[Pw_forum] Input for Quantum Espresso

Mohan maruthi sena maruthi.sena at gmail.com
Mon Jan 19 14:41:09 CET 2015


Thank you  very much sir  for  valuable time and reply.

Thanks & Regards,
K. Mohan

On Mon, Jan 19, 2015 at 1:47 PM, Carlo Nervi <carlo.nervi at unito.it> wrote:

> Dear Moan,
> please pay attention to the following points:
> 1. make sure you use the latest version of cif2qe.sh. It's an experimental
> code with no time (from my side) to develop it, and time to time new bugs
> are fixed.
> 2. you have more than one structure in your cif file. Please simplify as
> much as you can your cif file, removing the unnecessary  stuff. Expecially
> leave only one structure. cif2qe.sh is not thinked to deal with multiple
> structure cif files.
>
> I tried cut the unecessary stuff from the cif cile:
>
> _audit_creation_method            SHELXL-97
> _chemical_name_systematic
> _chemical_name_common             'cellulose'
> _chemical_melting_point           ?
> _chemical_formula_moiety          'C12 H14 O10'
> _chemical_formula_sum  'C12 H24 O10'
> _chemical_formula_weight          318.23
> _symmetry_cell_setting            1
> _symmetry_space_group_name_H-M    'P1'
> _cell_length_a                    10.400(10)
> _cell_length_b                    6.717(6)
> _cell_length_c                    5.962(7)
> _cell_angle_alpha                 80.37(5)
> _cell_angle_beta                  118.08(5)
> _cell_angle_gamma                 114.80(5)
> _cell_volume                      333.3(6)
> _cell_formula_units_Z             1
> _cell_measurement_temperature     293(2)
> _cell_measurement_reflns_used     255
> _cell_measurement_theta_min       2.45
> _cell_measurement_theta_max       21.10
> _symmetry_cell_setting            1
> _symmetry_space_group_name_H-M    'P1'
>
> loop_
> _symmetry_equiv_pos_as_xyz
> 'x, y, z'
>
> loop_
>  _atom_site_label
>  _atom_site_type_symbol
>  _atom_site_fract_x
>  _atom_site_fract_y
>  _atom_site_fract_z
>  _atom_site_U_iso_or_equiv
>  _atom_site_adp_type
>  _atom_site_occupancy
>  _atom_site_symmetry_multiplicity
>  _atom_site_calc_flag
>  _atom_site_refinement_flags
>  _atom_site_disorder_assembly
>  _atom_site_disorder_group
> O51 O 0.239(2) 0.152(4) -0.044(6) 0.016(3) Uiso 1 1 d D . .
> C11 C 0.254(3) -0.054(4) 0.031(6) 0.016(3) Uiso 1 1 d D . .
> H11 H 0.1973 -0.1585 -0.1140 0.019 Uiso 1 1 calc R . .
> O11 O 0.416(3) -0.009(4) 0.157(5) 0.016(3) Uiso 1 1 d D . .
> C21 C 0.193(3) -0.143(4) 0.234(6) 0.016(3) Uiso 1 1 d D . .
> H21 H 0.2550 -0.0383 0.3792 0.019 Uiso 1 1 calc R . .
> C31 C 0.022(3) -0.174(5) 0.114(6) 0.016(3) Uiso 1 1 d D . .
> H31 H -0.0404 -0.2902 -0.0201 0.019 Uiso 1 1 calc R . .
> C41 C 0.000(2) 0.035(4) -0.003(6) 0.016(3) Uiso 1 1 d D . .
> H41 H 0.0464 0.1410 0.1359 0.019 Uiso 1 1 calc R . .
> C51 C 0.079(2) 0.138(4) -0.175(5) 0.016(3) Uiso 1 1 d D . .
> H51 H 0.0220 0.0485 -0.3333 0.019 Uiso 1 1 calc R . .
> C61 C 0.092(3) 0.374(4) -0.236(7) 0.016(3) Uiso 1 1 d D . .
