[Pw_forum] Regarding supercell dimensions
I am nobe to quantum espresso and using supercell for first time.
Can any one help me in understanding few things regarding the supecell
determination?
The following is a typical input file I am using (copied from one of the
earlier post).
CONTROL
title = 'Graphene mono layer'
calculation = "relax" ,
restart_mode = 'from_scratch' ,
outdir='/home/usuarios/baldini/espresso-4.2.1/tmp/' ,
pseudo_dir = '/home/usuarios/baldini/espresso-4.2.1/pseudo' ,
etot_conv_thr = 1.0E-4 ,
forc_conv_thr = 1.0D-3 ,
nstep=50,
dt=40,
prefix='1MLG_Ti_H2',
/
&SYSTEM
ibrav = 0.,
ntyp = 2 ,
nat = 33 ,
ecutwfc = 50.0 ,
ecutrho = 400.0,
/
&ELECTRONS
electron_maxstep = 300.,
conv_thr = 1.0d-8 ,
mixing_mode = 'plain',
mixing_beta = 0.5,
diagonalization = 'cg' ,
diago_cg_maxiter = 50,
/
&IONS
/
CELL_PARAMETERS
16.12131954 9.383047808 0.000
0. 18.658162370 0.000
0.0000.00056.6893424
ATOMIC_SPECIES
C 12.0107 C.pbe-van_ak.UPF
Ti 47.8670 Ti.pbe-sp-van_ak.UPF
ATOMIC_POSITIONS angstrom
C 2.891637.402191.8862
C 3.592928.638321.8826
C 3.603496.167021.8884
C 5.0186 8.645011.8612
C 5.0215 6.165981.8904
C 5.733027.405221.8718
C 1.471847.396161.891
C 2.891129.870661.886
C 2.894714.932641.8916
C 5.733199.8885 1.8612
C 5.736434.9413 1.8924
C 7.163487.412031.882
C 1.474744.9269 1.8924
C 0.762281 8.627831.8946
C 0.763134 6.161721.8914
C 1.4715 9.863351.8934
C 3.6034111.10951.8868
C 5.0212411.12391.882
C 3.605123.701561.8932
C 5.026453.707891.891
C 7.878078.655321.8816
C 7.163739.894971.872
C 7.162034.948141.8954
C 7.876196.176771.8996
C 5.7363412.35221.8872
C 0.772689 3.691021.898
C 0.762793 1.220031.8968
C 7.8764511.13371.8894
C 7.1620312.35871.889
C 7.8720113.59221.8942
C 2.894792.466191.8922
C 1.474822.458781.8952
Ti 6.416048.659743.74
K_POINTS {automatic}
6.0 6.0 1.0 1.0 1.0 1.0
Can anyone help me understanding how are these Cell parameters calculated?
Also in some cases celld(m) are used. Can anyone comment on these also?
How are the cell parameters and lattice constant or atomic spacing related?
Any clue would be of great help.
Thanks in advance.
Rgds
Deepak
-- next part --
An HTML attachment was scrubbed...
URL:
http://www.democritos.it/pipermail/pw_forum/attachments/20110803/6951fbc5/attachment.htm
[Pw_forum] problem with creating the pseudopotential of Zn
thanks for your valuable advice,my problem was resolved at once.You are so kind to give me the help! And I'm so sorry to reply the letter late because of a vacation. ? 2011?7?23? ??11:29?GAO Zhe ??? > when lloc=2, d orbital should be the last one~ > I am not good at PP generation and theory, but your problem can be fixed > with such modifications ( I am not sure whether LD1 code supports > Revised-PBE, and I met a negative rho problem if I used RRKJ method ): > *&input > zed = 30. > rel = 1, > config = '[Ar] 3d10 4s1 4p1' , > iswitch = 3, > dft = 'PBE' > / > &inputp >lloc = 1 , >pseudotype = 3 , >file_pseudopw = 'Zn.PBE.UPF' , >nlcc = .true. , >tm = .true. , > > / > 5 > 3D 3 2 10.00 0.00 1.80 2.00 > 3D 3 2 0.00 0.05 1.80 2.00 > 4S 1 0 1.00 0.00 1.80 2.00 > 4S 1 0 0.00 0.05 1.80 2.00 > 4P 2 1 1.00 0.00 1.80 2.10 > * > -- > GAO Zhe > CMC Lab, MSE, SNU, Seoul, S.Korea > > At 2011-07-23 16:45:13,"Robin H" wrote: > > Hi,everyone.I have tried many times to creat the PP of Zn,but the problems > come out everytime.Even if I correct the one,then there will be anthoer.Zn > is one of the transition iron atom,and I'm not sure my input items are all > proper for it.This is my input file for ld1.x .And the next is the wrong > information.I need some help. > *input :* > &input > title='Zn' > zed=30. > rel=1, > config='[Ar] 3d10.00 4s1.00 4p1.00', > iswitch=3, > dft='revPBE' > / > &inputp >lloc=2, >pseudotype=3, >file_pseudopw='Zn.revPBE.UPF', >author='ADC', > / > 6 > 3D 3 2 10.00 0.00 1.80 2.00 > 3D 3 2 0.00 0.05 1.80 2.00 > 4S 1 0 1.00 0.00 1.80 2.00 > 4S 1 0 0.00 0.05 1.80 2.00 > 4P 2 1 1.00 0.00 1.80 2.10 > 4P 2 1 0.00 0.05 1.80 2.10 > > > > *wrong information :* > * *Program LD1 v.4.3.1starts on 23Jul2011 at 16:29: 5 > This program is part of the open-source Quantum ESPRESSO suite > for quantum simulation of materials; please cite > "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); > URL http://www.quantum-espresso.org";, > in publications or presentations arising from this work. More details > at > > http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO > Parallel version (MPI), running on 1 processors > > > %% > from ld1_readin : error # 1 > only one local channel > > > %% > stopping ... > [unset]: aborting job: > application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 > > > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110803/b06b30cf/attachment.htm
[Pw_forum] problem with Sc-pseudo
Dear all ... I have been working with the pseudo Sc.pbe-nsp-van.UPF obtained from the database at the quantum-espresso web page. In order to test it I set up a calculation for ScN, with Rs and Zb structure but I got really bad frequencies. After some check, it seems to me that the problem relies on the Sc pseudo. Does anybody have experience with this pseudos or if you happen to have a good Sc soft pseudo it will greatly appreciate it? or if no, can somebody help me or giving me some hints on how to create a good soft pseudo? Thanks in advance -- Henry Ortiz CINVESTAV-Quer?taro Mexico -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110803/f4fd420b/attachment.htm
[Pw_forum] compiling error during the installation of the GPU release of Quantum ESpresso
Dear all, during the installation of the GPU-enabled release of QE on a 64-bit Linux Pc with (gfortran+gcc+openmpi), the following error occurs: make[1]: Entering directory `/home/fabri/espresso-PRACE/PW' [] mpif90 -O3 -g -x f95-cpp-input -D__GFORTRAN -D__STD_F95 -D__FFTW3 -D__CUDA -D__CUDA_MEM_PINNED -D__GPU_NVIDIA_20 -D__CUDA_QE_TIMING -D__MPI -D__PARA -I../include -I/usr/local/cuda//include -I../iotk/src -I../Modules -I. -c addusdens.f90 addusdens.f90:121.12: IF (err) THEN 1 Error: IF clause at (1) requires a scalar LOGICAL expression make[1]: *** [addusdens.o] Error 1 make[1]: Leaving directory `/home/fabri/espresso-PRACE/PW' make: *** [pw] Error 2 Could anybody give me some hints? thank you in advance -- Dr. Fabrizio Gala Dipartimento di Scienze di Base e Applicate per l'Ingegneria, Sezione di Fisica. La Sapienza,University of Rome and Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia (CNISM) via A. Scarpa 14-16 00161 Rome - ITALY phone: +390649766545 fax: +390644240183 -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110803/d61ddf57/attachment.htm
[Pw_forum] IOTK error while restarting using QE4.3.1
Dear all,
I am using Quantum espresso 4.3.1. It has been compiled with gfortran
4.1.2 and openmpi-1.5. The code has been compiled on a desktop having
Intel(R) Core(TM)2 Quad CPU Q9650.
When I am trying to restart the scf calculation it is giving me the
following IOTK error:
# FROM IOTK LIBRARY, VERSION 1.2.0
# UNRECOVERABLE ERROR (ierr=1)
# ERROR IN: iotk_scan_end (iotk_scan.spp:233)
# CVS Revision: 1.23
# foundl
# ERROR IN: iotk_close_read (iotk_files.spp:645)
# CVS Revision: 1.20
However, the same input file restarts perfectly fine for QE-4.2.1
compiled in the same machine using the same versions of gfortran and
mpi.
