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gpawsolve.py
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gpawsolve.py
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#!/usr/bin/env python
'''
gpawsolve.py: High-level Interaction Script for GPAW
More information: $ gpawsolve.py -h
'''
Description = f'''
Usage:
$ mpirun -np <corenumbers> gpawsolve.py <args>
-------------------------------------------------------------
Calculation selector
-------------------------------------------------------------
| Method | XCs | Structure optim. | Spin | Ground | Elastic | DOS | DFT+U | Band | Density | Optical |
| ------ | --------------- | ---------------- | ---- | ------ | ------- | --- | ----- | ---- | ------- | ------- |
| PW | Local and LibXC | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes |
| PW | GLLBSC / M | No | Yes | Yes | Yes | Yes | No | Yes | Yes | Yes |
| PW | HSE03, HSE06 | No | Yes | Yes | n/a | Yes | No | No | No | No |
| PW-G0W0| Local and LibXC | No | No | Yes | No | No | No | Some | No | No |
| LCAO | Local and LibXC | No | Yes | Yes | Yes | Yes | Yes | Yes | Yes | No |
*: Just some ground state energy calculations.
'''
import getopt, sys, os, time, shutil
import textwrap
import requests
import pickle
from argparse import ArgumentParser, HelpFormatter
from ase import *
from ase.spacegroup import get_spacegroup
from ase.dft.kpoints import get_special_points
from ase.parallel import paropen, world, parprint, broadcast
from gpaw import GPAW, PW, Davidson, FermiDirac, MixerSum, MixerDif, Mixer
from ase.optimize import QuasiNewton
from ase.io import read, write
from ase.eos import calculate_eos
from ase.units import Bohr, GPa, kJ
import matplotlib.pyplot as plt
from ase.constraints import FixSymmetry
from ase.filters import FrechetCellFilter
from ase.io.cif import write_cif
from pathlib import Path
from gpaw.response.df import DielectricFunction
from gpaw.response.bse import BSE
from gpaw.response.g0w0 import G0W0
from gpaw.response.gw_bands import GWBands
from gpaw.dos import DOSCalculator
from gpaw.utilities.dos import raw_orbital_LDOS
import numpy as np
from numpy import genfromtxt
from elastic import get_elastic_tensor, get_elementary_deformations
from phonopy import Phonopy
from phonopy.structure.atoms import PhonopyAtoms
from phonopy.phonon.band_structure import get_band_qpoints_and_path_connections
import phonopy
import pandas as pd
import warnings
warnings.filterwarnings('ignore')
class RawFormatter(HelpFormatter):
"""To print Description variable with argparse"""
def _fill_text(self, text, width, indent):
return "\n".join([textwrap.fill(line, width) for line in textwrap.indent(textwrap.dedent(text), indent).splitlines()])
def struct_from_file(inputfile, geometryfile):
"""Load variables from parse function"""
global bulk_configuration
# Works like from FILE import *
inputf = __import__(Path(inputfile).stem, globals(), locals(), ['*'])
for k in dir(inputf):
# Still can not get rid of global variable usage :(
globals()[k] = getattr(inputf, k)
# If there is a CIF input, use it. Otherwise use the bulk configuration provided above.
if geometryfile is None:
if Outdirname !='':
struct = Outdirname
else:
struct = 'results' # All files will get their names from this file
else:
struct = Path(geometryfile).stem
bulk_configuration = read(geometryfile, index='-1')
parprint("Number of atoms imported from CIF file:"+str(bulk_configuration.get_global_number_of_atoms()))
parprint("Spacegroup of CIF file:",get_spacegroup(bulk_configuration, symprec=1e-2))
parprint("Special Points usable for this spacegroup:",get_special_points(bulk_configuration.get_cell()))
# Output directory
if Outdirname != '':
structpath = os.path.join(os.getcwd(),Outdirname)
else:
structpath = os.path.join(os.getcwd(),struct)
if not os.path.isdir(structpath):
os.makedirs(structpath, exist_ok=True)
struct = os.path.join(structpath,struct)
return struct
def autoscale_y(ax,margin=0.1):
"""This function rescales the y-axis based on the data that is visible given the current xlim of the axis.
ax -- a matplotlib axes object
margin -- the fraction of the total height of the y-data to pad the upper and lower ylims"""
import numpy as np
def get_bottom_top(line):
xd = line.get_xdata()
yd = line.get_ydata()
lo,hi = ax.get_xlim()
y_displayed = yd[((xd>lo) & (xd<hi))]
h = np.max(y_displayed) - np.min(y_displayed)
bot = np.min(y_displayed)-margin*h
top = np.max(y_displayed)+margin*h
return bot,top
lines = ax.get_lines()
bot,top = np.inf, -np.inf
for line in lines:
new_bot, new_top = get_bottom_top(line)
if new_bot < bot: bot = new_bot
if new_top > top: top = new_top
ax.set_ylim(bot,top)
class gpawsolve:
"""
The gpawsolve class is a high-level interaction script for GPAW calculations.
It handles various types of calculations such as ground state, structure optimization,
elastic properties, density of states, band structure, density, and optical properties.
The class takes input parameters from a configuration file and performs the calculations
accordingly.
