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Added GROMACS and Amber packages
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moisesalvarez committed Feb 2, 2022
1 parent 5c87165 commit 9db6fad
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Showing 468 changed files with 16,696 additions and 3,790 deletions.
16 changes: 10 additions & 6 deletions codes/adf/adf-d3e1030.rst
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Expand Up @@ -20,9 +20,9 @@ adf
+----------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------------------------------------------------------------+
| Type | Status |
+============================================================================================================================+============================================================================================================================+
| CML extraction template | |image0| |
| CML extraction template | |image1| |
+----------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------------------------------------------------------------+
| HTML5 representation | |image1| |
| HTML5 representation | |image2| |
+----------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------------------------------------------------------------+

.. table:: Template attributes
Expand All @@ -49,7 +49,9 @@ adf
| xml:base | adf/adf.xml |
+----------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------------------------------------------------------------+

**Comment.**
.. container:: formalpara-title

**Comment**

::

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A D F E X I T

**Template definition.**
.. container:: formalpara-title

**Template definition**

.. code:: xml
<templateList> <xi:include href="adf/../program.header.xml" /> <xi:include href="adf/init/modelparameters/model.parameters.xml" /> <xi:include href="adf/runtype/runtype.xml" /> <xi:include href="adf/build/build_fragments.xml" /> <xi:include href="adf/technical/technical.xml" /> <xi:include href="adf/computation/computation.xml" /> <xi:include href="adf/results/results.xml" /> <xi:include href="adf/frequencyanalysis/frequencyanalysis.xml" />
</templateList>
.. |image0| image:: ../../imgs/Total.png
.. |image1| image:: ../../imgs/None.png
.. |image1| image:: ../../imgs/Total.png
.. |image2| image:: ../../imgs/None.png
16 changes: 10 additions & 6 deletions codes/adf/adf.build-d3e2260.rst
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Expand Up @@ -8,9 +8,9 @@ adf.build
+----------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------------------------------------------------------------+
| Type | Status |
+============================================================================================================================+============================================================================================================================+
| CML extraction template | |image0| |
| CML extraction template | |image1| |
+----------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------------------------------------------------------------+
| HTML5 representation | |image1| |
| HTML5 representation | |image2| |
+----------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------------------------------------------------------------+

.. table:: Template attributes
Expand All @@ -35,7 +35,9 @@ adf.build
| xml:base | adf/build/build_fragments.xml |
+----------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------------------------------------------------------------+

**Comment.**
.. container:: formalpara-title

**Comment**

::

Expand All @@ -57,12 +59,14 @@ adf.build

**Template definition.**
.. container:: formalpara-title

**Template definition**

.. code:: xml
<xi:include href="build/scanfreq.xml" />
<xi:include href="build/../frequencyanalysis/thermochemistry.xml" />
.. |image0| image:: ../../imgs/Total.png
.. |image1| image:: ../../imgs/None.png
.. |image1| image:: ../../imgs/Total.png
.. |image2| image:: ../../imgs/None.png
16 changes: 10 additions & 6 deletions codes/adf/adf.computation-d3e2502.rst
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Expand Up @@ -14,9 +14,9 @@ adf.computation
+----------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------------------------------------------------------------+
| Type | Status |
+============================================================================================================================+============================================================================================================================+
| CML extraction template | |image0| |
| CML extraction template | |image1| |
+----------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------------------------------------------------------------+
| HTML5 representation | |image1| |
| HTML5 representation | |image2| |
+----------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------------------------------------------------------------+

.. table:: Template attributes
Expand All @@ -41,7 +41,9 @@ adf.computation
| xml:base | adf/computation/computation.xml |
+----------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------------------------------------------------------------+

**Comment.**
.. container:: formalpara-title

**Comment**

::

Expand All @@ -68,12 +70,14 @@ adf.computation

**Template definition.**
.. container:: formalpara-title

**Template definition**

.. code:: xml
<templateList> <xi:include href="computation/scf.xml" /> <xi:include href="computation/geometry.cycle.xml" />
</templateList>
.. |image0| image:: ../../imgs/Total.png
.. |image1| image:: ../../imgs/None.png
.. |image1| image:: ../../imgs/Total.png
.. |image2| image:: ../../imgs/None.png
14 changes: 9 additions & 5 deletions codes/adf/adf.frequencyanalysis-d3e4488.rst
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Expand Up @@ -17,9 +17,9 @@ adf.frequencyanalysis
+----------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------------------------------------------------------------+
| Type | Status |
+============================================================================================================================+============================================================================================================================+
| CML extraction template | |image0| |
| CML extraction template | |image1| |
+----------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------------------------------------------------------------+
| HTML5 representation | |image1| |
| HTML5 representation | |image2| |
+----------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------------------------------------------------------------+

.. table:: Template attributes
Expand All @@ -46,7 +46,9 @@ adf.frequencyanalysis
| xml:base | adf/frequencyanalysis/frequencyanalysis.xml |
+----------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------------------------------------------------------------+

**Comment.**
.. container:: formalpara-title

**Comment**

::

Expand Down Expand Up @@ -116,12 +118,14 @@ adf.frequencyanalysis

**Template definition.**
.. container:: formalpara-title

**Template definition**

.. code:: xml
<templateList> <xi:include href="frequencyanalysis/masses.xml" /> <xi:include href="frequencyanalysis/zeropoint.xml" /> <xi:include href="frequencyanalysis/vibrations.xml" /> <xi:include href="frequencyanalysis/intensities.xml" /> <xi:include href="frequencyanalysis/thermochemistry.xml" />
</templateList>
.. |image0| image:: ../../imgs/Total.png
.. |image1| image:: ../../imgs/Total.png
.. |image2| image:: ../../imgs/Total.png
16 changes: 10 additions & 6 deletions codes/adf/adf.results-d3e2979.rst
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Expand Up @@ -24,9 +24,9 @@ adf.results
+----------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------------------------------------------------------------+
| Type | Status |
+============================================================================================================================+============================================================================================================================+
| CML extraction template | |image0| |
| CML extraction template | |image1| |
+----------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------------------------------------------------------------+
| HTML5 representation | |image1| |
| HTML5 representation | |image2| |
+----------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------------------------------------------------------------+

.. table:: Template attributes
Expand Down Expand Up @@ -55,7 +55,9 @@ adf.results
| xml:base | adf/results/results.xml |
+----------------------------------------------------------------------------------------------------------------------------+----------------------------------------------------------------------------------------------------------------------------+

**Comment.**
.. container:: formalpara-title

**Comment**

::

Expand Down Expand Up @@ -118,12 +120,14 @@ adf.results
***************************************************************************************************

**Template definition.**
.. container:: formalpara-title

**Template definition**

.. code:: xml
<templateList> <xi:include href="results/orbital.energies.spin.zora.xml" /> <xi:include href="results/orbital.energies.zora.xml" /> <xi:include href="results/orbital.energies.xml" /> <xi:include href="results/orbital.energies.spin.xml" /> <xi:include href="results/fit.test.xml" /> <xi:include href="results/mulliken.xml" /> <xi:include href="results/multipole/multipole.xml" /> <xi:include href="results/quadrupole.moment.xml" /> <xi:include href="results/s2.xml" /> <xi:include href="results/bonding.energy.xml" /> <xi:include href="results/sfopopulation/sfo.population.xml" /> <xi:include href="results/excitationenergy/excitation.energy.xml" />
</templateList>
.. |image0| image:: ../../imgs/Total.png
.. |image1| image:: ../../imgs/None.png
.. |image1| image:: ../../imgs/Total.png
.. |image2| image:: ../../imgs/None.png

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