cosmo
Type |
Status |
|---|---|
CML extraction template |
|
HTML5 representation |
|
Attribute |
Value |
|---|---|
source |
Orca log |
id |
cosmo |
name |
Cosmo section |
pattern |
\s*-{10,}$\s*COSMO\sINITIALIZATION.* |
endPattern |
\s*-{10,}$\s*\w.* |
repeat |
* |
xml:base |
job/cosmo/cosmo.xml |
Input
--------------------
COSMO INITIALIZATION
--------------------
Epsilon ... 80.4000
Refractive Index ... 1.3300
Potential Evaluation ... ANALYTIC
Technical COSMO parameters:
rsolv ... 1.3000
routf ... 0.8500
disex ... 10.0000
nppa ... 1082
nspa ... 92
Radii:
Radius for O used is 3.2503 Bohr (= 1.7200 Ang.)
Radius for C used is 3.7795 Bohr (= 2.0000 Ang.)
Radius for H used is 2.4566 Bohr (= 1.3000 Ang.)
Initializing COSMO package ... done
Setting COSMO radii ... done
Setting atoms and making cavity ... USING 1082 GRID
done
Cholesky decomposition of A ... done
--------------
Output text
1<comment class="example.output" id="cosmo">
2 <module cmlx:templateRef="cosmo" dictRef="cc:userDefinedModule">
3 <list cmlx:templateRef="technical">
4 <list>
5 <scalar dataType="xsd:string" dictRef="cc:parameter">rsolv</scalar>
6 <scalar dataType="xsd:string" dictRef="cc:value">1.3000</scalar>
7 </list>
8 <list>
9 <scalar dataType="xsd:string" dictRef="cc:parameter">routf</scalar>
10 <scalar dataType="xsd:string" dictRef="cc:value">0.8500</scalar>
11 </list>
12 <list>
13 <scalar dataType="xsd:string" dictRef="cc:parameter">disex</scalar>
14 <scalar dataType="xsd:string" dictRef="cc:value">10.0000</scalar>
15 </list>
16 <list>
17 <scalar dataType="xsd:string" dictRef="cc:parameter">nppa</scalar>
18 <scalar dataType="xsd:string" dictRef="cc:value">1082</scalar>
19 </list>
20 <list>
21 <scalar dataType="xsd:string" dictRef="cc:parameter">nspa</scalar>
22 <scalar dataType="xsd:string" dictRef="cc:value">92</scalar>
23 </list>
24 </list>
25 <list cmlx:templateRef="radii">
26 <array dataType="xsd:string" dictRef="cc:elementType" size="3">O C H</array>
27 <array dataType="xsd:double" dictRef="o:radius" size="3" units="nonsi:angstrom">1.7200 2.0000 1.3000</array>
28 </list>
29 <list cmlx:templateRef="parameters" dictRef="parameters">
30 <list>
31 <scalar dataType="xsd:string" dictRef="cc:parameter">Epsilon</scalar>
32 <scalar dataType="xsd:string" dictRef="cc:value">80.4000</scalar>
33 </list>
34 <list>
35 <scalar dataType="xsd:string" dictRef="cc:parameter">Refractive Index</scalar>
36 <scalar dataType="xsd:string" dictRef="cc:value">1.3300</scalar>
37 </list>
38 <list>
39 <scalar dataType="xsd:string" dictRef="cc:parameter">Potential Evaluation</scalar>
40 <scalar dataType="xsd:string" dictRef="cc:value">ANALYTIC</scalar>
41 </list>
42 <list>
43 <scalar dataType="xsd:string" dictRef="cc:parameter">Initializing COSMO package</scalar>
44 <scalar dataType="xsd:string" dictRef="cc:value">done</scalar>
45 </list>
46 <list>
47 <scalar dataType="xsd:string" dictRef="cc:parameter">Setting COSMO radii</scalar>
48 <scalar dataType="xsd:string" dictRef="cc:value">done</scalar>
49 </list>
50 <list>
51 <scalar dataType="xsd:string" dictRef="cc:parameter">Setting atoms and making cavity</scalar>
52 <scalar dataType="xsd:string" dictRef="cc:value">USING 1082 GRID</scalar>
53 </list>
54 <list>
55 <scalar dataType="xsd:string" dictRef="cc:parameter">Cholesky decomposition of A</scalar>
56 <scalar dataType="xsd:string" dictRef="cc:value">done</scalar>
57 </list>
58 </list>
59 </module>
60 </comment>
Template definition
1<templateList> <template pattern="\s*Technical\sCOSMO\sparameters.*" endPattern="\s*Radii.*" endPattern2="\w.*" endPattern3="~" repeat="*"> <record /> <record id="technical" repeat="*">{X,cc:parameter}\.\.\.{X,cc:value}</record>
2 </template> <template pattern="\s*Radii:\s*" endPattern="\s*(?!.*Radius).+" endPattern2="~" repeat="*"> <record /> <record id="radii" repeat="*" makeArray="true">\s*Radius\sfor{A,cc:elementType}used\sis.*\(={F,o:radius}.*</record>
3 </template> <template id="parameter" pattern=".*\.\.\..*" endPattern=".*" endPattern2="~" repeat="*"> <record>{X,cc:parameter}\.\.\.{X,cc:value}</record>
4 </template>
5 </templateList>
6<transform process="move" xpath=".//cml:module[@cmlx:templateRef='parameter']/cml:list/cml:list" to="." />
7<transform process="pullup" xpath=".//cml:list[@cmlx:templateRef='radii']" />
8<transform process="pullup" xpath=".//cml:list[@cmlx:templateRef='technical']" />
9<transform process="delete" xpath=".//cml:list[count(*)=0]" />
10<transform process="delete" xpath=".//cml:module[count(*)=0]" />
11<transform process="delete" xpath=".//cml:module" />
12<transform process="addUnits" xpath=".//cml:array[@dictRef='o:radius']" value="nonsi:angstrom" />
13<transform process="addChild" elementName="cml:list" xpath="." dictRef="parameters" />
14<transform process="addAttribute" xpath=".//cml:list[@dictRef='parameters']" name="cmlx:templateRef" value="parameters" />
15<transform process="move" xpath="./cml:list[not(@cmlx:templateRef)]" to="./cml:list[@cmlx:templateRef='parameters']" />