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Added YouTube videos, refactored templates
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@moisesalvarez
moisesalvarez committed Feb 21, 2020
1 parent fbd5c45 commit e67d1a8
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1 change: 0 additions & 1 deletion README.md
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2 changes: 1 addition & 1 deletion codes/adf/adf-d3e850.rst
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Expand Up @@ -123,7 +123,7 @@ adf

.. code:: xml
<templateList> <xi:include href="../program.header.xml" /> <xi:include href="init/modelparameters/model.parameters.xml" /> <xi:include href="runtype/runtype.xml" /> <xi:include href="build/build_fragments.xml" /> <xi:include href="technical/technical.xml" /> <xi:include href="computation/computation.xml" /> <xi:include href="results/results.xml" /> <xi:include href="frequencyanalysis/frequencyanalysis.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
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2 changes: 1 addition & 1 deletion codes/adf/adf.build-d3e1991.rst
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Expand Up @@ -34,7 +34,7 @@ adf.build
+-----------------------------------+-----------------------------------+
| endOffset | 2 |
+-----------------------------------+-----------------------------------+
| xml:base | build/build_fragments.xml |
| xml:base | adf/build/build_fragments.xml |
+-----------------------------------+-----------------------------------+

**Comment.**
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4 changes: 2 additions & 2 deletions codes/adf/adf.computation-d3e2003.rst
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Expand Up @@ -40,7 +40,7 @@ adf.computation
+-----------------------------------+-----------------------------------+
| repeat | \* |
+-----------------------------------+-----------------------------------+
| xml:base | computation/computation.xml |
| xml:base | adf/computation/computation.xml |
+-----------------------------------+-----------------------------------+

**Comment.**
Expand Down Expand Up @@ -74,7 +74,7 @@ adf.computation

.. code:: xml
<templateList> <xi:include href="scf.xml" /> <xi:include href="geometry.cycle.xml" />
<templateList> <xi:include href="computation/scf.xml" /> <xi:include href="computation/geometry.cycle.xml" />
</templateList>
.. |image0| image:: ../../imgs/Total.png
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4 changes: 2 additions & 2 deletions codes/adf/adf.frequencyanalysis-d3e3989.rst
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Expand Up @@ -44,7 +44,7 @@ adf.frequencyanalysis
+-----------------------------------+-----------------------------------+
| repeat | \* |
+-----------------------------------+-----------------------------------+
| xml:base | freque |
| xml:base | adf/freque |
| | ncyanalysis/frequencyanalysis.xml |
+-----------------------------------+-----------------------------------+

Expand Down Expand Up @@ -122,7 +122,7 @@ adf.frequencyanalysis

.. code:: xml
<templateList> <xi:include href="zeropoint.xml" /> <xi:include href="vibrations.xml" /> <xi:include href="intensities.xml" /> <xi:include href="thermochemistry.xml" />
<templateList> <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
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4 changes: 2 additions & 2 deletions codes/adf/adf.results-d3e2480.rst
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Expand Up @@ -50,7 +50,7 @@ adf.results
+-----------------------------------+-----------------------------------+
| repeat | \* |
+-----------------------------------+-----------------------------------+
| xml:base | results/results.xml |
| xml:base | adf/results/results.xml |
+-----------------------------------+-----------------------------------+

**Comment.**
Expand Down Expand Up @@ -120,7 +120,7 @@ adf.results

.. code:: xml
<templateList> <xi:include href="orbital.energies.spin.zora.xml" /> <xi:include href="orbital.energies.zora.xml" /> <xi:include href="orbital.energies.xml" /> <xi:include href="orbital.energies.spin.xml" /> <xi:include href="fit.test.xml" /> <xi:include href="mulliken.xml" /> <xi:include href="multipole/multipole.xml" /> <xi:include href="quadrupole.moment.xml" /> <xi:include href="s2.xml" /> <xi:include href="bonding.energy.xml" /> <xi:include href="sfopopulation/sfo.population.xml" /> <xi:include href="excitationenergy/excitation.energy.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
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4 changes: 2 additions & 2 deletions codes/adf/adf.runtype-d3e1534.rst
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Expand Up @@ -39,7 +39,7 @@ adf.runtype
+-----------------------------------+-----------------------------------+
| repeat | \* |
+-----------------------------------+-----------------------------------+
| xml:base | runtype/runtype.xml |
| xml:base | adf/runtype/runtype.xml |
+-----------------------------------+-----------------------------------+

