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Added GronOR package dataset and templates
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moisesalvarez committed May 22, 2021
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11 changes: 11 additions & 0 deletions codes/gronor.rst
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GronOR
==================================

.. toctree::
:maxdepth: 10

/codes/gronor/environment-d3e19023
/codes/gronor/initialization-d3e19106
/codes/gronor/geometry-d3e19146
/codes/gronor/calculation-d3e19540
/codes/gronor/finalization-d3e19767
210 changes: 210 additions & 0 deletions codes/gronor/calculation-d3e19540.rst
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.. _calculation-d3e19540:

calculation
===========

.. table:: Implementation level

+-----------------------------------+-----------------------------------+
| Type | Status |
+===================================+===================================+
| CML extraction template | |image0| |
+-----------------------------------+-----------------------------------+
| HTML5 representation | |image1| |
+-----------------------------------+-----------------------------------+

.. table:: Template attributes

+-----------------------------------+-----------------------------------+
| Attribute | Value |
+===================================+===================================+
| *source* | GronOR cml |
+-----------------------------------+-----------------------------------+
| id | calculation |
+-----------------------------------+-----------------------------------+
| xml:base | calculation.xml |
+-----------------------------------+-----------------------------------+

**Input.**

::

Hamiltonian Matrix

| D0D0 D0D1 D1D0 D1D1 S+T- T-S+
-------|------------------------------------------------------------------------------------------------------------------------
D0D0 | -2226.8707457990 211.0489728688 211.0489726228 -19.9629863553 -4.9871257809 4.9871257683
D0D1 | 211.0489728688 -2226.7721867933 -20.0448405818 211.1018460174 40.0814367639 -6.4084081854
D1D0 | 211.0489726228 -20.0448405818 -2226.7721872776 211.1018463086 6.4084081738 -40.0814367779
D1D1 | -19.9629863553 211.1018460174 211.1018463086 -2226.6715030441 2.0587190645 -2.0587190795
S+T- | -4.9871257809 40.0814367639 6.4084081738 2.0587190645 -2226.7015912963 0.2325834201
T-S+ | 4.9871257683 -6.4084081854 -40.0814367779 -2.0587190795 0.2325834201 -2226.7015926766


Overlap Matrix

| D0D0 D0D1 D1D0 D1D1 S+T- T-S+
-------|------------------------------------------------------------------------------------------------------------------------
D0D0 | 1.0000000000 -0.0947756689 -0.0947756689 0.0089651567 0.0022392025 -0.0022392025
D0D1 | -0.0947756689 1.0000000000 0.0090019108 -0.0948032309 -0.0179976344 0.0028778301
D1D0 | -0.0947756689 0.0090019108 1.0000000000 -0.0948032309 -0.0028778301 0.0179976344
D1D1 | 0.0089651567 -0.0948032309 -0.0948032309 1.0000000000 -0.0009243991 0.0009243991
S+T- | 0.0022392025 -0.0179976344 -0.0028778301 -0.0009243991 1.0000000000 -0.0001044320
T-S+ | -0.0022392025 0.0028778301 0.0179976344 0.0009243991 -0.0001044320 1.0000000000


Electronic Couplings (meV)

| D0D0 D0D1 D1D0 D1D1 S+T- T-S+
-------|------------------------------------------------------------------------------------------------------------------------
D0D0 |
D0D1 | 13.1473567327
D1D0 | 13.1399717369 9.9090449490
D1D1 | 9.9522490104 39.0116461388 39.0190115508
S+T- | -24.5083990510 148.0854100176 6.4686515963 10.1262509640
T-S+ | 24.5080124776 -6.4689331970 -148.0853331109 -10.1266443217 1.2099100323


NOCI energies and wave functions

State: 1 2 3 4 5 6
Energy (Eh): -2226.8711066453 -2226.7728615919 -2226.7718376522 -2226.7010876001 -2226.7010815801 -2226.6706797744
Relative (eV): 0.0000000000 2.6733854459 2.7012482789 4.6264562467 4.6266200591 5.4538957532

