Molcas

General Info

Molcas - General Info - Main fields

Field

Source

Sample value

Title

Set on Browse calculation publication

Sample calculation

Browse Item

URL pointing Browse published item

https://rodi.urv.es:8080/browse/handle/123456789/6

Program

program.header template

Molcas 8.0 - service pack 1

Author

Username fullname

Doe, John

Formula

Atom count from final geometry

C 8 H 12 N 8 O 2

Calculation type

Custom logic 1

Geometry optimization

Method

Custom logic 2

RASSCF RASPT2
../_images/MOLCAS_header.png

Atomics 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).

../_images/MOLCAS_geometry.png

Molecular Info

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

Symmetry information

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

../_images/MOLCAS_symmetry.png

Molecular Info

Molecular Info - Main fields

Field

Source

Sample value

Charge

Readed from “charge” scalar on molcharge line or from mulliken module

0.000

Multiplicity

Readed from scalar[m:spinquantumnum] inside wave.specs module OR from scalar[m:spin] inside scf-ksdft module

3
../_images/MOLCAS_molecularinfo.png

Solvation input

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

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

../_images/MOLCAS_solvation.png

Integrals

Data source: <module cmlx:templateRef=’seward.generate’>

../_images/MOLCAS_sewardgenerate.png

Bond distances

Data source (to read molecule and calculate bonds): <module cmlx:templateRef=’coordinates’>

../_images/MOLCAS_bonddistances.png

Restrictions in the Geometry Optimization

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

../_images/MOLCAS_restrictions.png

Modules

Wave function specification

Data source: <module cmlx:templateRef=’wave.specs’>

../_images/MOLCAS_module_wavefunction.png

Orbital specifications

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

../_images/MOLCAS_module_orbitalspecs.png

CI expansion specifications

Data source: <module cmlx:templateRef=’ci.expansion’>

../_images/MOLCAS_module_ciexpansion.png

Energies

Data source: <module cmlx:templateRef=’wave.printout’>

../_images/MOLCAS_module_energies.png

Wave functions / Weights of the most important CSFs

Data source <module cmlx:templateRef=’wave.printout’>

../_images/MOLCAS_module_wavefunctioncsf.png

Natural Occupation numbers

Data source: <module cmlx:templateRef=’wave.printout’>, module “natural”

../_images/MOLCAS_module_natural.png

Mulliken Spin Population

Data source: <module cmlx:templateRef=’mulliken’>, submodule “mulliken.spin”

../_images/MOLCAS_module_mullikenspin.png

Electrostatic moments

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

../_images/MOLCAS_module_electrostaticmoments.png

Population analysis / Mulliken atomic charges

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

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

../_images/MOLCAS_module_loprop.png ../_images/MOLCAS_module_mulliken.png

Single-State CASPT2

Data source: <module cmlx:templateRef=”final.caspt2”>

../_images/MOLCAS_module_singlestate_caspt2.png

Final energy

Data source: <module cmlx:templateRef=”scf-ksdft”> scalar dictRef=’m:scfener’

Data source: <module cmlx:templateRef=”cchc”> scalar dictRef=’m:e2mp2energy’

Data source: <module cmlx:templateRef=”cchc”> scalar dictRef=’m:e2ccsdenergy’

Data source: <module cmlx:templateRef=”ccsdt”> scalar dictRef=’m:ccsdtcorrenergy’

../_images/MOLCAS_module_finalenergy.png ../_images/MOLCAS_module_finalenergy2.png

HZERO

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

../_images/MOLCAS_module_hzero.png

Harmonic frequencies

This module also allows displaying harmonic frequency intensities on a customizable chart.

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

../_images/MOLCAS_module_harmonicfreq.png ../_images/MOLCAS_module_harmonicfreq2.png

