMMAND is not set")
print("Will set CASTEP_COMMAND = castep for the sake of this test")
print(
"Please change it if this does not run castep in your environment")
os.environ['CASTEP_COMMAND'] = 'castep'
if not (os.system(
'which %s > /dev/null 2>&1' % os.environ['CASTEP_COMMAND']) == 0):
raise NotAvailable("""Could not find CASTEP. If you have it
installed make sure, you set the CASTEP_COMMAND
environment variable correctly""")
return True
def main():
if "ASE_CP2K_COMMAND" not in os.environ:
raise NotAvailable('$ASE_CP2K_COMMAND not defined')
inp = """&FORCE_EVAL
&DFT
&QS
LS_SCF ON
&END QS
&END DFT
&END FORCE_EVAL"""
calc = CP2K(label='test_H2_LS', inp=inp)
h2 = molecule('H2', calculator=calc)
h2.center(vacuum=2.0)
energy = h2.get_potential_energy()
energy_ref = -30.6989581747
diff = abs((energy - energy_ref) / energy_ref)
assert diff < 5e-7
print('passed test "H2_LS"')
def main():
if "ASE_CP2K_COMMAND" not in os.environ:
raise NotAvailable('$ASE_CP2K_COMMAND not defined')
calc = CP2K(label='test_H2_GOPT')
atoms = molecule('H2', calculator=calc)
atoms.center(vacuum=2.0)
# Run Geo-Opt
gopt = BFGS(atoms, logfile=None)
gopt.run(fmax=1e-6)
# check distance
dist = atoms.get_distance(0, 1)
dist_ref = 0.7245595
assert (dist - dist_ref) / dist_ref < 1e-7
# check energy
energy_ref = -30.7025616943
energy = atoms.get_potential_energy()
assert (energy - energy_ref) / energy_ref < 1e-10
print('passed test "H2_GEO_OPT"')
def main():
if "ASE_CP2K_COMMAND" not in os.environ:
raise NotAvailable('$ASE_CP2K_COMMAND not defined')
calc = CP2K(label='test_H2_MD')
positions = [(0, 0, 0), (0, 0, 0.7245595)]
atoms = Atoms('HH', positions=positions, calculator=calc)
atoms.center(vacuum=2.0)
# Run MD
MaxwellBoltzmannDistribution(atoms, 0.5 * 300 * units.kB, force_temp=True)
energy_start = atoms.get_potential_energy() + atoms.get_kinetic_energy()
dyn = VelocityVerlet(atoms, 0.5 * units.fs)
#def print_md():
# energy = atoms.get_potential_energy() + atoms.get_kinetic_energy()
# print("MD total-energy: %.10feV" % energy)
#dyn.attach(print_md, interval=1)
dyn.run(20)
energy_end = atoms.get_potential_energy() + atoms.get_kinetic_energy()
assert energy_start - energy_end < 1e-4
print('passed test "H2_MD"')
def main():
if sys.version_info < (2, 7):
raise NotAvailable('read_xml requires Python version 2.7 or greater')
assert installed()
# simple test calculation of CO molecule
d = 1.14
co = Atoms('CO', positions=[(0, 0, 0), (0, 0, d)], pbc=True)
co.center(vacuum=5.)