"""
def __init__(self, struct):
global np
self.Mode = Mode
self.Geo_optim = Geo_optim
self.Elastic_calc = Elastic_calc
self.DOS_calc = DOS_calc
self.Band_calc = Band_calc
self.Density_calc = Density_calc
self.Optical_calc = Optical_calc
self.Optimizer = Optimizer
self.Max_F_tolerance = Max_F_tolerance
self.Max_step = Max_step
self.Alpha = Alpha
self.Damping = Damping
self.Fix_symmetry = Fix_symmetry
self.Relax_cell = Relax_cell
self.Hydrostatic_pressure = Hydrostatic_pressure
self.Cut_off_energy = Cut_off_energy
self.Ground_kpts_density = Ground_kpts_density
self.Ground_kpts_x = Ground_kpts_x
self.Ground_kpts_y = Ground_kpts_y
self.Ground_kpts_z = Ground_kpts_z
self.Ground_gpts_density = Ground_gpts_density
self.Ground_gpts_x = Ground_gpts_x
self.Ground_gpts_y = Ground_gpts_y
self.Ground_gpts_z = Ground_gpts_z
self.Setup_params = Setup_params
self.XC_calc = XC_calc
self.Ground_convergence = Ground_convergence
self.Occupation = Occupation
self.Mixer_type = Mixer_type
self.Spin_calc = Spin_calc
self.Magmom_per_atom = Magmom_per_atom
self.Magmom_single_atom = Magmom_single_atom
self.DOS_npoints = DOS_npoints
self.DOS_width = DOS_width
self.DOS_convergence = DOS_convergence
self.Gamma = Gamma
self.Band_path = Band_path
self.Band_npoints = Band_npoints
self.Energy_max = Energy_max
self.Energy_min = Energy_min
self.Band_convergence = Band_convergence
self.Refine_grid = Refine_grid
self.Phonon_PW_cutoff = Phonon_PW_cutoff
self.Phonon_kpts_x = Phonon_kpts_x
self.Phonon_kpts_y = Phonon_kpts_y
self.Phonon_kpts_z = Phonon_kpts_z
self.Phonon_supercell = Phonon_supercell
self.Phonon_displacement = Phonon_displacement
self.Phonon_path = Phonon_path
self.Phonon_npoints = Phonon_npoints
self.Phonon_acoustic_sum_rule = Phonon_acoustic_sum_rule
self.GW_calc_type = GW_calc_type
self.GW_kpoints_list = GW_kpoints_list
self.GW_truncation = GW_truncation
self.GW_cut_off_energy = GW_cut_off_energy
self.GW_valence_band_no = GW_valence_band_no
self.GW_conduction_band_no = GW_conduction_band_no
self.GW_PPA = GW_PPA
self.GW_q0_correction = GW_q0_correction
self.GW_nblocks_max = GW_nblocks_max
self.GW_interpolate_band = GW_interpolate_band
self.Opt_calc_type = Opt_calc_type
self.Opt_shift_en = Opt_shift_en
self.Opt_BSE_valence = Opt_BSE_valence
self.Opt_BSE_conduction = Opt_BSE_conduction
self.Opt_BSE_min_en = Opt_BSE_min_en
self.Opt_BSE_max_en = Opt_BSE_max_en
self.Opt_BSE_num_of_data = Opt_BSE_num_of_data
self.Opt_num_of_bands = Opt_num_of_bands
self.Opt_FD_smearing = Opt_FD_smearing
self.Opt_eta = Opt_eta
self.Opt_domega0 = Opt_domega0
self.Opt_omega2 = Opt_omega2
self.Opt_cut_of_energy = Opt_cut_of_energy
self.Opt_nblocks = Opt_nblocks
self.MPI_cores = MPI_cores
self.Localisation = Localisation
self.bulk_configuration = bulk_configuration
self.struct = struct
self.dos_xlabel = dos_xlabel
self.dos_ylabel = dos_ylabel
self.band_ylabel = band_ylabel
def structurecalc(self):
"""
This method calculates and writes the spacegroup and special points of the given structure.
It reads the bulk configuration from the CIF file and prints the number of atoms, spacegroup,
and special points usable for the spacegroup to a text file.
"""
# -------------------------------------------------------------
# Step 0 - STRUCTURE
# -------------------------------------------------------------
with paropen(struct+'-0-Result-Spacegroup-and-SpecialPoints.txt', "w") as fd:
print("Number of atoms imported from CIF file:"+str(bulk_configuration.get_global_number_of_atoms()), file=fd)
print("Spacegroup of CIF file:",get_spacegroup(bulk_configuration, symprec=1e-2), file=fd)
print("Special Points usable for this spacegroup:",get_special_points(bulk_configuration.get_cell()), file=fd)
def groundcalc(self):
"""
This method performs ground state calculations for the given structure using various settings
and parameters specified in the configuration file. It handles different XC functionals,
spin calculations, and geometry optimizations. The results are saved in appropriate files,
including the final configuration as a CIF file and the ground state results in a GPW file.
"""
# -------------------------------------------------------------
# Step 1 - GROUND STATE
# -------------------------------------------------------------
# Start ground state timing
time11 = time.time()
if Mode == 'PW':
if Spin_calc == True:
if 'Magmom_single_atom' in globals() and Magmom_single_atom is not None:
numm = [0.0]*bulk_configuration.get_global_number_of_atoms()
numm[Magmom_single_atom[0]] = Magmom_single_atom[1]
else:
numm = [Magmom_per_atom]*bulk_configuration.get_global_number_of_atoms()
bulk_configuration.set_initial_magnetic_moments(numm)
if Ground_calc == True:
# PW Ground State Calculations
parprint("Starting PW ground state calculation...")
if True in Relax_cell:
if XC_calc in ['GLLBSC', 'GLLBSCM', 'HSE06', 'HSE03','B3LYP', 'PBE0','EXX']:
parprint("\033[91mERROR:\033[0m Structure optimization LBFGS can not be used with "+XC_calc+" xc.")
parprint("Do manual structure optimization, or do with PBE, then use its final CIF as input.")
parprint("Quiting...")
quit()
if XC_calc in ['HSE06', 'HSE03','B3LYP', 'PBE0','EXX']:
parprint('Starting Hybrid XC calculations...')
if 'Ground_kpts_density' in globals() and Ground_kpts_density is not None:
calc = GPAW(mode=PW(ecut=Cut_off_energy, force_complex_dtype=True), xc={'name': XC_calc, 'backend': 'pw'}, nbands='200%',
parallel={'band': 1, 'kpt': 1}, eigensolver=Davidson(niter=1), mixer=Mixer_type, charge=Total_charge,
spinpol=Spin_calc, kpts={'density': Ground_kpts_density, 'gamma': Gamma}, txt=struct+'-1-Log-Ground.txt',
convergence = Ground_convergence, occupations = Occupation)
else:
calc = GPAW(mode=PW(ecut=Cut_off_energy, force_complex_dtype=True), xc={'name': XC_calc, 'backend': 'pw'}, nbands='200%',
parallel={'band': 1, 'kpt': 1}, eigensolver=Davidson(niter=1), mixer=Mixer_type, charge=Total_charge,
spinpol=Spin_calc, kpts={'size': (Ground_kpts_x, Ground_kpts_y, Ground_kpts_z), 'gamma': Gamma}, txt=struct+'-1-Log-Ground.txt',
convergence = Ground_convergence, occupations = Occupation)
else:
parprint('Starting calculations with '+XC_calc+'...')
