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Add tools to prepare for STM-like scanning of additional positions
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also refactor tools for combine imps and move some to imp_cluster_tools
to reuse the functions in there for the new STM-scanning feature
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@PhilippRue
PhilippRue committed Nov 30, 2023
1 parent 0ac4137 commit 014413b
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36 changes: 24 additions & 12 deletions aiida_kkr/calculations/kkrimp.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,15 +14,16 @@
from aiida_kkr.tools.tools_kkrimp import modify_potential, make_scoef, write_scoef_full_imp_cls, get_imp_info_from_parent
from aiida_kkr.tools.common_workfunctions import get_username
from aiida_kkr.tools.ldau import get_ldaupot_text
from aiida_kkr.tools.imp_cluster_tools import get_scoef_single_imp
from masci_tools.io.common_functions import search_string, get_ef_from_potfile
import os
import tarfile
from numpy import array, array_equal, sqrt, sum, where, loadtxt
import numpy as np

__copyright__ = (u'Copyright (c), 2018, Forschungszentrum Jülich GmbH, '
'IAS-1/PGI-1, Germany. All rights reserved.')
__license__ = 'MIT license, see LICENSE.txt file'
__version__ = '0.10.0'
__version__ = '0.10.1'
__contributors__ = (u'Philipp Rüßmann', u'Fabian Bertoldo')

#TODO: implement 'ilayer_center' consistency check
Expand Down Expand Up @@ -330,18 +331,29 @@ def _get_and_verify_hostfiles(self, tempfolder):
# case, raise an error
if found_impurity_inputnode and found_host_parent:
check_consistency_imp_info = False
#TODO: implement also 'ilayer_center' check
if 'imp_cls' in imp_info_inputnode.get_dict().keys():
input_imp_cls_arr = array(imp_info_inputnode.get_dict()['imp_cls'])
parent_imp_cls_arr = array(imp_info.get_dict()['imp_cls'])
is_identical = array_equal(input_imp_cls_arr[:, 0:4], parent_imp_cls_arr[:, 0:4])
input_imp_cls_arr = np.array(imp_info_inputnode.get_dict()['imp_cls'])

try:
parent_imp_cls_arr = np.array(imp_info.get_dict()['imp_cls'])
except:
host_structure, _ = VoronoiCalculation.find_parent_structure(parent_calc)
parent_imp_cls_arr = get_scoef_single_imp(host_structure, imp_info)

is_identical = np.array_equal(
np.round(input_imp_cls_arr[:, 0:4], 5), np.round(parent_imp_cls_arr[:, 0:4], 5)
)

if is_identical:
check_consistency_imp_info = True
else:
self.report('impurity_info node from input and from previous GF calculation are NOT compatible!.')
self.report(f'impurity_info node from input: {input_imp_cls_arr[:, 0:4]}')
self.report(f'impurity_info node from previous GF calculation: {parent_imp_cls_arr[:, 0:4]}')

#TODO: implement also 'ilayer_center' check
elif imp_info_inputnode.get_dict().get('Rcut') == imp_info.get_dict().get('Rcut'):

check_consistency_imp_info = True
try:
if (
Expand Down Expand Up @@ -554,9 +566,9 @@ def _change_atominfo(self, imp_info, kkrflex_file_paths, tempfolder):
n_rows = len(scoeffile.readlines()) - 1
with tempfolder.open(KkrCalculation._SCOEF, u'r') as scoeffile:
if n_rows > 1:
scoef = loadtxt(scoeffile, skiprows=1)[:, :3]
scoef = np.loadtxt(scoeffile, skiprows=1)[:, :3]
else:
scoef = loadtxt(scoeffile, skiprows=1)[:3]
scoef = np.loadtxt(scoeffile, skiprows=1)[:3]

# find replaceZimp list from Zimp and Rimp_rel
imp_info_dict = imp_info.get_dict()
Expand All @@ -567,14 +579,14 @@ def _change_atominfo(self, imp_info, kkrflex_file_paths, tempfolder):
self.report(f'DEBUG: Rimp_rel_list: {Rimp_rel_list}.')

for iatom in range(len(Zimp_list)):
rtmp = array(Rimp_rel_list[iatom])[:3]
rtmp = np.array(Rimp_rel_list[iatom])[:3]
self.report(f'INFO: Rimp_rel {iatom}, {rtmp}')
if n_rows > 1:
diff = sqrt(sum((rtmp - scoef)**2, axis=1))
diff = np.sqrt(np.sum((rtmp - scoef)**2, axis=1))
else:
diff = sqrt(sum((rtmp - scoef)**2, axis=0))
diff = np.sqrt(np.sum((rtmp - scoef)**2, axis=0))
Zimp = Zimp_list[iatom]
ipos_replace = where(diff == diff.min())[0][0]
ipos_replace = np.where(diff == diff.min())[0][0]
replace_zatom_imp.append([ipos_replace, Zimp])