calc = Vasp(xc='PBE',
prec='Low',
algo='Fast',
ismear=0,
sigma=1.,
istart=0,
lwave=False,
lcharg=False,
ldipol=True)
co.set_calculator(calc)
energy = co.get_potential_energy()
forces = co.get_forces()
dipole_moment = co.get_dipole_moment()
# check that parsing of vasprun.xml file works
conf = read('vasprun.xml')
assert conf.calc.parameters['kpoints_generation']
assert conf.calc.parameters['sigma'] == 1.0
assert conf.calc.parameters['ialgo'] == 68
assert energy - conf.get_potential_energy() == 0.0
assert np.allclose(conf.get_forces(), forces)
assert np.allclose(conf.get_dipole_moment(), dipole_moment, atol=1e-6)
# Cleanup
calc.clean()
def installed():
import os
import subprocess
from ase.test import NotAvailable
# check if CASTEP_COMMAND is set an environment variable
if 'CASTEP_COMMAND' not in os.environ:
print("WARNING: Environment variable CASTEP_COMMAND is not set")
print("Will set CASTEP_COMMAND = castep for the sake of this test")
print(
"Please change it if this does not run castep in your environment")
os.environ['CASTEP_COMMAND'] = 'castep'
try:
# not python 2.6-safe
#subprocess.check_output([os.environ['CASTEP_COMMAND']])
devnull = open(os.devnull)
subprocess.Popen([os.environ['CASTEP_COMMAND']],
stdout=devnull,
stderr=devnull)
except OSError:
raise NotAvailable("""Could not find CASTEP. If you have it
installed make sure, you set the CASTEP_COMMAND
environment variable correctly""")
return True
def main():
"""add the following line in .bash_profile and source the .bash_profile to
define the varialbe "ASE_CP2K_COMMAND":
export ASE_CP2K_COMMAND="mpiexec.hydra -n NCORES cp2k_shell.popt"
where NCORES is the total number of cores used for calculation.
mpiexec.hydra is the mpi command used for the parrallel running.
"""
if "ASE_CP2K_COMMAND" not in os.environ:
raise NotAvailable('$ASE_CP2K_COMMAND not defined')
# Basically, the entire CP2K input is passed in explicitly.
# Disable ASE's input generation by setting everything to None.
# ASE should only add the CELL and the COORD section.
calc = CP2K(basis_set=None,
basis_set_file=None,
max_scf=None,
cutoff=None,
force_eval_method=None,
potential_file=None,
poisson_solver=None,
pseudo_potential=None,
stress_tensor=False,
xc=None,
label='N2O4-NH4', inp=inp)
from ase.test import NotAvailable
try:
import cmr
except ImportError:
raise NotAvailable('CMR is required')
from cmr.ui import DirectoryReader
from cmr.test.examples.ase_reaction_energy import ASEReactionEnergy
# see the module for the required format of reactions definition
from ase.test.cmr.reactions import reactions
from ase.test.cmr.reactions import reference
# assure that all reactions define a reaction_id
for r in reactions:
assert r[-1][0] == 'reaction_id'
# project id: must uniquely identify the project!
project_id = 'EMT' + ' reaction energies'
# if True, then results are uploaded to the database
database = False
# create assisting class for project with project_id,
# that allows one to convert trajectory files into
# db-files and perform analysis
re = ASEReactionEnergy(project_id, reactions, prefix='', verbose=False)
# compounds names
import os
from ase.test import NotAvailable
try:
nwchem_command = os.getenv('NWCHEM_COMMAND')
if nwchem_command == None:
raise NotAvailable('NWCHEM_COMMAND not defined')
except NotAvailable:
raise NotAvailable('Nwchem required')
import numpy as np
from ase.tasks.main import run
atoms, task = run("nwchem molecule O2 O -l -p task=gradient")
atoms, task = run('nwchem molecule O2 O -s')
ae = 2 * task.data['O']['energy'] - task.data['O2']['energy']
assert abs(ae - 6.605) < 1e-3
import os
from ase.test import NotAvailable
try:
fleur = os.getenv('FLEUR')
if fleur == None:
raise NotAvailable('FLEUR not defined')
except NotAvailable:
raise NotAvailable('Fleur required')
import numpy as np
from ase.tasks.main import run
atoms, task = run("fleur bulk Al -x fcc -a 4.04 --k-point-density=3.0 -p xc=PBE")
atoms, task = run('fleur bulk Al -s')
try:
import scipy
except ImportError:
from ase.test import NotAvailable
raise NotAvailable('This test needs scipy module.')