# Fix the spacegroup in the geometric optimization if wanted
if Fix_symmetry == True:
bulk_configuration.set_constraint(FixSymmetry(bulk_configuration))
if 'Ground_kpts_density' in globals() and Ground_kpts_density is not None:
calc = GPAW(mode=PW(ecut=Cut_off_energy, force_complex_dtype=True), xc=XC_calc, nbands='200%', setups= Setup_params,
parallel={'domain': world.size}, spinpol=Spin_calc, kpts={'density': Ground_kpts_density, 'gamma': Gamma},
mixer=Mixer_type, txt=struct+'-1-Log-Ground.txt', charge=Total_charge,
convergence = Ground_convergence, occupations = Occupation)
else:
calc = GPAW(mode=PW(ecut=Cut_off_energy, force_complex_dtype=True), xc=XC_calc, nbands='200%', setups= Setup_params,
parallel={'domain': world.size}, spinpol=Spin_calc, kpts={'size': (Ground_kpts_x, Ground_kpts_y, Ground_kpts_z), 'gamma': Gamma},
mixer=Mixer_type, txt=struct+'-1-Log-Ground.txt', charge=Total_charge,
convergence = Ground_convergence, occupations = Occupation)
bulk_configuration.calc = calc
if Geo_optim == True:
if True in Relax_cell:
if Hydrostatic_pressure > 0.0:
uf = FrechetCellFilter(bulk_configuration, mask=Relax_cell, hydrostatic_strain=True, scalar_pressure=Hydrostatic_pressure)
else:
uf = FrechetCellFilter(bulk_configuration, mask=Relax_cell)
# Optimizer Selection
if Optimizer == 'FIRE':
from ase.optimize.fire import FIRE
relax = FIRE(uf, maxstep=Max_step, trajectory=struct+'-1-Result-Ground.traj')
elif Optimizer == 'LBFGS':
from ase.optimize.lbfgs import LBFGS
relax = LBFGS(uf, maxstep=Max_step, alpha=Alpha, damping=Damping, trajectory=struct+'-1-Result-Ground.traj')
elif Optimizer == 'GPMin':
from ase.optimize import GPMin
relax = GPMin(uf, trajectory=struct+'-1-Result-Ground.traj')
else:
relax = QuasiNewton(uf, maxstep=Max_step, trajectory=struct+'-1-Result-Ground.traj')
else:
# Optimizer Selection
if Optimizer == 'FIRE':
from ase.optimize.fire import FIRE
relax = FIRE(bulk_configuration, maxstep=Max_step, trajectory=struct+'-1-Result-Ground.traj')
elif Optimizer == 'LBFGS':
from ase.optimize.lbfgs import LBFGS
relax = LBFGS(bulk_configuration, maxstep=Max_step, alpha=Alpha, damping=Damping, trajectory=struct+'-1-Result-Ground.traj')
elif Optimizer == 'GPMin':
from ase.optimize import GPMin
relax = GPMin(bulk_configuration, trajectory=struct+'-1-Result-Ground.traj')
else:
relax = QuasiNewton(bulk_configuration, maxstep=Max_step, trajectory=struct+'-1-Result-Ground.traj')
relax.run(fmax=Max_F_tolerance) # Consider tighter fmax!
else:
bulk_configuration.set_calculator(calc)
bulk_configuration.get_potential_energy()
if Density_calc == True:
#This line makes huge GPW files. Therefore it is better to use this if else
calc.write(struct+'-1-Result-Ground.gpw', mode="all")
else:
calc.write(struct+'-1-Result-Ground.gpw')
# Writes final configuration as CIF file
write_cif(struct+'-Final.cif', bulk_configuration)
else:
parprint("Passing PW ground state calculation...")
# Control the ground state GPW file
if not os.path.exists(struct+'-1-Result-Ground.gpw'):
parprint('\033[91mERROR:\033[0m'+struct+'-1-Result-Ground.gpw file can not be found. It is needed in other calculations. Firstly, finish the ground state calculation. You must have \033[95mGround_calc = True\033[0m line in your input file. Quiting.')
quit()
elif Mode == 'PW-GW':
if Ground_calc == True:
# PW Ground State Calculations
parprint("Starting PW only ground state calculation for GW calculation...")
# Fix the spacegroup in the geometric optimization if wanted
if Fix_symmetry == True:
bulk_configuration.set_constraint(FixSymmetry(bulk_configuration))
if 'Ground_kpts_density' in globals() and Ground_kpts_density is not None:
calc = GPAW(mode=PW(Cut_off_energy), xc=XC_calc, parallel={'domain': 1}, kpts={'density': Ground_kpts_density, 'gamma': Gamma},
convergence = Ground_convergence, charge=Total_charge,
mixer=Mixer_type, occupations = Occupation, txt=struct+'-1-Log-Ground.txt')
else:
calc = GPAW(mode=PW(Cut_off_energy), xc=XC_calc, parallel={'domain': 1}, kpts={'size':(Ground_kpts_x, Ground_kpts_y, Ground_kpts_z), 'gamma': Gamma},
convergence = Ground_convergence, charge=Total_charge,
mixer=Mixer_type, occupations = Occupation, txt=struct+'-1-Log-Ground.txt')
bulk_configuration.calc = calc
if Hydrostatic_pressure > 0.0:
uf = FrechetCellFilter(bulk_configuration, mask=Relax_cell, hydrostatic_strain=True, scalar_pressure=Hydrostatic_pressure)
else:
uf = FrechetCellFilter(bulk_configuration, mask=Relax_cell)
# Optimizer Selection
if Optimizer == 'FIRE':
from ase.optimize.fire import FIRE
relax = FIRE(uf, maxstep=Max_step, trajectory=struct+'-1-Result-Ground.traj')
elif Optimizer == 'LBFGS':
from ase.optimize.lbfgs import LBFGS
relax = LBFGS(uf, maxstep=Max_step, alpha=Alpha, damping=Damping, trajectory=struct+'-1-Result-Ground.traj')
elif Optimizer == 'GPMin':
from ase.optimize import GPMin
relax = GPMin(uf, trajectory=struct+'-1-Result-Ground.traj')
else:
relax = QuasiNewton(uf, maxstep=Max_step, trajectory=struct+'-1-Result-Ground.traj')
relax.run(fmax=Max_F_tolerance) # Consider tighter fmax!
bulk_configuration.get_potential_energy()
calc.diagonalize_full_hamiltonian()
calc.write(struct+'-1-Result-Ground.gpw', mode="all")
# Writes final configuration as CIF file
write_cif(struct+'-Final.cif', bulk_configuration)
# Print final spacegroup information
parprint("Final Spacegroup:",get_spacegroup(bulk_configuration, symprec=1e-2))
else:
parprint("Passing ground state calculation for GW calculation...")
# Control the ground state GPW file
if not os.path.exists(struct+'-1-Result-Ground.gpw'):
parprint('\033[91mERROR:\033[0m'+struct+'-1-Result-Ground.gpw file can not be found. It is needed in other calculations. Firstly, finish the ground state calculation. You must have \033[95mGround_calc = True\033[0m line in your input file. Quiting.')
quit()
# We start by setting up a G0W0 calculator object
gw = G0W0(struct+'-1-Result-Ground.gpw', filename=struct+'-1-', bands=(GW_valence_band_no, GW_conduction_band_no),
method=GW_calc_type,truncation=GW_truncation, nblocksmax=GW_nblocks_max,
maxiter=5, q0_correction=GW_q0_correction, charge=Total_charge,
mixing=0.5,savepckl=True,
ecut=GW_cut_off_energy, ppa=GW_PPA)
parprint("Starting PW ground state calculation with G0W0 approximation...")
gw.calculate()
results = pickle.load(open(struct+'-1-_results.pckl', 'rb'))
with paropen(struct+'-1-BandGap.txt', "w") as fd:
print('Quasi particle (QP) energies in eV. Take CB-VB for the bandgap', file=fd)
print('To see other energy contributions, use python -mpickle <picklefile>', file=fd)
for x in zip(results['qp']):
print(*x, sep=", ", file=fd)
elif Mode == 'LCAO':
if Spin_calc == True:
if 'Magmom_single_atom' in globals() and Magmom_single_atom is not None:
numm = [0.0]*bulk_configuration.get_global_number_of_atoms()
numm[Magmom_single_atom[0]] = Magmom_single_atom[1]
else:
numm = [Magmom_per_atom]*bulk_configuration.get_global_number_of_atoms()
bulk_configuration.set_initial_magnetic_moments(numm)
if Ground_calc == True:
parprint("Starting LCAO ground state calculation...")
