### Basic Configuration with Setup Script

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/doc/source/installation.guide/install.rst

Recommended for new users, this script interactively guides through the configuration process. Run it from the main MOLCAS directory after unpacking the source.

```bash
./setup
```

--------------------------------

### Setup OpenMolcas Environment

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/README.md

Run the setup script for your first OpenMolcas installation to configure the environment.

```bash
./pymolcas -setup
```

--------------------------------

### Example 2: Intel Compilers, GA, IntelMPI, MKL Setup

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/doc/source/installation.guide/install.rst

Illustrates the initial steps for configuring Molcas with Intel compilers and MPI, assuming Intel toolchain and Infiniband are preinstalled on a 64-bit Linux OS.

```bash
# make sure Intel compilers/MPI are loaded
module load ...
```

--------------------------------

### ExpBas Program Input Example

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/doc/source/users.guide/programs/expbas.rst

This is a basic input example for the ExpBas program. It shows the program name and the start of the input section.

```input
&EXPBAS
```

--------------------------------

### Example prologue script

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/doc/source/users.guide/environment.rst

A simple prologue script that echoes the project name and the start time of the calculation. Ensure this script is executable.

```shell
echo Calculation of $Project input will start at `date`
```

--------------------------------

### MC-PDFT Calculation Setup with RASSCF

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/doc/source/users.guide/programs/rasscf.rst

Example input for running MC-PDFT calculations using the RASSCF program. It involves an initial CASSCF run followed by a second call with CIRESTART and CIONLY keywords for MC-PDFT.

```input
&RASSCF
  Ras2
  1 0 0 0 1 0 0 0

  >>COPY $CurrDir/$Project.JobIph JOBOLD

  &RASSCF
  JOBIPH
  CIRESTART
  CIONLY
  Ras2
  1 0 0 0 1 0 0 0
  FUNC
  ROKS; T:PBE
```

--------------------------------

### OPT.product.input Example

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/doc/source/advanced.examples/ex-rp.rst

This snippet shows an example input file for the OPT.product calculation, including basis set definitions and SCF settings.

```input
>>> Do while <<<

&Seward

Basis set
C.cc-pVDZ....
C1            -2.0983667072        0.1000525724        0.5196668948
C2            -2.1177298783       -0.0920244467        3.0450747772
C3             0.5639781563        0.0024463770       -0.5245225314
End of Basis
Basis set
H.cc-pVDZ....
H1            -3.8870548756       -0.0558560582        4.1138131865
H2            -0.4133953535       -0.2946498869        4.2050068095
H3            -1.3495534119        0.3499572533       -3.3741881412
End of Basis
Basis set
O.cc-pVDZ....
O1             0.5100106099        0.2023808294       -3.0720173949
O2             2.5859515474       -0.2102046338        0.4795705925
End of Basis
End of input

>>> IF ( ITER = 1 ) <<<
&SCF
Core
Charge = -1
>>> ENDIF <<<
&SCF
LUMORB
Charge = -1

&Slapaf
Iterations = 20
>>> EndDo <<<

```

--------------------------------

### Get Starting Orbitals from File

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/doc/source/users.guide/programs/rasscf.rst

Use the LUMOrb keyword to specify an ASCII file (default INPORB) for reading starting molecular orbitals.

```text
%%Keyword: LUMOrb <basic>
<HELP>
Get starting molecular orbitals from an ASCII file called INPORB.
</HELP>
</KEYWORD>
```

--------------------------------

### CPF Module Input Example

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/doc/source/users.guide/programs/cpf.rst

Example of how to use the CPF module with a title and MCPF keyword.

```input
&CPF
 Title
  Water molecule. 1S frozen in transformation.
 MCPF

```

--------------------------------

### Install and Configure GA Library

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/doc/source/installation.guide/install.rst

