diff --git a/.github/workflows/process.yml b/.github/workflows/process.yml
index ed60185904..698459855a 100644
--- a/.github/workflows/process.yml
+++ b/.github/workflows/process.yml
@@ -178,7 +178,6 @@ jobs:
uses: Fusion-Power-Plant-Framework/fppf-actions/setup-hatch@main
with:
python-version: ${{ env.python-version }}
- - run: hatch run python scripts/vardes.py
- run: git config --global --add safe.directory '*'
- name: Download STF_TF.json files
uses: actions/download-artifact@v4
diff --git a/.gitignore b/.gitignore
index 93f469d2f4..a6236b708a 100644
--- a/.gitignore
+++ b/.gitignore
@@ -46,10 +46,8 @@ process/io/python_fortran_dicts.json
fortran.py
.coverage
dist/*
-documentation/io/vardes.md
lcov_results/
env/
-env_process/
.venv
*.DAT
!scenario_examples/*/*.DAT
diff --git a/documentation/examples b/documentation/examples
deleted file mode 120000
index a6573af9c9..0000000000
--- a/documentation/examples
+++ /dev/null
@@ -1 +0,0 @@
-../examples
\ No newline at end of file
diff --git a/documentation/python/process.io.md b/documentation/python/process.io.md
deleted file mode 100644
index d4a708633f..0000000000
--- a/documentation/python/process.io.md
+++ /dev/null
@@ -1,23 +0,0 @@
-# process.io
-
-::: process.io.configuration
-
-::: process.io.in_dat
-
-::: process.io.mfile_comparison
-
-::: process.io.mfile
-
-::: process.io.ndscan_funcs
-
-::: process.io.obsolete_vars
-
-::: process.io.plot_proc
-
-::: process.io.plot_sankey
-
-
-
-::: process.io.process_funcs
-
-::: process.io.python_fortran_dicts
\ No newline at end of file
diff --git a/documentation/python/process.md b/documentation/python/process.md
deleted file mode 100644
index 9a707e67d4..0000000000
--- a/documentation/python/process.md
+++ /dev/null
@@ -1,15 +0,0 @@
-# process
-
-::: process.main
-
-::: process.caller
-
-::: process.evaluators
-
-::: process.optimiser
-
-::: process.scan
-
-::: process.vmcon
-
-::: process.final
\ No newline at end of file
diff --git a/documentation/scripts/gen_api_ref.py b/documentation/scripts/gen_api_ref.py
new file mode 100644
index 0000000000..38eb4f7986
--- /dev/null
+++ b/documentation/scripts/gen_api_ref.py
@@ -0,0 +1,37 @@
+# SPDX-FileCopyrightText: 2023-present The Bluemira Developers
+#
+# SPDX-License-Identifier: LGPL-2.1-or-later
+"""Generate the API reference pages and navigation."""
+
+from pathlib import Path
+
+import mkdocs_gen_files
+from mkdocs_gen_files.nav import Nav
+
+nav = Nav()
+
+root = Path(__file__).parent.parent.parent
+package_name = "process"
+src = root / package_name
+reference = Path("source", "reference")
+
+for path in sorted(src.rglob("*.py")):
+ module_path = path.relative_to(root).with_suffix("")
+ doc_path = path.relative_to(root).with_suffix(".md")
+ full_doc_path = Path(reference, doc_path)
+
+ parts = tuple(module_path.parts)
+
+ if parts[-1] in {"__init__", "__main__", "_version"}:
+ continue
+
+ p = ".".join(parts)
+ nav[parts] = doc_path.as_posix()
+
+ with mkdocs_gen_files.open(full_doc_path, "w") as fd:
+ fd.write(f"::: {p}")
+
+ mkdocs_gen_files.set_edit_path(full_doc_path, path.relative_to(root))
+
+with mkdocs_gen_files.open(Path(reference, "overview.md"), "w") as nav_file:
+ nav_file.writelines(nav.build_literate_nav())
diff --git a/documentation/scripts/plotting_scripts/menard_beta_norm_plot.py b/documentation/scripts/plotting_scripts/menard_beta_norm_plot.py
index 98eb0a9f34..5d079b4964 100644
--- a/documentation/scripts/plotting_scripts/menard_beta_norm_plot.py
+++ b/documentation/scripts/plotting_scripts/menard_beta_norm_plot.py
@@ -11,13 +11,13 @@
y_range=(2, 8),
width=400,
height=400,
- title="Menard Normalized Beta Limit",
+ title="Menard Normalised Beta Limit",
)
plot.xaxis.axis_label = r"Aspect ratio, \ $$[A]$$"
-plot.yaxis.axis_label = r"Normalized beta limit, \ $$[\beta_N]$$"
+plot.yaxis.axis_label = r"Normalised beta limit, \ $$[\beta_N]$$"
plot.line("x", "y", source=source, line_width=3, line_alpha=0.6)
# Save the plot as HTML
-output_file("menard_beta_norm.html", title="Menard Normalized Beta Limit")
+output_file("menard_beta_norm.html", title="Menard Normalised Beta Limit")
save(plot)
diff --git a/documentation/scripts/plotting_scripts/original_beta_norm_plot.py b/documentation/scripts/plotting_scripts/original_beta_norm_plot.py
index ad0bf9e4f1..38a8407fa4 100644
--- a/documentation/scripts/plotting_scripts/original_beta_norm_plot.py
+++ b/documentation/scripts/plotting_scripts/original_beta_norm_plot.py
@@ -11,13 +11,13 @@
y_range=(2, 15),
width=400,
height=400,
- title="Original Normalized Beta Limit",
+ title="Original Normalised Beta Limit",
)
plot.xaxis.axis_label = r"Aspect ratio, \ $$[A]$$"
-plot.yaxis.axis_label = r"Normalized beta limit, \ $$[\beta_N]$$"
+plot.yaxis.axis_label = r"Normalised beta limit, \ $$[\beta_N]$$"
plot.line("x", "y", source=source, line_width=3, line_alpha=0.6)
# Save the plot as HTML
-output_file("original_beta_norm.html", title="Original Normalized Beta Limit")
+output_file("original_beta_norm.html", title="Original Normalised Beta Limit")
save(plot)
diff --git a/documentation/scripts/plotting_scripts/profile_hastie_current.py b/documentation/scripts/plotting_scripts/profile_hastie_current.py
index 3a1644a89d..a7c08ac3d2 100644
--- a/documentation/scripts/plotting_scripts/profile_hastie_current.py
+++ b/documentation/scripts/plotting_scripts/profile_hastie_current.py
@@ -16,7 +16,7 @@
height=400,
title="PROCESS vs Hastie Current Profile",
)
-plot.xaxis.axis_label = "Normalized Plasma Radius"
+plot.xaxis.axis_label = "Normalised Plasma Radius"
plot.yaxis.axis_label = "Current Density, J"
plot.line(
diff --git a/documentation/scripts/plotting_scripts/profile_parabolic_plot.py b/documentation/scripts/plotting_scripts/profile_parabolic_plot.py
index 2a1fc471ed..f6f232ff10 100644
--- a/documentation/scripts/plotting_scripts/profile_parabolic_plot.py
+++ b/documentation/scripts/plotting_scripts/profile_parabolic_plot.py
@@ -15,7 +15,7 @@
height=400,
title="Parabolic Profile | L-mode",
)
-plot.xaxis.axis_label = r"Normalized Radius, $$ \rho $$"
+plot.xaxis.axis_label = r"Normalised Radius, $$ \rho $$"
plot.yaxis.axis_label = r"Density, $$n_e$$"
plot.line("x", "y", source=source, line_width=3, line_alpha=0.6)
diff --git a/documentation/scripts/plotting_scripts/profile_pedestal_plot.py b/documentation/scripts/plotting_scripts/profile_pedestal_plot.py
index e31b6f88e5..576cd55783 100644
--- a/documentation/scripts/plotting_scripts/profile_pedestal_plot.py
+++ b/documentation/scripts/plotting_scripts/profile_pedestal_plot.py
@@ -29,7 +29,7 @@
height=400,
title="Pedestal Profile | H-mode",
)
-plot.xaxis.axis_label = r"Normalized Radius, $$ \rho $$"
+plot.xaxis.axis_label = r"Normalised Radius, $$ \rho $$"
plot.yaxis.axis_label = r"Density, $$n_e$$"
plot.line("x", "y", source=source, line_width=3, line_alpha=0.6)
diff --git a/documentation/scripts/sort_vardes.py b/documentation/scripts/sort_vardes.py
deleted file mode 100644
index bbef41d9cd..0000000000
--- a/documentation/scripts/sort_vardes.py
+++ /dev/null
@@ -1,34 +0,0 @@
-"""
-
-Script to tidy up vardes.md for the GitLab Page
-
-J. Morris
-10/08/19
-UKAEA
-
-"""
-
-import sys
-
-with open(sys.argv[1]) as vardes:
- lines = vardes.readlines()
-
-new_lines = []
-
-for counter, line in enumerate(lines):
- if "PROCESS Variable Descriptor File : dated" in line:
- date = line.split("dated")[-1].replace(" ", "")
- new_date = date[:4] + "." + date[4:6] + "." + date[6:]
- new_line = f"# PROCESS Variable Descriptions {new_date}\n"
- elif counter == 3:
- new_line = "## Introduction"
- elif "###" in line:
- new_line = line.split("]")[0].replace("[", "").replace(r"\_", " ")
- else:
- new_line = line
-
- new_lines.append(new_line)
-
-with open(sys.argv[1], "w") as new_vardes:
- new_vardes.writelines(new_lines)
- new_vardes.close()
diff --git a/documentation/cost-models/cost-models.md b/documentation/source/cost-models/cost-models.md
similarity index 95%
rename from documentation/cost-models/cost-models.md
rename to documentation/source/cost-models/cost-models.md
index 1947ea324c..4b3f0221fa 100644
--- a/documentation/cost-models/cost-models.md
+++ b/documentation/source/cost-models/cost-models.md
@@ -4,7 +4,7 @@ Two cost models are available, determined by the switch `cost_model`.
