Basics Input Programs Output Examples
Introduction to Molcas
Ignacio Fernández Galván
Uppsala University, Sweden
CASMolcas WorkshopJerusalem, February 6th 2017
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 1 / 29 >
CAS
Basics Input Programs Output Examples
1 Basics
2 Input
3 Programs
4 Output
5 Examples• Molecular oxygen with Hartree–Fock• Geometry optimization of aniline
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 2 / 29 >
CAS
Basics Input Programs Output Examples
1 Basics
2 Input
3 Programs
4 Output
5 Examples• Molecular oxygen with Hartree–Fock• Geometry optimization of aniline
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 2 / 29 >
CAS
Basics Input Programs Output Examples
1 Basics
2 Input
3 Programs
4 Output
5 Examples• Molecular oxygen with Hartree–Fock• Geometry optimization of aniline
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 2 / 29 >
CAS
Basics Input Programs Output Examples
1 Basics
2 Input
3 Programs
4 Output
5 Examples• Molecular oxygen with Hartree–Fock• Geometry optimization of aniline
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 2 / 29 >
CAS
Basics Input Programs Output Examples
1 Basics
2 Input
3 Programs
4 Output
5 Examples• Molecular oxygen with Hartree–Fock• Geometry optimization of aniline
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 2 / 29 >
CAS
Basics Input Programs Output Examples
Brief history of Molcas
MOLCAS = MOLECULE (1970s) + CASSCF (1980s)Björn O. Roos, Jan Almlöf, Per E. M. Siegbahn, Ulf Wahlgren
• First public release: 1989
• Molcas-2: 1991
• Molcas-3: 1993 (CASPT2, gradients)
• Molcas-4: 1997
• Molcas 5: 2000 (MS-CASPT2, spin–orbit, relativistic)
• Molcas 6: 2003 (UHF, DFT, CC, ANO-RCC, MEP)
• Molcas 7: 2007 (CD, DKH, RASPT2, QM/MM)
• Molcas 8: 2014 (magnetism, GASSCF, RICD gradients)
• Future: . . . (DMRG, HDF5, open source)
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 3 / 29 >
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Basics Input Programs Output Examples
Key features of Molcas
• Multiconfigurational SCF:CASSCF, RASSCF, GASSCF, DMRG
• Multiconfigurational perturbation theory:CASPT2, RASPT2, GASPT2
• Efficient handling of integrals:ANO, Cholesky decomposition, symmetry
• General-purpose geometry optimization:minima, TSs, conical intersections, constraints, etc.
• Hartree–Fock, DFT, MP2, CCSD(T), MRCI...
• Properties, relativistic corrections
• Vibrational analysis and thermochemistry
• QM/MM interfaces
• Molecular dynamics
• . . .
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 4 / 29 >
CAS
Basics Input Programs Output Examples
Key features of Molcas
• Multiconfigurational SCF:CASSCF, RASSCF, GASSCF, DMRG
• Multiconfigurational perturbation theory:CASPT2, RASPT2, GASPT2
• Efficient handling of integrals:ANO, Cholesky decomposition, symmetry
• General-purpose geometry optimization:minima, TSs, conical intersections, constraints, etc.
• Hartree–Fock, DFT, MP2, CCSD(T), MRCI...
• Properties, relativistic corrections
• Vibrational analysis and thermochemistry
• QM/MM interfaces
• Molecular dynamics
• . . .
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 4 / 29 >
CAS
Basics Input Programs Output Examples
Some technical details
• Source code: Fortran, C
• Scripts: Perl, Python, sh
• Platforms: Linux, Unix, MacOS, Windows (Cygwin)
• Compilers: GCC, Intel, PGI, NAG, SunStudio
• Parallelization: Distributed memory through MPI
• Math libraries: MKL, ACML, OpenBLAS . . .
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 5 / 29 >
CAS
Basics Input Programs Output Examples
Structure of Molcas
• Independent, task-specific programsintegrals, wavefunction, gradient, geometry . . .
• Communication through scratch (work) directory:RunFile, integrals, wavefunction . . .
• Main parser (molcas.exe)Extended Molcas Input Language (EMIL)
• Driver script (molcas)find Molcas, run calculation or tool
molcas
tool
molcas.exe
[$WorkDir]
SEWARD
SCF
RASSCF
CASPT2
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 6 / 29 >
CAS
Basics Input Programs Output Examples
Structure of Molcas
• Independent, task-specific programsintegrals, wavefunction, gradient, geometry . . .
• Communication through scratch (work) directory:RunFile, integrals, wavefunction . . .
• Main parser (molcas.exe)Extended Molcas Input Language (EMIL)
• Driver script (molcas)find Molcas, run calculation or tool
molcas
tool
molcas.exe
[$WorkDir]
SEWARD
SCF
RASSCF
CASPT2
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 6 / 29 >
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Basics Input Programs Output Examples
Documentation and help
• Online manual:www.molcas.org/documentation/manual/www.molcas.org/documentation/manual.pdf
• Locally compiled manuals (make doc)
• Command-line help: molcas help
• Forum: cobalt.itc.univie.ac.at/molcasforum/
$ molcas helptype molcas help module to get the list of keywordstype molcas help module keyword to get the description of keywordtype molcas help -t text to locate texttype molcas help ENVIRONMENT to list ENV variablestype molcas help EMIL to list EMIL commandstype molcas help basis A to list basis set for the element A
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 7 / 29 >
CAS
Basics Input Programs Output Examples
Documentation and help
• Online manual:www.molcas.org/documentation/manual/www.molcas.org/documentation/manual.pdf
• Locally compiled manuals (make doc)
• Command-line help: molcas help
• Forum: cobalt.itc.univie.ac.at/molcasforum/
$ molcas helptype molcas help module to get the list of keywordstype molcas help module keyword to get the description of keywordtype molcas help -t text to locate texttype molcas help ENVIRONMENT to list ENV variablestype molcas help EMIL to list EMIL commandstype molcas help basis A to list basis set for the element A
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 7 / 29 >
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Basics Input Programs Output Examples
An example
water.input
&GATEWAYCoord = water.xyzBasis = ANO-RCC-MBGroup = NoSym
&SEWARD
&SCFUHFKSDFT = B3LYP
molcas -f water.input
• Input for each program startswith &name
• Keywords may needarguments
• The programs are run insequence
• Output goes to water.log,errors to water.err
• Additional files:water.GssOrb,water.scf.molden . . .
• Scratch directoryinstallation-dependent
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 8 / 29 >
CAS
Basics Input Programs Output Examples
An example
water.input
&GATEWAYCoord = water.xyzBasis = ANO-RCC-MBGroup = NoSym
&SEWARD
&SCFUHFKSDFT = B3LYP
molcas -f water.input
• Input for each program startswith &name
• Keywords may needarguments
• The programs are run insequence
• Output goes to water.log,errors to water.err
• Additional files:water.GssOrb,water.scf.molden . . .
• Scratch directoryinstallation-dependent
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 8 / 29 >
CAS
Basics Input Programs Output Examples
An example
water.input
&GATEWAYCoord = water.xyzBasis = ANO-RCC-MBGroup = NoSym
&SEWARD
&SCFUHFKSDFT = B3LYP
molcas -f water.input
• Input for each program startswith &name
• Keywords may needarguments
• The programs are run insequence
• Output goes to water.log,errors to water.err
• Additional files:water.GssOrb,water.scf.molden . . .
• Scratch directoryinstallation-dependent
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 8 / 29 >
CAS
Basics Input Programs Output Examples
An example
water.input
&GATEWAYCoord = water.xyzBasis = ANO-RCC-MBGroup = NoSym
&SEWARD
&SCFUHFKSDFT = B3LYP
molcas -f water.input
• Input for each program startswith &name
• Keywords may needarguments
• The programs are run insequence
• Output goes to water.log,errors to water.err
• Additional files:water.GssOrb,water.scf.molden . . .
• Scratch directoryinstallation-dependent
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 8 / 29 >
CAS
Basics Input Programs Output Examples
An example
water.input
&GATEWAYCoord = water.xyzBasis = ANO-RCC-MBGroup = NoSym
&SEWARD
&SCFUHFKSDFT = B3LYP
molcas -f water.input
• Input for each program startswith &name
• Keywords may needarguments
• The programs are run insequence
• Output goes to water.log,errors to water.err
• Additional files:water.GssOrb,water.scf.molden . . .
• Scratch directoryinstallation-dependent
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 8 / 29 >
CAS
Basics Input Programs Output Examples
An example
water.input
&GATEWAYCoord = water.xyzBasis = ANO-RCC-MBGroup = NoSym
&SEWARD
&SCFUHFKSDFT = B3LYP
molcas -f water.input
• Input for each program startswith &name
• Keywords may needarguments
• The programs are run insequence
• Output goes to water.log,errors to water.err
• Additional files:water.GssOrb,water.scf.molden . . .
• Scratch directoryinstallation-dependent
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 8 / 29 >
CAS
Basics Input Programs Output Examples
Configuration
Per calculation
Project base name for generated files
WorkDir scratch directory
Preferences
molcas setuprc → ~/.Molcas/molcasrc
MOLCAS location of the Molcas installation
MOLCAS_WORKDIR base name for scratch directories
MOLCAS_OUTPUT location for extra output files
MOLCAS_REDUCE_PRT reduce print during optimizations
MOLCAS_NPROCS number of parallel processes
MOLCAS_MEM maximum memory per process
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 9 / 29 >
CAS
Basics Input Programs Output Examples
Configuration
Per calculation
Project base name for generated files
WorkDir scratch directory
Preferences
molcas setuprc → ~/.Molcas/molcasrc
MOLCAS location of the Molcas installation
MOLCAS_WORKDIR base name for scratch directories
MOLCAS_OUTPUT location for extra output files
MOLCAS_REDUCE_PRT reduce print during optimizations
MOLCAS_NPROCS number of parallel processes
MOLCAS_MEM maximum memory per process
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 9 / 29 >
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Basics Input Programs Output Examples
Input syntax
&GATEWAY &ENDCOORwater.xyzBASIANO-RCC-MBGROUNOSYMRICDNOMOEnd of input
&GATEWAYCoordinates = water.xyzBasis set = ANO-RCC-MBGroup = NoSymRICD ; NoMove
• &END unnecessary
• End of input unnecessary
• only first 4 characterssignificant
• = and ; as newlines
• arbitrary indentation andmost empty lines
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 10 / 29 >
CAS
Basics Input Programs Output Examples
Input syntax
&GATEWAY &ENDCOORwater.xyzBASIANO-RCC-MBGROUNOSYMRICDNOMOEnd of input
&GATEWAYCoordinates = water.xyzBasis set = ANO-RCC-MBGroup = NoSymRICD ; NoMove
• &END unnecessary
• End of input unnecessary
• only first 4 characterssignificant
• = and ; as newlines
• arbitrary indentation andmost empty lines
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 10 / 29 >
CAS
Basics Input Programs Output Examples
Input syntax
&GATEWAY &ENDCOORwater.xyzBASIANO-RCC-MBGROUNOSYMRICDNOMOEnd of input
&GATEWAYCoordinates = water.xyzBasis set = ANO-RCC-MBGroup = NoSymRICD ; NoMove
• &END unnecessary
• End of input unnecessary
• only first 4 characterssignificant
• = and ; as newlines
• arbitrary indentation andmost empty lines
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 10 / 29 >
CAS
Basics Input Programs Output Examples
Input syntax
&GATEWAY &ENDCOORwater.xyzBASIANO-RCC-MBGROUNOSYMRICDNOMOEnd of input
&GATEWAYCoordinates = water.xyzBasis set = ANO-RCC-MBGroup = NoSymRICD ; NoMove
• &END unnecessary
• End of input unnecessary
• only first 4 characterssignificant
• = and ; as newlines
• arbitrary indentation andmost empty lines
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 10 / 29 >
CAS
Basics Input Programs Output Examples
Input syntax
&GATEWAY &ENDCOORwater.xyzBASIANO-RCC-MBGROUNOSYMRICDNOMOEnd of input
