diff --git a/docs/Contribute.md b/docs/Contribute.md index 3d57b96..594cc4d 100644 --- a/docs/Contribute.md +++ b/docs/Contribute.md @@ -41,7 +41,7 @@ Our tutorials are written in [Markdown](https://www.markdownguide.org/cheat-shee - **Respect the existing documentation structure.** Before you write a tutorial, figure out if an equivalent is already present, and amend that if necessary. - *My first SOLPS-ITER simulation*: A beginner's first contact with SOLPS-ITER, step-by-step instructions toward creating one's first SOLPS-ITER simulation with the narrow grids version. Keep it simple. Document frequently encountered problems, but don't explain anything in depth. If needed, describe the issue at length elsewhere (e.g. in [Common pitfalls](supplementary/Common_pitfalls.md)) and link to it. - *Feature blog*: Largely independent ways to make a SOLPS simulation more complicated. Explain why one would want to adopt a particular feature, what are the benefits and costs, and how to do it. You can go into detail, but don't paraphrase or copy-paste existing documentation. Link to it instead. - - *Supplementary material*: Everything that didn't fit in the first two categories. + - *Supplementary material*: Everything that didn't fit in the first two categories. - **Do not duplicate.** If something is explained elsewhere (SOLPS manual, ITER SharePoint...) and you find yourself paraphrasing it or, God forbid, copy-pasting it, link to it instead. @@ -69,7 +69,7 @@ First, clean your local copy of SOLPS Tutorials. cd SOLPS-Tutorials git fetch git status - + If you see you're up-to-date with `master`, you're good to go. If you are on `master` but you're missing the last updates, download them to your local copy. git pull @@ -80,16 +80,16 @@ Usually I find myself a different, long-forgotten branch, from the last time I w git clone git@github.com:iterorganization/SOLPS-Tutorials.git Then proceed according to the instructions below. At the point where you're supposed to start writing your contributions, copy over the files from your old folder `SOLPS-Tutorials_definitely_not`. More on that below. - + Once you are on the latest update of the `master` branch, your work table is clean. You can start on your latest contribution. - + 1. Visit the [list of `SOLPS-Tutorials` branches](https://github.com/iterorganization/SOLPS-Tutorials/branches)open_in_new on its GitHub page. On the upper right, click `New branch`. Select `master` as the source. Name the branch using the [common conventions](https://medium.com/@abhay.pixolo/naming-conventions-for-git-branches-a-cheatsheet-8549feca2534)open_in_new, using branch prefixes such as `feature/`, `fix/` or `refactor/`. 2. Switch to the new branch on your local machine. git fetch # this downloads the information that there is a new remote branch git checkout -b feature/my_new_branch origin/feature/my_new_branch - + The `-b` will create your own local branch which tracks the remote branch. It prevents the detached HEAD state. 3. If you have any accumulated past changes, integrate them. Simply copy all the contents of `SOLPS-Tutorials_definitely_not` and paste them into your new shiny `SOLPS-Tutorials`. **Immediately** after that, resolve conflicts/deletions. The `Source Control` tab in our editor of choice, [Visual Studio Code](#recommended-editors), works well. Compare your old files with the newest `master`, get familiar with what has been done while you were sleeping and modify your past contributions accordingly. Use the `Revert` button/option to undo your "deletions". You don't want to overwrite any work others have done in the meantime. I know you're impatient to get started on the actual work, but if you postpone dealing with the conflicts, they will become a headache. You'll invest effort into rewriting documentation that's out-of-date. At the end of it, when you're making your commits and merging into `master`, you will have to deal with the conflicts anyway. And it will be harder, because you've *just* polished your contribution, you want to send it out there already, and now not only you are bogged down by Git conflicts, but you also have to rewrite your contribution to accommodate the work of others. @@ -110,7 +110,7 @@ Once you are on the latest update of the `master` branch, your work table is cle 6. Once you have a series of commits, ideally acknowledging all the changes you've made to the tutorials, upload them to the central GitLab repository. git push - + (You can also do this in Visual Studio Code `Source Control` tab.) 7. On the [`SOLPS-Tutorials` GitHub page](https://github.com/iterorganization/SOLPS-Tutorials/pulls)open_in_new, create a new pull request which merges your new branch back into `master`. Add Katka as a reviewer so she can check the changes and give you a deserved pat on the back. Expect a response within 3 days. @@ -119,7 +119,7 @@ Once you are on the latest update of the `master` branch, your work table is cle git checkout master git pull - + Thank you for contributing to SOLPS Tutorials! @@ -350,13 +350,11 @@ Katka's PhD thesis ``` -## Render SOLPS Tutorials locally with MkDocs - -Quick edits of SOLPS Tutorials are best done in a [Markdown editor](#recommended-editors), which will render the files in real time. However, most of the fancy [extensions](#markdown-extensions) will not be rendered in that way. There are two options to view the final result before it goes live with a Git pull request into the `master` branch: +## Preview your changes to SOLPS Tutorials -> **TODO** construction: Update the pipeline artifact information. +Quick edits of SOLPS Tutorials are best done in a [Markdown editor](#recommended-editors), which will render the files in real time. However, most of the fancy [extensions](#markdown-extensions) will not be rendered in that way. There