> H61A H 0.1302 0.4540 -0.0814 0.019 Uiso 1 1 calc R . .
> H61B H 0.1664 0.4464 -0.3072 0.019 Uiso 1 1 calc R . .
> O21 O 0.211(4) -0.346(5) 0.313(7) 0.016(3) Uiso 1 1 d D . .
> O31 O -0.031(4) -0.243(7) 0.307(7) 0.016(3) Uiso 1 1 d D . .
> O61 O -0.059(4) 0.371(7) -0.413(7) 0.016(3) Uiso 1 1 d D . .
> O52 O 0.680(3) -0.158(4) 0.046(6) 0.016(3) Uiso 1 1 d D . .
> C12 C 0.766(3) 0.048(4) -0.026(6) 0.016(3) Uiso 1 1 d D . .
> H12 H 0.8462 0.1471 0.1231 0.019 Uiso 1 1 calc R . .
> O12 O 0.837(2) 0.003(5) -0.152(5) 0.016(3) Uiso 1 1 d D . .
> C22 C 0.650(3) 0.147(4) -0.218(6) 0.016(3) Uiso 1 1 d D . .
> H22 H 0.5732 0.0483 -0.3680 0.019 Uiso 1 1 calc R . .
> C32 C 0.566(3) 0.180(5) -0.086(6) 0.016(3) Uiso 1 1 d D . .
> H32 H 0.6442 0.2833 0.0593 0.019 Uiso 1 1 calc R . .
> C42 C 0.483(3) -0.038(4) 0.008(6) 0.016(3) Uiso 1 1 d D . .
> H42 H 0.3980 -0.1353 -0.1395 0.019 Uiso 1 1 calc R . .
> C52 C 0.596(3) -0.148(4) 0.175(5) 0.016(3) Uiso 1 1 d D . .
> H52 H 0.6716 -0.0623 0.3350 0.019 Uiso 1 1 calc R . .
> C62 C 0.512(4) -0.382(4) 0.231(7) 0.016(3) Uiso 1 1 d D . .
> H62A H 0.4236 -0.4600 0.0751 0.019 Uiso 1 1 calc R . .
> H62B H 0.5849 -0.4562 0.2993 0.019 Uiso 1 1 calc R . .
> O22 O 0.740(4) 0.352(5) -0.288(7) 0.016(3) Uiso 1 1 d D . .
> O32 O 0.455(4) 0.270(6) -0.261(7) 0.016(3) Uiso 1 1 d D . .
> O62 O 0.457(5) -0.387(6) 0.409(7) 0.016(3) Uiso 1 1 d D . .
>
> #END
>
>
> and the output from cif2qe.sh is:
>
> ! Generated by using cif2qe Version 1.1 - Date: Mon Jan 19 10:16:16 CET
> 2015
> !   _symmetry_space_group_name_H-M =
> !   _symmetry_Int_Tables_number =
> !   _symmetry_cell_setting = 1
> ! a=10.4  b=6.717  c=5.962  alpha=80.37  beta=118.08  gamma=114.8
> ! Found by cif2qe: lattice = triclinic    Space group =    ibrav = 14
> !
> ! Symmetry found:
> !   1                        x, y, z    [x]  [ y]  [ z]
> &CONTROL
>                        title = 't'
>                  calculation = 'relax'
>                 restart_mode = 'from_scratch'
>                       outdir = './1'
>                   pseudo_dir = '/home/nervi/PP'
>                       prefix = 't'
>                      disk_io = 'none'
>                    verbosity = 'default'
>                etot_conv_thr = 0.0001
>                forc_conv_thr = 0.001
>                        nstep = 400
>                      tstress = .true.
>                      tprnfor = .true.
>  /
>  &SYSTEM
>                        ibrav = 0
>                          nat = 36
>                         ntyp = 3
>                      ecutwfc = 50
>                      ecutrho = 400
>                       london = .true.
