Fixed Molcas children templates display

ioChem-BD · Oct 9, 2021 · 765b6c1 · 765b6c1
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diff --git a/codes/molcas.rst b/codes/molcas.rst
@@ -19,19 +19,19 @@ MOLCAS
    /codes/molcas/mixed.ci.coeffs-d3e22229
    /codes/molcas/caspt2.root-d3e22331
    /codes/molcas/mulliken-d3e22352
-   /codes/molcas/symmetry-d3e22681
-   /codes/molcas/properties-d3e22794
-   /codes/molcas/loprop-d3e22967
-   /codes/molcas/extras-d3e23031
-   /codes/molcas/multicaspt2-d3e23105
-   /codes/molcas/final.caspt2-d3e23487
-   /codes/molcas/spin.orbit-d3e23592
-   /codes/molcas/spin.free-d3e23702
-   /codes/molcas/energy.statistics-d3e23869
-   /codes/molcas/vibrations-d3e24007
-   /codes/molcas/thermochemistry-d3e24108
-   /codes/molcas/constraint-d3e24139
-   /codes/molcas/cchc-d3e24362
-   /codes/molcas/atom.expansion-d3e24431
-   /codes/molcas/dynamic.loprop-d3e24547
-   /codes/molcas/molcas.input-d3e42112
+   /codes/molcas/symmetry-d3e22684
+   /codes/molcas/properties-d3e22797
+   /codes/molcas/loprop-d3e22973
+   /codes/molcas/extras-d3e23037
+   /codes/molcas/multicaspt2-d3e23111
+   /codes/molcas/final.caspt2-d3e23493
+   /codes/molcas/spin.orbit-d3e23598
+   /codes/molcas/spin.free-d3e23708
+   /codes/molcas/energy.statistics-d3e23875
+   /codes/molcas/vibrations-d3e24013
+   /codes/molcas/thermochemistry-d3e24191
+   /codes/molcas/constraint-d3e24225
+   /codes/molcas/cchc-d3e24448
+   /codes/molcas/atom.expansion-d3e24517
+   /codes/molcas/dynamic.loprop-d3e24633
+   /codes/molcas/molcas.input-d3e42198
diff --git a/codes/molcas/atom.expansion-d3e24431.rst → codes/molcas/atom.expansion-d3e24517.rst b/codes/molcas/atom.expansion-d3e24431.rst → codes/molcas/atom.expansion-d3e24517.rst
@@ -1,4 +1,4 @@
-.. _atom.expansion-d3e24431:
+.. _atom.expansion-d3e24517:
 
 atom.expansion
 ==============

diff --git a/codes/molcas/cchc-d3e24362.rst → codes/molcas/cchc-d3e24448.rst b/codes/molcas/cchc-d3e24362.rst → codes/molcas/cchc-d3e24448.rst
@@ -1,4 +1,4 @@
-.. _cchc-d3e24362:
+.. _cchc-d3e24448:
 
 cchc
 ====

diff --git a/codes/molcas/constraint-d3e24139.rst → codes/molcas/constraint-d3e24225.rst b/codes/molcas/constraint-d3e24139.rst → codes/molcas/constraint-d3e24225.rst
@@ -1,4 +1,4 @@
-.. _constraint-d3e24139:
+.. _constraint-d3e24225:
 
 constraint
 ==========

diff --git a/codes/molcas/dynamic.loprop-d3e24547.rst → codes/molcas/dynamic.loprop-d3e24633.rst b/codes/molcas/dynamic.loprop-d3e24547.rst → codes/molcas/dynamic.loprop-d3e24633.rst
@@ -1,4 +1,4 @@
-.. _dynamic.loprop-d3e24547:
+.. _dynamic.loprop-d3e24633:
 
 dynamic.loprop
 ==============

diff --git a/codes/molcas/eigenvalues-d3e23600.rst → codes/molcas/eigenvalues-d3e23606.rst b/codes/molcas/eigenvalues-d3e23600.rst → codes/molcas/eigenvalues-d3e23606.rst
@@ -1,4 +1,4 @@
-.. _eigenvalues-d3e23600:
+.. _eigenvalues-d3e23606:
 
 eigenvalues
 ===========

diff --git a/codes/molcas/eigenvalues-d3e23710.rst → codes/molcas/eigenvalues-d3e23716.rst b/codes/molcas/eigenvalues-d3e23710.rst → codes/molcas/eigenvalues-d3e23716.rst
@@ -1,4 +1,4 @@
-.. _eigenvalues-d3e23710:
+.. _eigenvalues-d3e23716:
 
 eigenvalues
 ===========

diff --git a/codes/molcas/energy.statistics-d3e23869.rst → codes/molcas/energy.statistics-d3e23875.rst b/codes/molcas/energy.statistics-d3e23869.rst → codes/molcas/energy.statistics-d3e23875.rst
@@ -1,4 +1,4 @@
-.. _energy.statistics-d3e23869:
+.. _energy.statistics-d3e23875:
 
