solvation

Implementation level
Type Status
CML extraction template image0
HTML5 representation image1
Template attributes
Attribute Value
source ADF log
id solvation
name ADF Init solvation parameters
pattern \s*SOLVATION.*$—.*
endPattern \s*$—.*
endOffset 1
repeat *
xml:base i nit/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.

<comment class="example.output" id="solvation">
        <module cmlx:lineCount="30" cmlx:templateRef="solvation">
          <list id="cosmo">
                <scalar dataType="xsd:integer" dictRef="a:ndiv">5</scalar>
                <scalar dataType="xsd:integer" dictRef="a:nfdiv">1</scalar>
                <scalar dataType="xsd:double" dictRef="a:rsol" units="nonsi:angstrom">1.4</scalar>
                <scalar dataType="xsd:double" dictRef="a:rminsolv" units="nonsi:angstrom">0.5</scalar>
                <scalar dataType="xsd:double" dictRef="a:ofac">0.8</scalar>
                <scalar dataType="xsd:double" dictRef="a:epsl">78.4</scalar>
                <scalar dataType="xsd:string" dictRef="a:cosmomethod">conjugate-gradient</scalar>
                <scalar dataType="xsd:double" dictRef="a:ncix">1000.0</scalar>
                <scalar dataType="xsd:double" dictRef="a:ccnv">1.0E-10</scalar>
                <scalar dataType="xsd:double" dictRef="a:gdsf">0.0</scalar>
            </list>
        </module>
    </comment>

Template definition.

<templateList>  <template pattern="\s*Division\sLevel\sfor\sSurface\sTriangles.*" endPattern=".*">    <record id="ndiv">.*\(NDIV\){I,a:ndiv}</record>
        </template>  <template pattern="\s*Final\sDivision\sLevel\sfor\sTriangles.*" endPattern=".*">    <record id="nfdiv">.*\(NFDIV\){I,a:nfdiv}</record>
        </template>  <template pattern="\s*Radius\sof\sthe\sSolvent.*" endPattern=".*">    <record id="rsol">.*\(RSOL\){F,a:rsol}.*</record>
        </template>  <template pattern="\s*Minimum\sRadius\sfor\snew\ssphere.*" endPattern=".*">    <record id="rminsolv">.*\(RMINSOLV\){F,a:rminsolv}.*</record>
        </template>  <template pattern="\s*Overlapping\sFactor.*" endPattern=".*">    <record id="ofac">.*\(OFAC\){F,a:ofac}</record>
        </template>  <template pattern="\s*Dielectric\sConstant.*" endPattern=".*">    <record id="epsl">.*\(EPSL\){F,a:epsl}</record>
        </template>  <template pattern="\s*COSMO\sequation\sis\ssolved\siteratively.*" endPattern=".*">    <record id="cosmomethod">.*iteratively-{X,a:cosmomethod}</record>
        </template>  <template pattern="\s*Maximun\sof\sIterations\sfor\sCharges.*" endPattern=".*">    <record id="ncix">.*\(NCIX\){F,a:ncix}</record>
        </template>  <template pattern="\s*Criterion\sfor\sCharge\sconvergence.*" endPattern=".*">    <record id="ccnv">.*\(CCNV\){E,a:ccnv}</record>
        </template>  <template pattern="\s*Geometry-dependent\sempirical\sfactor.*" endPattern=".*">    <record id="gdsf">\s*Geometry-dependent\sempirical\sfactor{F,a:gdsf}</record>
        </template>
    </templateList>
<transform process="addUnits" xpath=".//cml:scalar[@dictRef='a:rsol']" value="nonsi:angstrom" />
<transform process="addUnits" xpath=".//cml:scalar[@dictRef='a:rminsolv']" value="nonsi:angstrom" />
<transform process="pullup" xpath=".//cml:scalar" repeat="2" />
<transform process="delete" xpath=".//cml:list[count(*)=0]" />
<transform process="delete" xpath=".//cml:list[count(*)=0]" />
<transform process="delete" xpath=".//cml:module[count(*)=0]" />
<transform process="addChild" xpath="." elementName="cml:list" id="cosmo" />
<transform process="move" xpath=".//cml:scalar" to=".//cml:list" />