l301.pcm.standard ​
Implementation level ​
| Type | Status |
|---|---|
| CML extraction template |  |
| HTML5 representation |  |
Template attributes ​
| Attribute | Value |
|---|---|
| source | Gaussian log |
| id | l301.pcm.standard |
| pattern | \sPolarizable\sContinuum\sModel\s+\(PCM\).* |
| endPattern | \s*\-+.* |
| name | Polarizable continuum model - standard |
| endOffset | 1 |
| repeat | * |
| xml:base | l301/l301.pcm.standard.xml |
Input ​
Polarizable Continuum Model (PCM)
=================================
Model : PCM.
Atomic radii : UA0 (Simple United Atom Topological Model).
Polarization charges : Total charges.
Charge compensation : None.
Solution method : Matrix inversion.
Cavity : GePol (RMin=0.200 OFac=0.890).
Default sphere list used, NSphG= 54.
Tesserae with average area of 0.200 Ang**2.
Solvent : Acetone, Eps = 20.700000
Eps(inf)= 1.841000
RSolv = 2.380000 Ang.
------------------------------------------------------------------------------
Input ​
Polarizable Continuum Model (PCM)
=================================
Model : PCM.
Atomic radii : UA0 (Simple United Atom Topological Model).
Polarization charges : Total charges.
Charge compensation : None.
Solution method : Matrix inversion.
Cavity : GePol (RMin=0.200 OFac=0.890).
Default sphere list used, NSphG= 45.
Tesserae with average area of 0.200 Ang**2.
Solvent : non-standard Water,
Eps = 37.800000
Eps(infinity) = 1.776000
d(Eps)/dT = -0.356200 K**-1
Molar volume = 18.070000 Ang**3
Numeral density = 0.033480 Ang**-3
Absolute temperature = 298.150000 K
Thermal expansion coefficient = 0.000257 K**-1
RSolv = 2.642000 Ang.
------------------------------------------------------------------------------
Input ​
Polarizable Continuum Model (PCM)
=================================
Model : PCM.
Atomic radii : SMD-Coulomb.
Polarization charges : Total charges.
Charge compensation : None.
Solution method : Matrix inversion.
Cavity type : VdW (van der Waals Surface) (Alpha=1.000).
Cavity algorithm : GePol (No added spheres)
Default sphere list used, NSphG= 2.
Lebedev-Laikov grids with approx. 5.0 points / Ang**2.
Smoothing algorithm: Karplus/York (Gamma=1.0000).
Polarization charges: spherical gaussians, with
point-specific exponents (IZeta= 3).
Self-potential: point-specific (ISelfS= 7).
Self-field : sphere-specific E.n sum rule (ISelfD= 2).
1st derivatives : Analytical E(r).r(x)/FMM algorithm (CHGder, D1EAlg=3).
Cavity 1st derivative terms included.
Solvent : Water, Eps= 78.355300 Eps(inf)= 1.777849
------------------------------------------------------------------------------
Input ​
Polarizable Continuum Model (PCM)
=================================
Model : C-PCM.
Atomic radii : UFF (Universal Force Field).
Polarization charges : Total charges.
Charge compensation : None.
Solution method : Matrix inversion.
Cavity type : Scaled VdW (van der Waals Surface) (Alpha=1.100).
Cavity algorithm : GePol (No added spheres)
Default sphere list used, NSphG= 2.
Lebedev-Laikov grids with approx. 5.0 points / Ang**2.
Smoothing algorithm: Karplus/York (Gamma=1.0000).
Polarization charges: spherical gaussians, with
point-specific exponents (IZeta= 3).
Self-potential: point-specific (ISelfS= 7).
Self-field : sphere-specific E.n sum rule (ISelfD= 2).
1st derivatives : Analytical E(r).r(x)/FMM algorithm (CHGder, D1EAlg=3).
Cavity 1st derivative terms included.
Solvent : Water, Eps= 78.355300 Eps(inf)= 1.777849
------------------------------------------------------------------------------
Input ​
Polarizable Continuum Model (PCM)
=================================
Model : PCM.
Atomic radii : UFF (Universal Force Field).
