Hello,
I am optimizing the stanene nanoribbon and cluster on it surface, but even 3,4 days it's not converging. I have attached the input file - Can some one guide me what would be the issue due to which it's not converging even after 3,4 days?
# -*- coding: utf-8 -*-
# -------------------------------------------------------------
# Bulk Configuration
# -------------------------------------------------------------
# Set up lattice
vector_a = [87.7884, 0.0, 0.0]*Angstrom
vector_b = [0.0, 175.0, 0.0]*Angstrom
vector_c = [0.0, 0.0, 32.51127454211999]*Angstrom
lattice = UnitCell(vector_a, vector_b, vector_c)
# Define elements
elements = [Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin,
Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin,
Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin,
Tin, Hydrogen, Hydrogen, Hydrogen, Hydrogen, Hydrogen, Hydrogen,
Hydrogen, Hydrogen, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin,
Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin,
Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin, Tin,
Tin, Tin, Tin, Tin, Tin, Hydrogen, Hydrogen, Hydrogen, Hydrogen,
Hydrogen, Hydrogen, Hydrogen, Hydrogen, Tin, Tin, Tin, Tin, Tin,
Tin, Tin, Tin, Tin, Iron, Iron, Tin, Tin, Tin, Tin, Tin, Tin, Tin,
Tin, Tin, Iron]
# Define coordinates
fractional_coordinates = [[ 0.545001091377, 0.439667441783, 0.008394265003],
[ 0.545001091377, 0.439667441783, 0.258394265003],
[ 0.545001091377, 0.439667441783, 0.508394265003],
[ 0.545001091377, 0.439667441783, 0.758394265003],
[ 0.545001091377, 0.466482059909, 0.008394265003],
[ 0.545001091377, 0.466482059909, 0.258394265003],
[ 0.545001091377, 0.466482059909, 0.508394265003],
[ 0.545001091377, 0.466482059909, 0.758394265003],
[ 0.545001091377, 0.493296678034, 0.008394265003],
[ 0.545001091377, 0.493296678034, 0.258394265003],
[ 0.545001091377, 0.493296678034, 0.508394265003],
[ 0.545001091377, 0.493296678034, 0.758394265003],
[ 0.545001091377, 0.520111296159, 0.008394265003],
[ 0.545001091377, 0.520111296159, 0.258394265003],
[ 0.545001091377, 0.520111296159, 0.508394265003],
[ 0.545001091377, 0.520111296159, 0.758394265003],
[ 0.545001091377, 0.546925914284, 0.008394265003],
[ 0.545001091377, 0.546925914284, 0.258394265003],
[ 0.545001091377, 0.546925914284, 0.508394265003],
[ 0.545001091377, 0.546925914284, 0.758394265003],
[ 0.534447034618, 0.439666890916, 0.091815649394],
[ 0.534447034618, 0.439666890916, 0.341815649394],
[ 0.534447034618, 0.439666890916, 0.591815649394],
[ 0.534447034618, 0.439666890916, 0.841815649394],
[ 0.534447034618, 0.466481509041, 0.091815649394],
[ 0.534447034618, 0.466481509041, 0.341815649394],
[ 0.534447034618, 0.466481509041, 0.591815649394],
[ 0.534447034618, 0.466481509041, 0.841815649394],
[ 0.534447034618, 0.520110745291, 0.091815649394],
[ 0.534447034618, 0.520110745291, 0.341815649394],
[ 0.534447034618, 0.520110745291, 0.591815649394],
[ 0.534447034618, 0.520110745291, 0.841815649394],
[ 0.534447034618, 0.546925363416, 0.091815649394],
[ 0.534447034618, 0.546925363416, 0.341815649394],
[ 0.534447034618, 0.546925363416, 0.591815649394],
[ 0.534447034618, 0.546925363416, 0.841815649394],
[ 0.534447034618, 0.493296127166, 0.091815649395],
[ 0.534447034618, 0.493296127166, 0.341815649395],
[ 0.534447034618, 0.493296127166, 0.591815649395],
[ 0.534447034618, 0.493296127166, 0.841815649395],
[ 0.538725180092, 0.568336949088, 0.108590434607],
[ 0.538725180092, 0.568336949088, 0.358590434607],
[ 0.538725180092, 0.568336949088, 0.608590434607],
[ 0.538725180092, 0.568336949088, 0.858590434607],
[ 0.540784511345, 0.431663050912, 0.116665156977],
[ 0.540784511345, 0.431663050912, 0.366665156977],
[ 0.540784511345, 0.431663050912, 0.616665156977],
[ 0.540784511345, 0.431663050912, 0.866665156977],
[ 0.545062656885, 0.533518490939, 0.133439941882],
[ 0.545062656885, 0.533518490939, 0.383439941882],
[ 0.545062656885, 0.533518490939, 0.633439941882],
[ 0.545062656885, 0.533518490939, 0.883439941882],
[ 0.545062656885, 0.453074636564, 0.133439941882],
[ 0.545062656885, 0.453074636564, 0.383439941882],
[ 0.545062656885, 0.453074636564, 0.633439941882],
[ 0.545062656885, 0.453074636564, 0.883439941882],
[ 0.545062656885, 0.479889254689, 0.133439941882],
[ 0.545062656885, 0.479889254689, 0.383439941882],
[ 0.545062656885, 0.479889254689, 0.633439941882],
[ 0.545062656885, 0.479889254689, 0.883439941882],
