def get_aims_calculator(n):
#"gas" for gas-phase reactants and "periodic" for a periodic systems
if (n == "gas"):
return Aims(
xc='pbe',
spin='none',
vdw_correction_hirshfeld="True",
relativistic=('atomic_zora', 'scalar'),
#use_dipole_correction='True',
#default_initial_moment=2.0,
compute_forces="true"
#output=['mulliken']
)
else:
if (n == "periodic"):
return Aims(
xc='pbe',
spin='none',
k_grid=(3, 3, 1),
vdw_correction_hirshfeld="True",
relativistic=('atomic_zora', 'scalar'),
use_dipole_correction='True',
# default_initial_moment=2.0,
compute_forces="true",
output=['mulliken'],
elsi_restart=("write", 1))
def read_aims_calculator(file):
""" found instructions for building an FHI-aims calculator in the output file,
read its specifications and return it. """
from ase.calculators.aims import Aims
calc = Aims()
while True:
line = file.readline()
if "=======================================================" in line:
break
else:
args = line.split()
key = '#'
if len(args) > 0:
key = args[0]
if key == '#':
comment = True
elif calc.float_params.has_key(key):
calc.float_params[key] = float(args[1])
elif calc.exp_params.has_key(key):
calc.exp_params[key] = float(args[1])
elif calc.string_params.has_key(key):
calc.string_params[key] = args[1]
if len(args) > 2:
for s in args[2:]:
calc.string_params[key] += " "+s
elif calc.int_params.has_key(key):
calc.int_params[key] = int(args[1])
elif calc.bool_params.has_key(key):
try:
calc.bool_params[key] = bool(args[1])
except:
if key == 'vdw_correction_hirshfeld':
calc.bool_params[key] = True
elif calc.list_params.has_key(key):
if key == 'output':
# build output string from args:
out_option = ''
for arg in args[1:]:
out_option +=str(arg)+' '
if calc.list_params['output'] is not None:
calc.list_params['output'] += [out_option]
else:
calc.list_params['output'] = [out_option]
else:
calc.list_params[key] = list(args[1:])
elif '#' in key:
key = key[1:]
if calc.input_parameters.has_key(key):
calc.input_parameters[key] = args[1]
if len(args) > 2:
for s in args[2:]:
calc.input_parameters[key] += " "+s
else:
raise TypeError('FHI-aims keyword not defined in ASE: ' + key + '. Please check.')
return calc
def __init__(self, h2indices=[0,1], restart=None, ignore_bad_restart_file=False,
label=os.curdir, atoms=None, cubes=None, radmul=None,
tier=None, **kwargs):
Aims.__init__(self,restart=restart, ignore_bad_restart_file=\
ignore_bad_restart_file, label=label,atoms=atoms, \
cubes=cubes, radmul=radmul, tier=tier, **kwargs)
h2pes.pes_init()
self.h2indices = h2indices
implemented_properties = ['energy', 'forces', 'friction']
self.implemented_properties = implemented_properties
def get_aims_calculator(dimensions,
k_grid=None,
xc="pbe",
compute_forces="true",
**kwargs):
'''
Method to return a "default" FHI-aims calculator.
Note: This file should not be changed without consultation,
as changes could affect many users in the group.
Parameters:
dimensions: Integer
Determines whether we have a "gas"-phase (0) or "periodic" structure (2 or 3)
k_grid: List of integers
Gives the k-grid sampling in x-, y- and z- direction. e.g. [3, 3, 3]
xc: String
XC of choice
compute_forces: String
Determines whether forces are enabled ("true") or not enabled ("false").
**kwargs:
Any other keyword arguments that a user wants to set.
TODO: Reorder inputs so most necessary are first i.e. xc, compute_forces, k_grid (I think?)
