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updated from deprecated sphinx-panel package to sphinx-design package (…
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…#108)

updated from sphinx-panel to sphinx-design for fixing tabs
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@gorges97
gorges97 committed Sep 29, 2023
1 parent 81b5e25 commit 12549f0
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5 changes: 4 additions & 1 deletion README.rst
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Expand Up @@ -58,11 +58,14 @@ Contributors
* Eike Caldeweyher
* Sebastian Dohm
* Sebastian Ehlert
* Johannes Gorges
* Abylay Katbashev
* Jeroen Koopman
* Julia Kohn
* Hagen Neugebauer
* Christoph Plett
* Philipp Pracht
* Karola Schmitz
* Sarah Schmitz
* Jakob Seibert
* Sebastian Spicher
* Johannes Gorges
2 changes: 1 addition & 1 deletion env.yml
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Expand Up @@ -4,7 +4,7 @@ channels:
dependencies:
- python
- sphinx
- sphinx-panels
- sphinx-design
- sphinx-togglebutton
- sphinx-copybutton
- sphinx_rtd_theme
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1,729 changes: 867 additions & 862 deletions source/CENSO_docs/censo_nmr.rst
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1,367 changes: 690 additions & 677 deletions source/CENSO_docs/censo_setup.rst
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7 changes: 4 additions & 3 deletions source/CENSO_docs/censo_solvation.rst
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Expand Up @@ -7,14 +7,15 @@ CENSO uses several QM-packages and not all solvents are available for all solvat
models throughout the QM-codes. For this reason a user editable file is created
in the folder *~/.censo_assets*:

.. tabbed:: -->
.. tab-set::

.. tab-item::
.. code:: sh
$ ~/.censo_assets/censo_solvents.json
.. tabbed:: censo_solvents.json

.. tab-item:: censo_solvents.json
.. code:: sh
{
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19,575 changes: 9,784 additions & 9,791 deletions source/CENSO_docs/censo_usage.rst
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2 changes: 1 addition & 1 deletion source/conf.py
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Expand Up @@ -32,7 +32,7 @@
# ones.
extensions = [
"ablog",
"sphinx_panels",
"sphinx_design",
"sphinx_copybutton",
"sphinx_togglebutton",
]
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270 changes: 136 additions & 134 deletions source/dipro.rst
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Expand Up @@ -88,143 +88,145 @@ This is a very simple example of a cofacial NCI complex of benzene and nitrobenz

.. figure:: ../figures/dipro.png

.. tabbed:: cml input
.. tab-set::

.. code-block:: none
.. tab-item:: cml input

.. code-block:: none
> xtb coord.xyz --dipro --gfn 1
.. tabbed:: input.xyz

.. code-block:: none
26
C -1.20618 0.69599 1.75211
C -1.20379 -0.70017 1.75215
C 0.00616 -1.39690 1.75210
C 1.21824 -0.70002 1.75171
C 1.23033 0.70989 1.75117
C 0.00125 1.40067 1.75172
H 2.14504 -1.25925 1.74975
H -0.02278 2.48280 1.74976
H -2.14520 1.23405 1.75041
H -2.14028 -1.24255 1.75044
H 0.00554 -2.47919 1.75040
C -1.21072 0.69984 -1.75114
C -1.21074 -0.69902 -1.75149
C 0.00072 -1.39843 -1.75114
C 1.21220 -0.69897 -1.75037
C 1.21222 0.69988 -1.74995
C 0.00077 1.39929 -1.75036
H 2.14941 -1.24008 -1.74839
H 2.14945 1.24099 -1.74755
H 0.00077 2.48148 -1.74837
H -2.14799 1.24091 -1.74971
H -2.14800 -1.24014 -1.75028
H 0.00066 -2.48066 -1.74972
N 2.46723 1.42685 1.74737
O 2.47280 2.62117 1.74468
O 3.50640 0.83800 1.74471
.. tabbed:: output