&GATEWAYCoordinates = water.xyzBasis set = ANO-RCC-MBGroup = NoSymRICD ; NoMove
• &END unnecessary
• End of input unnecessary
• only first 4 characterssignificant
• = and ; as newlines
• arbitrary indentation andmost empty lines
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 10 / 29 >
CAS
Basics Input Programs Output Examples
Input syntax
&GATEWAY &ENDCOORwater.xyzBASIANO-RCC-MBGROUNOSYMRICDNOMOEnd of input
&GATEWAYCoordinates = water.xyzBasis set = ANO-RCC-MBGroup = NoSymRICD ; NoMove
• &END unnecessary
• End of input unnecessary
• only first 4 characterssignificant
• = and ; as newlines
• arbitrary indentation andmost empty lines
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 10 / 29 >
CAS
Basics Input Programs Output Examples
Extended input
&GATEWAY
* Coord = water.xyzCoord = acrolein.xyzBasis = ANO-RCC-MBGroup = NoSymRICD // Faster
&SEWARD
/*&SCFKSDFT = B3LYP
*/
• Comments with *, // or/* */
• Variables with $ (can bedefined externally)
• Extra commands with >
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 11 / 29 >
CAS
Basics Input Programs Output Examples
Extended input
> Export BASIS = ANO-RCC-MB
> ForEach NUM in (1, ..., 5)
&GATEWAYCoord = geom_$NUM.xyzBasis = $BASISGroup = NoSym
&SEWARD
&SCF
>>> EndDo <<<
• Comments with *, // or/* */
• Variables with $ (can bedefined externally)
• Extra commands with >
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 11 / 29 >
CAS
Basics Input Programs Output Examples
Extended input
> Export BASIS = ANO-RCC-MB
> ForEach NUM in (1, ..., 5)
&GATEWAYCoord = geom_$NUM.xyzBasis = $BASISGroup = NoSym
&SEWARD
&SCF
>>> EndDo <<<
• Comments with *, // or/* */
• Variables with $ (can bedefined externally)
• Extra commands with >
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 11 / 29 >
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Basics Input Programs Output Examples
EMIL commands
> Unix ls > list
> Copy $CurrDir/init_orb↩ $Project.RasOrb
> Rm list
> Exit 1
> DoWhile> If (ITER .ne. 1)...> EndIf
> EndDo
> Eval R = 0.1 * $NUM
• Commands are run in$WorkDir
• $CurrDir refers to inputdirectory
• Copy, delete files
• Interrupt a calculation
• Loops, conditionals
• Simple expressions
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 12 / 29 >
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Basics Input Programs Output Examples
A partial map to Molcas
GATEWAY
Define system, ba-sis set, externalfield, etc.
1 518 800 km2 @ $4.74/km2
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 13 / 29 >
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Basics Input Programs Output Examples
A partial map to Molcas
SEWARD
Compute one- andtwo-electron inte-grals
1 518 800 km2 @ $4.74/km2
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 13 / 29 >
CAS
Basics Input Programs Output Examples
A partial map to Molcas
ALASKA
Compute integralderivatives andmolecular gradient
1 518 800 km2 @ $4.74/km2
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 13 / 29 >
CAS
Basics Input Programs Output Examples
A partial map to Molcas
DENALI/MCKINLEY
Compute secondderivatives and fre-quencies
1 518 800 km2 @ $4.74/km2
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 13 / 29 >
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Basics Input Programs Output Examples
Other important programs
SCF Hartree–Fock and DFT calculations
MBPT2 MP2 calculations
RASSCF CASSCF, RASSCF, GASSCF calculations
CASPT2 CASPT2, RASPT2 calculations
RASSI Spin–orbit and transition properties
SLAPAF Geometry optimization
DYNAMIX Molecular dynamics simulations
ESPF QM/MM interface
GRID_IT Generate volumetric data (grid) files
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 14 / 29 >
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Basics Input Programs Output Examples
GATEWAY
Native input
&GATEWAYBasis functionsO.ANO-RCC-MBO1 0.000 0.000 0.225
End of basisBasis functionsH.ANO-RCC-MBH2 0.000 1.442 -0.901
End of basisSymmetry = x y
• Default: bohr
• Symmetry-uniqueatoms
• Unique atom labels
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 15 / 29 >
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Basics Input Programs Output Examples
GATEWAY
Native input
&GATEWAYBasis functionsO.ANO-RCC-MBO1 0.000 0.000 0.119 angstrom
End of basisBasis functionsH.ANO-RCC-MBH2 0.000 0.763 -0.477 angstrom
End of basisSymmetry = x y
• Default: bohr
• Symmetry-uniqueatoms
• Unique atom labels
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 15 / 29 >
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Basics Input Programs Output Examples
GATEWAY
XYZ input
&GATEWAYCoord = 3
A sample water moleculeO 0.000 0.000 0.119H 0.000 0.763 -0.477H 0.000 0.763 -0.477
Group = FullBasis = ANO-RCC-MB
• Default: ångström
• All atoms
• Detect symmetry
• External file
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 15 / 29 >
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Basics Input Programs Output Examples
GATEWAY
XYZ input
&GATEWAYCoord = 3
A sample water molecule, in bohrO 0.000 0.000 0.225H 0.000 1.442 -0.901H 0.000 1.442 -0.901
Group = NoSymBasis = O.ANO-RCC-MB, H.ANO-RCC-VDZP
• Default: ångström
• All atoms
• Detect symmetry
• External file
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 15 / 29 >
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Basics Input Programs Output Examples
Basis sets
$ molcas help basis C...C.ANO-RCC-VTZP...C.ECP.Dolg.4s4p1d.2s2p1d.4e-MWB....C.STO-3G.Hehre.6s3p.2s1p.