AL, March 2021: Doesn't matter - if named, the arguments are dynamic (i.e. can be any order)
'''
from ase.calculators.aims import Aims
# Default is suitable for molecular calculations
fhi_calc = Aims(spin='none',
relativistic=('atomic_zora', 'scalar'),
compute_forces=compute_forces,
**kwargs)
# Set the XC for the calculation. For LibXC, override_warning_libxc *needs*
# to be set first, otherwise we get a termination.
if "libxc" in xc:
fhi_calc.set(override_warning_libxc="true")
fhi_calc.set(xc=xc)
if dimensions == 2:
fhi_calc.set(use_dipole_correction='true')
if dimensions >= 2:
fhi_calc.set(k_grid=k_grid)
return fhi_calc
def my_calc():
return Aims(xc='pbesol',
spin='none',
relativistic=('atomic_zora', 'scalar'),
vdw_correction_hirshfeld='true',
k_grid=(
2,
2,
2,
),
compute_forces=True,
final_forces_cleaned=True)
def setup_control(self, overwrite=False):
control = self.dirpath.joinpath("control.in")
if control.exists() and (overwrite == False):
logger.warning(
"File control.in already exists. Set overwrite=True to force overwrite."
)
elif not control.exists() or overwrite:
logger.info("Writing {} ...".format(control))
calc = Aims(**self.aseargs)
calc.write_control(self.structure, str(control), debug=False)
calc.write_species(self.structure, filename=control)
self.__adjust_control(control)
def test_H2O_aims():
water = Atoms('HOH', [(1, 0, 0), (0, 0, 0), (0, 1, 0)])
water_cube = AimsCube(points=(29, 29, 29),
plots=('total_density', 'delta_density',
'eigenstate 5', 'eigenstate 6'))
calc = Aims(xc='PBE',
output=['dipole'],
sc_accuracy_etot=1e-6,
sc_accuracy_eev=1e-3,
sc_accuracy_rho=1e-6,
sc_accuracy_forces=1e-4,
cubes=water_cube)
water.calc = calc
dynamics = QuasiNewton(water, trajectory='square_water.traj')
dynamics.run(fmax=0.01)
def run(self):
self.prepare_calc_dir()
Aims.run(self)
calc = Aims(
xc='PBE',
run_command='mpirun -np 4 <insert_path>/bin/aims.160210.mpi.x > aims.out',
species_dir='<insert path>/aimsfiles/species_defaults/' + basisset,
occupation_type=['gaussian', 0.1],
sc_iter_limit=100,
#spin = 'collinear',
relativistic=['atomic_zora', 'scalar'],
#default_initial_moment = 0,
sc_accuracy_etot=1e-6,
sc_accuracy_eev=0.001,
sc_accuracy_rho=1e-5,
sc_accuracy_forces=1e-3,
load_balancing=True,
#empty_states=10,
k_grid=[12, 12, 1],
restart_aims='wvfn.dat',
output=[
"eigenvectors",
"k_point_list",
"hamiltonian_matrix",
"overlap_matrix",
"band 0.0000 0.0000 0.0000 0.0000 0.0833 0.0000 2 ",
"band 0.0000 0.2500 0.0000 0.0000 0.3333 0.0000 2 ",
"band 0.0000 0.4167 0.0000 0.0000 0.5000 0.0000 2 ",
"band 0.0000 0.8333 0.0000 0.0833 0.0000 0.0000 2 ",
"band 0.0833 0.0833 0.0000 0.0833 0.1667 0.0000 2 ",
"band 0.0833 0.3333 0.0000 0.0833 0.4167 0.0000 2 ",
"band 0.0833 0.5000 0.0000 0.0833 0.6667 0.0000 2 ",
"band 0.0833 0.7500 0.0000 0.0833 0.8333 0.0000 2 ",
"band 0.1667 0.0000 0.0000 0.1667 0.0833 0.0000 2 ",
"band 0.1667 0.1667 0.0000 0.1667 0.3333 0.0000 2 ",
"band 0.1667 0.4167 0.0000 0.1667 0.5000 0.0000 2 ",
"band 0.1667 0.6667 0.0000 0.1667 0.7500 0.0000 2 ",