 energy.statistics
 =================

diff --git a/codes/molcas/extras-d3e23031.rst → codes/molcas/extras-d3e23037.rst b/codes/molcas/extras-d3e23031.rst → codes/molcas/extras-d3e23037.rst
@@ -1,4 +1,4 @@
-.. _extras-d3e23031:
+.. _extras-d3e23037:
 
 extras
 ======

diff --git a/codes/molcas/final.caspt2-d3e23487.rst → codes/molcas/final.caspt2-d3e23493.rst b/codes/molcas/final.caspt2-d3e23487.rst → codes/molcas/final.caspt2-d3e23493.rst
@@ -1,4 +1,4 @@
-.. _final.caspt2-d3e23487:
+.. _final.caspt2-d3e23493:
 
 final.caspt2
 ============

diff --git a/codes/molcas/loprop-d3e22967.rst → codes/molcas/loprop-d3e22973.rst b/codes/molcas/loprop-d3e22967.rst → codes/molcas/loprop-d3e22973.rst
@@ -1,4 +1,4 @@
-.. _loprop-d3e22967:
+.. _loprop-d3e22973:
 
 loprop
 ======

diff --git a/codes/molcas/mol.props-d3e22815.rst b/codes/molcas/mol.props-d3e22815.rst
@@ -0,0 +1,96 @@
+.. _mol.props-d3e22815:
+
+mol.props
+=========
+
+.. table:: Implementation level
+
+   +-----------------------------------+-----------------------------------+
+   | Type                              | Status                            |
+   +===================================+===================================+
+   | CML extraction template           | |image0|                          |
+   +-----------------------------------+-----------------------------------+
+   | HTML5 representation              | |image1|                          |
+   +-----------------------------------+-----------------------------------+
+
+.. table:: Template attributes
+
+   +-----------------------------------+-----------------------------------+
+   | Attribute                         | Value                             |
+   +===================================+===================================+
+   | *source*                          | MOLCAS log                        |
+   +-----------------------------------+-----------------------------------+
+   | id                                | mol.props                         |
+   +-----------------------------------+-----------------------------------+
+   | name                              | Molecular properties              |
+   +-----------------------------------+-----------------------------------+
+   | pattern                           | \\s*(?:\+\+                       |
+   |                                   | )?\s*Molecular\s[Pp]roperties:.\* |
+   +-----------------------------------+-----------------------------------+
+   | pattern2                          | \\s*Charge.\*                     |
+   +-----------------------------------+-----------------------------------+
+   | pattern3                          | \\s*Dipole\sMoment.\*             |
+   +-----------------------------------+-----------------------------------+
+   | endPattern                        | \\s*\-\-\s\*                      |
+   +-----------------------------------+-----------------------------------+
+   | endPattern2                       | ~                                 |
+   +-----------------------------------+-----------------------------------+
+   | repeat                            | \*                                |
+   +-----------------------------------+-----------------------------------+
+   | xml:base                          | modules/properties/mol.props.xml  |
+   +-----------------------------------+-----------------------------------+
+
+**Input.**
+
+::
+
+   ++    Molecular properties:
+         ---------------------
+    
+         Charge (e):
+                         =   -0.0000
+         Dipole Moment (Debye):
+         Origin of the operator (Ang)=    0.0000    0.0000    0.0000
+                        X=    0.0000               Y=    0.0000               Z=    0.0000           Total=    0.0000
+         Quadrupole Moment (Debye*Ang):
+         Origin of the operator (Ang)=    0.0000    0.0000    0.0000
+                       XX=  -92.8211              XY=    0.0000              XZ=    0.0000              YY= -101.7054
+                       YZ=    0.0000              ZZ= -128.7810
+         In traceless form (Debye*Ang)
+                       XX=   22.4221              XY=    0.0000              XZ=    0.0000              YY=    9.0956
+                       YZ=    0.0000              ZZ=  -31.5177
+   --  
+       
+
+**Output text.**
+
+.. code:: xml
+
+   <comment class="example.output" id="mol.props">
+            <module cmlx:templateRef="mol.props">
+              <scalar dataType="xsd:double" dictRef="cc:charge">-0.0000</scalar>
+              <list cmlx:templateRef="dipole">
+                 <array dataType="xsd:double" dictRef="m:dipole" size="3">0.0000 0.0000 0.0000</array>
+                 <scalar dataType="xsd:double" dictRef="m:total">0.0000</scalar>
+                 <array dataType="xsd:double" dictRef="m:operatororig" size="3">0.0000 0.0000 0.0000</array>
+              </list>
+              <list cmlx:templateRef="quadrupole">
+                 <array dataType="xsd:double" dictRef="m:quadvalue" size="6">-92.8211 0.0000 0.0000 -101.7054 0.0000 -128.7810</array>
+                 <array dataType="xsd:double" dictRef="m:operatororig" size="3">0.0000 0.0000 0.0000</array>
+                 <array dataType="xsd:double" dictRef="m:quadtracevalue" size="6">22.4221 0.0000 0.0000 9.0956 0.0000 -31.5177</array>
+              </list>
+           </module>
+       </comment>
+
+**Template definition.**
+
+.. code:: xml
+
+   <templateList>  <template id="charge" name="Charge" pattern="\s*Charge.*" endPattern=".*[0-9]\s*" endOffset="1">    <record />    <record>\s*={F,cc:charge}</record>
+           </template>  <template id="dipole" name="Dipole/Quadripole moment" pattern="\s*Dipole\sMoment.*" endPattern="\s*" endPattern2="~">    <record />    <record>\s*Origin\sof\sthe\soperator\s\(Ang\)=\s*{3F,m:operatororig}</record>    <record id="dipole">\s*X={E,m:dipole}Y={E,m:dipole}Z={E,m:dipole}Total={E,m:total}</record>    <record />    <record>\s*Origin\sof\sthe\soperator\s\(Ang\)=\s*{3F,m:operatororig}</record>    <record id="quadrupole">\s*XX={E,m:quadvalue}XY={E,m:quadvalue}XZ={E,m:quadvalue}YY={E,m:quadvalue}</record>    <record id="quadrupole">\s*YZ={E,m:quadvalue}ZZ={E,m:quadvalue}</record>    <record />    <record id="quadrupole">\s*XX={E,m:quadtracevalue}XY={E,m:quadtracevalue}XZ={E,m:quadtracevalue}YY={E,m:quadtracevalue}</record>    <record id="quadrupole">\s*YZ={E,m:quadtracevalue}ZZ={E,m:quadtracevalue}</record>       
+           </template>  <transform process="createArray" xpath="." from=".//cml:scalar[@dictRef='m:dipole']" />  <transform process="createArray" xpath="." from=".//cml:scalar[@dictRef='m:quadvalue']" />  <transform process="createArray" xpath="." from=".//cml:scalar[@dictRef='m:quadtracevalue']" />  <transform process="move" xpath="(.//cml:array[@dictRef='m:operatororig'])[1]" to=".//cml:list[@cmlx:templateRef='dipole']" />  <transform process="move" xpath="(.//cml:array[@dictRef='m:operatororig'])[2]" to="(.//cml:list[@cmlx:templateRef='quadrupole'])[1]" />  <transform process="move" xpath=".//cml:array[@dictRef='m:quadtracevalue']" to="(.//cml:list[@cmlx:templateRef='quadrupole'])[1]" />  <transform process="pullup" xpath=".//cml:list[@cmlx:templateRef='dipole' or @cmlx:templateRef='quadrupole']/cml:list/*" />  <transform process="pullup" xpath=".//cml:scalar[@dictRef='cc:charge']" repeat="2" />  <transform process="pullup" xpath=".//cml:list[@cmlx:templateRef='dipole']" repeat="1" />  <transform process="pullup" xpath=".//cml:list[@cmlx:templateRef='quadrupole']" repeat="1" />  <transform process="delete" xpath=".//cml:list[count(*) = 0]" />  <transform process="delete" xpath=".//cml:list[count(*) = 0]" />  <transform process="delete" xpath=".//cml:module[count(*) = 0]" />
+
+       </templateList>
+
+.. |image0| image:: ../../imgs/Total.png
+.. |image1| image:: ../../imgs/None.png
diff --git a/codes/molcas/molcas.input-d3e42112.rst → codes/molcas/molcas.input-d3e42198.rst b/codes/molcas/molcas.input-d3e42112.rst → codes/molcas/molcas.input-d3e42198.rst
@@ -1,4 +1,4 @@
-.. _molcas.input-d3e42112:
+.. _molcas.input-d3e42198:
 