## 1990 cost model (`cost_model = 0`)
-This combines methods[^1] used in the TETRA code [^2] and the Generomak[^3] scheme. The costs are split into accounting categories[^4]. The best references for the algorithms used are[^5], and source file `costs.f90` in the code itself. The majority of the costed items have a unit cost associated with them. These values scale with (for example) power output, volume, component mass etc., and many are avaiable to be changed via the input file. All costs and their algorithms correspond to 1990 dollars.
+This combines methods[^1] used in the TETRA code [^2] and the Generomak[^3] scheme. The costs are split into accounting categories[^4]. The best references for the algorithms used are[^5], and source file `costs.f90` in the code itself. The majority of the costed items have a unit cost associated with them. These values scale with (for example) power output, volume, component mass etc., and many are available to be changed via the input file. All costs and their algorithms correspond to 1990 dollars.
The unit costs of the components of the fusion power core are relevant to "first-of-a-kind" items. That is to say, the items are assumed to be relatively expensive to build as they are effectively prototypes and specialised tools and machines have perhaps been made specially to create them. However, if a "production line" has been set up, and R & D progress has allowed more experience to be gained in constructing the power core components, the cost will be reduced as a result. Variable `fkind` may be used to multiply the raw unit costs of the fusion power core items (by a factor less than one) to simulate this cost reduction for an *Nth*-of-a-kind device. In other systems studies of fusion power plants[^6], values for this multiplier have ranged from 0.5 to 0.8.
@@ -14,7 +14,7 @@ The first wall, blanket, divertor, centrepost (if present) and current drive sys
If the switch `ireactor = 0`, no cost of electricity calculation is performed. If `ireactor = 1`, then the cost of electricity is evaluated, with the value quoted in units of $/MWh.
-The net electric power is calculated in routine `POWER` It is possible that the net electric power can become negative due to a high recirculating power. Switch `ipnet` determines whether the net electric power is scaled to always reamin positive (`ipnet = 0`, or whether it is allowed to become negative (`ipnet = 1`), in which case no cost of electricity calculation is performed.
+The net electric power is calculated in routine `POWER` It is possible that the net electric power can become negative due to a high recirculating power. Switch `ipnet` determines whether the net electric power is scaled to always remain positive (`ipnet = 0`, or whether it is allowed to become negative (`ipnet = 1`), in which case no cost of electricity calculation is performed.
## 2015 Kovari model (`cost_model = 1`)
diff --git a/documentation/development/add-vars.md b/documentation/source/development/add-vars.md
similarity index 91%
rename from documentation/development/add-vars.md
rename to documentation/source/development/add-vars.md
index d3299bb05f..67206c71cb 100644
--- a/documentation/development/add-vars.md
+++ b/documentation/source/development/add-vars.md
@@ -58,7 +58,7 @@ To add a `PROCESS` iteration variable please follow the steps below, in addition
1. The parameter `ipnvars` in module `numerics` of `numerics.f90` will normally be greater than the actual number of iteration variables, and does not need to be changed.
2. Append a new iteration number key to the end of the `ITERATION_VARIABLES` dictionary in `iteration_variables.py`. The associated variable is the corresponding key value.
3. Set the variable origin file and then the associated lower and upper bounds
-4. Update the `lablxc` derscription in `numerics.f90`.
+4. Update the `lablxc` description in `numerics.f90`.
It should be noted that iteration variables must not be reset elsewhere in the
code. That is, they may only be assigned new values when originally
@@ -110,7 +110,7 @@ After following the instruction to add an input variable, you can make the varia
2. Add a short description of the new scanning variable in the `nsweep` comment in `scan_variables.py`, alongside its identification number.
-3. Update the `SCAN_VARIABLES` dictionary in the `scan.py` file by adding a new case statement connecting the variable to the scan integer switch, the variable name and a short description.
+3. Update the `ScanVariables` enum in the `scan.py` file by adding a new case statement connecting the variable to the scan integer switch, the variable name and a short description.
4. Add a comment in the corresponding variable file in the data_structure directory, eg, `data_structure/[XX]_variables.py`, to add the variable description indicating the scan switch number.
@@ -130,12 +130,12 @@ After following the instruction to add an input variable, you can make the varia
`SCAN_VARIABLES` case example:
```python
- SCAN_VARIABLES = {
- 1: ScanVariable("aspect", "Aspect_ratio"),
- 2: ScanVariable("pflux_div_heat_load_max_mw", "Div_heat_limit_(MW/m2)"),
+ class ScanVariables(Enum):
+ aspect: ScanVariable("aspect", "Aspect_ratio", 1),
+ pflux_div_heat_load_max_mw: ScanVariable("pflux_div_heat_load_max_mw", "Div_heat_limit_(MW/m2)", 2),
...
- 54: ScanVariable("Bc2(0K)", "GL_NbTi Bc2(0K)"),
- 55: ScanVariable("dr_shld_inboard", "Inboard neutronic shield"),
+ Bc2_0K: ScanVariable("Bc2(0K)", "GL_NbTi Bc2(0K)", 54),
+ dr_shld_inboard : ScanVariable("dr_shld_inboard", "Inboard neutronic shield", 55),
```
---------------
@@ -170,4 +170,4 @@ def my_constraint_function():
value = ...
error = ...
return ConstraintResult(normalised_residual, value, error)
-```
\ No newline at end of file
+```
diff --git a/documentation/development/ci-guide.md b/documentation/source/development/ci-guide.md
similarity index 100%
rename from documentation/development/ci-guide.md
rename to documentation/source/development/ci-guide.md
diff --git a/documentation/development/debugging.md b/documentation/source/development/debugging.md
similarity index 98%
rename from documentation/development/debugging.md
rename to documentation/source/development/debugging.md
index 4b3a8e5942..aab5462a69 100644
--- a/documentation/development/debugging.md
+++ b/documentation/source/development/debugging.md
@@ -3,7 +3,7 @@
Debugging allows you stop a program mid-execution (called 'breaking') and explore the current state (e.g. print the current value of variables or attributes). In Python, this is done using `pdb` which comes as-standard with Python.
First, you must decide where in the code you would like to break. When debugging, a useful way to
-decide is to look at the terminal for where the error may have occured and break there. To insert a
+decide is to look at the terminal for where the error may have occurred and break there. To insert a
breakpoint in the code, insert the following code where you want the code to break:
```python
diff --git a/documentation/development/git-usage.md b/documentation/source/development/git-usage.md
similarity index 100%
rename from documentation/development/git-usage.md
rename to documentation/source/development/git-usage.md
diff --git a/documentation/development/numba.md b/documentation/source/development/numba.md
similarity index 100%
rename from documentation/development/numba.md
rename to documentation/source/development/numba.md
diff --git a/documentation/development/pre-commit.md b/documentation/source/development/pre-commit.md
similarity index 100%
rename from documentation/development/pre-commit.md
rename to documentation/source/development/pre-commit.md
diff --git a/documentation/development/standards.md b/documentation/source/development/standards.md
similarity index 95%
rename from documentation/development/standards.md
rename to documentation/source/development/standards.md
index 34a142e130..d4c4773068 100644
--- a/documentation/development/standards.md
+++ b/documentation/source/development/standards.md
@@ -8,7 +8,7 @@ You can check if your code meets the `ruff` standards by running:
2. `pre-commit run --all-files`
!!! Info "ruff automatic fixes"
- Many problems that `ruff` can detect it can also safely fix. Simply run `ruff check --fix` and it will try and automatically fix the mistakes, rewritting your source code.