"band 0.1667 0.8333 0.0000 0.2500 0.0000 0.0000 2 ",
"band 0.2500 0.0833 0.0000 0.2500 0.1667 0.0000 2 ",
"band 0.2500 0.3333 0.0000 0.2500 0.4167 0.0000 2 ",
"band 0.2500 0.5000 0.0000 0.2500 0.6667 0.0000 2 ",
"band 0.2500 0.7500 0.0000 0.2500 0.8333 0.0000 2 ",
"band 0.3333 0.0000 0.0000 0.3333 0.0833 0.0000 2 ",
"band 0.3333 0.1667 0.0000 0.3333 0.3333 0.0000 2 ",
"band 0.3333 0.4167 0.0000 0.3333 0.5000 0.0000 2 ",
"band 0.3333 0.6667 0.0000 0.3333 0.7500 0.0000 2 ",
"band 0.3333 0.8333 0.0000 0.4167 0.0000 0.0000 2 ",
"band 0.4167 0.0833 0.0000 0.4167 0.1667 0.0000 2 ",
"band 0.4167 0.3333 0.0000 0.4167 0.4167 0.0000 2 ",
"band 0.4167 0.5000 0.0000 0.4167 0.6667 0.0000 2 ",
"band 0.4167 0.7500 0.0000 0.4167 0.8333 0.0000 2 ",
"band 0.5000 0.0000 0.0000 0.5000 0.0833 0.0000 2 ",
"band 0.5000 0.1667 0.0000 0.5000 0.3333 0.0000 2 ",
"band 0.5000 0.4167 0.0000 0.5000 0.5000 0.0000 2 ",
"band 0.5000 0.7500 0.0000 0.5833 0.0833 0.0000 2 ",
"band 0.5833 0.4167 0.0000 0.5833 0.7500 0.0000 2 ",
"band 0.6667 0.0833 0.0000 0.6667 0.4167 0.0000 2 ",
"band 0.6667 0.7500 0.0000 0.7500 0.0833 0.0000 2 ",
"band 0.7500 0.4167 0.0000 0.7500 0.7500 0.0000 2 ",
"band 0.8333 0.0833 0.0000 0.8333 0.4167 0.0000 2 ",
"band 0.8333 0.7500 0.0000 0.9167 0.0833 0.0000 2 ",
"band 0.9167 0.4167 0.0000 0.9167 0.7500 0.0000 2 ",
],
)
def __init__(self, nodes=1, ppn=8, **kwargs):
Aims.__init__(self, **kwargs)
self.nodes=nodes
self.ppn=ppn
def run(self):
self.prepare_calc_dir()
Aims.run(self)
def read_aims_calculator(file):
""" found instructions for building an FHI-aims calculator in the output file,
read its specifications and return it. """
from ase.calculators.aims import Aims
calc = Aims()
while True:
line = file.readline()
if "=======================================================" in line:
break
else:
args = line.split()
key = '#'
if len(args) > 0:
key = args[0]
if key == '#':
comment = True
elif calc.float_params.has_key(key):
calc.float_params[key] = float(args[1])
elif calc.exp_params.has_key(key):
calc.exp_params[key] = float(args[1])
elif calc.string_params.has_key(key):
calc.string_params[key] = args[1]
if len(args) > 2:
for s in args[2:]:
calc.string_params[key] += " " + s
elif calc.int_params.has_key(key):
calc.int_params[key] = int(args[1])
elif calc.bool_params.has_key(key):
try:
calc.bool_params[key] = bool(args[1])
except:
if key == 'vdw_correction_hirshfeld':
calc.bool_params[key] = True
elif calc.list_params.has_key(key):
if key == 'output':
# build output string from args:
out_option = ''
for arg in args[1:]:
out_option += str(arg) + ' '
if calc.list_params['output'] is not None:
calc.list_params['output'] += [out_option]
else:
calc.list_params['output'] = [out_option]
else:
calc.list_params[key] = list(args[1:])
elif '#' in key or calc.input_parameters.has_key(key):
key = key[1:]
if calc.input_parameters.has_key(key):
calc.input_parameters[key] = args[1]
if len(args) > 2:
for s in args[2:]:
calc.input_parameters[key] += " " + s
else:
raise TypeError('FHI-aims keyword not defined in ASE: ' + key +
'. Please check.')
