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Merging dev onto release #2890

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Jan 26, 2024
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46fba6a
updating the init files in a few places with docstrings
jgostick Jul 23, 2023
be976f3
Merge branch 'dev' into fixing-basic-usage-docs
jgostick Sep 26, 2023
64f3a9f
fixing typos generator tutorial
jgostick Sep 28, 2023
1777992
fixed typos in tutorial No.3: data and topology storage
MohammadMehrnia787 Oct 5, 2023
2e05f38
Deleted line that adds pore.coords property to bcc network
mkaguer Oct 26, 2023
5e600bc
Improved spheres_and_cylinders conduit lengths model to catch more ed…
jgostick Nov 3, 2023
4270b12
enhanced tests to catch additional case
jgostick Nov 3, 2023
cb48a8c
updating shape factor tests
jgostick Nov 3, 2023
99a4fe0
added hydraulic conductance integration tests
jgostick Nov 3, 2023
12b6f45
oops, forgot to add assert before isclose
jgostick Nov 3, 2023
6d663d7
comparing conduits to analytical solution in integration test
jgostick Nov 3, 2023
7bb0564
Merge branch 'dev' into fixing-basic-usage-docs
jgostick Nov 22, 2023
9648d71
adding a network extraction example
jgostick Nov 22, 2023
95c7a7e
fixing a pep8 error
jgostick Nov 22, 2023
b301339
Merge pull request #2866 from PMEAL/fixing-basic-usage-docs
jgostick Nov 22, 2023
eed4136
Bump version number (build part)
actions-user Nov 22, 2023
5bab78e
Update docs.txt
jgostick Nov 22, 2023
5e2404c
Bump version number (build part)
actions-user Nov 22, 2023
a905ae1
fixing typos
MohammadMehrnia787 Nov 23, 2023
bc04bda
typos in examples #1-10
MohammadMehrnia787 Dec 6, 2023
4d5b844
Merge pull request #2831 from PMEAL/fixing_typos_in_examples
jgostick Dec 22, 2023
0baf355
Bump version number (build part)
actions-user Dec 22, 2023
9e31311
Fixed bug in pore surface area models
jgostick Jan 26, 2024
c6a4333
updating tests
jgostick Jan 26, 2024
93b5bb5
updating tests
jgostick Jan 26, 2024
51c3715
adding check to prevent negative numbers
jgostick Jan 26, 2024
47e0ac7
Merge pull request #2889 from PMEAL/fix_pore_surface_area
jgostick Jan 26, 2024
1668355
Bump version number (build part)
actions-user Jan 26, 2024
cc3012b
Merge branch 'release' into dev
jgostick Jan 26, 2024
53b6e6c
Bump version number (build part)
actions-user Jan 26, 2024
478890c
Merge pull request #2848 from PMEAL/issue2847_bcc
jgostick Jan 26, 2024
3677802
Bump version number (build part)
actions-user Jan 26, 2024
4d41843
Merge pull request #2853 from PMEAL/more_robust_conduit_lengths
jgostick Jan 26, 2024
223b0c0
Bump version number (build part)
actions-user Jan 26, 2024
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6 changes: 3 additions & 3 deletions examples/applications/absolute_permeability.ipynb
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"The example explains absolute permeabilty calculations on a cubic network. Note that permeability calcualtion for an extracted network from PoreSpy follows similar steps in assigning phase, algorithm and calculating permeability."
"The example explains absolute permeabilty calculations on a cubic network. Note that permeability calculation for an extracted network from PoreSpy follows similar steps in assigning phase, algorithm and calculating permeability."
]
},
{
Expand Down Expand Up @@ -66,7 +66,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"It is assumed that a generic phase flowsthrough the porous medium. As absolute permeability is the porous medium property and not the fluid property, any other fluid with an assigned viscosity value can be used as the phase."
"It is assumed that a generic phase flows through the porous medium. As absolute permeability is the porous medium property and not the fluid property, any other fluid with an assigned viscosity value can be used as the phase."
]
},
{
Expand Down Expand Up @@ -313,7 +313,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.16"
"version": "3.10.13"
}
},
"nbformat": 4,
Expand Down
20,259 changes: 20,246 additions & 13 deletions examples/applications/adjusting_pore_size_distributions.ipynb

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1,776 changes: 1,768 additions & 8 deletions examples/applications/dispersion_coefficient.ipynb

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1,695 changes: 1,690 additions & 5 deletions examples/applications/effective_diffusivity_and_tortuosity.ipynb

