#!/usr/bin/env runaiida
# -*- coding: utf-8 -*-
from __future__ import absolute_import
from __future__ import print_function
import sys
import os
from aiida.plugins import DataFactory, CalculationFactory
from aiida.orm import List, Dict
from aiida.engine import submit
from aiida_yambo.workflows.yamboconvergence import YamboConvergence
from aiida_quantumespresso.utils.pseudopotential import validate_and_prepare_pseudos_inputs
from ase import Atoms
import argparse
[docs]def get_options():
parser = argparse.ArgumentParser(description='YAMBO calculation.')
parser.add_argument(
'--yambocode',
type=str,
dest='yambocode_id',
required=True,
help='The yambo(main code) codename to use')
parser.add_argument(
'--parent',
type=int,
dest='parent_pk',
required=False,
help='The parent to use')
parser.add_argument(
'--inputparent',
type=int,
dest='inputparent_pk',
required=False,
help='yambo input to use')
parser.add_argument(
'--yamboprecode',
type=str,
dest='yamboprecode_id',
required=True,
help='The precode to use')
parser.add_argument(
'--pwcode',
type=str,
dest='pwcode_id',
required=True,
help='The pw to use')
parser.add_argument(
'--pseudo',
type=str,
dest='pseudo_family',
required=True,
help='The pseudo_family')
parser.add_argument(
'--time',
type=int,
dest='max_wallclock_seconds',
required=False,
default=24*60*60,
help='max wallclock in seconds')
parser.add_argument(
'--nodes',
type=int,
dest='num_machines',
required=False,
default=1,
help='number of machines')
parser.add_argument(
'--mpi',
type=int,
dest='num_mpiprocs_per_machine',
required=False,
default=1,
help='number of mpi processes per machine')
parser.add_argument(
'--threads',
type=int,
dest='num_cores_per_mpiproc',
required=False,
default=1,
help='number of threads per mpi process')
parser.add_argument(
'--queue_name',
type=str,
dest='queue_name',
required=False,
default=None,
help='queue(PBS) or partition(SLURM) name')
parser.add_argument(
'--qos',
type=str,
dest='qos',
required=False,
default=None,
help='qos name')
parser.add_argument(
'--account',
type=str,
dest='account',
required=False,
default=None,
help='account name')
parser.add_argument(
'--group_label',
type=str,
dest='group_label',
required=False,
default=None,
help='group name')
args = parser.parse_args()
###### setting the machine options ######
options = {
'yambocode_id': args.yambocode_id,
'yamboprecode_id': args.yamboprecode_id,
'pwcode_id': args.pwcode_id,
'pseudo_family': args.pseudo_family,
'max_wallclock_seconds': args.max_wallclock_seconds,
'resources': {
"num_machines": args.num_machines,
"num_mpiprocs_per_machine": args.num_mpiprocs_per_machine,
"num_cores_per_mpiproc": args.num_cores_per_mpiproc,
},
'prepend_text': u"export OMP_NUM_THREADS="+str(args.num_cores_per_mpiproc),
}
if args.parent_pk:
options['parent_pk']=args.parent_pk
if args.inputparent_pk:
options['inputparent_pk']=args.inputparent_pk
if args.queue_name:
options['queue_name']=args.queue_name
if args.qos:
options['qos']=args.qos
if args.account:
options['account']=args.account
if args.group_label:
options['group_label']=args.group_label
return options
[docs]def main(options):
###### setting the lattice structure ######
alat = 2.4955987320 # Angstrom
the_cell = [[1.000000*alat, 0.000000, 0.000000],
[-0.500000*alat, 0.866025*alat, 0.000000],
[0.000000, 0.000000, 6.4436359260]]
atoms = Atoms('BNNB', [(1.2477994910, 0.7204172280, 0.0000000000),
(-0.0000001250, 1.4408346720, 0.0000000000),
(1.2477994910, 0.7204172280, 3.2218179630),
(-0.0000001250,1.4408346720, 3.2218179630)],
cell = [1,1,1])
atoms.set_cell(the_cell, scale_atoms=False)
atoms.set_pbc([True,True,True])
StructureData = DataFactory('structure')
structure = StructureData(ase=atoms)
###### setting the kpoints mesh ######
KpointsData = DataFactory('array.kpoints')
kpoints = KpointsData()
kpoints.set_kpoints_mesh([6,6,2])
###### setting the scf parameters ######
Dict = DataFactory('dict')
params_scf = {
'CONTROL': {
'calculation': 'scf',
'verbosity': 'high',
'wf_collect': True
},
'SYSTEM': {
'ecutwfc': 80.,
'force_symmorphic': True,
'nbnd': 20
},
'ELECTRONS': {
'mixing_mode': 'plain',
'mixing_beta': 0.7,
'conv_thr': 1.e-8,
'diago_thr_init': 5.0e-6,
'diago_full_acc': True
},
}
params_nscf = {
'CONTROL': {
'calculation': 'nscf',
'verbosity': 'high',
'wf_collect': True
},
'SYSTEM': {
'ecutwfc': 80.,
'force_symmorphic': True,
'nbnd': 100,
},
'ELECTRONS': {
'mixing_mode': 'plain',
'mixing_beta': 0.7,
'conv_thr': 1.e-8,
'diagonalization': 'david',
'diago_thr_init': 5.0e-6,
'diago_full_acc': True
},
}
params_gw = {
'arguments': [
'dipoles',
'HF_and_locXC',
'dipoles',
'gw0',
'ppa',],
'variables': {
'Chimod': 'hartree',
'DysSolver': 'n',
'GTermKind': 'BG',
'NGsBlkXp': [2, 'Ry'],
'BndsRnXp': [[1, 50], ''],
'GbndRnge': [[1, 50], ''],
'QPkrange': [[[1, 1, 8, 9]], ''],}}
params_gw = Dict(dict=params_gw)
builder = YamboConvergence.get_builder()
##################scf+nscf part of the builder
builder.ywfl.scf.pw.structure = structure
builder.ywfl.nscf.pw.structure = structure
builder.ywfl.scf.kpoints = kpoints
builder.ywfl.nscf.kpoints = kpoints
builder.ywfl.scf.pw.metadata.options.max_wallclock_seconds = \
options['max_wallclock_seconds']
builder.ywfl.scf.pw.metadata.options.resources = \
dict = options['resources']
if 'queue_name' in options:
builder.ywfl.scf.pw.metadata.options.queue_name = options['queue_name']
if 'qos' in options:
builder.ywfl.scf.pw.metadata.options.qos = options['qos']
if 'account' in options:
builder.ywfl.scf.pw.metadata.options.account = options['account']
if 'group_label' in options:
builder.group_label = Str(options['group_label'])
builder.ywfl.scf.pw.metadata.options.prepend_text = options['prepend_text']
builder.ywfl.scf.pw.metadata.options.mpirun_extra_params = []
builder.ywfl.nscf.pw.parameters = Dict(dict=params_nscf)
builder.ywfl.scf.pw.parameters = Dict(dict=params_scf)
builder.ywfl.nscf.pw.metadata = builder.ywfl.scf.pw.metadata
builder.ywfl.scf.pw.code = load_code(options['pwcode_id'])
builder.ywfl.nscf.pw.code = load_code(options['pwcode_id'])
family = load_group(options['pseudo_family'])
builder.ywfl.scf.pw.pseudos = family.get_pseudos(structure=structure)
builder.ywfl.nscf.pw.pseudos = family.get_pseudos(structure=structure)
##################yambo part of the builder
try:
builder.ywfl.parent_folder = load_node(options['parent_pk']).outputs.remote_folder
except:
pass
builder.ywfl.yres.yambo.metadata.options.max_wallclock_seconds = \
options['max_wallclock_seconds']
builder.ywfl.yres.yambo.metadata.options.resources = \
dict = options['resources']
if 'queue_name' in options:
builder.ywfl.yres.yambo.metadata.options.queue_name = options['queue_name']
if 'qos' in options:
builder.ywfl.yres.yambo.metadata.options.qos = options['qos']
if 'account' in options:
builder.ywfl.yres.yambo.metadata.options.account = options['account']
builder.ywfl.yres.yambo.metadata.options = builder.ywfl.scf.pw.metadata.options
builder.ywfl.yres.yambo.parameters = params_gw
builder.ywfl.yres.yambo.precode_parameters = Dict(dict={})
builder.ywfl.yres.yambo.settings = Dict(dict={'INITIALISE': False, 'COPY_DBS': False})
builder.ywfl.yres.max_iterations = Int(3)
builder.ywfl.yres.max_number_of_nodes = Int(0)
builder.ywfl.yres.yambo.preprocessing_code = load_code(options['yamboprecode_id'])
builder.ywfl.yres.yambo.code = load_code(options['yambocode_id'])
builder.ywfl.additional_parsing = List(list=['gap_'])
builder.workflow_settings = Dict(dict={
'type': 'cheap', # or heavy; cheap uses initial value for the parameters that we already converged.
'what': ['gap_'], # all the possible quantities that we may parse in the YamboWorkflow.
})
#inputs for builder.parameters_space, see below
builder.parameters_space = List([
{
'var': ['BndsRnXp', 'GbndRnge', 'NGsBlkXp'],
'start': [50, 50, 2],
'stop': [400, 400, 10],
'delta': [50, 50, 2],
'max': [1000, 1000, 36],
'steps': 6,
'max_iterations': 8,
'conv_thr': 1,
'conv_thr_units': 'eV',
'convergence_algorithm': 'new_algorithm_2D',
},
{
'var': ['FFTGvecs'],
'start': 21,
'stop': 58,
'delta': 8,
'max': 84,
'steps': 4,
'max_iterations': 4,
'conv_thr': 10,
'conv_thr_units': '%',
'convergence_algorithm': 'new_algorithm_1D' #we are converging 1 parameter
},
])
dict_para_medium = {}
dict_para_medium['X_and_IO_CPU'] = '1 1 1 8 1'
dict_para_medium['X_and_IO_ROLEs'] = 'q k g c v'
dict_para_medium['DIP_CPU'] = '1 8 1'
dict_para_medium['DIP_ROLEs'] = 'k c v'
dict_para_medium['SE_CPU'] = '1 1 8'
dict_para_medium['SE_ROLEs'] = 'q qp b'
dict_res_medium = {"num_machines": 1, "num_mpiprocs_per_machine":8, "num_cores_per_mpiproc":2,}
dict_para_high = {}
dict_para_high['X_and_IO_CPU'] = '2 1 1 8 1'
dict_para_high['X_and_IO_ROLEs'] = 'q k g c v'
dict_para_high['DIP_CPU'] = '1 16 1'
dict_para_high['DIP_ROLEs'] = 'k c v'
dict_para_high['SE_CPU'] = '1 2 8'
dict_para_high['SE_ROLEs'] = 'q qp b'
dict_res_high = {"num_machines": 1, "num_mpiprocs_per_machine":16, "num_cores_per_mpiproc":1,}
parallelism_instructions_manual = Dict(dict={'manual' : {
'low':{
'BndsRnXp':[1,100],
'NGsBlkXp':[2,18],
'parallelism':dict_para_medium,
'resources':dict_res_medium,
},
'medium':{
'BndsRnXp':[101,1000],
'NGsBlkXp':[2,18],
'parallelism':dict_para_high,
'resources':dict_res_high,
},}})
parallelism_instructions_auto = Dict(dict={'automatic' : {
'std_1':{
'BndsRnXp':[1,100],
'NGsBlkXp':[1,18],
'mode':'balanced',
'resources':dict_res_medium,
},
'std_2':{
'BndsRnXp':[101,1000],
'NGsBlkXp':[1,18],
'mode':'memory',
'resources':dict_res_high,
},}})
builder.parallelism_instructions = parallelism_instructions_manual
#for i in range(len(var_to_conv)):
# print('{}-th variable will be {}'.format(i+1,var_to_conv[i]['var']))
#builder.parameters_space = List(list = var_to_conv)
return builder
if __name__ == "__main__":
[docs] options = get_options()
builder = main(options)
running = submit(builder)
running.label = 'hBN test'
print("Submitted YamboConvergence for bulk hBN; with pk=< {} >".format(running.pk))
