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
../_images/ADF_header.png

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
../_images/ADF_geometry.png

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
../_images/ADF_molecularinfo.png

Modules

Bonding energy

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

../_images/ADF_module_bondingenergies.png

Fit test

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

../_images/ADF_module_fittest.png

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’>

../_images/ADF_module_mullikenatomiccharges.png

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’>

../_images/ADF_module_quadrupolemoment.png

S**2

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

../_images/ADF_module_s2.png

Vibrational Frequencies and Intensities

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

../_images/ADF_module_intensities.png

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.

../_images/ADF_module_frequencies.png

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’>

../_images/ADF_module_thermochemistry.png

Final Excitation Energies

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

../_images/ADF_module_finalexcitationenergies.png

Rotatory Strengths

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

../_images/ADF_module_rotatory_str.png

NMR Shielding Tensors

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

../_images/ADF_module_nmr.png

Timing

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

../_images/ADF_module_timing.png

Input file

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

../_images/ADF_module_inputfile.png
1

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

 1    $runtype        Refers to <scalar dataType="xsd:string" dictRef="cc:runtype">
 2    $hasVibrations  Exists module <module cmlx:templateRef="vibrations" > ?
 3    $isMinimum      All frequencies from <module cmlx:templateRef="vibrations" > are positive?
 4    $isQuild        Exists module <module cmlx:templateRef="quild.iteration" > ?
 5    $isNMR          Exists module <module cmlx:templateRef="nucleus" > ?
 6
 7
 8    <!-- Calculation type related constants -->
 9    <xsl:variable name="adf:GeometryOptimization" select="'Geometry optimization'" />
10    <xsl:variable name="adf:SinglePoint" select="'Single point'" />
11    <xsl:variable name="adf:TransitionState" select="'TS'" />
12    <xsl:variable name="adf:Frequencies" select="'Frequencies'" />
13    <xsl:variable name="adf:Minimum" select="'Minimum'"/>
14    <xsl:variable name="adf:Quild" select="'Quild'" />
15    <xsl:variable name="adf:NMR" select="'NMR'" />
16
17    <!-- Calculation type variables -->
18    <xsl:variable name="calcType" select="
19        if(compare($runType,'GEOMETRY OPTIMIZATION') = 0)
20            then $adf:GeometryOptimization
21        else
22            if(compare($runType,'SINGLE POINT') = 0)
23                then $adf:SinglePoint
24            else
25                if(compare($runType,'TRANSITION STATE') = 0)
26                    then $adf:TransitionState
27                else
28                    if(compare($runType,'FREQUENCIES') = 0)
29                        then $adf:Frequencies
30                    else
31                        $adf:SinglePoint" />
32
33    <xsl:variable name="vibrations" select="
34        if($hasVibrations)
35            then if($isMinimum)
36                    then concat(' ', $adf:Minimum)
37                 else
38                     if(compare($calcType,$adf:TransitionState) != 0)
39                         then concat(' ',$adf:TransitionState)
40                     else
41                         ''
42        else ''" />
43
44    <xsl:variable name="quild" select="
45        if($isQuild)
46            then concat(' ',$adf:Quild)
47        else
48            ''" />
49
50    <xsl:variable name="nmr" select="
51        if($isNMR)
52            then concat(' ',$adf:NMR)
53        else
54            ''"
55    />
56    <xsl:sequence select="concat($calcType, $vibrations, $quild, $nmr)"/>