+ Many problems that `ruff` can detect it can also safely fix. Simply run `ruff check --fix` and it will try and automatically fix the mistakes, rewriting your source code.
--------------------
@@ -601,7 +601,7 @@ ii
| `b_t_onaxis` | Toroidal field on-axis | T |
| `b_t_max` | Max toroidal field | T |
| `nd_electron_vol` | Volume average electron density | m-3 |
-| `temp_electron_vol_eV` | Volume avgerage electron temperature | eV |
+| `temp_electron_vol_eV` | Volume average electron temperature | eV |
| `m_steel` | Mass of steel | kg |
| `m_steel_tonne` | Mass of steel | tonne |
| `e_neutron_eV` | Energy of neutron | eV |
@@ -634,26 +634,39 @@ The docstring style is that of the [Sphinx type](https://www.sphinx-doc.org/en/m
If writing in new Python functions please use the docstring template below.
```python
-def function_name(param1, param2):
+def function_name(param1: Any, param2: Any) -> Any:
"""
Brief description of what the function does.
Detailed description of the function. This can include information about the algorithm,
any important notes, and other relevant details.
- :param type param1: Description of the first parameter.
- :param type param2: Description of the second parameter.
- :returns: Description of the return value.
- :rtype: return_type
- :raises ExceptionType: Description of the exception raised (if any).
-
- :notes:
- - Additional notes about the function.
- - Any important considerations or caveats.
-
- :references:
- - Reference 1: Description of the reference.
- - Reference 2: Description of the reference.
+ Parameters
+ ----------
+ param1:
+ Description of the first parameter.
+ param2:
+ Description of the second parameter.
+
+ Returns
+ -------
+ :
+ Description of the return value.
+
+ Raises
+ ------
+ ExceptionType
+ Description of the exception raised (if any).
+
+ Notes
+ -----
+ - Additional notes about the function.
+ - Any important considerations or caveats.
+
+ References
+ ----------
+ - Reference 1: Description of the reference.
+ - Reference 2: Description of the reference.
"""
```
@@ -700,4 +713,4 @@ class ExampleClass:
- Use inline comments sparingly.
-- Comments above apply to code below.
\ No newline at end of file
+- Comments above apply to code below.
diff --git a/documentation/development/testing.md b/documentation/source/development/testing.md
similarity index 100%
rename from documentation/development/testing.md
rename to documentation/source/development/testing.md
diff --git a/documentation/development/versioning.md b/documentation/source/development/versioning.md
similarity index 100%
rename from documentation/development/versioning.md
rename to documentation/source/development/versioning.md
diff --git a/documentation/eng-models/blanket_overview.md b/documentation/source/eng-models/blanket_overview.md
similarity index 96%
rename from documentation/eng-models/blanket_overview.md
rename to documentation/source/eng-models/blanket_overview.md
index a04afb1a77..71ea951c26 100644
--- a/documentation/eng-models/blanket_overview.md
+++ b/documentation/source/eng-models/blanket_overview.md
@@ -48,7 +48,7 @@ Using the Reynolds number we calculate the Darcy friction factor using the Haala
For the radius of the pipe bend we assume it to be 3 times the radius of the coolant channel.
-The elbow coefficients for the 90 and 180 degree bends $\left(f_{\text{90,elbow}}, f_{\text{180,elbow}}\right)$ are clalculated via [`elbow_coeff()`](#pipe-bend-elbow-coefficient--elbow_coeff).
+The elbow coefficients for the 90 and 180 degree bends $\left(f_{\text{90,elbow}}, f_{\text{180,elbow}}\right)$ are calculated via [`elbow_coeff()`](#pipe-bend-elbow-coefficient--elbow_coeff).
The pressure drop for the straights along the entire pipe length is the same as above:
diff --git a/documentation/eng-models/buildings.md b/documentation/source/eng-models/buildings.md
similarity index 100%
rename from documentation/eng-models/buildings.md
rename to documentation/source/eng-models/buildings.md
diff --git a/documentation/eng-models/ccfe_hcpb.md b/documentation/source/eng-models/ccfe_hcpb.md
similarity index 100%
rename from documentation/eng-models/ccfe_hcpb.md
rename to documentation/source/eng-models/ccfe_hcpb.md
diff --git a/documentation/eng-models/central-solenoid.md b/documentation/source/eng-models/central-solenoid.md
similarity index 99%
rename from documentation/eng-models/central-solenoid.md
rename to documentation/source/eng-models/central-solenoid.md
index 8346dfb1ad..354aa3ae10 100644
--- a/documentation/eng-models/central-solenoid.md
+++ b/documentation/source/eng-models/central-solenoid.md
@@ -80,7 +80,7 @@ $$
where $\alpha = \frac{r_{\text{CS,outer}}}{r_{\text{CS,inner}}}$, is the ratio of the outer and inner radii of the solenoid and $\beta = \frac{z_{\text{CS,half}}}{r_{\text{CS,outer}}}$, is the ratio of the solenoid half height to its inboard radius.
-The peak field at the bore of the central solenoid will not be the same as that felt by the conductors inside the structures. We require to know the peak field on the conductor if we are to design a superconducting central solenoid that has enough margin. Fits to data[^1] for different ranges of $\beta$ have been calulated as follows:
+The peak field at the bore of the central solenoid will not be the same as that felt by the conductors inside the structures. We require to know the peak field on the conductor if we are to design a superconducting central solenoid that has enough margin. Fits to data[^1] for different ranges of $\beta$ have been calculated as follows:
- $\beta > 3.0$
diff --git a/documentation/eng-models/cryostat-and-vacuum-system.md b/documentation/source/eng-models/cryostat-and-vacuum-system.md
similarity index 100%
rename from documentation/eng-models/cryostat-and-vacuum-system.md
rename to documentation/source/eng-models/cryostat-and-vacuum-system.md
diff --git a/documentation/eng-models/divertor.md b/documentation/source/eng-models/divertor.md
similarity index 98%
rename from documentation/eng-models/divertor.md
rename to documentation/source/eng-models/divertor.md
index c031cbb91d..7eb1d26c5d 100644
--- a/documentation/eng-models/divertor.md
+++ b/documentation/source/eng-models/divertor.md
@@ -95,7 +95,7 @@ $$
The main assumption of the Peng gaseous divertor model is that the power radiated to the divertor is equally radiated in the divertor box across all three surfaces. This may not truly be the case in reality.
-The interactive graph below can be used to investigate how changing the key prameters changes the divertor configuration. The grey box represents the first wall, the far right red line represents the right hand edge of the divertor region ($r_{\text{outer}}$), the far left red line represents the left hand edge of the divertor region ($r_{\text{inner}}$) and the blue line represents the bottom of the divertor region ($\Delta z_{\text{plasma,div}}$).
+The interactive graph below can be used to investigate how changing the key parameters changes the divertor configuration. The grey box represents the first wall, the far right red line represents the right hand edge of the divertor region ($r_{\text{outer}}$), the far left red line represents the left hand edge of the divertor region ($r_{\text{inner}}$) and the blue line represents the bottom of the divertor region ($\Delta z_{\text{plasma,div}}$).
-------------
diff --git a/documentation/eng-models/fw-blanket.md b/documentation/source/eng-models/fw-blanket.md
similarity index 98%
rename from documentation/eng-models/fw-blanket.md
rename to documentation/source/eng-models/fw-blanket.md
index 5dd5fc460a..d1ca05bcaa 100644
--- a/documentation/eng-models/fw-blanket.md
+++ b/documentation/source/eng-models/fw-blanket.md
@@ -269,22 +269,22 @@ $$
### Model Switches
There are three blanket model options, chosen by the user to match their selected blanket design using the switch 'i_blkt_dual_coolant' (default=0):
- 0. Solid breeder - nuclear heating in the blanket is exctrated by the primary coolant.
+ 0. Solid breeder - nuclear heating in the blanket is extracted by the primary coolant.
1. Liquid metal breeder, single-coolant
- - nuclear heating in the blanket is exctrated by the primary coolant.