are two options to view the final result before it goes live after merging a pull request into the `master` branch: -- A complete build of pages is generated after each push as a downloadable artifact in the automatic [Pipelines](https://repo.tok.ipp.cas.cz/solps/solps-doc/-/pipelines)open_in_new (see download button on the right). +- A complete webpage preview is generated once you open a [pull request](https://github.com/iterorganization/SOLPS-Tutorials/pulls)open_in_new to `master`. Simply wait a couple of minutes for the ReadTheDocs bot to post the link in the pull request's thread. - Build the pages locally: diff --git a/docs/feature_blog/Drifts.md b/docs/feature_blog/Drifts.md index f7c85d0..ebed738 100644 --- a/docs/feature_blog/Drifts.md +++ b/docs/feature_blog/Drifts.md @@ -117,7 +117,7 @@ It's hard to say what are sensible values (1.5, 1.1, 1.0001) for any of the ramp ## Modify boundary conditions in `b2.boundary.parameters` -This is the most complicated step, but at the same time, it might not be important to make the simulation stable (Honza's conjecture). It is, at any rate, important for the simulation to be physically correct. Most of the information here is based on the documentation of the boundary conditions and on the official example `ITER_2588_Donly_standalone_drifts` from the `solps-iter/examples` directory. Refer to that example for more details. See the [B2.5 switches](/solps-doc/extras/b2input) for a documentation on the boundary conditions. The main idea is: +This is the most complicated step, but at the same time, it might not be important to make the simulation stable (Honza's conjecture). It is, at any rate, important for the simulation to be physically correct. Most of the information here is based on the documentation of the boundary conditions and on the official example `ITER_2588_Donly_standalone_drifts` from the `solps-iter/examples` directory. Refer to that example for more details. See the [B2.5 switches](/extras/b2input) for a documentation on the boundary conditions. The main idea is: - There are special versions of the sheath boundary conditions that are modified to properly account for drifts. - It is advisable to use leakage conditions instead of decay lengths for the radial boundaries. But I'm not sure if that is important for drifts or just a good idea in general. diff --git a/docs/feature_blog/Gas_puffing_and_pumping.md b/docs/feature_blog/Gas_puffing_and_pumping.md index 9f4c634..25b8795 100644 --- a/docs/feature_blog/Gas_puffing_and_pumping.md +++ b/docs/feature_blog/Gas_puffing_and_pumping.md @@ -150,7 +150,7 @@ Deuterium is just the most common main ion species in SOLPS-ITER simulations. If one has [implemented a pump](#gas-pumping), the lost particles must be compensated for. Under default boundary conditions, where the plasma density is controlled by the D1+ density at the core boundary $n_{i,core}$ (`BCCON = 1`), this refuelling is done mainly through the particle flux from the core. The flux is automatically adjusted to such a value that matches the density required in `CONPAR`. To get a proper particle balance, however, one needs to control the plasma density is through the *gas puff throughput* $\Gamma_{\text{puff}}$. /// tip | When gas puff is off in experiment -In short, low-density tokamak discharges, experimental density feedback system can find that it does not need to puff gas into the plasma to maintain the desired plasma density. Recycling is sustained by the pre-filled particles and pumping only removes them slowly (due to low neutral pressure). In the corresponding interpretative SOLPS-ITER simulation, gas puff throughput should still be non-zero. Even though your experimental plasma was not entirely steady-state, your simulation is. If you turn the gas puff off and introduce no additional fuelling, the particle content in your simulation will go down over time and you won't achieve convergence. +In short, low-density tokamak discharges, experimental density feedback system can find that it does not need to puff gas into the plasma to maintain the desired plasma density. Recycling is sustained by the pre-filled particles and pumping only removes them slowly (due to low neutral pressure). In the corresponding interpretative SOLPS-ITER simulation, gas puff throughput should still be non-zero. Even though your experimental plasma was not entirely steady-state, your simulation is. If you turn the gas puff off and introduce no additional fuelling, the particle content in your simulation will go down over time and you won't achieve convergence. /// @@ -273,7 +273,7 @@ Examples of gas puff feedback schemes among the SOLPS examples include: - `ITER_2588_D+He+N`: feedback on the deuterium gas puff intensity to preserve "the total particle content for that species" (not clear whether deuterium ions or neutrals) summed over a given rectangle of B2.5 cells - `ITER_2308_Honly_20MW`: feedback on the core boundary hydrogen particle (not clear whether neutrals or ions) flux to preserve the neutral hydrogen particle flux through the core boundary -All available feedback schemes are documented primarily in the description of switches specified in the `b2.feedback_control.parameters` file (refer to the [B2.5 switch database](/solps-doc/extras/b2input)open_in_new). +All available feedback schemes are documented primarily in the description of switches specified in the `b2.feedback_control.parameters` file (refer to the [B2.5 switch database](/extras/b2input)open_in_new). /// warning | The NEW and OLD feedback scheme switches Historically, there are two ways how to set up feedback schemes. You might run into a number of switches in `b2mn.dat`, which are documented as "feedback switches", e.g. `b2stbc_isfeedback` - those are the old-style switches and they are