### DFT+U Tutorial: Basic Setup

Source: https://docs.abinit.org/tutorial/dftu

This is the initial setup for the DFT+U tutorial, defining spin polarization, structural parameters, and k-point grid. It is used as a base for subsequent examples.

```Abinit Input
#Spin
nsppol 1
nspden 2
nspinor 1
spinat 0 0 1
       0 0 -1
       0 0 0
       0 0 0

#Parameters
nstep  50
ecut 15
pawecutdg 30
toldfe 1.0d-8
nband  40
occopt 7  tsmear 0.015

#Structural parameters
natom 4
ntypat 2
typat 1 1 2 2
znucl 28 8
xred 0 0 0
    0.0 0.0 0.5
    0.5 0.5 0.25
    0.5 0.5 0.75

acell   3*7.92

rprim 0.0 1/2 1/2
      1/2 0.0 1/2
      1.0 1.0 0.0

# Kpoint Grid
ngkpt 2 2 2
chksymbreak 0  # The k point grid is not symmetric, but the calculations being for the ground-state, this is not a problem.

 pp_dirpath "$ABI_PSPDIR"
 pseudos "Psdj_paw_pbe_std/Ni.xml, Psdj_paw_pbe_std/O.xml"

##############################################################
# This section is used only for regression testing of ABINIT #
##############################################################
#%%<BEGIN TEST_INFO>
#%% [setup]
#%% executable = abinit
#%% [files]
#%% files_to_test =
#%%   tdftu_1.abo, tolnlines=  4, tolabs=  2.000e-06, tolrel=  2.000e-03, fld_options = -medium
#%% output_file = "tdftu_1.abo"
#%% [paral_info]
#%% max_nprocs = 1
#%% [extra_info]
#%% authors = Unknown
#%% keywords = DFTU, PAW
#%% description =  first run of the DFT+U tutorial
#%%<END TEST_INFO>

```

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

### Example Input File for Ghost State Analysis

Source: https://docs.abinit.org/tutorial/paw2

This is an example input file used to demonstrate the presence and resolution of ghost states in ATOMPAW calculations. It serves as a starting point for troubleshooting.

```input
view tutorial/paw2_assets/Ni.ghost.atompaw.input
```

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

### Install ABINIT

Source: https://docs.abinit.org/INSTALL_MacOS

Install ABINIT to the system. This step is optional.

```bash
make install
```

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

### PAW2 Tutorial Test Setup

Source: https://docs.abinit.org/tutorial/paw2

This snippet outlines the setup for the PAW2 tutorial regression test. It specifies the executable, files to test with tolerance parameters, output file, and parallel processing information.

```bash
#%%<BEGIN TEST_INFO>
#%% [setup]
#%% executable = abinit
#%% [files]
#%% files_to_test =
#%%   tpaw2_2.abo, tolnlines= 25, tolabs=  1.1e-1,    tolrel=  5.0e-1, fld_options=-easy
#%% output_file = "tpaw2_2.abo"
#%% [paral_info]
#%% max_nprocs = 6
#%% [extra_info]
#%% authors = M. Torrent
#%% keywords = PAW
#%% description =
#%%   Input for PAW2 tutorial
#%%   Nickel ferromagnetic fcc structure
#%%   Testing ecut convergence
#%%<END TEST_INFO>
```

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

### Input File Path Example

Source: https://docs.abinit.org/tutorial/paw2

Specifies an input file path for a test case related to the RSO tutorial.

```text
tests/tutorial/Input/tpaw2_1.abi
```

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

### RSO Configuration Example

Source: https://docs.abinit.org/tutorial/paw2

This snippet shows a basic configuration for the Real Space Optimization (RSO) method, including numerical parameters and output format selection.

```text
3 0. troulliermartins
2.0
2.0
2.0
2.0
2.0
2.0
XMLOUT
default
END
```

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

### Install ATOMPAW using Homebrew (macOS)

Source: https://docs.abinit.org/tutorial/paw2

Installs the ATOMPAW package on macOS using the Homebrew package manager.

```bash
brew install atompaw/repo/atompaw
```

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

### Close Command Example

Source: https://docs.abinit.org/tutorial/paw2

Demonstrates the 'Close' command, likely used to finalize or exit a process related to the RSO configuration.

```text
Close
```

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

### AtomPaw Calculation Summary

Source: https://docs.abinit.org/tutorial/paw2

Example output from an AtomPaw calculation, showing a summary of PAW energies. This output is used to assess the convergence and accuracy of the calculation.

```text
   Summary of PAW energies
         Total valence energy       -185.18230027710337
           Smooth energy             11.634042318422193
           One center               -196.81634259552555
           Smooth kinetic            15.117782033814152
           Vloc energy              -2.8024659321861067
           Smooth exch-corr         -3.3712015132649102
           One-center xc            -123.08319475096027

```

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

### Partial-Waves Basis - Generation Scheme (Bloechl)

Source: https://docs.abinit.org/tutorial/paw2

Specifies the generation scheme for pseudo partial waves and projectors. 'bloechl' is used as a starting point.

```atompaw
bloechl
```

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

### ABINIT Output: Total Energy Convergence (RRKJ Pseudization)

Source: https://docs.abinit.org/tutorial/paw2

This output shows the total energy convergence using the RRKJ pseudization scheme. It indicates improved convergence compared to the initial Bloechl projector setup.

```text
  ecut1     8.00000000E+00 Hartree
  ecut2     1.00000000E+01 Hartree
  ecut3     1.20000000E+01 Hartree
  ecut4     1.40000000E+01 Hartree
  ecut5     1.60000000E+01 Hartree
  ecut6     1.80000000E+01 Hartree
  ecut7     2.00000000E+01 Hartree
  ecut8     2.20000000E+01 Hartree
etotal1    -3.9599860476E+01
etotal2    -3.9626919903E+01
etotal3    -3.9627249378E+01
etotal4    -3.9627836846E+01
etotal5    -3.9628304332E+01
etotal6    -3.9628429611E+01
etotal7    -3.9628436662E+01
etotal8    -3.9628455467E+01


```

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

### MPICH Installation Confirmation Message

Source: https://docs.abinit.org/tutorial/abinit_build

Example output message indicating where libraries have been installed and how to link against them.

```text
----------------------------------------------------------------------
Libraries have been installed in:
   /home/gmatteo/local/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the '-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the 'LD_LIBRARY_PATH' environment variable
     during execution
   - add LIBDIR to the 'LD_RUN_PATH' environment variable
     during linking
   - use the '-Wl,-rpath -Wl,LIBDIR' linker flag
   - have your system administrator add LIBDIR to '/etc/ld.so.conf'

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------

```

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

### Setup Calculation Directory

Source: https://docs.abinit.org/tutorial/z2pack

Navigate to the tutorial directory, create a working subdirectory, and copy the initial ABINIT input file.

```bash
cd $ABI_TESTS/tutoplugs/Input
mkdir Work_z2pack && cd Work_z2pack
cp ../tz2_2.abi .

```

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

### Core and Valence Electron Designation

Source: https://docs.abinit.org/tutorial/paw2

Designates shells as core ('c') or valence ('v'). This example marks 1s, 2s, 3s, 2p as core and 4s, 4p, 3d as valence.

```atompaw
c
c
c
v
c
c
v
v
```

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

### Wannier90 Configuration File Example

Source: https://docs.abinit.org/tutorial/wannier90

Example content for a configuration file (myconf.ac9) to enable Wannier90 support during ABINIT compilation. It specifies the installation path for the PSML I/O library.

```shell
#Install prefix of the PSML I/O library (e.g.
#                          /usr/local).
with_wannier90="/usr/local"
```

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

### Setup Working Directory and Copy Input File

Source: https://docs.abinit.org/tutorial/dmft_triqs

Navigate to the tutorial input directory, create a new working folder, and copy the initial ABINIT input file for the calculation.

```bash
cd $ABI_TESTS/tutoparal/Input
mkdir Work_dmft_triqs
cd Work_dmft_triqs
cp ../tdmft_triqs_1.abi .

```

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

### Setup Working Directory and Copy Input File

Source: https://docs.abinit.org/tutorial/gw2

Creates a new directory for the GW2 calculations, changes into it, and copies the necessary input file. This is the initial setup step for the tutorial.

```bash
    mkdir Work_gw2
    cd Work_gw2
    cp $ABI_TESTS/tutorial/Input/tgw2_1.abi .

```

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

### Get gfortran Version

Source: https://docs.abinit.org/tutorial/abinit_build

Retrieves the version information for the installed GNU Fortran compiler.

```bash
gfortran --version
GNU Fortran (GCC) 5.3.1 20160406 (Red Hat 5.3.1-6)
Copyright (C) 2015 Free Software Foundation, Inc.
```

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

### Set up Input Directory and Files

Source: https://docs.abinit.org/tutorial/elastic

Navigate to the input directory, create a working directory, and copy the necessary input file.

```bash
cd $ABI_TESTS/tutorespfn/Input
mkdir Work_elast
cd Work_elast
cp ../telast_1.abi .

```

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

### Setting up Working Directory and Input File

Source: https://docs.abinit.org/tutorial/base4

Prepare a working directory for the tutorial, copy the input file, and navigate into the directory. This sets up the environment for running the ABINIT calculation.

```shell
cd $ABI_TESTS/tutorial/Input
mkdir Work4
cd Work4
cp ../tbase4_1.abi .
```

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

### Install ABINIT Dependencies via MacPorts

Source: https://docs.abinit.org/INSTALL_MacOS

Install essential libraries for ABINIT using MacPorts, including GCC, OpenBLAS, OpenMPI, FFTW, HDF5, NetCDF, and libxc. This example uses GCC 11.

```bash
sudo port install gcc11
sudo port install OpenBLAS +gcc11+fortran
sudo port install openmpi-gcc11 +gfortran
sudo port install fftw-3 +gfortran
sudo port install fftw-3-single +gfortran
sudo port install fftw-3-long +gfortran
sudo port install hdf5 +cxx+gcc11+hl+openmpi
sudo port install netcdf +cdf5+dap+x+gcc11+netcdf4+openmpi
sudo port install netcdf-fortran +gcc11+openmpi
sudo port install libxc4 +gcc11
```

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

### Setting up Working Directory and Input File

Source: https://docs.abinit.org/tutorial/base3

Prepare a working directory for the tutorial calculations and copy the necessary input file. This involves changing directories, creating a new directory, and copying the input file.

```shell
cd $ABI_TESTS/tutorial/Input
mkdir Work3
cd Work3
cp ../tbase3_1.abi .

```

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

### ABINIT File Header Example

Source: https://docs.abinit.org/tutorial/eph4zpr

An example of the ABINIT file header, showing various parameters such as code version, system dimensions, perturbation case, and energy cutoffs. This information is crucial for understanding the calculation setup.

```text
===============================================================================
 ECHO of part of the ABINIT file header

 First record :
.codvsn,headform,fform = 9.2.0      80  111

 Second record :
 bantot,intxc,ixc,natom  =   480     0    11     2
 ngfft(1:3),nkpt         =    32    32    32    40
 nspden,nspinor          =     1     1
 nsppol,nsym,npsp,ntypat =     1    48     2     2
 occopt,pertcase,usepaw  =     1     4     0
 ecut,ecutdg,ecutsm      =  3.5000000000E+01  3.5000000000E+01  0.0000000000E+00
 ecut_eff                =  3.5000000000E+01
 qptn(1:3)               =  5.0000000000E-01  0.0000000000E+00  0.0000000000E+00
 rprimd(1:3,1)           =  0.0000000000E+00  4.0182361526E+00  4.0182361526E+00
 rprimd(1:3,2)           =  4.0182361526E+00  0.0000000000E+00  4.0182361526E+00
 rprimd(1:3,3)           =  4.0182361526E+00  4.0182361526E+00  0.0000000000E+00
 stmbias,tphysel,tsmear  =  0.0000000000E+00  0.0000000000E+00  1.0000000000E-02

 The header contain   4 additional records.

```

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

### Navigate to Tutorial Directory

Source: https://docs.abinit.org/tutorial/base3

Change the current directory to the ABINIT tutorial work directory and copy the input file for the k-point convergence study.

```bash
cd $ABI_TESTS/tutorial/Work3
cp ../tbase3_3.abi .
```

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

### Setup Working Directory and Copy Input Files

Source: https://docs.abinit.org/tutorial/lruj

Navigate to the tutorial input directory, create a working directory for LRUJ calculations, and copy the necessary input files.

```bash
cd $ABI_TESTS/tutorial/Input
mkdir work_lruj
cd work_lruj
cp ../tlruj_1.abi .
cp ../tlruj_2.abi .

```

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

### Example of Negative getXXX Variable Usage

Source: https://docs.abinit.org/variables/files

This example illustrates how a negative value for a 'get' variable indicates the number of datasets to go backward to find the needed file. It refers to dataset 2 when dataset 4 is initialized.

```fortran
ndtset 3   jdtset 1 2 4  getXXX -1
```

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

### Configure NetCDF-Fortran Prefix (Detailed)

Source: https://docs.abinit.org/developers/autoconf_examples

Specifies the installation prefix for the NetCDF-Fortran library, including version details. This path should be accurate for your setup.

```shell
with_netcdf_fortran="${FALLBACKS_HOME}_10.6/${FB}/netcdf4_fortran/4.6.2"
```

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

### Range Object Example

Source: https://docs.abinit.org/developers/abimkdocs

This YAML-like structure defines a range of values from start to stop, used for default values in Abinit input files.

```yaml
!range
   start: 1
   stop: N

```

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

### Example Configuration File Syntax

Source: https://docs.abinit.org/tutorial/abinit_build

Illustrates the syntax for an ABINIT configuration file, showing how to normalize configure options and use shell variables.

```text
# -------------------------------------------------------------------------- #

```

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

### Create and Navigate to Working Directory

Source: https://docs.abinit.org/tutorial/eph4vpq

Prepare a working directory for tutorial execution by creating a subdirectory and navigating into it.

```shell
cd $ABI_TESTS/tutorespfn/Input
mkdir Work_eph4vpq
cd Work_eph4vpq

```

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

### Relaxed Ion Calculation Setup

Source: https://docs.abinit.org/tutorial/polarization

This section indicates the start of a calculation for relaxed-ion piezoelectric constants. It uses the same Berry phase method and dataset configuration as the clamped-ion calculation.

```abinit
# Finite difference calculation of the relaxed ion
# piezoelectric constants of AlP
#
# The calculation proceeds by computing the change in cell
# polarization by a Berrys phase formula, due to changes
# in the strain of the unit cell. In this case, the ion positions
# will be allowed to relax to to their new equilibrium positions
# within the strain cell.

# Berry phase calculation of the polarization
# berryopt -1 triggers the implementation of M. Viethen
berryopt -1

# three cell geometries will be computed
ndtset 3

#Definition of the unit cell
acell     3*7.2728565836E+00

# rprim = strain tensor x rprim0, where
# rprim0 is the unstrained rprim

```

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

### Timing Results for Different Distributions

Source: https://docs.abinit.org/tutorial/paral_bandpw

Example output showing the processor timing for various `npband` x `npfft` configurations. This data is used to determine the most efficient setup.

```text
tparal_bandpw_02.04.16.abo:- Proc.   0 individual time (sec): cpu=         62.9  wall=         69.4
tparal_bandpw_02.08.08.abo:- Proc.   0 individual time (sec): cpu=         57.9  wall=         64.0
tparal_bandpw_02.16.04.abo:- Proc.   0 individual time (sec): cpu=         56.0  wall=         61.8
tparal_bandpw_02.32.02.abo:- Proc.   0 individual time (sec): cpu=         57.1  wall=         62.8
tparal_bandpw_02.64.01.abo:- Proc.   0 individual time (sec): cpu=         60.7  wall=         66.4
```

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

### Setup Working Directory and Copy Input Files

Source: https://docs.abinit.org/tutorial/eph_tdep_legacy

Prepare a working directory for the Abinit calculation by creating a subdirectory and copying necessary input files.

```bash
cd ~/abinit/tests/tutorespfn/Input
mkdir Work
cd Work
cp ../teph_tdep_legacy*in .

```

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

### Set up Input Directory and Copy File

Source: https://docs.abinit.org/tutorial/base2

Navigate to the input directory, create a new working directory, and copy the necessary input file.

```bash
cd $ABI_TESTS/tutorial/Input
mkdir Work2
cd Work2
cp ../tbase2_1.abi .

```

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

### Plane-Wave Basis and k-point Grid Setup

Source: https://docs.abinit.org/tutorial/paw1

Defines the kinetic energy cut-off for plane waves and the PAW double grid, and specifies the k-point grid generation. This example uses a 10x10x10 grid.

```abinit
ecut 20.0
ecutsm 0.5
pawecutdg 50.
kptopt 1
ngkpt 10 10 10
nshiftk 4
shiftk
  0.5 0.5 0.5
  0.5 0.0 0.0
  0.0 0.5 0.0
  0.0 0.0 0.5
```

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

### ABINIT Parallelization Output Example

Source: https://docs.abinit.org/tutorial/paral_bandpw

This output shows a sample of ABINIT's suggested processor distributions for parallel execution, based on the number of CPUs. It includes columns for np_spkpt, npfft, npband, bandpp, #MPI(proc), and WEIGHT, guiding the user to select an optimal configuration.

```text
 Searching for all possible proc distributions for this input with #CPUs<=64:

 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 |    np_spkpt|       npfft|      npband|      bandpp|  #MPI(proc)|    WEIGHT|
 |    1<<    1|    1<<   22|    1<<   64|    1<<  640|    1<<   64|  <=    64|
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 |           1|           4|          16|          10|          64|    42.328|
 |           1|           8|           8|          20|          64|    41.844|
 |           1|          16|           4|          40|          64|    41.730|
 |           1|           6|          10|          16|          60|    40.093|
 |           1|          15|           4|          40|          60|    39.054|
 |           1|           4|          16|           8|          64|    39.043|
 |           1|          12|           5|          32|          60|    39.026|
 |           1|           8|           8|          16|          64|    38.598|
 |           1|          16|           4|          32|          64|    38.493|
 |           1|           3|          20|           8|          60|    38.319|
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 Only the best possible choices for nproc are printed...
 
```

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

### Create and Navigate to Working Directory

Source: https://docs.abinit.org/tutorial/eph4zpr

Prepare a working directory for tutorial execution. This involves changing to the input directory, creating a new subdirectory for the tutorial, and then navigating into it.

```shell
cd $ABI_TESTS/tutorespfn/Input
mkdir Work_eph4zpr
cd Work_eph4zpr
```

