Integration with HTM

Objectives

• Use the hydrogen transport materials database HTM

• Directly integrate it with FESTIM

H-transport-materials (HTM) is a python library for accessing hydrogen transport properties such as diffusivities, solubilities, recombination coefficients, etc.

It is an open-source project and contributions to the database are more than welcome! Many materials are already available: Tungsten, copper, CuCrZr, Flinak, Flibe…

To install HTM simply run:

pip install h-transport-materials

👉 GitHub repository

👉 web dashboard

Now the interesting thing with HTM is that it can be used in FESTIM.

Let’s first have a look at the HTM api.

The HTM library

The diffusivities in the HTM database are stored in htm.diffusivities.

They can be filtered by material, isotope, author, year with the .filter() method.

import h_transport_materials as htm

# filter only tungsten and H
diffusivities = htm.diffusivities.filter(material="tungsten").filter(isotope="h")


# plot the properties
htm.plotting.plot(diffusivities)

import matplotlib.pyplot as plt

plt.yscale("log")
plt.ylabel("Diffusivity (m$^2$/s)")
plt.legend()
plt.show()

---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
Cell In[1], line 1
----> 1 import h_transport_materials as htm
      2 
      3 # filter only tungsten and H
      4 diffusivities = htm.diffusivities.filter(material="tungsten").filter(isotope="h")

File ~/checkouts/readthedocs.org/user_builds/festim-workshop/conda/festim1/lib/python3.11/site-packages/h_transport_materials/__init__.py:25
     22 Rg = 8.314 * ureg.Pa * ureg.m**3 * ureg.mol**-1 * ureg.K**-1
     23 avogadro_nb = 6.022e23 * ureg.particle * ureg.mol**-1
---> 25 from pybtex.database import parse_file
     26 from pathlib import Path
     28 bib_database = parse_file(str(Path(__file__).parent) + "/references.bib")

File ~/checkouts/readthedocs.org/user_builds/festim-workshop/conda/festim1/lib/python3.11/site-packages/pybtex/database/__init__.py:44
     42 from pybtex.errors import report_error
     43 from pybtex.py3compat import fix_unicode_literals_in_doctest, python_2_unicode_compatible
---> 44 from pybtex.plugin import find_plugin
     47 # for python2 compatibility
     48 def indent(text, prefix):

File ~/checkouts/readthedocs.org/user_builds/festim-workshop/conda/festim1/lib/python3.11/site-packages/pybtex/plugin/__init__.py:26
      2 # Copyright (c) 2006-2021  Andrey Golovizin
      3 # Copyright (c) 2014  Matthias C. M. Troffaes
      4 #
   (...)     21 # TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
     22 # SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
     25 import os.path  # splitext
---> 26 import pkg_resources
     28 from pybtex.exceptions import PybtexError
     31 class Plugin(object):

ModuleNotFoundError: No module named 'pkg_resources'

plt.figure()
# filter only tungsten and H
solubilities = htm.solubilities.filter(material="tungsten")

htm.plotting.plot(solubilities)


plt.yscale("log")
plt.ylabel("Solubility")
plt.legend()
plt.show()

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
Cell In[2], line 1
----> 1 plt.figure()
      2 # filter only tungsten and H
      3 solubilities = htm.solubilities.filter(material="tungsten")
      4 

NameError: name 'plt' is not defined

FESTIM integration

We want to use the properties of Frauenfelder for tungsten.

Let’s therefore filter the properties with .filter(author="frauenfelder").

We can obtain a single htm.ArrheniusProperty object:

diffusivities = htm.diffusivities.filter(material="tungsten").filter(isotope="h").filter(author="frauenfelder")
D = diffusivities[0]

print(type(diffusivities))
print(type(D))

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
Cell In[3], line 1
----> 1 diffusivities = htm.diffusivities.filter(material="tungsten").filter(isotope="h").filter(author="frauenfelder")
      2 D = diffusivities[0]
      3 
      4 print(type(diffusivities))

NameError: name 'htm' is not defined

A htm.ArrheniusProperty object has several useful attributes like .pre_exp which holds the pre-exponential factor, .act_energy for the activation energy but also .author and .year.

print(D)

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
Cell In[4], line 1
----> 1 print(D)

NameError: name 'D' is not defined

Let’s pick a solubility too:

S = htm.solubilities.filter(material="tungsten").filter(author="frauenfelder")[0]

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
Cell In[5], line 1
----> 1 S = htm.solubilities.filter(material="tungsten").filter(author="frauenfelder")[0]

NameError: name 'htm' is not defined

These properties can then be used inside a FESTIM.Material object.

This is extremely useful to avoid silly copy-pasting mistakes and typos in simulations.

import festim as F


tungsten = F.Material(
    id=1,
    D_0=D.pre_exp.magnitude, E_D=D.act_energy.magnitude,
    S_0=S.pre_exp.magnitude, E_S=S.act_energy.magnitude
    )

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
Cell In[6], line 6
      2 
      3 
      4 tungsten = F.Material(
      5     id=1,
----> 6     D_0=D.pre_exp.magnitude, E_D=D.act_energy.magnitude,
      7     S_0=S.pre_exp.magnitude, E_S=S.act_energy.magnitude
      8     )

NameError: name 'D' is not defined