>                    london_s6 = 0.75
>  /
>  &ELECTRONS
>             electron_maxstep = 200
>                     conv_thr = 1.0D-7
>               diago_thr_init = 1e-4
>                  startingpot = 'atomic'
>                  startingwfc = 'atomic'
>                  mixing_mode = 'plain'
>                  mixing_beta = 0.5
>                  mixing_ndim = 8
>              diagonalization = 'david'
>  /
> &IONS
>                 ion_dynamics = 'bfgs'
>  /
>
> ATOMIC_SPECIES
>     O   15.9994000000  O.pbe-n-rrkjus_psl.0.1.UPF
>     C   12.0107000000  C.pbe-n-rrkjus_psl.0.1.UPF
>     H    1.0079000000  H.pbe-rrkjus_psl.0.1.UPF
>
> ATOMIC_POSITIONS crystal
>  O     0.239000000000000     0.152000000000000     0.956000000000000
>  C     0.254000000000000     0.946000000000000     0.031000000000000
>  H     0.197300000000000     0.841500000000000     0.886000000000000
>  O     0.416000000000000     0.991000000000000     0.157000000000000
>  C     0.193000000000000     0.857000000000000     0.234000000000000
>  H     0.255000000000000     0.961700000000000     0.379200000000000
>  C     0.022000000000000     0.826000000000000     0.114000000000000
>  H     0.959600000000000     0.709800000000000     0.979900000000000
>  C     0.000000000000000     0.035000000000000     0.997000000000000
>  H     0.046400000000000     0.141000000000000     0.135900000000000
>  C     0.079000000000000     0.138000000000000     0.825000000000000
>  H     0.022000000000000     0.048500000000000     0.666700000000000
>  C     0.092000000000000     0.374000000000000     0.764000000000000
>  H     0.130200000000000     0.454000000000000     0.918600000000000
>  H     0.166400000000000     0.446400000000000     0.692800000000000
>  O     0.211000000000000     0.654000000000000     0.313000000000000
>  O     0.969000000000000     0.757000000000000     0.307000000000000
>  O     0.941000000000000     0.371000000000000     0.587000000000000
>  O     0.680000000000000     0.842000000000000     0.046000000000000
>  C     0.766000000000000     0.048000000000000     0.974000000000000
>  H     0.846200000000000     0.147100000000000     0.123100000000000
>  O     0.837000000000000     0.003000000000000     0.848000000000000
>  C     0.650000000000000     0.147000000000000     0.782000000000000
>  H     0.573200000000000     0.048300000000000     0.632000000000000
>  C     0.566000000000000     0.180000000000000     0.914000000000000
>  H     0.644200000000000     0.283300000000000     0.059300000000000
>  C     0.483000000000000     0.962000000000000     0.008000000000000
>  H     0.398000000000000     0.864700000000000     0.860500000000000
>  C     0.596000000000000     0.852000000000000     0.175000000000000
>  H     0.671600000000000     0.937700000000000     0.335000000000000
>  C     0.512000000000000     0.618000000000000     0.231000000000000
>  H     0.423600000000000     0.540000000000000     0.075100000000000
>  H     0.584900000000000     0.543800000000000     0.299300000000000
>  O     0.740000000000000     0.352000000000000     0.712000000000000
>  O     0.455000000000000     0.270000000000000     0.739000000000000
>  O     0.457000000000000     0.613000000000000     0.409000000000000
>
> K_POINTS automatic
> 1  2  2   0 0 0
>
> CELL_PARAMETERS
>    19.653151695476645     0.000000000000000     0.000000000000000
>    -5.324227082441216    11.522683134265510     0.000000000000000
>    -5.303208047623142    -0.374229849785373     9.933328808172122
>
>
> Hope this helps,
>   Carlo
>
>
> 2015-01-19 2:32 GMT+01:00 Mohan maruthi sena <maruthi.sena at gmail.com>:
>
>> Dear Ari Paavo Seitsonen,
>> Thank you sir for a reply. My apologies for not providing the input file.