# Fix the spacegroup in the geometric optimization if wanted
if Fix_symmetry == True:
bulk_configuration.set_constraint(FixSymmetry(bulk_configuration))
if 'Ground_gpts_density' in globals() and Ground_gpts_density is not None:
if 'Ground_kpts_density' in globals() and Ground_kpts_density is not None:
calc = GPAW(mode='lcao', basis='dzp', setups= Setup_params, kpts={'density': Ground_kpts_density, 'gamma': Gamma},
convergence = Ground_convergence, h=Ground_gpts_density, spinpol=Spin_calc, txt=struct+'-1-Log-Ground.txt',
mixer=Mixer_type, occupations = Occupation, nbands='200%', parallel={'domain': world.size}, charge=Total_charge)
else:
calc = GPAW(mode='lcao', basis='dzp', setups= Setup_params, kpts={'size':(Ground_kpts_x, Ground_kpts_y, Ground_kpts_z), 'gamma': Gamma},
convergence = Ground_convergence, h=Ground_gpts_density, spinpol=Spin_calc, txt=struct+'-1-Log-Ground.txt',
mixer=Mixer_type, occupations = Occupation, nbands='200%', parallel={'domain': world.size}, charge=Total_charge)
else:
if 'Ground_kpts_density' in globals() and Ground_kpts_density is not None:
calc = GPAW(mode='lcao', basis='dzp', setups= Setup_params, kpts={'density': Ground_kpts_density, 'gamma': Gamma},
convergence = Ground_convergence, gpts=(Ground_gpts_x, Ground_gpts_y, Ground_gpts_z), spinpol=Spin_calc, txt=struct+'-1-Log-Ground.txt',
mixer=Mixer_type, occupations = Occupation, nbands='200%', parallel={'domain': world.size}, charge=Total_charge)
else:
calc = GPAW(mode='lcao', basis='dzp', setups= Setup_params, kpts={'size':(Ground_kpts_x, Ground_kpts_y, Ground_kpts_z), 'gamma': Gamma},
convergence = Ground_convergence, gpts=(Ground_gpts_x, Ground_gpts_y, Ground_gpts_z), spinpol=Spin_calc, txt=struct+'-1-Log-Ground.txt',
mixer=Mixer_type, occupations = Occupation, nbands='200%', parallel={'domain': world.size}, charge=Total_charge)
bulk_configuration.calc = calc
if Geo_optim == True:
if True in Relax_cell:
#uf = FrechetCellFilter(bulk_configuration, mask=Relax_cell)
#relax = LBFGS(uf, maxstep=Max_step, alpha=Alpha, damping=Damping, trajectory=struct+'-1-Result-Ground.traj')
parprint('\033[91mERROR:\033[0mModifying supercell and atom positions with a filter (Relax_cell keyword) is not implemented in LCAO mode.')
quit()
else:
# Optimizer Selection
if Optimizer == 'FIRE':
from ase.optimize.fire import FIRE
relax = FIRE(bulk_configuration, maxstep=Max_step, trajectory=struct+'-1-Result-Ground.traj')
elif Optimizer == 'LBFGS':
from ase.optimize.lbfgs import LBFGS
relax = LBFGS(bulk_configuration, maxstep=Max_step, alpha=Alpha, damping=Damping, trajectory=struct+'-1-Result-Ground.traj')
elif Optimizer == 'GPMin':
from ase.optimize import GPMin
relax = GPMin(bulk_configuration, trajectory=struct+'-1-Result-Ground.traj')
else:
relax = QuasiNewton(bulk_configuration, maxstep=Max_step, trajectory=struct+'-1-Result-Ground.traj')
relax.run(fmax=Max_F_tolerance) # Consider tighter fmax!
else:
bulk_configuration.set_calculator(calc)
bulk_configuration.get_potential_energy()
#relax = LBFGS(bulk_configuration, maxstep=Max_step, alpha=Alpha, damping=Damping, trajectory=struct+'-1-Result-Ground.traj')
#relax.run(fmax=Max_F_tolerance) # Consider much tighter fmax!
#bulk_configuration.get_potential_energy()
if Density_calc == True:
#This line makes huge GPW files. Therefore it is better to use this if else
calc.write(struct+'-1-Result-Ground.gpw', mode="all")
else:
calc.write(struct+'-1-Result-Ground.gpw')
# Writes final configuration as CIF file
write_cif(struct+'-Final.cif', bulk_configuration)
# Print final spacegroup information
parprint("Final Spacegroup:",get_spacegroup(bulk_configuration, symprec=1e-2))
else:
parprint("Passing LCAO ground state calculation...")
# Control the ground state GPW file
if not os.path.exists(struct+'-1-Result-Ground.gpw'):
parprint('\033[91mERROR:\033[0m'+struct+'-1-Result-Ground.gpw file can not be found. It is needed in other calculations. Firstly, finish the ground state calculation. You must have \033[95mGround_calc = True\033[0m line in your input file. Quiting.')
quit()
elif Mode == 'FD':
parprint("\033[91mERROR:\033[0mFD mode is not implemented in gpaw-tools yet...")
quit()
else:
parprint("\033[91mERROR:\033[0mPlease enter correct mode information.")
quit()
# Finish ground state timing
time12 = time.time()
# Write timings of calculation
with paropen(struct+'-7-Result-Log-Timings.txt', 'a') as f1:
print('Ground state: ', round((time12-time11),2), end="\n", file=f1)
def elasticcalc(self, drawfigs = False):
"""
This method performs elastic property calculations for the given structure using the
ground state results. It computes the elastic constants, bulk modulus, shear modulus,
and other related properties. The results are saved in appropriate files for further
analysis and visualization.
"""
# -------------------------------------------------------------
# Step 1.5 - ELASTIC CALCULATION
# -------------------------------------------------------------
# Start elastic calc
time151 = time.time()
parprint('Starting elastic tensor calculations (\033[93mWARNING:\033[0mNOT TESTED FEATURE, PLEASE CONTROL THE RESULTS)...')
calc = GPAW(struct+'-1-Result-Ground.gpw').fixed_density(txt=struct+'-1.5-Log-Elastic.txt')
# Getting space group
parprint("Spacegroup:",get_spacegroup(bulk_configuration, symprec=1e-2))
# Calculating equation of state
parprint('Calculating equation of state...')
eos = calculate_eos(bulk_configuration, trajectory=struct+'-1.5-Result-Elastic.traj')
v, e, B = eos.fit()
# Calculating elastic tensor
parprint('Calculating elastic tensor...')
