Mopac

General Info

Mopac - 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/100/5672
Program	header template	Mopac 2016 - 16.041 64BITS
Author	Username fullname	Doe, John
Formula	Atom count from final geometry	C 4 H 6 O 4
Calculation type	Custom logic 1	Geometry optimization
Method	Custom logic 2	RASSCF RASPT2

Molecular Info

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

Molecular Info

Molecular Info - Main fields

Field	Source	Sample value
Charge	Readed from input file section of input.file module	0.000
Multiplicity	Readed from input file section input.file module with SINGLET, DOUBLE, TRIPLET … keywords.	3

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.

Initially its read from geometry module

Modules

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’>

Final results - energies

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

1

string molcas:getCalcType boolean isRestrictedOpt boolean isOptimization boolean isTS boolean isIncomplete

    $isOptimization   Exists module <module cmlx:templateRef="optimization" > ?
    $hasVibrations    Exists module <module cmlx:templateRef="vibrations" > ?

    $negativeFrequenciesCount  Negative frequencies count from <module cmlx:templateRef="vibrations" > module
    $isTS                      A TS calculation was setup on the <module cmlx:templateRef="inputlines" >

      <xsl:param name="isOptimization" as="xs:boolean"/>
        <xsl:param name="hasVibrations" as="xs:boolean"/>
        <xsl:param name="negativeFrequenciesCount" as="xs:integer"/>
        <xsl:param name="isTS" as="xs:boolean"/>

        <xsl:variable name="type">
            <xsl:choose>
                <xsl:when test="$isOptimization">
                    <xsl:value-of select="$mp:GeometryOptimization"/>
                </xsl:when>
                <xsl:otherwise>
                    <xsl:value-of select="$mp:SinglePoint"/>
                </xsl:otherwise>
            </xsl:choose>
        </xsl:variable>

        <xsl:variable name="type2">
            <xsl:if test="$hasVibrations">
                <xsl:choose>
                    <xsl:when test="$negativeFrequenciesCount = 1 and $isTS" >
                        <xsl:value-of select="$mp:TransitionState"/>
                    </xsl:when>
                    <xsl:when test="$negativeFrequenciesCount = 0">
                        <xsl:value-of select="$mp:Minimum"/>
                    </xsl:when >
                </xsl:choose>
            </xsl:if>
        </xsl:variable>
        <xsl:value-of select="concat($type, ' ', $type2)"/>

2

string* mp:getMethods nodes inputLines

    $inputLines   Input lines from <module cmlx:templateRef="inputlines" >

    <xsl:variable name="mp:methodsRegex" select="'^(HF|UHF|RHF|PM3|PM6|PM6-D3|PM6-DH\+|PM6-DH2|PM6-DH2X|PM6-D3H4|PM6-D3H4X|PMEP|PM7|PM7-TS|AM1|RM1|MNDO|MNDOD).*'"/>

    <xsl:for-each select="$inputLines//cml:scalar[@dictRef='mp:inputline']">
        <xsl:variable name="line" select="./text()"/>
        <xsl:for-each select="tokenize($line,'\s+')">
            <xsl:variable name="command" select="."/>
                <xsl:if test="matches(upper-case($command), $mp:methodsRegex)">
                    <xsl:value-of select="$command"/><xsl:text> </xsl:text>
                </xsl:if>
        </xsl:for-each>
    </xsl:for-each>