improved ORB; compatible with atomistic_tools v1.0

nanotech-empa · Aug 12, 2019 · e62587b · e62587b
1 parent 1bd53e7
commit e62587b
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Showing 12 changed files with 1,504 additions and 174 deletions.
diff --git a/common.py b/common.py
@@ -35,15 +35,22 @@
 
 workchain_preproc_and_viewer_info = {
     'STMWorkChain': OrderedDict([
-        ('stm', { # If no preprocess matches, error wrt first version is given
+        ('stm2', { # If no preprocess matches, error wrt first version is given
             'n_calls': 2,
             'viewer_path': "scanning_probe/stm/view_stm.ipynb",
             'retrieved_files': [(1, ["stm.npz"])], # [(step_index, list_of_retr_files), ...]
             'struct_label': 'structure',
+            'req_param': ('stm_params', '--fwhms'), # required parameterdata input and a key in it
+        }),
+        ('stm1', {
+            'n_calls': 2,
+            'viewer_path': "scanning_probe/stm/view_stm-v1.ipynb",
+            'retrieved_files': [(1, ["stm.npz"])],
+            'struct_label': 'structure',
         }),
         ('stm0', {
             'n_calls': 3,
-            'viewer_path': "scanning_probe/stm/view_stm-old.ipynb",
+            'viewer_path': "scanning_probe/stm/view_stm-v0.ipynb",
             'retrieved_files': [(2, ["stm_ch.npz"])],
             'struct_label': 'structure',
         })
@@ -65,16 +72,23 @@
         }),
     ]),
     'OrbitalWorkChain': OrderedDict([
-        ('orb', {
+        ('orb1', {
             'n_calls': 2,
             'viewer_path': "scanning_probe/orb/view_orb.ipynb",
             'retrieved_files': [(1, ["orb.npz"])],
             'struct_label': 'structure',
+            'req_param': ('stm_params', '--orb_fwhms'),
+        }),
+        ('orb0', {
+            'n_calls': 2,
+            'viewer_path': "scanning_probe/orb/view_orb-v0.ipynb",
+            'retrieved_files': [(1, ["orb.npz"])],
+            'struct_label': 'structure',
         }),
     ]),
 }
 
-PREPROCESS_VERSION = 0.95
+PREPROCESS_VERSION = 1.01
 
 def preprocess_one(workcalc):
     """
@@ -87,18 +101,21 @@ def preprocess_one(workcalc):
 
     prefix = None
     reason = None
+
     for prefix_version in version_preproc_dict:
         n_calls = version_preproc_dict[prefix_version]['n_calls']
         retr_list_per_step = version_preproc_dict[prefix_version]['retrieved_files']
 
-        success = True
-
+        # ---
+        # check if number of calls matches
         if len(workcalc.get_outputs()) < n_calls:
             if reason is None:
                 reason = "Not all calculations started."
-            success = False
-            break
+            continue
 
+        # ---
+        # check if all specified files are retrieved
+        success = True
         for rlps in retr_list_per_step:
             calc_step, retr_list = rlps
             calc = workcalc.get_outputs()[calc_step]
@@ -108,17 +125,31 @@ def preprocess_one(workcalc):
                     reason = "Not all files were retrieved."
                 success = False
                 break
-        if success:
-            prefix = prefix_version
-            break
+        if not success:
+            continue
+
+        # ---
+        # check if the required parameter is there
+        if 'req_param' in version_preproc_dict[prefix_version]:
+            req_param, req_key = version_preproc_dict[prefix_version]['req_param']
+            inp_dict = workcalc.get_inputs_dict()
+            if not (req_param in inp_dict and req_key in inp_dict[req_param].dict):
+                if reason is None:
+                    reason = "Required parameter not existing."
+                continue
+
+        # ---
+        # found match!    
+        prefix = prefix_version
+        break
 
     if prefix is None:
         raise(Exception(reason))
 
     structure = workcalc.get_inputs_dict()[version_preproc_dict[prefix]['struct_label']]
-    pk_numbers = [e for e in structure.get_extras() if e.startswith(prefix)]
+    pk_numbers = [e for e in structure.get_extras() if e.startswith(prefix[:-1])]
     pk_numbers = [int(e.split('_')[1]) for e in pk_numbers if e.split('_')[1].isdigit()]
-    pks = [e[1] for e in structure.get_extras().items() if e[0].startswith(prefix)]
+    pks = [e[1] for e in structure.get_extras().items() if e[0].startswith(prefix[:-1])]
     if workcalc.pk in pks:
         return
     nr = 1
@@ -139,7 +170,7 @@ def preprocess_spm_calcs(workchain_list = ['STMWorkChain', 'PdosWorkChain', 'Afm
                {'extras.preprocess_version': {'<': PREPROCESS_VERSION}},
            ],
     })
-    qb.order_by({WorkCalculation:{'ctime':'desc'}})
+    qb.order_by({WorkCalculation:{'ctime':'asc'}})
 
     for m in qb.all():
         n = m[0]

