Beginner’s Tutorial

Table of contents

Once PWTK is installed and configured (see Installation and Configuration Tutorial), we are ready to start using PWTK. It can be used interactively, but more often it is used to execute scripts. Among the first things to learn is how to specify QE input data and how to run QE programs in PWTK scripts.

Specifying input data

There are two ways how to specify input data for QE executables in PWTK scripts.

Input data can be loaded into PWTK from existing QE input files using the load_from command. For example, an existing pw.x input file (say pw.Si.in) can be loaded as:
```
load_from pw.x pw.Si.in
```
Hence, the usage of the load_from command is:

load_from program inputFile

where program is the name of the QE executable (e.g. pw.x, ph.x, pp.x) and inputFile is the name of the input file.

Alternatively, the pw.x input file can be loaded with the load_fromPWI command as:
```
load_fromPWI pw.Si.in
```
where PWI stands for PW.x Input. For other executables, analogous commands exist (e.g. load_fromPHI, load_fromPPI, load_fromNEBI). The load_fromXXI (XXI = PWI, PHI, PPI, NEBI…) commands exist for all explicitly supported QE programs in PWTK. Likewise, only the inputs for the explicitly supported QE programs can be loaded into PWTK with the load_from command. To get the list of explicitly supported programs, enter the PWTK interactive prompt (by typing pwtk in the terminal) and type report programs.

The second way of specifying input data is by entering them directly. The syntax is analogous to that of QE with the difference that namelists and cards are in encapsulated in curly braces (or double quotes), e.g.:

pw.x input file

PWTK script

&CONTROL
   calculation = 'scf'
/
&SYSTEM
     ibrav = 2
         A = 5.4
       nat = 2
      ntyp = 1
   ecutwfc = 18.0
 /
&ELECTRONS
   conv_thr = 1d-7
/

ATOMIC_SPECIES
   Si  1.00  Si.vbc 

ATOMIC_POSITIONS alat 
   Si    0.00  0.00  0.00    
   Si    0.25  0.25  0.25    

K_POINTS automatic 
   4 4 4   1 1 1

CONTROL {
   calculation = 'scf'
}
SYSTEM {
     ibrav = 2
         A = 5.4
       nat = 2
      ntyp = 1
   ecutwfc = 18.0
}
ELECTRONS {
   conv_thr = 1d-7
}
ATOMIC_SPECIES {
   Si  1.00  Si.vbc 
}
ATOMIC_POSITIONS alat  {
   Si    0.0  0.0  0.0    
   Si    1/4  1/4  1/4
}
K_POINTS automatic {
   4 4 4   1 1 1
}

BEWARE: PWTK scripts are case-sensitive, implying that also namelists, namelist variables, and cards are case-sensitive. Namelists and cards usually have the same names as in QE but are written in uppercase. Among exceptions are the generic namelists (e.g. INPUT and INPUTPP) that are used by several QE programs, which are renamed because PWTK requires unique names. To list all exceptions, enter the PWTK interactive prompt (by typing pwtk in the terminal) and type:

report exceptions

which lists all the namelist and card naming exceptions in PWTK, i.e.:

 -------------------------------------------------------------------------------
  executable      type       QE-name                             PWTK-name        
 -------------------------------------------------------------------------------
  cp.x            supercard  AUTOPILOT/ENDRULES                  AUTOPILOT        

  cppp.x          namelist   INPUTPP                             CPPP             

  d3hess.x        namelist   INPUT                               D3HESS           

  dynmat.x        namelist   INPUT                               DYNMAT           

  ...             ...        ...                                 ...

For further info about input data specs in PWTK, see section 2.2 Specifying Input Data.

Modifying and deleting namelist variables

In PWTK, input data can be changed on the fly. For example, consider the following snippet:

SYSTEM {
   nspin = 2
   tot_magnetization = 1
}

SYSTEM {
   nspin = 1
   tot_magnetization = 0
}

The current value of variables is now nspin = 1 and tot_magnetization = 0. But for nspin=1, we do not need to specify tot_magnetization. In PWTK, a defined namelist variable can be deleted as follows:

SYSTEM {
   tot_magnetization =
}

Inheritance of namelist variables

In PWTK, a few namelist variables are inherited from a “parent” namelist to “descendant” namelists. Examples of such variables are the prefix and outdir variables of the CONTROL namelist, INPUTPH’s fildyn, and flfrc of the q2r.x program. Hence, for example, if the prefix and outdir variables are set in the CONTROL namelist, their definition in the “descendant” namelists (INPUTPP, INPUTPH, PROJWFC…) can be omitted because PWTK automatically sets them. Here is an example:

