<div dir="ltr"><div>Thank you very much sir for valuable time and reply.<br><br></div><div>Thanks & Regards,<br></div><div>K. Mohan<br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Jan 19, 2015 at 1:47 PM, Carlo Nervi <span dir="ltr"><<a href="mailto:carlo.nervi@unito.it" target="_blank">carlo.nervi@unito.it</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Dear Moan,<div>please pay attention to the following points:</div><div>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.</div><div>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.</div><div><br></div><div>I tried cut the unecessary stuff from the cif cile:</div><div><br></div><div><div>_audit_creation_method SHELXL-97</div><div>_chemical_name_systematic</div><div>_chemical_name_common 'cellulose'</div><div>_chemical_melting_point ?</div><div>_chemical_formula_moiety 'C12 H14 O10'</div><div>_chemical_formula_sum 'C12 H24 O10'</div><div>_chemical_formula_weight 318.23</div><div>_symmetry_cell_setting 1</div><div>_symmetry_space_group_name_H-M 'P1'</div><div>_cell_length_a 10.400(10)</div><div>_cell_length_b 6.717(6)</div><div>_cell_length_c 5.962(7)</div><div>_cell_angle_alpha 80.37(5)</div><div>_cell_angle_beta 118.08(5)</div><div>_cell_angle_gamma 114.80(5)</div><div>_cell_volume 333.3(6)</div><div>_cell_formula_units_Z 1</div><div>_cell_measurement_temperature 293(2)</div><div>_cell_measurement_reflns_used 255</div><div>_cell_measurement_theta_min 2.45</div><div>_cell_measurement_theta_max 21.10</div><div>_symmetry_cell_setting 1</div><div>_symmetry_space_group_name_H-M 'P1'</div><div><br></div><div>loop_</div><div>_symmetry_equiv_pos_as_xyz</div><div>'x, y, z'</div><div> </div><div>loop_</div><div> _atom_site_label</div><div> _atom_site_type_symbol</div><div> _atom_site_fract_x</div><div> _atom_site_fract_y</div><div> _atom_site_fract_z</div><div> _atom_site_U_iso_or_equiv</div><div> _atom_site_adp_type</div><div> _atom_site_occupancy</div><div> _atom_site_symmetry_multiplicity</div><div> _atom_site_calc_flag</div><div> _atom_site_refinement_flags</div><div> _atom_site_disorder_assembly</div><div> _atom_site_disorder_group</div><div>O51 O 0.239(2) 0.152(4) -0.044(6) 0.016(3) Uiso 1 1 d D . .</div><div>C11 C 0.254(3) -0.054(4) 0.031(6) 0.016(3) Uiso 1 1 d D . .</div><div>H11 H 0.1973 -0.1585 -0.1140 0.019 Uiso 1 1 calc R . .</div><div>O11 O 0.416(3) -0.009(4) 0.157(5) 0.016(3) Uiso 1 1 d D . .</div><div>C21 C 0.193(3) -0.143(4) 0.234(6) 0.016(3) Uiso 1 1 d D . .</div><div>H21 H 0.2550 -0.0383 0.3792 0.019 Uiso 1 1 calc R . .</div><div>C31 C 0.022(3) -0.174(5) 0.114(6) 0.016(3) Uiso 1 1 d D . .</div><div>H31 H -0.0404 -0.2902 -0.0201 0.019 Uiso 1 1 calc R . .</div><div>C41 C 0.000(2) 0.035(4) -0.003(6) 0.016(3) Uiso 1 1 d D . .</div><div>H41 H 0.0464 0.1410 0.1359 0.019 Uiso 1 1 calc R . .</div><div>C51 C 0.079(2) 0.138(4) -0.175(5) 0.016(3) Uiso 1 1 d D . .</div><div>H51 H 0.0220 0.0485 -0.3333 0.019 Uiso 1 1 calc R . .</div><div>C61 C 0.092(3) 0.374(4) -0.236(7) 0.016(3) Uiso 1 1 d D . .</div><div>H61A H 0.1302 0.4540 -0.0814 0.019 Uiso 1 1 calc R . .</div><div>H61B H 0.1664 0.4464 -0.3072 0.019 Uiso 1 1 calc R . .</div><div>O21 O 0.211(4) -0.346(5) 0.313(7) 0.016(3) Uiso 1 1 d D . .</div><div>O31 O -0.031(4) -0.243(7) 0.307(7) 0.016(3) Uiso 1 1 d D . .</div><div>O61 O -0.059(4) 0.371(7) -0.413(7) 0.016(3) Uiso 1 1 d D . .</div><div>O52 O 0.680(3) -0.158(4) 0.046(6) 0.016(3) Uiso 1 1 d D . .</div><div>C12 C 0.766(3) 0.048(4) -0.026(6) 0.016(3) Uiso 1 1 d D . .</div><div>H12 H 0.8462 0.1471 0.1231 0.019 Uiso 1 1 calc R . .</div><div>O12 O 0.837(2) 0.003(5) -0.152(5) 0.016(3) Uiso 1 1 d D . .</div><div>C22 C 0.650(3) 0.147(4) -0.218(6) 0.016(3) Uiso 1 1 d D . .</div><div>H22 H 0.5732 0.0483 -0.3680 0.019 Uiso 1 1 calc R . .</div><div>C32 C 0.566(3) 0.180(5) -0.086(6) 0.016(3) Uiso 1 1 d D . .</div><div>H32 H 0.6442 0.2833 0.0593 0.019 Uiso 1 1 calc R . .</div><div>C42 C 0.483(3) -0.038(4) 0.008(6) 0.016(3) Uiso 1 1 d D . .</div><div>H42 H 0.3980 -0.1353 -0.1395 0.019 Uiso 1 1 calc R . .