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[pre-commit.ci] auto fixes from pre-commit.com hooks
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pre-commit-ci[bot] committed Jul 1, 2024
1 parent 99d6ee7 commit 7abf43e
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Showing 13 changed files with 266 additions and 264 deletions.
166 changes: 82 additions & 84 deletions aiida_fleur/cmdline/launch/launch.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -155,7 +155,7 @@ def launch_fleur(fleurinp, fleur, parent_folder, settings, daemon, max_num_machi


@click.command('scf')
@options.STRUCTURE_OR_FILE(default="inp.xml", show_default=True)
@options.STRUCTURE_OR_FILE(default='inp.xml', show_default=True)
@options.INPGEN()
@options.CALC_PARAMETERS()
@options.SETTINGS()
Expand All @@ -171,13 +171,13 @@ def launch_scf(structure, inpgen, calc_parameters, fleurinp, fleur, wf_parameter
"""
Launch a scf workchain
"""
fleurinp=None
fleurinp = None

if isinstance(structure, FleurinpData):
fleurinp=structure
structure=None
inpgen=None
fleurinp = structure
structure = None
inpgen = None

workchain_class = WorkflowFactory('fleur.scf')
inputs = {
'inpgen': inpgen,
Expand All @@ -194,31 +194,32 @@ def launch_scf(structure, inpgen, calc_parameters, fleurinp, fleur, wf_parameter
inputs = clean_nones(inputs)
builder = workchain_class.get_builder()
builder.update(inputs)
pk=utils.launch_process(builder, daemon)
pk = utils.launch_process(builder, daemon)

#Now create output files
if fleurinp and not daemon:
from aiida.orm import load_node
wf=load_node(pk)
scf_output=wf.outputs.output_scf_wc_para.get_dict()
scf_output["SCF-uuid"]=wf.uuid
wf = load_node(pk)
scf_output = wf.outputs.output_scf_wc_para.get_dict()
scf_output['SCF-uuid'] = wf.uuid

#json with dict
import json
with open("scf.json","w") as file:
json.dump(scf_output,file,indent=2)
with open('scf.json', 'w') as file:
json.dump(scf_output, file, indent=2)
#plot
from aiida_fleur.tools.plot.fleur import plot_fleur
plot_fleur(wf,save=True,show=False)
plot_fleur(wf, save=True, show=False)

#store files
for file in ["out.xml","cdn1","cdn_last.hdf"]:
for file in ['out.xml', 'cdn1', 'cdn_last.hdf']:
if file in wf.outputs.last_calc.retrieved.list_object_names():
with open(file,"wb") as f:
f.write(wf.outputs.last_calc.retrieved.get_object_content(file,"rb"))
with open(file, 'wb') as f:
f.write(wf.outputs.last_calc.retrieved.get_object_content(file, 'rb'))


@click.command('relax')
@options.STRUCTURE_OR_FILE(default="inp.xml", show_default=True)
@options.STRUCTURE_OR_FILE(default='inp.xml', show_default=True)
@options.INPGEN()
@options.CALC_PARAMETERS()
@options.FLEUR()
Expand All @@ -235,19 +236,16 @@ def launch_relax(structure, inpgen, calc_parameters, fleur, wf_parameters, scf_p
# TODO final scf input
"""
from aiida_fleur.workflows.relax import FleurRelaxWorkChain

if isinstance(structure, FleurinpData):
fleurinp=structure
structure=None
inpgen=None
fleurinp = structure
structure = None
inpgen = None

# we need a scf_paramters dict to change the forcemix if required later
if scf_parameters==None:
scf_parameters=Dict(dict= {
'force_dict': {'forcemix': 'BFGS'},
'inpxml_changes': []
})

if scf_parameters == None:
scf_parameters = Dict(dict={'force_dict': {'forcemix': 'BFGS'}, 'inpxml_changes': []})

#workchain_class = WorkflowFactory('fleur.base_relax')
inputs = {
'scf': {
Expand All @@ -262,37 +260,36 @@ def launch_relax(structure, inpgen, calc_parameters, fleur, wf_parameters, scf_p
'wf_parameters': wf_parameters
}


inputs = clean_nones(inputs)
builder = FleurRelaxWorkChain.get_builder()
builder.update(inputs)
pk=utils.launch_process(builder, daemon)
pk = utils.launch_process(builder, daemon)