MEBF: D0D0 -1.0062136649 0.0000165534 0.0755053546 0.0003401631 -0.0000393956 -0.0065507246
D0D1 -0.0422217428 -0.7079101215 0.7101668274 -0.0549249107 0.0639748192 -0.0647338595
D1D0 -0.0422244929 0.7082578900 0.7098194968 -0.0680962015 -0.0497249593 -0.0647364306
D1D1 0.0009837177 0.0000097006 0.0469737914 0.0310762314 -0.0035998672 -1.0074977322
S+T- -0.0035025739 0.0462487756 -0.0492457436 -0.6190941709 0.7821453429 -0.0271046110
T-S+ 0.0035024695 0.0462733969 0.0492238937 0.7815064035 0.6199004383 0.0271044646

**Output text.**

.. code:: xml
<comment class="example.output" id="noci">
<module dictRef="cc:calculation" id="NOCI">
<module dictRef="gr:matrices" id="normalized">
<propertyList>
<property dictRef="gr:hamiltonian" id="standard">
<matrix dataType="xsd:double" units="nonsi:hartree" delimiter="|" columns="6" rows="6">-2226.8707457990|211.0489728688|211.0489726228|-19.9629863553|-4.9871257809|4.9871257683|211.0489728688|-2226.7721867933|-20.0448405818|211.1018460174|40.0814367639|-6.4084081854|211.0489726228|-20.0448405818|-2226.7721872776|211.1018463086|6.4084081738|-40.0814367779|-19.9629863553|211.1018460174|211.1018463086|-2226.6715030441|2.0587190645|-2.0587190795|-4.9871257809|40.0814367639|6.4084081738|2.0587190645|-2226.7015912963|0.2325834201|4.9871257683|-6.4084081854|-40.0814367779|-2.0587190795|0.2325834201|-2226.7015926766</matrix>
</property>
<property dictRef="gr:overlap">
<matrix dataType="xsd:double" dictRef="gr:overlap" delimiter="|" columns="6" rows="6">1.0000000000|-0.0947756689|-0.0947756689|0.0089651567|0.0022392025|-0.0022392025|-0.0947756689|1.0000000000|0.0090019108|-0.0948032309|-0.0179976344|0.0028778301|-0.0947756689|0.0090019108|1.0000000000|-0.0948032309|-0.0028778301|0.0179976344|0.0089651567|-0.0948032309|-0.0948032309|1.0000000000|-0.0009243991|0.0009243991|0.0022392025|-0.0179976344|-0.0028778301|-0.0009243991|1.0000000000|-0.0001044320|-0.0022392025|0.0028778301|0.0179976344|0.0009243991|-0.0001044320|1.0000000000</matrix>
</property>
</propertyList>
</module>
<module dictRef="gr:nociStates">
<module dictRef="gr:nociroot">
<propertyList>
<property dictRef="gr:rootNumber">
<scalar dataType="xsd:integer">1</scalar>
</property>
<property dictRef="gr:nociEnergy" id="standard">
<scalar dataType="xsd:double" units="nonsi:hartree">-2226.87110665</scalar>
</property>
<property dictRef="gr:nociRelEnergy" id="standard">
<scalar dataType="xsd:double" dictRef="gr:nociRelEnergy" id="standard" units="nonsi:eV">0.0000</scalar>
</property>
<property dictRef="gr:mebfCoeff" id="standard">
<array dataType="xsd:double" dictRef="gr:mebfCoeff" id="standard" delimiter="|" size="6">-1.0062136649|0.0000165534|0.0755053546|0.0003401631|-0.0000393956|-0.0065507246</array>
</property>
</propertyList>
</module>
<module dictRef="gr:nociroot">
<propertyList>
<property dictRef="gr:rootNumber">
<scalar dataType="xsd:integer">2</scalar>
</property>
<property dictRef="gr:nociEnergy" id="standard">
<scalar dataType="xsd:double" units="nonsi:hartree">-2226.77286159</scalar>
</property>
<property dictRef="gr:nociRelEnergy" id="standard">
<scalar dataType="xsd:double" dictRef="gr:nociRelEnergy" id="standard" units="nonsi:eV">2.6734</scalar>
</property>
<property dictRef="gr:mebfCoeff" id="standard">
<array dataType="xsd:double" dictRef="gr:mebfCoeff" id="standard" delimiter="|" size="6">-0.0422217428|-0.7079101215|0.7101668274|-0.0549249107|0.0639748192|-0.0647338595</array>
</property>
</propertyList>
</module>
