[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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