#Now create output files
if fleurinp and not daemon:
from aiida.orm import load_node
wf=load_node(pk)
relax_output=wf.outputs.output_relax_wc_para.get_dict()
relax_output["Relax-uuid"]=wf.uuid
relax_output["retrieved-uuid"]=wf.outputs.last_scf.last_calc.retrieved.uuid


wf = load_node(pk)
relax_output = wf.outputs.output_relax_wc_para.get_dict()
relax_output['Relax-uuid'] = wf.uuid
relax_output['retrieved-uuid'] = wf.outputs.last_scf.last_calc.retrieved.uuid

#json with dict
import json
with open("relax.json","w") as file:
json.dump(relax_output,file,indent=2)
with open('relax.json', 'w') as file:
json.dump(relax_output, file, indent=2)
#plot
from aiida_fleur.tools.plot.fleur import plot_fleur
plot_fleur([wf],save=True,show=False)
plot_fleur([wf], save=True, show=False)

#store files
for file in ["relax.xml","out.xml","cdn1","cdn_last.hdf"]:
for file in ['relax.xml', 'out.xml', 'cdn1', 'cdn_last.hdf']:
if file in wf.outputs.last_scf.last_calc.retrieved.list_object_names():
with open(file,"wb") as f:
f.write(wf.outputs.last_scf.last_calc.retrieved.get_object_content(file,"rb"))
with open(file, 'wb') as f:
f.write(wf.outputs.last_scf.last_calc.retrieved.get_object_content(file, 'rb'))


@click.command('eos')
@options.STRUCTURE_OR_FILE(default="inp.xml", show_default=True)
@options.STRUCTURE_OR_FILE(default='inp.xml', show_default=True)
@options.INPGEN()
@options.CALC_PARAMETERS()
@options.FLEUR()
Expand All @@ -307,13 +304,13 @@ def launch_eos(structure, inpgen, calc_parameters, fleur, wf_parameters, scf_par
"""

workchain_class = WorkflowFactory('fleur.eos')
fleurinp=None

fleurinp = None

if isinstance(structure, FleurinpData):
fleurinp=structure
structure=None
fleurinp = structure
structure = None

inputs = {
'scf': {
'wf_parameters': scf_parameters,
Expand All @@ -329,34 +326,34 @@ def launch_eos(structure, inpgen, calc_parameters, fleur, wf_parameters, scf_par
inputs = clean_nones(inputs)
builder = workchain_class.get_builder()
builder.update(inputs)
pk=utils.launch_process(builder, daemon)
pk = utils.launch_process(builder, daemon)

#Now create output files
if fleurinp and not daemon:
from aiida.orm import load_node
wf=load_node(pk)
eos_output=wf.outputs.output_eos_wc_para.get_dict()
wf = load_node(pk)
eos_output = wf.outputs.output_eos_wc_para.get_dict()
#json with dict
import json
with open("eos.json","w") as file:
json.dump(eos_output,file,indent=2)
with open('eos.json', 'w') as file:
json.dump(eos_output, file, indent=2)
#cif file
if "output_eos_wc_structure" in wf.outputs:
if 'output_eos_wc_structure' in wf.outputs:
import os.path
if os.path.isfile("opt_struct.cif"): os.remove("opt_struct.cif")
cif_struct=wf.outputs.output_eos_wc_structure.get_cif()
cif_struct.export("opt_struct.cif")
if os.path.isfile('opt_struct.cif'):
os.remove('opt_struct.cif')
cif_struct = wf.outputs.output_eos_wc_structure.get_cif()
cif_struct.export('opt_struct.cif')
#plot
if eos_output["volume_gs"] >0 :
if eos_output['volume_gs'] > 0:
from aiida_fleur.tools.plot.fleur import plot_fleur
plot_fleur(wf,save=True,show=False)

for i,uuid in enumerate(eos_output["calculations"]):
scf=load_node(uuid)
scale=eos_output["scaling"][i]
with open(f"out_{scale}.xml","w") as f:
f.write(scf.outputs.last_calc.retrieved.get_object_content("out.xml"))
plot_fleur(wf, save=True, show=False)

for i, uuid in enumerate(eos_output['calculations']):
scf = load_node(uuid)
scale = eos_output['scaling'][i]
with open(f"out_{scale}.xml", 'w') as f:
f.write(scf.outputs.last_calc.retrieved.get_object_content('out.xml'))