redundant in SOLPS-ITER 3.0.8+. The new-style configuration of feedback is done almost entirely in the `b2.feedback_control.parameters` file. @@ -348,7 +348,7 @@ At low plasma densities, enabling density control using gas puff feedback can le This section discusses how such oscillations come to be and how to control them. -**Feedback formula example**: Using `NA_FEEDBACK_OPTION = 1` in `b2.feedback_control.parameters` (see the [switch description](/solps-doc/extras/b2input/b2.parameters.html#b2.feedback_control.parameters)) translates into the following formula: +**Feedback formula example**: Using `NA_FEEDBACK_OPTION = 1` in `b2.feedback_control.parameters` (see the [switch description](/extras/b2input/develop/b2.parameters.html#b2.feedback_control.parameters)) translates into the following formula: $$\Gamma_{\text{puff,new}} = \Gamma_{\text{puff,old}} \cdot \frac{1 + \alpha \cdot \frac{\text{target } n_{e,sep}}{\text{current } n_{e,sep}}}{1 + \alpha}$$ @@ -385,4 +385,4 @@ Lower $\alpha$ increases the oscillations magnitude and decreases the period. At *Three consequent simulations, gradually decreasing requested separatrix electron density. At 2.2 ms, $\alpha$ was increased from 0.1 to 1.0 to prompt faster convergence.* -I am not sure how (or if) this trick gets around the non-linearity described by Kukushkin and Krasheninnikov. On occasion, relaunching a converged low-density simulation with different parameters renews the oscillations. In the worst case, always start from a high-density case. \ No newline at end of file +I am not sure how (or if) this trick gets around the non-linearity described by Kukushkin and Krasheninnikov. On occasion, relaunching a converged low-density simulation with different parameters renews the oscillations. 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- - - - - - - image/svg+xml - - - - - - - - - doc - SOLPS - - - diff --git a/docs/img/tip.png b/docs/img/tip.png deleted file mode 100644 index 890b9d1..0000000 Binary files a/docs/img/tip.png and /dev/null differ diff --git a/docs/img/under_construction.png b/docs/img/under_construction.png deleted file mode 100644 index 5481bb0..0000000 Binary files a/docs/img/under_construction.png and /dev/null differ diff --git a/docs/img/warning.png b/docs/img/warning.png deleted file mode 100644 index f57220b..0000000 Binary files a/docs/img/warning.png and /dev/null differ diff --git a/docs/index.md b/docs/index.md index f94b61b..c412e32 100644 --- a/docs/index.md +++ b/docs/index.md @@ -23,7 +23,7 @@ SOLPS Tutorials are sorted into three basic categories parts: 2. **Feature blog**, or making your SOLPS simulation more complex. This includes [diffusion coefficients](feature_blog/Diffusion_coefficients.md), [gas puffing and pumping](feature_blog/Gas_puffing_and_pumping.md), [impurities](feature_blog/Impurities.md), [drifts](feature_blog/Drifts.md), [wide grids](feature_blog/Wide_grids.md), and deep dives on [magnetic equilibrium reconstructions](feature_blog/Magnetic_equilibrium_reconstructions.md), [energy fluxes](feature_blog/Energy_fluxes_deep_dive.md) and [interpretative simulations](feature_blog/Interpretative_simulations_of_COMPASS.md). -3. **Supplementary material**, which helps you use SOLPS aside from the physics. This includes [SOLPS-ITER user wisdom](supplementary/SOLPS-ITER_user_wisdom.md), a [library](supplementary/Library.md), [remote access](supplementary/Remote_access.md), [common pitfalls](supplementary/Common_pitfalls.md), [questions and answers](supplementary/Questions_and_answers.md) and [B2.5 switch documentation](/solps-doc/extras/b2input). +3. **Supplementary material**, which helps you use SOLPS aside from the physics. This includes [SOLPS-ITER user wisdom](supplementary/SOLPS-ITER_user_wisdom.md), a [library](supplementary/Library.md), [remote access](supplementary/Remote_access.md), [common pitfalls](supplementary/Common_pitfalls.md), [questions and answers](supplementary/Questions_and_answers.md) and [B2.5 switch documentation](/extras/b2input). When contributing to the tutorials, please respect this underlying structure. @@ -65,7 +65,7 @@ SOLPS-ITER is a suite of codes (B2.5, EIRENE, DivGeo, Carre...) which performs 2 /// tip | Your documentation could be here! -Although SOLPS Tutorials does not aim to substitute existing SOLPS documentation, they do aspire to become its central hub. If you have written any sort of SOLPS-related documentation, consider [contributing to SOLPS Tutorials](https://repo.tok.ipp.cas.cz/solps/solps-doc#solps-doc)open_in_new or adding your work to the [Useful links](supplementary/SOLPS-ITER_user_wisdom.md#useful-links) section. +Although SOLPS Tutorials does not aim to substitute existing SOLPS documentation, they do aspire to become its central hub. If you have written any sort of SOLPS-related documentation, consider [contributing to SOLPS Tutorials](Contribute.md) or adding your work to the [Useful links](supplementary/SOLPS-ITER_user_wisdom.md#useful-links) section. /// ## Contributors @@ -81,11 +81,11 @@ Katka was two years into her PhD on SOLPS-ITER when she got married, agreed on t /// hint | Jan Hečko *"The smaller and easier a task is, the lower it is on my to-do list."