IR spectrum / Vibrational frequencies

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

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

../_images/MOLCAS_module_frequencies.png

Multipole Expansion Analysis

Data source:<module cmlx:templateRef=”atom.expansion”>

../_images/MOLCAS_module_multipoleexpansion.png

LoProp Analysis

Data source: <module cmlx:templateRef=’dynamic.loprop’>

../_images/MOLCAS_module_loprop_analysis.png
1

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

 1    $isRestrictedOpt  Exists module <module cmlx:templateRef="constraint" > ?
 2    $isOptimization   Input file from <module cmlx:templateRef="molcas.input" > is setup to perform a geometry optimization?
 3    $isTS           TS keyword is defined inside <module cmlx:templateRef="molcas.input" > ?
 4    $isIncomplete   Convergence table from <module cmlx:templateRef="energy.statistics" > shows 'all converged' OR $isOptimization and $hasLastEnergySection ?
 5
 6
 7    <!-- Calculation type related constants -->
 8    <xsl:param name="isRestrictedOpt"/>
 9    <xsl:param name="isOptimization"/>
10    <xsl:param name="isTS"/>
11    <xsl:param name="isIncomplete"/>
12
13    <xsl:choose>
14        <xsl:when test="$isRestrictedOpt">
15            <xsl:value-of select="$molcas:RestrictedGeomOpt"/>
16        </xsl:when>
17        <xsl:when test="$isOptimization">
18            <xsl:value-of select="$molcas:GeometryOpt"/>
19        </xsl:when>
20        <xsl:otherwise>
21            <xsl:value-of select="$molcas:SinglePoint"/>
22        </xsl:otherwise>
23    </xsl:choose>
24    <xsl:if test="$isTS">
25        <xsl:text> </xsl:text><xsl:value-of select="$molcas:TS"/>
26    </xsl:if>
27    <xsl:if test="$isIncomplete">
28        <xsl:text> </xsl:text><xsl:value-of select="$molcas:Incomplete"/>
29    </xsl:if>
2

string molcas:getMethods node* modules node ksdft node wavespecs

 1    $modules    Array with all executed module names
 2    $ksdft      Module from <module cmlx:templateRef="scf-ksdft" >
 3    $wavespecs  Entire <module cmlx:templateRef="wave.specs" > module
 4
 5
 6        <xsl:param name="modules"/>
 7        <xsl:param name="ksdft" />
 8        <xsl:param name="wavespecs" />
 9
10        <xsl:variable name="isCASSCF" select="
11            if(exists($wavespecs) and contains($modules,$molcas:RASSCFmodule) and ($wavespecs/cml:scalar[@dictRef='m:ras1holes'] = '0') and ($wavespecs/cml:scalar[@dictRef='m:ras3holes'] = 0)) then
12                true()
13            else
14                false()"/>
15        <xsl:variable name="isRASSCF" select="
16            if(contains($modules,$molcas:RASSCFmodule)) then
17                true()
18            else
19                false()"/>
20
21        <xsl:variable name="moduleArray">
22            <xsl:for-each select="$modules">
23                <xsl:value-of select="concat(upper-case(string(.)),'|')"/>
24            </xsl:for-each>
25        </xsl:variable>
26
27        <xsl:for-each select="distinct-values(tokenize($moduleArray/text(),'[|]+'))">
28            <xsl:if test="matches(.,$molcas:methodsRegex)">
29                <xsl:choose>
30                    <xsl:when test="exists($ksdft) and matches(.,$molcas:SCFmodule)">
31                        <xsl:choose>
32                            <xsl:when test="matches($ksdft,$molcas:SCFmodule)">
33                                <xsl:text>HF </xsl:text>
34                            </xsl:when>
35                            <xsl:otherwise>
36                                <xsl:text>DFT </xsl:text>
37                            </xsl:otherwise>
38                        </xsl:choose>
39                    </xsl:when>
40                    <xsl:when test="matches(.,$molcas:RASSCFmodule)">
41                        <xsl:choose>
42                            <xsl:when test="$isCASSCF">
43                                <xsl:value-of select="$molcas:CASSCFmodule"/><xsl:text> </xsl:text>
44                            </xsl:when>
45                            <xsl:otherwise>
46                                <xsl:value-of select="."/><xsl:text> </xsl:text>
47                            </xsl:otherwise>
48                        </xsl:choose>
49                    </xsl:when>
50                    <xsl:when test="matches(.,$molcas:CASPT2module)">
51                        <xsl:choose>
52                            <xsl:when test="not($isCASSCF) and $isRASSCF">
53                                <xsl:value-of select="$molcas:RASPT2module"/><xsl:text> </xsl:text>
54                            </xsl:when>
55                            <xsl:otherwise>
56                                <xsl:value-of select="."/><xsl:text> </xsl:text>
57                            </xsl:otherwise>
58                        </xsl:choose>
59                    </xsl:when>
60                    <xsl:otherwise>
61                        <xsl:value-of select="."/><xsl:text> </xsl:text>
62                    </xsl:otherwise>
63                </xsl:choose>
64            </xsl:if>
65        </xsl:for-each>