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Basics Input Programs Output Examples Introduction to Molcas Ignacio Fernández Galván Uppsala University, Sweden CAS Molcas Workshop Jerusalem, February 6th 2017 UU.se Ignacio Fdez. Galván CAS Introduction to Molcas < 1 / 29 >
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Page 1: Ignacio Fernández Galván - huji.ac.il · BasicsInputProgramsOutputExamples Introduction to Molcas Ignacio Fernández Galván Uppsala University, Sweden CAS Molcas Workshop Jerusalem,

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 >

Page 2: Ignacio Fernández Galván - huji.ac.il · BasicsInputProgramsOutputExamples Introduction to Molcas Ignacio Fernández Galván Uppsala University, Sweden CAS Molcas Workshop Jerusalem,

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 >

Page 3: Ignacio Fernández Galván - huji.ac.il · BasicsInputProgramsOutputExamples Introduction to Molcas Ignacio Fernández Galván Uppsala University, Sweden CAS Molcas Workshop Jerusalem,

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 >

Page 4: Ignacio Fernández Galván - huji.ac.il · BasicsInputProgramsOutputExamples Introduction to Molcas Ignacio Fernández Galván Uppsala University, Sweden CAS Molcas Workshop Jerusalem,

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 >

Page 5: Ignacio Fernández Galván - huji.ac.il · BasicsInputProgramsOutputExamples Introduction to Molcas Ignacio Fernández Galván Uppsala University, Sweden CAS Molcas Workshop Jerusalem,

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 >

Page 6: Ignacio Fernández Galván - huji.ac.il · BasicsInputProgramsOutputExamples Introduction to Molcas Ignacio Fernández Galván Uppsala University, Sweden CAS Molcas Workshop Jerusalem,

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 >

Page 7: Ignacio Fernández Galván - huji.ac.il · BasicsInputProgramsOutputExamples Introduction to Molcas Ignacio Fernández Galván Uppsala University, Sweden CAS Molcas Workshop Jerusalem,

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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 >

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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 >

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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 >

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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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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 >

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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 >

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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 >

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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 >

Page 17: Ignacio Fernández Galván - huji.ac.il · BasicsInputProgramsOutputExamples Introduction to Molcas Ignacio Fernández Galván Uppsala University, Sweden CAS Molcas Workshop Jerusalem,

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 >

Page 18: Ignacio Fernández Galván - huji.ac.il · BasicsInputProgramsOutputExamples Introduction to Molcas Ignacio Fernández Galván Uppsala University, Sweden CAS Molcas Workshop Jerusalem,

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 >

Page 19: Ignacio Fernández Galván - huji.ac.il · BasicsInputProgramsOutputExamples Introduction to Molcas Ignacio Fernández Galván Uppsala University, Sweden CAS Molcas Workshop Jerusalem,

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 >

Page 20: Ignacio Fernández Galván - huji.ac.il · BasicsInputProgramsOutputExamples Introduction to Molcas Ignacio Fernández Galván Uppsala University, Sweden CAS Molcas Workshop Jerusalem,

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 >

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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 >

Page 22: Ignacio Fernández Galván - huji.ac.il · BasicsInputProgramsOutputExamples Introduction to Molcas Ignacio Fernández Galván Uppsala University, Sweden CAS Molcas Workshop Jerusalem,

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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 >

Page 24: Ignacio Fernández Galván - huji.ac.il · BasicsInputProgramsOutputExamples Introduction to Molcas Ignacio Fernández Galván Uppsala University, Sweden CAS Molcas Workshop Jerusalem,

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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 >

Page 25: Ignacio Fernández Galván - huji.ac.il · BasicsInputProgramsOutputExamples Introduction to Molcas Ignacio Fernández Galván Uppsala University, Sweden CAS Molcas Workshop Jerusalem,

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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 >

Page 26: Ignacio Fernández Galván - huji.ac.il · BasicsInputProgramsOutputExamples Introduction to Molcas Ignacio Fernández Galván Uppsala University, Sweden CAS Molcas Workshop Jerusalem,

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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 >

Page 27: Ignacio Fernández Galván - huji.ac.il · BasicsInputProgramsOutputExamples Introduction to Molcas Ignacio Fernández Galván Uppsala University, Sweden CAS Molcas Workshop Jerusalem,

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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 >

Page 28: Ignacio Fernández Galván - huji.ac.il · BasicsInputProgramsOutputExamples Introduction to Molcas Ignacio Fernández Galván Uppsala University, Sweden CAS Molcas Workshop Jerusalem,

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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 >

Page 29: Ignacio Fernández Galván - huji.ac.il · BasicsInputProgramsOutputExamples Introduction to Molcas Ignacio Fernández Galván Uppsala University, Sweden CAS Molcas Workshop Jerusalem,

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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 >

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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 >

Page 31: Ignacio Fernández Galván - huji.ac.il · BasicsInputProgramsOutputExamples Introduction to Molcas Ignacio Fernández Galván Uppsala University, Sweden CAS Molcas Workshop Jerusalem,

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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 >

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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 >

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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

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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

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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)

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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)

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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)

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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)

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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

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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

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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

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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

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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

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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

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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

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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/)

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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/)

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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)

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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)

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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!

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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!

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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!

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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!

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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!

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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

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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

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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

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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

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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

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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.

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Basics Input Programs Output Examples

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