* -Honza has awesome superpowers, such as being one with the source code. He is responsible for the [installation tutorials](installing/solps-iter-codebase.md), the [B2.5 switch documentation](/solps-doc/extras/b2input) and the website formatting. He also wrote most of the [Gas puffing and pumping](feature_blog/Gas_puffing_and_pumping.md) and [Drifts](feature_blog/Drifts.md) tutorials, and he got the [Wide grids](feature_blog/Wide_grids.md) tutorial started. +Honza has awesome superpowers, such as being one with the source code. He is responsible for the [installation tutorials](installing/solps-iter-codebase.md), the [B2.5 switch documentation](/extras/b2input) and the website formatting. He also wrote most of the [Gas puffing and pumping](feature_blog/Gas_puffing_and_pumping.md) and [Drifts](feature_blog/Drifts.md) tutorials, and he got the [Wide grids](feature_blog/Wide_grids.md) tutorial started. /// Other major contributors to the Tutorials are: - **Aleš Podolník** - wrote the [Energy fluxes deep dive](feature_blog/Energy_fluxes_deep_dive.md) -We would also like to thank, in alphabetic order, Xavier Bonnin, Irina Borodkina, David Coster, Michael Komm, Lukáš Kripner, Diana Naydenkova, Jakub Seidl, Oleg Shyshkin, Daniel Švorc, Matěj Tomeš, David Tskhakaya, and Sven Wiesen. \ No newline at end of file +We would also like to thank, in alphabetic order, Xavier Bonnin, Irina Borodkina, David Coster, Michael Komm, Lukáš Kripner, Diana Naydenkova, Jakub Seidl, Oleg Shyshkin, Daniel Švorc, Matěj Tomeš, David Tskhakaya, and Sven Wiesen. diff --git a/docs/my_first_simulation/Adjusting_SOLPS-ITER_input.md b/docs/my_first_simulation/Adjusting_SOLPS-ITER_input.md index 0d5c2bd..859a770 100644 --- a/docs/my_first_simulation/Adjusting_SOLPS-ITER_input.md +++ b/docs/my_first_simulation/Adjusting_SOLPS-ITER_input.md @@ -19,7 +19,7 @@ Once you have mastered these, you can move on to features described in the Featu - Switching to [wide grids](../feature_blog/Wide_grids.md) /// tip | Input parameter overview -To look up information on boundary conditions and SOLPS-ITER input parameters, use our [B2.5 switch database](https://solps.pages.tok.ipp.cas.cz/solps-doc/extras/b2input/). It has colours and a search function. +To look up information on boundary conditions and SOLPS-ITER input parameters, use our [B2.5 switch database](/extras/b2input/). It has colours and a search function. /// @@ -74,7 +74,7 @@ It's important to know the colloquial names for B2.5 boundaries because they are bcend= 65, 36, 36, 17, 84, 84, ``` -These lines mean that wherever boundary conditions are listed for all B2.5 boundaries, there will be **6 numbers** and they will correspond, respectively, to boundaries S2 (core), W (outer target), E (inner target), S1 and S3 (PFR) and N (far SOL). You can tell the difference between the three South boundaries using the indices. Perusing the [B2.5 switch documentation](/solps-doc/extras/b2input)open_in_new for the meaning of `BCPOS`, `BCSTART` and `BCEND`, you can learn that the S2 (core) boundary has the $y$ (radial) index -1 and poloidally (in $x$) spans from cell 18 to 65, that is, from inner X-point to outer X-point. +These lines mean that wherever boundary conditions are listed for all B2.5 boundaries, there will be **6 numbers** and they will correspond, respectively, to boundaries S2 (core), W (outer target), E (inner target), S1 and S3 (PFR) and N (far SOL). You can tell the difference between the three South boundaries using the indices. Perusing the [B2.5 switch documentation](/extras/b2input)open_in_new for the meaning of `BCPOS`, `BCSTART` and `BCEND`, you can learn that the S2 (core) boundary has the $y$ (radial) index -1 and poloidally (in $x$) spans from cell 18 to 65, that is, from inner X-point to outer X-point. Knowing the number of boundaries is useful for orientation in SOLPS input files. Wherever indices run from 1 to 6, you can be pretty sure they're listing the individual B2.5 boundaries in the order given by `BCCHAR`. Besides the 6 B2.5 boundaries, another recurring list that you'll encounter in the example `b2.boundary.parameters` file runs from 1 to 2. This is the **list of all ion species**. Its index is usually denoted `is` (Index of Species) and in this example file, it includes two "ion" species only: deuterium atom neutrals and deuterium (singly charged) ions. (Molecules are not covered by B2.5, only by EIRENE.) The boundary conditions of the continuity and momentum equation are given separately for every ion species. That's why you have: @@ -95,7 +95,7 @@ Knowing the number of boundaries is useful for orientation in SOLPS input files. mompar(0,3,2)= 0.00 , 0.00 , ``` -`BCMOM` is given on 6 lines (corresponding to each of the 6 B2.5 boundaries) and each line has 2 values (corresponding to D0 and D+). Perusing the description of `BCMOM = 2` in the [B2.5 switch documentation](/solps-doc/extras/b2input)open_in_new, you will find this boundary condition only has one free parameter: `MOMPAR(,,1)`. However, boundary condition `BCMOM = 3` has two free parameters: `MOMPAR(,,1)` and `MOMPAR(,,2)`. That is why there are 8 lines for `MOMPAR`: 6 of them list `MOMPAR(,,1)` and 2 of them list `MOMPAR(,,2)`. Reading the indices in the brackets, you can find the exact place where you need to edit a number to change a SOLPS input. +`BCMOM` is given on 6 lines (corresponding to each of the 6 B2.5 boundaries) and each line has 2 values (corresponding to D0 and D+). Perusing the description of `BCMOM = 2` in the [B2.5 switch documentation](/extras/b2input)open_in_new, you will find this boundary condition only has one free parameter: `MOMPAR(,,1)`. However, boundary condition `BCMOM = 3` has two free parameters: `MOMPAR(,,1)` and `MOMPAR(,,2)`. That is why there are 8 lines for `MOMPAR`: 6 of them list `MOMPAR(,,1)` and 2 of them list `MOMPAR(,,2)`. Reading the indices in the brackets, you can find the exact place where you need to edit a number to change a SOLPS input. /// tip | There are many available boundary conditions As of February 2026, there are 28 available boundary conditions for the ion energy equation `BCENI` in the "structured grids" SOLPS-ITER 3.0.9, and the list is growing. You can prescribe the sheath (`BCENI=3`), you can prescribe the sheath but different (`BCENI=11,12`), you can prescribe the sheath but compatible with drifts (`BCENI=15`)... At this point, as you read this introductory