for (iatom, zimp) in replace_zatom_imp:
Expand Down
245 changes: 6 additions & 239 deletions aiida_kkr/tools/combine_imps.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,10 +8,13 @@
from aiida.orm import Dict, SinglefileData, load_node, Bool
from aiida.common import InputValidationError
from aiida.common.folders import SandboxFolder
from aiida_kkr.tools.tools_kkrimp import modify_potential, create_scoef_array
from aiida_kkr.tools.tools_kkrimp import modify_potential
from aiida_kkr.calculations import VoronoiCalculation, KkrimpCalculation
from aiida_kkr.workflows import kkr_imp_sub_wc
from masci_tools.io.common_functions import get_alat_from_bravais
from .imp_cluster_tools import (
pos_exists_already, get_inplane_neighbor, get_scoef_single_imp, get_zimp, combine_clusters,
create_combined_imp_info, create_combined_imp_info_cf
)

__copyright__ = (u'Copyright (c), 2020, Forschungszentrum Jülich GmbH, '
'IAS-1/PGI-1, Germany. All rights reserved.')
Expand Down Expand Up @@ -146,245 +149,9 @@ def get_nspin_and_pot(imp):
return nspin, pot_imp


# combine clusters calcfunction


def get_zimp(impurity_info):
"""
extract zimp from impurity_info node and return as list
"""
zimp = impurity_info.get_dict().get('Zimp')

try:
zimp = list(zimp)
except TypeError:
zimp = [zimp]

return zimp


def get_scoef_single_imp(host_structure, impinfo_node):
"""
Create scoef cluster from host_structure and impurity info nodes
:para impinfo_node: Impurity info node (should have at least Rcut and ilayer_center in dict)
:type impinfo_node: aiida.orm.Dict
:para host_structure: structure of host crystal into which impurities are embedded
:type host_structure: aiida.orm.StructureData
:return: scoef array (positions [x,y,z], layer index, distance to first position in imp cluster)
:type: numpy.array
"""
impinfo = impinfo_node.get_dict()
Rcut = impinfo.get('Rcut', None)
hcut = impinfo.get('hcut', -1.)
cylinder_orient = impinfo.get('cylinder_orient', [0., 0., 1.])
ilayer_center = impinfo.get('ilayer_center', 0)

clust = create_scoef_array(host_structure, Rcut, hcut, cylinder_orient, ilayer_center)
# sort after distance
clust = clust[(clust[:, -1]).argsort()]

return clust


def get_inplane_neighbor(host_structure, i_neighbor, r_out_of_plane):
"""
create in-plane neighbor
"""
# if offset of second impurity is given in units of the host structure bravais vectors:
cell = np.array(host_structure.cell)

# find and sort list of nearest neighbors
dist = []
icount = 0
N_neighbor_search = 5 # define box in which neighbors are searched
for j in list(range(N_neighbor_search + 1)
) + list(range(-N_neighbor_search, 0)[::-1]): # use this to have better ordering (nicer numbers)
for i in list(range(N_neighbor_search + 1)) + list(range(-N_neighbor_search, 0)[::-1]):
# create position
r = cell[0] * i + cell[1] * j + r_out_of_plane
d = np.sqrt(np.sum(r**2))
# check if already in list
add_pair = False
if icount > 1:
if abs(np.array(dist)[:, -1] - d).min() > 10**-5:
add_pair = True
else:
add_pair = True
# add distance
if add_pair:
dist.append([i, j, r[0], r[1], r[2], d])
icount += 1

alat = get_alat_from_bravais(cell, host_structure.pbc[2])
dist = np.array(dist)
dist[:, 2:] = dist[:, 2:] / alat
dist_sort_list = dist[:, -1].argsort()

# find in-plane neighbor
r_offset = dist[dist_sort_list[i_neighbor]][2:5] # element 0 is no offset

return r_offset


def pos_exists_already(pos_list_old, pos_new, debug=False):
"""
check if pos_new is in pos_list_old
"""
sort_ref = np.array(pos_list_old)
dists = np.sqrt(np.sum((sort_ref - np.array(pos_new))**2, axis=1))
mask = (dists < 10**-5)

if debug:
print('check pos', dists.min())

if dists.min() < 10**-5:
return True, [i for i in range(len(mask)) if mask[i]]
else:
return False, None


def combine_clusters(clust1, clust2_offset, single_single, debug=False):
"""
combine impurity clusters and remove doubles in there
:return cluster_combined:
:return rimp_rel_combined: relative position of impurities in cluster
:return kickout_list: licst of positions doubled in clust 2
:return i_neighbor_inplane: position removed from cluster 1 (doubled with impurity position)
"""

# now combine cluster1 and cluster2
cluster_combined = list(clust1.copy())

# check if imp position of cluster 2 is inside and remove that position
# this ensures that imp2 is not kicked out
_, i_removed_from_1 = pos_exists_already(clust1[:, :3], clust2_offset[0, :3], debug)
if debug:
print('i_removed_from_1:', i_removed_from_1)

