solvation

Implementation level

Type	Status
CML extraction template
HTML5 representation

Template attributes

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

<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">.*\(NDIV\)&#123;I,a:ndiv&#125;</record>       
        </template>  <template pattern="\s*Final\sDivision\sLevel\sfor\sTriangles.*" endPattern=".*">    <record id="nfdiv">.*\(NFDIV\)&#123;I,a:nfdiv&#125;</record>
        </template>  <template pattern="\s*Radius\sof\sthe\sSolvent.*" endPattern=".*">    <record id="rsol">.*\(RSOL\)&#123;F,a:rsol&#125;.*</record>
        </template>  <template pattern="\s*Minimum\sRadius\sfor\snew\ssphere.*" endPattern=".*">    <record id="rminsolv">.*\(RMINSOLV\)&#123;F,a:rminsolv&#125;.*</record>
        </template>  <template pattern="\s*Overlapping\sFactor.*" endPattern=".*">    <record id="ofac">.*\(OFAC\)&#123;F,a:ofac&#125;</record>
        </template>  <template pattern="\s*Dielectric\sConstant.*" endPattern=".*">    <record id="epsl">.*\(EPSL\)&#123;F,a:epsl&#125;</record>
        </template>  <template pattern="\s*COSMO\sequation\sis\ssolved\siteratively.*" endPattern=".*">    <record id="cosmomethod">.*iteratively-&#123;X,a:cosmomethod&#125;</record>
        </template>  <template pattern="\s*Maximun\sof\sIterations\sfor\sCharges.*" endPattern=".*">    <record id="ncix">.*\(NCIX\)&#123;F,a:ncix&#125;</record>
        </template>  <template pattern="\s*Criterion\sfor\sCharge\sconvergence.*" endPattern=".*">    <record id="ccnv">.*\(CCNV\)&#123;E,a:ccnv&#125;</record>
        </template>  <template pattern="\s*Geometry-dependent\sempirical\sfactor.*" endPattern=".*">    <record id="gdsf">\s*Geometry-dependent\sempirical\sfactor&#123;F,a:gdsf&#125;</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" />