Steps to download, configure, compile, and install the General Atomic (GA) library with specific Intel MPI and MKL optimizations.

```bash
type mpiicc
type mpiifort
echo $MKLROOT
tar zxvf /path/to/ga-5-4b.tgz
cd ga-5-4b/
./configure --prefix=/opt/ga54b-ilp64.IntelMPI --enable-i8 --with-openib \
              --with-blas8="-L$MKLROOT/lib/intel64 -lmkl_intel_ilp64
                            -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm" \
              --with-scalapack8="-L$MKLROOT/lib/intel64 -lmkl_scalapack_ilp64
                                 -lmkl_intel_ilp64 -lmkl_intel_thread -lmkl_core
                                 -lmkl_blacs_intelmpi_ilp64 -liomp5 -lpthread -lm"
make
[sudo]make install
```

--------------------------------

### CHCC Module Configuration Example

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/doc/source/users.guide/programs/chcc.rst

An example of an input file for the CHCC module, demonstrating the use of various keywords to configure a calculation.

```input
&CHCC &END
  Title
  Benzene dimer
  Frozen
  12
  Deleted
  0
  Large
  4
  Small
  2
  CHSEgment
  100
  Precalculate
  Join
  2
  Maxiter
  50
  Threshold
  1.0d-6
  Print
  2
  End of Input
```

--------------------------------

### Out-of-Source Installation with configure

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/doc/source/installation.guide/install.rst

Demonstrates how to perform an out-of-source installation of Molcas by creating a separate directory and running the configure script with specific flags.

```bash
mkdir $HOME/molcas
cd $HOME/molcas
/sw/molcas_dist/configure -speed safe
```

--------------------------------

### MOTRA Configuration Example

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/doc/source/users.guide/programs/motra.rst

Example of a MOTRA configuration block with various keywords.

```input
&MOTRA
  Title  =  Water molecule.
  * Don't correlate 1s on oxygen
  Frozen =  1 0 0 0
  Lumorb
```

--------------------------------

### SEWARD Program Input Example

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/doc/source/users.guide/programs/seward.rst

This is a basic example of how to initiate the SEWARD program. It shows the program name followed by the '&SEWARD' directive.

```input
&SEWARD
```

--------------------------------

### Build and Install Executables

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/Tools/rf2asc/CMakeLists.txt

Iterates through a list of programs (rf2asc, asc2rf, testrf), adds them as executables, links necessary libraries, and installs them to the specified destination.

```cmake
foreach (prog IN ITEMS rf2asc asc2rf testrf)
  add_executable (${prog}.exe ${prog}.F90)
  target_link_libraries (${prog}.exe libmolcas)
  target_link_libraries (${prog}.exe ${EXTERNAL_LIBRARIES})
  install (PROGRAMS
           ${EXECUTABLE_OUTPUT_PATH}/${prog}.exe
           DESTINATION ${CMAKE_INSTALL_PREFIX}/${tooldir}
  )
endforeach (prog)
```

--------------------------------

### RHODYN Input Example 1

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/doc/source/users.guide/programs/rhodyn.rst

Example input for the RHODYN module, setting up manifold and state properties for dipole and emission calculations.

```input
  > copy /path/to/file/s3.rasscf.h5  RASSD1
  > copy /path/to/file/s1.rasscf.h5  RASSD2
  > copy /path/to/file/si.rassisd.h5 RASSISD
  > copy /path/to/file/kmatrix.dat   HRFACT

  &RHODYN

  NRSManifolds          = 2
  NRDEt,CSF,STATES,SPIN = 25   25   25   3
                          30   30   30   1
  NSTAte                = 105 all
  FINAltime             = 10
  IFSO
  AMPLitude             = 9.0
  TAUShift              = 1.
  SIGMa                 = 0.3
  OMEGa                 = 875
  IfDissipation
  KEXTernal
```

--------------------------------

### LEVEL Input Example

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/doc/source/users.guide/programs/level.rst

An example input file for the LEVEL module, specifying parameters for calculating the vibrational-rotation spectrum of Li2 using the MLR potential.

```fortran
&LEVEL
  IAN1 = 3
  IMN1 = 6
  IAN2 = 3
  IMN2 = 6
  CHARGE = 0
  NUMPOT = 1
  RH = 0.0005
  RMIN = 0.125
  PRV = 1
  ARV = 5.0d0
  EPS = 2.d-10
  NTP = -1
  LPPOT = 0
  IOMEG1 = 0
  VLIM = 0.0d0
  IPOTL = 4
  PPAR = 5
  QPAR = 3
  NSR = 3
  NLR = 3
  IBOB = -1
  DSCM = 3.337678701485D+02
  REQ = 4.170010583477D+00
  RREF = 8.0d0
  NCMM = 3
  IVSR = -2
  TDSTT = 1
  RHOAB = 0.54d0
  MMLR = 6 8 10
  CMM = 6.719000000d+06 1.126350000d+08  2.786940000d+09
  PARM = -5.156803528943D-01 -9.585070416286D-02 1.170797201140D-01 -2.282814434665D-02
  NLEV1 = -999
  AUTO1 = 1
  LCDC = 2
  LXPCT = 0
  NJM = 0
  JDJR = 1
  LPRWF = 0

```

--------------------------------

### Installing HDF5 Development Libraries on Ubuntu

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/doc/source/users.guide/programs/wfa.rst

Use this command to install the necessary HDF5 development libraries on Ubuntu systems.

```bash
sudo apt install libhdf5-dev libhdf5-cpp-103

```

--------------------------------

### RHODYN Input Example 2

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/doc/source/users.guide/programs/rhodyn.rst

Example input for the RHODYN module, configuring population style, time evolution, and pulse properties for emission calculations.

```input
  &RHODYN

  NRSManifolds          = 2
  NRDEt,CSF,STATES,SPIN = 25   25   25   3
                          30   30   30   1
  POPUlatedstyle        = SO_THERMAL
  NSTAte                = 105 all
  FINAltime             = 6
  Tout                  = 0.0005
  METHod                = RKCK
  IFSO
  DMBAsis               = SO
  PROPbasis             = SO
  TFDM                  = 0.005

  PTYPe                 = Gaussian
  NPULses               = 1
  AMPLitude             = 9.0
  TAUShift              = 1.
  POLArization          = (1.0,0.0) (0.0,0.0) (0.0,0.0)
  SIGMa                 = 0.3
  OMEGa                 = 875
  PHASe                 = 0
  Dipole
  Emission
```

--------------------------------

### Parallel Build and Install of Molcas with Configure

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/doc/source/installation.guide/install.rst

Two-step process for parallel compilation and installation of Molcas when configured with the 'configure' script, using N threads.

```bash
make -jN build
make install
```

--------------------------------

### ExpBas File Preparation Example

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/doc/source/users.guide/programs/expbas.rst

This example demonstrates how to prepare the necessary input files for the ExpBas program using copy commands. It includes the orbital file and two runfiles.

```shell
>>COPY name.InpOrb INPORB
>>COPY name.RunFil1 RUNFIL1
>>COPY name.Runfil2 RUNFIL2
 &EXPBAS
```

--------------------------------

### ESPF Input Example

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/doc/source/users.guide/programs/espf.rst

A typical input for calculating the energy and gradient of a molecule in an external potential field. This example demonstrates ESPF setup with QM/MM interactions.

```input
&Gateway
  Basis set
  C.sto-3g.....
    C1   1.11820     0.72542    -2.75821 angstrom
    C2   1.20948     0.66728    -1.25125 angstrom
  End of basis
  Basis set
  O.sto-3g.....
    O1   2.19794     1.10343    -0.67629 angstrom
  End of basis
  Basis set
  H.sto-3g.....
    H1   2.02325     1.18861    -3.14886 angstrom
    H2   0.25129     1.31794    -3.04374 angstrom
    H3   1.02458    -0.28460    -3.15222 angstrom
  End of basis
  Basis set
  N.sto-3g.....
    N1   0.17609     0.12714    -0.61129 angstrom
  End of basis
  Basis set
  C.sto-3g.....
    C3   0.09389    -0.01123     0.84259 angstrom
    C4  -1.21244    -0.67109     1.28727 angstrom
  End of basis
  Basis set
  O.sto-3g.....
    O2  -2.06502    -1.02710     0.48964 angstrom
  End of basis
  Basis set
  H.sto-3g.....
    H4  -0.61006    -0.21446    -1.14521 angstrom
    H5   0.92981    -0.61562     1.19497 angstrom
    H6   0.16338     0.97444     1.30285 angstrom
  End of basis
  Basis set
  N.sto-3g.....
    N2  -1.41884    -0.85884     2.57374 angstrom
  End of basis
  Basis set
  H.sto-3g.....
    H7  -0.73630    -0.57661     3.25250 angstrom
    H8  -2.28943    -1.29548     2.82140 angstrom
  End of basis

  &seward

  &espf
  MultipoleOrder = 0
  External = 0
  1  -0.048 -0.002 -0.006 -0.001  0.007 -0.009  0.002 -0.001  0.001 -0.001
  2  -0.047 -0.002  0.001 -0.002  0.003  0.000 -0.004  0.000 -0.001  0.000
  3  -0.053  0.004  0.000 -0.011  0.002  0.002 -0.004  0.002  0.003 -0.007
  4  -0.046  0.011 -0.009 -0.001  0.006 -0.005 -0.001  0.003  0.003 -0.004
  5  -0.042 -0.016 -0.011 -0.006  0.005 -0.007  0.003 -0.004 -0.001 -0.005
  6  -0.050  0.000  0.008  0.001  0.006 -0.006  0.000 -0.002  0.000 -0.001
  7  -0.039 -0.008  0.001  0.000  0.001 -0.002  0.001 -0.001 -0.001 -0.001
  8  -0.032 -0.007 -0.002  0.004  0.002 -0.003  0.001 -0.002  0.002 -0.001
  9  -0.011 -0.009  0.004  0.001  0.002  0.000 -0.002 -0.001  0.001  0.001
  10  0.000 -0.011  0.003  0.004  0.001  0.002 -0.003  0.001 -0.001  0.001
  11 -0.028 -0.008  0.004 -0.001 -0.001 -0.002  0.002 -0.001  0.001 -0.002
  12 -0.026  0.003 -0.008  0.014  0.002 -0.001 -0.001 -0.008  0.006 -0.009

```

--------------------------------

### Initial CMake Configuration

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/doc/source/installation.guide/install.rst

Sets up the build environment by creating a build directory and running CMake with the source directory path.

```bash
mkdir ~/molcas-build
cd ~/molcas-build/
cmake ~/molcas/
```

--------------------------------

### Defining Constraints in GATEWAY

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/doc/source/users.guide/programs/gateway.rst

Example of how to start and end the definition of constraints for an optimization within the GATEWAY input.

```GATEWAY
:kword:`CONStraints`
  This marks the start of the definition of the constraints
  which the optimization is subject to.
  This section is always ended by the keyword
  :kword:`End of Constraints`.
  This option can be used in conjunction with any definition of the
  internal coordinates.
```

--------------------------------

### Excluding Degrees of Freedom from Numerical Differentiation

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/doc/source/users.guide/programs/gateway.rst

Example showing the start and end of a section to define additional restrictions for numerical differentiation.

```GATEWAY
:kword:`NGEXclude`
  This marks the start of the definition of additional restrictions for numerical differentiation.
  This section is always ended by the keyword :kword:`End of NGExclude`.
  The syntax of this section is like that of normal constraints, and the degrees of
  freedom specified here will be excluded from numerical differentiation (like phantom constraints).
  If a line containing only "Invert" is included inside the section,
  the definition is reversed and only these degrees of freedom are differentiated.
  :kword:`NGEXclude` is intended for use with the :kword:`KEEPOldGradient` keyword in :program:`ALASKA`,
  and can be combined with :kword:`CONStraints`, which will further reduce
  the numerical differentiation subspace :cite:`Stenrup2015`.
  Note that the value assigned to the constraints in this section is unused, but a ``Value`` block
  must still be included.
```

--------------------------------

### Display configure Help Options

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/doc/source/installation.guide/install.rst

Lists all available options for the configure script to customize the build process.

```bash
./configure -help
```

--------------------------------

### Z-matrix Construction: First Atom

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/doc/source/users.guide/programs/geo.rst

Example of the first step in constructing a z-matrix for the GEO module, starting with the first atom of a fragment.

```text
H
```

--------------------------------

### Setup Environment Variables and Working Directory

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/doc/source/advanced.examples/ex-rc.rst

Sets up essential environment variables for project directories and creates a temporary working directory. It also creates symbolic links to necessary input files.

```bash
export HomeDir=/u/$LOGNAME/$Project
export TempDir=/temp/$LOGNAME
export WorkDir=$TempDir/$RANDOM
mkdir $WorkDir
cd $WorkDir
ln -fs  $TempDir/$Project.OrdInt ORDINT
ln -fs  $TempDir/$Project.OneInt.$Solvent ONEINT
```

--------------------------------

### Example CASVB Input File

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/doc/source/users.guide/programs/casvb.rst

A sample input file demonstrating the setup for a CASVB calculation, including basis set definitions and SCF/RASSCF/CASVB parameters.

```OpenMolcas Input
&seward
symmetry
x y
basis set
c.sto-3g....
c 0 0 -0.190085345
end of basis
basis set
h.sto-3g....
h 0 1.645045225 1.132564974
end of basis
&scf
occupied
3 0 1 0
&rasscf
inactive
1 0 0 0
ras2
3 1 2 0
nactel
6 0 0
lumorb
&casvb
```

--------------------------------

### Example 1: GCC, GA, OpenMPI, OpenBLAS Configuration

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/doc/source/installation.guide/install.rst

Builds OpenBLAS, GA, and then Molcas using GCC compilers, OpenMPI for parallelization, and OpenBLAS for linear algebra. Assumes a 64-bit Linux OS and preinstalled MPI.

```bash
# OpenBLAS
tar zxvf OpenBLAS-v0.2.15.tar.gz
cd OpenBLAS-0.2.15/
make USE_OPENMP=1 NO_LAPACK=0 INTERFACE64=1 BINARY=64 DYNAMIC_ARCH=1 libs netlib shared
[sudo] make PREFIX=/opt/openblas-lapack-ilp64 install
# GA
tar zxvf /path/to/ga-5-4b.tgz
cd ga-5-4b/
./configure --enable-i8 --with-blas8 --with-lapack8 --with-scalapack8 --prefix=/opt/ga54b-ilp64.OpenMPI
make
[sudo] make install
# Molcas
tar zxvf molcas.tgz
cd molcas
mkdir build && cd build/
export GA=/opt/ga54b-ilp64.OpenMPI
export OPENBLASROOT=/opt/openblas-lapack-ilp64
CC=mpicc FC=mpifort cmake -DMPI=ON -DGA=ON -DLINALG=OpenBLAS ../
make -j4
```

--------------------------------

### Generating Initial Conditions with Dynamixtools

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/doc/source/users.guide/programs/dynamix.rst

Example command to generate 200 initial conditions for a molecular dynamics simulation using a specified molden file, seed, and temperature.

```bash
$ python3 dynamixtools.py -i water.freq.molden -t 300 -c 200 -s 3435432
```

--------------------------------

### AlignOnly Keyword Example

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/doc/source/users.guide/programs/gateway.rst

Use the AlignOnly keyword to align two starting structures without further computation. An input block for SEWARD is still required, but no integrals will be computed.

```text
.. xmldoc:: <KEYWORD MODULE="GATEWAY" NAME="ALIGNONLY" APPEAR="Align only" KIND="SINGLE" LEVEL="ADVANCED" EXCLUSIVE="NOALIGN">
              %%Keyword: AlignOnly <advanced>
              <HELP>
              The two starting structures are aligned, but nothing more is done.
              An input block for SEWARD is still needed, but no integrals are computed.
              </HELP>
              </KEYWORD>
```

--------------------------------

### Configure Main Include Directory and Version Header

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/CMakeLists.txt

Sets up the main include directory and configures the molcasversion.h header file from a template.

```cmake
# global include directory
#=========================

set (MAIN_INCLUDE_DIR ${PROJECT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/include)
configure_file (${OPENMOLCAS_DIR}/src/Include/molcasversion.h.in ${MAIN_INCLUDE_DIR}/molcasversion.h)

```

--------------------------------

### Verify MO Integral Dumping to FCIDUMP

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/doc/source/installation.guide/stochcas.rst

After installing OpenMolcas, this command can be used to verify that Molecular Orbital integrals are correctly dumped into the FCIDUMP file, a basic test for Stochastic-CASSCF setup.

```bash
molcas verify limannig
```

--------------------------------

### Molcas Usage Example

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/doc/source/tutorials/tut_errors.rst

Demonstrates the basic usage syntax for running a Molcas module. This command structure is used when Molcas driver scripts are not found.

```text
Usage: molcas module_name input
```

--------------------------------

### Basic SCF Calculation Setup

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/doc/source/tutorials/tut_ex.rst

Sets up a basic Self-Consistent Field (SCF) calculation for a molecule, including title and basis set information. This is often a starting point for more complex calculations.

```input
&SEWARD

>>> If ( Iter = 1 ) <<<

 &SCF
Title= acrolein minimum optimization

>>> EndIf <<<
```

--------------------------------

### WFA Program Installation with CMake

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/doc/source/users.guide/programs/wfa.rst

This command demonstrates how to install the WFA module using CMake, specifying the Fortran compiler, linear algebra backend (MKL), and enabling WFA and Armadillo.

```bash
FC=ifort cmake -D LINALG=MKL -D WFA=ON -D ARMADILLO_INC=../armadillo-7.300.0/include ..

```

--------------------------------

### Install analyze-molcas with pip

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/Tools/analyze_molcas/docs/installation.md

Use this command to install the analyze-molcas package. Ensure you have pip installed and configured.

```bash
pip install analyze-molcas
```

--------------------------------

### Configure Parallel Installation

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/doc/source/installation.guide/parainst.rst

Installs the parallel version of Molcas using the configure script. Specify the -parallel flag for parallel installation.

```bash
./configure -parallel
```

--------------------------------

### Verify GA4GUGA Installation

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/Tools/GA4GUGA/readme.md

Run the test_installation.py script to verify that the GA4GUGA package has been installed correctly. This script checks the integrity of the installation.

```bash
python test_installation.py
```

--------------------------------

### Install GA4GUGA Package

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/Tools/GA4GUGA/readme.md

Install the GA4GUGA package in editable mode using pip. Navigate to the package directory and run the installation command.

```bash
cd GA4GUGA
pip install -e .
```

--------------------------------

### Molcasrc Configuration for Working Directory and Project

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/doc/source/tutorials/nutshell.rst

An example molcasrc file demonstrating how to configure the working directory, memory, and project naming conventions for Molcas.

```shell
# Version 1.0
MOLCAS_MEM=256
MOLCAS_WORKDIR=/scratch
MOLCAS_NEW_WORKDIR=YES
MOLCAS_KEEP_WORKDIR=YES
MOLCAS_PROJECT=NAME
```

--------------------------------

### Install Auger-OCA Package

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/Tools/AugerOca/README.md

Install the auger-oca package using pip.

```bash
pip install auger-oca
```

--------------------------------

### ALASKA OFEMbedding Input Example

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/doc/source/users.guide/programs/alaska.rst

This snippet shows an example input for the OFEMbedding keyword, specifying functionals for kinetic energy and exchange-correlation. It also includes an example for the DFMD keyword.

```input
OFEMbedding
 ldtf/pbe
dFMD
 1.0
```

--------------------------------

### GRID_IT Input Example with Orbital Selection

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/doc/source/tutorials/tut_grid_it.rst

This example shows a basic input for GRID_IT, including specifying a dense grid and selecting specific orbitals by range and symmetry.

```input
&GRID_IT
 Dense
 * compute orbitals from 20 to 23 form symmetry 1 and orbital 4 from symmetry 2
 SELECT
 1:20-23,2:4
```

--------------------------------

### Configure Parallel Installation with External GA

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/doc/source/installation.guide/parainst.rst

Installs the parallel version of Molcas with an external Global Arrays (GA) library. Pass the location of the GA installation using the -ga flag.

```bash
./configure -parallel -ga /opt/ga-5.1
```

--------------------------------

### Prepare RDM Templates

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/doc/source/tutorials/tut_nevpt2.rst

Copy the prepare_rdm_template.sh script to your scratch directory and run it to create subdirectories for each state's 4-RDM calculation.

```bash
cp $MOLCAS/Tools/distributed-4rdm/prepare_rdm_template.sh .
./prepare_rdm_template.sh 0 1 2
```

--------------------------------

### Dynamixtools Command Line Help

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/doc/source/users.guide/programs/dynamix.rst

Displays the usage information for the dynamixtools.py script, outlining available arguments for generating initial conditions for molecular dynamics calculations.

```bash
$ python3 dynamixtools.py -h
usage: dynamixtools.py [-h] [-s SEED] [-l LABEL] [-i I] [-c CONDITION] [-t TEMP] [-v] [-T] [-D] [-m METHOD]

optional arguments:
  -h, --help            show this help message and exit
  -s SEED, --seed SEED  indicate the SEED to use for the generation of randoms
  -l LABEL, --label LABEL
                        label for your project (default is "geom")
  -i I, --input I       path of the frequency h5 or molden file
  -c CONDITION, --condition CONDITION
                        number of initial conditions (default 1)
  -t TEMP, --temperature TEMP
                        temperature in kelvin for the initial conditions
  -v, --verbose         more verbose output
  -T, --TEST            keyword use to test the routines
  -D, --DIGIT           keyword to suppress the counter in the filename (needed for debug)
  -m METHOD, --method METHOD
                        Keyword to specify the sampling method:
                        1 Initial conditions based on the molecular vibrational frequencies and energies sampled from a Boltzmann distribution (Default).
                        2 Thermal normal mode sampling where the cumulitative distribution function for a classical boltzmann distribution at temperature T is used to approximate the energy of each mode.
                        3 Wigner distribution for the ground vibrational state, n=0.
```

--------------------------------

### Poly_Aniso NNEQ Keyword Examples

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/doc/source/users.guide/programs/poly_aniso.rst

Examples of the NNEQ keyword for defining the number of non-equivalent magnetic centers and specifying ab initio computation status. These examples are for situations where all sites have been computed ab initio.

```input
NNEQ
2  T  F
```

```input
NNEQ
3  T  F
```

```input
NNEQ
6  T  F
```

--------------------------------

### BSSE Calculation Setup

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/doc/source/tutorials/tut_gateway.rst