The input file for bulk PbS is given below:
&CONTROL
calculation = 'scf',
prefix='Pb-S',
restart_mode = 'restart',
tstress = .TRUE.,
tprnfor=.true.
pseudo_dir ='.',
outdir='.'
wf_collect=.true.
/
&SYSTEM
ibrav= 2,
celldm(1) = 11.37,
nat= 2,
ntyp= 2,
nspin = 1,
ecutwfc = 40.,
ecutrho=400
/
&ELECTRONS
conv_thr=1.0d-8,
mixing_mode = 'plain'
mixing_beta = 0.3,
/
ATOMIC_SPECIES
Pb 196.966569 Pb.pbe-d-van.UPF
S 32.0 S.pbe-van_bm.UPF
ATOMIC_POSITIONS (crystal)
Pb 0.0 0.0 0.0
S 0.5 0.5 0.5
K_POINTS {automatic}
8 8 8 0 0 0
Does anyone have similar experience with version 4.3.1 and gfortran
compilers? Is it some problem with the compiler or there is some bug
in QE4.3.1?
With regards,
Prasenjit
--
PRASENJIT GHOSH,
Assistant Professor,
IISER Pune,
First floor, Central Tower, Sai Trinity Building
Garware Circle, Sutarwadi, Pashan
Pune, Maharashtra 411021, India
Phone: +91 (20) 2590 8203
Fax: +91 (20) 2589 9790
[Pw_forum] Raman on DFT-false-metals
Hi, I would like to calculate a Raman spectrum with PHONON for an insulator that is metallic in LDA and GGA. Is it possible to introduce easily a scissors shift to open the gap and allow the Raman calculation? -- Eduardo Menendez Proupin Departamento de Qu?mica Fisica Aplicada Facultad de Ciencias Universidad Aut?noma de Madrid Phone: +34 91 497 6706 On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad de Chile URL: http://fisica.ciencias.uchile.cl/~emenendez "*Padece, espera y trabaja para gentes que nunca conocer? y que a su vez padecer?n, esperar?n y trabajar?n para otros, que tampoco ser?n felices, pues el hombre ans?a siempre una felicidad situada m?s all? de la porci?n que le es otorgada. Pero la grandeza del hombre est? precisamente en querer mejorar lo que es. En imponerse Tareas. En el Reino de los Cielos no hay grandeza que conquistar, puesto que all? todo es jerarqu?a establecida, inc?gnita despejada, existir sin t?rmino, imposibilidad de sacrificio, reposo y deleite. Por ello, agobiado de penas y de Tareas, hermoso dentro de su miseria, capaz de amar en medio de las plagas, el hombre puede hallar su grandeza, su m?xima medida en el Reino de este Mundo*". Alejo Carpentier, El reino de este mundo, (1949). Translate from spanish here http://translate.google.com/?hl=&ie=UTF-8&text=&sl=es&tl=en -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110803/dc935be2/attachment-0001.htm
[Pw_forum] Doubt in input file
Il giorno 02/ago/2011, alle ore 19.47, Padmaja Patnaik ha scritto: > Hi All > While doing fully relativistic calculations one has to mention "noncolin= > .TRUE., lspinorb= .TRUE.," in the scf input. > Yes > If then I proceed to do nscf calculations for DOS then should I mention > these to variables again in the input? > Yes > Please suggest. > I did > > With thanks and regards > You're welcome Padmaja Patnaik Research Scholar Dept of Physics IIT Bombay Mumbai, India ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110803/c52f5a94/attachment.htm
[Pw_forum] ld1.x generate Sb PP
Dear PP experts, I spend long long time to generate the Sb PBE pseudopotential. The "best" one I get is still not very successful to get the good experimental or VASP-PAW lattice constants. exp??? :??? 4.3084200 4.30841850220 11.274600 PAW-PBE: 4.387963702059904 4.387963701901805 11.42545713239960 PP-PBE:??? 4.44711025 ? ? ? ? ? ? ? ? ? ?? 4.44858214 ? ? ? ? ? ? ? ? ? ? 11.81877927 The c-direction is significantly different to the experimental data and PAW results. And I notice in the PP database, there has a PW91 Sb PP. Using the PW91 PP, the theoretical lattice constants are quite good. (4.35479533, 4.35557221,? 11.32102582). The my Sb PP input file is: &input ??? title='Sb' ??? zed=51. ??? rel=1, ??? rlderiv=2.2, ??? eminld=-2.0, ??? emaxld=2.0, ??? deld=0.01, ??? nld=3, ??? config='[Kr] 4d10.0 5s2.0 5p3.0' ??? iswitch=3, ??? dft='PBE' ?/ ?&inputp ?? pseudotype=3, ?? lloc=1, ?? rho0=0.001, ?? file_pseudopw='Sb.pbe.UPF', ?? nlcc = .true., ?? author='YS-Zhang', ?/ 4 4D? 3? 2 10.00? 0.00? 1.60? 2.00? 1 4D? 3? 2? 0.00 -1.70? 1.60? 2.00? 1 5S? 1? 0? 2.00? 0.00? 2.10? 2.10? 1 5P? 2? 1? 3.00? 0.00? 2.30? 2.30? 1 During the tests, I didn't find any ghost state and the largest difference between PP and AE is 3 2 4D?? 1(10.00)?? -6.59082?? -6.55589?? -0.03493 1 0 5S?? 1( 0.00)?? -4.49315?? -4.49962??? 0.00647 2 1 5P?? 1( 0.00)?? -3.63377?? -3.64128??? 0.00751 dEtot_ae =? 10.908350 Ry dEtot_ps =? 10.913263 Ry,?? Delta E=? -0.004913 Ry Please help me improve the Sb PP input file. Thank you very much. Yongsheng Zhang Northwestern University Dept. of Materials Science and Eng. 2220 Campus Dr. Evanston, IL 60208