@click.command('dos')
Expand All @@ -371,15 +368,15 @@ def launch_dos(fleurinp, fleur, wf_parameters, parent_folder, daemon, settings,
"""
Launch a banddos workchain (special command to set the dos as a default mode)
"""
if wf_parameters==None:
wf_parameters=Dict({"mode":"dos"})
if wf_parameters == None:
wf_parameters = Dict({'mode': 'dos'})
else:
wf_dict=wf_parameters.get_dict()
wf_dict["mode"]="dos"
wf_parameters=Dict(wf_dict)
wf_dict = wf_parameters.get_dict()
wf_dict['mode'] = 'dos'
wf_parameters = Dict(wf_dict)

launch_banddos(fleurinp, fleur, wf_parameters, parent_folder, daemon, settings, option_node)


@click.command('band')
@options.FLEURINP(default='inp.xml')
Expand All @@ -395,11 +392,12 @@ def launch_band(fleurinp, fleur, wf_parameters, parent_folder, daemon, settings,
"""
#Band is default
launch_banddos(fleurinp, fleur, wf_parameters, parent_folder, daemon, settings, option_node)



def launch_banddos(fleurinp, fleur, wf_parameters, parent_folder, daemon, settings, option_node):
"""
Launch a banddos workchain
"""
"""
workchain_class = WorkflowFactory('fleur.banddos')
inputs = {
'wf_parameters': wf_parameters,
Expand All @@ -411,23 +409,23 @@ def launch_banddos(fleurinp, fleur, wf_parameters, parent_folder, daemon, settin
inputs = clean_nones(inputs)
builder = workchain_class.get_builder()
builder.update(inputs)
pk=utils.launch_process(builder, daemon)
pk = utils.launch_process(builder, daemon)

#Now create output files
from aiida.orm import load_node
wf=load_node(pk)
banddos_output=wf.outputs.output_banddos_wc_para.get_dict()
wf = load_node(pk)
banddos_output = wf.outputs.output_banddos_wc_para.get_dict()
#json with dict
import json
with open("banddos.json","w") as file:
json.dump(banddos_output,file,indent=2)
#the banddos.hdf file
with open(f"banddos.hdf","wb") as f:
f.write(wf.outputs.banddos_calc.retrieved.get_object_content("banddos.hdf",'rb'))
with open('banddos.json', 'w') as file:
json.dump(banddos_output, file, indent=2)
#the banddos.hdf file
with open(f"banddos.hdf", 'wb') as f:
f.write(wf.outputs.banddos_calc.retrieved.get_object_content('banddos.hdf', 'rb'))

#plot
from aiida_fleur.tools.plot.fleur import plot_fleur
plot_fleur(wf,save=True,show=False)
plot_fleur(wf, save=True, show=False)


@click.command('init_cls')
Expand Down
23 changes: 10 additions & 13 deletions aiida_fleur/cmdline/util/__init__.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -13,8 +13,8 @@
'''
import click
import json
from .defaults import get_code_interactive,get_default_dict

from .defaults import get_code_interactive, get_default_dict
from aiida.cmdline.utils import decorators


Expand All @@ -24,20 +24,17 @@
def cmd_defaults():
"""Interactively create/modify the default settings for aiida-fleur CLI."""

dict=get_default_dict()
dict = get_default_dict()

#default codes
dict["fleur"]=get_code_interactive("fleur.fleur",dict["fleur"])
dict["inpgen"]=get_code_interactive("fleur.inpgen",dict["inpgen"])
dict['fleur'] = get_code_interactive('fleur.fleur', dict['fleur'])
dict['inpgen'] = get_code_interactive('fleur.inpgen', dict['inpgen'])

import os
HOME=os.getenv("HOME")
HOME = os.getenv('HOME')
try:
os.mkdir(f"{HOME}/.aiida-fleur")
except:
pass #dir might exist already
with open(f"{HOME}/.aiida-fleur/cli.json","w") as f:
json.dump(dict,f)



pass #dir might exist already
with open(f"{HOME}/.aiida-fleur/cli.json", 'w') as f:
json.dump(dict, f)
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