Merge pull request #117 from JuDFTteam/develop

Release 1.1.13

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.1.12
+current_version = 1.1.13
 commit = True
 tag = True
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+))?

aiida_kkr/__init__.py

@@ -2,4 +2,4 @@
 AiiDA KKR
 """
 
-__version__ = '1.1.12'
+__version__ = '1.1.13'

aiida_kkr/calculations/kkr.py

@@ -7,7 +7,7 @@
 import os
 import numpy as np
 from aiida.engine import CalcJob
-from aiida.orm import CalcJobNode, load_node, RemoteData, Dict, StructureData, KpointsData, Bool
+from aiida.orm import CalcJobNode, load_node, RemoteData, Dict, StructureData, KpointsData, Bool, FolderData
 from .voro import VoronoiCalculation
 from ..tools.common_workfunctions import get_natyp
 from aiida.common.utils import classproperty
@@ -27,7 +27,7 @@
 __copyright__ = (u'Copyright (c), 2017, Forschungszentrum Jülich GmbH, '
                  'IAS-1/PGI-1, Germany. All rights reserved.')
 __license__ = 'MIT license, see LICENSE.txt file'
-__version__ = '0.12.2'
+__version__ = '0.12.5'
 __contributors__ = ('Jens Bröder', 'Philipp Rüßmann')
 
 verbose = False
@@ -55,6 +55,7 @@ class KkrCalculation(CalcJob):
     # List of optional input files (may be mandatory for some settings in inputcard)
     _SHAPEFUN = 'shapefun'  # mandatory if nonspherical calculation
     _SCOEF = 'scoef'  # mandatory for KKRFLEX calculation and some functionalities
+    _BFIELD = 'bfield.dat'  # mandatory if <NONCOBFIELD>= True
     _NONCO_ANGLES = 'nonco_angle.dat'  # mandatory if noncollinear directions are used that are not (theta, phi)= (0,0) for all atoms
     _NONCO_ANGLES_IMP = 'nonco_angle_imp.dat'  # mandatory for GREENIMP option (scattering code)
     _SHAPEFUN_IMP = 'shapefun_imp'  # mandatory for GREENIMP option (scattering code)
@@ -101,6 +102,7 @@ class KkrCalculation(CalcJob):
     _DECIFILE = 'decifile'
     # BdG mode
     _BDG_POT = 'den_lm_ir.%0.3i.%i.txt'
+    _BDG_CHI_NS = 'den_lm_ns_*.npy'
 
     # template.product entry point defined in setup.json
     _default_parser = 'kkr.kkrparser'
@@ -215,6 +217,25 @@ def define(cls, spec):
             equal to the number of atoms.
             """
         )
+        spec.input(
+            'bfield',
+            valid_type=Dict,
+            required=False,
+            help="""Non-collinear exteral B-field used for constraint calculations.
+
+            The Dict node should be of the form
+            initial_noco_angles = Dict(dict={
+                'theta': [theta_at1, theta_at2, ..., theta_atN],
+                # list theta values in degrees (0..180)
+                'phi': [phi_at1, phi_at2, ..., phi_atN],
+                # list phi values in degrees (0..360)
+                'magnitude': [magnitude at_1, ..., magnitude at_N]
+                # list of magnitude of the applied fields in Ry units
+            })
+            Note: The length of the theta, phi and magnitude lists have to be
+            equal to the number of atoms.
+            """
+        )
         spec.input(
             'deciout_parent',
             valid_type=RemoteData,
@@ -230,6 +251,15 @@ def define(cls, spec):
             the kkrflex_* files are copied to the retrieved (can clutter the
             database) or are ony left in the remote folder."""
         )
+        spec.input(
+            'anomalous_density',
+            valid_type=FolderData,
+            required=False,
+            help="""FolderData that contains anomalous density input files for
+            the KKRhost BdG calculation. If these are not give the code looks
+            for them in the retrieved of the parent calculation and takes them
+            from there."""
+        )
 
         # define outputs
         spec.output(
@@ -295,6 +325,10 @@ def prepare_for_submission(self, tempfolder):
         if 'initial_noco_angles' in self.inputs:
             parameters = self._use_initial_noco_angles(parameters, structure, tempfolder)
 