Full specification (parts can be omitted):
1 Element symbol
2 Basis set name
3 Source/author
4 Primitives
5 Contracted functions
6 Auxiliary label
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Basics Input Programs Output Examples
SEWARD
• Computes integrals
• Almost always needed(especially change of geometry, basis set)
• Use Cholesky decomposition (RICD in GATEWAY)
• Typically no keywords
• Produces guessed orbitals ($Project.GssOrb)
&GATEWAY...RICD // Faster SEWARD, lower memory requirement
&SEWARD
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Basics Input Programs Output Examples
SCF
&SCFFileOrb = $Project.GssOrbUHFSpin = 1KSDFT = B3LYP
• All keywords optional
• Will use the “best”available orbitals
• Produces SCF orbitals($Project.ScfOrb)
• Several functionalsavailable for DFT
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Basics Input Programs Output Examples
SCF
&SCFFileOrb = $Project.GssOrbUHFSpin = 1KSDFT = B3LYP
• All keywords optional
• Will use the “best”available orbitals
• Produces SCF orbitals($Project.ScfOrb)
• Several functionalsavailable for DFT
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 18 / 29 >
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Basics Input Programs Output Examples
SCF
&SCFFileOrb = $Project.GssOrbUHFSpin = 1KSDFT = B3LYP
• All keywords optional
• Will use the “best”available orbitals
• Produces SCF orbitals($Project.ScfOrb)
• Several functionalsavailable for DFT
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 18 / 29 >
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Basics Input Programs Output Examples
SCF
&SCFFileOrb = $Project.GssOrbUHFSpin = 1KSDFT = B3LYP
• All keywords optional
• Will use the “best”available orbitals
• Produces SCF orbitals($Project.ScfOrb)
• Several functionalsavailable for DFT
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 18 / 29 >
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Basics Input Programs Output Examples
RASSCF
&RASSCFFileOrb = $Project.ScfOrbSpin = 3Charge = 0NActEl = 8 0 0RAS1 = 0RAS2 = 6RAS3 = 0CIRoot = 5 5 1
• Initial orbitals are crucial
• Different ways to specifyactive space
• State-average for excitedstates
• Produces MCSCF orbitals($Project.RasOrb)
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 19 / 29 >
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Basics Input Programs Output Examples
RASSCF
&RASSCFFileOrb = $Project.ScfOrbSpin = 3Charge = 0NActEl = 8 0 0RAS1 = 0RAS2 = 6RAS3 = 0CIRoot = 5 5 1
• Initial orbitals are crucial
• Different ways to specifyactive space
• State-average for excitedstates
• Produces MCSCF orbitals($Project.RasOrb)
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 19 / 29 >
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Basics Input Programs Output Examples
RASSCF
&RASSCFFileOrb = $Project.ScfOrbSpin = 3Charge = 0NActEl = 8 0 0RAS1 = 0RAS2 = 6RAS3 = 0CIRoot = 5 5 1
• Initial orbitals are crucial
• Different ways to specifyactive space
• State-average for excitedstates
• Produces MCSCF orbitals($Project.RasOrb)
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 19 / 29 >
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Basics Input Programs Output Examples
RASSCF
&RASSCFFileOrb = $Project.ScfOrbSpin = 3Charge = 0NActEl = 8 0 0RAS1 = 0RAS2 = 6RAS3 = 0CIRoot = 5 5 1
• Initial orbitals are crucial
• Different ways to specifyactive space
• State-average for excitedstates
• Produces MCSCF orbitals($Project.RasOrb)
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 19 / 29 >
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Basics Input Programs Output Examples
External programs
MolGUI molcas.altervista.org/Graphical interface, input generator, structure builder,job manager
GV www.molcas.org/GV/Graphical interface, structure generator, grid viewer,unmaintained
Luscus luscus.sourceforge.net/Graphical interface, structure generator, grid viewer
Molden www.cmbi.ru.nl/molden/Graphical interface, structure generator, orbital viewer
TheoDORE theodore-qc.sourceforge.net/Python scripts, wavefunction analysis
Molpy github.com/steabert/molpy/Python scripts, wavefunction and orbital handling
