Debug changes from lwave and stability calculations

gaspy/fireworks_helper_scripts.py

@@ -282,7 +282,11 @@ def get_atoms_from_fw(fw, index=-1):
         atoms   `ase.Atoms` instance from the Firework you provided
     '''
     # Get the `ase.Atoms` object from FireWork's results
-    atoms_trajhex = fw.launches[-1].action.stored_data['opt_results'][1]
+    try:
+        atoms_trajhex = fw.launches[-1].action.stored_data['opt_results'][1]
+    except IndexError:
+        atoms_trajhex = fw.archived_launches[-1].action.stored_data['opt_results'][1]
+        warnings.warn('Getting atoms from an archive Fireworks launch', RuntimeWarning)
     atoms = decode_trajhex_to_atoms(atoms_trajhex, index=index)
 
     # Get the Firework task that was meant to convert the original hexstring to

gaspy/gasdb.py

@@ -12,7 +12,7 @@
 from pymongo import MongoClient
 from pymongo.collection import Collection
 from pymatgen.ext.matproj import MPRester
-from pymatgen.analysis.pourbaix_diagram import PourbaixDiagram, ELEMENTS_HO, PourbaixPlotter
+from pymatgen.analysis.pourbaix_diagram import PourbaixDiagram, ELEMENTS_HO
 from . import defaults
 from .utils import read_rc
 from .fireworks_helper_scripts import get_launchpad
@@ -812,6 +812,7 @@ def purge_adslabs(fwids):
     with get_mongo_collection('adsorption') as collection:
         collection.delete_many({'fwids.slab+adsorbate': {'$in': fwids}})
 
+
 def get_electrochemical_stability(mpid, pH, potential):
     '''
     A wrapper for pymatgen to construct Pourbaix amd calculate electrochemical

gaspy/tasks/calculation_finders.py

@@ -215,8 +215,10 @@ def _load_attributes(self):
         self.fw_query = {'name.calculation_type': 'gas phase optimization',
                          'name.gasname': self.gas_name}
         for key, value in self.vasp_settings.items():
-            self.gasdb_query['fwname.vasp_settings.%s' % key] = value
-            self.fw_query['name.vasp_settings.%s' % key] = value
+            # We don't care if these VASP settings change
+            if key not in set(['nsw', 'isym', 'symprec', 'lwave', 'lcharg']):
+                self.gasdb_query['fwname.vasp_settings.%s' % key] = value
+                self.fw_query['name.vasp_settings.%s' % key] = value
         self.dependency = MakeGasFW(self.gas_name, self.vasp_settings)
 
 
@@ -253,8 +255,10 @@ def _load_attributes(self):
         self.fw_query = {'name.calculation_type': 'unit cell optimization',
                          'name.mpid': self.mpid}
         for key, value in self.vasp_settings.items():
-            self.gasdb_query['fwname.vasp_settings.%s' % key] = value
-            self.fw_query['name.vasp_settings.%s' % key] = value
+            # We don't care if these VASP settings change
+            if key not in set(['nsw', 'isym', 'symprec', 'lwave', 'lcharg']):
+                self.gasdb_query['fwname.vasp_settings.%s' % key] = value
+                self.fw_query['name.vasp_settings.%s' % key] = value
         self.dependency = MakeBulkFW(self.mpid, self.vasp_settings)
 
 
@@ -363,7 +367,7 @@ def _load_attributes(self):
 
         for key, value in self.vasp_settings.items():
             # We don't care if these VASP settings change
-            if key not in set(['nsw', 'isym', 'symprec']):
+            if key not in set(['nsw', 'isym', 'symprec', 'lwave', 'lcharg']):
                 self.gasdb_query['fwname.vasp_settings.%s' % key] = value
                 self.fw_query['name.vasp_settings.%s' % key] = value
 
@@ -485,7 +489,7 @@ def _load_attributes(self):
         # Parse the VASP settings
         for key, value in self.vasp_settings.items():
             # We don't care if these VASP settings change
-            if key != 'isym':
+            if key not in set(['isym', 'lwave', 'lcharg']):
                 self.gasdb_query['fwname.vasp_settings.%s' % key] = value
                 self.fw_query['name.vasp_settings.%s' % key] = value
 

gaspy/tests/gasdb_test.py

@@ -36,6 +36,7 @@
                      get_electrochemical_stability)
 
 # Things we need to do the tests
+import math
 import pytest
 import warnings
 import copy
@@ -507,10 +508,11 @@ def test_get_low_coverage_ml_docs(adsorbate, model_tag):
         low_cov_energy = low_coverage_docs_by_surface[surface]['energy']
         assert low_cov_energy <= energy
 
+
 def test_get_electrochemical_stability():
     # at pH=0, V=0.9
-    expected_stabilities = {'mp-126':0.884,  # Pt
+    expected_stabilities = {'mp-126': 0.884,  # Pt
                             'mp-81': 0.0}    # Au
     for mpid, expected_stability in expected_stabilities.items():
         stability = get_electrochemical_stability(mpid, 0, 0.9)
-        assert stability == expected_stability
+        assert math.isclose(stability, expected_stability, rel_tol=1e-6)

gaspy/tests/tasks_tests/calculation_finders_test.py

@@ -113,7 +113,11 @@ def _assert_vasp_settings(doc, vasp_settings):
 
             # If we're looking at a slab, then we don't care about certain
             # vasp settings
-            elif doc['fwname']['calculation_type'] == 'slab+adsorbat optimizatione' and key in set(['isym']):
+            elif doc['fwname']['calculation_type'] == 'surface energy optimization' and key in set(['isym']):
+                pass
+
+            # We never really care if the electronic files are saved or not
+            elif key in set(['lwave', 'lcharg']):
                 pass
 
             else: