Merge pull request #141 from JuDFTteam/fix_issue_137

Fix finding parent structure for KkrimpCalculation and `strucplot` input to `plot_kkr`

.github/workflows/cd.yml

@@ -94,7 +94,7 @@ jobs:
       fail-fast: false
       matrix:
         python-version: ["3.8", "3.9", "3.10"]
-        aiida: [{version: 'aiida-core==2.1.2', name: '2.1.2'}]
+        aiida: [{version: 'aiida-core==2.3.0', name: '2.3.0'}]
         masci-tools: [{version: 'git+https://github.com/JuDFTteam/masci-tools.git@develop', name: '-masci-develop'}]
         allowed-to-fail: [false]
 
@@ -125,7 +125,7 @@ jobs:
     - uses: actions/checkout@v3
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 

.github/workflows/ci.yml

@@ -88,7 +88,7 @@ jobs:
       fail-fast: false
       matrix:
         python-version: ["3.8", "3.9", "3.10"]
-        aiida: [{version: 'aiida-core==2.1.2', name: '2.1.2'}]
+        aiida: [{version: 'aiida-core==2.3.0', name: '2.3.0'}]
         masci-tools: [{version: 'git+https://github.com/JuDFTteam/masci-tools.git@develop', name: '-masci-develop'}]
         allowed-to-fail: [false]
 

aiida_kkr/parsers/kkrimp.py

@@ -41,8 +41,8 @@ def __init__(self, calc):
         super(KkrimpParser, self).__init__(calc)
 
     # pylint: disable=protected-access
-
-    def parse(self, debug=False, ignore_nan=True, **kwargs):  # pylint: disable=unexpected-keyword-arg
+    # pylint: disable=unexpected-keyword-arg
+    def parse(self, debug=False, ignore_nan=True, **kwargs):
         """
         Parse output data folder, store results in database.
 

aiida_kkr/tools/find_parent.py

@@ -30,7 +30,11 @@ def get_remote(parent_folder):
     try:
         parent_folder_tmp = parent_folder_tmp0.get_incoming().get_node_by_label('remote_folder')
     except NotExistent:
-        parent_folder_tmp = parent_folder_tmp0
+        try:
+            # check if GFhost_folder is there, this is the case for a KkrimpCalculation
+            parent_folder_tmp = parent_folder_tmp0.get_incoming().get_node_by_label('GFhost_folder')
+        except NotExistent:
+            parent_folder_tmp = parent_folder_tmp0
     return parent_folder_tmp
 
 

aiida_kkr/tools/plot_kkr.py

@@ -13,10 +13,51 @@
 __copyright__ = (u'Copyright (c), 2018, Forschungszentrum Jülich GmbH, '
                  'IAS-1/PGI-1, Germany. All rights reserved.')
 __license__ = 'MIT license, see LICENSE.txt file'
-__version__ = '0.7.1'
+__version__ = '0.7.2'
 __contributors__ = ('Philipp Rüßmann')
 
 
+def get_datetime_from_str(calc, verbose=False):
+    """
+    Return a datetime object from the last time a calculation was checked by the scheduler.
+
+    Every calculation should have the  'scheduler_lastchecktime' attribute which has the
+    following format: '2023-11-08T22:44:13.543215+00:00'.
+    This is converted to a datetime object that can be sorted.
+    """
+    from datetime import datetime
+    # get last time stamp of scheduler from calculation attribute
+    try:
+        last_time_on_computer = calc.attributes['scheduler_lastchecktime']
+    except:
+        raise ValueError('Failed to get "scheduler_lastchecktime" from calculation.')
+    # parse date and time from string
+    date = last_time_on_computer.split('T')[0]
+    time = last_time_on_computer.split('T')[1].split('.')[0]
+    # change format
+    datetime_str = date[2:].replace('-', '/') + ' ' + time
+    # convert to datetime object
+    datetime_object = datetime.strptime(datetime_str, '%y/%m/%d %H:%M:%S')
+
+    if verbose:
+        print(datetime_object)  # printed in default format
+
+    #return datetime object of the last time the calculation was checked
+    return datetime_object
+
+
+def get_sorting_indices(calcs):
+    """
+    Get the sorting index for a list of calculations.
+
+    For each calculation the datetime object of the last time the scheduler checked the
+    calculation is extracted. This is then sorted and the sorting index array is returned.
+    """
+    datetimes = [get_datetime_from_str(calc) for calc in calcs]
+    isort = np.array(datetimes).argsort()
+    return isort
+
+
 def remove_empty_atoms(show_empty_atoms, structure, silent=False):
     # check if empty sphere need to be removed for plotting (ase structgure cannot be constructed for alloys or vacancies)
     #print('in remove empty atoms:', structure.has_vacancies, ('X' in [i.kind_name for i in structure.sites]) )
@@ -341,6 +382,8 @@ class plot_kkr(object):
     :type switch_xy: bool
     :param iatom: list of atom indices which are supposed to be plotted (default: [], i.e. show all atoms)
     :type iatom: list
+    :param debug: activate debug output
+    :type debug: bool
 
     additional keyword arguments are passed onto the plotting function which allows, for example,
     to change the markers used in a DOS plot to crosses via `marker='x'`
@@ -359,8 +402,17 @@ def __init__(self, nodes=None, **kwargs):
         from aiida import load_profile
         load_profile()
 
