solvation
Type |
Status |
|---|---|
CML extraction template |
|
HTML5 representation |
|
Attribute |
Value |
|---|---|
source |
AMS ADF log |
id |
solvation |
name |
ADF Init solvation parameters |
pattern |
\s*SOLVATION.*$\-\-\-.* |
endPattern |
\s*$\-\-\-.* |
endOffset |
1 |
repeat |
* |
xml:base |
init/modelparameters/solvation.xml |
Input
SOLVATION
-------------------------------------------
The Solvent-Excluding surface is calculated
Division Level for Surface Triangles (NDIV) 5
Final Division Level for Triangles (NFDIV) 1
Radius of the Solvent (RSOL) 1.40000 angstr
Minimum Radius for new sphere (RMINSOLV) 0.50000 angstr
Overlapping Factor (OFAC) 0.80000
New spheres will be assigned to the initials using ASSG1
Dielectric Constant (EPSL) 78.40000
COSMO equation is solved iteratively- conjugate-gradient
Maximun of Iterations for Charges (NCIX) 1000
Criterion for Charge convergence (CCNV) 1.0E-10
Geometry-dependent empirical factor 0.00000
COSMO charges included variationally in SCF
COSMO started at end of SCF
C-Matrix calculated in cspmtx
In cspmtx, C-Matrix calculated using fitted potential
-------------------------------------------
Output text
1<comment class="example.output" id="solvation">
2 <module cmlx:lineCount="30" cmlx:templateRef="solvation">
3 <list id="cosmo">
4 <scalar dataType="xsd:integer" dictRef="a:ndiv">5</scalar>
5 <scalar dataType="xsd:integer" dictRef="a:nfdiv">1</scalar>
6 <scalar dataType="xsd:double" dictRef="a:rsol" units="nonsi:angstrom">1.4</scalar>
7 <scalar dataType="xsd:double" dictRef="a:rminsolv" units="nonsi:angstrom">0.5</scalar>
8 <scalar dataType="xsd:double" dictRef="a:ofac">0.8</scalar>
9 <scalar dataType="xsd:double" dictRef="a:epsl">78.4</scalar>
10 <scalar dataType="xsd:string" dictRef="a:cosmomethod">conjugate-gradient</scalar>
11 <scalar dataType="xsd:double" dictRef="a:ncix">1000.0</scalar>
12 <scalar dataType="xsd:double" dictRef="a:ccnv">1.0E-10</scalar>
13 <scalar dataType="xsd:double" dictRef="a:gdsf">0.0</scalar>
14 </list>
15 </module>
16 </comment>
Template definition
1<templateList> <template pattern="\s*Division\sLevel\sfor\sSurface\sTriangles.*" endPattern=".*"> <record id="ndiv">.*\(NDIV\){I,a:ndiv}</record>
2 </template> <template pattern="\s*Final\sDivision\sLevel\sfor\sTriangles.*" endPattern=".*"> <record id="nfdiv">.*\(NFDIV\){I,a:nfdiv}</record>
3 </template> <template pattern="\s*Radius\sof\sthe\sSolvent.*" endPattern=".*"> <record id="rsol">.*\(RSOL\){F,a:rsol}.*</record>
4 </template> <template pattern="\s*Minimum\sRadius\sfor\snew\ssphere.*" endPattern=".*"> <record id="rminsolv">.*\(RMINSOLV\){F,a:rminsolv}.*</record>
5 </template> <template pattern="\s*Overlapping\sFactor.*" endPattern=".*"> <record id="ofac">.*\(OFAC\){F,a:ofac}</record>
6 </template> <template pattern="\s*Dielectric\sConstant.*" endPattern=".*"> <record id="epsl">.*\(EPSL\){F,a:epsl}</record>
7 </template> <template pattern="\s*COSMO\sequation\sis\ssolved\siteratively.*" endPattern=".*"> <record id="cosmomethod">.*iteratively-{X,a:cosmomethod}</record>
8 </template> <template pattern="\s*Maximun\sof\sIterations\sfor\sCharges.*" endPattern=".*"> <record id="ncix">.*\(NCIX\){F,a:ncix}</record>
9 </template> <template pattern="\s*Criterion\sfor\sCharge\sconvergence.*" endPattern=".*"> <record id="ccnv">.*\(CCNV\){E,a:ccnv}</record>
10 </template> <template pattern="\s*Geometry-dependent\sempirical\sfactor.*" endPattern=".*"> <record id="gdsf">\s*Geometry-dependent\sempirical\sfactor{F,a:gdsf}</record>
11 </template>
12 </templateList>
13<transform process="addUnits" xpath=".//cml:scalar[@dictRef='a:rsol']" value="nonsi:angstrom" />
14<transform process="addUnits" xpath=".//cml:scalar[@dictRef='a:rminsolv']" value="nonsi:angstrom" />
15<transform process="pullup" xpath=".//cml:scalar" repeat="2" />
16<transform process="delete" xpath=".//cml:list[count(*)=0]" />
17<transform process="delete" xpath=".//cml:list[count(*)=0]" />
18<transform process="delete" xpath=".//cml:module[count(*)=0]" />
19<transform process="addChild" xpath="." elementName="cml:list" id="cosmo" />
20<transform process="move" xpath=".//cml:scalar" to=".//cml:list" />