</div><div>C52 C 0.596(3) -0.148(4) 0.175(5) 0.016(3) Uiso 1 1 d D . .</div><div>H52 H 0.6716 -0.0623 0.3350 0.019 Uiso 1 1 calc R . .</div><div>C62 C 0.512(4) -0.382(4) 0.231(7) 0.016(3) Uiso 1 1 d D . .</div><div>H62A H 0.4236 -0.4600 0.0751 0.019 Uiso 1 1 calc R . .</div><div>H62B H 0.5849 -0.4562 0.2993 0.019 Uiso 1 1 calc R . .</div><div>O22 O 0.740(4) 0.352(5) -0.288(7) 0.016(3) Uiso 1 1 d D . .</div><div>O32 O 0.455(4) 0.270(6) -0.261(7) 0.016(3) Uiso 1 1 d D . .</div><div>O62 O 0.457(5) -0.387(6) 0.409(7) 0.016(3) Uiso 1 1 d D . .</div><div><br></div><div>#END </div></div><div><br></div><div><br></div><div>and the output from cif2qe.sh is:</div><div><div><br></div><div>! Generated by using cif2qe Version 1.1 - Date: Mon Jan 19 10:16:16 CET 2015</div><div>! _symmetry_space_group_name_H-M = </div><div>! _symmetry_Int_Tables_number = </div><div>! _symmetry_cell_setting = 1</div><div>! a=10.4 b=6.717 c=5.962 alpha=80.37 beta=118.08 gamma=114.8</div><div>! Found by cif2qe: lattice = triclinic Space group = ibrav = 14</div><div>!</div><div>! Symmetry found:</div><div>! 1 x, y, z [x] [ y] [ z]</div><div>&CONTROL</div><div> title = 't'</div><div> calculation = 'relax'</div><div> restart_mode = 'from_scratch'</div><div> outdir = './1'</div><div> pseudo_dir = '/home/nervi/PP'</div><div> prefix = 't'</div><div> disk_io = 'none'</div><div> verbosity = 'default'</div><div> etot_conv_thr = 0.0001</div><div> forc_conv_thr = 0.001</div><div> nstep = 400</div><div> tstress = .true.</div><div> tprnfor = .true.</div><div> /</div><div> &SYSTEM</div><div> ibrav = 0</div><div> nat = 36</div><div> ntyp = 3</div><div> ecutwfc = 50</div><div> ecutrho = 400</div><div> london = .true.</div><div> london_s6 = 0.75</div><div> /</div><div> &ELECTRONS</div><div> electron_maxstep = 200</div><div> conv_thr = 1.0D-7</div><div> diago_thr_init = 1e-4</div><div> startingpot = 'atomic'</div><div> startingwfc = 'atomic'</div><div> mixing_mode = 'plain'</div><div> mixing_beta = 0.5</div><div> mixing_ndim = 8</div><div> diagonalization = 'david'</div><div> /</div><div>&IONS</div><div> ion_dynamics = 'bfgs'</div><div> /</div><div><br></div><div>ATOMIC_SPECIES</div><div> O 15.9994000000 O.pbe-n-rrkjus_psl.0.1.UPF</div><div> C 12.0107000000 C.pbe-n-rrkjus_psl.0.1.UPF</div><div> H 1.0079000000 H.pbe-rrkjus_psl.0.1.UPF</div><div><br></div><div>ATOMIC_POSITIONS crystal</div><div> O 0.239000000000000 0.152000000000000 0.956000000000000</div><div> C 0.254000000000000 0.946000000000000 0.031000000000000</div><div> H 0.197300000000000 0.841500000000000 0.886000000000000</div><div> O 0.416000000000000 0.991000000000000 0.157000000000000</div><div> C 0.193000000000000 0.857000000000000 0.234000000000000</div><div> H 0.255000000000000 0.961700000000000 0.379200000000000</div><div> C 0.022000000000000 0.826000000000000 0.114000000000000</div><div> H 0.959600000000000 0.709800000000000 0.979900000000000</div><div> C 0.000000000000000 0.035000000000000 0.997000000000000</div><div> H 0.046400000000000 0.141000000000000 0.135900000000000</div><div> C 0.079000000000000 0.138000000000000 0.825000000000000</div><div> H 0.022000000000000 0.048500000000000 0.666700000000000</div><div> C 0.092000000000000 0.374000000000000 0.764000000000000</div><div> H 0.130200000000000 0.454000000000000 0.918600000000000</div><div> H 0.166400000000000 0.446400000000000 0.692800000000000</div><div> O 0.211000000000000 0.654000000000000 0.313000000000000</div><div> O 0.969000000000000 0.757000000000000 0.307000000000000</div><div> O 0.941000000000000 0.371000000000000 0.587000000000000</div><div> O 0.680000000000000 0.842000000000000 0.046000000000000</div><div> C 0.766000000000000 0.048000000000000 0.974000000000000</div><div> H 0.846200000000000 0.147100000000000 0.123100000000000</div><div> O 0.837000000000000 0.003000000000000 0.848000000000000</div><div> C 0.650000000000000 0.147000000000000 0.782000000000000</div><div> H 0.573200000000000 0.048300000000000 0.632000000000000</div><div> C 0.566000000000000 0.180000000000000 0.914000000000000</div><div> H 