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Increase code readability #32

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Nov 22, 2024
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Increase code readability #32

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7220af1
small refactoring
KulaginVladimir Nov 9, 2024
a15946e
upd H_Ti
KulaginVladimir Nov 20, 2024
c92e21b
TESSIM -> TESSIM-X
KulaginVladimir Nov 21, 2024
df05fa1
X for TESSIM
KulaginVladimir Nov 22, 2024
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35 changes: 16 additions & 19 deletions D_EUROFER/D_EUROFER.ipynb
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8 changes: 4 additions & 4 deletions D_EUROFER/reference_data/README.md
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@@ -1,6 +1,6 @@
## Description of files

- **143hplasma.json** - TESSIM simulation data and experimental TDS data for the case of 143 h exposure of Eurofer without damaged-induced traps
- **DPA+48hplasma.json** - TESSIM simulation data and experimental TDS data for the case of 48 h exposure of Eurofer with damaged-induced traps
- **DPA+143hplasma.json** - TESSIM simulation data and experimental TDS data for the case of 143 h exposure of Eurofer with damaged-induced traps
- **DPA+D+48hplasma.json** - TESSIM simulation data and experimental TDS data for the case of 48 h exposure of Eurofer with damaged-induced traps. Damaging was performed with already D-loaded sample.
- **143hplasma.json** - TESSIM-X simulation data and experimental TDS data for the case of 143 h exposure of Eurofer without damaged-induced traps
- **DPA+48hplasma.json** - TESSIM-X simulation data and experimental TDS data for the case of 48 h exposure of Eurofer with damaged-induced traps
- **DPA+143hplasma.json** - TESSIM-X simulation data and experimental TDS data for the case of 143 h exposure of Eurofer with damaged-induced traps
- **DPA+D+48hplasma.json** - TESSIM-X simulation data and experimental TDS data for the case of 48 h exposure of Eurofer with damaged-induced traps. Damaging was performed with already D-loaded sample.
210 changes: 108 additions & 102 deletions D_WO/D_WO.ipynb
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74 changes: 33 additions & 41 deletions D_damagedW/D_damagedW.ipynb
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153 changes: 88 additions & 65 deletions H_Ti/H_Ti.ipynb
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Expand Up @@ -24,53 +24,15 @@
},
{
"cell_type": "code",
"execution_count": 1,
"execution_count": 8,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Defining initial values\n",
"Defining variational problem\n",
"Defining source terms\n",
"Defining boundary conditions\n",
"Time stepping...\n",
"Calling FFC just-in-time (JIT) compiler, this may take some time.\n",
"Calling FFC just-in-time (JIT) compiler, this may take some time.\n",
"100.0 % 1.5e+03 s Elapsed time so far: 8.5 s\n",
"Defining initial values\n",
"Defining variational problem\n",
"Defining source terms\n",
"Defining boundary conditions\n",
"Time stepping...\n",
"100.0 % 1.5e+03 s Elapsed time so far: 6.0 s\n",
"Defining initial values\n",
"Defining variational problem\n",
"Defining source terms\n",
"Defining boundary conditions\n",
"Time stepping...\n",
"100.0 % 1.5e+03 s Elapsed time so far: 5.2 s\n",
"Defining initial values\n",
"Defining variational problem\n",
"Defining source terms\n",
"Defining boundary conditions\n",
"Time stepping...\n",
"100.0 % 1.5e+03 s Elapsed time so far: 5.2 s\n",
"Defining initial values\n",
"Defining variational problem\n",
"Defining source terms\n",
"Defining boundary conditions\n",
"Time stepping...\n",
"100.0 % 1.5e+03 s Elapsed time so far: 4.9 s\n"
]
}
],
"outputs": [],
"source": [
"import festim as F\n",
"import fenics as f\n",
"import numpy as np\n",
"import h_transport_materials as htm\n",
"import matplotlib.pyplot as plt\n",
"\n",
"################### PARAMETERS ###################\n",
"N_A_const = 6.022e23 # Avogadro, mol^-1\n",
Expand All @@ -83,7 +45,7 @@
"V = A * L # Ti volume (1cm x 1.3cm x 1mm), m^-3\n",
"\n",
"# Ti properties\n",
"X_max = 3\n",
"X_max = 3 # maximum number of H atoms per a Ti atom in the bulk\n",
"n_b = 9.4e4 * N_A_const # the number of atomic sites per unit of volume of Ti, m^-3\n",
"n_surf = (\n",
" X_max * 2.16e-5 * N_A_const\n",
Expand All @@ -98,7 +60,7 @@
"E_diff = D.act_energy.magnitude # diffusion activation energy, eV\n",
"\n",
"E_des = F.kJmol_to_eV(1.17e5 / 1e3) # activateion energy for desorption, eV\n",
"k_des = 1.08e8 * N_A_const # frequency factor for the surface desorption\n",
"k_des = 1.08e8 * N_A_const / n_surf**2 # desorption rate, m^2 s^-1\n",
"\n",
"E_sb = F.kJmol_to_eV(\n",
" 1.18e2\n",
Expand All @@ -114,14 +76,6 @@