+        # used to keep track of structure plotting
         self.sview = None
 
+        # debug mode
+        self.debug = False
+        if 'debug' in kwargs:
+            self.debug = kwargs.pop('debug')
+            print('start plot_kkr')
+            print('kwargs:', kwargs)
+
+        # grouping of node if a list of nodes is the input instead of a single node
         groupmode = False
         if type(nodes) == list:
             if len(nodes) > 1:
@@ -1006,8 +1058,12 @@ def plot_voro_calc(self, node, **kwargs):
     def plot_kkrimp_calc(self, node, return_rms=False, return_stot=False, plot_rms=True, **kwargs):
         """plot things from a kkrimp Calculation node"""
 
+        if self.debug:
+            print('in plot_kkrimp_calc')
+            print('kwargs:', kwargs)
+
         # plot impurity cluster
-        if kwargs.get('strucplot', True):
+        if kwargs.get('strucplot', False):
             if _has_ase_notebook():
                 self.sview = plot_imp_cluster(node, **kwargs)
             else:
@@ -1048,7 +1104,7 @@ def plot_kkrimp_calc(self, node, return_rms=False, return_stot=False, plot_rms=T
             else:
                 ptitle = f'pk= {node.pk}'
 
-            self.make_kkrimp_rmsplot([rms], [stot], [0], rms_goal, ptitle, **kwargs)
+            self.make_kkrimp_rmsplot([rms], [stot], [node], rms_goal, ptitle, **kwargs)
 
         # now return values
         return_any, return_list = False, []
@@ -1074,10 +1130,14 @@ def plot_kkrimp_sub_wc(self, node, **kwargs):
         """plot things from a kkrimp_sub_wc workflow"""
         from aiida_kkr.calculations import KkrimpCalculation
 
+        if self.debug:
+            print('in plot_kkrimp_sub_wc')
+            print('kwargs:', kwargs)
+
         impcalcs = [i.node for i in node.get_outgoing(node_class=KkrimpCalculation).all()]
 
         # plot impurity cluster
-        if len(impcalcs) > 0 and kwargs.get('strucplot', True):
+        if len(impcalcs) > 0 and kwargs.get('strucplot', False):
             if _has_ase_notebook():
                 self.sview = plot_imp_cluster(impcalcs[0], **kwargs)
             else:
@@ -1088,10 +1148,9 @@ def plot_kkrimp_sub_wc(self, node, **kwargs):
                 kwargs.pop(k)
 
         # extract rms from calculations
-        rms_all, pks_all, stot_all = [], [], []
+        rms_all, stot_all = [], []
         rms_goal = None
         for impcalc in impcalcs:
-            pks_all.append(impcalc.pk)
             rms_tmp, rms_goal_tmp, stot_tmp = self.plot_kkrimp_calc(
                 impcalc, return_rms=True, return_stot=True, plot_rms=False
             )
@@ -1108,9 +1167,9 @@ def plot_kkrimp_sub_wc(self, node, **kwargs):
         else:
             ptitle = f'pk= {node.pk}'
 
-        self.make_kkrimp_rmsplot(rms_all, stot_all, pks_all, rms_goal, ptitle, **kwargs)
+        self.make_kkrimp_rmsplot(rms_all, stot_all, impcalcs, rms_goal, ptitle, **kwargs)
 
-    def make_kkrimp_rmsplot(self, rms_all, stot_all, pks_all, rms_goal, ptitle, **kwargs):
+    def make_kkrimp_rmsplot(self, rms_all, stot_all, list_of_impcalcs, rms_goal, ptitle, **kwargs):
         """
         plot rms and total spin moment of kkrimp calculation or series of kkrimp calculations
         """
@@ -1141,7 +1200,7 @@ def make_kkrimp_rmsplot(self, rms_all, stot_all, pks_all, rms_goal, ptitle, **kw
         # plotting of convergence properties (rms etc.)
         if len(rms_all) > 0:
             # sort rms values and flatten array
-            reorder_rms = array(pks_all).argsort()[::-1]
+            reorder_rms = get_sorting_indices(list_of_impcalcs)
             rms, niter_calcs, stot = [], [0], []
             rms_all_sorted = [rms_all[i] for i in reorder_rms]
             for i in rms_all_sorted:
@@ -1192,6 +1251,10 @@ def plot_kkrimp_dos_wc(self, node, **kwargs):
         from masci_tools.vis.kkr_plot_dos import dosplot
         from matplotlib.pyplot import show, figure, title, xticks, xlabel, axvline
 
+        if self.debug:
+            print('in plot_kkrimp_dos_wc')
+            print('kwargs:', kwargs)
+
         interpol, all_atoms, l_channels, sum_spins, switch_xy = True, False, True, False, False
         ptitle = None
         if 'ptitle' in list(kwargs.keys()):

tests/tools/test_find_parent.py

@@ -23,6 +23,21 @@ def test_find_parent_structure():
     assert voro_parent.uuid == '559b9d9b-3525-402e-9b24-ecd8b801853c'
 
 
+def test_find_structure_kkrimp():
+    """
+    find parent structure from a KkrimpCalculation
+    """
+    import_with_migration('files/db_dump_kkrimp_out.tar.gz')
+    kkrimp_calc = load_node('eab8db1b-2cc7-4b85-a524-0df4ff2b7da6')
+
+    # now find voronoi parent and structure
+    struc, voro_parent = find_parent_structure(kkrimp_calc)
+
+    # check result
+    assert struc.uuid == 'e51ee6a1-bd27-4901-9612-7bac256bf117'
+    assert voro_parent.uuid == '559b9d9b-3525-402e-9b24-ecd8b801853c'
+
+
 def test_get_calc_from_remote():
     """
     find parent calc from remote