AMS / ADF¶

General Info¶

ADF - General Info - Main fields¶
Field	Source	Sample value
Title	Set on Browse calculation publication	Sample calculation
Browse Item	URL pointing Browse published item	https://iochem-bd.iciq.es/browse/handle/100/1722
Program	program.header template	ADF 2007
Author	Username fullname	Doe, John
Formula	Atom count from final geometry	H 1 O 40 P 1 Ti 1 W 11
Calculation type	Custom logic [1]	Geometry optimization Minimum
Method	DFT	DFT

ADF - General Info - Additional fields (if thermochemistry module exists)¶
Field	Source	Sample value
Temperature	<scalar dictRef=”cc:temp”>	300 K
Pressure	<scalar dictRef=”cc:press”>	1.0 atm

Atoms and Basis Sets¶

After header section, our HTML resume will output a xyz coordinates table with current molecule atoms.

For every atom, we will output it’s serial number, atom type, coordinates in angstroms, basis used and contraction.

In geometry optimizations calculations, next to geometry section header there will appear the word (optimized), pointing that this geometry is the last one from all optimization steps and has converged.

If the geometry optimization did not converge, there will appear the phrase (calculation did not converge).

If there are multiple geometries we’ll capture them acording with the following table order :

Atomic coordinates - Possible candidates (most important first)¶
Section	Note
<module cmlx:templateRef=”geometry.cycle”>	Latest geometry cycle(Coordinates on Input orientation)
<module cmlx:templateRef=”geometry.cycle”>	Lastest geom.opt. (Coordinates)
<module cmlx:templateRef=”quild.coord”>	Latest quild iteration
<module cmlx:templateRef=”nuclear.coordinates”>	NMR geometry
<module cmlx:templateRef=”geometry”>	Single point initial geometry

Molecular Info¶

This section captures molecule additional information not captured on previous section.

Molecular Info - Main fields¶
Field	Source	Description
Spin polarization	<scalar dictRef=”a:spinPolarization”>	Variable found inside logfile module (last instance is captured)
Multiplicity	Depends on spin polarization	If spin polarization exists, multiplicity = spinpolarization + 1, otherwise multiplicity = 1
Charge	<scalar dictRef=”a:charge”>	Variable found inside logfile module (last instance is captured)
Solvation	<module cmlx:templateRef=”solvation”>	Solvation parameters

Modules¶

Bonding energy¶

Data source: <module cmlx:templateRef=’bonding.energy’>

../_images/ADF_module_bondingenergies.png

Fit test¶

Data source: <module cmlx:templateRef=’fit.test’>

MOs / SFO gross populations¶

Data source: <module cmlx:templateRef=’molecular-orbitals’>

../_images/ADF_module_molecularorbitals.png

MOs Energies¶

Data source: <module cmlx:templateRef=’orbital.energies’>

Data source: <module cmlx:templateRef=’orbital.energies.spin’>

../_images/ADF_module_orbitalenergies.png

Data source: <module cmlx:templateRef=’orbital.energies.spin’>

../_images/ADF_module_orbitalenergiesspin.png

Mulliken Atomic Charges¶

Data source <module cmlx:templateRef=’mulliken’>

Multipole Derived Atomic Charges¶

Data source: <module cmlx:templateRef=’atomic.charges’>

Data source: <module cmlx:templateRef=’atomic.charges.spin’>

Data source: <module cmlx:templateRef=’spin.density’>

../_images/ADF_module_multipolederivedatomiccharges.png

../_images/ADF_module_multipolederivedatomiccharges2.png

../_images/ADF_module_multipolederivedatomiccharges3.png

Quadrupole Moment¶

Data source: <module cmlx:templateRef=’quadrupole.moment’>

S**2¶

Data source: <module cmlx:templateRef=”s2”>

Vibrational Frequencies and Intensities¶

Data source: <module cmlx:templateRef=’intensities’>

IR spectrum¶

Data source: <module cmlx:templateRef=’vibrations’>

This module will display JSpecView + JSmol plugins (using javascript libraries) working together to represent molecule IR spectrum.

Zero Point Energy¶

Data source:

<module cmlx:templateRef=”zeropoint”><scalar dictRef=”cc:zeropoint”>

../_images/ADF_module_zeropointenergy.png

Thermochemistry¶

Data source: <module cmlx:templateRef=’thermochemistry’>

Final Excitation Energies¶

Data source: <module cmlx:templateRef=’excitation.energy’>

Rotatory Strengths¶

Data source: <module cmlx:templateRef=’excitation.energy’>

NMR Shielding Tensors¶

Data source: <module cmlx:templateRef=’nmr’>

Timing¶

Data source: <module cmlx:templateRef=’timing’>

Input file¶

Data source: <module cmlx:templateRef=’input.file’>

[1]

string adf:getCalcType string runtype boolean hasVibrations boolean isMininum boolean isQuild boolean isNMR

$runtype        Refers to <scalar dataType="xsd:string" dictRef="cc:runtype">
$hasVibrations  Exists module <module cmlx:templateRef="vibrations" > ?
$isMinimum      All frequencies from <module cmlx:templateRef="vibrations" > are positive?
$isQuild        Exists module <module cmlx:templateRef="quild.iteration" > ?
$isNMR          Exists module <module cmlx:templateRef="nucleus" > ?


<!-- Calculation type related constants -->
<xsl:variable name="adf:GeometryOptimization" select="'Geometry optimization'" />
<xsl:variable name="adf:SinglePoint" select="'Single point'" />
<xsl:variable name="adf:TransitionState" select="'TS'" />
<xsl:variable name="adf:Frequencies" select="'Frequencies'" />
<xsl:variable name="adf:Minimum" select="'Minimum'"/>
<xsl:variable name="adf:Quild" select="'Quild'" />
<xsl:variable name="adf:NMR" select="'NMR'" />

<!-- Calculation type variables -->
<xsl:variable name="calcType" select="
    if(compare($runType,'GEOMETRY OPTIMIZATION') = 0)
        then $adf:GeometryOptimization
    else
        if(compare($runType,'SINGLE POINT') = 0)
            then $adf:SinglePoint
        else
            if(compare($runType,'TRANSITION STATE') = 0)
                then $adf:TransitionState
            else
                if(compare($runType,'FREQUENCIES') = 0)
                    then $adf:Frequencies
                else
                    $adf:SinglePoint" />

<xsl:variable name="vibrations" select="
    if($hasVibrations)
        then if($isMinimum)
                then concat(' ', $adf:Minimum)
             else
                 if(compare($calcType,$adf:TransitionState) != 0)
                     then concat(' ',$adf:TransitionState)
                 else
                     ''
    else ''" />

<xsl:variable name="quild" select="
    if($isQuild)
        then concat(' ',$adf:Quild)
    else
        ''" />

<xsl:variable name="nmr" select="
    if($isNMR)
        then concat(' ',$adf:NMR)
    else
        ''"
/>
<xsl:sequence select="concat($calcType, $vibrations, $quild, $nmr)"/>