[Pw_forum] About the Frozen Phonon Method
Dear Prof. Baroni, Thank you so much. It clarified a lot. Yours, Mohaddeseh On Tue, Aug 2, 2011 at 10:20 PM, Stefano Baroni wrote: > > On Aug 2, 2011, at 8:18 AM, mohaddeseh abbasnejad wrote: > > Dear Prof. Baroni > > Thanks again > >> Dear Prof. Baroni >> >> Thanks for your reply. >> I wonder shouldn't the plot show the same frequency for a range of >> displacements? >> >> >> what range? why should it? >> >> > -- Because if we are in the neighberhood of a minimum "where a quadratic > could be fitted", any displacement in that range should result the same > frequency. By displacement, I mean the same pattern but different in > amplitude. > > > who said this? around a minimum, the only thing you can say is that the > Taylor expansion of the energy in powers of the atomic displacements lacks > any linear terms. In general, it has both quadratic terms (which are the one > you are interested in), as well as higher order terms ... No reason why the > Taylor expansion should be *exactly* quadratic (which is what would give > rise to a "same frequency"). Note however, that it is your definition of > frequency that is probably flawed. I suspect that you define the frequency > as the ratio between the energy variation and the square of the > displacement, which obviously depends on the magnitude of the displacement, > if the energy variation is not exactly quadratic. The correct definition, > instead, is the *limit* of that ration when the displacement goes to zero. > That limit is obviously well defined, independently of the magnitude of any > particular distortion that you may consider. > > > >> And the same freq. for the range to be the harmonic frequency? or the >> zero displacement limit, is the harmonic frequency? >> >> >> yes, by definition >> > > See the above discussion > > >> And when I test the displacements with the same amplitude, but different >> in sign (regarding the inward and outward atomic movements in the basis) I >> do not get the same results. >> >> >> why should you? >> >> Shouldn't the plot have symmetry vs. the vertical axis? >> >> >> why? >> > > -- Consider for example a linear chain of atoms, with 2 atoms per basis. > The optical mode is the result of the outward movement of the atoms (The one > in +a/2 moves towards +x and the one in -a/2 moves towards -x). I expect > that if I displace the atoms in an inward movement with the same amplitude > as the outward, I should see the same frequency (The one in +a/2 moves > towards -x and the one in -a/2 moves towards +x) because the 2 patterns > present the same mode, right? That is what I've done in the case of Diamond. > Is my expectation wrong? > > > Yes. If the Taylor expansion of the energy difference vs displacement has > cubic terms (as it usually has, but in very special cases dictated by > symmetry), there is no reason why the energy difference should be even with > respect to energy displacement. Actually, it usually isn't ... > > Hope this clarifies a bit the situation ... > > Take care > SB > > --- > Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste > http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / > stefanobaroni (skype) > > La morale est une logique de l'action comme la logique est une morale de la > pens?e - Jean Piaget > > Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html > > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- - Mohaddeseh Abbasnejad, Room No. 323, Department of Physics, University of Tehran, North Karegar Ave., Tehran, P.O. Box: 14395-547- IRAN Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 4781 Cellphone: +98 917 731 7514 E-Mail: m.abbasnejad at gmail.com Website: http://physics.ut.ac.ir - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110803/9523c4fc/attachment-0001.htm