return calc
import sys
from ase.build import molecule
from ase.optimize import BFGS
from ase.calculators.aims import Aims
from ase.calculators.socketio import SocketIOCalculator
# Environment-dependent parameters -- please configure according to machine
# Note that FHI-aim support for the i-PI protocol must be specifically
# enabled at compile time, e.g.: make -f Makefile.ipi ipi.mpi
species_dir = '/home/aimsuser/src/fhi-aims.171221_1/species_defaults/light'
command = 'ipi.aims.171221_1.mpi.x'
# This example uses INET; see other examples for how to use UNIX sockets.
port = 31415
atoms = molecule('H2O', vacuum=3.0)
atoms.rattle(stdev=0.1)
aims = Aims(command=command,
use_pimd_wrapper=('localhost', port),
compute_forces=True,
xc='LDA',
species_dir=species_dir)
opt = BFGS(atoms, trajectory='opt.aims.traj', logfile='opt.aims.log')
with SocketIOCalculator(aims, log=sys.stdout, port=port) as calc:
atoms.calc = calc
opt.run(fmax=0.05)
import sys
from ase.io.gromos import read_gromos
RUN_COMMAND = '/home/mka/bin/aims.071711_6.serial.x'
SPECIES_DIR = '/home/mka/Programs/fhi-aims.071711_6/species_defaults/light/'
LOG_FILE = open("ase-qm-mm-output.log","w")
sys.stdout = LOG_FILE
infile_name = sys.argv[1]
CALC_QM1 = Aims(charge = 0,
xc = 'pbe',
sc_accuracy_etot = 1e-5,
sc_accuracy_eev = 1e-2,
sc_accuracy_rho = 1e-5,
sc_accuracy_forces = 1e-3,
species_dir = SPECIES_DIR,
run_command = RUN_COMMAND)
CALC_QM1.set(output = 'hirshfeld')
CALC_QM2 = Aims(charge = 0,
xc = 'pbe',
sc_accuracy_etot = 1e-5,
sc_accuracy_eev = 1e-2,
sc_accuracy_rho = 1e-5,
sc_accuracy_forces = 1e-3,
species_dir = SPECIES_DIR,
run_command = RUN_COMMAND)
CALC_QM2.set(output = 'hirshfeld')
"outfilename": "aims.out",
}
dft_settings = {
# system settings
"xc": "pbe",
"spin": "none",
"compute_forces": True,
}
# ################# Set aims calculator ######################
workdir = "aims_rundir"
port_aims = 12345
aux_settings = {"label": workdir, "use_pimd_wrapper": ("localhost", port_aims)}
calc = Aims(**usr_settings, **dft_settings, **aux_settings)
# atoms.set_calculator(calc)
# ################# Create Client ############################
# inet
port_ipi = 10200
host_ipi = "localhost"
client = SocketClient(host=host_ipi, port=port_ipi)
# ################# Create ASE SERVER ############################
with SocketIOCalculator(calc, log="socketio.log", port=port_aims) as io_calc:
atoms.set_calculator(io_calc)
client.run(atoms)
from ase.io import read
molecule = read('azo.xyz')
slab = molecule
aims_bin = 'mpirun -np 4' + ' /data/michelitsch/devAIMS/bin/aims.150528.mpi.x > aims.out'
basis_set = '/data/michelitsch/devAIMS/fhiaims_doc/species_defaults/light/'
if True:
QM1 = Aims(command=aims_bin,
xc='PBE',
relativistic=('atomic_zora scalar 1.0e-09'),
spin='none',
species_dir=basis_set,
tier=1,
#k_grid=cluster_kgrid,
smearing=('gaussian', 0.1),
sc_accuracy_etot=1e-4,
sc_accuracy_rho=1e-6,
sc_accuracy_forces=1e-3,
output=['hirshfeld'],
)
calc_vdw = mbdio(INPUT_FILE='azo.mbd',
SETTING_FILE='azo_setting.in',
OUTPUT_FILE='azo.log',
xc='1',
mbd_cfdm_dip_cutoff='200.d0',
mbd_scs_dip_cutoff='200.0',
mbd_supercell_cutoff='15.d0',
mbd_scs_vacuum_axis='.true. .true. .false.',
import os
from ase import Atoms
from ase.optimize import BFGS
from ase.calculators.aims import Aims
os.environ['ASE_AIMS_COMMAND'] = 'aims.x'
os.environ[
'AIMS_SPECIES_DIR'] = '/home/alumne/software/FHIaims/species_defaults/light'