.. code-block:: none
-------------------------------------------------
| D I P R O |
-------------------------------------------------
Calculation for dimer
---------------------
.
.
.
Found 2 fragments!
Fragment 1: 1-11, 24-26
Fragment 2: 12-23
Calculation for fragment 1
------------------------------
charge of fragment : 0
unpaired e- of fragment : 0
.
.
.
Calculation for fragment 2
------------------------------
charge of fragment : 0
unpaired e- of fragment : 0
.
.
.
::::::::::::::::::::::::::::::::::::::::::::::
:: D I P R O C O U P L I N G S ::
::::::::::::::::::::::::::::::::::::::::::::::
energy threshhold for near-degenerate orbitals near HOMO and LUMO considered for DIPRO: 0.100 eV
no. of orbitals within energy window of frag 1 2
no. of orbitals within energy window of frag 2 4
Fragment 1 HOMO Fragment 2 HOMO-1
--------------------------------------
E_mon(orb) frag1 frag2 -12.966 -12.094 eV
|J(AB)|: 0.001 eV
S(AB): 0.00002581 Eh
|J(AB,eff)|: 0.000 eV
Fragment 1 HOMO Fragment 2 HOMO
--------------------------------------
E_mon(orb) frag1 frag2 -12.966 -12.099 eV
|J(AB)|: 0.238 eV
S(AB): -0.00998928 Eh
|J(AB,eff)|: 0.113 eV
Fragment 1 HOMO Fragment 2 LUMO
--------------------------------------
E_mon(orb) frag1 frag2 -12.966 -7.366 eV
|J(AB)|: 0.002 eV
S(AB): -0.00009192 Eh
|J(AB,eff)|: 0.001 eV
Fragment 1 HOMO Fragment 2 LUMO+1
-------------------------------------
E_mon(orb) frag1 frag2 -12.966 -7.361 eV
|J(AB)|: 0.000 eV
S(AB): 0.00001124 Eh
|J(AB,eff)|: 0.000 eV
Fragment 1 LUMO Fragment 2 HOMO-1
--------------------------------------
E_mon(orb) frag1 frag2 -9.417 -12.094 eV
|J(AB)|: 0.035 eV
S(AB): -0.00153946 Eh
|J(AB,eff)|: 0.019 eV
.
.
.
..............................................................................
: total |J(AB,eff)| for hole transport (occ. MOs) : 0.113 eV :
: total |J(AB,eff)| for charge transport (unocc. MOs) : 0.062 eV :
: total |J(AB,eff)| for charge transfer (CT) : 0.019 eV :
..............................................................................
Please remember, DIPRO is not available for restart!
normal termination of dipro
----------------------------------------------------------
* finished run on 2023/08/25 at 16:43:22.737
----------------------------------------------------------
dipro:
* wall-time: 0 d, 0 h, 0 min, 0.084 sec
* cpu-time: 0 d, 0 h, 0 min, 0.337 sec
* ratio c/w: 3.996 speedup
> xtb coord.xyz --dipro --gfn 1
.. tab-item:: input.xyz

.. code-block:: none
26
C -1.20618 0.69599 1.75211
C -1.20379 -0.70017 1.75215
C 0.00616 -1.39690 1.75210
C 1.21824 -0.70002 1.75171
C 1.23033 0.70989 1.75117
C 0.00125 1.40067 1.75172
H 2.14504 -1.25925 1.74975
H -0.02278 2.48280 1.74976
H -2.14520 1.23405 1.75041
H -2.14028 -1.24255 1.75044
H 0.00554 -2.47919 1.75040
C -1.21072 0.69984 -1.75114
C -1.21074 -0.69902 -1.75149
C 0.00072 -1.39843 -1.75114
C 1.21220 -0.69897 -1.75037
C 1.21222 0.69988 -1.74995
C 0.00077 1.39929 -1.75036
H 2.14941 -1.24008 -1.74839
H 2.14945 1.24099 -1.74755
H 0.00077 2.48148 -1.74837
H -2.14799 1.24091 -1.74971
H -2.14800 -1.24014 -1.75028
H 0.00066 -2.48066 -1.74972
N 2.46723 1.42685 1.74737
O 2.47280 2.62117 1.74468
O 3.50640 0.83800 1.74471
.. tab-item:: output

