[Pw_forum] Input for Quantum Espresso
Carlo Nervi
carlo.nervi at unito.it
Mon Jan 19 09:17:06 CET 2015
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.
>>>
>>>
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>
>
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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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