+ - nuclear heating in the blanket is extracted by the primary coolant.
- liquid metal is circulated for tritium extraction, specified by number of circulations/day.
2. Liquid metal breeder, dual-coolant
- nuclear heating in the liquid breeder/coolant is extracted by the liquid breeder/coolant.
- nuclear heating in the blanket structure is extracted by the primary coolant
The default assuption for all blanket models is that the first wall and breeding blanket have the same coolant (flow = FW inlet -> FW outlet -> BB inlet-> BB outlet).
-It is possible to choose a different coolant for the FW and breeding blanket, in which case the mechanical pumping powers for the FW and BB are calculated seperately.
+It is possible to choose a different coolant for the FW and breeding blanket, in which case the mechanical pumping powers for the FW and BB are calculated separately.
The model has three mechanical pumping power options, chosen by the user to match their selected blanket design using the switch 'i_fw_blkt_shared_coolant' (default=0):
0. Same coolant for FW and BB ('i_fw_coolant_type`=`i_blkt_coolant_type`)
1. Different coolant for FW and BB ('i_fw_coolant_type`/=`i_blkt_coolant_type`)
!!! Note "Note"
- For the dual-coolant blanket the 'i_fw_blkt_shared_coolant' switch is relavent for the blanket structure coolant and not the liquid metal breeder/coolant choice.
+ For the dual-coolant blanket the 'i_fw_blkt_shared_coolant' switch is relevant for the blanket structure coolant and not the liquid metal breeder/coolant choice.
The user can select the number poloidal and toroidal modules for the IB and OB BB. The 'i_blkt_module_segmentation' switch can be set to 1 for a single-module-segment blanket (default=0):
0. Multi-module segment
diff --git a/documentation/eng-models/heating_and_current_drive/NBI/culham_nb.md b/documentation/source/eng-models/heating_and_current_drive/NBI/culham_nb.md
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diff --git a/documentation/eng-models/heating_and_current_drive/NBI/iter_nb.md b/documentation/source/eng-models/heating_and_current_drive/NBI/iter_nb.md
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diff --git a/documentation/eng-models/heating_and_current_drive/NBI/nbi_overview.md b/documentation/source/eng-models/heating_and_current_drive/NBI/nbi_overview.md
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index 0f200e1469..65e86a3360 100644
--- a/documentation/eng-models/heating_and_current_drive/NBI/nbi_overview.md
+++ b/documentation/source/eng-models/heating_and_current_drive/NBI/nbi_overview.md
@@ -100,7 +100,7 @@ It is recommended that only one of these two constraint equations is used
| $\mathtt{rnfe}$ | Iron density /$n_{\text{e}}$ |
-Both the [ITER](./iter_nb.md) and [Culham](culham_nb.md) NBI models both use the `sigbeam` method to calculate the stopping cross section[^1]. It finds a suitable analytic epressing for $\sigma_s^{(Z)}(E,n_{\text{e}},T_{\text{e}},Z_{\text{eff}})$ for fitting $\sigma_s$ data for a single impurity $(\text{Z)}$ plasma:
+Both the [ITER](./iter_nb.md) and [Culham](culham_nb.md) NBI models both use the `sigbeam` method to calculate the stopping cross section[^1]. It finds a suitable analytic expression for $\sigma_s^{(Z)}(E,n_{\text{e}},T_{\text{e}},Z_{\text{eff}})$ for fitting $\sigma_s$ data for a single impurity $(\text{Z)}$ plasma:
diff --git a/documentation/eng-models/heating_and_current_drive/RF/culham_electron_cyclotron.md b/documentation/source/eng-models/heating_and_current_drive/RF/culham_electron_cyclotron.md
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diff --git a/documentation/eng-models/heating_and_current_drive/RF/culham_lower_hybrid.md b/documentation/source/eng-models/heating_and_current_drive/RF/culham_lower_hybrid.md
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rename from documentation/eng-models/heating_and_current_drive/RF/culham_lower_hybrid.md
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index c6ed5d4d37..3247ac1f7b 100644
--- a/documentation/eng-models/heating_and_current_drive/RF/culham_lower_hybrid.md
+++ b/documentation/source/eng-models/heating_and_current_drive/RF/culham_lower_hybrid.md
@@ -14,10 +14,10 @@ AEA FUS 172: Physics Assessment for the European Reactor Study[^1]
5. Calculate the local toroidal magnetic field, `blocal`, using the formula `b_plasma_toroidal_on_axis * rmajor / (rmajor - rpenet)`. Here, `b_plasma_toroidal_on_axis` is the toroidal magnetic field at the magnetic axis, and `rmajor` is the major radius of the plasma.
6. Calculate the parallel refractive index, `nplacc`, which is needed for plasma access. It uses the local density `dlocal` and the local magnetic field `blocal` to calculate a fraction `frac`. `nplacc` is then obtained by adding `frac` to the square root of `1.0 + frac * frac`.
7. Calculate the local inverse aspect ratio, `epslh`, by dividing `rpenet` by `rmajor`.
-8. Calculate the LH normalized efficiency, `x`, using the formula `24.0 / (nplacc * sqrt(tlocal))`.
+8. Calculate the LH normalised efficiency, `x`, using the formula `24.0 / (nplacc * sqrt(tlocal))`.
9. Calculate several intermediate terms, `term01`, `term02`, `term03`, and `term04`, using different formulas involving `nplacc`, `physics_variables.zeff`, `tlocal`, `epslh`, and `x`.
10. Calculate the current drive efficiency, `gamlh`, using the formula `term01 * term02 * (1.0e0 - term03 / term04)`.
-11. Return the current drive efficiency normalized by the product of `0.1e0 * dlocal` and `physics_variables.rmajor`.
+11. Return the current drive efficiency normalised by the product of `0.1e0 * dlocal` and `physics_variables.rmajor`.
[^1]: T. C. Hender, M. K. Bevir, M. Cox, R. J. Hastie, P. J. Knight, C. N. Lashmore-Davies, B. Lloyd, G. P. Maddison, A. W. Morris, M. R. O'Brien, M.F. Turner abd H. R. Wilson, *"Physics Assessment for the European Reactor Study"*, AEA Fusion Report AEA FUS 172 (1992)
diff --git a/documentation/eng-models/heating_and_current_drive/RF/cutoff_ecrh.md b/documentation/source/eng-models/heating_and_current_drive/RF/cutoff_ecrh.md
similarity index 93%
rename from documentation/eng-models/heating_and_current_drive/RF/cutoff_ecrh.md
rename to documentation/source/eng-models/heating_and_current_drive/RF/cutoff_ecrh.md
index 7b6770e2c7..915aca5ac0 100644
--- a/documentation/eng-models/heating_and_current_drive/RF/cutoff_ecrh.md
+++ b/documentation/source/eng-models/heating_and_current_drive/RF/cutoff_ecrh.md
@@ -4,8 +4,8 @@
| Input | Description |
|-------|-------------|
-| `nd_plasma_electrons_vol_avg`, $n_{\text{e}}$ | Avergae electron temperature $\left[10^{19}\text{m}^{-3}\right]$ |
-| `temp_plasma_electron_vol_avg_kev`, $T_{\text{e}}$ | Avergae electron temperature $\left[\text{keV}\right]$ |
+| `nd_plasma_electrons_vol_avg`, $n_{\text{e}}$ | Average electron temperature $\left[10^{19}\text{m}^{-3}\right]$ |
+| `temp_plasma_electron_vol_avg_kev`, $T_{\text{e}}$ | Average electron temperature $\left[\text{keV}\right]$ |
| `rmajor`, $R_0$ | Major radius $\left[\text{m}\right]$ |
| `b_plasma_toroidal_on_axis`, $B_{\text{T}}$ | Toroidal magnetic field $\left[\text{T}\right]$ |
| `zeff`, $Z_{\text{eff}}$ | Effective charge |
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diff --git a/documentation/eng-models/machine-build.md b/documentation/source/eng-models/machine-build.md
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diff --git a/documentation/eng-models/pf-coil.md b/documentation/source/eng-models/pf-coil.md
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rename from documentation/eng-models/pf-coil.md
rename to documentation/source/eng-models/pf-coil.md
index 8160d2b04b..abf79e8df8 100644
--- a/documentation/eng-models/pf-coil.md
+++ b/documentation/source/eng-models/pf-coil.md
@@ -48,7 +48,7 @@ The four possible values of `i_pf_location(j)` correspond to the following PF co
R = R_0 + \texttt{rpf2} \times \delta \times a
$$
- Due to the nautre of the TF coils not being top-down symmetric for single null cases the positioning slightly differs if the coil is above or below the midplane.
