encyclopedia-gui issueshttps://gitlab.mpcdf.mpg.de/nomad-lab/encyclopedia-gui/-/issues2019-07-31T16:01:07Zhttps://gitlab.mpcdf.mpg.de/nomad-lab/encyclopedia-gui/-/issues/135Ideas for refactorings2019-07-31T16:01:07ZGeorg HuhsIdeas for refactorings## Materials list in the new search page
The whole result-related part of the page is encapsulated in a `<div class="results-panel">` element, which contains only one other element `<div id="matlist">`
* Why are there two elements, on...## Materials list in the new search page
The whole result-related part of the page is encapsulated in a `<div class="results-panel">` element, which contains only one other element `<div id="matlist">`
* Why are there two elements, one referenced by its class, another one by its id?
* Is this a system or a relict?
* Could they be mergedGeorg HuhsGeorg Huhshttps://gitlab.mpcdf.mpg.de/nomad-lab/encyclopedia-gui/-/issues/131"undefined" strings in Methodology filters2018-10-31T10:51:31ZGeorg Huhs"undefined" strings in Methodology filtersSome Code names in the filters on the methodology details page are given as "undefined", while they are listed correctly on the overview page.
Example: material https://encyclopedia.nomad-coe.eu/gui/#/material/14
![methodology_filters...Some Code names in the filters on the methodology details page are given as "undefined", while they are listed correctly on the overview page.
Example: material https://encyclopedia.nomad-coe.eu/gui/#/material/14
![methodology_filters_problem_overview](/uploads/80271119c4219b5492870bbcd972849e/methodology_filters_problem_overview.png)
![methodology_filters_problem_detail](/uploads/674a07bdc1c08b3c0535f95f8b930ae1/methodology_filters_problem_detail.png)https://gitlab.mpcdf.mpg.de/nomad-lab/encyclopedia-gui/-/issues/130filter labels2018-10-09T08:10:07ZGeorg Huhsfilter labelsOn the methodology details page the labels of the filters are capitalized, while the values in the table are all lowercase. This should be aligned (all lowercase)
* to be confirmed by ClaudiaOn the methodology details page the labels of the filters are capitalized, while the values in the table are all lowercase. This should be aligned (all lowercase)
* to be confirmed by Claudiahttps://gitlab.mpcdf.mpg.de/nomad-lab/encyclopedia-gui/-/issues/129Show Fermi surface data2018-09-29T17:51:18ZGeorg HuhsShow Fermi surface data**Needs:**
* API providing x3d file
* Correct entries in DB**Needs:**
* API providing x3d file
* Correct entries in DBhttps://gitlab.mpcdf.mpg.de/nomad-lab/encyclopedia-gui/-/issues/126Error reporting feedback2018-06-29T12:06:19ZGeorg HuhsError reporting feedbackIt would be good to give the user the confirmation that the error report has been sent (does the API confirm it?).It would be good to give the user the confirmation that the error report has been sent (does the API confirm it?).https://gitlab.mpcdf.mpg.de/nomad-lab/encyclopedia-gui/-/issues/123Add material classification2018-06-26T10:17:27ZGeorg HuhsAdd material classificationTwo fields are to be added to the _material details_ page, just after _strukturbericht designation_.
| quantity | name to be shown in GUI |
|--|--|
| `springer classification` | material class |
| `springer compound class` | compound cl...Two fields are to be added to the _material details_ page, just after _strukturbericht designation_.
| quantity | name to be shown in GUI |
|--|--|
| `springer classification` | material class |
| `springer compound class` | compound class |
* To be shown only if there is data
* For both there can be various entries (for list of options see data description system).
Each entry gets its own line
**Blocked by**: new parse, API extensionhttps://gitlab.mpcdf.mpg.de/nomad-lab/encyclopedia-gui/-/issues/122API-changes2018-06-21T12:01:01ZGeorg HuhsAPI-changesProbably the API might change for some points:
* [ ] Geometry data (atom positions): in a collection instead of the `elements` endpoint - taking out the elements endpoint if it is not needed. (see [material refactoring](https://gitlab.m...Probably the API might change for some points:
* [ ] Geometry data (atom positions): in a collection instead of the `elements` endpoint - taking out the elements endpoint if it is not needed. (see [material refactoring](https://gitlab.mpcdf.mpg.de/nomad-lab/encyclopedia-general/wikis/refactoring-concept).)