tutorial, don't worry about all of these options and stick to the default ones, which were pre-generated in the `stencil` files. But later, once you've mastered the basics and you move on to the Feature blog, you will study this list of boundary conditions and choose the best one for your simulation. diff --git a/docs/my_first_simulation/Creating_a_new_SOLPS-ITER_simulation.md b/docs/my_first_simulation/Creating_a_new_SOLPS-ITER_simulation.md index 7bc8765..a08b4df 100644 --- a/docs/my_first_simulation/Creating_a_new_SOLPS-ITER_simulation.md +++ b/docs/my_first_simulation/Creating_a_new_SOLPS-ITER_simulation.md @@ -301,8 +301,8 @@ SOLPS-ITER input files are the text files you will edit while running your simul /// tip | Resources **`b2mn.dat`** -- `$SOLPSTOP/modules/B2.5/src/documentation/b2input.xml` - mother source of B2.5 switch descriptions -- [B2.5 switches](/solps-doc/extras/b2input) - our pretty, searchable viewport of the `b2input.xml` file, also great for browsing boundary conditions +- `$SOLPSTOP/modules/B2.5/src/documentation/b2input.xml` - mother source of B2.5 switch descriptions +- [B2.5 switches](/extras/b2input) - our pretty, searchable viewport of the `b2input.xml` file, also great for browsing boundary conditions **`input.dat`** - [EIRENE manual](https://eirene.de/Documentation/eirene.pdf)open_in_new @@ -368,7 +368,7 @@ Usually, you'll have `b2ah.dat` in the `baserun` and `b2mn.dat`, `b2.boundary.pa We recommend starting from our [annotated basic `b2mn.dat`](../files/annotated_basic_b2mn.dat)download. The annotations explain what the switches mean and what their default values are. Note that this was made for SOLPS version 3.0.6. You may be running a newer version, where some of the listed switches are obsolete. -To learn more about B2.5 switches, peruse our [B2 switches documentation](/solps-doc/extras/b2input). Kateřina has compiled the [switches she found interesting](../files/annotated_interesting_switches_in_b2mn.dat)download on her October 2023 read-through. +To learn more about B2.5 switches, peruse our [B2 switches documentation](/extras/b2input). Kateřina has compiled the [switches she found interesting](../files/annotated_interesting_switches_in_b2mn.dat)download on her October 2023 read-through. An important part of `b2mn.dat` is switching between the "standard” and "physics” boundary conditions. To use `b2.boundary.parameters` instead of `b2ah.dat` etc., paste these line into `b2mn.dat`: ``` diff --git a/docs/my_first_simulation/Running_SOLPS-ITER.md b/docs/my_first_simulation/Running_SOLPS-ITER.md index 269f485..cea368c 100644 --- a/docs/my_first_simulation/Running_SOLPS-ITER.md +++ b/docs/my_first_simulation/Running_SOLPS-ITER.md @@ -150,7 +150,7 @@ SOLPS-ITER keeps dozens of files in the `run` directory, hundreds if you use the b2.neutrals.parameters input.dat # or eirene.input.json b2.transport.inputfile # and other input files - + # For spotting unwanted reversal to flat profiles b2ai.dat b2ar.dat @@ -165,7 +165,7 @@ SOLPS-ITER keeps dozens of files in the `run` directory, hundreds if you use the # Other b2fplasmf b2plot.ps - + 5. Save the text file and, in your file browser, hit `Ctrl+H` a few times. Refresh if needed. @@ -201,7 +201,7 @@ To restart a simulation: /// warning | Remove `b2mn.prt`, not `b2mn.dat` Everyone raise your hand if you once didn't pay attention and by mistake removed the B2.5 master control file `b2mn.dat` instead of `b2mn.prt`... OTL - /// + /// 4. Rewrite `b2fstati` (`i` for "initial" plasma state) with `b2fstate` (`e` for "end" plasma state). @@ -214,13 +214,13 @@ The simulation will start from whichever plasma state is present in `b2fstati`. - **Create a checkpoint** of the simulation state so you can come back to it later: `cp b2fstate b2fstate_before_gas_puff` (You can archive EIRENE results as well (files `fort.13`, `14`, `15`, `44` and `46`), but only `b2fstate` is essential.) - **Return to a checkpoint**: `cp b2fstate_before_gas_puff b2fstati` -- **Adopt a completely different solution** (with the same geometry/number of cells): `cp ../another_run/b2fstate b2fstati` +- **Adopt a completely different solution** (with the same geometry/number of cells): `cp ../another_run/b2fstate b2fstati` /// ## Branching out a SOLPS-ITER run -Sometimes, you'll want to see what happens when you tweak a simulation a little (e.g. trying this weird switch you've just found in [B2.5 documentation](/solps-doc/extras/b2input)), but you don't want to lose the original simulation in case something goes wrong. Other times, you'll want to conduct a parameter scan. That is when you need to branch out an existing run. +Sometimes, you'll want to see what happens when you tweak a simulation a little (e.g. trying this weird switch you've just found in [B2.5 documentation](/extras/b2input)), but you don't want to lose the original simulation in case something goes wrong. Other times, you'll want to conduct a parameter scan. That is when you need to branch out an existing run. **Simple and dirty**: ``` @@ -274,7 +274,7 @@ This will end the simulation after the current iteration is finished, write the ## Defining how long SOLPS-ITER should run -SOLPS-ITER keeps running until one of its stops is pulled. All of them are defined in `b2mn.dat`. Browse them in [B2.5 switches](/solps-doc/extras/b2input). +SOLPS-ITER keeps running until one of its stops is pulled. All of them are defined in `b2mn.dat`. Browse them in [B2.5 switches](/extras/b2input). Set the number of iterations (iteration = 1 EIRENE call + several B2.5 calls): ``` @@ -375,7 +375,7 @@ When you compute the left-hand side for each cell of the B2.5 grid, you get some
2D maps of residuals of individual B2.5 equations. Standalone run, Wide Grids, COMPASS Upgrade. Red = positive residuals, blue = negative residuals.