+        # write bfield.dat file and add '<NONCOBFIELD>= True' to input parameters
+        if 'bfield' in self.inputs:
+            parameters = self._use_nonco_bfield(parameters, structure, tempfolder)
+
         # activate decimation mode and copy decifile from deciout parent
         if 'deciout_parent' in self.inputs:
             parameters = self._use_decimation(parameters, tempfolder)
@@ -802,10 +836,13 @@ def _get_BdG_filelist(self, parameters, natom, nspin):
             self.report(f'retrieve BdG? {retrieve_BdG_files}')
 
         if retrieve_BdG_files:
+            # anomalous density files for all atoms if present
             for iatom in range(natom):
                 for ispin in range(nspin):
                     print('adding files for BdG mode')
                     add_files += [self._BDG_POT % (iatom + 1, ispin + 1)]
+            # radially-averaged anomalous density matrix (for triplet components etc.)
+            add_files.append(self._BDG_CHI_NS)
 
             #also retrieve BdG DOS files for anomalous density and hole part
             for BdGadd in ['_eh', '_he', '_hole']:
@@ -1015,6 +1052,51 @@ def _use_initial_noco_angles(self, parameters, structure, tempfolder):
 
         return parameters
 
+    def _use_nonco_bfield(self, parameters, structure, tempfolder):
+        """
+        Set external non-collinear bfield (writes bfield.dat to tempfolder) used in constraint calculations.
+        """
+        self.report('Found `bfield` input node, writing nonco_angle.dat file')
+
+        # extract number of atoms for length comparison
+        natom = get_natyp(structure)
+
+        change_values = [['<NONCOBFIELD>', True]]
+        parameters = _update_params(parameters, change_values)
+
+        # extract magnitude, theta and phi values from input node
+        mags = self.inputs.bfield['magnitude']
+        if len(mags) != natom:
+            raise InputValidationError(
+                'Error: `magnitude` list in `bfield` input node needs to have the same length as number of atoms!'
+            )
+        thetas = self.inputs.bfield['theta']
+        if len(thetas) != natom:
+            raise InputValidationError(
+                'Error: `theta` list in `bfield` input node needs to have the same length as number of atoms!'
+            )
+        phis = self.inputs.bfield['phi']
+        if len(phis) != natom:
+            raise InputValidationError(
+                'Error: `phi` list in `bfield` input node needs to have the same length as number of atoms!'
+            )
+
+        # now write kkrflex_angle file
+        with tempfolder.open(self._BFIELD, 'w') as bfield_file:
+            bfield_file.write('# theta [deg]  phi [deg]  magnitude [Ry]\n')
+            for iatom in range(natom):
+                theta, phi = thetas[iatom], phis[iatom]
+                magnitude = mags[iatom]
+                # check consistency
+                if theta < 0. or theta > 180.:
+                    raise InputValidationError(
+                        f'Error: theta value out of range (0..180): iatom={iatom}, theta={theta}'
+                    )
+                # write line
+                bfield_file.write(f'   {theta}    {phi}    {magnitude}\n')
+
+        return parameters
+
     def _use_decimation(self, parameters, tempfolder):
         """
         Activate decimation mode and copy decifile from output of deciout_parent calculation
@@ -1063,13 +1145,26 @@ def _copy_BdG_pot(self, retrieved, tempfolder):
         Activate BdG mode and copy den_lm_ir files of the previous output to the input of this calculation.
         """
 
-        BDG_POT_FILES = [i for i in retrieved.list_object_names() if self._BDG_POT.split('.')[0] in i]
+        if 'anomalous_density' in self.inputs:
+            # this means we have a FolderData input that contains the
+            # anomalous density files
+            adens_folder = self.inputs.anomalous_density
+        else:
+            # if no anomalous density is given as an input node we check
+            # if there are any anomalous density files in the parent retrieved
+            # and take them from there if present
+            adens_folder = retrieved
+
+        # list of den_lm_ir files (anomalous density per atom)
+        BDG_POT_FILES = [i for i in adens_folder.list_object_names() if self._BDG_POT.split('.')[0] in i]
 