+ Due to the nature of the TF coils not being top-down symmetric for single null cases the positioning slightly differs if the coil is above or below the midplane.
For above the midplane:
diff --git a/documentation/eng-models/plant-availability.md b/documentation/source/eng-models/plant-availability.md
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rename from documentation/eng-models/plant-availability.md
rename to documentation/source/eng-models/plant-availability.md
index e0a1a513d1..db46fa38f4 100644
--- a/documentation/eng-models/plant-availability.md
+++ b/documentation/source/eng-models/plant-availability.md
@@ -4,7 +4,7 @@ Switch `i_plant_availability` is used to control how the overall plant availabil
If `i_plant_availability = 0`, the input value of `f_t_plant_available` is used.
-If `i_plant_availability = 1`, a model by N. Taylor and D. Ward[^1] is used instead, in which `f_t_plant_available` is calculated taking into account the time taken to replace certain components of the fusion power core, and various unplanned unavailability fractions which may be set by the user, as summerised in Table 1.
+If `i_plant_availability = 1`, a model by N. Taylor and D. Ward[^1] is used instead, in which `f_t_plant_available` is calculated taking into account the time taken to replace certain components of the fusion power core, and various unplanned unavailability fractions which may be set by the user, as summarised in Table 1.
------------------
@@ -122,7 +122,7 @@ where $t_{\text{burn}}$ is the burn time and $t_{\text{cycle}}$ is the full cycl
--------------
-All availability models in PROCESS require the calculation of the centerpost lifetime, which is detailed here.
+All availability models in PROCESS require the calculation of the centrepost lifetime, which is detailed here.
!!! Note "Note"
The centrepost lifetime is calculated in full-power years (FPY).
diff --git a/documentation/eng-models/power-conversion-and-heat-dissipation-systems.md b/documentation/source/eng-models/power-conversion-and-heat-dissipation-systems.md
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diff --git a/documentation/eng-models/superconductors.md b/documentation/source/eng-models/superconductors.md
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rename to documentation/source/eng-models/superconductors.md
index cbf303c754..e1d4ae15c4 100644
--- a/documentation/eng-models/superconductors.md
+++ b/documentation/source/eng-models/superconductors.md
@@ -355,7 +355,7 @@ The fit values are:
- $u: 33450.0$
- $v: -176577.0$
-The output of the model only gives the critical current ($I_c$) and not the critical current density ($J_c$). Therefore the value is multiplied by the tape paramters to find the critical current density in the REBCO strand
+The output of the model only gives the critical current ($I_c$) and not the critical current density ($J_c$). Therefore the value is multiplied by the tape parameters to find the critical current density in the REBCO strand
$$
J_c = I_c \frac{w_{\text{tape}} \times \Delta x_{\text{REBCO}}}{w_{\text{tape}} \times \Delta x_{\text{tape}} }
@@ -509,4 +509,4 @@ Indico, 2017. https://indico.cern.ch/event/588810/contributions/2473740/ (access
[^10]: Y. Zhai, D. van der Laan, P. Connolly, and C. Kessel, “Conceptual design of HTS magnets for fusion nuclear science facility,” Fusion Engineering and Design, vol. 168, p. 112611, Jul. 2021, doi: https://doi.org/10.1016/j.fusengdes.2021.112611.
-
\ No newline at end of file
+
diff --git a/documentation/eng-models/tf-coil-resistive.md b/documentation/source/eng-models/tf-coil-resistive.md
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rename from documentation/eng-models/tf-coil-resistive.md
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diff --git a/documentation/eng-models/tf-coil-superconducting.md b/documentation/source/eng-models/tf-coil-superconducting.md
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rename from documentation/eng-models/tf-coil-superconducting.md
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index a5c771ba49..1c4f03cbd5 100644
--- a/documentation/eng-models/tf-coil-superconducting.md
+++ b/documentation/source/eng-models/tf-coil-superconducting.md
@@ -255,7 +255,7 @@ $$
P(t)dt = \sum_i c_{P,i}\rho_{i} V_{i} dT
$$
-Where $P(t)$ is the power deposited in the copper through Joule heating at time t, and the sum on the RHS is over the conductor consitutents (copper, helium, superconductor), where $V_{i}$ is the volume of said constituent. This can be rewritten as:
+Where $P(t)$ is the power deposited in the copper through Joule heating at time t, and the sum on the RHS is over the conductor constituents (copper, helium, superconductor), where $V_{i}$ is the volume of said constituent. This can be rewritten as:
$$
\int J(t)^2 dt = \int_{T_{0}}^{T_{max}} \sum_i f_{i}\dfrac{c_{P,i}\rho_{i}}{\nu_{Cu}} dT
@@ -263,7 +263,7 @@ $$
The LHS is solved analytically, assuming that the current is at the operational value $J_{op}$ for some quench detection time $t_{detection}$ and then decays exponentially with a time constant $\tau_{discharge}$. The RHS is solved numerically by integration of the temperature-dependent material properties over $dT$.
-The resistivity of copper, $\nu_{Cu}$, is an extremely important parameter in this model. The residual-resistance-ratio (RRR) of the copper can be specified, and magneto-resistive and irradiation-induced increases in resistivity are accounted for. The magnetic field at which the copper resisitivity is calculated is kept constant at $B_{TF,peak}$. This is conservative, and to simplify the implementation (keeping the separation of the $t$ and $T$ integrations).
+The resistivity of copper, $\nu_{Cu}$, is an extremely important parameter in this model. The residual-resistance-ratio (RRR) of the copper can be specified, and magneto-resistive and irradiation-induced increases in resistivity are accounted for. The magnetic field at which the copper resistivity is calculated is kept constant at $B_{TF,peak}$. This is conservative, and to simplify the implementation (keeping the separation of the $t$ and $T$ integrations).
Formally this gives:
diff --git a/documentation/eng-models/tf-coil.md b/documentation/source/eng-models/tf-coil.md
similarity index 98%
rename from documentation/eng-models/tf-coil.md
rename to documentation/source/eng-models/tf-coil.md
index e0710eb2dc..ca33896dae 100644
--- a/documentation/eng-models/tf-coil.md
+++ b/documentation/source/eng-models/tf-coil.md
@@ -28,7 +28,7 @@ Resistive coils can benefit in having a larger outboard conductor area than
the inboard one, to reduce resistive heating without increasing the plasma
major radius or increasing its aspect ratio. For this reason, thicker outboard
can be set using the f_dr_tf_outboard_inboard user input defined as the ratio between
-ouboard and inboard TF coil legs. The possibility of having different coil
+outboard and inboard TF coil legs. The possibility of having different coil
thicknesses is only available for resistive coils and f_dr_tf_outboard_inboard
would have no effect if superconducting coils are selected (`i_tf_sup = 1`)
@@ -63,7 +63,7 @@ Two different plasma side casing shapes can be selected using the `i_tf_case_geo
## Topology of TF coils and Central Solenoid
The engineering models are based on a topology like that used in ITER: the central solenoid and the TF coils are not linked: the central solenoid can be inserted or removed without cutting the TF coils.
-However, an option does exist wich permits the alternative topology, in which the inboard legs of the TF coils pass through the middle of the central solenoid. This layout is used in MAST, where the copper TF coils can be dismantled to allow the central solenoid to be inserted or removed.
+However, an option does exist which permits the alternative topology, in which the inboard legs of the TF coils pass through the middle of the central solenoid. This layout is used in MAST, where the copper TF coils can be dismantled to allow the central solenoid to be inserted or removed.
The topology is set as follows:
- `i_tf_inside_cs = 0` (default) ITER-like topology: the central solenoid and the TF coils are not linked.
@@ -452,7 +452,7 @@ $$
this configuration in theory. The radial and toroidal stress calculations
are made assuming no vertical tension. A constant vertical stress is then
estimated *a posteriori* by dividing the inboard vertical tension by the
- support sutructure area to obtain the 3 normal stress necessary to for the
+ support structure area to obtain the 3 normal stress necessary to for the
*TRESCA* yield stress estimate as described in [1]. Although using
un-adapted model hypothesis this model is still used by default as it
has been validated on FEA analysis and benchmarked with the *MADMAX* *CEA*
@@ -472,7 +472,7 @@ $$
complete this model is not yet used by default as more FEA validations
are needed. `i_tf_stress_model = 0` is the older model, which is O(n^3)
in the number of layers and fails if there is a solid dr_bore.