atoms = Atoms('HOH', positions=[[0, 0, -1], [0, 1, 0], [0, 0, 1]])
calc = Aims(xc='LDA', compute_forces=True)
atoms.calc = calc
opt = BFGS(atoms, trajectory='opt-aims.traj')
opt.run(fmax=0.05)
#!/usr/bin/env python
from ase.calculators.aims import Aims
from ase import Atom, Atoms
#
calc = Aims(restart='cluster/pt-relax')
Ept=calc.get_potential_energy()
#
calc = Aims(restart='molecules/co-relax')
Eco=calc.get_potential_energy()
#
calc = Aims(restart='cluster/pt-co-relax')
Eptco=calc.get_potential_energy()
#
CE=Eptco - Ept - Eco
print('binding energy = {0} eV'.format(CE))
#!/usr/bin/env python
from ase.units import *
from ase.calculators.aims import Aims
bond_lengths = [1.05, 1.1, 1.15, 1.2, 1.25]
energies = []
for d in bond_lengths:
calc = Aims(label='molecules/co-{0}'.format(d))
atoms = calc.get_atoms()
energies.append(atoms.get_potential_energy())
# fit the data
pars = np.polyfit(bond_lengths, energies, 3)
xfit = np.linspace(1.05, 1.25)
efit = np.polyval(pars, xfit)
# first derivative
dpars = np.polyder(pars)
# find where the minimum is. chose the second one because it is the
# minimum we need.
droots = np.roots(dpars)
# second derivative
ddpars = np.polyder(dpars)
d_min = droots[np.polyval(ddpars, droots) > 0]
# curvature at minimum = force constant in SI units
k = np.polyval(ddpars, d_min) / (J / m**2)
# mu, reduced mass
from ase.data import atomic_masses
C_mass = atomic_masses[6] / kg
O_mass = atomic_masses[8] / kg
mu = 1.0 / (1.0 / C_mass + 1.0 / O_mass)
frequency = 1. / (2. * np.pi) * np.sqrt(k / mu)
print('The CO vibrational frequency is {0} Hz'.format(*frequency))
print('The CO vibrational frequency is {0} cm^{{-1}}'.format(frequency / 3e10))
import sys
from ase.io import read
RUN_COMMAND = '/home/mka/bin/aims.071711_6.serial.x'
SPECIES_DIR = '/home/mka/Programs/fhi-aims.071711_6/species_defaults/light/'
LOG_FILE = open("ase-qm-mm-output.log", "w")
sys.stdout = LOG_FILE
infile_name = sys.argv[1]
CALC_QM1 = Aims(charge=0,
xc='pbe',
sc_accuracy_etot=1e-5,
sc_accuracy_eev=1e-2,
sc_accuracy_rho=1e-5,
sc_accuracy_forces=1e-3,
species_dir=SPECIES_DIR,
run_command=RUN_COMMAND)
CALC_QM1.set(output='hirshfeld')
CALC_QM2 = Aims(charge=0,
xc='pbe',
sc_accuracy_etot=1e-5,
sc_accuracy_eev=1e-2,
sc_accuracy_rho=1e-5,
sc_accuracy_forces=1e-3,
species_dir=SPECIES_DIR,
run_command=RUN_COMMAND)
CALC_QM2.set(output='hirshfeld')
width=width,
basis_threshold=basis_threshold,
relativistic=relativistic,
x=x)
if id is None:
continue
# perform EOS step
atoms.set_cell(cell * x, scale_atoms=True)
# set calculator
atoms.calc = Aims(
label=name + '_' + code + '_' + str(n),
species_dir=os.path.join(os.environ['AIMS_SPECIES_DIR'], basis),
xc='PBE',
kpts=kpts,
KS_method='elpa',
sc_accuracy_rho=1.e-4,
sc_accuracy_eev=5.e-3,
occupation_type=['gaussian', width],
override_relativity=True,
override_illconditioning=True,
basis_threshold=basis_threshold,
charge_mix_param=0.01,
)
atoms.calc.set(**kwargs) # remaining calc keywords
t = time.time()
atoms.get_potential_energy()
c.write(atoms,
name=name,
basis=basis,
linspacestr=linspacestr,
kptdensity=kptdensity,
width=width,
def calc(self, **kwargs):
from ase.calculators.aims import Aims
kwargs1 = dict(xc='LDA')
kwargs1.update(kwargs)
return Aims(command=self.executable, **kwargs1)
from ase import Atoms
from ase.visualize import view