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 20 / 29 >
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Basics Input Programs Output Examples
Text output
MOLMOL
MOL CASMOMOLCA SM OLMO LC AS MOMO LC AS MOMO L CAS MOM O LCA S MOMOL CA SMO L
MOL CAS M OLCA SMMOLCASM OLCAS MOLCA SMOLCA
MOLCASMOL CASMOLCASMOLCAS MOLCASMOLMOLCASMOLC AS MO LCA SMOMOLCASMOLC ASMOLCA S MOLMOLCASMOLC ASMOLCASMOLCA S MOLMOLCASMOLC ASMOLCASMOLCASM O LCAMOLCASMOL CASMOLCASMOLCASMO L CAS MOLC AS MOLMOLCASMOL CASMOLCASMOLCASMOL C ASM OL CA SM O LMOLCASMOL CASMOLCASMOLCASMO LCA S M O LMOLCASMO LCASMOLCASMOLCA SMO L C A SMOMOLCAS MOLCASMOLCASM OLC A SMOL CMOL CASM OLCASMO L C ASM O L CA SM O L
MOLCASMOL CASM O LCAS M O LCASMOLCASMOLCASMOLCASMOLCASMOLCASMOLCASMOL
MOLCASMOLCASMOLCASMOLCASMOLCASMOLMOLCASMOLCASMOLCASMOLCASM
MOLCASMOLCASMOLCASM version v8.0.16-08-07MOLCASMOLCA Molcas 8 service pack 1
MOL fixed ANO-RCC and CASPT2
• Banner with version
• Environment
• Input file
• Output for eachprogram
• Final energies with::
• Final return code
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 21 / 29 >
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Basics Input Programs Output Examples
Text output
-------------------------------------------------------------------|| Project = water| Submitted from = /scr/user/test/| Scratch area = /scr/user/test/Work| Save outputs to = Save| Molcas = /home/user/molcas-8.0|| Scratch area is empty|| MOLCAS_REDUCE_PRT = NO| MOLCAS_MEM = 2000| MOLCAS_MOLDEN = ON| MOLCAS_NPROCS = 1| MOLCAS_GRID = NO| MOLCAS_THREADS = 1| MOLCAS_SOURCE = /home/user/molcas-8.0|-------------------------------------------------------------------
• Banner with version
• Environment
• Input file
• Output for eachprogram
• Final energies with::
• Final return code
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 21 / 29 >
CAS
Basics Input Programs Output Examples
Text output
++ --------- Input file ---------
&GATEWAYCoordwater.xyzBasisANO-RCC-MBGroupNoSymRICDNoMove
&SEWARD&SCF&RASSCFFileOrb$Project.ScfOrbSpin1
Charge0
NActEl8 0 0
RAS26
-- ----------------------------------
• Banner with version
• Environment
• Input file
• Output for eachprogram
• Final energies with::
• Final return code
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 21 / 29 >
CAS
Basics Input Programs Output Examples
Text output
--- Start Module: scf at Tue Jan 17 16:46:21 2017
()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()MOLCAS executing module SCF with 2000 MB of memory
at 16:46:21 Tue Jan 17 2017()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()
:: Total SCF energy -75.9949351623One-electron energy -122.6959001160Two-electron energy 37.6091445437Nuclear repulsion energy 9.0918204100Kinetic energy (interpolated) 76.6296875583Virial theorem 0.9917166255Total spin, S(S+1) 0.0000000000Total spin, S 0.0000000000Max non-diagonal density matrix element 0.0000000000Max non-diagonal Fock matrix element 0.0000013314
--- Stop Module: scf at Tue Jan 17 16:46:21 2017 /rc=0 ---
• Banner with version
• Environment
• Input file
• Output for eachprogram
• Final energies with::
• Final return code
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 21 / 29 >
CAS
Basics Input Programs Output Examples
Text output
--- Start Module: scf at Tue Jan 17 16:46:21 2017
()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()MOLCAS executing module SCF with 2000 MB of memory
at 16:46:21 Tue Jan 17 2017()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()
:: Total SCF energy -75.9949351623One-electron energy -122.6959001160Two-electron energy 37.6091445437Nuclear repulsion energy 9.0918204100Kinetic energy (interpolated) 76.6296875583Virial theorem 0.9917166255Total spin, S(S+1) 0.0000000000Total spin, S 0.0000000000Max non-diagonal density matrix element 0.0000000000Max non-diagonal Fock matrix element 0.0000013314
--- Stop Module: scf at Tue Jan 17 16:46:21 2017 /rc=0 ---
• Banner with version
• Environment
• Input file
• Output for eachprogram
• Final energies with::
• Final return code
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 21 / 29 >
CAS
Basics Input Programs Output Examples
Text output
Happy landing!