**Input.**
Expand Down Expand Up @@ -117,7 +117,7 @@ adf.runtype
.. code:: xml
<templateList> <template pattern=".*R\sU\sN\s+T\sY\sP\sE.*" endPattern=".*" endOffset="0"> <record id="runtype">.*R\sU\sN\s+T\sY\sP\sE\s\:{X,cc:runtype}\*.*</record> <transform process="pullup" repeat="2" xpath=".//cml:scalar[@dictRef='cc:runtype']" />
</template> <xi:include href="geometry.xml" /> <xi:include href="symmetry.xml" />
</template> <xi:include href="runtype/geometry.xml" /> <xi:include href="runtype/symmetry.xml" />
</templateList>
<transform process="delete" xpath=".//cml:list[count(*)=0]" />
<transform process="delete" xpath=".//cml:module[count(*)=0]" />
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2 changes: 1 addition & 1 deletion codes/adf/adf.technical-d3e1997.rst
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Expand Up @@ -34,7 +34,7 @@ adf.technical
+-----------------------------------+-----------------------------------+
| repeat | \* |
+-----------------------------------+-----------------------------------+
| xml:base | technical/technical.xml |
| xml:base | adf/technical/technical.xml |
+-----------------------------------+-----------------------------------+

**Comment.**
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2 changes: 1 addition & 1 deletion codes/adf/atomic.charges-d3e3025.rst
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Expand Up @@ -35,7 +35,7 @@ atomic.charges
+-----------------------------------+-----------------------------------+
| repeat | \* |
+-----------------------------------+-----------------------------------+
| xml:base | atomic.charges.xml |
| xml:base | multipole/atomic.charges.xml |
+-----------------------------------+-----------------------------------+

**Input.**
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2 changes: 1 addition & 1 deletion codes/adf/atomic.charges.spin-d3e3076.rst
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Expand Up @@ -36,7 +36,7 @@ atomic.charges.spin
+-----------------------------------+-----------------------------------+
| repeat | \* |
+-----------------------------------+-----------------------------------+
| xml:base | atomic.charges.spin.xml |
| xml:base | multipole/atomic.charges.spin.xml |
+-----------------------------------+-----------------------------------+

**Input.**
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2 changes: 1 addition & 1 deletion codes/adf/bonding.energy-d3e3240.rst
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Expand Up @@ -35,7 +35,7 @@ bonding.energy
+-----------------------------------+-----------------------------------+
| repeat | \* |
+-----------------------------------+-----------------------------------+
| xml:base | bonding.energy.xml |
| xml:base | results/bonding.energy.xml |
+-----------------------------------+-----------------------------------+

**Input.**
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2 changes: 1 addition & 1 deletion codes/adf/dirac-d3e721.rst
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Expand Up @@ -87,7 +87,7 @@ dirac

.. code:: xml
<templateList> <xi:include href="../program.header.xml" />
<templateList> <xi:include href="dirac/../program.header.xml" />
</templateList>
.. |image0| image:: ../../imgs/Total.png
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2 changes: 1 addition & 1 deletion codes/adf/excitation.energy-d3e3767.rst
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Expand Up @@ -37,7 +37,7 @@ excitation.energy
+-----------------------------------+-----------------------------------+
| repeat | \* |
+-----------------------------------+-----------------------------------+
| xml:base | excit |
| xml:base | results/excit |
| | ationenergy/excitation.energy.xml |
+-----------------------------------+-----------------------------------+

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2 changes: 1 addition & 1 deletion codes/adf/fit.test-d3e2777.rst
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Expand Up @@ -32,7 +32,7 @@ fit.test
+-----------------------------------+-----------------------------------+
| repeat | \* |
+-----------------------------------+-----------------------------------+
| xml:base | fit.test.xml |
| xml:base | results/fit.test.xml |
+-----------------------------------+-----------------------------------+

**Input.**
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3 changes: 2 additions & 1 deletion codes/adf/fragment.files-d3e1113.rst
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Expand Up @@ -32,7 +32,8 @@ fragment.files
+-----------------------------------+-----------------------------------+
| repeat | \* |
+-----------------------------------+-----------------------------------+
| xml:base | fragment.files.xml |
| xml:base | init/m |
| | odelparameters/fragment.files.xml |
+-----------------------------------+-----------------------------------+