- `i_tf_stress_model = 2` is the newr model, which is O(n) and accepts a solid
+ `i_tf_stress_model = 2` is the newer model, which is O(n) and accepts a solid
dr_bore, but is otherwise identical to the older model `i_tf_stress_model = 0`.
@@ -729,22 +729,22 @@ selected with the `i_tf_bucking` integer switch.
-
**Bucked and wedged (`i_tf_bucking == 2,3`):** the TF coil uses the CS coil
as centering forces structural support. This design allows to substantially
- reduce the thickness of the TF coil individual suport structure if a large
+ reduce the thickness of the TF coil individual support structure if a large
CS coil is present. As the CS coil current generates a beneficial CS radial
outward forces, the most critical instant for structural support is the
moment when no current flows in the CS coil. The CS coil is therefore
- represented as an additionnal stress layer with `e.m.` no body forces.
- The layer strctural properties are defined using using similar smearing/
+ represented as an additional stress layer with `e.m.` no body forces.
+ The layer structural properties are defined using using similar smearing/
unsmeating procedure as the TF coil, as detailed in issue [4]. The maximum
between the CS stress from the this model and the on calculated in the
`pfcoil` module is taken as the CS coil stress limit (constraint 72). A fast
version, neglecting the interface layer properties is implemented
(`i_tf_bucking == 2`). And a more complete one, taking explicitly the Kapton
- interface into account in the stress calcualtions (`i_tf_bucking == 3`) is
+ interface into account in the stress calculations (`i_tf_bucking == 3`) is
also implemented. Before using this design option, the user must know two
major potential issues not captured by *PROCESS*. The first is the fatigue
introduced by the CS on the TF coil. The second is the nature of the CS-TF
- coil interface that has to allow vertical slinding at cryogenic temperatures,
+ coil interface that has to allow vertical sliding at cryogenic temperatures,
as the CS vertical size reduces when energized and the TF coil vertical
tension makes TF grow taller with current flowing in it. The CS and the TF
coil are therefore strain insulated, therefore all the vertical tension is
@@ -824,7 +824,7 @@ and the maximum field (on coil toroidal direction) respectively, measured at
the mid-plane plasma outer limit (separatrix).
To prevent intolerable fast particles losses and plasma instabilities,
-$\delta$ must be limited to a few percent, approximatively \( \delta \in
+$\delta$ must be limited to a few percent, approximately \( \delta \in
[0.5-1]\) . If intolerable, the plasma ripple can be reduced with many
different techniques, for example the TF coil shape, stabilisation coils can
be added, more coils can be used or the coil outboard radius can be increased.
@@ -880,7 +880,7 @@ $$
$$
-with \(x\) the lateral thickness of the winding pack normalized to the coil
+with \(x\) the lateral thickness of the winding pack normalised to the coil
dimensions defined as:
diff --git a/documentation/eng-models/vacuum-vessel.md b/documentation/source/eng-models/vacuum-vessel.md
similarity index 100%
rename from documentation/eng-models/vacuum-vessel.md
rename to documentation/source/eng-models/vacuum-vessel.md
diff --git a/documentation/source/examples b/documentation/source/examples
new file mode 120000
index 0000000000..d15735c1df
--- /dev/null
+++ b/documentation/source/examples
@@ -0,0 +1 @@
+../../examples
\ No newline at end of file
diff --git a/documentation/fusion-devices/inertial.md b/documentation/source/fusion-devices/inertial.md
similarity index 100%
rename from documentation/fusion-devices/inertial.md
rename to documentation/source/fusion-devices/inertial.md
diff --git a/documentation/fusion-devices/spherical-tokamak.md b/documentation/source/fusion-devices/spherical-tokamak.md
similarity index 100%
rename from documentation/fusion-devices/spherical-tokamak.md
rename to documentation/source/fusion-devices/spherical-tokamak.md
diff --git a/documentation/fusion-devices/stellarator.md b/documentation/source/fusion-devices/stellarator.md
similarity index 99%
rename from documentation/fusion-devices/stellarator.md
rename to documentation/source/fusion-devices/stellarator.md
index aad1b1c691..4687498df3 100644
--- a/documentation/fusion-devices/stellarator.md
+++ b/documentation/source/fusion-devices/stellarator.md
@@ -34,7 +34,7 @@ The user can switch between these models by using the switch variable `istell`:
- `istell=5`: A W7-X variation with 30 coils
- `istell-6`: Use the `stella_conf.json` file.
-The stellarator version of PROCESS assumes the coil-set itself to be **fixed in shape** and can only scale the *overall* size of the machine in major radius `rmajor`. There is no capability in PROCESS to seperately scale the minor coil radius -- in other words: the coil aspect ratio is fixed. Also the number of coils is considered fixed and is given by the configuration.
+The stellarator version of PROCESS assumes the coil-set itself to be **fixed in shape** and can only scale the *overall* size of the machine in major radius `rmajor`. There is no capability in PROCESS to separately scale the minor coil radius -- in other words: the coil aspect ratio is fixed. Also the number of coils is considered fixed and is given by the configuration.
## Input File Specifications
@@ -88,7 +88,7 @@ The model call is in the following order
1. Stellarator New Configuration setup (`stnewconfig`)
2. Stellarator Geometry (`stgeom`)
- 3. Stellarator Physics Loop Routine (containing steps requiring to evalute the physics model at different operation points) (`stopt`)
+ 3. Stellarator Physics Loop Routine (containing steps requiring to evaluate the physics model at different operation points) (`stopt`)
4. Stellarator Physics (`stphys`)
5. Stellarator radial and toroidal build (`stbild`)
6. Stellarator Structure Mass (`ststrc`)
@@ -156,7 +156,7 @@ Here $\bar{\iota}$ is the rotational transform, which is equivalent to the recip
As no 1D solver options are available for stellarators yet, PROCESS prints several neoclassics parameters as obtained from the 1/$\nu$ regime.
The two most important parameters are `q_PROCESS` and `total_q_neo_e`.
-`q_PROCESS` is the heat flux that PROCESS obtaines from the 0D confinement time scalings.
+`q_PROCESS` is the heat flux that PROCESS obtains from the 0D confinement time scalings.
`total_q_neo_e` is the estimated total neoclassical flux as obtained from the 1/$\nu$ electron transport regime, multiplied by a factor of 4 (2 for the ion contribution and another factor of 2 for the radial electrical field influence).
The user should check if `q_PROCESS>total_q_neo_e`. If not, the design point is likely not feasible.
diff --git a/documentation/images/2D_contour_plot_example.png b/documentation/source/images/2D_contour_plot_example.png
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rename from documentation/img/Once_Through-Cooling_Pond.png
rename to documentation/source/img/Once_Through-Cooling_Pond.png
diff --git a/documentation/img/Once_Through.png b/documentation/source/img/Once_Through.png
similarity index 100%
rename from documentation/img/Once_Through.png
rename to documentation/source/img/Once_Through.png
diff --git a/documentation/img/Wet_Cooling-Mechanical_Draft.png b/documentation/source/img/Wet_Cooling-Mechanical_Draft.png
similarity index 100%
rename from documentation/img/Wet_Cooling-Mechanical_Draft.png
rename to documentation/source/img/Wet_Cooling-Mechanical_Draft.png
diff --git a/documentation/img/Wet_Cooling-Natural_Draft.png b/documentation/source/img/Wet_Cooling-Natural_Draft.png
similarity index 100%
rename from documentation/img/Wet_Cooling-Natural_Draft.png
rename to documentation/source/img/Wet_Cooling-Natural_Draft.png
diff --git a/documentation/index.md b/documentation/source/index.md
similarity index 100%
rename from documentation/index.md
rename to documentation/source/index.md
diff --git a/documentation/installation/installation.md b/documentation/source/installation/installation.md
similarity index 100%
rename from documentation/installation/installation.md
rename to documentation/source/installation/installation.md
diff --git a/documentation/installation/vs-code.md b/documentation/source/installation/vs-code.md
similarity index 100%
rename from documentation/installation/vs-code.md
rename to documentation/source/installation/vs-code.md
diff --git a/documentation/io/input-guide.md b/documentation/source/io/input-guide.md
similarity index 87%
rename from documentation/io/input-guide.md
rename to documentation/source/io/input-guide.md
index 749c844f50..0fcff23c1a 100644
--- a/documentation/io/input-guide.md
+++ b/documentation/source/io/input-guide.md
@@ -8,6 +8,9 @@ If the code encounters a problem reading the input file, it will stop immediatel
with an error message. The last line of the output file `OUT.DAT` may give an
indication of where in the input file the problem lies.
