Orca
General Info
Field |
Source |
Sample value |
---|---|---|
Title |
Set on Browse calculation publication |
Sample calculation |
Browse Item |
URL pointing Browse published item |
|
Program |
Orca 3.0.1 |
|
Author |
Username fullname |
Doe, John |
Formula |
Atom count from final geometry |
H 2 Fe 1 O 1 |
Calculation type |
Custom logic 1 |
Geometry optimization Minimum |
Method(s) |
Custom logic 2 |
DFT ( PBE0 ) |
Modules
Atomic coordinates
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.
Molecular Info
This section captures molecule additional information not captured on previous section.
Field |
Source |
Sample value |
---|---|---|
Multiplicity |
Readed from Mul parameter on General settings section of scfsettings module |
1 |
Charge |
Readed from Charge parameter on General settings section of scfsettings module |
0 |
Bond distances
Data source (to read molecule and calculate bonds): <module cmlx:templateRef=’input’>
Data source (to read molecule and calculate bonds): <module cmlx:templateRef=’geometry’>
Solvation input
Data source: <module cmlx:templateRef=’cosmo’>
Restrictions in the Geometry Optimization
Data source: <module cmlx:templateRef=’optsetup’>
Total SCF energy
Data source: <module cmlx:templateRef=’totalenergy’>
Data source: <module cmlx:templateRef=’mp2’>
Data source: <module cmlx:templateRef=’ci’>
Data source: <module cmlx:templateRef=’d3’>
IR spectrum / Vibrational frequencies
This module will display JSpecView + JSmol plugins (using javascript libraries) working together to represent molecule IR spectrum.
Data source: <module cmlx:templateRef=’vibrations’>
Data source: <module cmlx:templateRef=’irspectrum’>
Population analysis
Data source <module cmlx:templateRef=’loewdin’>
Data source <module cmlx:templateRef=’mullikenpopulation’>
Electrostatic moments
Data source: Charge parameter on General settings section of scfsettings
Data source: modulecmlx:templateRef=’electricproperties’
Broken symmetry magnetic coupling analysis
Data source: <module cmlx:templateRef=”brokensym”>
Frontier orbitals
Data source: <module cmlx:templateRef=’orbitalenergies’>
Natural orbitals
Data source: <module cmlx:templateRef=’natural’>
NMR Shielding tensors
Data source:
<module cmlx:templateRef=”nmr”>
TDHF / TDDFT
This section displays an interative chart to visualize root energies and an additional table with most relevant dominant contributions to each root
Data source: <module cmlx:templateRef=’tddft’>
Data source: <module cmlx:templateRef=’orbitalenergies’>
g-matrix and ZFS
Data source: <module cmlx:templateRef=’eprnmr’>
Final results
Data source: <module cmlx:templateRef=’totalenergy’>
Data source: <module cmlx:templateRef=’spincontamination’>
Data source: <module cmlx:templateRef=’innerenergy’>
Data source: <module cmlx:templateRef=’mp2’>
Data source: <module cmlx:templateRef=’ci’>
Data source: <module cmlx:templateRef=’dftd3’>
- 1
string
orca:getCalcType
booleanisOptimization
booleanisBrokenSymm
booleanhasVibrations
integernegativeFrequenciesCount