-You can reduce these 2D maps to a single number if you take the absolute value in each cell and sum them all (see section C.10 of the manual). Such residual sums are periodically saved to the `b2fstrace` file by SOLPS-ITER. The *absolute value* of residuals is usually inconsequential. (There are `b2mn.dat` [switches](/solps-doc/extras/b2input) which stop the calculation once a certain residuals value is reached, such as `b2mndr_min_areshe`. Their usefulness is, however, limited.) Generally, you are interested in *relative values* of residual sums, and whether they are going down with subsequent iterations. To plot the time evolution of residuals (can be done while the simulation is running): +You can reduce these 2D maps to a single number if you take the absolute value in each cell and sum them all (see section C.10 of the manual). Such residual sums are periodically saved to the `b2fstrace` file by SOLPS-ITER. The *absolute value* of residuals is usually inconsequential. (There are `b2mn.dat` [switches](/extras/b2input) which stop the calculation once a certain residuals value is reached, such as `b2mndr_min_areshe`. Their usefulness is, however, limited.) Generally, you are interested in *relative values* of residual sums, and whether they are going down with subsequent iterations. To plot the time evolution of residuals (can be done while the simulation is running): ``` resall_D # all residuals of fluid D0 and D1 diff --git a/docs/supplementary/Common_pitfalls.md b/docs/supplementary/Common_pitfalls.md index 0208fc7..e2d29fc 100644 --- a/docs/supplementary/Common_pitfalls.md +++ b/docs/supplementary/Common_pitfalls.md @@ -6,7 +6,7 @@ Pitfalls covered here: - [The danger of timestamps](#the-danger-of-timestamps), or "Why did my simulation jump to the flat profiles state?" - [Divergence](#divergence), or "Why is the separatrix temperature 5 keV?" -- [Make SOLPS-ITER run faster](#make-solps-iter-run-faster), or "I only have four years for my PhD, how am I supposed to model DEMO with impurities and drifts?" +- [Make SOLPS-ITER run faster](#make-solps-iter-run-faster), or "I only have four years for my PhD, how am I supposed to model DEMO with impurities and drifts?" /// warning | Your expertise is needed! Ever since the IPP Prague team switched from modelling the COMPASS tokamak to COMPASS Upgrade, divergence and infinite runtime has been our bane. Your expertise is especially welcome in *Common pitfalls*! @@ -307,13 +307,13 @@ echo "phys te 0.0 fmin 40.0 fmax surf" | b2plot Carbon ionisation energy is 11.16 eV (as stated in the `b2plot` output), so there should have been some neutral carbon surviving in the PFR at least. Why was there none? -I tried breaking the simulation up into smaller parts and drawing the results in individual time snaps. It turned out that C0 density fell with every iteration, from 1015 m-3 (flat profiles solution) to what you see above. The moment it hit 104 m-3, the C0 continuity equation residuals stopped evolving. It seemed like there was a floor limit to how low a density can get? Eventually, I discovered the B2.5 switch `b2mndr_na_min` (see its description in our [B2.5 switch documentation viewer](/solps-doc/extras/b2input)), which sets the minimum ion species density. Its default value is 104 m-3. +I tried breaking the simulation up into smaller parts and drawing the results in individual time snaps. It turned out that C0 density fell with every iteration, from 1015 m-3 (flat profiles solution) to what you see above. The moment it hit 104 m-3, the C0 continuity equation residuals stopped evolving. It seemed like there was a floor limit to how low a density can get? Eventually, I discovered the B2.5 switch `b2mndr_na_min` (see its description in our [B2.5 switch documentation viewer](/extras/b2input)), which sets the minimum ion species density. Its default value is 104 m-3. So! It appeared that neutral carbon was depleted from the simulation domain, globally hit the minimum density, and its solution stopped evolving with time. Where did it go? And why was there still plenty of ionised carbon remaining? The question how the crash happened receded into the background, because I *wanted* neutral carbon in my simulation. Fixing that took priority before finding the physical nature of the crash. Since neutral carbon should have been produced by sputtering, I searched how sputtering was controlled. The manual confused me initially. In reality, there are two sets of sputtering switches: -- A group of "sputtering model switches" in `b2mn.dat`, all beginning with `b2stbr`. These control sputtering in B2.5 calculations, that is, in standalone simulations. See them in the [B2.5 switch documentation viewer](/solps-doc/extras/b2input). +- A group of "sputtering model switches" in `b2mn.dat`, all beginning with `b2stbr`. These control sputtering in B2.5 calculations, that is, in standalone simulations. See them in the [B2.5 switch documentation viewer](/extras/b2input). - Paragraph *\*\*\* 6B. Data for local reflection and sputtering models* in `input.dat`, most importantly switches `ILSPT`, `ISRS` and `ISRC`. These control sputtering in EIRENE calculations, that is, in coupled simulations. See the [EIRENE manual](https://eirene.de/Documentation/eirene.pdf)open_in_new, section *Input data for surface interaction models*. The SOLPS manual doesn't say that these are independent groups of inputs which come into effect depending on who's handling the neutrals. Eventually, I gathered as much from the SOLPS Slack and experience. I zeroed in on the EIRENE input file, `input.dat`. @@ -341,7 +341,7 @@ Written like this, the divergence hunt seems like a logical progression of steps Browsing my notes from 2021, I see mentions of diverging carbon simulations from May to August. There is a detailed study of B2.5 boundary conditions (but no sputtering switches), repeated calls to contact Fabio Subba (which I never did), and a list of thirteen measures to fix the simulation (of which I tried nine, to no effect). 