from ase.calculators.aims import Aims, AimsCube
from ase.optimize import QuasiNewton
water = Atoms('HOH', [(1, 0, 0), (0, 0, 0), (0, 1, 0)])
water_cube = AimsCube(points=(29, 29, 29),
plots=('total_density', 'delta_density', 'eigenstate 5',
'eigenstate 6'))
calc = Aims(
xc='pbe',
sc_accuracy_etot=1e-6,
sc_accuracy_eev=1e-3,
sc_accuracy_rho=1e-6,
sc_accuracy_forces=1e-4,
species_dir=
'/home/hanke/codes/fhi-aims/fhi-aims.workshop/species_defaults/light/',
run_command='aims.workshop.serial.x',
cubes=water_cube)
water.set_calculator(calc)
dynamics = QuasiNewton(water, trajectory='square_water.traj')
dynamics.run(fmax=0.01)
view(water)
from ase.io import read
from ase import Atoms
from ase.calculators.aims import Aims
BEA = read('x.cif')
calc = Aims(xc='pbesol',
k_grid=(2, 2, 2),
spin='none',
relativistic=('atomic_zora', 'scalar'),
vdw_correction_hirshfeld='true',
relax_geometry='trm 1E-2',
relax_unit_cell='full',
sc_accuracy_forces='1E-3')
BEA.set_calculator(calc)
e_BEA = BEA.get_potential_energy()
print(e_BEA)
import os
from ase import Atoms
from ase.optimize import BFGS
from ase.calculators.aims import Aims
from ase.calculators.socketio import SocketIOCalculator
os.environ['ASE_AIMS_COMMAND'] = 'aims.x'
os.environ[
'AIMS_SPECIES_DIR'] = '/home/alumne/software/FHIaims/species_defaults/light'
atoms = Atoms('HOH', positions=[[0, 0, -1], [0, 1, 0], [0, 0, 1]])
opt = BFGS(atoms, trajectory='opt-aims-socketio.traj')
aims = Aims(xc='LDA',
compute_forces=True,
use_pimd_wrapper=('UNIX:mysocket', 31415))
with SocketIOCalculator(aims, unixsocket='mysocket') as calc:
atoms.calc = calc
opt.run(fmax=0.05)
def test_aims_interface():
import tempfile
import os
from ase.calculators.aims import Aims
from ase import Atoms
# test the new command handling + legacy behavior
aims_command = 'aims.x'
aims_command_alternative = 'mpirun -np 4 fhiaims.x'
outfilename = 'alternative_aims.out'
outfilename_default = 'aims.out'
command = '{0:s} > {1:s}'.format(aims_command, outfilename)
#command_alternative = '{0:s} > {1:s}'.format(aims_command_alternative, outfilename)
command_default = '{0:s} > {1:s}'.format(aims_command, outfilename_default)
legacy_command = 'aims.version.serial.x > aims.out'
legacy_aims_command = legacy_command.split('>')[0].strip()
legacy_outfilename = legacy_command.split('>')[-1].strip()
# legacy behavior of empty init
calc = Aims()
assert calc.command == legacy_command
assert calc.outfilename == legacy_outfilename
assert calc.aims_command == legacy_aims_command
# behavior of empty init with env variable
os.environ['ASE_AIMS_COMMAND'] = aims_command_alternative
calc = Aims()
assert calc.command == '{0} > {1}'.format(aims_command_alternative,
outfilename_default)
assert calc.outfilename == outfilename_default
assert calc.aims_command == aims_command_alternative
# legacy behavior of "proper" command
calc = Aims(run_command=command)
assert calc.command == command
assert calc.outfilename == outfilename
assert calc.aims_command == aims_command
# legacy behavior of an "improper" command
calc = Aims(run_command=aims_command)
assert calc.command == command_default
assert calc.aims_command == aims_command
assert calc.outfilename == outfilename_default
# fixed "command" behavior
calc = Aims(command=command)
assert calc.command == command
assert calc.outfilename == outfilename
assert calc.aims_command == aims_command