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8 changes: 4 additions & 4 deletions examples/applications/formation_factor.ipynb
Original file line number Diff line number Diff line change
Expand Up @@ -11,13 +11,13 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"The formation factor is the ratio of the conducitivity of the pure brine to the measured conductivity \n",
"The formation factor is the ratio of the conductivity of the pure brine to the measured conductivity \n",
"\n",
"$$\n",
"F = \\frac{\\sigma_{brine}}{\\sigma_{measured}}\\\\\n",
"$$\n",
"\n",
"This example shows how to calculate the formation factor from a fickian diffusion simulation on a cubic network. Note that formation factior calculation on an extracted network from Porespy follows similar steps in assigning phase, algorithm and calculating the effective property."
"This example shows how to calculate the formation factor from a Fickian diffusion simulation on a cubic network. Note that formation factor calculation on an extracted network from Porespy follows similar steps in assigning phase, algorithm and calculating the effective property."
]
},
{
Expand Down Expand Up @@ -174,7 +174,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"In porous media research, the effective transport properties of one process can be used as a substitute for another, for example, electron conduction and diffusion are analagous.\n",
"In porous media research, the effective transport properties of one process can be used as a substitute for another, for example, electron conduction and diffusion are analogous.\n",
"\n",
"$$\n",
"\\frac{D_{eff}}{D_{AB}} = \\frac{\\sigma_{eff}}{\\sigma}\\\\\n",
Expand Down Expand Up @@ -258,7 +258,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.16"
"version": "3.10.13"
}
},
"nbformat": 4,
Expand Down
16 changes: 8 additions & 8 deletions examples/applications/mercury_intrusion.ipynb
Original file line number Diff line number Diff line change
Expand Up @@ -305,7 +305,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"This looks pretty good. The minimum value (`loc`) was set to 100 nm, and the `scale` of 20 um positions the distribution well within our expected range. Lastly, the `c` value controls the skew, which has created a slighly elongated tail, but nothing too extreme. Only a few values will be larger than the network spacing of 40 um, which we will revisit later."
"This looks pretty good. The minimum value (`loc`) was set to 100 nm, and the `scale` of 20 um positions the distribution well within our expected range. Lastly, the `c` value controls the skew, which has created a slightly elongated tail, but nothing too extreme. Only a few values will be larger than the network spacing of 40 um, which we will revisit later."
]
},
{
Expand Down Expand Up @@ -350,9 +350,9 @@
"source": [
"There are two important advantages to this approach.\n",
"\n",
"Firstly, we can limit the range of seed values, for instance from 0.1 to 0.9, which will prevent any abnormally large values that might occur if a point far out on the tail end of the distribution is choosen (like 0.9999). \n",
"Firstly, we can limit the range of seed values, for instance from 0.1 to 0.9, which will prevent any abnormally large values that might occur if a point far out on the tail end of the distribution is chosen (like 0.9999). \n",
"\n",
"Seconly, this simplifies the process of creating spatially correlated pore sizes since there are many way to generate correlated random numbers bewteen 0 and 1 (i.e. `porespy.generators.fractal_noise`). We won't go into that here, but it was used to create anisotropic networks in [this work](https://doi.org/10.1016/j.jpowsour.2007.04.059)."
"Secondly, this simplifies the process of creating spatially correlated pore sizes since there are many way to generate correlated random numbers between 0 and 1 (i.e. `porespy.generators.fractal_noise`). We won't go into that here, but it was used to create anisotropic networks in [this work](https://doi.org/10.1016/j.jpowsour.2007.04.059)."
]
},
{
Expand Down Expand Up @@ -476,7 +476,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"And we can chose which of these becomes the \"official\" throat diameter, and apply some scaling to the values if needed using:"
"And we can choose which of these becomes the \"official\" throat diameter, and apply some scaling to the values if needed using:"
]
},
{
Expand Down Expand Up @@ -594,7 +594,7 @@
"source": [
"## Add Physics\n",
"\n",
"To simulate mercury intrusion, we will need to calulate the capillary pressure of the throats in the network. The capillary pressure can be calculated using the Washburn equation as provided below.\n",
"To simulate mercury intrusion, we will need to calculate the capillary pressure of the throats in the network. The capillary pressure can be calculated using the Washburn equation as provided below.\n",
"\n",
"$$ P_C = \\frac{-2\\sigma cos(\\theta)}{R_T} $$\n"
]
Expand Down Expand Up @@ -694,7 +694,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"The agreement is surprizingly good for a first guess. We probably want to make the throat sizes in the network a little bit larger to shift the curve left. Recall that to compute the throat sizes we took the minimum size of the two neighboring pores and scaled it by 0.5. Let's adjust this scale factor. We could readd a new model over the old one, or just adjust the stored parameters of the current one:"
"The agreement is surprisingly good for a first guess. We probably want to make the throat sizes in the network a little bit larger to shift the curve left. Recall that to compute the throat sizes we took the minimum size of the two neighboring pores and scaled it by 0.5. Let's adjust this scale factor. We could readd a new model over the old one, or just adjust the stored parameters of the current one:"
]
},
{
Expand Down Expand Up @@ -847,7 +847,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"Now teh fit in the low pressure region is nearly perfect. Of course the high pressure region is not fitting at all, but as dicussed by Tsakiroglou and Payatakes in their paper, this sandstone has a dual porosity or microporosity, which is not resolved by the basic network used here. "
"Now teh fit in the low pressure region is nearly perfect. Of course the high pressure region is not fitting at all, but as discussed by Tsakiroglou and Payatakes in their paper, this sandstone has a dual porosity or microporosity, which is not resolved by the basic network used here. "
]
},
{
Expand Down Expand Up @@ -1020,7 +1020,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.15"
"version": "3.10.13"
},
"toc": {
"base_numbering": 1,
Expand Down
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