CONTROL {
   prefix = 'example1'
   outdir = '.'
}

# 'outdir' and 'prefix' are inherited from the CONTROL namelist; 
# no need to set them here
PROJWFC {
   ngauss  = 0
   degauss = 0.01
   DeltaE  = 0.1
}

The qe2pwtk program

An easy way to learn how to specify input data in PWTK is by using its qe2pwtk program, which converts the QE input into the PWTK script. The usage is:

qe2pwtk ?-p program? inputFile

where the pair of question marks (?…?) indicates optional arguments, program is the name of QE executable and inputFile is the input file. For example, a neb.x input file (say, neb.H2+H.in) can be converted to PWTK syntax as:

qe2pwtk -p neb.x neb.H2+H.in

which gives:

PATH {
   CI_scheme     = 'auto'
   num_of_images = 7
   nstep_path    = 100
   string_method = 'neb'
}

CONTROL {
   prefix = 'H2+H'
}

SYSTEM {
   ecutwfc           = 20.0
   ibrav             = 0
   nat               = 3
   nspin             = 2
   ntyp              = 1
   tot_magnetization = 1.0
}

ELECTRONS {
   conv_thr    = 1.e-8
}

ATOMIC_SPECIES {
    H  1.00794  H.pbe-rrkjus.UPF
}

CELL_PARAMETERS bohr {
    12.000000000000000    0.000000000000000    0.000000000000000
     0.000000000000000    5.000000000000000    0.000000000000000
     0.000000000000000    0.000000000000000    5.000000000000000
}

K_POINTS gamma

POSITIONS {
FIRST_IMAGE
ATOMIC_POSITIONS bohr
  H       -5.274278671000   0.000000000000   0.000000000000   1  0  0
  H        0.000000000000   0.000000000000   0.000000000000   0  0  0
  H        1.490737029000   0.000000000000   0.000000000000   1  0  0
LAST_IMAGE
ATOMIC_POSITIONS bohr
  H       -1.490737127000   0.000000000000   0.000000000000
  H        0.000000000000   0.000000000000   0.000000000000
  H        5.274284748000   0.000000000000   0.000000000000
}

Note that for neb.x, the PWTK syntax is slightly simpler than the QE syntax because its omits the BEGIN- and END-type keywords.

Running QE executables

Analogously to specifying input data, there are two ways of how to run QE executables in PWTK.

They can be run by using the existing QE input files with the run command, i.e.:
```
run pw.x pw.Si.in
```
which is equivalent to the following shell command:
```
$PREFIX pw.x < pw.Si.in > pw.Si.out
```
where pw.Si.in is an existing pw.x input file and the value of PREFIX is, e.g., mpirun -np 4. The run command is similar to the Tcl exec command but takes into account the PWTK specs, such as bin_dir, prefix, postfix…

The second way of running QE executables is by first loading the input data into PWTK and then using the runXX command. The advantage of loading the input data into PWTK is that one can change them on the fly. For example: tcl load_from pw.x pw.Si.in SYSTEM { ecutwfc = 25.0 } runXX pw.x pw.Si-e25.in Alternatively, the pw.x program can be run with the runPW command as: runPW pw.Si-e25.in Analogous commands exist for other QE programs (e.g., runPH, runPP, runNEB).

BEWARE: load_from and runXX commands are available only for explicitly supported QE programs in PWTK. To get the list of them, enter the PWTK interactive prompt (by typing pwtk in the terminal) and type:

report programs

which gives:

 -------------------------------------------------------------------------------
  executable             runCmd                rerunCmd      input namespace     
 -------------------------------------------------------------------------------
  all_currents.x         runALL_CURRENTS                     ::pwtk::all_curri   
  band_interpolation.x   runBAND_INTERPOLATION               ::pwtk::band_inti   
  bands.x                runBANDS                            ::pwtk::bi          
  bgw2pw.x               runBGW2PW                           ::pwtk::bgw2pwi     
  cp.x                   runCP                 rerunCP       ::pwtk::cpi         
  cppp.x                 runCPPP                             ::pwtk::cpppi       
  d3hess.x               runD3HESS                           ::pwtk::d3hessi     
  dos.x                  runDOS                              ::pwtk::di          
  dynmat.x               runDYNMAT                           ::pwtk::dmi         
  hp.x                   runHP                               ::pwtk::hpi         
  kcw.x                  runKCW                              ::pwtk::kcwi        
  ld1.x                  runLD1                              ::pwtk::ld1i        
  matdyn.x               runMATDYN                           ::pwtk::mdi         
  molecularpdos.x        runMOPDOS                           ::pwtk::mpdi        
  neb.x                  runNEB                rerunNEB      ::pwtk::nebi        
  oscdft_et.x            runOSCDFT_ET                        ::pwtk::oscdft_eti  
  oscdft_pp.x            runOSCDFT_PP                        ::pwtk::oscdft_ppi  
  ph.x                   runPH                 rerunPH       ::pwtk::phi         
  postahc.x              runPOSTAHC                          ::pwtk::postahci    
  pp.x                   runPP                               ::pwtk::ppi         
  ppacf.x                runPPACF                            ::pwtk::ppacfi      
  pprism.x               runPPRISM                           ::pwtk::pprismi     
  projwfc.x              runPROJWFC                          ::pwtk::pri         
  pw.x                   runPW                 rerunPW       ::pwtk::pwi         
  pw2bgw.x               runPW2BGW                           ::pwtk::pw2bgwi     
  pw2gw.x                runPW2GW                            ::pwtk::pw2gwi      
  pw2wannier90.x         runPW2WANNIER90                     ::pwtk::pw2wan90i   
  pwcond.x               runPWCOND             rerunPWCOND   ::pwtk::pwcondi     
  q2r.x                  runQ2R                              ::pwtk::q2ri        
  turbo_davidson.x       runDAVIDSON           rerunDAVIDSON ::pwtk::davi        
  turbo_eels.x           runEELS               rerunEELS     ::pwtk::eelsi       
  turbo_lanczos.x        runLANCZOS            rerunLANCZOS  ::pwtk::lani        
  turbo_magnon.x         runMAGNON             rerunMAGNON   ::pwtk::magi        
  turbo_spectrum.x       runSPECTRUM                         ::pwtk::speci
 -------------------------------------------------------------------------------

Simple script: a parameter scan

As seen above, loading input data into PWTK allows for changing them on the fly, which is a handy feature that, among others, makes parameter-scan calculations quite easy to script. For example, the following script loads the pw.Si.in input files and makes a series of pw.x calculations where the value of the ecutwfc variable (i.e., kinetic energy wavefunction cutoff) is scanned:

load_fromPWI pw.Si.in

scanpar ecut [seq 12 4 40] {
    SYSTEM " ecutwfc = $ecut "
    write ecutwfc.dat [pwo_totene [runPW pw.Si-e$ecut.in]]
}

plot -xr 10:40 -yf %.3f -xl "ecutwfc (Ry)" -yl "Total energy (Ry)" ecutwfc.dat

In this script, the following new PWTK commands are used:

scanpar – loops over parameter values (similar to the one-dimension Tcl foreach loop)
seq – returns a sequence of numbers (currently: 12 16 20 24 28 32 36 40)
write – writes data to a datafile
pwo_totene – extract total energy from the pw.x output file (pwo = pw.x output)
plot – plots the results from the ecutwfc.dat datafile as shown below

In addition to performing the scan, this script also extracts the total energy from the pw.x output file and writes it to the ecutwfc.dat file, which is plotted at the end with the plot command. Let us save the above script into the ecut.pwtk file and run it from the terminal as:

pwtk ecut.pwtk

After the calculations are completed, we obtain the following plot:

Input-data stacking

Input-data stacking is a useful mechanism when performing multiple calculations, and we do not want input data modification for the preceding calculation to affect the input data for subsequent calculations. The concept is graphically presented here:

Here is the PWTK script example to illustrate the point; it utilizes the input_pushpop command which provides the stacking mechanism (read the comments):

   load_fromPWI pw.Si.in
   
   
   # the value of 'ecutwfc' in 'pw.Si.in' is 18.0 Ry;
   # let's perform the calculation at higher 'ecutwfc'
   
   input_pushpop {
      SYSTEM { ecutrho = 30.0 }
      # now the value of ecutrho = 30.0 Ry
      runPW pw.Si-e30.0.in
   }

   # here, the value of ecutrho = 18.0 Ry again
   
   # K_POINTS specs in 'pw.Si.in' are 4x4x4;
   # let's perform the calculation with a denser K-grid
   input_pushpop {
      K_POINTS (automatic) {
         8 8 8   1 1 1
      }
      runPW pw.Si-k8x8x8.in
   }
   
   # here K_POINTS specs are 4x4x4 again

Explanation of the “scanpar” command

To further illustrate the input-data stacking mechanism, let us explain the scanpar command used above. It is similar to a one-parameter Tcl foreach loop but, in addition, uses the input-data stacking mechanism and, in combination with the write command, keeps track of the scanned parameter. Here is a comparison between equivalent script snippets using the scanpar and foreach commands:

using scanpar using foreach

scanpar ecut [seq 12 4 40] {
   SYSTEM " ecutwfc = $ecut "
   write ecut.dat \
      [pwo_totene [runPW pw.Si-e$ecut.in]]
}

# the above modifications of 'ecutwfc' 
# have no effect here

foreach ecut [seq 12 4 40] {
   input_pushpop {
      SYSTEM " ecutwfc = $ecut "
      write ecut.dat \
        "$ecut  [pwo_totene [runPW pw.Si-e$ecut.in]]"
   }
}
# the above modifications of 'ecutwfc'
# have no effect here

This implies that all input data modifications performed inside the scanpar loop are removed after the loop finishes. Note also that within the scanpar loop, the $ecut variable is not specified on the write command line because write knows which parameter(s) is (are) being scanned and adds them automatically.