* [ ] Probably new API endpoint for ranges of floating point value quantities, or somehow integrated into the _suggestions_ endpoint
**Blocked** as it is a matter of coordination with the API
Involved: @mscheidg, @ghuhshttps://gitlab.mpcdf.mpg.de/nomad-lab/encyclopedia-gui/-/issues/121Review of search and materials pages2018-07-13T09:08:39ZGeorg HuhsReview of search and materials pages# Full description
[see wiki](https://gitlab.mpcdf.mpg.de/nomad-lab/encyclopedia-general/wikis/M30%20review%20search%20and%20materials%20list)
# Full description
[see wiki](https://gitlab.mpcdf.mpg.de/nomad-lab/encyclopedia-general/wikis/M30%20review%20search%20and%20materials%20list)
https://gitlab.mpcdf.mpg.de/nomad-lab/encyclopedia-gui/-/issues/119QHA2018-06-16T08:14:51ZGeorg HuhsQHA# TODO
* Show data from QHA calculations (thermal properties details page)
:question: link to userimpatience-prototype
**Blocked** by the availability of data# TODO
* Show data from QHA calculations (thermal properties details page)
:question: link to userimpatience-prototype
**Blocked** by the availability of datahttps://gitlab.mpcdf.mpg.de/nomad-lab/encyclopedia-gui/-/issues/118New structure types and structure presentation review2018-06-16T08:02:47ZGeorg HuhsNew structure types and structure presentation reviewSurface and adsorbate systems will be added, which require also a general review of how structures are displayed, mainly in the structure details page.
[More info](https://gitlab.mpcdf.mpg.de/nomad-lab/encyclopedia-general/wikis/M36-ma...Surface and adsorbate systems will be added, which require also a general review of how structures are displayed, mainly in the structure details page.
[More info](https://gitlab.mpcdf.mpg.de/nomad-lab/encyclopedia-general/wikis/M36-material-definition-review)
**Blocked** by definition of the concept, data extension, actual datahttps://gitlab.mpcdf.mpg.de/nomad-lab/encyclopedia-gui/-/issues/117GW2018-06-16T07:58:13ZGeorg HuhsGW# ToDo
* Compare-mode for results in electronic structure page
* Reference/link to basic calculation
**Blocked** by calculation type review and full description of the concept# ToDo
* Compare-mode for results in electronic structure page
* Reference/link to basic calculation
**Blocked** by calculation type review and full description of the concepthttps://gitlab.mpcdf.mpg.de/nomad-lab/encyclopedia-gui/-/issues/116EoS extension2018-06-16T07:49:42ZGeorg HuhsEoS extension# ToDo
The two main changes for _Equation of state_ calculations:
* show a fit in the curve plus some additional information (see graph below)
* show as proper calculation type (treated in the calculation type review)
**blocked** by i...# ToDo
The two main changes for _Equation of state_ calculations:
* show a fit in the curve plus some additional information (see graph below)
* show as proper calculation type (treated in the calculation type review)
**blocked** by implementation of calculation type review and availability of the extra-data
# Details
## Fitting formula
![birch-murnaghan_formula.svg](/uploads/163807fe3c59c54586e8fad06a6ad84d/birch-murnaghan_formula.svg)
The parameters will be delivered by the API
## GUI-changes
![eos](/uploads/448b5311dac8aeb45f4e6aba9376648a/eos.png)https://gitlab.mpcdf.mpg.de/nomad-lab/encyclopedia-gui/-/issues/115calculation type2018-05-04T14:49:20ZGeorg Huhscalculation typeThe weirdly constructed `calculation type` will be replaced by the extended `run type`.
See [commit](https://gitlab.mpcdf.mpg.de/nomad-lab/encyclopedia-general/commit/429e192079e117b27272db9c8b71e0e6b5810809)
and [Wiki](https://gitlab...The weirdly constructed `calculation type` will be replaced by the extended `run type`.