Polarization charges : Total charges.
Charge compensation : None.
Solution method : Matrix inversion.
Cavity type : Scaled VdW (van der Waals Surface) (Alpha=1.100).
Cavity algorithm : GePol (No added spheres)
Default sphere list used, NSphG= 2.
Lebedev-Laikov grids with approx. 5.0 points / Ang**2.
Smoothing algorithm: Karplus/York (Gamma=1.0000).
Polarization charges: spherical gaussians, with
point-specific exponents (IZeta= 3).
Self-potential: point-specific (ISelfS= 7).
Self-field : sphere-specific E.n sum rule (ISelfD= 2).
1st derivatives : Analytical E(r).r(x)/FMM algorithm (CHGder, D1EAlg=3).
Cavity 1st derivative terms included.
Solvent : Water, Eps= 78.355300 Eps(inf)= 1.777849
------------------------------------------------------------------------------
Output text ​
xml
<comment class="example.output" id="l301.pcm.standard1">
<module cmlx:lineCount="14" cmlx:templateRef="l301.pcm.standard">
<scalar dataType="xsd:string" dictRef="g:model">PCM</scalar>
<scalar dataType="xsd:string" dictRef="g:atomicradii">UA0</scalar>
<scalar dataType="xsd:string" dictRef="g:polarcharges">Total charges</scalar>
<scalar dataType="xsd:string" dictRef="g:chargecompensation">None</scalar>
<scalar dataType="xsd:string" dictRef="g:solutionmethod">Matrix inversion</scalar>
<scalar dataType="xsd:string" dictRef="g:solvent">Acetone</scalar>
<scalar dataType="xsd:double" dictRef="g:eps">20.7</scalar>
<scalar dataType="xsd:double" dictRef="g:epsinfinity">1.841</scalar>
</module>
</comment>Output text ​
xml
<comment class="example.output" id="l301.pcm.standard2">
<module cmlx:lineCount="20" cmlx:templateRef="l301.pcm.standard">
<scalar dataType="xsd:string" dictRef="g:model">PCM</scalar>
<scalar dataType="xsd:string" dictRef="g:atomicradii">UA0</scalar>
<scalar dataType="xsd:string" dictRef="g:polarcharges">Total charges</scalar>
<scalar dataType="xsd:string" dictRef="g:chargecompensation">None</scalar>
<scalar dataType="xsd:string" dictRef="g:solutionmethod">Matrix inversion</scalar>
<scalar dataType="xsd:string" dictRef="g:solvent">non-standard Water</scalar>
<scalar dataType="xsd:double" dictRef="g:eps">37.8</scalar>
<scalar dataType="xsd:double" dictRef="g:epsinfinity">1.776</scalar>
</module>
</comment>Output text ​
xml
<comment class="example.output" id="l301.pcm.standard3">
<module cmlx:lineCount="20" cmlx:templateRef="l301.pcm.standard">
<scalar dataType="xsd:string" dictRef="g:model">PCM</scalar>
<scalar dataType="xsd:string" dictRef="g:atomicradii">SMD-Coulomb.</scalar>
<scalar dataType="xsd:string" dictRef="g:polarcharges">Total charges</scalar>
<scalar dataType="xsd:string" dictRef="g:chargecompensation">None</scalar>
<scalar dataType="xsd:string" dictRef="g:solutionmethod">Matrix inversion</scalar>
<scalar dataType="xsd:string" dictRef="g:solvent">Water</scalar>
<scalar dataType="xsd:double" dictRef="g:eps">78.3553</scalar>
<scalar dataType="xsd:double" dictRef="g:epsinfinity">1.777849</scalar>
</module>
</comment>Output text ​
xml
<comment class="example.output" id="l301.pcm.standard4">
<module cmlx:lineCount="20" cmlx:templateRef="l301.pcm.standard">
<scalar dataType="xsd:string" dictRef="g:model">C-PCM</scalar>
<scalar dataType="xsd:string" dictRef="g:atomicradii">UFF</scalar>