 molcas.input
 ============

diff --git a/codes/molcas/mulliken-d3e22352.rst b/codes/molcas/mulliken-d3e22352.rst
@@ -1,6 +1,13 @@
-.. _mulliken-d3e22352:
-
 mulliken
+=====================================
+
+.. toctree::
+   :maxdepth: 5  
+
+   /codes/molcas/mulliken.header-d3e22361
+   /codes/molcas/mulliken.charges-d3e22411
+   /codes/molcas/mulliken.spin-d3e22582
+
 ========
 
 .. table:: Implementation level
@@ -93,9 +100,8 @@ mulliken
 
 .. code:: xml
 
-   <xi:include href="modules/mulliken/mulliken.header.xml" />
-   <xi:include href="modules/mulliken/mulliken.charges.xml" />
-   <xi:include href="modules/mulliken/mulliken.spin.xml" />
+   <templateList>  <xi:include href="modules/mulliken/mulliken.header.xml" />  <xi:include href="modules/mulliken/mulliken.charges.xml" />  <xi:include href="modules/mulliken/mulliken.spin.xml" />
+       </templateList>
    <transform process="addChild" xpath="." elementName="cml:module" dictRef="mulliken.header" />
    <transform process="addAttribute" xpath=".//cml:module[@dictRef='mulliken.header']" name="cmlx:templateRef" value="mulliken.header" />
    <transform process="addChild" id="root" xpath="./cml:module[@dictRef='mulliken.header' and count(*) = 0]" elementName="cml:scalar" dictRef="m:rootnumber" value="$string((preceding::cml:module[@cmlx:templateRef='caspt2.root'])[last()]//cml:scalar/text())" />