95 % of the notes concern other things. Then there's a one-month break... and the issue of diverging carbon simulation vanishes. -My point is: **Take heart**. You will find a solution to your divergence eventually, even if it's "I don't need carbon *that* badly". And if you uncover the root of the problem and are able to address it, [write about it here](https://repo.tok.ipp.cas.cz/solps/solps-doc#solps-doc)open_in_new! The leads I should have followed are more apparent in hindsight. Hopefully, by accumulating stories of mending divergence, we can distill rules of thumb to shorten the Brownian fumbling. +My point is: **Take heart**. You will find a solution to your divergence eventually, even if it's "I don't need carbon *that* badly". And if you uncover the root of the problem and are able to address it, [write about it here](../Contribute.md)! The leads I should have followed are more apparent in hindsight. Hopefully, by accumulating stories of mending divergence, we can distill rules of thumb to shorten the Brownian fumbling. /// @@ -435,4 +435,4 @@ Here tips and tricks for accelerating SOLPS-ITER runs are given. Some have been > Convergence of the run and even the result might depend on the starting profiles. Flat profile case is not the best choice. Fastest convergence is reached when restarting from the similar run. Important to have the same grids structure and can be even different machine. The main reasons of this dependence is the following: the transport equations are strongly nonlinear and unphysical, or far from real (like flat profiles) can drive to wrong metastable solutions. -**Switch to fluid neutrals**. As [[Carli, 2021]](https://onlinelibrary.wiley.com/doi/10.1002/ctpp.202100184)open_in_new argues, the latest version of fluid neutrals (or standalone B2.5) is accurate enough to replace EIRENE if you really gotta go fast. \ No newline at end of file +**Switch to fluid neutrals**. As [[Carli, 2021]](https://onlinelibrary.wiley.com/doi/10.1002/ctpp.202100184)open_in_new argues, the latest version of fluid neutrals (or standalone B2.5) is accurate enough to replace EIRENE if you really gotta go fast. diff --git a/docs/supplementary/Questions_and_answers.md b/docs/supplementary/Questions_and_answers.md index aa67fc5..23279c5 100644 --- a/docs/supplementary/Questions_and_answers.md +++ b/docs/supplementary/Questions_and_answers.md @@ -239,9 +239,9 @@ Internally, SOLPS-ITER doesn't use the parallel coordinate at all. All calculati The figures show a B2.5 grid based on a COMPASS equilibrium, field lines traced using PLEQUE from the outer target cell centres (red dots) and the connection length from the OMP to the inner and outer target. Two observations can be made: 1. The poloidal cell rows follow PLEQUE field lines, but the field lines do not necessarily pass through the cell centres. This is most readily seen in the top left part of the equilibrium, but it is also true at the outer midplane (OMP). The takeaways are: - + 1. Poloidal cell rows in B2.5 truly constitute **flux tubes**, and the transport through them is purely parallel transport. - + 2. If, nevertheless, you want to trace field lines from the cell centres with PLEQUE, don't start from the OMP. You will follow a field line which does not pass through the poloidal cell row. 2. The discretised calculation of `b2plot`, SOLPSpy and SOLPS-postproc is, to a large degree, **accurate**. The only sizable deviation is seen near the separatrix, where the connection length goes to infinity near the X-point. This is a pretty good result for such coarse discretisation. @@ -305,7 +305,7 @@ Refer to the tutorial [installing SOLPS-ITER on a properly configured site](../i **What is a "stratum"?**
A stratum (plural strata) is a neutral particle source of (in some regard) homogeneous properties. When sampling Monte Carlo neutrals whose trajectories it will follow, EIRENE splits its total neutral particle source into strata according to their origin - mostly "originating on a plasma boundary" or "volumetric neutral particle source". If it samples, say, 7000 neutral particles for each stratum, it achieves lower statistical variance than if it sampled from the total neutral particle source at random. This is because stratified sampling provides more representative samples of neutral particles in each EIRENE run. -More information can be found via Google (general understanding of stratified sampling in Monte Carlo techniques), in the EIRENE manual, sections *1.3.3.2 Stratified Source Sampling* (particular implementation of stratified sampling in EIRENE) and *2.7 Input data for Initial Distribution of Test Particles* (description of block 7 in `input.dat`, where strata description is given), and `b2.neutrals.parameters` along with the [description of its switches](https://solps.pages.tok.ipp.cas.cz/solps-doc/extras/b2input/b2.parameters.html#b2.neutrals.parameters). +More information can be found via Google (general understanding of stratified sampling in Monte Carlo techniques), in the EIRENE manual, sections *1.3.3.2 Stratified Source Sampling* (particular implementation of stratified sampling in EIRENE) and *2.7 Input data for Initial Distribution of Test Particles* (description of block 7 in `input.dat`, where strata description is given), and `b2.neutrals.parameters` along with the [description of its switches](/extras/b2input/develop/b2.parameters.html#b2.neutrals.parameters). For instance, the beginning of the `b2.neutrals.parameters` file in a D+C simulation reads: diff --git a/docs/supplementary/SOLPS-ITER_user_wisdom.md b/docs/supplementary/SOLPS-ITER_user_wisdom.md index 11ae13f..eeb91d6 100644 --- a/docs/supplementary/SOLPS-ITER_user_wisdom.md +++ b/docs/supplementary/SOLPS-ITER_user_wisdom.md @@ -54,14 +54,14 @@ If you compiled all of these sources and made them fully searchable, you'd get a - Our [Library](Library.md), especially if you're looking for physics understanding. - History of the [SOLPS Slack](http://solps.slack.com)open_in_new. Lamentably, you need a paid Slack account to see the entire history. However, searching for keywords in the `solps-iter`, `q_and_a`, `beginner-advice` and `general` channels should be a gold mine for solutions. - The [SOLPS User Forum minutes](https://confluence.iter.org/spaces/IMP/pages/178135134/SOLPS-ITER#SOLPSITER-UserForumdebriefings)open_in_new. Often you'll find mentions of recent updates and bugfixes relevant to your problems. -- The [SOLPS-ITER source code](https://github.com/iterorganization/SOLPS-ITER/tree/master/modules)open_in_new. To view and search its content, use a high-level code editor such as [Visual Studio