# novel way to use aims_command, no specific outfile
calc = Aims(aims_command=aims_command)
assert calc.command == command_default
assert calc.outfilename == outfilename_default
assert calc.aims_command == aims_command
calc = Aims(aims_command=aims_command, outfilename=outfilename)
assert calc.command == command
assert calc.outfilename == outfilename
assert calc.aims_command == aims_command
# # testing the setters
calc.command = command_default
assert calc.outfilename == outfilename_default
assert calc.aims_command == aims_command
assert calc.command == command_default
#calc.set_aims_command(aims_command_alternative)
calc.aims_command = aims_command_alternative
assert calc.aims_command == aims_command_alternative
assert calc.outfilename == outfilename_default
assert calc.command == '{} > {}'.format(aims_command_alternative,
outfilename_default)
calc.outfilename = outfilename
assert calc.command == '{} > {}'.format(aims_command_alternative,
outfilename)
assert calc.aims_command == aims_command_alternative
assert calc.outfilename == outfilename
# test writing files
tmp_dir = tempfile.mkdtemp()
water = Atoms('HOH', [(1, 0, 0), (0, 0, 0), (0, 1, 0)])
calc = Aims(
xc='PBE',
output=['dipole'],
sc_accuracy_etot=1e-6,
sc_accuracy_eev=1e-3,
sc_accuracy_rho=1e-6,
species_dir="/data/rittmeyer/FHIaims/species_defaults/light/",
sc_accuracy_forces=1e-4,
label=tmp_dir,
)
try:
calc.prepare_input_files()
raise AssertionError
except ValueError:
pass
calc.atoms = water
calc.prepare_input_files()
for f in ['control.in', 'geometry.in']:
assert os.path.isfile(os.path.join(tmp_dir, f))
from ase.calculators.aims import Aims
from ase.visualize import view
from ase.build import fcc111, bulk, surface
from ase.constraints import FixAtoms, FixBondLengths
from ase.io import write
from ase.io import read
from ase.calculators.emt import EMT
a = 3.909 # approximate lattice constant
b = a / 2
calc = Aims(xc='pbe',
spin='none',
k_grid=(9,9,9),
vdw_correction_hirshfeld="True",
relativistic=('atomic_zora','scalar'),
#use_dipole_correction='True',
compute_forces="true",
output=['mulliken'],
# elsi_restart=("write",1)
)
bulk = Atoms('Pd',
cell=[(0, b, b), (b, 0, b), (b, b, 0)],
pbc=1,
calculator=calc) # use EMT potential
bulk.get_potential_energy()
#traj.write(bulk)
energy_bulk=bulk.get_potential_energy()
print ("potential-energy-bulk", energy_bulk)
#print (energy_bulk)
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import numpy as np
mydb = connect("mydb.db")
atoms = mydb.get_atoms(name='ceo2')
energies = []
lattices = []
thetas = []
calc = Aims(label='bulk/ceo2-relax',
xc='pbe',
spin='none',
relativistic = 'atomic_zora scalar',
kpts=(9, 9, 9), # specifies the Monkhorst-Pack grid
sc_accuracy_etot=1e-5,
sc_accuracy_eev=1e-2,
sc_accuracy_rho=1e-4,
sc_accuracy_forces=1e-3,
relax_geometry = 'bfgs 5e-3',
relax_unit_cell = 'full')
atoms.set_calculator(calc)
energies.append(atoms.get_potential_energy())
mydb.write(atoms, name='ceo2-relax', relax=True)
lattices.append(norm(atoms.cell[0]))
thetas.append(arccos(dot(atoms.cell[0], atoms.cell[1]) /
(norm(atoms.cell[0]) * norm(atoms.cell[0])))/pi*180)
print('----------------------------')
print('# U lattice constant (A) angle (degree) energy (eV) ')
print(' {0:1.2f} {1:1.4f} {2:1.2f} {3:1.5f}'
# test the new command handling + legacy behavior
aims_command = 'aims.x'
aims_command_alternative = 'mpirun -np 4 fhiaims.x'