1 $isOptimization Refers to function orca:isOptimization($commands), which searches optimitzation keywords from <module cmlx:templateRef="input" > module 2 $isBrokenSymm Refers to function orca:isBrokenSymm($commands) which searches BrokenSymm keyword from <module cmlx:templateRef="input" > module 3 $hasVibrations Exists module <module cmlx:templateRef="vibrations" > ? 4 $negativeFrequenciesCount Count negative frequencies from <module cmlx:templateRef="vibrations" > ? 5 6 7 <!-- Calculation type related constants --> 8 <xsl:variable name="orca:GeometryOptimization" select="'Geometry optimization'" /> 9 <xsl:variable name="orca:SinglePoint" select="'Single point'" /> 10 <xsl:variable name="orca:BrokenSymmetry" select="'Broken symmetry'" /> 11 <xsl:variable name="orca:TransitionState" select="'TS'" /> 12 <xsl:variable name="orca:Minimum" select="'Minimum'"/> 13 14 <!-- Calculation type variables --> 15 <xsl:param name="isOptimization" as="xs:boolean"/> 16 <xsl:param name="isBrokenSymm" as="xs:boolean"/> 17 <xsl:param name="hasVibrations" as="xs:boolean"/> 18 <xsl:param name="negativeFrequenciesCount" as="xs:integer"/> 19 20 <xsl:variable name="type"> 21 <xsl:choose> 22 <xsl:when test="$isOptimization"> 23 <xsl:value-of select="$orca:GeometryOptimization"/> 24 </xsl:when> 25 <xsl:when test="$isBrokenSymm"> 26 <xsl:value-of select="$orca:BrokenSymmetry"/> 27 </xsl:when> 28 <xsl:otherwise> 29 <xsl:value-of select="$orca:SinglePoint"/> 30 </xsl:otherwise> 31 </xsl:choose> 32 </xsl:variable> 33 34 <xsl:variable name="type2"> 35 <xsl:if test="$hasVibrations"> 36 <xsl:choose> 37 <xsl:when test="$negativeFrequenciesCount > 0"> 38 <xsl:value-of select="$orca:TransitionState"/> 39 </xsl:when> 40 <xsl:otherwise> 41 <xsl:value-of select="$orca:Minimum"/> 42 </xsl:otherwise> 43 </xsl:choose> 44 </xsl:if> 45 </xsl:variable> 46 47 <xsl:value-of select="concat($type, ' ', $type2)"/>
- 2
string
orca:getMehods
nodesetsection
booleanisTddft
1 $section Input section elements from <module cmlx:templateRef="input"> module 2 $isTddft Refers to function orca:isTddft($commands) which searches tddft keywords from <module cmlx:templateRef="input" > module 3 4 <xsl:for-each select="$section/cml:array[@dictRef='cc:keywords']"> 5 <xsl:variable name="line" select="./text()"/> 6 <xsl:for-each select="tokenize($line,'\s+')"> 7 <xsl:variable name="command" select="."/> 8 <xsl:choose> 9 <xsl:when test="matches(upper-case($command), $orca:methodsRegex)"> 10 <xsl:if test="$isTddft and matches(upper-case($command), '(DFT|HF)')">TD</xsl:if><xsl:value-of select="$command"/><xsl:text> </xsl:text> 11 </xsl:when> 12 <xsl:when test="matches(upper-case($command),$orca:calculationLevelRegex)"> 13 <xsl:if test="$isTddft">TD</xsl:if><xsl:value-of select="$orca:calculationLevels/level[@id=upper-case($command)]/@method"/><xsl:text> </xsl:text> 14 </xsl:when> 15 </xsl:choose> 16 </xsl:for-each> 17 </xsl:for-each> 18 19 <xsl:variable name="blocklines" select="$section//cml:module[@cmlx:templateRef='block']/cml:scalar"/> 20 <xsl:for-each select="$blocklines"> 21 <xsl:variable name="line" select="./text()"/> 22 <xsl:for-each select="tokenize($line,'\s+')"> 23 <xsl:variable name="command" select="."/> 24 <xsl:choose> 25 <xsl:when test="matches(upper-case($command), $orca:methodsRegex)"> 26 <xsl:if test="$isTddft and matches(upper-case($command), '(DFT|HF)')">TD</xsl:if><xsl:value-of select="$command"/><xsl:text> </xsl:text> 27 </xsl:when> 28 <xsl:when test="matches(upper-case($command),$orca:calculationLevelRegex)"> 29 <xsl:if test="$isTddft">TD</xsl:if><xsl:value-of select="$orca:calculationLevels/level[@id=upper-case($command)]/@method"/><xsl:text> </xsl:text> 30 </xsl:when> 31 </xsl:choose> 32 </xsl:for-each> 33 </xsl:for-each>