"V_ch = 2.95e-3 # the chamber volume, m^3\n",
"P0 = 1.3e4 # the initial pressure, Pa\n",
"\n",
"T_list = [\n",
" 450 + 273,\n",
" 500 + 273,\n",
" 550 + 273,\n",
" 600 + 273,\n",
" 650 + 273,\n",
"] # reference data is given in deg C\n",
"\n",
"\n",
"################### FUNCTIONS ###################\n",
"def S0(T):\n",
Expand All @@ -143,7 +97,7 @@
" * P_H2(T, X)\n",
" / (2 * np.pi * M_H2 * F.k_B * T * e) ** 0.5\n",
" )\n",
" J_des = 2 * k_des * (surf_conc / n_surf) ** 2 * f.exp(-E_des / F.k_B / T)\n",
" J_des = 2 * k_des * surf_conc**2 * f.exp(-E_des / F.k_B / T)\n",
" return J_ads - J_des\n",
"\n",
"\n",
Expand All @@ -168,10 +122,22 @@
" X = 2 * (f.assemble(self.mobile.solution * self.mesh.dx) + surf) * A\n",
"\n",
" # Normalised content parameter\n",
" self.h_transport_problem.boundary_conditions[0].prms[\"X\"].assign(X)\n",
"\n",
"\n",
"################### MODEL ###################\n",
" self.h_transport_problem.boundary_conditions[0].prms[\"X\"].assign(X)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"We can now define a function that will run a FESTIM model for different cases:"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [],
"source": [
"def run_sim(T0):\n",
" Ti_model_impl = CustomSimulation()\n",
"\n",
Expand Down Expand Up @@ -223,8 +189,68 @@
" Ti_model_impl.initialise()\n",
" Ti_model_impl.run()\n",
"\n",
" return derived_quantities\n",
"\n",
" return derived_quantities"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"We now run the FESTIM model for the five cases with different material temperatures:"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Defining initial values\n",
"Defining variational problem\n",
"Defining source terms\n",
"Defining boundary conditions\n",
"Time stepping...\n",
"Calling FFC just-in-time (JIT) compiler, this may take some time.\n",
"Calling FFC just-in-time (JIT) compiler, this may take some time.\n",
"100.0 % 1.5e+03 s Elapsed time so far: 8.0 s\n",
"Defining initial values\n",
"Defining variational problem\n",
"Defining source terms\n",
"Defining boundary conditions\n",
"Time stepping...\n",
"100.0 % 1.5e+03 s Elapsed time so far: 5.8 s\n",
"Defining initial values\n",
"Defining variational problem\n",
"Defining source terms\n",
"Defining boundary conditions\n",
"Time stepping...\n",
"100.0 % 1.5e+03 s Elapsed time so far: 5.2 s\n",
"Defining initial values\n",
"Defining variational problem\n",
"Defining source terms\n",
"Defining boundary conditions\n",
"Time stepping...\n",
"100.0 % 1.5e+03 s Elapsed time so far: 5.3 s\n",
"Defining initial values\n",
"Defining variational problem\n",
"Defining source terms\n",
"Defining boundary conditions\n",
"Time stepping...\n",
"100.0 % 1.5e+03 s Elapsed time so far: 5.4 s\n"
]
}
],
"source": [
"T_list = [\n",
" 450 + 273,\n",
" 500 + 273,\n",
" 550 + 273,\n",
" 600 + 273,\n",
" 650 + 273,\n",
"] # reference data is given in deg C\n",
"\n",
"results = {}\n",
"for T0 in T_list:\n",
Expand All @@ -247,7 +273,7 @@
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": 11,
"metadata": {},
"outputs": [
{
Expand All @@ -262,9 +288,6 @@
}
],
"source": [
"import matplotlib.pyplot as plt\n",
"\n",
"\n",
"def plot_inventory(T0, FESTIM_data):\n",
" retention = np.array(FESTIM_data[1].data) + np.array(\n",
" FESTIM_data[0].data\n",
Expand Down Expand Up @@ -315,7 +338,7 @@
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": 12,
"metadata": {},
"outputs": [
{
Expand All @@ -338,7 +361,6 @@
}
],
"source": [
"import matplotlib.pyplot as plt\n",
"from pypalettes import load_cmap\n",
"\n",
"cmap = load_cmap(\"Sunset2\")\n",
Expand All @@ -354,6 +376,8 @@
" ),\n",
" \"font.size\": 8,\n",
" \"font.family\": \"Times New Roman\",\n",
" \"axes.spines.right\": False,\n",
" \"axes.spines.top\": False,\n",
"}\n",
"plt.rcParams.update(params)\n",
"\n",
Expand Down Expand Up @@ -386,7 +410,6 @@
" va=\"center\",\n",
" color=cmap(i),\n",
" )\n",
" axis.spines[[\"right\", \"top\"]].set_visible(False)\n",
"\n",
"(dummy_line,) = axs[0].plot([-1], [-1], color=\"black\", lw=1.5, label=\"FESTIM\")\n",
"dummy_dot = axs[0].scatter([-1], [-1], color=\"black\", s=10, label=\"Exp.\")\n",
Expand Down
3 changes: 1 addition & 2 deletions MMS/MMS.ipynb
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Expand Up @@ -282,7 +282,7 @@
},
{
"cell_type": "code",
"execution_count": 9,
"execution_count": null,
"metadata": {},
"outputs": [
{
Expand All @@ -305,7 +305,6 @@
}
],
"source": [
"import matplotlib.pyplot as plt\n",
"from pypalettes import load_cmap\n",
"\n",
"cmap = load_cmap(\"Sunset2\", reverse=False)\n",
Expand Down
4 changes: 2 additions & 2 deletions README.md
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Expand Up @@ -14,9 +14,9 @@ The repository includes several validation cases and one verification test on th