Cij, Bij=get_elastic_tensor(bulk_configuration,get_elementary_deformations(bulk_configuration, n=5, d=2))
with paropen(struct+'-1.5-Result-Elastic.txt', "w") as fd:
print("Elastic calculation results (NOT TESTED FEATURE, PLEASE CONTROL THE RESULTS):", file=fd)
print("EoS: Stabilized jellium equation of state (SJEOS)", file=fd)
print("Refs: Phys.Rev.B 63, 224115 (2001) and Phys.Rev.B 67, 026103 (2003)", file=fd)
print("Elastic constants: Standart elasticity theory calculated by -Elastic- library", file=fd)
print("Ref: European Physical Journal B; 15, 2 (2000) 265-268", file=fd)
print("-----------------------------------------------------------------------------", file=fd)
print("Spacegroup: "+str(get_spacegroup(bulk_configuration, symprec=1e-2)), file=fd)
print("B (GPa): "+str(B / kJ * 1.0e24), file=fd)
print("e (eV): "+str(e), file=fd)
print("v (Ang^3): "+str(v), file=fd)
print("Cij (GPa): ",Cij/GPa, file=fd)
print("The general ordering of Cij components is (except triclinic): C11,C22,C33,C12,C13,C23,C44,C55,C66,C16,C26,C36,C45.", file=fd)
# Finish elastic calc
time152 = time.time()
# Write timings of calculation
with paropen(struct+'-7-Result-Log-Timings.txt', 'a') as f1:
print('Elastic calculation: ', round((time152-time151),2), end="\n", file=f1)
# Draw or write the figure
if drawfigs == True:
# Draw graphs only on master node
if world.rank == 0:
# Elastic
eos.plot(struct+'-1.5-Graph-Elastic-EOS.png', show=True)
else:
# Draw graphs only on master node
if world.rank == 0:
# Elastic
eos.plot(struct+'-1.5-Result-Elastic-EOS.png')
def doscalc(self, drawfigs = False):
"""
This method performs density of states (DOS) calculations for the given structure using
the ground state results. It computes the DOS for various energy levels and saves the
results in appropriate files for further electronic analysis and visualization.
"""
# -------------------------------------------------------------
# Step 2 - DOS CALCULATION
# -------------------------------------------------------------
# Start DOS calc
time21 = time.time()
parprint("Starting DOS calculation...")
if XC_calc in ['HSE06', 'HSE03','B3LYP', 'PBE0','EXX']:
parprint('Passing DOS NSCF calculations...')
calc = GPAW().read(filename=struct+'-1-Result-Ground.gpw')
ef=0.0 # Can not find the use get_fermi_level()
else:
calc = GPAW(struct+'-1-Result-Ground.gpw').fixed_density(txt=struct+'-2-Log-DOS.txt', convergence = DOS_convergence, occupations = Occupation)
ef = calc.get_fermi_level()
chem_sym = bulk_configuration.get_chemical_symbols()
if Spin_calc == True:
#Spin down
# RAW PDOS for spin down
parprint("Calculating and saving Raw PDOS for spin down...")
if ef==0.0:
rawdos = DOSCalculator.from_calculator(filename=struct+'-1-Result-Ground.gpw',soc=False, theta=0.0, phi=0.0, shift_fermi_level=True)
else:
rawdos = DOSCalculator.from_calculator(filename=struct+'-1-Result-Ground.gpw',soc=False, theta=0.0, phi=0.0, shift_fermi_level=False)
energies = rawdos.get_energies(npoints=DOS_npoints)
# Weights
pdossweightsdown = [0.0] * DOS_npoints
pdospweightsdown = [0.0] * DOS_npoints
pdospxweightsdown = [0.0] * DOS_npoints
pdospyweightsdown = [0.0] * DOS_npoints
pdospzweightsdown = [0.0] * DOS_npoints
pdosdweightsdown = [0.0] * DOS_npoints
pdosdxyweightsdown = [0.0] * DOS_npoints
pdosdyzweightsdown = [0.0] * DOS_npoints
pdosd3z2_r2weightsdown = [0.0] * DOS_npoints
pdosdzxweightsdown = [0.0] * DOS_npoints
pdosdx2_y2weightsdown = [0.0] * DOS_npoints
pdosfweightsdown = [0.0] * DOS_npoints
totaldosweightsdown = [0.0] * DOS_npoints
# Writing RawPDOS
with paropen(struct+'-2-Result-RawPDOS-EachAtom-Down.csv', "w") as fd:
print("Energy, s-total, p-total, px, py, pz, d-total, dxy, dyz, d3z2_r2, dzx, dx2_y2, f-total, TOTAL", file=fd)
for j in range(0, bulk_configuration.get_global_number_of_atoms()):
print("Atom no: "+str(j+1)+", Atom Symbol: "+chem_sym[j]+" --------------------", file=fd)
pdoss = rawdos.raw_pdos(energies, a=j, l=0, m=None, spin=0, width=DOS_width)
pdosp = rawdos.raw_pdos(energies, a=j, l=1, m=None, spin=0, width=DOS_width)
pdospx = rawdos.raw_pdos(energies, a=j, l=1, m=2, spin=0, width=DOS_width)
pdospy = rawdos.raw_pdos(energies, a=j, l=1, m=0, spin=0, width=DOS_width)
pdospz = rawdos.raw_pdos(energies, a=j, l=1, m=1, spin=0, width=DOS_width)
pdosd = rawdos.raw_pdos(energies, a=j, l=2, m=None, spin=0, width=DOS_width)
pdosdxy = rawdos.raw_pdos(energies, a=j, l=2, m=0, spin=0, width=DOS_width)
pdosdyz = rawdos.raw_pdos(energies, a=j, l=2, m=1, spin=0, width=DOS_width)
pdosd3z2_r2 = rawdos.raw_pdos(energies, a=j, l=2, m=2, spin=0, width=DOS_width)
pdosdzx = rawdos.raw_pdos(energies, a=j, l=2, m=3, spin=0, width=DOS_width)
pdosdx2_y2 = rawdos.raw_pdos(energies, a=j, l=2, m=4, spin=0, width=DOS_width)
pdosf = rawdos.raw_pdos(energies, a=j, l=3, m=None, spin=0, width=DOS_width)
dosspdf = pdoss + pdosp + pdosd + pdosf
# Weights
pdossweightsdown = pdossweightsdown + pdoss
pdospweightsdown = pdospweightsdown + pdosp
pdospxweightsdown = pdospxweightsdown + pdospx
pdospyweightsdown = pdospyweightsdown + pdospy
pdospzweightsdown = pdospzweightsdown + pdospz
pdosdweightsdown = pdosdweightsdown + pdosd
pdosdxyweightsdown = pdosdxyweightsdown + pdosd
pdosdyzweightsdown = pdosdyzweightsdown + pdosd
pdosd3z2_r2weightsdown = pdosd3z2_r2weightsdown + pdosd
pdosdzxweightsdown = pdosdzxweightsdown + pdosd
pdosdx2_y2weightsdown = pdosdx2_y2weightsdown + pdosd
pdosfweightsdown = pdosfweightsdown + pdosf
totaldosweightsdown = totaldosweightsdown + dosspdf
for x in zip(energies, pdoss, pdosp, pdospx, pdospy, pdospz, pdosd, pdosdxy, pdosdyz, pdosd3z2_r2, pdosdzx, pdosdx2_y2, pdosf, dosspdf):
print(*x, sep=", ", file=fd)
# Writing DOS
parprint("Saving DOS for spin down...")
