Skip to content

Commit

Permalink
add upload file
Browse files Browse the repository at this point in the history
  • Loading branch information
mori0711 committed Nov 5, 2019
1 parent 6c20e30 commit b0a017d
Show file tree
Hide file tree
Showing 2 changed files with 15 additions and 5 deletions.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
20 changes: 15 additions & 5 deletions docs/usage/make_molecular_parameter/upload_file.rst
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ Users push the following image in PolyParGen front page.
| :align: center |
+--------------------------------------------------------------------------+

At first, users have to registrate their information to use PolyParGen.
Step1, users have to registrate their information to use PolyParGen.
E-mail address certainly is needed in user's informaiton, because PolyParGen sends that parameter file to user's e-mail after generation of molecular parameter.
The users, which already registrated, pass this step.

Expand All @@ -27,28 +27,38 @@ The users, which already registrated, pass this step.
| :align: center |
+--------------------------------------------------------------------------+

| Next, users upload the molecule file from the following buttom.
Step2, users upload the molecule file from the following buttom.

+--------------------------------------------------------------------------+
| .. image:: ./imgs/upload_file_004.png |
| :scale: 70 % |
| :align: center |
+--------------------------------------------------------------------------+

|
.. note::

The uploaded file format, which we recommend, is `CML file format <https://en.wikipedia.org/wiki/Chemical_Markup_Language>`_ ,
because CML file format has more detail for each bond infromation.
CML file can be generated by `Avogadro <https://avogadro.cc/>`_ or `Open Babel <http://openbabel.org/wiki/Main_Page>`_ .



.. warning::

- The current version can not apply for cation and anion molecule.
- Users have to add hydrogens atom for molecules without hydrogenation.
- Users have to add hydrogen atoms for molecules which are made without hydrogenation.
- 1 file have to set absolutely 1 molecule without solvent.


Step3, users select PolyParGen version, a kind of parameter and atomic charge.
- Select PolyParGen version
In the case of simple linear polymer, users select v1 because v1 faster than v2.
However, we recomended users select v2.

+--------------------------------------------------------------------------+
| .. image:: ./imgs/upload_file_005.png |
| :scale: 70 % |
| :align: center |
+--------------------------------------------------------------------------+



0 comments on commit b0a017d

Please sign in to comment.