import numpy as np
from ase.io import read, PickleTrajectory
from ase.lattice import bulk
from ase.calculators.emt import EMT
a0 = 3.52 / np.sqrt(2)
c0 = np.sqrt(8 / 3.0) * a0
print '%.4f %.3f' % (a0, c0 / a0)
for i in range(3):
traj = PickleTrajectory('Ni.traj', 'w')
eps = 0.01
for a in a0 * np.linspace(1 - eps, 1 + eps, 4):
for c in c0 * np.linspace(1 - eps, 1 + eps, 4):
ni = bulk('Ni', 'hcp', a=a, covera=c / a)
ni.set_calculator(EMT())
ni.get_potential_energy()
traj.write(ni)
configs = read('Ni.traj@:')
energies = [config.get_potential_energy() for config in configs]
ac = [(config.cell[0, 0], config.cell[2, 2]) for config in configs]
from ase.optimize import polyfit
p = polyfit(ac, energies)
from scipy.optimize import fmin_bfgs
a0, c0 = fmin_bfgs(p, (a0, c0))
from ase.test import NotAvailable
import ase.io.netcdftrajectory as netcdftrajectory
if not netcdftrajectory.have_nc:
raise NotAvailable('No NetCDF module available (netCDF4-python, '
'scipy.io.netcdf)')
import os
from ase import Atom, Atoms
from ase.io import NetCDFTrajectory
co = Atoms([Atom('C', (0, 0, 0)), Atom('O', (0, 0, 1.2))], pbc=True)
traj = NetCDFTrajectory('1.nc', 'w', co)
for i in range(5):
co.positions[:, 2] += 0.1
traj.write()
del traj
if netcdftrajectory.have_nc == netcdftrajectory.NC_IS_NETCDF4:
traj = NetCDFTrajectory('1.nc', 'a')
co = traj[-1]
print(co.positions)
co.positions[:] += 1
traj.write(co)
del traj
t = NetCDFTrajectory('1.nc', 'a')
else:
t = NetCDFTrajectory('1.nc', 'r')
print(t[-1].positions)
print('.--------')
# do some tests here before we import
# Right version of Scientific?
from ase.test import NotAvailable
import os
try:
import Scientific
version = Scientific.__version__.split(".")
print 'Found ScientificPython version: ', Scientific.__version__
if map(int, version) < [2, 8]:
print 'ScientificPython 2.8 or greater required for numpy support in NetCDF'
raise NotAvailable(
'ScientificPython version 2.8 or greater is required')
except (ImportError, NotAvailable):
print "No Scientific python found. Check your PYTHONPATH"
raise NotAvailable('ScientificPython version 2.8 or greater is required')
if not (os.system('which dacapo.run') == 0):
print "No Dacapo Fortran executable (dacapo.run) found. Check your path settings."
raise NotAvailable(
'dacapo.run is not installed on this machine or not in the path')
# Now Scientific 2.8 and dacapo.run should both be available
from ase import Atoms, Atom
from ase.calculators.jacapo import Jacapo
atoms = Atoms([Atom('H', [0, 0, 0])], cell=(2, 2, 2))
calc = Jacapo('Jacapo-test.nc',
pw=200,
nbands=2,
import sys
from ase.test import NotAvailable, must_raise
if sys.platform in ['win32']:
raise NotAvailable('Fails on Windows '
'https://trac.fysik.dtu.dk/projects/ase/ticket/62')
import os
from ase import Atom, Atoms
from ase.io import Trajectory, read
from ase.constraints import FixBondLength
co = Atoms([Atom('C', (0, 0, 0)),
Atom('O', (0, 0, 1.2))])
traj = Trajectory('1.traj', 'w', co)
for i in range(5):
co.positions[:, 2] += 0.1
traj.write()
traj = Trajectory('1.traj', 'a')
co = read('1.traj')
print(co.positions)
co.positions[:] += 1
traj.write(co)
for a in Trajectory('1.traj'):
print(1, a.positions[-1, 2])
co.positions[:] += 1
t = Trajectory('1.traj', 'a')
t.write(co)
#!/usr/bin/python
"""
Run some VASP tests to ensure that the VASP calculator works. This
is conditional on the existence of the VASP_COMMAND or VASP_SCRIPT
environment variables
"""
from ase.test import NotAvailable
import os
vcmd = os.getenv('VASP_COMMAND')
vscr = os.getenv('VASP_SCRIPT')
if vcmd == None and vscr == None:
raise NotAvailable('Neither VASP_COMMAND nor VASP_SCRIPT defined')
from ase import Atoms
from ase.calculators.vasp import Vasp
import numpy as np
def array_almost_equal(a1, a2, tol=np.finfo(type(1.0)).eps):
"""Replacement for old numpy.testing.utils.array_almost_equal."""