0.644200000000000 0.283300000000000 0.059300000000000</div><div> C 0.483000000000000 0.962000000000000 0.008000000000000</div><div> H 0.398000000000000 0.864700000000000 0.860500000000000</div><div> C 0.596000000000000 0.852000000000000 0.175000000000000</div><div> H 0.671600000000000 0.937700000000000 0.335000000000000</div><div> C 0.512000000000000 0.618000000000000 0.231000000000000</div><div> H 0.423600000000000 0.540000000000000 0.075100000000000</div><div> H 0.584900000000000 0.543800000000000 0.299300000000000</div><div> O 0.740000000000000 0.352000000000000 0.712000000000000</div><div> O 0.455000000000000 0.270000000000000 0.739000000000000</div><div> O 0.457000000000000 0.613000000000000 0.409000000000000</div><div><br></div><div>K_POINTS automatic</div><div>1 2 2 0 0 0</div><div><br></div><div>CELL_PARAMETERS</div><div> 19.653151695476645 0.000000000000000 0.000000000000000</div><div> -5.324227082441216 11.522683134265510 0.000000000000000</div><div> -5.303208047623142 -0.374229849785373 9.933328808172122</div><div><br></div><div><br></div><div>Hope this helps,</div></div><div> Carlo</div><div><br></div></div><div class="gmail_extra"><div><div class="h5"><br><div class="gmail_quote">2015-01-19 2:32 GMT+01:00 Mohan maruthi sena <span dir="ltr"><<a href="mailto:maruthi.sena@gmail.com" target="_blank">maruthi.sena@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div><div><div><div><div>Dear Ari Paavo Seitsonen,<br>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.<br><br></div>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]<br><br></div>2) Please find the attached input obtained as output form cif2qsh.<br><br><br></div>Thank you so much for a reply,<br></div><br></div>with regards,<br></div>K. Mohan<br></div><div class="gmail_extra"><br><div class="gmail_quote"><div><div>On Mon, Jan 19, 2015 at 3:45 AM, Ari P Seitsonen <span dir="ltr"><<a href="mailto:Ari.P.Seitsonen@iki.fi" target="_blank">Ari.P.Seitsonen@iki.fi</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div><br>
Dear Mohan maruthi sena,<br>
<br>
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:<br>
<br>
- Are your atomic coordinates in the crystal coordinates? Does your input file have the correct option for that?<br>
<br>
- 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.<br>
<br>
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).<br>
<br>
Hopefully this helps you at least a little bit forward.<br>
<br>
Greetings from Rome,<br>
<br>
apsi<br>
<br>
-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=<u></u>*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=<u></u>-=*=-=*=-=*=-=*=-<br>
Ari Paavo Seitsonen / <a href="mailto:Ari.P.Seitsonen@iki.fi" target="_blank">Ari.P.Seitsonen@iki.fi</a> / <a href="http://www.iki.fi/~apsi/" target="_blank">http://www.iki.fi/~apsi/</a><br>
Ecole Normale Supérieure (ENS), Département de Chimie, Paris<br>
Mobile (F) : +33 789 37 24 25 (CH) : +41 79 71 90 935<div><div><br>
<br>
<br>
On Sun, 18 Jan 2015, Mohan maruthi sena wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi all,<br>
I recently started using espresso. I want to optimize a crystal structure. By looking at the previous posts , I tried to<br>
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<br>
file for the attached cif file. I have visualized the cif file in vesta, gaussian and then saved those .cif file. It prepared input<br>
files but the atoms are too close.<br>
<br>
1) Can some please let me how to give prepare input file for espresso 5.1.1, using cif or pdb file?<br>
<br>
2) If want to create a slab structure and maintain 10 angstorms distance between the slabs? How can i do this in espresso?<br>
<br>
3) I have used the following server (<a href="http://j-ice.sourceforge.net/ondemand/index.html" target="_blank">http://j-ice.sourceforge.net/<u></u>ondemand/index.html</a>) but could not get the input file.<br>
<br>
Please find the attached cif and espresso input files.<br>
<br>
</blockquote>
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