# remove doubled position from impcls1 if there is any
if i_removed_from_1 is not None:
#removed = cluster_combined.pop(i_removed_from_1)
cluster_combined = [clust1[i] for i in range(len(clust1)) if i not in i_removed_from_1]

# add the rest of the imp cluster of imp 2 if position does not exist already in cluster of imp 1
kickout_list = []
for ipos, pos_add in enumerate(clust2_offset):
if ipos == 0 or not pos_exists_already(np.array(cluster_combined)[:, :3], pos_add[:3], debug)[0]:
cluster_combined.append(pos_add)
else:
kickout_list.append(ipos)
cluster_combined = np.array(cluster_combined)

# fix distances for second half
cluster_combined[:, -1] = np.sqrt(np.sum(cluster_combined[:, :3]**2, axis=1))

# construct Rimp_rel list
rimp_rel_combined = [clust1[0, :3]] + [clust2_offset[0, :3]]

return cluster_combined, rimp_rel_combined, kickout_list, i_removed_from_1


def create_combined_imp_info(
host_structure, impinfo1, impinfo2, offset_imp2, imps_info_in_exact_cluster, single_single, debug=False
):
"""
create impurity clusters from impinfo nodes and combine these putting the second
impurity to the i_neighbor_inplane-th in-plane neighbor
"""
#TODO: Try it with the self object in the in the input

imps_info_in_exact_cluster = imps_info_in_exact_cluster.get_dict()
if single_single:
zimp1 = imps_info_in_exact_cluster['Zimps'][0]
zimp2 = imps_info_in_exact_cluster['Zimps'][-1]

if 'imp_cls' in impinfo1.get_dict():
clust1 = np.array(impinfo1['imp_cls'])

elif single_single:
# create cluster of imp1
clust1 = get_scoef_single_imp(host_structure, impinfo1)

# do the same for imp2
clust2 = get_scoef_single_imp(host_structure, impinfo2)

# set zimp in scoef file (not used by the code but makes it easier to read the files / debug)
if single_single:
clust1[0][4] = zimp1
clust2[0][4] = zimp2
#if debug:
# print('cls1:', clust1)
# print('cls2:', clust2)

if 'r_offset' in offset_imp2.get_dict():
# use offset given in input
r_offset = offset_imp2['r_offset']
else:
# find offset taking into account the possible out-of-plane vector if the imps are in different layers
r_out_of_plane = np.array([0, 0, 0])
center_imp = imps_info_in_exact_cluster['ilayers'][0]
layer2 = imps_info_in_exact_cluster['ilayers'][-1]
if center_imp != layer2:
pos1 = np.array(host_structure.sites[center_imp].position)
pos2 = np.array(host_structure.sites[layer2].position)
r_out_of_plane = pos2 - pos1
i_neighbor_inplane = imps_info_in_exact_cluster['offset_imps'][-1]
r_offset = get_inplane_neighbor(host_structure, i_neighbor_inplane, r_out_of_plane)
if debug:
print('r_offset:', r_offset)

# add offset to cluster 2
clust2_offset = clust2.copy()
clust2_offset[:, :3] += r_offset

cluster_combined, rimp_rel_combined, kickout_list, i_removed_from_1 = combine_clusters(
clust1, clust2_offset, single_single, debug
)

if 'Rimp_rel' in impinfo1.get_dict():
rimp_rel_combined = impinfo1['Rimp_rel'] + rimp_rel_combined[1:]

if debug:
#print('cls_combined:', cluster_combined)
print('rimp_rel_combined:', rimp_rel_combined)
print('kickout_list:', kickout_list)
print('i_removed_from_1:', i_removed_from_1)

zimp_combined = imps_info_in_exact_cluster['Zimps']

# create new imp_info node with imp_cls, Rimp_rel and Zimp definig the cluster and impurity location
imp_info_combined = Dict({'imp_cls': cluster_combined, 'Zimp': zimp_combined, 'Rimp_rel': rimp_rel_combined})

# kickout info (used later in cfreation of combined potential)
kickout_info = Dict({
'i_removed_from_1': i_removed_from_1,
'kickout_list': kickout_list,
'Ncls1': len(clust1),
'Ncls2': len(clust2),
'Ncls_combined': len(cluster_combined)
})

return {'imp_info_combined': imp_info_combined, 'kickout_info': kickout_info}


@calcfunction
def create_combined_imp_info_cf(
host_structure, impinfo1, impinfo2, offset_imp2, imps_info_in_exact_cluster, single_single
):
"""
create impurity clusters from impinfo nodes and combine these putting the second
impurity to the i_neighbor_inplane-th in-plane neighbor
"""

return create_combined_imp_info(
host_structure, impinfo1, impinfo2, offset_imp2, imps_info_in_exact_cluster, single_single
)
# combine potentials calcfunction


# combine potentials calcfunction
def combine_potentials(kickout_info, pot_imp1, pot_imp2, nspin_node):

# unpack kickout info
Expand Down
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