tri-amdd / piro Goto Github PK

Was attempting to run the BaTiO3 notebook on colab and have had some errors installing from pip as that notebooks do not match the release.

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-17-d8c3c8f46d03> in <module>()
      7     allow_gas_release=True,
      8     confine_competing_to_icsd=False,
----> 9     add_elements=['C']
     10 )

TypeError: __init__() got an unexpected keyword argument 'confine_competing_to_icsd'

Hi!
I am encountering a problem when running the BaTiO3 notebook.
After the imports, running

router = SynthesisRoutes(
    mp_id, 
    confine_to_icsd=True, 
    confine_to_stables=True, 
    explicit_includes=[TiO2_rutile,BaCO3_beta,TiO_ordered, BaTi2O5], 
    exclude_compositions=['BaTiO3'],
    allow_gas_release=True,
    confine_competing_to_icsd=False,
    add_elements=['C']
)

returns an IndexError with traceback:

IndexError                                Traceback (most recent call last)
      10 TiO2_rutile = 'mp-2657' # Additional relevant phase to explicitly include
      11 BaCO3_beta = 'mp-4559'  # Additional relevant phase to explicitly include
----> 13 router = SynthesisRoutes(
      14     mp_id, 
     15     confine_to_icsd=True, 
     16     confine_to_stables=True, 
     17     explicit_includes=[TiO2_rutile,BaCO3_beta,TiO_ordered, BaTi2O5], 
     18     exclude_compositions=['BaTiO3'],
     19     allow_gas_release=True,
     20     confine_competing_to_icsd=False,
     21     add_elements=['C']
     22 )

File .\site-packages\piro\route.py:129, in SynthesisRoutes.__init__(self, target_entry_id, confine_to_icsd, confine_to_stables, hull_distance, simple_precursors, explicit_includes, exclude_compositions, allow_gas_release, add_elements, flexible_competition, entries, epitaxies, similarities, sigma, transport_constant, custom_target_entry, confine_competing_to_icsd)
    126 else:
    127     self.elts = list(self.target_entry.composition.as_dict().keys())
--> 129 self.get_precursor_library()
    130 print("Precursor library ready.")
    131 self.epitaxies = (
    132     epitaxies
    133     if epitaxies
    134     else get_epitaxies(self.precursor_library, self.target_entry)
...
    194     return self.custom_target_entry
    195 else:
--> 196     return [e for e in self.entries if e.entry_id == self.target_entry_id][0]

IndexError: list index out of range

Any idea on how to fix this?

Installed piro via:

conda create -n piro python==3.7
conda activate piro
pip install piro

from piro.route import SynthesisRoutes

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
~\AppData\Local\Temp/ipykernel_27028/3824750463.py in <module>
      1 import pandas as pd
----> 2 from piro.route import SynthesisRoutes
      3 pd.set_option('display.width', 700)
      4 pd.set_option('display.max_colwidth', 300)

~\Miniconda3\envs\piro\lib\site-packages\piro\route.py in <module>
      7 import json
      8 
----> 9 from pymatgen.core import Composition
     10 from pymatgen.analysis.phase_diagram import PhaseDiagram
     11 from pymatgen.util.string import latexify

~\Miniconda3\envs\piro\lib\site-packages\pymatgen\core\__init__.py in <module>
     59 
     60 
---> 61 SETTINGS = _load_pmg_settings()
     62 locals().update(SETTINGS)

~\Miniconda3\envs\piro\lib\site-packages\pymatgen\core\__init__.py in _load_pmg_settings()
     49         with open(SETTINGS_FILE) as f:
     50             d_yml = yaml.safe_load(f)
---> 51         d.update(d_yml)
     52     except OSError:
     53         # If there are any errors, default to using environment variables

TypeError: 'NoneType' object is not iterable

Not essential, but might help people to get up and running sooner if there's a dependency issue so they can install a known set of compatible dependencies via pip install -r requirements.txt as a last resort.

Just gonna leave this to track issue derivative from #45 .

MP_API_KEY = '' #@param {type:"string"}
!pmg config --add PMG_MAPI_KEY {MP_API_KEY}

Traceback (most recent call last):
  File "/usr/local/bin/pmg", line 5, in <module>
    from pymatgen.cli.pmg import main
  File "/usr/local/lib/python3.7/dist-packages/pymatgen/cli/pmg.py", line 15, in <module>
    from pymatgen.core import SETTINGS
  File "/usr/local/lib/python3.7/dist-packages/pymatgen/core/__init__.py", line 61, in <module>
    SETTINGS = _load_pmg_settings()
  File "/usr/local/lib/python3.7/dist-packages/pymatgen/core/__init__.py", line 51, in _load_pmg_settings
    d.update(d_yml)
TypeError: 'NoneType' object is not iterable

Workaround is to just use export MAPI_KEY=<your API key>, but then another error ensues (which appears regardless of using Google Colab or not). See #58

I think it would be nice to be able to display known syntheses alongside the plot. Structural information is often missing from these, but I think even a table of synthesis of equivalent compositions would be helpful.