Account recent updates

Author: blokhin

mpds_aiida/workflows/cif.py

@@ -3,9 +3,11 @@
 The MPDS workflow using structure from CIF file
 """
 from aiida_crystal_dft.utils import get_data_class
+
+from metis_backend.datasources.fmt import detect_format
+from metis_backend.structures.cif_utils import cif_to_ase
+
 from .crystal import MPDSCrystalWorkChain
-from mpds_ml_labs.struct_utils import detect_format
-from mpds_ml_labs.cif_utils import cif_to_ase
 
 
 class CIFStructureWorkChain(MPDSCrystalWorkChain):

requirements.txt

@@ -2,6 +2,6 @@ reentry >= 1.3.1
 six >= 1.16.0
 numpy >= 1.17.5
 ase >= 3.19
-mpds-ml-labs @ git+https://github.com/mpds-io/mpds-ml-labs
 aiida-crystal-dft @ git+https://github.com/tilde-lab/aiida-crystal-dft
 yascheduler >= 1.0.12
+metis-backend @ git+https://github.com/basf/metis-backend

scripts/aiida_submit_cif.py

@@ -9,8 +9,9 @@
 
 import spglib
 
-from mpds_ml_labs.struct_utils import detect_format, refine, get_formula
-from mpds_ml_labs.cif_utils import cif_to_ase
+from metis_backend.datasources.fmt import detect_format
+from metis_backend.structures.struct_utils import refine, get_formula
+from metis_backend.structures.cif_utils import cif_to_ase
 
 
 load_profile()

scripts/aiida_submit_ht_test.py

@@ -6,27 +6,20 @@
 from aiida.plugins import DataFactory
 from aiida.orm import Code
 from aiida.engine import submit
-from mpds_aiida.workflows.crystal import MPDSCrystalWorkchain
+from mpds_aiida.workflows.mpds import MPDSStructureWorkChain
 
 from mpds_client import MPDSDataRetrieval
-from mpds_aiida.common import get_template, get_mpds_phases
+from mpds_aiida.common import get_mpds_phases
 
 
 ela = ['Li', 'Na', 'K']
 elb = ['F', 'Cl', 'Br']
 
 client = MPDSDataRetrieval()
 
-calc_setup = get_template()
-
 load_profile()
 
-inputs = MPDSCrystalWorkchain.get_builder()
-inputs.crystal_code = Code.get_from_string('{}@{}'.format(calc_setup['codes'][0], calc_setup['cluster']))
-inputs.crystal_parameters = DataFactory('dict')(dict=calc_setup['parameters']['crystal'])
-
-inputs.basis_family, _ = DataFactory('crystal_dft.basis_family').get_or_create(calc_setup['basis_family'])
-inputs.options = DataFactory('dict')(dict=calc_setup['options'])
+inputs = MPDSStructureWorkChain.get_builder()
 
 for elem_pair in product(ela, elb):
     print(elem_pair)
@@ -36,5 +29,5 @@
         formula, sgs, pearson = phase.split('/')
         inputs.metadata = {'label': phase}
         inputs.mpds_query = DataFactory('dict')(dict={'formulae': formula, 'sgs': int(sgs)})
-        wc = submit(MPDSCrystalWorkchain, **inputs)
+        wc = submit(MPDSStructureWorkChain, **inputs)
         print("Submitted WorkChain %s for %s" % (wc.pk, phase))

scripts/run_properties.py

@@ -1,16 +1,22 @@
 #!/usr/bin/env python3
 
 import os, sys
+from io import BytesIO
 import json
 #from pprint import pprint
 
 import numpy as np
 import matplotlib.pyplot as plt
 
+from PIL import Image
+from ase.data import chemical_symbols
+
 from aiida import load_profile
 from aiida_crystal_dft.io.f9 import Fort9
-from mpds_aiida.common import get_template
-from mpds_aiida.properties import properties_run_direct, properties_export
+from aiida_crystal_dft.utils.dos import get_dos_projections_atoms
+
+from mpds_aiida.common import get_template, fix_label_names, formula_to_latex
+from mpds_aiida.properties import properties_run_direct, properties_export, dos_colors
 
 
 load_profile()
@@ -50,6 +56,7 @@
 f.close()
 
 print("Writing e_props.png")
+bands.attributes['labels'] = fix_label_names(bands.attributes['labels'])
 
 fig, (ax0, ax1) = plt.subplots(1, 2, gridspec_kw={'width_ratios': [3, 1]}, figsize=(10, 8))
 x = np.arange(bands.get_array('kpoints').shape[0])
@@ -61,11 +68,26 @@
 
 ax1.set_xlim(0, 2000)
 ax1.set_ylim(-10, 20)
+ax1.set_prop_cycle(color=dos_colors)
 ax1.plot(dos['dos_up'].T, (dos['e'] - dos['e_fermi']))
 
-fig.suptitle(wf.get_ase().get_chemical_formula(empirical=True))
+atsymbs = [chemical_symbols[x] for x in wf.get_atomic_numbers()]
+count, padding = 0, 70
+for proj in get_dos_projections_atoms(wf.get_atomic_numbers()):
+    ax1.annotate(atsymbs[proj[0] - 1], xy=(count * padding, -150), xycoords='axes pixels', size=7, c=dos_colors[count])
+    count += 1
+ax1.annotate('Total', xy=(count * padding, -150), xycoords='axes pixels', size=7, c=dos_colors[count])
+
+fig.suptitle(formula_to_latex(wf.get_ase().get_chemical_formula(empirical=True)))
 plt.margins(0.2)
 plt.subplots_adjust(bottom=0.15)
-plt.savefig('e_props.png', dpi=250)
+#plt.savefig('e_props.png', dpi=250)
+
+mem = BytesIO()
+plt.savefig(mem, format='png', dpi=250)
+mem.seek(0)
+im = Image.open(mem)
+im2 = im.convert('RGB').convert('P', palette=Image.ADAPTIVE)
+im2.save('e_props.png')
 
 print('E_dir, E_ind = ', result['direct_gap'], result['indirect_gap'])

scripts/ya_submit_ht_test.py

@@ -3,20 +3,24 @@
 import sys
 import random
 from itertools import product
+from configparser import ConfigParser
 
 import numpy as np
 from aiida_crystal_dft.io.f34 import Fort34
 
-from yascheduler import Yascheduler
+from yascheduler import CONFIG_FILE
+from yascheduler.scheduler import Yascheduler
 
 from mpds_client import MPDSDataRetrieval
 from mpds_aiida.common import get_template, get_basis_sets, get_mpds_structures, get_input
 
 
-ela = ['Li', 'Na', 'K', 'Rb', 'Be', 'Mg']
-elb = ['F', 'Cl', 'Br', 'I', 'O', 'S']
+ela = ['Li', 'Na', 'K']
+elb = ['F', 'Cl', 'Br']
 
-yac = Yascheduler()
+config = ConfigParser()
+config.read(CONFIG_FILE)
+yac = Yascheduler(config)
 
 client = MPDSDataRetrieval()
 
@@ -59,5 +63,5 @@
         struct_input = str(struct_input)
         setup_input = str(setup_input)
 
-        yac.queue_submit_task(target_obj.info['phase'], {"fort.34": struct_input, "INPUT": setup_input}, "pcrystal")
+        yac.queue_submit_task(target_obj.info['phase'], dict(structure=struct_input, input=setup_input))
         counter += 1