gabor1
commented
3 years ago When you compiled QUIP, did you turn on "TB support" ?
-- Gábor
Gábor Csányi Professor of Molecular Modelling Engineering Laboratory, University of Cambridge Pembroke College Cambridge
Pembroke College supports CARA. A Lifeline to Academics at Risk. http://www.cara.ngo/
On 8 Dec 2020, at 16:24, Computational-Chem-Nanocluster notifications@github.com wrote:
Hi all,
I was doing a tutorial examples in: https://libatoms.github.io/GAP/gap_si_surface.html?highlight=gap_3b However the below script (copied from the link) gives an error at qm_pot = Potential('TB DFTB', param_filename='dftb-params.xml') line. (Error message is attached in the bottom of the page)
I am not sure how to resolve the error.
Could you please give any advice on this error?
Many thanks.
import os import numpy as np import matplotlib.pylab as plt from quippy.potential import Potential from quippy.descriptors import Descriptor from ase import Atoms, units from ase.build import add_vacuum from ase.lattice.cubic import Diamond from ase.io import write from ase.constraints import FixAtoms from ase.md.velocitydistribution import MaxwellBoltzmannDistribution from ase.md.verlet import VelocityVerlet from ase.md.langevin import Langevin from ase.optimize.precon import PreconLBFGS, Exp sys.path.append('/home/uccatka/software/QUIP/src/GAP/doc_src/gap_si_surface/') from visualise import ViewStructure
T = 1000.0 # Temperature [Kelvin] timestep = 1.0 * units.fs
def build_slab(size=(1,2,2), vacuum=10.):
Build Si lattice.
# lattice = Diamond('Si', directions=([1, 0, 0], [0, 1, 0], [0, 0, 1]), latticeconstant=5.44, size=size) lattice = Diamond('Si', latticeconstant=5.44, size=size) atoms = Atoms(lattice) # Fixing the bottom layer bottom = atoms.positions[:,2].min() fixed_mask = (abs(atoms.positions[:,2] - bottom) < 2.0) atoms.set_constraint(FixAtoms(mask=fixed_mask)) # build surface by adding space to z direction add_vacuum(atoms, vacuum) # atoms.center(vacuum=10.0, axis=2) return atomsatoms = build_slab() print('Number of atoms:', len(atoms))
attach tight binding calculator
qm_pot = Potential('TB DFTB', param_filename='dftb-params.xml') atoms.set_calculator(qm_pot)
Thermalize atoms
MaxwellBoltzmannDistribution(atoms, 2.0 T units.kB)
dynamics = VelocityVerlet(atoms, timestep)
dynamics = Langevin(atoms, timestep, T * units.kB, 0.002)
attach observer to dynamics to track quantity of interest (temperature)
def print_status(): print('Step = {}, time = {} [fs], T = {} [K]'.format( dynamics.nsteps, dynamics.nsteps dynamics.dt / units.fs, atoms.get_kinetic_energy() / (1.5 units.kB * len(atoms)) ))
def print_energy(a=atoms): # store a reference to atoms in the definition. """Function to print the potential, kinetic and total energy.""" epot = a.get_potential_energy() / len(a) ekin = a.get_kinetic_energy() / len(a) print('Energy per atom: Epot = %.3feV Ekin = %.3feV (T=%3.0fK) ' 'Etot = %.3feV' % (epot, ekin, ekin / (1.5 * units.kB), epot + ekin))
dynamics.attach(print_status, interval=10) dynamics.attach(print_energy, interval=1)
reported Error is:
Traceback (most recent call last): File "input.py", line 63, in
qm_pot = Potential('TB DFTB', param_filename='dftb-params.xml') File "/home/uccatka/.local/lib/python3.7/site-packages/quippy-https_github.com_libAtoms_QUIP.git_357e28d_dirty-py3.7-linux-x86_64.egg/quippy/potential.py", line 82, in init param_filename=param_filename) File "/home/uccatka/.local/lib/python3.7/site-packages/quippy-https_github.com_libAtoms_QUIP.git_357e28d_dirty-py3.7-linux-x86_64.egg/quippy/potential_module.py", line 134, in filename_initialise if bulk_scale is None else bulk_scale._handle, error=error) RuntimeError Exception ignored in: <function Potential.del at 0x2ab14599c9d8> Traceback (most recent call last): File "/home/uccatka/.local/lib/python3.7/site-packages/quippy-https_github.com_libAtoms_QUIP.git_357e28d_dirty-py3.7-linux-x86_64.egg/quippy/potential_module.py", line 258, in del _quippy.f90wrap_potential_finalise(this=self._handle, error=error) TypeError: int() argument must be a string, a bytes-like object or a number, not 'NoneType' — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe.
DGKang234
leoil
jiapeng-liu
Amitcuhp
bernstei
wanggrun
Hi all,
I was doing a tutorial examples in: https://libatoms.github.io/GAP/gap_si_surface.html?highlight=gap_3b However the below script (copied from the link) gives an error at qm_pot = Potential('TB DFTB', param_filename='dftb-params.xml') line. (Error message is attached in the bottom of the page)
I am not sure how to resolve the error.
Could you please give any advice on this error?
Many thanks.
reported Error is: