initialization ​
Implementation level ​
| Type | Status |
|---|---|
| CML extraction template |  |
| HTML5 representation | |
Template attributes ​
| Attribute | Value |
|---|---|
| source | xTB log |
| id | initialization |
| name | Input file setup |
| pattern | \s+-{10,}\s*$\s*\|\s*G\sF\sN.*\-\sx\sT\sB.* |
| endPattern | \s*$\s*\.{10,}\s* |
| endPattern2 | ~ |
| endOffset | 0 |
| xml:base | initialization.xml |
Input
-------------------------------------------------
| G F N 2 - x T B |
-------------------------------------------------
Reference 10.1021/acs.jctc.8b01176
* Hamiltonian:
H0-scaling (s, p, d) 1.850000 2.230000 2.230000
zeta-weighting 0.500000
* Dispersion:
s8 2.700000
a1 0.520000
a2 5.000000
s9 5.000000
* Repulsion:
kExp 1.500000 1.000000
rExp 1.000000
* Coulomb:
alpha 2.000000
third order shell-resolved
anisotropic true
a3 3.000000
a5 4.000000
cn-shift 1.200000
cn-exp 4.000000
max-rad 5.000000
* Solvation model: GBSA
Solvent toluene
Parameter file internal GFN2-xTB/GBSA
Dielectric constant 7.0000E+00
Reference state gsolv [1 M gas/solution]
Free energy shift 4.5239E-03 Eh 2.8388E+00 kcal/mol
Temperature 2.9815E+02 K
Density 8.6700E-01 kg/L
Solvent mass 9.2140E+01 g/mol
Interaction kernel Still
Born radius scaling (c1) 1.5686E+00
Born radii integrator GBOBC
Born offset 0.0000E+00 a0 0.0000E+00 AA
H-bond correction false
Ion screening false
Surface tension 1.0000E-05 Eh 1.5569E+01 dyn/cm
Grid points 230 per atom
q/qsh data taken from xtbrestart
CAMM data taken from xtbrestart
Output text
xml
<comment class="example.output" id="initialization">
<module cmlx:templateRef="initialization">
<list cmlx:templateRef="Hamiltonian">
<list>
<scalar dataType="xsd:string" dictRef="x:parameter">H0-scaling (s, p, d)</scalar>
<scalar dataType="xsd:string" dictRef="x:value">1.850000 2.230000 2.230000</scalar>
</list>
<list>
<scalar dataType="xsd:string" dictRef="x:parameter">zeta-weighting</scalar>
<scalar dataType="xsd:string" dictRef="x:value">0.500000</scalar>
</list>
</list>
<list cmlx:templateRef="Dispersion">
<list>
<scalar dataType="xsd:string" dictRef="x:parameter">s8</scalar>
<scalar dataType="xsd:string" dictRef="x:value">2.700000</scalar>
</list>
<list>
<scalar dataType="xsd:string" dictRef="x:parameter">a1</scalar>
<scalar dataType="xsd:string" dictRef="x:value">0.520000</scalar>
</list>
<list>
<scalar dataType="xsd:string" dictRef="x:parameter">a2</scalar>
<scalar dataType="xsd:string" dictRef="x:value">5.000000</scalar>
</list>
<list>
<scalar dataType="xsd:string" dictRef="x:parameter">s9</scalar>
<scalar dataType="xsd:string" dictRef="x:value">5.000000</scalar>
</list>
</list>
<list cmlx:templateRef="Repulsion">
<list>
<scalar dataType="xsd:string" dictRef="x:parameter">kExp</scalar>
<scalar dataType="xsd:string" dictRef="x:value">1.500000 1.000000</scalar>
</list>
<list>
<scalar dataType="xsd:string" dictRef="x:parameter">rExp</scalar>
<scalar dataType="xsd:string" dictRef="x:value">1.000000</scalar>
</list>
</list>
<list cmlx:templateRef="Coulomb">
<list>
<scalar dataType="xsd:string" dictRef="x:parameter">alpha</scalar>
<scalar dataType="xsd:string" dictRef="x:value">2.000000</scalar>
</list>
<list>
<scalar dataType="xsd:string" dictRef="x:parameter">third order</scalar>
<scalar dataType="xsd:string" dictRef="x:value">shell-resolved</scalar>
</list>
<list>
<scalar dataType="xsd:string" dictRef="x:parameter">anisotropic</scalar>
<scalar dataType="xsd:string" dictRef="x:value">true</scalar>
</list>
<list>
<scalar dataType="xsd:string" dictRef="x:parameter">a3</scalar>
<scalar dataType="xsd:string" dictRef="x:value">3.000000</scalar>
</list>
<list>
<scalar dataType="xsd:string" dictRef="x:parameter">a5</scalar>
<scalar dataType="xsd:string" dictRef="x:value">4.000000</scalar>
</list>
<list>
<scalar dataType="xsd:string" dictRef="x:parameter">cn-shift</scalar>
<scalar dataType="xsd:string" dictRef="x:value">1.200000</scalar>
</list>
<list>
<scalar dataType="xsd:string" dictRef="x:parameter">cn-exp</scalar>
<scalar dataType="xsd:string" dictRef="x:value">4.000000</scalar>
</list>
<list>
<scalar dataType="xsd:string" dictRef="x:parameter">max-rad</scalar>
<scalar dataType="xsd:string" dictRef="x:value">5.000000</scalar>
</list>
</list>
<list cmlx:templateRef="Solvation model">
<list>
<scalar dataType="xsd:string" dictRef="x:parameter">Solvent</scalar>
<scalar dataType="xsd:string" dictRef="x:value">toluene</scalar>
</list>
<list>
<scalar dataType="xsd:string" dictRef="x:parameter">Parameter file</scalar>
<scalar dataType="xsd:string" dictRef="x:value">internal GFN2-xTB/GBSA</scalar>
</list>
<list>
<scalar dataType="xsd:string" dictRef="x:parameter">Dielectric constant</scalar>
<scalar dataType="xsd:string" dictRef="x:value">7.0000E+00</scalar>
</list>
<list>
<scalar dataType="xsd:string" dictRef="x:parameter">Reference state</scalar>
<scalar dataType="xsd:string" dictRef="x:value">gsolv [1 M gas/solution]</scalar>
</list>
<list>
<scalar dataType="xsd:string" dictRef="x:parameter">Free energy shift</scalar>
<scalar dataType="xsd:string" dictRef="x:value">4.5239E-03 Eh 2.8388E+00 kcal/mol</scalar>
</list>
<list>
<scalar dataType="xsd:string" dictRef="x:parameter">Temperature</scalar>
<scalar dataType="xsd:string" dictRef="x:value">2.9815E+02 K</scalar>
</list>
<list>
<scalar dataType="xsd:string" dictRef="x:parameter">Density</scalar>
<scalar dataType="xsd:string" dictRef="x:value">8.6700E-01 kg/L</scalar>
</list>
<list>
<scalar dataType="xsd:string" dictRef="x:parameter">Solvent mass</scalar>
<scalar dataType="xsd:string" dictRef="x:value">9.2140E+01 g/mol</scalar>
</list>
<list>
<scalar dataType="xsd:string" dictRef="x:parameter">Interaction kernel</scalar>
<scalar dataType="xsd:string" dictRef="x:value">Still</scalar>
</list>
<list>
<scalar dataType="xsd:string" dictRef="x:parameter">Born radius scaling (c1)</scalar>
<scalar dataType="xsd:string" dictRef="x:value">1.5686E+00</scalar>
</list>
<list>
<scalar dataType="xsd:string" dictRef="x:parameter">Born radii integrator</scalar>
<scalar dataType="xsd:string" dictRef="x:value">GBOBC</scalar>
</list>
<list>
<scalar dataType="xsd:string" dictRef="x:parameter">Born offset</scalar>
<scalar dataType="xsd:string" dictRef="x:value">0.0000E+00 a0 0.0000E+00 AA</scalar>
</list>
<list>
<scalar dataType="xsd:string" dictRef="x:parameter">H-bond correction</scalar>
<scalar dataType="xsd:string" dictRef="x:value">false</scalar>
</list>
<list>
<scalar dataType="xsd:string" dictRef="x:parameter">Ion screening</scalar>
<scalar dataType="xsd:string" dictRef="x:value">false</scalar>
</list>
<list>
<scalar dataType="xsd:string" dictRef="x:parameter">Surface tension</scalar>
<scalar dataType="xsd:string" dictRef="x:value">1.0000E-05 Eh 1.5569E+01 dyn/cm</scalar>
</list>
<list>
<scalar dataType="xsd:string" dictRef="x:parameter">Grid points</scalar>
<scalar dataType="xsd:string" dictRef="x:value">230 per atom</scalar>
</list>
<list>
<scalar dataType="xsd:string" dictRef="x:parameter">Solvation model</scalar>
<scalar dataType="xsd:string" dictRef="x:value">GBSA</scalar>
</list>
</list>
</module>
</comment>Template definition
xml
<templateList> <template id="section" pattern="\s*\*\s+.*:\s*" endPattern="\s*\*\s+.*:\s*" endPattern2="\s*" endPattern3="\w.*" repeat="*"> <record>\s+\*\s*{X,xtb:header}:\s*</record> <record repeat="*">\s{6,}{X,x:parameter}\s{4}{X,x:value}</record> <transform process="addAttribute" xpath=".//cml:list[@cmlx:templateRef='missingID']" name="cmlx:templateRef" value="$string(..//cml:scalar[@dictRef='xtb:header']/text())" /> <transform process="delete" xpath=".//cml:list[./cml:scalar[@dictRef='xtb:header']]" />
</template> <template id="section" pattern="\s*\*\s+.*:\s*\S.*" endPattern="\s*\*\s+.*:\s*" endPattern2="\s*" endPattern3="\w.*" repeat="*"> <record id="header">\s+\*\s*{X,x:parameter}:\s*{X,x:value}</record> <record repeat="*">\s{6,}{X,x:parameter}\s{4}{X,x:value}</record> <transform process="addAttribute" xpath=".//cml:list[@cmlx:templateRef='missingID']" name="cmlx:templateRef" value="$string(..//cml:list[@cmlx:templateRef='header']//cml:scalar[@dictRef='x:parameter']/text())" /> <transform process="moveRelative" xpath=".//cml:list[@cmlx:templateRef='header']/cml:list" to="../../cml:list[position()=last()]" /> <transform process="delete" xpath=".//cml:list[./cml:scalar[@dictRef='xtb:header']]" />
</template>
</templateList>
<transform process="pullup" xpath=".//cml:list[@cmlx:templateRef]" />
<transform process="delete" xpath=".//cml:list[count(*)=0]" />
<transform process="delete" xpath=".//cml:module[count(*)=0]" />