outfilename = 'alternative_aims.out'
outfilename_default = 'aims.out'
command = '{0:s} > {1:s}'.format(aims_command, outfilename)
command_alternative = '{0:s} > {1:s}'.format(aims_command_alternative,
outfilename)
command_default = '{0:s} > {1:s}'.format(aims_command, outfilename_default)
legacy_command = 'aims.version.serial.x > aims.out'
legacy_aims_command = legacy_command.split('>')[0].strip()
legacy_outfilename = legacy_command.split('>')[-1].strip()
# legacy behavior of empty init
calc = Aims()
assert calc.command == legacy_command
assert calc.outfilename == legacy_outfilename
assert calc.aims_command == legacy_aims_command
# behavior of empty init with env variable
os.environ['ASE_AIMS_COMMAND'] = aims_command_alternative
calc = Aims()
assert calc.command == '{0} > {1}'.format(aims_command_alternative,
outfilename_default)
assert calc.outfilename == outfilename_default
assert calc.aims_command == aims_command_alternative
# legacy behavior of "proper" command
calc = Aims(run_command=command)
assert calc.command == command
def __init__(self, nodes=1, ppn=8, **kwargs):
Aims.__init__(self, **kwargs)
self.nodes = nodes
self.ppn = ppn
from ase.calculators.socketio import SocketIOCalculator
# Environment-dependent parameters -- please configure according to machine
# Note that FHI-aim support for the i-PI protocol must be specifically
# enabled at compile time, e.g.: make -f Makefile.ipi ipi.mpi
species_dir = '/home/aimsuser/src/fhi-aims.171221_1/species_defaults/light'
command = 'ipi.aims.171221_1.mpi.x'
# This example uses INET; see other examples for how to use UNIX sockets.
port = 31415
atoms = molecule('H2O', vacuum=3.0)
atoms.rattle(stdev=0.1)
aims = Aims(
command=command,
use_pimd_wrapper=('localhost', port),
# alternative: ('UNIX:mysocketname', 31415)
# (numeric port must be given even with Unix socket)
compute_forces=True,
xc='LDA',
species_dir=species_dir)
opt = BFGS(atoms, trajectory='opt.aims.traj', logfile='opt.aims.log')
with SocketIOCalculator(aims, log=sys.stdout, port=port) as calc:
# For running with UNIX socket, put unixsocket='mysocketname'
# instead of port cf. aims parameters above
atoms.calc = calc
opt.run(fmax=0.05)
from ase import Atoms
from ase.calculators.aims import Aims, AimsCube
from ase.optimize import QuasiNewton
water = Atoms('HOH', [(1, 0, 0), (0, 0, 0), (0, 1, 0)])
water_cube = AimsCube(points=(29, 29, 29),
plots=('total_density', 'delta_density', 'eigenstate 5',
'eigenstate 6'))
calc = Aims(xc='PBE',
output=['dipole'],
sc_accuracy_etot=1e-6,
sc_accuracy_eev=1e-3,
sc_accuracy_rho=1e-6,
sc_accuracy_forces=1e-4,
cubes=water_cube)
water.set_calculator(calc)
dynamics = QuasiNewton(water, trajectory='square_water.traj')
dynamics.run(fmax=0.01)
from ase import Atoms
from ase.io import read
from ase.constraints import FixAtoms
from ase.optimize import QuasiNewton
from ase.calculators.aims import Aims
from ase.vibrations import Vibrations
BEAH = read('BEAH.cif')
calc = Aims(xc='pbesol',
relativistic='atomic_zora', 'scalar',
k_grid=(2,2,2),
vdw_correction='hirshfeld',
sc_accuracy_etot=1e-4,
sc_accuracy_eev=1e-4,
sc_accuracy_rho=1e-4,
sc_accuracy_forces=1e-4))
BEAH.set_calculator(calc)
from ase.constraints import FixAtoms
c = FixAtoms(indices=[i for i in range(0,192)])
BEAH.set_constraint(c)
e0 = BEAH.get_potential_energy()
QuasiNewton(BEAH).run(fmax=0.05)
from ase.vibrations import Vibrations