<scalar dataType="xsd:string" dictRef="g:polarcharges">Total charges</scalar>
<scalar dataType="xsd:string" dictRef="g:chargecompensation">None</scalar>
<scalar dataType="xsd:string" dictRef="g:solutionmethod">Matrix inversion</scalar>
<scalar dataType="xsd:string" dictRef="g:solvent">Water</scalar>
<scalar dataType="xsd:double" dictRef="g:eps">78.3553</scalar>
<scalar dataType="xsd:double" dictRef="g:epsinfinity">1.777849</scalar>
</module>
</comment>Output text ​
xml
<comment class="example.output" id="l301.pcm.standard5">
<module cmlx:lineCount="20" cmlx:templateRef="l301.pcm.standard">
<scalar dataType="xsd:string" dictRef="g:model">PCM</scalar>
<scalar dataType="xsd:string" dictRef="g:atomicradii">UFF</scalar>
<scalar dataType="xsd:string" dictRef="g:polarcharges">Total charges</scalar>
<scalar dataType="xsd:string" dictRef="g:chargecompensation">None</scalar>
<scalar dataType="xsd:string" dictRef="g:solutionmethod">Matrix inversion</scalar>
<scalar dataType="xsd:string" dictRef="g:solvent">Water</scalar>
<scalar dataType="xsd:double" dictRef="g:eps">78.3553</scalar>
<scalar dataType="xsd:double" dictRef="g:epsinfinity">1.777849</scalar>
</module>
</comment>Template definition ​
xml
<record repeat="2" />
<record id="model">\sModel\s+\:\s*{X,g:model}\..*</record>
<record id="atomicradii">\sAtomic\sradii\s+\:\s*{A,g:atomicradii}\.*\s*(\(.*\))*\.*\s*</record>
<record id="polarcharges">\sPolarization\scharges\s+\:\s*{X,g:polarcharges}\.\s*</record>
<record id="chargecompensation">\sCharge\scompensation\s+\:\s*{X,g:chargecompensation}\.\s*</record>
<record id="solutionmethod">\sSolution\smethod\s+\:\s*{X,g:solutionmethod}\.\s*</record>
<templateList> <template pattern="\s+Solvent.*Eps.*Eps.*" endPattern=".*" endOffset="0" repeat="*"> <record id="solventeps">\s+Solvent\s+\:{X,g:solvent},\s+Eps\s*\=\s*{F,g:eps}\s*Eps\(inf\)\=\s*{F,g:epsinfinity}\s*</record>
</template> <template pattern="\s+Solvent\s+\:\s+.*Eps.*" endPattern=".*" endOffset="0"> <record id="solventeps">\s+Solvent\s+\:\s+{X,g:solvent},\s+Eps\s+\=\s+{F,g:eps}</record>
</template> <template pattern="^\s+Solvent((?!Eps).)*$" endPattern=".*" endOffset="0"> <record id="solvent">\s+Solvent\s*\:\s*{X,g:solvent}\s*,.*</record>
</template> <template pattern="\s+Eps\s*\=.*" endPattern=".*" endOffset="0"> <record id="eps">\s+Eps\s*\={F,g:eps}</record>
</template> <template pattern="\s+Eps\(inf.*" endPattern=".*" endOffset="0"> <record id="epsinfinity">.*\={F,g:epsinfinity}</record>
</template> <template pattern="^(?!(\s*Solvent)|(\s*Eps)).*" endPattern=".*" endPattern2="~" repeat="*" endOffset="0"> <record />
</template>
</templateList>
<transform process="pullup" xpath="./cml:module/cml:list/cml:list/cml:scalar" />
<transform process="pullup" xpath="./cml:module/cml:list/cml:scalar" repeat="2" />
<transform process="pullup" xpath="./cml:list/cml:scalar" repeat="1" />
<transform process="delete" xpath="./descendant-or-self::cml:list[count(*)=0]" />
<transform process="delete" xpath="./descendant-or-self::cml:list[count(*)=0]" />
<transform process="delete" xpath="./descendant-or-self::cml:module[count(*)=0]" />
<transform process="delete" xpath="./cml:module[@cmlx:templateRef='NULL_ID']" />