.. code-block:: none
-------------------------------------------------
| D I P R O |
-------------------------------------------------
Calculation for dimer
---------------------
.
.
.
Found 2 fragments!
Fragment 1: 1-11, 24-26
Fragment 2: 12-23
Calculation for fragment 1
------------------------------
charge of fragment : 0
unpaired e- of fragment : 0
.
.
.
Calculation for fragment 2
------------------------------
charge of fragment : 0
unpaired e- of fragment : 0
.
.
.
::::::::::::::::::::::::::::::::::::::::::::::
:: D I P R O C O U P L I N G S ::
::::::::::::::::::::::::::::::::::::::::::::::
energy threshhold for near-degenerate orbitals near HOMO and LUMO considered for DIPRO: 0.100 eV
no. of orbitals within energy window of frag 1 2
no. of orbitals within energy window of frag 2 4
Fragment 1 HOMO Fragment 2 HOMO-1
--------------------------------------
E_mon(orb) frag1 frag2 -12.966 -12.094 eV
|J(AB)|: 0.001 eV
S(AB): 0.00002581 Eh
|J(AB,eff)|: 0.000 eV
Fragment 1 HOMO Fragment 2 HOMO
--------------------------------------
E_mon(orb) frag1 frag2 -12.966 -12.099 eV
|J(AB)|: 0.238 eV
S(AB): -0.00998928 Eh
|J(AB,eff)|: 0.113 eV
Fragment 1 HOMO Fragment 2 LUMO
--------------------------------------
E_mon(orb) frag1 frag2 -12.966 -7.366 eV
|J(AB)|: 0.002 eV
S(AB): -0.00009192 Eh
|J(AB,eff)|: 0.001 eV
Fragment 1 HOMO Fragment 2 LUMO+1
-------------------------------------
E_mon(orb) frag1 frag2 -12.966 -7.361 eV
|J(AB)|: 0.000 eV
S(AB): 0.00001124 Eh
|J(AB,eff)|: 0.000 eV
Fragment 1 LUMO Fragment 2 HOMO-1
--------------------------------------
E_mon(orb) frag1 frag2 -9.417 -12.094 eV
|J(AB)|: 0.035 eV
S(AB): -0.00153946 Eh
|J(AB,eff)|: 0.019 eV
.
.
.
..............................................................................
: total |J(AB,eff)| for hole transport (occ. MOs) : 0.113 eV :
: total |J(AB,eff)| for charge transport (unocc. MOs) : 0.062 eV :
: total |J(AB,eff)| for charge transfer (CT) : 0.019 eV :
..............................................................................
Please remember, DIPRO is not available for restart!
normal termination of dipro
----------------------------------------------------------
* finished run on 2023/08/25 at 16:43:22.737
----------------------------------------------------------
dipro:
* wall-time: 0 d, 0 h, 0 min, 0.084 sec
* cpu-time: 0 d, 0 h, 0 min, 0.337 sec
* ratio c/w: 3.996 speedup
DIPRO first performs a singlepoint calculation on the complex and yields the fragmentation of your input coordinates. Then, two singlepoint calculations on the fragments structures are performed. The DIPRO output lists which orbitals from the couplings fragments were considered for the coupling calculations, e.g. the HOMO from fragment 1 (here nitrobenzene) and the HOMO-1 from fragment 2 (here benzene), and their corresponding energies. The most important parts are the results for the coupling integrals |J(AB)| and |J(AB,eff)|. Furthermore, a total coupling averaged over the square sum of all individual couplings is printed.

.. math::
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