[Pw_forum] forrtl: severe (59)
Dear all users,
When I was about to calculate the fermisurface, after it have done
a nscf run, it gave the error message like this in the turn of which
bands_FS.x should be run:
forrtl: severe (59): list-directed I/O syntax error, unit 5, file stdin
I have no idea what happened.And my inputs for the bands_FS.x.
input_FS
16 23
11.6147
LaFeAsO
10 10 10
1.00 0.00 0.00
0.00 1.00 0.00
0.00 0.00 0.461340
and another input is the output of the nscf run, here is the input of
nscf running.
&control
calculation = 'nscf'
prefix='LaFeAsO',
pseudo_dir = '/disk2/xgwan/Quantum-Espresso/espresso-4.0.3/pseudo/',
outdir='/disk2/xgwan/tmp/'
/
&system
ibrav=6,
celldm(1)=7.6232,
celldm(3)=2.1676,
nat=8,
ntyp=4,
ecutwfc = 40.0,
ecutrho = 300.0,
occupations= 'smearing'
degauss = 0.03
smearing = 'marzari-vanderbilt'
/
&electrons
mixing_beta = 0.7
conv_thr = 1.0d-11
/
ATOMIC_SPECIES
La 57.0 La.pbe-nsp-van.UPF
Fe 28.0 Fe.pbe-sp-van.UPF
As 33.0 As.pbe-n-van.UPF
O 16.0 O.pbe-rrkjus.UPF
ATOMIC_POSITIONS {crystal}
La 0.25 0.25 0.14134
La 0.75 0.75 0.85866
Fe 0.75 0.25 0.5
Fe 0.25 0.75 0.5
As 0.25 0.25 0.65166
As 0.75 0.75 0.34834
O 0.75 0.25 0.0
O 0.25 0.75 0.0
K_POINTS
1331
0.000.000.00 1.00
0.000.000.046134 1.00
0.000.000.092268 1.00
0.000.000.138402 1.00
0.000.000.184536 1.00
I omitted others K_points here which is generated by kvecs_FS.x.
I am appraciate for any suggest and comment.
Have a nice day.
Pan Deng
Nanjing University
[Pw_forum] roblem with bfgs algorithm optimizer for spin polarized system
Thanks, the solution to the? problem was cell_dofree, removing the optimization works fine,? even if at the second SCF hemaite starts with absolute magnetization equal to 0.47, and after some cycles it's becoming higher 13.34 Bohr mag /cell. It is allright ? Thanks Piero - Original Message - From: pc...@kent.ac.uk Date: Friday, March 13, 2009 6:05 pm Subject: Re: [Pw_forum] roblem with bfgs algorithm optimizer for spin polarized system To: PWSCF Forum > Thanks, > the solution to the? problem was cell_dofree, removing it . It's > work even if at the second SCF hemaite starts with absolute > magnetization equal to 0.47, and after some cycles it's becoming > higher 13 34 Bohr mag /cell. It is allright ? > > - Original Message - > From: Lorenzo Paulatto > Date: Friday, March 13, 2009 4:20 pm > Subject: Re: [Pw_forum] roblem with bfgs algorithm optimizer for > spin polarized system > To: PWSCF Forum > > > On Fri, 13 Mar 2009 17:16:22 +0100, Giuseppe Mattioli > > wrote: > > > > > I still suspect that > > > Piero's problem concerns some "electronic" stuff. > > > > yes, of course, but if the minimization algorithm doesn't work > > well it can take the system to some weird configuration that > > have trouble converging... this is only a theory of course. > Also > > disabling charge and potential interpolation may help. > > > > cheers > > > > > > > > > > -- > > Lorenzo Paulatto > > SISSA? &? DEMOCRITOS (Trieste) > > phone: +39 040 3787 511 > > skype: paulatz > > www:?? http://people.sissa.it/~paulatto/ > > > > *** save italian brains *** > > ?http://saveitalianbrains.wordpress.com/ > > ___ > > 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/20090313/14b5fa3e/attachment.htm
[Pw_forum] roblem with bfgs algorithm optimizer for spin polarized system
Thanks, the solution to the? problem was cell_dofree, removing it . It's work even if at the second SCF hemaite starts with absolute magnetization equal to 0.47, and after some cycles it's becoming higher 13 34 Bohr mag /cell. It is allright ? - Original Message - From: Lorenzo Paulatto Date: Friday, March 13, 2009 4:20 pm Subject: Re: [Pw_forum] roblem with bfgs algorithm optimizer for spin polarized system To: PWSCF Forum > On Fri, 13 Mar 2009 17:16:22 +0100, Giuseppe Mattioli > wrote: > > > I still suspect that > > Piero's problem concerns some "electronic" stuff. > > yes, of course, but if the minimization algorithm doesn't work > well it can take the system to some weird configuration that > have trouble converging... this is only a theory of course. Also > disabling charge and potential interpolation may help. > > cheers > > > > > -- > Lorenzo Paulatto > SISSA? &? DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > skype: paulatz > www:?? http://people.sissa.it/~paulatto/ > > *** save italian brains *** > ?http://saveitalianbrains.wordpress.com/ > ___ > 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/20090313/cf9fd721/attachment.htm
[Pw_forum] roblem with bfgs algorithm optimizer for spin polarized system
On Fri, 13 Mar 2009 17:16:22 +0100, Giuseppe Mattioli wrote: > I still suspect that > Piero's problem concerns some "electronic" stuff. yes, of course, but if the minimization algorithm doesn't work well it can take the system to some weird configuration that have trouble converging... this is only a theory of course. Also disabling charge and potential interpolation may help. cheers -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/
[Pw_forum] roblem with bfgs algorithm optimizer for spin polarized system
> If I were you, I would try without the "cell_dofree" option, which has not
> been maintained in awhile, to the point I'm not sure it is working as it
> should, especially for BFGS.
I may have missed it, but if not I suggest including a comprehensive example
regarding the use of different vc-relax schemes within the next QE
distribution...
However I used recently the bfgs (both on the ions and on the cell parameters)
method and the cell_dofree option without problems. I still suspect that
Piero's problem concerns some "electronic" stuff.
export FILE="anat12-vcr-bfgs"
export INPFILE=$FILE-2.inp
export OUTFILE=$FILE-2.out
echo " $FILE"
echo " $INPFILE"
echo " $OUTFILE"
cat > $INPFILE << EOF
&control
calculation = 'vc-relax'
restart_mode='restart',
prefix='$FILE',
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/',
tstress=.true.,
tprnfor=.true.,
nstep=200,
etot_conv_thr=1.0E-5,
forc_conv_thr=1.0D-4,
/
&system
ibrav=6, celldm(1)=7.15262, celldm(3)=2.51360,
nat=12, ntyp=2,
ecutwfc=25.0,
ecutrho=150.,
occupations='smearing', degauss=0.01,
nspin=1,
/
&electrons
mixing_mode='plain'
mixing_beta=0.3
conv_thr=1.0d-9
electron_maxstep=200
/
&ions
ion_dynamics='bfgs'
/
&cell
cell_dynamics='bfgs',
press =0.00,
cell_dofree='xyz',
/
ATOMIC_SPECIES
Ti 47.900 Ti12_pbe.van.UPF
O15.999 O_pbe.van.UPF
ATOMIC_POSITIONS {crystal}
Ti 0. 0. 0.
Ti 0. 0.5000 0.2500
Ti 0.5000 0.5000 0.5000
Ti 0.5000 1. 0.7500
O 0. 0. 0.2066
O 0. 0. -0.2066
O 0. 0.5000 0.4566
O 0. 0.5000 0.0434
O 0.5000 0.5000 0.7066
O 0.5000 0.5000 0.2934
O 0.5000 1. 0.9566
O 0.5000 1. 0.5434
K_POINTS {automatic}
4, 4, 2, 0, 0, 0
EOF
$PARA_PREFIX $ESPRESSO/pw.x $PARA_POSTFIX < $INPFILE >> $OUTFILE
On Friday 13 March 2009 15:09:42 Lorenzo Paulatto wrote:
> On Fri, 13 Mar 2009 15:07:22 +0100, wrote:
> > Thanks for the reply,
> > buT I am still thinking that should be a bug in the optimizer, since I
> > also tried to run my system like a metal and nothing gonna change.
>
>
> cheers
--
- Article premier - Les hommes naissent et demeurent
libres et ?gaux en droits. Les distinctions sociales
ne peuvent ?tre fond?es que sur l'utilit? commune
- Article 2 - Le but de toute association politique
est la conservation des droits naturels et
imprescriptibles de l'homme. Ces droits sont la libert?,
la propri?t?, la s?ret? et la r?sistance ? l'oppression.
Giuseppe Mattioli
CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
v. Salaria Km 29,300 - C.P. 10
I 00016 - Monterotondo Stazione (RM)
Tel + 39 06 90672836 - Fax +39 06 90672316
E-mail:
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[Pw_forum] "charge is wrong" error
Aihua Zhang wrote: > from electrons : error # 1 > charge is wrong on which machine (hardware and software) do you get this error? P. -- Paolo Giannozzi, Democritos and University of Udine, Italy
[Pw_forum] roblem with bfgs algorithm optimizer for spin polarized system
On Fri, 13 Mar 2009 15:07:22 +0100, wrote: > Thanks for the reply, > buT I am still thinking that should be a bug in the optimizer, since I > also tried to run my system like a metal and nothing gonna change. If I were you, I would try without the "cell_dofree" option, which has not been maintained in awhile, to the point I'm not sure it is working as it should, especially for BFGS. cheers -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/
[Pw_forum] forrtl: severe (59)
?? wrote: > forrtl: severe (59): list-directed I/O syntax error, unit 5, file stdin > > I have no idea what happened then you better learn how to have an idea: these are trivial problems whose solution can be found more often than not by just searching the net. If you search the above message in the mailing list archive, you will find an explanation of what the message means: "wrong input data read from input" (and, by the way, "forrtl" = "fortran run-time library") P. -- Paolo Giannozzi, Democritos and University of Udine, Italy
[Pw_forum] roblem with bfgs algorithm optimizer for spin polarized system
??? ntyp = 3, > > ecutwfc = 50 , > > ?? nosym = .true. , > > ??? nbnd = 70, > > ?? nelec = 100, > > ? tot_charge = 0.00, > > occupations = 'fixed' , > > ?? nspin = 2 , > > ?? starting_magnetization(1) = 1., > > ?? starting_magnetization(2) = -1., > > ?? starting_magnetization(3) = 0., > > ?? tot_magnetization = 0 , > > ?/ > > ?&ELECTRONS > > ?/ > > ?&IONS > > ??? ion_dynamics = 'bfgs' , > > ?/ > > ?&CELL > > ?? cell_dynamics = 'bfgs' , > > ?? wmass = 2001.0060 , > > cell_dofree = 'all' , > > ?/ > > ATOMIC_SPECIES > > ?? Fe?? 55.62000? Fe.pbe-sp-van_ak.UPF? > > ? Fe1?? 55.62000? Fe.pbe-sp-van_ak.UPF? > > ??? O?? 15.99000? O.pbe-van_ak.UPF? > > ATOMIC_POSITIONS crystal? > > ? Fe?? 0.144358141?? 0.144342247?? 0.144393006 > > ? Fe1? 0.355605889?? 0.355642696?? 0.355656118 > > ? Fe1? 0.644394003?? 0.644359012?? 0.644344959 > > ? Fe?? 0.855641399?? 0.855655859?? 0.855605070 > > ? O??? 0.556470421?? 0.943529173?? 0.250007053 > > ? O??? 0.250006034?? 0.556470770?? 0.943529639 > > ? O??? 0.943529367?? 0.250006711?? 0.556470944 > > ? O??? 0.443532949?? 0.056467967?? 0.749992942 > > ? O??? 0.749994148?? 0.443532454?? 0.056467520 > > ? O??? 0.056467649?? 0.749993110?? 0.443532750 > > K_POINTS automatic? > > ? 4 4 4?? 0 0 0 > > > > > > --? > > Pieremanuele Canepa > > Room 230 > > School of Physical Science? > > Ingram Building > > University of Kent, > > ?Canterbury, > > ?Kent, CT2 7NH? > > United Kingdom > > Cell: +44-7768685833 > > ID Skype: pieremanuele > > ID msn:?pieremanuele83 at hotmail.com > > ---- > > -- > > - Article premier - Les hommes naissent et demeurent > libres et ?gaux en droits. Les distinctions sociales > ne peuvent ?tre fond?es que sur l'utilit? commune > - Article 2 - Le but de toute association politique > est la conservation des droits naturels et > imprescriptibles de l'homme. Ces droits sont la libert?, > la propri?t?, la s?ret? et la r?sistance ? l'oppression. > > > ?? Giuseppe > Mattioli??? > ?? CNR - ISTITUTO DI STRUTTURA DELLA > MATERIA?? > ?? v. Salaria Km 29,300 - C.P. > 10??? > ?? I 00016 - Monterotondo Stazione > (RM)? > ?? Tel + 39 06 90672836 - Fax +39 06 > 90672316??? > ?? E-mail: > -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090313/8f287951/attachment-0001.htm
[Pw_forum] roblem with bfgs algorithm optimizer for spin polarized system
0.355605889?? 0.355642696?? 0.355656118 > ? Fe1? 0.644394003?? 0.644359012?? 0.644344959 > ? Fe?? 0.855641399?? 0.855655859?? 0.855605070 > ? O??? 0.556470421?? 0.943529173?? 0.250007053 > ? O??? 0.250006034?? 0.556470770?? 0.943529639 > ? O??? 0.943529367?? 0.250006711?? 0.556470944 > ? O??? 0.443532949?? 0.056467967?? 0.749992942 > ? O??? 0.749994148?? 0.443532454?? 0.056467520 > ? O??? 0.056467649?? 0.749993110?? 0.443532750 > K_POINTS automatic? > ? 4 4 4?? 0 0 0 > > > --? > Pieremanuele Canepa > Room 230 > School of Physical Science? > Ingram Building > University of Kent, > ?Canterbury, > ?Kent, CT2 7NH? > United Kingdom > Cell: +44-7768685833 > ID Skype: pieremanuele > ID msn:?pieremanuele83 at hotmail.com > -- - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00016 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090313/ea4f6c17/attachment-0001.htm
[Pw_forum] fixed spin moment calculation
about 2.5? Ni should have 10 electrons in >> valence, so I would >> expect to get a number around 10 for the charge (unless the atom goes in a >> very ionized >> state, but that seems highly unprobable to me). >> Are you sure PPs and all the rest is OK? >> >> >> GS >> >> yumin qian wrote: >> > thanks for your reply ,I changed the lambda=5.0 and used >> >occupations='tetrahedra' but the magnetization still did not >> > converge to the initial value ,but the total energy converged. >> > I do know what is the problem. >> > >> >> == >> > > atom number5 relative position : -0.1652 0.2839 >> 0.5083 >> > > charge : 2.373353 >> > > magnetization : 1.544423 >> > > magnetization/charge:0.650735 >> > > constrained moment : 1.80 >> > > >> > > >> > >> >> == >> > > the output file gives a magnetic moment of 1.5444 ,how should I >> do to >> > > make the calculation converge to the starting_magnetization 1.8 >> ? >> > >> >> -- >> >> >> o o >> | Gabriele Sclauzero, PhD Student | >> | c/o: SISSA & CNR-INFM Democritos, | >> |via Beirut 2-4, 34014 Trieste (Italy) | >> | email: sclauzer at sissa.it | >> | phone: +39 040 3787 511 | >> | skype: gurlonotturno | >> o o >> ___ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > > -- > Sincerely Y. M. Qian > Lab.of Condensed Matter Theory and Materials Computation > Institute of Physics > Chinese Academy of Sciences > Tel: + 8610 8264 9147 > E-Mail:yuminqian at gmail.com > P.O.Box 603 Beijing 100190 > China > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Sincerely Y. M. Qian Lab.of Condensed Matter Theory and Materials Computation Institute of Physics Chinese Academy of Sciences Tel: + 8610 8264 9147 E-Mail:yuminqian at gmail.com P.O.Box 603 Beijing 100190 China -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090313/9b3bbfe0/attachment-0001.htm
[Pw_forum] fixed spin moment calculation
Thanks for your reply , It's very kind of you ,I will try your it again following you suggestion 2009/3/12 Gabriele Sclauzero > > yumin qian wrote: > > Sorry for confuse you , After checking the input and output file , I > > found that I also did a LiVO2 crystal calcualtion with the same > > problem, the input file I posted is for LiNiO2 and the output file I > > posted is for LiVO2 , here is the complete input and output file from > > the same calcualtion > > This does not help me to help you... why didn'y you post the full input > file from the > beginning? > > > > > > > > > == > > atom number5 relative position : -0.1652 0.2839 0.5083 > > charge : 2.371448 > > magnetization : 1.554551 > > magnetization/charge:0.655528 > > constrained moment : 1.80 > > > > > > I also changed lambda from 1 to 5 and the final magnetic moment > > changed from 1.55 to 1.50 > > It sounds strange to me that it decreases if you increase lambda, should be > the opposite. > > > so the parameter lambda seems have no impact on the final magnetic > > moment, there should be something wrong with my calcualtion but I can't > > spot this error. > > Maybe a state with such a high local magnetization (consider that you have > only 2.37 > "local electrons") is energetically quite unfavored and putting the penalty > with this > lambda is not enough. > You can try to increase more lambda. If it doesn't work, maybe there's some > other problem > I cannot see. > > GS > -- > > > o o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > |via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o o > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Sincerely Y. M. Qian Lab.of Condensed Matter Theory and Materials Computation Institute of Physics Chinese Academy of Sciences Tel: + 8610 8264 9147 E-Mail:yuminqian at gmail.com P.O.Box 603 Beijing 100190 China -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090313/bc587e39/attachment.htm
[Pw_forum] xcrysden+cygwin can't display relax process
On Fri, 2009-03-13 at 09:04 +0100, Paolo Giannozzi wrote: > Dr. Shu-jun Hu wrote: > > > The string '0 0 0' means the position of corresponding ions has been > > fix. When > > such strings have been removed from the output file, the whole relax > > process can > > be displayed correctly. I suggest removing the 0 0 0 string from the output > > file > > or fix the bug of xcrysden. > > which version of xcrysden are you using? I think this is fixed > in the most recent versions It is! Regards, Tone PS: If the error still persists in the new versions, follow the guidelines of Gabriele: send the output file. -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html
[Pw_forum] xcrysden+cygwin can't display relax process
Dr. Shu-jun Hu wrote: > The string '0 0 0' means the position of corresponding ions has been fix. > When > such strings have been removed from the output file, the whole relax process > can > be displayed correctly. I suggest removing the 0 0 0 string from the output > file > or fix the bug of xcrysden. which version of xcrysden are you using? I think this is fixed in the most recent versions P. -- Paolo Giannozzi, Democritos and University of Udine, Italy
[Pw_forum] xcrysden+cygwin can't display relax process
Dr. Shu-jun Hu wrote: > Dear All, > > When I use the xcyrsden installed on cygwin to display the relaxing process, > it > just shows the initio structure (only one slide) rather than the whole > process. > Since some ions have been fixed in the input file, the new structure after > each > dynamic step is like: > > * > atom 140 type 1 force = 0.00621763 -0.00424409 -0.00889158 > > Total force = 0.061794 Total SCF correction = 0.002797 > > Entering Dynamics:iteration =27 > > = 0.99727388 > > ATOMIC_POSITIONS (angstrom) > Zn 0.0 0.0 0.00 0 0 > Zn 2.81560 1.62560 0.00 0 0 > O0.0 0.0 1.986200 0 0 > *** > > The string '0 0 0' means the position of corresponding ions has been fix. > When > such strings have been removed from the output file, the whole relax process > can > be displayed correctly. I suggest removing the 0 0 0 string from the output > file > or fix the bug of xcrysden. Which bug? For me (on Linux...) xcrysden works perfectly in displaying the atomic coordinates of relax calculations. If you have clear evidence that this is a bug (and it has not been solved already in a later release... BTW, you did not mention which version of Xcrysden you're using, I suppose you already tried the last one) and it is reproducible, please send a pw output file that gives the error to the xcrysden mailing list (which is not this one). Removing that string from pw output is not good idea, since the atomic positions on the output can be reused as starting configuration for a successive relaxation in case one is obliged to restart from_scratch for some reason. Cheers GS > > Best > > Shujun > > > > > > > > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- o o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | |via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o o
[Pw_forum] xcrysden+cygwin can't display relax process
Dear All, When I use the xcyrsden installed on cygwin to display the relaxing process, it just shows the initio structure (only one slide) rather than the whole process. Since some ions have been fixed in the input file, the new structure after each dynamic step is like: * atom 140 type 1 force = 0.00621763 -0.00424409 -0.00889158 Total force = 0.061794 Total SCF correction = 0.002797 Entering Dynamics:iteration =27 = 0.99727388 ATOMIC_POSITIONS (angstrom) Zn 0.0 0.0 0.00 0 0 Zn 2.81560 1.62560 0.00 0 0 O0.0 0.0 1.986200 0 0 *** The string '0 0 0' means the position of corresponding ions has been fix. When such strings have been removed from the output file, the whole relax process can be displayed correctly. I suggest removing the 0 0 0 string from the output file or fix the bug of xcrysden. Best Shujun
[Pw_forum] xcrysden+cygwin can't display relax process
Hello Dr. Hu, XCrysDen uses an awk script to parse the relaxation output file. It doesn't like the 0 0 0 because it searches (as I recall) for lines that have 4 entries. It's relatively easy to change it so it'll search for lines that have 4 OR 7 entries. Cheers, Lex Kemper Department of Physics University of Florida Dr. Shu-jun Hu wrote: > Dear All, > > When I use the xcyrsden installed on cygwin to display the relaxing process, > it > just shows the initio structure (only one slide) rather than the whole > process. > Since some ions have been fixed in the input file, the new structure after > each > dynamic step is like: > > * > atom 140 type 1 force = 0.00621763 -0.00424409 -0.00889158 > > Total force = 0.061794 Total SCF correction = 0.002797 > > Entering Dynamics:iteration =27 > > = 0.99727388 > > ATOMIC_POSITIONS (angstrom) > Zn 0.0 0.0 0.00 0 0 > Zn 2.81560 1.62560 0.00 0 0 > O0.0 0.0 1.986200 0 0 > *** > > The string '0 0 0' means the position of corresponding ions has been fix. > When > such strings have been removed from the output file, the whole relax process > can > be displayed correctly. I suggest removing the 0 0 0 string from the output > file > or fix the bug of xcrysden. > > Best > > Shujun > > > > > > > > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum
[Pw_forum] ld1.x & US requires...
Dear Paul, For 3d, I guess you can use the Fe psp input in the paw_library. Try commenting the? PAW tags if you want to have an input sample for ultrasoft to work on.. But, you may as well start using PAW instead. Emine Kucukbenli, PhD student, SISSA, Italy --- On Thu, 3/12/09, Paul M. Grant wrote: From: Paul M. Grant Subject: Re: [Pw_forum] ld1.x & US requires... To: "'PWSCF Forum'" Date: Thursday, March 12, 2009, 5:10 PM Thanks, Paolo. Actually, I was aware of that library of ld1.x input examples, but what I was actually asking about were there any similar examples for the 3d TMs around somewhere. I should have been more specific. Paul M. Grant, PhD Principal, W2AGZ Technologies Visiting Scholar, Applied Physics, Stanford (2005-2008) EPRI Science Fellow (Retired) IBM Research Staff Member Emeritus w2agz at pacbell.net http://www.w2agz.com ? ? -Original Message- From: pw_forum-bounces at pwscf.org [mailto:pw_forum-boun...@pwscf.org] On Behalf Of Paolo Giannozzi Sent: Thursday, March 12, 2009 12:21 AM To: PWSCF Forum Subject: Re: [Pw_forum] ld1.x & US requires... On Mar 12, 2009, at 5:29 , Paul M. Grant wrote: > as far as I could find, none provided a large number of input examples > one could play around with see atomic_doc/pseudo_library --- Paolo Giannozzi, Democritos and University of Udine, Italy ___ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum ___ 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/20090313/06408946/attachment.htm
[Pw_forum] roblem with bfgs algorithm optimizer for spin polarized system
Dear PWscf developers,? I am trying to? optimize, on the latest version of the espresso code (v4.0.4 ),? the cell parameter and also the ionic coordinate of hematite.? Initially I treat hematite like an insulator using? the following pseudo-potential :Fe.pbe-sp-van_ak.UPF for? Iron and O.pbe-van_ak.UPF for oxygen (I attached the input at the bottom). To optimize? both atomic coordinates and cell parameters I used bfgs algorithm . As you know hematite is an open-shell system, and you need to define the spin orientation in order to describe it like a ferro-magnetic or anti-ferromagnetic system. I choose the anti-ferromagnetic one, that means? to have? the total magnetization equal to 0 every SCF cycle and absolute magnetization ranging from 11-16 (this highly pseudo potential dependent).?? Anyway, for the first SCF cycle the magnetization carried out is correct, while after the first geometry optimization step hematite starts to lose the spin and the energy? also dancing between two value not allowing the SCF to converge.? So attempting to managed this problem I try to run it like a metal introducing? a methfessel-paxton? smearing. Nothing seems to change, the SCF of the second optimization step doesn't converge as previously. Then I tried to restart my calculation from the first point coordinates and the first SCF step converged, whilst the next no as in the previous cases . This is very strange and get me frustrated ! Then I run the same calculation changing both optimization algorithm to damp for the ionic coordinate and damp-w for the cell. In this way the SCFs after the first optimization cycle seem to converge with the right magnetization and the next as well.? I did also a further trial, because I need to use the bfgs algorithm to optimize my structure. I tried to run the same system on a previous version of espresso (v.2.1.2), and treating it like a metal? (with methfessel-paxton? smering) and using bfgs for ionic coordinate and damp for cell optimization (since bfgs wasn't implemented to optimize the cell parameter in this version) the first SCF? reached the convergence and the following as well.?? How can I solve it ?? I also read in the documents related to PWscf that bfgs? for optimizing cell parameters (vc-relax) is still in a experimental version. Would it be possible that It has some problem with spin polarized systems?? How can I manage this problem? I need desperately to use bfgs to optimize the hematite.? ?? Best Regards, Piero ?&CONTROL ?? title = 'opt_bulk_PBE_van3.inp' , calculation = 'vc-relax' , ??? restart_mode = 'from_scratch' , ? wf_collect = .true. , ? outdir = '/home/pc229/backup/Counts/PWscf/Fe2O3_bulk/PWSCF/Fe2O3_bulk/opt_bulk_PBE_van/' , ? pseudo_dir = '/home/pc229/backup/Counts/PWscf/Fe2O3_bulk/PWSCF/Fe2O3_bulk/pseudo/' , ? prefix = 'opt_bulk_PBE_van3.inp' , ?/ ?&SYSTEM ?? ibrav = 5, ?? celldm(1) = 11.091428, ?? celldm(4) = 0.587237106, nat = 10, ??? ntyp = 3, ecutwfc = 50 , ?? nosym = .true. , ??? nbnd = 70, ?? nelec = 100, ? tot_charge = 0.00, occupations = 'fixed' , ?? nspin = 2 , ?? starting_magnetization(1) = 1., ?? starting_magnetization(2) = -1., ?? starting_magnetization(3) = 0., ?? tot_magnetization = 0 , ?/ ?&ELECTRONS ?/ ?&IONS ??? ion_dynamics = 'bfgs' , ?/ ?&CELL ?? cell_dynamics = 'bfgs' , ?? wmass = 2001.0060 , cell_dofree = 'all' , ?/ ATOMIC_SPECIES ?? Fe?? 55.62000? Fe.pbe-sp-van_ak.UPF? ? Fe1?? 55.62000? Fe.pbe-sp-van_ak.UPF? ??? O?? 15.99000? O.pbe-van_ak.UPF? ATOMIC_POSITIONS crystal? ? Fe?? 0.144358141?? 0.144342247?? 0.144393006 ? Fe1? 0.355605889?? 0.355642696?? 0.355656118 ? Fe1? 0.644394003?? 0.644359012?? 0.644344959 ? Fe?? 0.855641399?? 0.855655859?? 0.855605070 ? O??? 0.556470421?? 0.943529173?? 0.250007053 ? O??? 0.250006034?? 0.556470770?? 0.943529639 ? O??? 0.943529367?? 0.250006711?? 0.556470944 ? O??? 0.443532949?? 0.056467967?? 0.749992942 ? O??? 0.749994148?? 0.443532454?? 0.056467520 ? O??? 0.056467649?? 0.749993110?? 0.443532750 K_POINTS automatic? ? 4 4 4?? 0 0 0 --? Pieremanuele Canepa Room 230 School of Physical Science? Ingram Building University of Kent, ?Canterbury, ?Kent, CT2 7NH? United Kingdom Cell: +44-7768685833 ID Skype: pieremanuele ID msn:?pieremanuele83 at hotmail.com ------ next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090313/9e16eaf1/attachment.htm