Code](https://code.visualstudio.com/)open_in_new. This allows, for instance, searching for keywords across multiple files using `Ctrl+Shift+F`. +- The [SOLPS-ITER source code](https://github.com/iterorganization/SOLPS-ITER/tree/master/modules)open_in_new. To view and search its content, use a high-level code editor such as [Visual Studio Code](https://code.visualstudio.com/)open_in_new. This allows, for instance, searching for keywords across multiple files using `Ctrl+Shift+F`. - SOLPS routine description (e.g. `b2stbc`): Search for the keyword. In the best case, you'll find docstrings. In a worse case, you can inspect the Fortran code line by line to figure out what the simulation actually does. - Some DivGeo documentation: `$SOLPSTOP/modules/DivGeo/equtrn/doxygen/refman.pdf` - [Useful links](#useful-links) below. - To find out what B2.5 switches do: - - Search them in our [B2.5 switch documentation](/solps-doc/extras/b2input). Be sure to use the correct SOLPS version, as some switches may be recently added. + - Search them in our [B2.5 switch documentation](/extras/b2input). Be sure to use the correct SOLPS version, as some switches may be recently added. - The [SOLPS GUI](https://static.iter.org/imas/assets/solps-iter/html/index.html)open_in_new includes an `Input` tab which not only collapses `input.dat` into individual sections but also automatically displays switch descriptions upon clicking/hovering. Charming! @@ -215,7 +215,7 @@ Follow the instructions in this order and don't go straight to `Ctrl+F`. It's te - Created by Leon Kos, the SOLPS-ITER GUI (Graphical User Interface) aims to make SOLPS-ITER more user-friendly. - Even if you do not plan to use the tool itself, the documentation provides nicely written (but often brief) guides and overviews such as [SOLPS Structure](https://static.iter.org/imas/assets/solps-iter/html/introduction.html#solps-structure)open_in_new and [SOLPS-ITER installation with `easybuild-local.sh`](https://static.iter.org/imas/assets/solps-iter/html/howto/install.html#solps-iter-installation)open_in_new. -**[B2.5 switches documentation](/solps-doc/extras/b2input)** +**[B2.5 switches documentation](/extras/b2input)** - Created by Jan Hečko, this semi-detached part of SOLPS Tutorials lists the switches of B2, their meaning and default values, in a human-readable way. - Switch descriptions are taken from the official SOLPS/B2.5 documentation (`$SOLPSTOP/B2.5/src/documentation/b2input.xml`). @@ -360,4 +360,4 @@ Czech: "Do prdele!" (In the ass!) *** -> To have a laugh, we suggest browsing the `gateway` channel of the [SOLPS Slack](http://solps.slack.com)open_in_new. \ No newline at end of file +> To have a laugh, we suggest browsing the `gateway` channel of the [SOLPS Slack](http://solps.slack.com)open_in_new. diff --git a/extras/b2input/README.md b/extras/b2input/README.md index 7e820af..f1f9218 100644 --- a/extras/b2input/README.md +++ b/extras/b2input/README.md @@ -1,10 +1,10 @@ # B2 input docs viewer -The [B2 input docs viewer]([https://solps.pages.tok.ipp.cas.cz/solps-doc/extras/b2input/) is a lucid guide to the switches in all B2.5 input files, including `b2mn.dat`, `b2.boundary.parameters` and more. It generates a webpage based on the official SOLPS documentation, where the switch names, default values and descriptions are given. +The [B2 input docs viewer](https://solps-tutorials.readthedocs.io/extras/b2input/) is a lucid guide to the switches in all B2.5 input files, including `b2mn.dat`, `b2.boundary.parameters` and more. It generates a webpage based on the official SOLPS documentation, where the switch names, default values and descriptions are given. ## Generate the webpage -The viewer webpage is pre-generated by `solps-doc` from several SOLPS-ITER versions, but you are free to generate it yourself. +The viewer webpage is pre-generated by `solps-tutorials` from several SOLPS-ITER versions, but you are free to generate it yourself. ### Prerequisites @@ -21,7 +21,7 @@ The viewer webpage is pre-generated by `solps-doc` from several SOLPS-ITER versi ### Usage -Go to this directory, i.e. `cd solps-doc/extras/b2input`, before running the commands below. Check the documentation of the script: +Go to this directory, i.e. `cd solps-tutorials/extras/b2input`, before running the commands below. Check the documentation of the script: ```bash python generate_html.py --help @@ -44,10 +44,10 @@ python fetch_b2input_xml_files.py --help ``` ```bash -python fetch_b2input_xml_files.py --token $MY_SECRET_TOKEN versions.yaml +python fetch_b2input_xml_files.py versions.yaml ``` -Now, instead of passing one file, one can pass a directory with multiple suffixed `b2input.xml` files as produced by `fetch_b2input_xml_files.py`. This will generate a webpage for multiple SOLPS-ITER versions, similar to what is found in `solps-doc`. +Now, instead of passing one file, one can pass a directory with multiple suffixed `b2input.xml` files as produced by `fetch_b2input_xml_files.py`. This will generate a webpage for multiple SOLPS-ITER versions, similar to what is found at [https://solps-tutorials.readthedocs.io/extras/b2input/]. ```bash python generate_html.py -d "./public" ./ diff --git a/extras/b2input/src_html/base.html b/extras/b2input/src_html/base.html index cc919ce..f5de427 100644 --- a/extras/b2input/src_html/base.html +++ b/extras/b2input/src_html/base.html @@ -8,6 +8,10 @@ {% block page_title %}b2 input – {{ header_label or 'SOLPS-ITER' }}{% endblock %} + {% endblock %} diff --git a/extras/b2input/src_html/index_toplevel_template.html b/extras/b2input/src_html/index_toplevel_template.html index 945209d..38a7414 100644 --- a/extras/b2input/src_html/index_toplevel_template.html +++ b/extras/b2input/src_html/index_toplevel_template.html @@ -28,8 +28,6 @@ -

Available SOLPS-ITER versions

- {% for label in labels %}

diff --git a/mkdocs.yml b/mkdocs.yml index d8dd454..6699da9 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -1,5 +1,5 @@ site_name: 'SOLPS Tutorials' -site_url: https://solps.pages.tok.ipp.cas.cz/solps-doc/ +site_url: https://solps-tutorials.readthedocs.io/ site_dir: public theme: name: material @@ -55,4 +55,4 @@ nav: - supplementary/Remote_access.md - supplementary/Common_pitfalls.md - supplementary/Questions_and_answers.md - - 'B2.5 switches': /solps-doc/extras/b2input + - 'B2.5 switches': /extras/b2input