See [commit](https://gitlab.mpcdf.mpg.de/nomad-lab/encyclopedia-general/commit/429e192079e117b27272db9c8b71e0e6b5810809)
and [Wiki](https://gitlab.mpcdf.mpg.de/nomad-lab/encyclopedia-general/wikis/M36-review-calculations)
This needs first the changes in the backend to be implemented.https://gitlab.mpcdf.mpg.de/nomad-lab/encyclopedia-gui/-/issues/113Infrastructure changes (API URLs and auth token) that require code update2018-04-19T10:28:51ZIker HurtadoInfrastructure changes (API URLs and auth token) that require code updateThe objective of this issue is to document the required client code update because of the two recent changes on the infrastructure:
- A new and long run auth token (default token - unauthenticated user)
- API domains/URLs changes for dif...The objective of this issue is to document the required client code update because of the two recent changes on the infrastructure:
- A new and long run auth token (default token - unauthenticated user)
- API domains/URLs changes for different environments
### New authentication token
This change has required two changes:
- The new token has been inserted manually in the production executable code (`bundle-es5.js`) (not recommendable practice, a temporary patch until the next deployment)
- The new token has been inserted in the developing code and it's been tested in stagging (it is still necessary to test it in production)
### API domains/URLs changes
These has required two changes:
- The new API domain/URL has been inserted manually in the production executable code (bundle-es5.js). The value of the API_HOST variable was changed from `encyclopedia-api.nomad-coe.eu` to `encyclopedia.nomad-coe.eu` and the API_BASE_URL is the API_HOST plus the `api/v1.0/` string now (`v1.0/` before)
- The API domains/URLs has been changed for all the cases (different environments) in the developing code and they've been tested in local dev and stagging environments (it is still necessary to test it in production)
In addition, it'd be good to take the opportunity to check if the configuration specified in the current code is right or it can be improved (@ivancea):
- Production server. API HOST: `https://encyclopedia.nomad-coe.eu/` API PATH: `api/v1.0/`
- Staging/local installations server. API HOST: `/` API PATH: `v1.0/`
As said above, **in the next production deployment we should be attentive and check that everything works fine** (as expected)https://gitlab.mpcdf.mpg.de/nomad-lab/encyclopedia-gui/-/issues/112PIDs as calculation IDs2018-06-16T08:22:18ZGeorg HuhsPIDs as calculation IDs# Todo
* [ ] Use PID as visible "name" for calculations
**Blocked** by:
* [ ] Only calculations with PIDs are in the DMSS
* [ ] Probably the definition of a new ID to be shown (calculations defined only in enc)
see also [calc ...# Todo
* [ ] Use PID as visible "name" for calculations
**Blocked** by:
* [ ] Only calculations with PIDs are in the DMSS
* [ ] Probably the definition of a new ID to be shown (calculations defined only in enc)
see also [calc type review](https://gitlab.mpcdf.mpg.de/nomad-lab/encyclopedia-general/wikis/M36-review-calculations)
https://gitlab.mpcdf.mpg.de/nomad-lab/encyclopedia-gui/-/issues/111DOS quantities (from API data) transformation for graphs2020-07-01T14:45:15ZIker HurtadoDOS quantities (from API data) transformation for graphsThis issue has been created to track the changes in the transformation of the DOS data (coming form the API) needed to be drawn on graphs properly. It's something (the changes) that's been happening all the time (different transformation...This issue has been created to track the changes in the transformation of the DOS data (coming form the API) needed to be drawn on graphs properly. It's something (the changes) that's been happening all the time (different transformations for different types of calculation) and has become a mess. This post will try to prevent that since now.
## General case:
* **Energy** (Y axis) = `dos_energies`/1.602176565e-19
* **DOS** (X axis) = `dos_values` * 1.602176565e-19
## Particular cases
### Staging based on production 1.11.6
The values for VASP, AIMS, and exciting are O(1e19), thus the general case should apply.
### Staging based on prod-032
This is meant as "intermediate" update until the latest production becomes usable.
#### AIMS
* Values are O(1)
* So this seems to be from the state where we were not sure about the relation to the cell volume
* For now: let's keep them as they are.