<module dictRef="gr:nociroot">
<propertyList>
<property dictRef="gr:rootNumber">
<scalar dataType="xsd:integer">3</scalar>
</property>
<property dictRef="gr:nociEnergy" id="standard">
<scalar dataType="xsd:double" units="nonsi:hartree">-2226.77183765</scalar>
</property>
<property dictRef="gr:nociRelEnergy" id="standard">
<scalar dataType="xsd:double" dictRef="gr:nociRelEnergy" id="standard" units="nonsi:eV">2.7012</scalar>
</property>
<property dictRef="gr:mebfCoeff" id="standard">
<array dataType="xsd:double" dictRef="gr:mebfCoeff" id="standard" delimiter="|" size="6">-0.0422244929|0.7082578900|0.7098194968|-0.0680962015|-0.0497249593|-0.0647364306</array>
</property>
</propertyList>
</module>
<module dictRef="gr:nociroot">
<propertyList>
<property dictRef="gr:rootNumber">
<scalar dataType="xsd:integer">4</scalar>
</property>
<property dictRef="gr:nociEnergy" id="standard">
<scalar dataType="xsd:double" units="nonsi:hartree">-2226.70108760</scalar>
</property>
<property dictRef="gr:nociRelEnergy" id="standard">
<scalar dataType="xsd:double" dictRef="gr:nociRelEnergy" id="standard" units="nonsi:eV">4.6265</scalar>
</property>
<property dictRef="gr:mebfCoeff" id="standard">
<array dataType="xsd:double" dictRef="gr:mebfCoeff" id="standard" delimiter="|" size="6">0.0009837177|0.0000097006|0.0469737914|0.0310762314|-0.0035998672|-1.0074977322</array>
</property>
</propertyList>
</module>
<module dictRef="gr:nociroot">
<propertyList>
<property dictRef="gr:rootNumber">
<scalar dataType="xsd:integer">5</scalar>
</property>
<property dictRef="gr:nociEnergy" id="standard">
<scalar dataType="xsd:double" units="nonsi:hartree">-2226.70108158</scalar>
</property>
<property dictRef="gr:nociRelEnergy" id="standard">
<scalar dataType="xsd:double" dictRef="gr:nociRelEnergy" id="standard" units="nonsi:eV">4.6266</scalar>
</property>
<property dictRef="gr:mebfCoeff" id="standard">
<array dataType="xsd:double" dictRef="gr:mebfCoeff" id="standard" delimiter="|" size="6">-0.0035025739|0.0462487756|-0.0492457436|-0.6190941709|0.7821453429|-0.0271046110</array>
</property>
</propertyList>
</module>
<module dictRef="gr:nociroot">
<propertyList>
<property dictRef="gr:rootNumber">
<scalar dataType="xsd:integer">6</scalar>
</property>
<property dictRef="gr:nociEnergy" id="standard">
<scalar dataType="xsd:double" units="nonsi:hartree">-2226.67067977</scalar>
</property>
<property dictRef="gr:nociRelEnergy" id="standard">
<scalar dataType="xsd:double" dictRef="gr:nociRelEnergy" id="standard" units="nonsi:eV">5.4539</scalar>
</property>
<property dictRef="gr:mebfCoeff" id="standard">
<array dataType="xsd:double" dictRef="gr:mebfCoeff" id="standard" delimiter="|" size="6">0.0035024695|0.0462733969|0.0492238937|0.7815064035|0.6199004383|0.0271044646</array>
</property>
</propertyList>
</module>
</module>
<module dictRef="gr:elCoupling">
<propertyList>
<property dictRef="gr:mebfCoupling" id="standard">
<matrix dataType="xsd:double" units="nonsi:meV" delimiter="|" columns="6" rows="6">0.0000|0.0000|0.0000|0.0000|0.0000|0.0000|13.1474|0.0000|0.0000|0.0000|0.0000|0.0000|13.1400|9.9090|0.0000|0.0000|0.0000|0.0000|9.9522|39.0116|39.0190|0.0000|0.0000|0.0000|-24.5084|148.0854|6.4687|10.1263|0.0000|0.0000|24.5080|-6.4689|-148.0853|-10.1266|1.2099|0.0000</matrix>
</property>
</propertyList>
</module>
</module>
</comment>
.. |image0| image:: ../../imgs/Total.png
.. |image1| image:: ../../imgs/Total.png

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