USPEX and SIESTA error, generating input for QE

[Ryan Yarbrough]

Hello USPEX community,

I have been using USPEX for a while with Quantum Espresso, but I am switching to SIESTA for molecular dynamics. I have successfully compiled SIESTA and tested it with USPEX using the SIESTA_300 example included with USPEX 9.4.4; it works flawlessly.

I am trying to compute a molecular crystal using a MOL file. When I start up USPEX it goes through initialization steps like it would with Quantum Espresso, It builds crystals. The following is an example of the output:

Please see the calculated Zmatrix in OUTPUT.txt
Default Volume for MOLs :
     Volume of MOL_1 : 308.06  A^3
     --   Total Volume of MOLs : 616.12  A^3
 
Default IonDistances for Atoms :    Zn    O    C
    Minimum distances:       Zn: 0.80  0.60  0.60 
    Minimum distances:        O: 0.60  0.30  0.30 
    Minimum distances:        C: 0.60  0.30  0.40 
 
===============================================================================================
=   When you cannot generate structures for a long time, for the INPUT.txt                    =
=    (1) check your "IonDistances" and "MolCenters" parameters, or reduce them;               =
=    (2) increase the above default volume and set "Latticevalues" parameter.                 =
===============================================================================================
Molecular Crystal 1 built with the symmetry group 38 (C2mm)
Molecular Crystal 2 built with the symmetry group 12 (A2/m)
Molecular Crystal 3 built with the symmetry group 9 (Aa)
Molecular Crystal 4 built with the symmetry group 59 (Pmmn)
Molecular Crystal 5 built with the symmetry group 182 (P6_322)
Molecular Crystal 6 built with the symmetry group 35 (Cmm2)
Molecular Crystal 7 built with the symmetry group 49 (Pccm)
Molecular Crystal 8 built with the symmetry group 160 (R3m)
Molecular Crystal 9 built with the symmetry group 137 (P4_2/nmc)
Molecular Crystal 10 built with the symmetry group 63 (Cmcm)
Molecular Crystal 11 built with the symmetry group 28 (Pma2)
Molecular Crystal 12 built with the symmetry group 2 (P-1)
Molecular Crystal 13 built with the symmetry group 191 (P6/mmm)
Molecular Crystal 14 built with the symmetry group 98 (I4_122)
Molecular Crystal 15 built with the symmetry group 14 (P2_1/a)
Molecular Crystal 16 built with the symmetry group 119 (I-4m2)
Molecular Crystal 17 built with the symmetry group 83 (P4/m)
Molecular Crystal 18 built with the symmetry group 156 (P3m1)
Molecular Crystal 19 built with the symmetry group 55 (Pbam)
Molecular Crystal 20 built with the symmetry group 194 (P6_3/mmc)
 
After this USPEX crashes with the following error:

Read Seeds ...
 
Structure1 step1 at CalcFold1
Error using /
Matrix dimensions must agree.

Error in Read_QE_Structure (line 18)
numIons = size(COOR,1)/scf;

Error in Read_Structure

Error in Reading (line 25)
[COORDINATES, LATTICE] = Read_Structure(code, Const_Lat);

Error in ReadJobs_310 (line 20)
Error = Reading(ORG_STRUC.abinitioCode(Step),whichInd, indic);

Error in EA_310 (line 10)
ReadJobs_310();

Error in Start (line 77)
eval(['EA_' calcTypeStr '()']);

When I go the the CalcFold1 folder I see the inputs for SIESTA, but I am also seeing a 'qe.in' file that is generated. When I start out, the folder has the INPUT.txt and a MOL_1 file. In the Specif folder I have three SIESTA files and the potentials. It appears that after running USPEX I am getting an input for the Quantum Espresso and it seems like QE is trying to run. I have no idea why. I am attaching my input, mol file and the potentials as well as the SIESTA inputs.

Any help understanding this error would be greatly appreciated.

Thanks!

Ryan

[ivan.k...@phystech.edu]

Dear Ryan,

Thank you for noticing this error, I will try to reproduce your results and deal with this problem.

Best,

Ivan.

четверг, 17 мая 2018 г., 6:36:26 UTC+3 пользователь Ryan Yarbrough написал:

[Aleksandra Oranskaia]

Hi Ryan,

% abinitioCode

8 8 8

% ENDabinit

Change it for Siesta (#2)

Do you have experience with VCNEB in USPEX-QE? If Yes, could you please share an example with all outputs for > 3 VCNEB cycles?

And why do you switch to Siesta for MD: sth wrong with cp.x?

Best,
Alex.

___
Aleksandra Oranskaia (M.Sc.)
ChemS PhD student, KAUST
Phone: +966 50 1335254

On May 17, 2018, at 6:36 AM, Ryan Yarbrough <raya...@gmail.com> wrote:

<INPUT.txt>

---

This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.