--- Stop Module: auto at Tue Jan 17 16:46:22 2017 /rc=0 ---
• Banner with version
• Environment
• Input file
• Output for eachprogram
• Final energies with::
• Final return code
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 21 / 29 >
CAS
Basics Input Programs Output Examples
Orbitals
*Orb format
• Generated by some Molcas programs(SCF, RASSCF, MP2, CASPT2. . . )
• Can be used directly by many of these programs(cf. FileOrb keyword)
• Can be visualized by generating “grids” with GRID_IT(runs by default unless MOLCAS_GRID = NO)
Molden format
• Generated by some Molcas programs(with MOLCAS_MOLDEN = ON)
• Understood by other programs outside Molcas
• Can be visualized with Molden(www.cmbi.ru.nl/molden/)
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 22 / 29 >
CAS
Basics Input Programs Output Examples
Orbitals
*Orb format
• Generated by some Molcas programs(SCF, RASSCF, MP2, CASPT2. . . )
• Can be used directly by many of these programs(cf. FileOrb keyword)
• Can be visualized by generating “grids” with GRID_IT(runs by default unless MOLCAS_GRID = NO)
Molden format
• Generated by some Molcas programs(with MOLCAS_MOLDEN = ON)
• Understood by other programs outside Molcas
• Can be visualized with Molden(www.cmbi.ru.nl/molden/)
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 22 / 29 >
CAS
Basics Input Programs Output Examples
Structures
XYZ format
• Generated by SLAPAF and DYNAMIX
• Optimized geometries ($Project.Opt.xyz)
• Trajectories ($Project.md.xyz)
• Widely supported format
Molden format
• Generated by SLAPAF and MCKINLEY
• Optimization process ($Project.geo.molden)
• Reaction paths ($Project.mep.molden,$Project.irc.molden)
• Normal modes ($Project.freq.molden)
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 23 / 29 >
CAS
Basics Input Programs Output Examples
Structures
XYZ format
• Generated by SLAPAF and DYNAMIX
• Optimized geometries ($Project.Opt.xyz)
• Trajectories ($Project.md.xyz)
• Widely supported format
Molden format
• Generated by SLAPAF and MCKINLEY
• Optimization process ($Project.geo.molden)
• Reaction paths ($Project.mep.molden,$Project.irc.molden)
• Normal modes ($Project.freq.molden)
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 23 / 29 >
CAS
Basics Input Programs Output Examples O2 PhNH2
Molecular oxygen with Hartree–Fock
&GATEWAYCoord = 2Oxygen, experimental bond lengthO -0.604 0.0 0.0O 0.604 0.0 0.0
Basis = ANO-RCC-VTZPGroup = NoSymRICD
&SEWARD
&SCF>>> Copy $Project.scf.molden
↩ $CurrDir/S-RHF.molden
&SCFUHFSpin = 3
>>> Copy $Project.scf.molden↩ $CurrDir/T-UHF.molden
&SCFUHFSpin = 1
>>> Copy $Project.scf.molden↩ $CurrDir/S-UHF.molden
Three calculations in one:
1 Closed-shell singlet
2 Open-shell triplet
3 Open-shell singlet(using triplet orbitals asinitial guess)
Orbitals are saved before theyare overwritten
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 24 / 29 >
CAS
Basics Input Programs Output Examples O2 PhNH2
Molecular oxygen with Hartree–Fock
&GATEWAYCoord = 2Oxygen, experimental bond lengthO -0.604 0.0 0.0O 0.604 0.0 0.0
Basis = ANO-RCC-VTZPGroup = NoSymRICD
&SEWARD
&SCF>>> Copy $Project.scf.molden
↩ $CurrDir/S-RHF.molden
&SCFUHFSpin = 3
>>> Copy $Project.scf.molden↩ $CurrDir/T-UHF.molden
&SCFUHFSpin = 1
>>> Copy $Project.scf.molden↩ $CurrDir/S-UHF.molden
Three calculations in one:
1 Closed-shell singlet
2 Open-shell triplet
3 Open-shell singlet(using triplet orbitals asinitial guess)
Orbitals are saved before theyare overwritten
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 24 / 29 >
CAS
Basics Input Programs Output Examples O2 PhNH2
Molecular oxygen with Hartree–Fock
&GATEWAYCoord = 2Oxygen, experimental bond lengthO -0.604 0.0 0.0O 0.604 0.0 0.0
Basis = ANO-RCC-VTZPGroup = NoSymRICD
&SEWARD
&SCF>>> Copy $Project.scf.molden
↩ $CurrDir/S-RHF.molden
&SCFUHFSpin = 3
>>> Copy $Project.scf.molden↩ $CurrDir/T-UHF.molden
&SCFUHFSpin = 1
>>> Copy $Project.scf.molden↩ $CurrDir/S-UHF.molden
Three calculations in one:
1 Closed-shell singlet
2 Open-shell triplet
3 Open-shell singlet(using triplet orbitals asinitial guess)
Orbitals are saved before theyare overwritten
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 24 / 29 >
CAS
Basics Input Programs Output Examples O2 PhNH2
Molecular oxygen with Hartree–Fock
&GATEWAYCoord = 2Oxygen, experimental bond lengthO -0.604 0.0 0.0O 0.604 0.0 0.0
Basis = ANO-RCC-VTZPGroup = NoSymRICD
&SEWARD
&SCF>>> Copy $Project.scf.molden
↩ $CurrDir/S-RHF.molden
&SCFUHFSpin = 3
>>> Copy $Project.scf.molden↩ $CurrDir/T-UHF.molden
&SCFUHFSpin = 1
>>> Copy $Project.scf.molden↩ $CurrDir/S-UHF.molden
Three calculations in one:
1 Closed-shell singlet
2 Open-shell triplet
3 Open-shell singlet(using triplet orbitals asinitial guess)
Orbitals are saved before theyare overwritten
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 24 / 29 >
CAS
Basics Input Programs Output Examples O2 PhNH2
Molecular oxygen with Hartree–Fock
&GATEWAYCoord = 2Oxygen, experimental bond lengthO -0.604 0.0 0.0O 0.604 0.0 0.0
Basis = ANO-RCC-VTZPGroup = NoSymRICD
&SEWARD
&SCF>>> Copy $Project.scf.molden
↩ $CurrDir/S-RHF.molden
&SCFUHFSpin = 3
>>> Copy $Project.scf.molden↩ $CurrDir/T-UHF.molden
&SCFUHFSpin = 1
>>> Copy $Project.scf.molden↩ $CurrDir/S-UHF.molden
Three calculations in one:
1 Closed-shell singlet
2 Open-shell triplet
3 Open-shell singlet(using triplet orbitals asinitial guess)
Orbitals are saved before theyare overwritten
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 24 / 29 >
CAS
Basics Input Programs Output Examples O2 PhNH2
Oxygen orbitals
$ grep "::" O2.output:: Total SCF energy -149.7065256135:: Total SCF energy -149.7926121539:: Total SCF energy -149.7645733861
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 25 / 29 >
CAS
Basics Input Programs Output Examples O2 PhNH2
Oxygen orbitals
$ grep "::" O2.output:: Total SCF energy -149.7065256135:: Total SCF energy -149.7926121539:: Total SCF energy -149.7645733861
S-RHF
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 25 / 29 >
CAS
Basics Input Programs Output Examples O2 PhNH2
Oxygen orbitals
$ grep "::" O2.output:: Total SCF energy -149.7065256135:: Total SCF energy -149.7926121539:: Total SCF energy -149.7645733861
S-UHF
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 25 / 29 >
CAS
Basics Input Programs Output Examples O2 PhNH2
Oxygen orbitals
$ grep "::" O2.output:: Total SCF energy -149.7065256135:: Total SCF energy -149.7926121539:: Total SCF energy -149.7645733861
T-UHF
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 25 / 29 >
CAS
Basics Input Programs Output Examples O2 PhNH2
Geometry optimization of aniline
&GATEWAYCoord = aniline.xyzBasis = cc-pVDZGroup = NoSymRICD
>>> DoWhile
&SEWARD
&SCFKSDFT = B3LYP
&SLAPAF
>>> EndDo
• SLAPAF requests gradient(ALASKA) automatically, obtainsnew geometry, signalsconvergence
• DFT functional as option to SCF
• SEWARD inside the loop!
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 26 / 29 >
CAS
Basics Input Programs Output Examples O2 PhNH2
Geometry optimization of aniline
&GATEWAYCoord = aniline.xyzBasis = cc-pVDZGroup = NoSymRICD
>>> DoWhile
&SEWARD
&SCFKSDFT = B3LYP
&SLAPAF
>>> EndDo
• SLAPAF requests gradient(ALASKA) automatically, obtainsnew geometry, signalsconvergence
• DFT functional as option to SCF
• SEWARD inside the loop!
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 26 / 29 >
CAS
Basics Input Programs Output Examples O2 PhNH2
Geometry optimization of aniline
&GATEWAYCoord = aniline.xyzBasis = cc-pVDZGroup = NoSymRICD
>>> DoWhile
&SEWARD
&SCFKSDFT = B3LYP
&SLAPAF
>>> EndDo
• SLAPAF requests gradient(ALASKA) automatically, obtainsnew geometry, signalsconvergence
• DFT functional as option to SCF
• SEWARD inside the loop!
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 26 / 29 >
CAS
Basics Input Programs Output Examples O2 PhNH2
Geometry optimization of aniline
&GATEWAYCoord = aniline.xyzBasis = cc-pVDZGroup = NoSymRICD
>>> DoWhile
&SEWARD
&SCFKSDFT = B3LYP
&SLAPAF
>>> EndDo
• SLAPAF requests gradient(ALASKA) automatically, obtainsnew geometry, signalsconvergence
• DFT functional as option to SCF
• SEWARD inside the loop!
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 26 / 29 >
CAS
Basics Input Programs Output Examples O2 PhNH2
Geometry optimization of aniline
&GATEWAYCoord = aniline.xyzBasis = cc-pVDZGroup = NoSymRICD
>>> DoWhile
&SEWARD
&SCFKSDFT = B3LYP
&SLAPAF
>>> EndDo
• SLAPAF requests gradient(ALASKA) automatically, obtainsnew geometry, signalsconvergence
• DFT functional as option to SCF
• SEWARD inside the loop!
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 26 / 29 >
CAS
Basics Input Programs Output Examples O2 PhNH2
Aniline structures
14Aniline HF/cc-pVDZ planar optimizationH 1.51867690 2.54059252 0.00000000C 0.96547983 1.61185812 0.00000000C -0.42282694 1.61174200 0.00000000H -0.96244358 2.55050225 0.00000000C -1.13911140 0.42643438 0.00000000H -2.22191527 0.44825140 0.00000000C -0.47333499 -0.80364213 0.00000000N -1.17610492 -1.98339965 0.00000000H -2.16976459 -1.98523860 0.00000000H -0.70474578 -2.85800915 0.00000000C 0.92539708 -0.80326751 0.00000000H 1.46021746 -1.74501591 0.00000000C 1.62655807 0.39101218 0.00000000H 2.70901812 0.36358008 0.00000000
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 27 / 29 >
CAS
Basics Input Programs Output Examples O2 PhNH2
Aniline structures
****************************************************************************************************************** Energy Statistics for Geometry Optimization ******************************************************************************************************************
Energy Grad Grad Step Estimated Geom HessianIter Energy Change Norm Max Element Max Element Final Energy Update Update Index1 -287.61954204 0.00000000 0.028779 0.022431 nrc017 0.031503 nrc016 -287.62050293 RS-RFO None 02 -287.62080607 -0.00126404 0.008676 0.008423 nrc017 0.017355 nrc017 -287.62096615 RS-RFO BFGS 03 -287.62096870 -0.00016263 0.001166 0.000453 nrc017 -0.001370 nrc016 -287.62096963 RS-RFO BFGS 04 -287.62096991 -0.00000121 0.000389-0.000165 nrc016 -0.000871 nrc016 -287.62097007 RS-RFO BFGS 0
+----------------------------------+----------------------------------++ Cartesian Displacements + Gradient in internals ++ Value Threshold Converged? + Value Threshold Converged? +
+-----+----------------------------------+----------------------------------++ RMS + 0.3175E-03 0.1200E-02 Yes + 0.9716E-04 0.3000E-03 Yes ++-----+----------------------------------+----------------------------------++ Max + 0.6179E-03 0.1800E-02 Yes + 0.1649E-03 0.4500E-03 Yes ++-----+----------------------------------+----------------------------------+
Geometry is converged in 4 iterations to a Minimum Structure
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 27 / 29 >
CAS
Basics Input Programs Output Examples O2 PhNH2
Aniline structures
14Aniline, out-of-plane NH 1.51867690 2.54059252 0.00000000C 0.96547983 1.61185812 0.00000000C -0.42282694 1.61174200 0.00000000H -0.96244358 2.55050225 0.00000000C -1.13911140 0.42643438 0.00000000H -2.22191527 0.44825140 0.00000000C -0.47333499 -0.80364213 0.00000000N -1.17610492 -1.98339965 0.10000000H -2.16976459 -1.98523860 0.00000000H -0.70474578 -2.85800915 0.00000000C 0.92539708 -0.80326751 0.00000000H 1.46021746 -1.74501591 0.00000000C 1.62655807 0.39101218 0.00000000H 2.70901812 0.36358008 0.00000000
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 27 / 29 >
CAS
Basics Input Programs Output Examples O2 PhNH2
Aniline structures
****************************************************************************************************************** Energy Statistics for Geometry Optimization ******************************************************************************************************************
Energy Grad Grad Step Estimated Geom HessianIter Energy Change Norm Max Element Max Element Final Energy Update Update Index
14 -287.62281527 -0.00000415 0.000756-0.000351 nrc017 0.005464 nrc029 -287.62281626 RS-RFO BFGS 015 -287.62281658 -0.00000131 0.000354 0.000173 nrc006 -0.002304 nrc036 -287.62281689 RS-RFO BFGS 016 -287.62281697 -0.00000038 0.000099 0.000052 nrc036 0.001605 nrc036 -287.62281702 RS-RFO BFGS 0
+----------------------------------+----------------------------------++ Cartesian Displacements + Gradient in internals ++ Value Threshold Converged? + Value Threshold Converged? +
+-----+----------------------------------+----------------------------------++ RMS + 0.7523E-03 0.1200E-02 Yes + 0.1901E-04 0.3000E-03 Yes ++-----+----------------------------------+----------------------------------++ Max + 0.1337E-02 0.1800E-02 Yes + 0.5247E-04 0.4500E-03 Yes ++-----+----------------------------------+----------------------------------+
Geometry is converged in 16 iterations to a Minimum Structure
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 27 / 29 >
CAS
Basics Input Programs Output Examples O2 PhNH2
Aniline structures
****************************************************************************************************************** Energy Statistics for Geometry Optimization ******************************************************************************************************************
Energy Grad Grad Step Estimated Geom HessianIter Energy Change Norm Max Element Max Element Final Energy Update Update Index
14 -287.62281527 -0.00000415 0.000756-0.000351 nrc017 0.005464 nrc029 -287.62281626 RS-RFO BFGS 015 -287.62281658 -0.00000131 0.000354 0.000173 nrc006 -0.002304 nrc036 -287.62281689 RS-RFO BFGS 016 -287.62281697 -0.00000038 0.000099 0.000052 nrc036 0.001605 nrc036 -287.62281702 RS-RFO BFGS 0
+----------------------------------+----------------------------------++ Cartesian Displacements + Gradient in internals ++ Value Threshold Converged? + Value Threshold Converged? +
+-----+----------------------------------+----------------------------------++ RMS + 0.7523E-03 0.1200E-02 Yes + 0.1901E-04 0.3000E-03 Yes ++-----+----------------------------------+----------------------------------++ Max + 0.1337E-02 0.1800E-02 Yes + 0.5247E-04 0.4500E-03 Yes ++-----+----------------------------------+----------------------------------+
Geometry is converged in 16 iterations to a Minimum Structure
Planar −287.620 969 91 Eh
Pyramidalized −287.622 816 97 Eh
Difference 1.16 kcal/mol
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 27 / 29 >
Basics Input Programs Output Examples
Citation and new features
Molcas 8: New Capabilities for MulticonfigurationalQuantum Chemical Calculations across the Periodic Ta-bleF. Aquilante, J. Autschbach, R. K. Carlson, L. F. Chibotaru,M. G. Delcey, L. De Vico, I. Fdez. Galván, N. Ferré, L. M. Fru-tos, L. Gagliardi, M. Garavelli, A. Giussani, C. E. Hoyer, G.Li Manni, H. Lischka, D. Ma, P. Å. Malmqvist, T. Müller, A.Nenov, M. Olivucci, T. B. Pedersen, D. Peng, F. Plasser, B.Pritchard, M. Reiher, I. Rivalta, I. Schapiro, J. Segarra-Martí,M. Stenrup, D. G. Truhlar, L. Ungur, A. Valentini, S. Vancoil-lie, V. Veryazov, V. P. Vysotskiy, O. Weingart, F. Zapata, R.LindhJ. Comput. Chem. 37 (2016) 506–541.
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 28 / 29 >
Basics Input Programs Output Examples
UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 29 / 29 >