with paropen(struct+'-2-Result-DOS-Down.csv', "w") as fd:
for x in zip(energies, totaldosweightsdown):
print(*x, sep=", ", file=fd)
# Writing PDOS
parprint("Saving PDOS for spin down...")
with paropen(struct+'-2-Result-PDOS-Down.csv', "w") as fd:
print("Energy, s-total, p-total, px, py, pz, d-total, dxy, dyz, d3z2_r2, dzx, dx2_y2, f-total, TOTAL", file=fd)
for x in zip(energies, pdossweightsdown, pdospweightsdown, pdospxweightsdown, pdospyweightsdown, pdospzweightsdown, pdosdweightsdown,
pdosdxyweightsdown, pdosdyzweightsdown, pdosd3z2_r2weightsdown, pdosdzxweightsdown, pdosdx2_y2weightsdown, pdosfweightsdown, totaldosweightsdown):
print(*x, sep=", ", file=fd)
#Spin up
# RAW PDOS for spin up
parprint("Calculating and saving Raw PDOS for spin up...")
rawdos = DOSCalculator.from_calculator(struct+'-1-Result-Ground.gpw',soc=False, theta=0.0, phi=0.0, shift_fermi_level=True)
energies = rawdos.get_energies(npoints=DOS_npoints)
# Weights
pdossweightsup = [0.0] * DOS_npoints
pdospweightsup = [0.0] * DOS_npoints
pdospxweightsup = [0.0] * DOS_npoints
pdospyweightsup = [0.0] * DOS_npoints
pdospzweightsup = [0.0] * DOS_npoints
pdosdweightsup = [0.0] * DOS_npoints
pdosdxyweightsup = [0.0] * DOS_npoints
pdosdyzweightsup = [0.0] * DOS_npoints
pdosd3z2_r2weightsup = [0.0] * DOS_npoints
pdosdzxweightsup = [0.0] * DOS_npoints
pdosdx2_y2weightsup = [0.0] * DOS_npoints
pdosfweightsup = [0.0] * DOS_npoints
totaldosweightsup = [0.0] * DOS_npoints
#Writing RawPDOS
with paropen(struct+'-2-Result-RawPDOS-EachAtom-Up.csv', "w") as fd:
print("Energy, s-total, p-total, px, py, pz, d-total, dxy, dyz, d3z2_r2, dzx, dx2_y2, f-total, TOTAL", file=fd)
for j in range(0, bulk_configuration.get_global_number_of_atoms()):
print("Atom no: "+str(j+1)+", Atom Symbol: "+chem_sym[j]+" --------------------", file=fd)
pdoss = rawdos.raw_pdos(energies, a=j, l=0, m=None, spin=1, width=DOS_width)
pdosp = rawdos.raw_pdos(energies, a=j, l=1, m=None, spin=1, width=DOS_width)
pdospx = rawdos.raw_pdos(energies, a=j, l=1, m=2, spin=1, width=DOS_width)
pdospy = rawdos.raw_pdos(energies, a=j, l=1, m=0, spin=1, width=DOS_width)
pdospz = rawdos.raw_pdos(energies, a=j, l=1, m=1, spin=1, width=DOS_width)
pdosd = rawdos.raw_pdos(energies, a=j, l=2, m=None, spin=1, width=DOS_width)
pdosdxy = rawdos.raw_pdos(energies, a=j, l=2, m=0, spin=1, width=DOS_width)
pdosdyz = rawdos.raw_pdos(energies, a=j, l=2, m=1, spin=1, width=DOS_width)
pdosd3z2_r2 = rawdos.raw_pdos(energies, a=j, l=2, m=2, spin=1, width=DOS_width)
pdosdzx = rawdos.raw_pdos(energies, a=j, l=2, m=3, spin=1, width=DOS_width)
pdosdx2_y2 = rawdos.raw_pdos(energies, a=j, l=2, m=4, spin=1, width=DOS_width)
pdosf = rawdos.raw_pdos(energies, a=j, l=3, m=None, spin=1, width=DOS_width)
dosspdf = pdoss + pdosp + pdosd + pdosf
# Weights
pdossweightsup = pdossweightsup + pdoss
pdospweightsup = pdospweightsup + pdosp
pdospxweightsup = pdospxweightsup + pdospx
pdospyweightsup = pdospyweightsup + pdospy
pdospzweightsup = pdospzweightsup + pdospz
pdosdweightsup = pdosdweightsup + pdosd
pdosdxyweightsup = pdosdxyweightsup + pdosd
pdosdyzweightsup = pdosdyzweightsup + pdosd
pdosd3z2_r2weightsup = pdosd3z2_r2weightsup + pdosd
pdosdzxweightsup = pdosdzxweightsup + pdosd
pdosdx2_y2weightsup = pdosdx2_y2weightsup + pdosd
pdosfweightsup = pdosfweightsup + pdosf
totaldosweightsup = totaldosweightsup + dosspdf
for x in zip(energies, pdoss, pdosp, pdospx, pdospy, pdospz, pdosd, pdosdxy, pdosdyz, pdosd3z2_r2, pdosdzx, pdosdx2_y2, pdosf, dosspdf):
print(*x, sep=", ", file=fd)
# Writing DOS
parprint("Saving DOS for spin up...")
with paropen(struct+'-2-Result-DOS-Up.csv', "w") as fd:
for x in zip(energies, totaldosweightsup):
print(*x, sep=", ", file=fd)
# Writing PDOS
parprint("Saving PDOS for spin up...")
with paropen(struct+'-2-Result-PDOS-Up.csv', "w") as fd:
print("Energy, s-total, p-total, px, py, pz, d-total, dxy, dyz, d3z2_r2, dzx, dx2_y2, f-total, TOTAL", file=fd)
for x in zip(energies, pdossweightsup, pdospweightsup, pdospxweightsup, pdospyweightsup, pdospzweightsup, pdosdweightsup, pdosdxyweightsup,
pdosdyzweightsup, pdosd3z2_r2weightsup, pdosdzxweightsup, pdosdx2_y2weightsup, pdosfweightsup, totaldosweightsup):
print(*x, sep=", ", file=fd)
else:
# RAW PDOS
parprint("Calculating and saving Raw PDOS...")