**Input.**
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2 changes: 1 addition & 1 deletion codes/adf/geometry-d3e1550.rst
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Expand Up @@ -32,7 +32,7 @@ geometry
+-----------------------------------+-----------------------------------+
| endOffset | 1 |
+-----------------------------------+-----------------------------------+
| xml:base | geometry.xml |
| xml:base | runtype/geometry.xml |
+-----------------------------------+-----------------------------------+

**Input.**
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2 changes: 1 addition & 1 deletion codes/adf/geometry.cycle-d3e2041.rst
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Expand Up @@ -39,7 +39,7 @@ geometry.cycle
+-----------------------------------+-----------------------------------+
| repeat | \* |
+-----------------------------------+-----------------------------------+
| xml:base | geometry.cycle.xml |
| xml:base | computation/geometry.cycle.xml |
+-----------------------------------+-----------------------------------+

**Input.**
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2 changes: 1 addition & 1 deletion codes/adf/intensities-d3e4107.rst
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Expand Up @@ -35,7 +35,7 @@ intensities
+-----------------------------------+-----------------------------------+
| repeat | \* |
+-----------------------------------+-----------------------------------+
| xml:base | intensities.xml |
| xml:base | frequencyanalysis/intensities.xml |
+-----------------------------------+-----------------------------------+

**Input.**
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4 changes: 2 additions & 2 deletions codes/adf/model.parameters-d3e977.rst
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Expand Up @@ -42,7 +42,7 @@ model.parameters
+-----------------------------------+-----------------------------------+
| offset | -1 |
+-----------------------------------+-----------------------------------+
| xml:base | init/mod |
| xml:base | adf/init/mod |
| | elparameters/model.parameters.xml |
+-----------------------------------+-----------------------------------+

Expand All @@ -68,7 +68,7 @@ model.parameters

.. code:: xml
<templateList> <xi:include href="parameters.xml" /> <xi:include href="fragment.files.xml" /> <xi:include href="solvation.xml" />
<templateList> <xi:include href="init/modelparameters/parameters.xml" /> <xi:include href="init/modelparameters/fragment.files.xml" /> <xi:include href="init/modelparameters/solvation.xml" />
</templateList>
.. |image0| image:: ../../imgs/Total.png
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3 changes: 2 additions & 1 deletion codes/adf/molecular.orbitals-d3e3351.rst
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Expand Up @@ -34,7 +34,8 @@ molecular.orbitals
+-----------------------------------+-----------------------------------+
| endOffset | 0 |
+-----------------------------------+-----------------------------------+
| xml:base | molecular.orbitals.xml |
| xml:base | sfo |
| | population/molecular.orbitals.xml |
+-----------------------------------+-----------------------------------+

**Input.**
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2 changes: 1 addition & 1 deletion codes/adf/mulliken-d3e2828.rst
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Expand Up @@ -35,7 +35,7 @@ mulliken
+-----------------------------------+-----------------------------------+
| repeat | \* |
+-----------------------------------+-----------------------------------+
| xml:base | mulliken.xml |
| xml:base | results/mulliken.xml |
+-----------------------------------+-----------------------------------+

**Input.**
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10 changes: 5 additions & 5 deletions codes/adf/multipole-d3e3018.rst
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Expand Up @@ -44,7 +44,7 @@ multipole
+-----------------------------------+-----------------------------------+
| repeat | \* |
+-----------------------------------+-----------------------------------+
| xml:base | multipole/multipole.xml |
| xml:base | results/multipole/multipole.xml |
+-----------------------------------+-----------------------------------+

**Comment.**
Expand Down Expand Up @@ -77,7 +77,7 @@ multipole

.. code:: xml
<templateList> <xi:include href="atomic.charges.xml" /> <xi:include href="atomic.charges.spin.xml" /> <xi:include href="spin.density.xml" />
<templateList> <xi:include href="multipole/atomic.charges.xml" /> <xi:include href="multipole/atomic.charges.spin.xml" /> <xi:include href="multipole/spin.density.xml" />
</templateList>
.. _atomic.charges-d3e3025:
Expand Down Expand Up @@ -117,7 +117,7 @@ atomic.charges
+-----------------------------------+-----------------------------------+
| repeat | \* |
+-----------------------------------+-----------------------------------+
| xml:base | atomic.charges.xml |
| xml:base | multipole/atomic.charges.xml |
+-----------------------------------+-----------------------------------+