[2] [D adsorption on oxidised W](./D_WO): The case reproduces simulation results of [E. A. Hodille et al.](https://iopscience.iop.org/article/10.1088/1741-4326/ad2a29) on the D adsorption/desorption on/from oxidised W. The simulations are based on experiments performed by [A. Dunand et al.](https://iopscience.iop.org/article/10.1088/1741-4326/ac583a)

[3] [D implantation in damaged W](./D_damagedW): The case reproduces simulation results of [E. A. Hodille et al.](https://iopscience.iop.org/article/10.1088/1741-4326/aa5aa5/meta) on the isothermal D implantation in self-damaged W, followed by isothermal desorption. The simulations are based on experiments performed by [S. Markelj et al.](https://www.sciencedirect.com/science/article/pii/S0022311515303470?via%3Dihub)
[3] [D atom exposure of self-damaged W](./D_damagedW): The case reproduces simulation results of [E. A. Hodille et al.](https://iopscience.iop.org/article/10.1088/1741-4326/aa5aa5/meta) on the isothermal D implantation in self-damaged W, followed by isothermal desorption. The simulations are based on experiments performed by [S. Markelj et al.](https://www.sciencedirect.com/science/article/pii/S0022311515303470?via%3Dihub)

[4] [D implantation in damaged EUROFER](./D_EUROFER): The case reproduces experimental results of [K. Schmid et al.](https://www.sciencedirect.com/science/article/pii/S2352179122002228) on the D implantation in damaged EUROFER, followed by TDS measurements. The FESTIM model is mainly based on the simulations of [K. Schmid et al.](https://www.sciencedirect.com/science/article/pii/S2352179123001333?via%3Dihub)
[4] [D implantation in W-damaged EUROFER](./D_EUROFER): The case reproduces experimental results of [K. Schmid et al.](https://www.sciencedirect.com/science/article/pii/S2352179122002228) on the D implantation in damaged EUROFER, followed by TDS measurements. The FESTIM model is mainly based on the simulations of [K. Schmid et al.](https://www.sciencedirect.com/science/article/pii/S2352179123001333?via%3Dihub)

[5] [MMS](./MMS) test

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