The QE input is formatted incorrectly

[ignaciomigliaro]

Hello, I have taken great interest in your code and have tried running it with QE but have ran into multiple problems. For example in the code for interface/QE/strucuture.py, the code has it that the order of the elements are wrong. This is the example QE file I get from CRYSPY for a RS.

` &control title = 'Si8' calculation = 'relax' nstep = 100 restart_mode = 'from_scratch', pseudo_dir = '~/calculations/subbig/pseudo' outdir='./out.d/' /

&system ibrav = 0 nat = 8 ntyp = 1 ecutwfc = 44.0 occupations = 'smearing' degauss = 0.01 /

&electrons /

&ions /

&cell /

ATOMIC_SPECIES C 6 C.pbesol-n-kjpaw_psl.1.0.0.UPF N 7 N.pbesol-theos.UPF O 8 O.pbesol-n-kjpaw_psl.0.1.UPF H 1 H.pbesol-rrkjus_psl.1.0.0.UPF CELL_PARAMETERS angstrom 8.1848068865698647 0.7595598784348114 -3.3614435519497508 0.0000000000000000 4.4085364017832651 1.5179270290575053 0.0000000000000000 0.0000000000000000 8.4052731466826653 ATOMIC_POSITIONS crystal H 1.0272744478181299 0.2627384881289004 0.0937040858057427 H 0.7599491902187562 0.4420509409689334 -0.0379224401397704 H 1.3007095992936761 -0.1762893569218246 0.1301253103079126 H 1.3893435394195548 -0.0918628105280647 0.3098480415925064 H 0.4922202182767800 0.4226243674907904 -0.0430278705054866 H 1.2803379384555376 0.1694080055216949 0.1230441804720760 H 0.4340795085209237 0.0087842692283943 0.1757403461623094 H 0.6500865178911813 -0.3590159214232218 0.4058724455370528 H 0.9157461409670384 -0.3277890657827509 0.4067927517420840 C 0.6714343797682183 -0.1906154698147080 0.3120322805532349 C 0.8609280385192991 0.0556383934057273 0.1807914373508377 C 1.1426173714168577 -0.1350332890639422 0.2454986051209205 C 0.7357180528581425 0.2795152402424241 0.0506878208188995 C 0.5793394500253902 0.2630572865696528 0.0503723761544435 C 1.2879407348735656 -0.0447281851573187 0.1963193557811781 C 0.5462998709944149 0.0248704954110217 0.1798608171398284 C 0.8290013795207284 -0.1775005144063645 0.3144883205869253 N 1.0157177154294088 0.0828068224690623 0.1677794035480051 O 1.1406391373372478 -0.3925329060627208 0.3486125988670675 K_POINTS automatic 2 4 2 0 0 0 `

1. After each section there shouldn't be a line break , it should end with forward slash only.
2. The order for the input is Atomic species, ATOMIC_positions angstrom, K_points automatic, and in the end cell_parameters.

With the input file provided from the code I get the following error: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Error in routine read_cards (1): species H in ATOMIC_POSITIONS is nonexistent %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

Most likely due to the wrong order of the elements in the code.

Thank you so much for anything, any way I can help please reach out to me.

[Tomoki-YAMASHITA]

Could you give us your cryspy.in?

[yw-fang]

I think you have to make yourself exposed to several examples of quantum espresso first. Please refer to the input parameters for pw.x https://www.quantum-espresso.org/Doc/INPUT_PW.html Then you will realize that many errors in this input file for quantum espresso calculations.

To me, it's more likely that you are a bit new to quantum espresso, which leads yourself to set the parameters wrongly with CrySPY. For example, nat = 8 means you should have 8 atoms in the compound, however, the number of atoms in your input file obviously exceeds 8. There are many other errors. I highly recommend making the test calculations with the official examples of Quantum ESPRESSO before using CrySPY code.

[yw-fang]

By the way, the empty lines after /, and the order of the different sections will NOT affect the execution of calculations. This is also one of the major reasons that certifies that you should do example calculations of QE first. If you don't understand the workflow of QE, using CrySPY as well as its interface to QE will waste your time and your CPU time.

[Tomoki-YAMASHITA]

I see. @ignaciomigliaro, try the following:

&system
ibrav = 0
nat = 19
ntyp = 3
/

The cutoff needs to be changed as well.

[ignaciomigliaro]

Thank you for your prompt response, I have multiple scripts running that are generating the cryspy.in from xyz data, and I forgot to change the pwscf file. I wasn't aware that the order of the items on the QE input file could be re-arranged, because if we look the link @yw-fang has posted, it goes from atomic species > atomic positions > k-points > cell parameters.