l301.pcm.standard

Implementation level
Type Status
CML extraction template image0
HTML5 representation image1
Template attributes
Attribute Value
source Gaussian log
id l301.pcm.standard
pattern \sPolarizab lesContinuumsModels+(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.

<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.

<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.

<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.

<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.

<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.

<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']" />