+!!! Info "Variable Descriptions"
+ A full list of inputs variables is given in the PROCESS data structure API documentation [here](../../source/reference/process/data_structure/blanket_library).
+
## File Naming Convention
The default PROCESS input file name is `IN.DAT`. The user can provide a named
@@ -47,7 +50,7 @@ icc = 2 * Global power balance (consistency equation)
!!! Info "Constraints"
A full list of constraints is given on the variable description page in the row labelled
- `lablcc` [here](vardes.md#numerics).
+ `lablcc` [here](../../source/reference/process/data_structure/numerics/#process.data_structure.numerics.lablcc).
See [solver](../solver/solver-guide.md) page for more info
## Iteration Variables
@@ -80,7 +83,7 @@ the default, if no value is specified), will be used as the starting value.
!!! Note "Iteration Variables"
A full list of iteration variables is given on the variable description page in the row labelled
- `lablxc` [here](vardes.md#numerics).
+ `lablxc` [here](../../source/reference/process/data_structure/numerics/#process.data_structure.numerics.lablxc).
(See [solver](../solver/solver-guide.md) page for more info)
## Bounds
@@ -131,7 +134,7 @@ epsvmc = 1.0e-8 * Error tolerance for vmcon
!!! Info "Figure of Merit"
A full list of figures of merit is given on the variable description page in the row labelled
- `lablmm` [here](vardes.md#numerics).
+ `lablmm` [here](../../source/reference/process/data_structure/numerics/#process.data_structure.numerics.lablmm).
## Input Variables
@@ -149,8 +152,7 @@ one can add a `*` to the beginning of the line, as below:
```
!!! Info "Variable Descriptions"
- A full list of inputs variables is given in the PROCESS `html` documentation
- file `vardes.html` and on the variable description page [here](vardes.md).
+ A full list of inputs variables is given in the PROCESS data structure API documentation [here](../../source/reference/process/data_structure/blanket_library).
## Scan
@@ -166,7 +168,7 @@ isweep = 4
sweep = 2.8, 2.9, 3.0, 3.1
```
-where `nsweep` is the scan variable chosen (see [variable descriptions](vardes.md)),
+where `nsweep` is the scan variable chosen (see [variable descriptions](../../source/reference/process/scan/#process.scan.ScanVariables)),
`isweep` is the number of scan points and `sweep` is the array of scan values. In this example,
PROCESS runs for each of the four values given of the plasma aspect ratio variable `aspect`.
@@ -198,7 +200,7 @@ Scan variables should not be confused with iteration variables.
!!! Info "Scanning"
For obvious reasons, the active scanning variable or variables must not also be active
iteration variables.
- A full list of scan variables is [here](vardes.md#scan_module).
+ A full list of scan variables is [here](../../source/reference/process/scan/#process.scan.ScanVariables).
## Examples
diff --git a/documentation/io/output-guide.md b/documentation/source/io/output-guide.md
similarity index 100%
rename from documentation/io/output-guide.md
rename to documentation/source/io/output-guide.md
diff --git a/documentation/io/python-lib-guide.md b/documentation/source/io/python-lib-guide.md
similarity index 100%
rename from documentation/io/python-lib-guide.md
rename to documentation/source/io/python-lib-guide.md
diff --git a/documentation/io/utilities.md b/documentation/source/io/utilities.md
similarity index 98%
rename from documentation/io/utilities.md
rename to documentation/source/io/utilities.md
index 091f592a6a..8a1ec5020d 100644
--- a/documentation/io/utilities.md
+++ b/documentation/source/io/utilities.md
@@ -133,7 +133,7 @@ for the reference year of the inflation used.
| Power flows |
| :------------------------------------------------------------------------------------------------------------------------------------------------- |
| Nominal neutron wall load[^2] |
-| Normalised radius of the 'core' region $\rho_{core}$ used in the radiation correction of the onfinement scaling[^3] [^4] |
+| Normalised radius of the 'core' region $\rho_{core}$ used in the radiation correction of the confinement scaling[^3] [^4] |
| The electron density at the pedestal top, $n_{\text{e,ped}}$ |
| The normalised radius $\rho=r/a$ at the pedestal top |
| The helium fraction relative to the electron density |
@@ -153,7 +153,7 @@ for the reference year of the inflation used.
| Physics |
| :-------------------------------------------------------------------------------------------------------------------------------------------- |
| Plasma current, $I_{\text{P}}$ |
-| Vaccuum magnetic field at in the plasma centre, $B_{\text{T}}(R_0)$ |
+| Vacuum magnetic field at in the plasma centre, $B_{\text{T}}(R_0)$ |
| Safety factor at the 95% flux surface, $q_{95}$ |
| Definitions of $\beta$ as given in [^1] |
| Volume averaged electron temperature $\langle T_e\rangle$ and density $\langle n_e\rangle$ |
@@ -183,7 +183,7 @@ for the reference year of the inflation used.
| Inboard TF nose case thickness |
| Inboard TF minimum distance between side case and WP |
| Radial width of inboard TF leg |
-| Thickness of insualtion surrounding WP |
+| Thickness of insulation surrounding WP |
| Number of turns in WP |
| WP current density |
| Radial width of WP |
@@ -241,7 +241,7 @@ plots in the `SIG_TF_plots/` folder, created if not existing.
### Discussion of the stress modelling assumptions
-In case of a resisitive coil, the stress is calculated from a generalized plane strain model, hence providing vertical
+In case of a resistive coil, the stress is calculated from a generalized plane strain model, hence providing vertical
stress radial distribution, alongside the radial and the toroidal ones. This is not the case for superconducting magnets
as a plane stress modelling is used for now. The reason is that a transverse orthotropic formulation of the generalized
plane strain is needed to correctly take the difference of the casing in the vertical direction properly. This will be
@@ -331,7 +331,7 @@ python process/io/plot_scans.py [-h] [-f path/to/MFILE(s)] [-yv output vars] [-y
| `-sf, --save_format` | Output format (default='pdf') |
| `-as, --axis_font_size` | Axis label font size selection (default=18) |
| `-ln, --label_name` | Label names for plot legend. If multiple input files used then list the same number of label names eg: -nl 'leg1 leg2', (default = MFile file name) |
-| `-2DC, --two_dimensional_contour` | Option to plot 2D scans as a coloured contour plot instead of a line plot. Note: Non convergent points will show up with a value of zero Note: The scan paramters must both be in increasing orderl |
+| `-2DC, --two_dimensional_contour` | Option to plot 2D scans as a coloured contour plot instead of a line plot. Note: Non convergent points will show up with a value of zero Note: The scan parameters must both be in increasing order |
| `-stc, --stack_plots` | Option to plot multiple 1D plots in a column of subplots. Variables will be plotted in order of input |
diff --git a/documentation/physics-models/current_vs_time.png b/documentation/source/physics-models/current_vs_time.png
similarity index 100%
rename from documentation/physics-models/current_vs_time.png
rename to documentation/source/physics-models/current_vs_time.png
diff --git a/documentation/physics-models/detailed_physics.md b/documentation/source/physics-models/detailed_physics.md
similarity index 100%
rename from documentation/physics-models/detailed_physics.md
rename to documentation/source/physics-models/detailed_physics.md
diff --git a/documentation/physics-models/fusion_reactions/beam_reactions.md b/documentation/source/physics-models/fusion_reactions/beam_reactions.md
similarity index 100%
rename from documentation/physics-models/fusion_reactions/beam_reactions.md
rename to documentation/source/physics-models/fusion_reactions/beam_reactions.md
diff --git a/documentation/physics-models/fusion_reactions/deuterium_branching_plot.png b/documentation/source/physics-models/fusion_reactions/deuterium_branching_plot.png
similarity index 100%
rename from documentation/physics-models/fusion_reactions/deuterium_branching_plot.png
rename to documentation/source/physics-models/fusion_reactions/deuterium_branching_plot.png
diff --git a/documentation/physics-models/fusion_reactions/plasma_bosch_hale.md b/documentation/source/physics-models/fusion_reactions/plasma_bosch_hale.md
similarity index 100%
rename from documentation/physics-models/fusion_reactions/plasma_bosch_hale.md
rename to documentation/source/physics-models/fusion_reactions/plasma_bosch_hale.md
diff --git a/documentation/physics-models/fusion_reactions/plasma_reactions.md b/documentation/source/physics-models/fusion_reactions/plasma_reactions.md
similarity index 100%
rename from documentation/physics-models/fusion_reactions/plasma_reactions.md
rename to documentation/source/physics-models/fusion_reactions/plasma_reactions.md
diff --git a/documentation/physics-models/plasma_beta/plasma_alpha_beta_contribution.md b/documentation/source/physics-models/plasma_beta/plasma_alpha_beta_contribution.md
similarity index 100%
rename from documentation/physics-models/plasma_beta/plasma_alpha_beta_contribution.md
rename to documentation/source/physics-models/plasma_beta/plasma_alpha_beta_contribution.md
diff --git a/documentation/physics-models/plasma_beta/plasma_beta.md b/documentation/source/physics-models/plasma_beta/plasma_beta.md
similarity index 100%
rename from documentation/physics-models/plasma_beta/plasma_beta.md
rename to documentation/source/physics-models/plasma_beta/plasma_beta.md
diff --git a/documentation/physics-models/plasma_composition.md b/documentation/source/physics-models/plasma_composition.md
similarity index 100%
rename from documentation/physics-models/plasma_composition.md
rename to documentation/source/physics-models/plasma_composition.md
diff --git a/documentation/physics-models/plasma_confinement.md b/documentation/source/physics-models/plasma_confinement.md
similarity index 100%
rename from documentation/physics-models/plasma_confinement.md
rename to documentation/source/physics-models/plasma_confinement.md
diff --git a/documentation/physics-models/plasma_current/bootstrap_current.md b/documentation/source/physics-models/plasma_current/bootstrap_current.md
similarity index 99%
rename from documentation/physics-models/plasma_current/bootstrap_current.md
rename to documentation/source/physics-models/plasma_current/bootstrap_current.md
index 8704199b1b..2bad25d1f3 100644
--- a/documentation/physics-models/plasma_current/bootstrap_current.md
+++ b/documentation/source/physics-models/plasma_current/bootstrap_current.md
@@ -272,7 +272,7 @@ $$
1 \times 10^6 \times \frac{-B_{0}\left[\rho\right]_{-1}\left[\frac{1}{q}\right]_{-1}}{0.2\pi R_0}\right)
$$
-In this case square brackets denote array variables equal in length to $\rho_{\text{max}}$ representing the normalized radius elements across the profile. The $-1$ subscript denotes the previous array element in the summation.