         # add 'den-lm_ir' files to input
         for BdG_pot in BDG_POT_FILES:
-            self.report(f'Copy BdG potential {BdG_pot}')
-            with retrieved.open(BdG_pot, 'r') as file_handle:
+            self.report(f'Copy BdG potential {BdG_pot} from {adens_folder.uuid}')
+            # read from parent
+            with adens_folder.open(BdG_pot, 'r') as file_handle:
                 file_txt = file_handle.readlines()
+            # write to tempfolder
             with tempfolder.open(BdG_pot, 'w') as file_handle:
                 file_handle.writelines(file_txt)
 

aiida_kkr/tools/__init__.py

@@ -18,6 +18,7 @@
 from .kick_out_core_states import *
 from .neworder_potential import *
 from .find_parent import get_calc_from_remote, get_remote, get_parent
+from .bdg_tools import get_anomalous_density_data
 
 
 # expose structure finder from VoronoiCalculation

aiida_kkr/tools/bdg_tools.py

@@ -0,0 +1,48 @@
+"""
+Helper tools that deal with the anomalous density of the BdG formalism in KKR
+"""
+
+from aiida.engine import calcfunction
+from aiida.orm import FolderData
+
+
+@calcfunction
+def get_anomalous_density_data(retrieved, rename_files=None):
+    """
+    Extract anomalous density files from a retrieved folder of a KkrCalculation
+    and copy into a new FolderData. This FolderData is then returned and can be
+    used as the anomalous_density FolderData input to a KkrCalculation.
+
+    :param retrieved: retrieved FolderData of a parent KKRhost BdG calculation where anomalous density files are stored (called `den_lm_ir.AAA.1.txt` where AAA is an atom index)
+
+    :param rename_files: Optional Dict node where mappings of file names are defined. This is helpful if the atom index in the new structure is different from the original calculation (e.g. atom N of the original structure corresponds to atom M of the new structure, then the renaming dict should be {N: M}). Indices that are not found or that map to None are skipped and will not appear in the returned FolderData!
+
+    :returns: anomalous_density FolderData which contains the (possibly renamed) anomalous density files
+    """
+    BdG_files = [i for i in retrieved.list_object_names() if 'den_lm_ir' in i]
+
+    anomalous_density = FolderData()
+    for fname in BdG_files:
+        with retrieved.open(fname, 'r') as _fin:
+            # default is to use the same name as in the input
+            fname_out = fname
+
+            # rename file, if natom is found in the renaming dict
+            if rename_files is not None:
+                # find atom index (should be integer)
+                natom = int(fname.split('.')[1])
+                # we pick the new atom index and recreate the filename
+                natom_new = {int(k): v for k, v in rename_files.get_dict().items()}.get(natom)
+                if natom_new is None:
+                    # if no renaming is mapping is found
+                    # we do not copy this anomalous density but leave it out
+                    fname_out = None
+                else:
+                    # construct changed name
+                    fname_out = 'den_lm_ir.%0.3i.1.txt' % natom_new
+
+            if fname_out is not None:
+                # copy input file to FolderData node, maybe with changed name
+                anomalous_density.put_object_from_filelike(_fin, fname_out)
+
+    return anomalous_density

aiida_kkr/tools/plot_kkr.py

@@ -16,7 +16,7 @@
 __copyright__ = (u'Copyright (c), 2018, Forschungszentrum Jülich GmbH, '
                  'IAS-1/PGI-1, Germany. All rights reserved.')
 __license__ = 'MIT license, see LICENSE.txt file'
-__version__ = '0.7.0'
+__version__ = '0.7.1'
 __contributors__ = ('Philipp Rüßmann')
 
 
@@ -1896,7 +1896,7 @@ def get_ef_from_parent(node):
     except:
         with node.outputs.retrieved.open('output.0.txt', mode='r') as file_handle:
             txt = file_handle.readlines()
-            iline = search_string('Fermi energy', txt)
+            iline = search_string('Fermi energy =', txt)
             if iline >= 0:
                 ef = txt[iline].split('=')[1]
                 ef = float(ef.split()[0])