[ 0.545062656885, 0.506703872814, 0.133439941882],
[ 0.545062656885, 0.506703872814, 0.383439941882],
[ 0.545062656885, 0.506703872814, 0.633439941882],
[ 0.545062656885, 0.506703872814, 0.883439941882],
[ 0.545062656885, 0.560333109065, 0.133439941882],
[ 0.545062656885, 0.560333109065, 0.383439941882],
[ 0.545062656885, 0.560333109065, 0.633439941882],
[ 0.545062656885, 0.560333109065, 0.883439941882],
[ 0.534391508784, 0.453074334526, 0.216743534207],
[ 0.534391508784, 0.453074334526, 0.466743534207],
[ 0.534391508784, 0.453074334526, 0.716743534207],
[ 0.534391508784, 0.453074334526, 0.966743534207],
[ 0.534391508784, 0.479888952651, 0.216743534207],
[ 0.534391508784, 0.479888952651, 0.466743534207],
[ 0.534391508784, 0.479888952651, 0.716743534207],
[ 0.534391508784, 0.479888952651, 0.966743534207],
[ 0.534391508784, 0.506703570776, 0.216743534207],
[ 0.534391508784, 0.506703570776, 0.466743534207],
[ 0.534391508784, 0.506703570776, 0.716743534207],
[ 0.534391508784, 0.506703570776, 0.966743534207],
[ 0.534391508784, 0.533518188901, 0.216743534207],
[ 0.534391508784, 0.533518188901, 0.466743534207],
[ 0.534391508784, 0.533518188901, 0.716743534207],
[ 0.534391508784, 0.533518188901, 0.966743534207],
[ 0.534391508784, 0.560332807026, 0.216743534207],
[ 0.534391508784, 0.560332807026, 0.466743534207],
[ 0.534391508784, 0.560332807026, 0.716743534207],
[ 0.534391508784, 0.560332807026, 0.966743534207],
[ 0.538668007478, 0.431664087298, 0.233532064004],
[ 0.538668007478, 0.431664087298, 0.483532064004],
[ 0.538668007478, 0.431664087298, 0.733532064004],
[ 0.538668007478, 0.431664087298, 0.983532064004],
[ 0.540724592801, 0.56833616151 , 0.241605734997],
[ 0.540724592801, 0.56833616151 , 0.491605734997],
[ 0.540724592801, 0.56833616151 , 0.741605734997],
[ 0.540724592801, 0.56833616151 , 0.991605734997],
[ 0.481191360607, 0.490116494889, 0.433668563691],
[ 0.454937343115, 0.51128640202 , 0.559207748975],
[ 0.457765726314, 0.510467556028, 0.433668031845],
[ 0.481191138358, 0.493838475594, 0.326063421612],
[ 0.457767592128, 0.496900652858, 0.510787308269],
[ 0.454940306488, 0.496082029735, 0.38524772928 ],
[ 0.498185776347, 0.50860527515 , 0.326062205358],
[ 0.46419187606 , 0.508606614722, 0.326063035667],
[ 0.481187018047, 0.518888042359, 0.385245850884],
[ 0.481189107277, 0.503683181452, 0.472227097958],
[ 0.481189352698, 0.503683318637, 0.398966408015],
[ 0.481186853947, 0.517249868015, 0.510785632225],
[ 0.507440871439, 0.496079960885, 0.385246446941],
[ 0.50461248824 , 0.496898806876, 0.510786164071],
[ 0.481187076197, 0.51352788731 , 0.618390774304],
[ 0.504610622426, 0.510465710046, 0.433666887647],
[ 0.507437908066, 0.511284333169, 0.559206466636],
[ 0.464192438208, 0.498761087755, 0.618391990558],
[ 0.498186338494, 0.498759748182, 0.618391160249],
[ 0.481191196508, 0.488478320545, 0.559208345032],
[ 0.481188861857, 0.503683044267, 0.545487787901]]
# Set up configuration
bulk_configuration = BulkConfiguration(
bravais_lattice=lattice,
elements=elements,
fractional_coordinates=fractional_coordinates
)
# -------------------------------------------------------------
# Calculator
# -------------------------------------------------------------
#----------------------------------------
# Exchange-Correlation
#----------------------------------------
exchange_correlation = SGGA.PBE
numerical_accuracy_parameters = NumericalAccuracyParameters(
density_mesh_cutoff=85.0*Hartree,
occupation_method=FermiDirac(0.01*eV),
)
calculator = LCAOCalculator(
exchange_correlation=exchange_correlation,
numerical_accuracy_parameters=numerical_accuracy_parameters,
)
bulk_configuration.setCalculator(calculator)
nlprint(bulk_configuration)
bulk_configuration.update()
nlsave('C-Pre.hdf5', bulk_configuration)
# -------------------------------------------------------------
# Optimize Geometry
# -------------------------------------------------------------
constraints = [FixStrain(x=False, y=False, z=True)]
bulk_configuration = OptimizeGeometry(
bulk_configuration,
max_forces=0.05*eV/Ang,
max_stress=0.1*GPa,
max_steps=200,
max_step_length=0.2*Ang,
constraints=constraints,
trajectory_filename='C-Pre_trajectory.hdf5',
trajectory_interval=5.0*Minute,
restart_strategy=RestartFromTrajectory(),
optimizer_method=LBFGS(),
enable_optimization_stop_file=True,
)
nlsave('C-Pre.hdf5', bulk_configuration)
nlprint(bulk_configuration)