Demonstrates how to set up a Basis Set Superposition Error (BSSE) calculation using the 'bsse' keyword in the GATEWAY input. The 'bsse' keyword followed by a number indicates a XYZ file to be treated as dummy atoms.

```molcas
&GATEWAY
coord = ethanol.xyz
coord = water.xyz
bsse  = 1
basis = ANO-S-MB
NOMOVE
&SEWARD; &SCF
&GRID_IT
NAME = water
***************
&GATEWAY
coord = ethanol.xyz
coord = water.xyz
bsse  = 2
basis = ANO-S-MB
NOMOVE
&SEWARD; &SCF
&GRID_IT
NAME = ethanol
**************
&GATEWAY
coord = ethanol.xyz
coord = water.xyz
basis = ANO-S-MB
NOMOVE
&SEWARD; &SCF
```

--------------------------------

### Z-matrix Example

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/doc/source/users.guide/programs/gateway.rst

An example of defining atomic coordinates using the Z-matrix format. Units are assumed to be angstroms.

```text
H.ANO-L...1s.
 H    -2.748759     0.819593     2.808729  / angstrom
End of basis
```

--------------------------------

### QM/MM Calculation Setup with TINKER

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/doc/source/users.guide/programs/espf.rst

This snippet shows a typical input file for a QM/MM calculation using the TINKER interface. It defines the gateway, basis set, and external program settings.

```molcas
&Gateway
  Tinker
  Basis = STO-3G
  Group = Nosym

  &Seward

  &Espf
  External = Tinker
  LAMorok

```

--------------------------------

### Set Installation Prefix

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/CMakeLists.txt

Configures the default installation directory for OpenMolcas. This option is used when the CMAKE_INSTALL_PREFIX has not been explicitly set.

```cmake
if (CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
  set (CMAKE_INSTALL_PREFIX "/opt/OpenMolcas" CACHE PATH "Location where OpenMolcas will be installed." FORCE)
endif ()
```

--------------------------------

### Verify Molcas Installation

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/doc/source/installation.guide/install.rst

Command to initiate the verification process for the Molcas installation, checking main modules and features.

```bash
molcas verify
```

--------------------------------

### Boys Localisation Example

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/doc/source/users.guide/programs/localisation.rst

Example input for performing Boys localisation on the CO molecule. Symmetry should not be used for this method.

```input
&GATEWAY
Coord = $MOLCAS/Coord/CO.xyz
Basis = STO-3G
Group = C1

&SEWARD ; &SCF

&LOCALISATION
Boys
```

--------------------------------

### MBPT2 Input Example with Orbital Specification

Source: https://gitlab.com/molcas/openmolcas/-/blob/master/doc/source/users.guide/programs/mbpt2.rst

This example demonstrates how to configure MBPT2 calculations by specifying frozen and deleted orbitals. It includes options for general orbital freezing/deletion and symmetry-specific settings.

```input
&MBPT2
 Title
  H2O:  O(9.5/4.2), H(4/2)
 * The lowest energy occupied orbital in the repr. no.1 will be frozen in
 * MBPT2 calculations. The number of representations is 4 and all zeros
 * must be explicitly given
 Frozen
 1 0 0 0
 * Two highest energy external orbitals in the repr. no.3 will be deleted
 * in MBPT2 calculations. The number of representations is 4 and all
 * zeros must be explicitly given
 Deleted
 0 0 2 0
 * One occupied orbital in symmetry no.1 will be additionally frozen by
 * using the SFRO option. Let it be the third SCF occupied orbital in
 * this symmetry
 sFrozen
 1 0 0 0   // Gives the number of frozen orbitals in each symmetry
 3         // Gives the frozen orbital reference number in symmetry no. 1
 * Two external orbitals in symmetry no.1 and one external orbital in
 * symmetry 3 will be deleted. In symmetry 1 let it be the second and
 * third external orbitals, and in symmetry 3 the third (already deleted
 * in by using the option DELE) external orbital
 sDeleted
 2 0 1 0   // Gives the number of orbitals to be deleted in each symmetry
 2 3       // Gives the reference numbers of external orbitals in sym. 1
 3         // Gives the reference number of the external orb. in sym. 3

```