Project-based configuration: the “import” command

With the import command it is possible to include a PWTK script into another script. This command can be exploited for kind-of project-based configuration, which helps systematizing its calculations. The idea is to create a project common file (let us name it common.pwtk), where default input data for the project are stored and then project scripts import it.

Let us say that we want to study the adsorption of small organic molecules (containing H, C, N, and O atoms) on low Miller index Rh surfaces. After performing the basic convergence tests calculations (as to determine the energy cutoff, lattice parameter, k-point sampling…), we can create the project common.pwtk, which could look something like this:

# default pw.x input data
CONTROL {
   calculation = 'relax'
   nstep       = 400
}
SYSTEM {
   ibrav       = 0   
   ecutwfc     = 50.
   ecutrho     = 400.   
   occupations = 'smearing' 
   degauss     = 0.02 
   smearing    = 'm-v'
}
ELECTRONS {
   conv_thr    = 1d-9
   mixing_beta = 0.3
}
IONS {
   upscale = 100.
}
ATOMIC_SPECIES {
   H  1.0079   H.pbe-rrkjus_psl.1.0.0.UPF
   C  12.011   C.pbe-n-rrkjus_psl.1.0.0.UPF
   N  14.0067  N.pbe-n-rrkjus_psl.1.0.0.UPF
   O  15.9994  O.pbe-n-rrkjus_psl.1.0.0.UPF
   Rh 102.906  Rh.pbe-spn-rrkjus_psl.1.0.0.UPF
}
# default k-points for Rh(111)-2x2 & Rh(100)-2x2
K_POINTS (automatic) {
   6 6 1   1 1 1
}

# default ph.x input data
INPUTPH {
   tr2_ph       = 1e-16
   trans        = .true.
   nogg         = .true.
   alpha_mix(1) = 0.3
} {
   0.0  0.0  0.0
}

# default projwfc.x input data
PROJWFC {
   ngauss  = 0
   degauss = 0.01
   DeltaE  = 0.1
}

REMARK: Note that all the pseudopotentials used in the project are listed in the ATOMIC_SPECIES card, and the SYSTEM’s ntyp variable is not assigned. For specific cases, PWTK uses only pseudopotentials for atomic types present in the ATOMIC_POSITIONS card and sets the ntyp variable accordingly.

Then from specific scripts we can include this common.pwtk file. For example, let us perform some calculations in the Rh100-2x2-4L/ subdirectory. In particular, we scan the lateral position of CH~3 over Rh(100)-2x2-4L slab (4L = four-layer). The script could look something like:

import ../common.pwtk

# load the CH3 @ Rh(100)-2x2-4L structure (4L = 4-layers)
CELL_PARAMETERS_and_ATOMIC_POSITIONS_fromXSF CH3-Rh100-2x2-4L.xsf

# fix the bottom-layer Rh atoms (i.e. atom from 1 to 4)
fixAtoms 1-4 

# fix the C atom (atom 17) laterally
fixAtoms 17 "0 0 1"

# the Rh-Rh distance is 2.687 Å
set dRhRh 2.687

# scan the CH3 laterally

scanpar dx [seq 0 0.2 1] {
   scanpar dy [seq 0 0.2 1] {
       set name CH3-$dx,$dy@Rh100-2x2-4L
       outdir_postfix $name       
       CONTROL " prefix = '$name' "
       
       # convert dx,dy to Å
       set dx [expr $dx*$dRhRh]
       set dy [expr $dy*$dRhRh]
       
       # CH3 atoms are atoms from 17 to 20
       displaceAtoms "$dx $dy 0.0" 17-20
       
       write CH3.dat [pwo_totene [runPW relax.$name]]
   }
}

# plot the result as a 3D surface-plot
splot -xl "Δx (Å)" -yl "Δy (Å)" -xf %.1f -yf %.1f -zf %.3f -t png CH3.dat

In this script, we used the following new PWTK commands:

CELL_PARAMETERS_and_ATOMIC_POSITIONS_fromXSF – loads a structure from an XSF file
fixAtoms – immobilizes the specified atoms
outdir_postfix – sets the outdir as outdir_prefix/outdir_postfix
displaceAtoms – displaces atoms
splot – creates a 3D surface plot

After the script finishes all calculations, splot creates the following CH3.png image:

TODO–insert-splot