rawdos = DOSCalculator.from_calculator(struct+'-1-Result-Ground.gpw',soc=False, theta=0.0, phi=0.0, shift_fermi_level=True)
energies = rawdos.get_energies(npoints=DOS_npoints)
totaldosweights = [0.0] * DOS_npoints
pdossweights = [0.0] * DOS_npoints
pdospweights = [0.0] * DOS_npoints
pdospxweights = [0.0] * DOS_npoints
pdospyweights = [0.0] * DOS_npoints
pdospzweights = [0.0] * DOS_npoints
pdosdweights = [0.0] * DOS_npoints
pdosdxyweights = [0.0] * DOS_npoints
pdosdyzweights = [0.0] * DOS_npoints
pdosd3z2_r2weights = [0.0] * DOS_npoints
pdosdzxweights = [0.0] * DOS_npoints
pdosdx2_y2weights = [0.0] * DOS_npoints
pdosfweights = [0.0] * DOS_npoints
# Writing RawPDOS
with paropen(struct+'-2-Result-RawPDOS-EachAtom.csv', "w") as fd:
print("Energy, s-total, p-total, px, py, pz, d-total, dxy, dyz, d3z2_r2, dzx, dx2_y2, f-total, TOTAL", file=fd)
for j in range(0, bulk_configuration.get_global_number_of_atoms()):
print("Atom no: "+str(j+1)+", Atom Symbol: "+chem_sym[j]+" ----------------------------------------", file=fd)
pdoss = rawdos.raw_pdos(energies, a=j, l=0, m=None, spin=None, width=DOS_width)
pdosp = rawdos.raw_pdos(energies, a=j, l=1, m=None, spin=None, width=DOS_width)
pdospx = rawdos.raw_pdos(energies, a=j, l=1, m=2, spin=None, width=DOS_width)
pdospy = rawdos.raw_pdos(energies, a=j, l=1, m=0, spin=None, width=DOS_width)
pdospz = rawdos.raw_pdos(energies, a=j, l=1, m=1, spin=None, width=DOS_width)
pdosd = rawdos.raw_pdos(energies, a=j, l=2, m=None, spin=None, width=DOS_width)
pdosdxy = rawdos.raw_pdos(energies, a=j, l=2, m=0, spin=None, width=DOS_width)
pdosdyz = rawdos.raw_pdos(energies, a=j, l=2, m=1, spin=None, width=DOS_width)
pdosd3z2_r2 = rawdos.raw_pdos(energies, a=j, l=2, m=2, spin=None, width=DOS_width)
pdosdzx = rawdos.raw_pdos(energies, a=j, l=2, m=3, spin=None, width=DOS_width)
pdosdx2_y2 = rawdos.raw_pdos(energies, a=j, l=2, m=4, spin=None, width=DOS_width)
pdosf = rawdos.raw_pdos(energies, a=j, l=3, m=None, spin=None, width=DOS_width)
# Weights
dosspdf = pdoss + pdosp + pdosd + pdosf
pdossweights = pdossweights + pdoss
pdospweights = pdospweights + pdosp
pdospxweights = pdospxweights + pdospx
pdospyweights = pdospyweights + pdospy
pdospzweights = pdospzweights + pdospz
pdosdweights = pdosdweights + pdosd
pdosdxyweights = pdosdxyweights + pdosd
pdosdyzweights = pdosdyzweights + pdosd
pdosd3z2_r2weights = pdosd3z2_r2weights + pdosd
pdosdzxweights = pdosdzxweights + pdosd
pdosdx2_y2weights = pdosdx2_y2weights + pdosd
pdosfweights = pdosfweights + pdosf
totaldosweights = totaldosweights + dosspdf
for x in zip(energies, pdoss, pdosp, pdospx, pdospy, pdospz, pdosd, pdosdxy, pdosdyz, pdosd3z2_r2, pdosdzx, pdosdx2_y2, pdosf, dosspdf):
print(*x, sep=", ", file=fd)
# Writing DOS
parprint("Saving DOS...")
with paropen(struct+'-2-Result-DOS.csv', "w") as fd:
for x in zip(energies, totaldosweights):
print(*x, sep=", ", file=fd)
# Writing PDOS
parprint("Saving PDOS...")
with paropen(struct+'-2-Result-PDOS.csv', "w") as fd:
print("Energy, s-total, p-total, px, py, pz, d-total, dxy, dyz, d3z2_r2, dzx, dx2_y2, f-total, TOTAL", file=fd)
for x in zip(energies, pdossweights, pdospweights, pdospxweights, pdospyweights, pdospzweights, pdosdweights, pdosdxyweights, pdosdyzweights,
pdosd3z2_r2weights, pdosdzxweights, pdosdx2_y2weights, pdosfweights, totaldosweights):
print(*x, sep=", ", file=fd)
# Finish DOS calc
time22 = time.time()
# Write timings of calculation
with paropen(struct+'-7-Result-Log-Timings.txt', 'a') as f1:
print('DOS calculation: ', round((time22-time21),2), end="\n", file=f1)
# Write or draw figures
if drawfigs == True:
# Draw graphs only on master node
if world.rank == 0:
# DOS
if Spin_calc == True:
downf = pd.read_csv(struct+'-2-Result-DOS-Down.csv', header=None)
upf = pd.read_csv(struct+'-2-Result-DOS-Up.csv', header=None)
downf[0]=downf[0]+ef
upf[0]=upf[0]+ef
ax = plt.gca()
ax.plot(downf[0], -1.0*downf[1], 'y')
ax.plot(upf[0], upf[1], 'b')
ax.set_xlabel(dos_xlabel[Localisation])
ax.set_ylabel(dos_ylabel[Localisation])
else:
dosf = pd.read_csv(struct+'-2-Result-DOS.csv', header=None)
dosf[0]=dosf[0]+ef
ax = plt.gca()
ax.plot(dosf[0], dosf[1], 'b')
ax.set_xlabel(dos_xlabel[Localisation])
ax.set_ylabel(dos_ylabel[Localisation])
plt.xlim(Energy_min+ef, Energy_max+ef)
autoscale_y(ax)
plt.savefig(struct+'-2-Graph-DOS.png', dpi=300)
#plt.show()
else:
# Draw graphs only on master node
if world.rank == 0:
# DOS
if Spin_calc == True:
downf = pd.read_csv(struct+'-2-Result-DOS-Down.csv', header=None)
upf = pd.read_csv(struct+'-2-Result-DOS-Up.csv', header=None)
downf[0]=downf[0]+ef
upf[0]=upf[0]+ef
ax = plt.gca()
ax.plot(downf[0], -1.0*downf[1], 'y')
ax.plot(upf[0], upf[1], 'b')
ax.set_xlabel(dos_xlabel[Localisation])
ax.set_ylabel(dos_ylabel[Localisation])
else:
dosf = pd.read_csv(struct+'-2-Result-DOS.csv', header=None)
dosf[0]=dosf[0]+ef
ax = plt.gca()
ax.plot(dosf[0], dosf[1], 'b')
ax.set_xlabel(dos_xlabel[Localisation])
ax.set_ylabel(dos_ylabel[Localisation])
plt.xlim(Energy_min+ef, Energy_max+ef)
autoscale_y(ax)
plt.savefig(struct+'-2-Graph-DOS.png', dpi=300)
def bandcalc(self, drawfigs = False):
"""
This method performs band structure calculations for the given structure using the
ground state results. It computes the electronic band structure along specified
k-point paths and saves the results in appropriate files for further analysis
and visualization.