diff --git a/manage_calcs.ipynb b/manage_calcs.ipynb
@@ -19,6 +19,7 @@
     "from aiida.orm.calculation.work import WorkCalculation\n",
     "from aiida.orm.calculation.job import JobCalculation\n",
     "from aiida.orm import load_node\n",
+    "from aiida.orm.data.structure import StructureData\n",
     "\n",
     "\n",
     "import ipywidgets as ipw\n",
@@ -38,6 +39,24 @@
     "}"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Delete all SPM extras:\n",
+    "\n",
+    "#qb = QueryBuilder()\n",
+    "#qb.append(StructureData)\n",
+    "#\n",
+    "#for struct_data in qb.all():\n",
+    "#    extras = struct_data[0].get_extras()\n",
+    "#    for key in extras.keys():\n",
+    "#        if key.endswith('_pk') and key.split('_')[1].isdigit():\n",
+    "#            struct_data[0].del_extra(key)"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,

diff --git a/orb/misc/run_cube_from_wfn.py b/orb/misc/run_cube_from_wfn.py
@@ -7,13 +7,17 @@
 
 mkdir $DIR/cubes
 
-$SCRIPT_PATH cube_from_wfn.py \
+"$SCRIPT_PATH"cube_from_wfn.py \
   --cp2k_input_file $DIR/aiida.inp \
   --basis_set_file $DIR/BASIS_MOLOPT \
   --xyz_file $DIR/geom.xyz \
   --wfn_file $DIR/aiida-RESTART.wfn \
   --output_dir $DIR/cubes/ \
-  --n_homo 5 \
-  --n_lumo 5 \
+  --n_homo 3 \
+  --n_lumo 3 \
   --dx 0.2 \
-#  --gen_rho \
+  --eval_cutoff 14.0 \
+#  --orb_square \
+#  --charge_dens \
+#  --spin_dens \
+
diff --git a/orb/orb_workchain.py b/orb/orb_workchain.py
@@ -47,7 +47,7 @@ def define(cls, spec):
     def run_scf_diag(self):
         self.report("Running CP2K diagonalization SCF")
 
-        n_lumo = int(self.inputs.stm_params.get_dict()['--n_lumo_ch'])
+        n_lumo = int(self.inputs.stm_params.get_dict()['--n_lumo'])
 
         inputs = self.build_cp2k_inputs(self.inputs.structure,
                                         self.inputs.cp2k_code,

diff --git a/orb/submit_orb.ipynb b/orb/submit_orb.ipynb
@@ -255,16 +255,24 @@
     "                              value='3.0 5.0',\n",
     "                              style=style, layout=layout)\n",
     "\n",
+    "isovals_text = ipw.Text(description='Isovalues',\n",
+    "                              value='1e-7',\n",
+    "                              style=style, layout=layout)\n",
+    "\n",
+    "fwhms_text = ipw.Text(description='FWHMs (eV)',\n",
+    "                              value='0.02 0.10',\n",
+    "                              style=style, layout=layout)\n",
+    "\n",
     "extrap_plane_floattext = ipw.BoundedFloatText(\n",
     "                        description='Extrap plane (ang)',\n",
     "                        min=1.0,\n",
     "                        max=10.0,\n",
     "                        step=0.1,\n",
-    "                        value=3.0,\n",
+    "                        value=3.5,\n",
     "                        style=style, layout=layout_small)\n",
     "\n",
     "\n",
-    "display(n_homo_inttext, n_lumo_inttext, heights_text, extrap_plane_floattext)"
+    "display(n_homo_inttext, n_lumo_inttext, heights_text, isovals_text, fwhms_text, extrap_plane_floattext)"
    ]
   },
   {
@@ -342,15 +350,15 @@
     "            '--wfn_file':           parent_dir+'aiida-RESTART.wfn',\n",
     "            '--hartree_file':       parent_dir+'aiida-HART-v_hartree-1_0.cube',\n",
     "            '--orb_output_file':    'orb.npz',\n",
-    "            '--emin':               '-2.0',\n",
-    "            '--emax':               '2.0',\n",
     "            '--eval_region':        ['G', 'G', 'G', 'G', 'n-1.0_C', 'p%.1f'%extrap_plane],\n",
     "            '--dx':                 '0.15',\n",
     "            '--eval_cutoff':        '14.0',\n",
     "            '--extrap_extent':      '5.0',\n",
+    "            '--n_homo':             str(n_homo_inttext.value),\n",
+    "            '--n_lumo':             str(n_lumo_inttext.value),\n",
     "            '--orb_heights':        heights_text.value.split(),\n",
-    "            '--n_homo_ch':          str(n_homo_inttext.value),\n",
-    "            '--n_lumo_ch':          str(n_lumo_inttext.value),\n",
+    "            '--orb_isovalues':      isovals_text.value.split(),\n",
+    "            '--orb_fwhms':          fwhms_text.value.split(),\n",
     "        })\n",
     "        \n",
     "        cp2k_code = cp2k_codes[drop_cp2k.index]\n",