>> I want to create a slab structure from the bulk structure.
>>
>> 1) I have understood that, if slab structure is in xy plane and if we add
>> +10 angstorms to the structure will suffice the need. [ the two slabs will
>> be separated by 10 angstorms]
>>
>> 2) Please find the attached input obtained as output form cif2qsh.
>>
>>
>> Thank you so much for a reply,
>>
>> with regards,
>> K. Mohan
>>
>> On Mon, Jan 19, 2015 at 3:45 AM, Ari P Seitsonen <Ari.P.Seitsonen at iki.fi>
>> wrote:
>>
>>>
>>> Dear Mohan maruthi sena,
>>>
>>>   I do not have an opportunity to look at your .cif-file in detail just
>>> now, and you do not provide the full input file, so I can just guess with
>>> two errors that I am particularly good at doing myself:
>>>
>>>  - Are your atomic coordinates in the crystal coordinates? Does your
>>> input file have the correct option for that?
>>>
>>>  - Maybe your .cif file contains fractional occupations and thus several
>>> configurations with different atomic positions might be possible; I do not
>>> know what 'cif2qe.sh' would do in that case.
>>>
>>>   Constructing the input file starting from a pdb file would probably
>>> not be too tedious (one might lose some symmetries, however, if present as
>>> the pdb uses few digits in the atomic positions, in Angstroms if I am not
>>> wrong). I do not fully understand your question 2), do you mean that the
>>> structure that you built from the .cif file is a slab structure? Or that
>>> the .cif contains a bulk structure and you want to create a slab starting
>>> from that input? Well, you have first to determine the direction along the
>>> surface of the slab and its normal (orthogonal to the surface), and then
>>> add 10 Angstroms or more in that direction (and naturally adjust the
>>> coordinates if they are in crystal coordiates).
>>>
>>>   Hopefully this helps you at least a little bit forward.
>>>
>>>     Greetings from Rome,
>>>
>>>        apsi
>>>
>>> -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=
>>> -=*=-=*=-=*=-=*=-
>>>   Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi /
>>> http://www.iki.fi/~apsi/
>>>   Ecole Normale Supérieure (ENS), Département de Chimie, Paris
>>>   Mobile (F) : +33 789 37 24 25    (CH) : +41 79 71 90 935
>>>
>>>
>>>
>>> On Sun, 18 Jan 2015, Mohan maruthi sena wrote:
>>>
>>>  Hi  all,
>>>>             I recently started using espresso. I want to  optimize a
>>>> crystal structure. By looking at the previous posts , I tried to
>>>> use cif2qe.sh script to convert from .cif to .inp file.  I tried with
>>>> various examples and it was working. I  could not prepare inp
>>>> file for the attached cif file. I have visualized the cif file in
>>>> vesta, gaussian and then saved those .cif file. It prepared input
>>>> files but the atoms are too close.
>>>>
>>>> 1) Can some please let me how to give prepare input file for espresso
>>>> 5.1.1, using cif or pdb file?
>>>>
>>>> 2) If want to create a slab structure and maintain 10 angstorms
>>>> distance between the slabs? How can i do this in espresso?
>>>>
>>>> 3) I have used the following server (http://j-ice.sourceforge.net/
>>>> ondemand/index.html) but could not get the input file.
>>>>
>>>> Please find the attached  cif and espresso input files.
>>>>
>>>>
>>> _______________________________________________
>>> Pw_forum mailing list
>>> Pw_forum at pwscf.org
>>> http://pwscf.org/mailman/listinfo/pw_forum
>>>
>>
>>
>> _______________________________________________
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>>
>
>
>
> --
>
> ------------------------------------------------------------
> Prof. Carlo Nervi carlo.nervi at unito.it  Tel:+39 0116707507/8
> Fax: +39 0116707855      -      Dipartimento di Chimica, via
> P. Giuria 7, 10125 Torino, Italy.    http://lem.ch.unito.it/
>
>
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