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

### BSE Input File Example for Crystalline Silicon

Source: https://docs.abinit.org/tutorial/bse

This input file demonstrates the setup for a Bethe-Salpeter Equation (BSE) calculation for crystalline silicon. It includes steps for ground-state calculation, NSCF runs for WFK file generation on symmetric and symmetry-breaking k-meshes, and SCR calculation for the screening matrix.

```input
# Crystalline silicon
# Preparatory run for BS calculations
#
# There are four datasets specified in this input:
# 1) Ground-state calculation to get the density.
# 2) NSCF run to generate the WFK file on a symmetric k-mesh (4x4x4, gamma-centered)
# 3) NSCF run to generate another WFK file on a shifted 4x4x4 k-mesh that breaks the symmetry of the BZ sampling
# 4) SCR calculation with the WFK file generated in the second dataset
#
ndtset 4

# Definition of the k-point grid
kptopt 1             # Option for the automatic generation of k points,
ngkpt  4 4 4         # This mesh is too coarse for optical properties.
nshiftk 1
shiftk  0.0 0.0 0.0  # Gamma-centered k-mesh

# Dataset1: self-consistent calculation
#
tolvrs1 1.0d-8
prtden1 1

# Dataset2: definition of parameters for the calculation of the WFK file on the symmetric k-mesh.
#
iscf2    -2       # NSCF run
getden2  1        # Read previous density file
tolwfr2  1.0d-8
nband2    105     # bands treated in the CG algorithm
nbdbuf2    5      # The last five states are excluded from the converge check
                  # to facilitate the convergence

# Dataset3: calculation of the WFK file on the shifted k-mesh to break the symmetry.
#
iscf3    -2
getden3   1
tolwfr3  1.0d-8
nband3    15               # Here we can reduce the number of bands since this WFK file
                           # will be used to construct the transition space
nbdbuf3    5
chksymbreak3 0             # To skip the check on the k-mesh.
shiftk3    0.11 0.21 0.31  # This shift breaks the symmetry of the k-mesh.

# Dataset3: creation of the screening (eps^-1) matrix
#
optdriver4 3
gwpara4    2
inclvkb4   2
awtr4      1
symchi4    1
getwfk4    2
ecuteps4   6
ecutwfn4   12
nband4    100  # This value leads to well converged QP energies, see the first GW tutorial
nfreqre4   1   # Only the static limit is needed for standard BSE calculations.
nfreqim4   0

# VARIABLES COMMON TO THE DIFFERENT DATASETS

# Definition of the unit cell: fcc
acell 3*10.217         # This is equivalent to   10.217 10.217 10.217
rprim  0.0  0.5  0.5   # FCC primitive vectors (to be scaled by acell)
       0.5  0.0  0.5
       0.5  0.5  0.0

# Definition of the atom types
ntypat 1         # There is only one type of atom
znucl 14         # The keyword "zatnum" refers to the atomic number of the
                 # possible type(s) of atom. The pseudopotential(s)
                 # mentioned in the "files" file must correspond
                 # to the type(s) of atom. Here, the only type is Silicon.

# Definition of the atoms
natom 2           # There are two atoms
typat 1 1         # They both are of type 1, that is, Silicon.
xred              # Reduced coordinate of atoms
   0.0  0.0  0.0
   0.25 0.25 0.25

```

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

### Prepare Working Directory and Copy Input File

Source: https://docs.abinit.org/tutorial/gwr1

Create a dedicated working directory for the tutorial and copy the initial input file (tgwr_1.abi) into it. This sets up the environment for the first calculation step.

```shell
mkdir Work_gwr
cd Work_gwr
cp ../tgwr_1.abi .

```

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

### List Installed Libraries

Source: https://docs.abinit.org/tutorial/abinit_build

Lists the OpenBLAS library files installed in the lib directory of the local installation. This confirms successful installation.

```bash
ls $HOME/local/lib/libopenblas*
```

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

### Setup Spin Calculation Directory

Source: https://docs.abinit.org/tutorial/spin

Prepare the working directory and copy the input file for the spin tutorial. This sets up the environment for the calculation.

```bash
cd $ABI_TESTS/tutorial/Input
mkdir Work_spin
cd Work_spin
cp ../tspin_1.abi .

```