return (np.abs(a1 - a2) < tol).all()
d = 1.14
co = Atoms('CO', positions=[(0, 0, 0), (0, 0, d)], pbc=True)
co.center(vacuum=5.)
calc = Vasp(xc='PBE',
if not os.path.exists('calcDelta.py'):
try:
resp = urllib.request.urlopen(src)
urllib.request.urlretrieve(src, filename=name)
z = zipfile.ZipFile(name)
try: # new in 2.6
z.extractall()
except AttributeError:
# http://stackoverflow.com/questions/7806563/how-to-unzip-a-zip-file-with-python-2-4
for f in z.namelist():
fd = open(f, "w")
fd.write(z.read(f))
fd.close()
# AttributeError if unzip not found
except (urllib.error.HTTPError, AttributeError):
raise NotAvailable('Retrieval of zip failed')
os.chdir('..')
task = Task(
tag=tag,
use_lock_files=True,
)
# header
h = ['#element', 'V0', 'B0', 'B1']
if not os.path.exists('%s_raw.csv' % tag):
# read calculated results from json file and write into csv
task.read()
task.analyse()
from ase.test import NotAvailable
from ase.calculators.mopac import Mopac
if Mopac().get_command() is None:
raise NotAvailable('MOPAC required')
from ase.tasks.main import run
atoms, task = run("mopac molecule O2 O")
atoms, task = run('mopac molecule O2 O -s')
ae = 2 * task.data['O']['energy'] - task.data['O2']['energy']
print ae
assert abs(ae - 12.658) < 1e-3
"""Check reading of a sample v_sim .ascii file, and I/O consistency"""
try:
from urllib.request import urlretrieve
from urllib.error import URLError
except ImportError:
from urllib import urlretrieve
from urllib2 import URLError
from socket import error as SocketError
from ase.test import NotAvailable
from ase.io import read
raise NotAvailable('The web site which this test depends upon. '
'TODO: Let us not depend on external websites.')
dest = 'demo.ascii'
src = 'http://inac.cea.fr/L_Sim/V_Sim/files/' + dest
copy = 'demo2.ascii'
try:
urlretrieve(src, filename=dest)
except (IOError, URLError, SocketError):
raise NotAvailable('Retrieval of ' + src + ' failed')
atoms = read(dest, format='v-sim')
atoms.write(copy)
atoms2 = read(copy)
tol = 1e-6
""" test run for gromacs calculator """
from ase.test import NotAvailable
from ase.calculators.gromacs import Gromacs
if Gromacs().get_command() is None:
raise NotAvailable(
'Gromacs required, setup your GMXCMD environmental variable')
GRO_INIT_FILE = 'hise_box.gro'
# write structure file
outfile = open('hise_box.gro', 'w')
outfile.write('HISE for testing \n')
outfile.write(' 20 \n')
outfile.write(' 3HISE N 1 1.966 1.938 1.722 \n')
outfile.write(' 3HISE H1 2 2.053 1.892 1.711 \n')
outfile.write(' 3HISE H2 3 1.893 1.882 1.683 \n')
outfile.write(' 3HISE H3 4 1.969 2.026 1.675 \n')
outfile.write(' 3HISE CA 5 1.939 1.960 1.866 \n')
outfile.write(' 3HISE HA 6 1.934 1.869 1.907 \n')
outfile.write(' 3HISE CB 7 2.055 2.041 1.927 \n')
outfile.write(' 3HISE HB1 8 2.141 2.007 1.890 \n')
outfile.write(' 3HISE HB2 9 2.043 2.137 1.903 \n')
outfile.write(' 3HISE ND1 10 1.962 2.069 2.161 \n')
outfile.write(' 3HISE CG 11 2.065 2.032 2.077 \n')
outfile.write(' 3HISE CE1 12 2.000 2.050 2.287 \n')
outfile.write(' 3HISE HE1 13 1.944 2.069 2.368 \n')
outfile.write(' 3HISE NE2 14 2.123 2.004 2.287 \n')
outfile.write(' 3HISE HE2 15 2.177 1.981 2.369 \n')
outfile.write(' 3HISE CD2 16 2.166 1.991 2.157 \n')