"""
# -------------------------------------------------------------
# Step 3 - BAND STRUCTURE CALCULATION
# -------------------------------------------------------------
# Start Band calc
time31 = time.time()
parprint("Starting band structure calculation...")
if Mode == 'PW-GW':
GW = GWBands(calc=struct+'-1-Result-Ground.gpw', fixdensity=True,
gw_file=struct+'-1-_results.pckl',kpoints=GW_kpoints_list)
# Getting results without spin-orbit
results = GW.get_gw_bands(SO=False, interpolate=GW_interpolate_band, vac=True)
# Extracting data
X = results['X']
ef = results['ef']
xdata = results['x_k']
banddata = results['e_kn']
np.savetxt(struct+'-3-Result-Band.dat', np.c_[xdata,banddata])
with open(struct+'-3-Result-Band.dat', 'a') as f:
print ('Symmetry points: ', X, end="\n", file=f)
print ('Fermi Level: ', ef, end="\n", file=f)
else:
if XC_calc in ['HSE06', 'HSE03','B3LYP', 'PBE0','EXX']:
calc = GPAW(struct+'-1-Result-Ground.gpw', symmetry='off',kpts={'path': Band_path, 'npoints': Band_npoints},
parallel={'band':1, 'kpt':1}, occupations = Occupation,
txt=struct+'-3-Log-Band.txt', convergence=Band_convergence)
ef=0.0
else:
calc = GPAW(struct+'-1-Result-Ground.gpw').fixed_density(kpts={'path': Band_path, 'npoints': Band_npoints},
txt=struct+'-3-Log-Band.txt', symmetry='off', occupations = Occupation, convergence=Band_convergence)
ef = calc.get_fermi_level()
calc.get_potential_energy()
bs = calc.band_structure()
Band_num_of_bands = calc.get_number_of_bands()
parprint('Num of bands:'+str(Band_num_of_bands))
# No need to write an additional gpaw file. Use json file to use with ase band-structure command
#calc.write(struct+'-3-Result-Band.gpw')
bs.write(struct+'-3-Result-Band.json')
if Spin_calc == True:
eps_skn = np.array([[calc.get_eigenvalues(k,s)
for k in range(Band_npoints)]
for s in range(2)]) - ef
parprint(eps_skn.shape)
with paropen(struct+'-3-Result-Band-Down.dat', 'w') as f1:
for n1 in range(Band_num_of_bands):
for k1 in range(Band_npoints):
print(k1, eps_skn[0, k1, n1], end="\n", file=f1)
print (end="\n", file=f1)
with paropen(struct+'-3-Result-Band-Up.dat', 'w') as f2:
for n2 in range(Band_num_of_bands):
for k2 in range(Band_npoints):
print(k2, eps_skn[1, k2, n2], end="\n", file=f2)
print (end="\n", file=f2)
# Thanks to Andrej Kesely (https://stackoverflow.com/users/10035985/andrej-kesely) for helping the problem of general XYYY writer
currentd, all_groupsd = [], []
with open(struct+'-3-Result-Band-Down.dat', 'r') as f_in1:
for line in map(str.strip, f_in1):
if line == "" and currentd:
all_groupsd.append(currentd)
currentd = []
else:
currentd.append(line.split(maxsplit=1))
if currentd:
all_groupsd.append(currentd)
try:
with paropen(struct+'-3-Result-Band-Down-XYYY.dat', 'w') as f1:
for g in zip(*all_groupsd):
print('{} {} {}'.format(g[0][0], g[0][1], ' '.join(v for _, v in g[1:])), file=f1)
except Exception as e:
print("\033[93mWARNING:\033[0m A problem occurred during writing XYYY formatted spin down Band file. Mostly, the file is created without any problem.")
print(e)
pass # Continue execution after encountering an exception
currentu, all_groupsu = [], []
with open(struct+'-3-Result-Band-Up.dat', 'r') as f_in2:
for line in map(str.strip, f_in2):
if line == "" and currentu:
all_groupsu.append(currentu)
currentu = []
else:
currentu.append(line.split(maxsplit=1))
if currentu:
all_groupsu.append(currentu)
try:
with paropen(struct+'-3-Result-Band-Up-XYYY.dat', 'w') as f2:
for g in zip(*all_groupsu):
print('{} {} {}'.format(g[0][0], g[0][1], ' '.join(v for _, v in g[1:])), file=f2)
except Exception as e:
print("\033[93mWARNING:\033[0m A problem occurred during writing XYYY formatted spin up Band file. Mostly, the file is created without any problem.")
print(e)
pass # Continue execution after encountering an exception
else:
eps_skn = np.array([[calc.get_eigenvalues(k,s)
for k in range(Band_npoints)]
for s in range(1)]) - ef
with paropen(struct+'-3-Result-Band.dat', 'w') as f:
for n in range(Band_num_of_bands):
for k in range(Band_npoints):
print(k, eps_skn[0, k, n], end="\n", file=f)
print (end="\n", file=f)
# Thanks to Andrej Kesely (https://stackoverflow.com/users/10035985/andrej-kesely) for helping the problem of general XYYY writer
current, all_groups = [], []
with open(struct+'-3-Result-Band.dat', 'r') as f_in:
for line in map(str.strip, f_in):
if line == "" and current:
all_groups.append(current)
current = []
else:
current.append(line.split(maxsplit=1))
if current:
all_groups.append(current)
try:
with paropen(struct+'-3-Result-Band-XYYY.dat', 'w') as f1:
for g in zip(*all_groups):
print('{} {} {}'.format(g[0][0], g[0][1], ' '.join(v for _, v in g[1:])), file=f1)
except Exception as e:
print("\033[93mWARNING:\033[0m A problem occurred during writing XYYY formatted Band file. Mostly, the file is created without any problem.")
print(e)
pass # Continue execution after encountering an exception
# Projected Band
Projected_band = False
if Projected_band == True:
with paropen(struct+'-3-Result-ProjectedBand.dat', 'w') as f3:
for i in range(len(sym_ang_mom_i)):
print('----------------------'+sym_ang_mom_i[i]+'---------------------------', end="\n", file=f3)
for n in range(Band_num_of_bands):
for k in range(Band_npoints):
print(k, projector_weight_skni[0, k, n, i], end="\n", file=f3)
print (end="\n", file=f3)
# Finish Band calc