+In this case square brackets denote array variables equal in length to $\rho_{\text{max}}$ representing the normalised radius elements across the profile. The $-1$ subscript denotes the previous array element in the summation.
It is not known fully if the $\left(\sigma_{\text {neo }}\left\langle E_{\|} B\right\rangle-I(\psi) p(\psi)\right)$ term is properly implemented into the `PROCESS` version. The $R_{pe}$ value is assumingly taken to be 0.5 as it is stated to approximately to be in Sauter et.al[^4].
diff --git a/documentation/physics-models/plasma_current/diamagnetic_current.md b/documentation/source/physics-models/plasma_current/diamagnetic_current.md
similarity index 100%
rename from documentation/physics-models/plasma_current/diamagnetic_current.md
rename to documentation/source/physics-models/plasma_current/diamagnetic_current.md
diff --git a/documentation/physics-models/plasma_current/inductive_plasma_current.md b/documentation/source/physics-models/plasma_current/inductive_plasma_current.md
similarity index 99%
rename from documentation/physics-models/plasma_current/inductive_plasma_current.md
rename to documentation/source/physics-models/plasma_current/inductive_plasma_current.md
index b32a95eb9d..80baa9bec9 100644
--- a/documentation/physics-models/plasma_current/inductive_plasma_current.md
+++ b/documentation/source/physics-models/plasma_current/inductive_plasma_current.md
@@ -69,7 +69,7 @@ $$
\overbrace{\Phi_{\text{ind,internal,ramp}}}^{\texttt{vs_plasma_internal}} = I_{\text{p}} \times \underbrace{\left[\frac{\mu_0 R l_i}{2}\right]}_{\texttt{ind_plasma_internal}}
$$
-Here $l_i$ is known as the normalized internal inductance defined for circular cross section plasmas with minor radius $a$:
+Here $l_i$ is known as the normalised internal inductance defined for circular cross section plasmas with minor radius $a$:
$$
l_i = \frac{\langle B_{\text{p}}^2 \rangle }{B_{\text{p}}^2(a)}
diff --git "a/documentation/physics-models/plasma_current/pfirsch_schl\303\274ter_current_drive.md" "b/documentation/source/physics-models/plasma_current/pfirsch_schl\303\274ter_current_drive.md"
similarity index 100%
rename from "documentation/physics-models/plasma_current/pfirsch_schl\303\274ter_current_drive.md"
rename to "documentation/source/physics-models/plasma_current/pfirsch_schl\303\274ter_current_drive.md"
diff --git a/documentation/physics-models/plasma_current/plasma_current.md b/documentation/source/physics-models/plasma_current/plasma_current.md
similarity index 100%
rename from documentation/physics-models/plasma_current/plasma_current.md
rename to documentation/source/physics-models/plasma_current/plasma_current.md
diff --git a/documentation/physics-models/plasma_current/plasma_inductance.md b/documentation/source/physics-models/plasma_current/plasma_inductance.md
similarity index 100%
rename from documentation/physics-models/plasma_current/plasma_inductance.md
rename to documentation/source/physics-models/plasma_current/plasma_inductance.md
diff --git a/documentation/physics-models/plasma_current/plasma_resistive_heating.md b/documentation/source/physics-models/plasma_current/plasma_resistive_heating.md
similarity index 100%
rename from documentation/physics-models/plasma_current/plasma_resistive_heating.md
rename to documentation/source/physics-models/plasma_current/plasma_resistive_heating.md
diff --git a/documentation/physics-models/plasma_density.md b/documentation/source/physics-models/plasma_density.md
similarity index 100%
rename from documentation/physics-models/plasma_density.md
rename to documentation/source/physics-models/plasma_density.md
diff --git a/documentation/physics-models/plasma_geometry.md b/documentation/source/physics-models/plasma_geometry.md
similarity index 100%
rename from documentation/physics-models/plasma_geometry.md
rename to documentation/source/physics-models/plasma_geometry.md
diff --git a/documentation/physics-models/plasma_h_mode.md b/documentation/source/physics-models/plasma_h_mode.md
similarity index 100%
rename from documentation/physics-models/plasma_h_mode.md
rename to documentation/source/physics-models/plasma_h_mode.md
diff --git a/documentation/physics-models/plasma_overview.md b/documentation/source/physics-models/plasma_overview.md
similarity index 80%
rename from documentation/physics-models/plasma_overview.md
rename to documentation/source/physics-models/plasma_overview.md
index 44f11bc531..9cbf90645b 100644
--- a/documentation/physics-models/plasma_overview.md
+++ b/documentation/source/physics-models/plasma_overview.md
@@ -2,7 +2,7 @@
!!! warning " Documentation re-write"
- The plasma documenation is slowly going through an update to ensure each section is properly decribed and up to date. Each section of the plasma now has its own dedicated page
+ The plasma documentation is slowly going through an update to ensure each section is properly described and up to date. Each section of the plasma now has its own dedicated page
## Introduction
diff --git a/documentation/physics-models/plasma_power_balance.md b/documentation/source/physics-models/plasma_power_balance.md
similarity index 100%
rename from documentation/physics-models/plasma_power_balance.md
rename to documentation/source/physics-models/plasma_power_balance.md
diff --git a/documentation/physics-models/plasma_radiation.md b/documentation/source/physics-models/plasma_radiation.md
similarity index 99%
rename from documentation/physics-models/plasma_radiation.md
rename to documentation/source/physics-models/plasma_radiation.md
index 8606e658a0..a4ec7603a7 100644
--- a/documentation/physics-models/plasma_radiation.md
+++ b/documentation/source/physics-models/plasma_radiation.md
@@ -66,7 +66,7 @@ For the regime above $40 \ \text{keV}$ whichc an be seen by the dashed lines in
The radiation emission is numerically integrated over the plasma profile,
using the corresponding temperature and density distributions. Emission is only considered from within the separatrix,
as the PROCESS model does not account for the scrape-off layer.
-The plasma inside the separatrix is divided into two regions: the “core” and the “edge,” separated by a normalized minor radius defined by the user.
+The plasma inside the separatrix is divided into two regions: the “core” and the “edge,” separated by a normalised minor radius defined by the user.
Radiation is calculated separately for the core and edge regions, except for synchrotron radiation, which is assumed to originate solely from the core.
--------------
@@ -200,7 +200,7 @@ A comparison of the different reflection functions can be seen in the graph belo