#### VASP
* Values are O(1e-49)
* For investigations see [wiki page](m36_dos_investigation_vasp), outcome: in prod-032 a transformation between A^3 and m^3 has been done, without considering the cell volume as it was at prod-028, thus
* Thus the transformation should be `dos_values` / (1.602176565e-19 * 1e-30)
#### exciting
* Values are O(1e-16)
* :new: Transformation `dos_values` / (1.602176565e-19 * (27.211^2))
* There is data for only 4 materials, all 2D
### Previous notes (most of 2018)
#### Code **AIMS** (**NOT IMPLEMENTED**)
Info from AIMS manual: "_The unit of output for the density of states is (eV · Vunit cell)^(−1), i.e., number of states per energy unit (eV) and unit cell volume._"
and it seems that the volume is given in A^3
Probably the Parser does not do the normalization to fulfill the metainfo definition
* **Energy** (Y axis) = `dos_energies`/1.602176565e-19
* **DOS** (X axis) = `dos_values` * cell_volume[A³] * 1e30 :question:
#### Code **VASP** (**NOT IMPLEMENTED**)
* **Energy** (Y axis) = `dos_energies`/1.602176565e-19
* **DOS** (X axis) = `dos_values`*(1.602176565E-19)^2****
https://gitlab.mpcdf.mpg.de/nomad-lab/encyclopedia-gui/-/issues/110License and make this project usable for others.2018-05-23T11:41:07ZMarkus ScheidgenLicense and make this project usable for others.Make this project usable for others:
1. comment and close this issue, if this project should **not** be part of NOMAD's open source software
2. apply a license: create a LICENSE file for the Apache 2.0 License ([LICENSE.txt](http://apach...Make this project usable for others:
1. comment and close this issue, if this project should **not** be part of NOMAD's open source software
2. apply a license: create a LICENSE file for the Apache 2.0 License ([LICENSE.txt](http://apache.org/licenses/LICENSE-2.0.txt))
3. document your code: create a README file
4. make your project available: set settings/general/permissions/public visibility to "Public"
5. close this issue if everything was done
You find more detailed information in our wiki [here](https://gitlab.mpcdf.mpg.de/nomad-lab/public-wiki/wikis/NOMAD-software-and-source-code-release).
If you have contributed to this project, please feel responsible.https://gitlab.mpcdf.mpg.de/nomad-lab/encyclopedia-gui/-/issues/103Bonds in structure viewer2018-01-18T14:05:15ZMartin KubanBonds in structure viewerThe bonds in the structure viewer sometimes exceed the possible number of bonds for an atom, e.g. Si with more than 4 bonds in clathrate compounds https://encyclopedia-gui.nomad-coe.eu/#/material/146293/structure:
![too_many_bonds_Si_cl...The bonds in the structure viewer sometimes exceed the possible number of bonds for an atom, e.g. Si with more than 4 bonds in clathrate compounds https://encyclopedia-gui.nomad-coe.eu/#/material/146293/structure:
![too_many_bonds_Si_clathrate_circle](/uploads/9a14000653c3949cc6499ee2daa62272/too_many_bonds_Si_clathrate_circle.png)https://gitlab.mpcdf.mpg.de/nomad-lab/encyclopedia-gui/-/issues/102Improve electronic structure details page2018-06-16T08:36:28ZGeorg HuhsImprove electronic structure details page**Problem**: All the electronic structure information we show is related to the original simulation cell. But the user sees in the structure category only the standardized cell.
**Suggested solution** (clarified with Claudia):
1. A tex...**Problem**: All the electronic structure information we show is related to the original simulation cell. But the user sees in the structure category only the standardized cell.
**Suggested solution** (clarified with Claudia):
1. A text informs the user that the data comes from the original simulation cell.
2. The structure of the simulation cell can be shown on demand (directly in the electronic structure page).
As the latter is a larger effort, we could at least implement the first temporarily.
**Needs concept, design, and text to show**https://gitlab.mpcdf.mpg.de/nomad-lab/encyclopedia-gui/-/issues/99Structure viewer: axis labels "in" atoms2022-12-16T11:13:31ZGeorg HuhsStructure viewer: axis labels "in" atomsIn cases where atoms sit in the middle of the cell edges, the axis label is printed like "in" the atom. It is readable, but not ideal.In cases where atoms sit in the middle of the cell edges, the axis label is printed like "in" the atom. It is readable, but not ideal.