**Input.**
Expand Down Expand Up @@ -289,7 +289,7 @@ atomic.charges.spin
+-----------------------------------+-----------------------------------+
| repeat | \* |
+-----------------------------------+-----------------------------------+
| xml:base | atomic.charges.spin.xml |
| xml:base | multipole/atomic.charges.spin.xml |
+-----------------------------------+-----------------------------------+

**Input.**
Expand Down Expand Up @@ -419,7 +419,7 @@ spin.density
+-----------------------------------+-----------------------------------+
| repeat | \* |
+-----------------------------------+-----------------------------------+
| xml:base | spin.density.xml |
| xml:base | multipole/spin.density.xml |
+-----------------------------------+-----------------------------------+

**Input.**
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2 changes: 1 addition & 1 deletion codes/adf/nmr-d3e19.rst
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Expand Up @@ -96,7 +96,7 @@ nmr

.. code:: xml
<templateList> <xi:include href="../program.header.xml" /> <xi:include href="nuclear.coordinates.xml" /> <xi:include href="nucleus.xml" />
<templateList> <xi:include href="nmr/../program.header.xml" /> <xi:include href="nmr/nuclear.coordinates.xml" /> <xi:include href="nmr/nucleus.xml" />
</templateList>
.. |image0| image:: ../../imgs/Total.png
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2 changes: 1 addition & 1 deletion codes/adf/nuclear.coordinates-d3e146.rst
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Expand Up @@ -33,7 +33,7 @@ nuclear.coordinates
+-----------------------------------+-----------------------------------+
| repeat | \* |
+-----------------------------------+-----------------------------------+
| xml:base | nuclear.coordinates.xml |
| xml:base | nmr/nuclear.coordinates.xml |
+-----------------------------------+-----------------------------------+

**Input.**
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2 changes: 1 addition & 1 deletion codes/adf/nucleus-d3e570.rst
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Expand Up @@ -36,7 +36,7 @@ nucleus
+-----------------------------------+-----------------------------------+
| repeat | \* |
+-----------------------------------+-----------------------------------+
| xml:base | nucleus.xml |
| xml:base | nmr/nucleus.xml |
+-----------------------------------+-----------------------------------+

**Input.**
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2 changes: 1 addition & 1 deletion codes/adf/orbital.energies-d3e2689.rst
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Expand Up @@ -33,7 +33,7 @@ orbital.energies
+-----------------------------------+-----------------------------------+
| repeat | \* |
+-----------------------------------+-----------------------------------+
| xml:base | orbital.energies.xml |
| xml:base | results/orbital.energies.xml |
+-----------------------------------+-----------------------------------+

**Input.**
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2 changes: 1 addition & 1 deletion codes/adf/orbital.energies.spin-d3e2732.rst
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Expand Up @@ -32,7 +32,7 @@ orbital.energies.spin
+-----------------------------------+-----------------------------------+
| endOffset | 1 |
+-----------------------------------+-----------------------------------+
| xml:base | orbital.energies.spin.xml |
| xml:base | results/orbital.energies.spin.xml |
+-----------------------------------+-----------------------------------+

**Input.**
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3 changes: 2 additions & 1 deletion codes/adf/orbital.energies.spin.zora-d3e2487.rst
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Expand Up @@ -39,7 +39,8 @@ orbital.energies.spin.zora
+-----------------------------------+-----------------------------------+
| repeat | \* |
+-----------------------------------+-----------------------------------+
| xml:base | orbital.energies.spin.zora.xml |
| xml:base | resul |
| | ts/orbital.energies.spin.zora.xml |
+-----------------------------------+-----------------------------------+

**Input.**
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2 changes: 1 addition & 1 deletion codes/adf/orbital.energies.zora-d3e2587.rst
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Expand Up @@ -38,7 +38,7 @@ orbital.energies.zora
+-----------------------------------+-----------------------------------+
| repeat | \* |
+-----------------------------------+-----------------------------------+
| xml:base | orbital.energies.zora.xml |
| xml:base | results/orbital.energies.zora.xml |
+-----------------------------------+-----------------------------------+

**Input.**
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