[Pw_forum] Re [8] : US-PP of Au
Dear Lorenzo Thank you to reply. It is always segmentation fault. My system is 3-atoms Au cluster. this cluster forms a chain of atoms but the calculations never finished because of segmentation fault. Dear Gabriele the work was completely don with kinetic-energy cutoff=32. Ry and charge density cutoff = 320. Ry . *Forces acting on atoms (Ry/au): atom 1 type 1 force =-0.9579 -0.95790. atom 2 type 1 force = 0.00013265 -0.36860. atom 3 type 1 force =-0.36860.000132650. Total force = 0.000237 Total SCF correction = 0.000290 SCF correction compared to forces is too large, reduce conv_thr bfgs converged in 24 scf cycles and 19 bfgs steps (criteria: energy < 0.10E-03, force < 0.10E-02) End of BFGS Geometry Optimization Final energy =-262.9046471560 Ry Begin final coordinates ATOMIC_POSITIONS (angstrom) Au 1.381049485 1.381049485 0.0 Au 3.868137287 -1.139186772 0.0 Au -1.139186772 3.868137287 0.0 End final coordinates* Best wishes. Reza.Shidpour Institute for Nanoscienec and Nanotechnology, SUT -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100915/97843a52/attachment.htm
[Pw_forum] Re [7] : US-PP of Au
Dear Gabriele Thank you for your comments in pwscf forum. I performed your suggestion that ecut is set to 32 Ry. The structure was relaxed and I repeated with ecut=20 , 22 Ry. It seems that the structure did not relaxed with this point " * . ... the Fermi energy is-5.0636 ev !total energy =-262.94392529 Ry Harris-Foulkes estimate =-262.94392533 Ry estimated scf accuracy< 0.0006 Ry The total energy is the sum of the following terms: one-electron contribution =-323.90644330 Ry hartree contribution = 178.85727642 Ry xc contribution =-104.02662243 Ry ewald contribution= -13.85257067 Ry smearing contrib. (-TS) = -0.01556530 Ry convergence has been achieved in 2 iterations Forces acting on atoms (Ry/au): negative rho (up, down): 0.998E-04 0.000E+00 atom 1 type 1 force = 0.0.002237110. atom 2 type 1 force =-0.00165978 -0.001118560. atom 3 type 1 force = 0.00165978 -0.001118560. Total force = 0.003608 Total SCF correction = 0.000988 SCF correction compared to forces is too large, reduce conv_thr The maximum number of steps has been reached. End of BFGS Geometry Optimization Begin final coordinates ATOMIC_POSITIONS (angstrom) Au 0.0 0.248435531 0.0 Au -2.339313337 1.325352234 0.0 Au 2.339313337 1.325352234 0.0 End final coordinates* Questions : 1) The electron_maxstep is equaled 100. What is purpose of "number of states" ? 2) Should I consider system to be semiconducting If I want to simulate 4-atoms cluster? Best Regards, Reza.Shidpour SUT -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100913/57452288/attachment.htm
[Pw_forum] Re [6] : US-PP of Au
Dear Paolo Thank you for reply. With ecut = 72 Ry , I repeated the simulation five times. The simulation proceeded several scf iterations and several bfgs iterations but the jobs were never finished. ( I attached one of the out puts. ) Is it possible the ecut is so great that RAM is not sufficient for 3-atoms cluster ? Best regards. Reza.Shidpour SUT -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100913/09d10f15/attachment-0001.htm -- next part -- A non-text attachment was scrubbed... Name: Au3_relax_6.out Type: application/octet-stream Size: 53837 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20100913/09d10f15/attachment-0002.obj -- next part -- A non-text attachment was scrubbed... Name: Au3_relax.in Type: application/octet-stream Size: 772 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20100913/09d10f15/attachment-0003.obj
[Pw_forum] Re [5] : PP-US of Au
Dear Gabriele and Dear Paolo
Thank you for previous comments.
I used your hints and I run small cluster with only 3 atoms but the previous
problem has remained.
Input file
&control
calculation='relax'
title='Au3Cluster'
restart_mode='from_scratch'
outdir='./tmp'
prefix='Au3'
etot_conv_thr=1.0D-4
pseudo_dir = './'
wf_collect=.true.
/
&system
ibrav= 2, celldm(1) = 26,nat= 3, ntyp= 1,
ecutwfc =72.0, ecutrho=560.0,
occupations='smearing', smearing='fd', degauss=0.01
nspin=1,
/
&electrons
electron_maxstep=100,
diagonalization='cg',
conv_thr=1.0D-6,
mixing_beta=0.1,
/
&ions
ion_dynamics='bfgs'
/
&cell
/
ATOMIC_SPECIES
Au 196.97 Au.pbe-nd-rrkjus.UPF
ATOMIC_POSITIONS {angstrom}
Au0.0000.0000.000
Au4.1100.0000.000
Au 0.000 4.1100.000
K_POINTS {automatic}
2 2 2 1 1 1
and
The Error :
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PCRoutineLine
Source
pw.x 0052089C addusdens_ 27
addusdens.f90
pw.x 004DCB76 sum_band_ 153
sum_band.f90
pw.x 0044B7D7 electrons_287
electrons.f90
pw.x 0040BA6E MAIN__ 92
pwscf.f90
pw.x 0040B8DC Unknown Unknown Unknown
libc.so.6 2AE29DCF2ABD Unknown Unknown Unknown
pw.x 0040B7D9 Unknown Unknown Unknown
Question : Is it possible that the source of error is related to be
semiconducting while I identified metal in input file with smearing keyword
?
Best Regards,
Reza.Shidpour
SUT
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[Pw_forum] Re [4] : PP-US of Au
Dear Gabriele and Dear Paolo I am very grateful to you for helping. To reply the Gabriele 's question , I mention that I use 4 cpu (Intel? Core?2 Quad Processor *Q9550* (12M Cache, 2.83 GHz, 1333 MHz FSB)). Dear gentlemans I try to perform your comments certainly and I will inform you the conclusion of process. Best Regards, Reza.Shidpour SUT -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100830/51735991/attachment.htm
[Pw_forum] Re [3] : PP-US of Au
*Dear Gabriele *
*Thank you for your comment. I know that you and co-workers attempt
perseveringly so
I apperciate from your efforts but I mention some points :
1 ) All of examples ( 35 examples ) has been run successfully.
2 ) The RAM of my system is sufficient for 13 atoms (RAM = 8 Gigabyte DDR3).
3 ) I tested a case . I used informations related to 01 example ( Si - scf
).
I constructed a input file from a imaginary 13-atom Si cluster that is
different from
previous input file in type of atoms and pseudopotential. Then I run scf
calculation both of them.*
*Input File related to Au :
&control
calculation='scf'
title='Au13Cluster'
restart_mode='from_scratch'
outdir='./tmp'
prefix='Au13'
etot_conv_thr=1.0D-4
pseudo_dir = './'
/
&system
ibrav= 2, celldm(1) = 38,nat= 13, ntyp= 1,
ecutwfc =40.0, ecutrho=400.0,
occupations='smearing',smearing='gaussian',degauss=0.01,
nspin=1,
/
&electrons
electron_maxstep=100,
diagonalization='cg',
conv_thr=1.0D-6,
mixing_beta=0.5,
/
&ions
ion_dynamics='bfgs'
/
&cell
/
ATOMIC_SPECIES
Au 196.97 Au.pbe-nd-van.UPF
ATOMIC_POSITIONS {angstrom}
Au 4.844 4.844 4.844
Au 0.000 4.844 7.833
Au 4.844 7.833 0.000
Au 4.844 7.833 9.688
Au 9.688 4.844 1.855
Au 1.855 0.000 4.844
Au 1.855 9.688 4.844
Au 4.844 1.855 9.688
Au 7.833 9.688 4.844
Au 4.844 1.855 0.000
Au 9.688 4.844 7.833
Au 7.833 0.000 4.844
Au 0.000 4.844 1.855
K_POINTS {automatic}
2 2 2 1 1 1*
*After of several minutes, the result was *
* Largest allocated arrays est. size (Mb) dimensions
Kohn-Sham Wavefunctions 110.74 Mb ( 84386, 86)
NL pseudopotentials 217.61 Mb ( 84386, 169)
Each V/rho on FFT grid 51.50 Mb (3375000)
Each G-vector array 9.18 Mb (1203541)
G-vector shells 0.03 Mb ( 3661)
Largest temporary arrays est. size (Mb) dimensions
Each subspace H/S matrix0.11 Mb ( 86, 86)
Each matrix 0.22 Mb (169, 86)
Arrays for rho mixing 411.99 Mb (3375000, 8)
Initial potential from superposition of free atoms
Check: negative starting charge= -0.356687
starting charge 142.84904, renormalised to 143.0
negative rho (up, down): 0.357E+00 0.000E+00
Starting wfc are 117 atomic wfcs
total cpu time spent up to now is255.53 secs
per-process dynamical memory: 1035.0 Mb
Self-consistent Calculation
iteration # 1 ecut=51.00 Ry beta=0.50
CG style diagonalization
ethr = 1.00E-02, avg # of iterations = 2.1
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PCRoutineLine
Source
pw.x 0052089C addusdens_ 27
addusdens.f90
pw.x 004DCB76 sum_band_ 153
sum_band.f90
pw.x 0044B7D7 electrons_287
electrons.f90
pw.x 0040BA6E MAIN__ 92
pwscf.f90
pw.x 0040B8DC Unknown Unknown Unknown
libc.so.6 2B500B54CABD Unknown Unknown Unknown
pw.x 0040B7D9 Unknown Unknown Unknown*
*Now , for input file related Si *
*&control
calculation='scf
title='Si13Cluster
restart_mode='from_scratch
outdir='./tmp
prefix='Si13
etot_conv_thr=1.0D-4
pseudo_dir = './
/
&system
ibrav= 2, celldm(1) = 38,nat= 13, ntyp= 1,
ecutwfc =40.0, ecutrho=400.0,
occupations='smearing',smearing='mp',degauss= 0.01,
nspin=1,
/
&electrons
electron_maxstep=100,
diagonalization='cg',
conv_thr=1.0D-6,
mixing_beta=0.5,
/
&ions
/
&cell
/
ATOMIC_SPECIES
Si 28.086 Si.pz-vbc.UPF
ATOMIC_POSITIONS {angstrom}
Si0.000 0.000 0.000
Si 0.000 4.844 7.833
Si 4.844 7.833 0.000
Si 4.844 7.833 9.688
Si 9.688 4.844 1.855
Si 1.855 0.000 4.844
Si 1.855 9.688 4.844
Si 4.844 1.855 9.688
Si 7.833 9.688 4.844
Si 4.844 1.855 0.000
Si 9.688 4.844 7.833
Si 7.833 0.000 4.844
Si 0.000 4.844 1.855
K_POINTS {automatic}
2 2 2 1 1 1
*
*And the result was :*
*...
...
iteration # 50 ecut=40.00 Ry beta=0.50
CG style diagonalization
ethr = 2.38E-05, avg # of iterations = 3.8
negative rho (up, down): 0.442E-07 0.000E+00
total cpu time spent up to now is 7717.21 secs
total energy = -97.69548088 Ry
Harris-Foulkes estimate = -97.70290819 Ry
estimated scf accuracy< 0.46657030 Ry
iteration # 51 ecut=40.00 Ry beta=0.50
CG sty
[Pw_forum] Re [2]: PP-US of Au
Dear Paolo I appreciate from your advise. I try to examine this on other machine. ( If I could find ) But I have a question . I did not use parallelism. With complete compiling of PWSCF and running all of examples without even one error ( I accentuate "all of examples" ) , Is it possible that the fault is included from hard/soft ware or parallelism ? Best regards. R.Shidpour SUT -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100829/f51d4cf8/attachment.htm
[Pw_forum] PP-US of Au
Dear QE Developers and Users
I use PWSCF for simulation of Au13 cluster. I complied software completely
and I run all of examples without error.
My system seems suitable for this purpose.(RAM = 8 GIGABYTE , PROCESSOR =
QUADCORE 2.8 , OPERATION SYSTEM =
UBUNTU 9.10) but the software stops with segmentation fault error (code 174)
frequently.
I studied user-guide and writings in forum and I performed these actions :
1) all of libraries are compiled completely (ifort & mkl & ic).
2) I checked position of atoms with xcrysden and I did not found any
problem.
3) I used almost of US pseudopotentials for Au in site and all of them have
problem.
4) I tried to use diagonalization='cg' but this error remained.
Is it possible that all of PP-US related to Au are bad pseudopotential,
typically with a ghost, or a USPP giving non-positive charge
density, leading to a violation of positiveness of the S matrix appearing in
the USPP formalism ? OR Is PWSCF unable to simulate heavy atoms such as Au
or Pd because of lack of suitable USPP?
I really appreciate you for solving this problem.
My input file :
&control
calculation='relax'
title='Au13'
restart_mode='from_scratch'
outdir='./tmp'
prefix='Au13'
etot_conv_thr=1.0D-4
pseudo_dir = './'
/
&system
ibrav= 2, celldm(1) = 38,nat= 13, ntyp= 1,
ecutwfc =52.0, ecutrho=520.0,
occupations='smearing',smearing='mv',degauss=0.01,
nspin=1,
/
&electrons
electron_maxstep=100,
diagonalization='cg',
conv_thr=1.0D-6,
mixing_beta=0.5,
/
&ions
ion_dynamics='bfgs'
/
&cell
/
ATOMIC_SPECIES
Au 196.97 Au.pbe-nd-van.UPF
ATOMIC_POSITIONS {angstrom}
Au 4.844 4.844 4.844
Au 0.000 4.844 7.833
Au 4.844 7.833 0.000
Au 4.844 7.833 9.688
Au 9.688 4.844 1.855
Au 1.855 0.000 4.844
Au 1.855 9.688 4.844
Au 4.844 1.855 9.688
Au 7.833 9.688 4.844
Au 4.844 1.855 0.000
Au 9.688 4.844 7.833
Au 7.833 0.000 4.844
Au 0.000 4.844 1.855
K_POINTS {automatic}
2 2 2 1 1 1
Reza . Shidpour
SUT
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[Pw_forum] Problem about applying US-PP in Au
Dear Pwscf users
I use pwscf for simulation of Au cluster (RAM = 8 GIGABYTE , PROCESSOR =
QUADCORE 2.8 , OPERATION SYSTEM =
UBUNTU 9.10) . With employing all of (ultrasoft) pseudopotentials*** *in
espresso site, I face to the segmentation
fault error but with employing a non-US pseudopotential this error
disappeares.
Would you please helping me about solving this error ?
input file :
&control
calculation='scf'
title='Au_ Pd_surface'
restart_mode='from_scratch'
outdir='./tmp'
prefix='Au_Pd'
etot_conv_thr=1.0D-4
pseudo_dir = '/home/reza/pseudo/'
/
&system
ibrav= 6, celldm(1) = 23.137,celldm(3)=2,nat= 72, ntyp= 1,
ecutwfc =40.0, ecutrho=400.0,
occupations='smearing',smearing='mp',degauss= 0.01,
nspin=1
/
&electrons
electron_maxstep=100,
conv_thr=1.0D-6,
mixing_beta=0.5,
/
&ions
/
&cell
/
ATOMIC_SPECIES
Au 196.97 Au.pbe-nd-rrkjus.UPF
ATOMIC_POSITIONS {angstrom}
Au 00 0
Au 2.042.04 0
Au 02.04 2.04
Au 2.040 2.04
Au 4.080 0
Au 6.122.04 0
Au 4.082.04 2.04
Au 6.120 2.04
Au 8.160 0
Au 10.22.04 0
Au 8.162.04 2.04
Au 10.20 2.04
Au 04.08 0
Au 2.046.12 0
Au 06.12 2.04
Au 2.044.08 2.04
Au 4.084.08 0
Au 6.126.12 0
Au 4.086.12 2.04
Au 6.124.08 2.04
Au 8.164.08 0
Au 10.26.12 0
Au 8.166.12 2.04
Au 10.24.08 2.04
Au 08.16 0
Au 2.0410.2 0
Au 010.2 2.04
Au 2.048.16 2.04
Au 4.088.16 0
Au 6.1210.2 0
Au 4.0810.2 2.04
Au 6.128.16 2.04
Au 8.168.16 0
Au 10.210.2 0
Au 8.1610.2 2.04
Au 10.28.16 2.04
Au 00 4.08
Au 2.042.04 4.08
Au 02.04 6.12
Au 2.040 6.12
Au 4.080 4.08
Au 6.122.04 4.08
Au 4.082.04 6.12
Au 6.120 6.12
Au 8.160 4.08
Au 10.22.04 4.08
Au 8.162.04 6.12
Au 10.20 6.12
Au 04.08 4.08
Au 2.046.12 4.08
Au 06.12 6.12
Au 2.044.08 6.12
Au 4.084.08 4.08
Au 6.126.12 4.08
Au 4.086.12 6.12
Au 6.124.08 6.12
Au 8.164.08 4.08
Au 10.26.12 4.08
Au 8.166.12 6.12
Au 10.24.08 6.12
Au 08.16 4.08
Au 2.0410.2 4.08
Au 010.2 6.12
Au 2.048.16 6.12
Au 4.088.16 4.08
Au 6.1210.2 4.08
Au 4.0810.2 6.12
Au 6.128.16 6.12
Au 8.168.16 4.08
Au 10.210.2 4.08
Au 8.1610.2 6.12
Au 10.28.16 6.12
K_POINTS {automatic}
2 2 1 1 1 1
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