Re: [QE-users] Question about optimizing the lattice constant of iron

[David Foster]

HiI think it is good enough with nearly 1% error.

Regards
 
 David 

On Tuesday, December 25, 2018, 7:06:01 AM GMT+3:30, Gui Wei 
<201707021...@cqu.edu.cn> wrote:  
 
 Hi, When optimizing the lattice constant of bcc Fe,the result is a=2.830A， 
which is in disagreement with experimentally derived structural parameter 
a=2.863A.Could someone give me some advice?
    calculation = 'vc-relax'    prefix='Fe1',    pseudo_dir = 
'/public/home/duan1/gw2/pseudo/',    outdir='/public/home/duan1/gw2/tempdir/'   
 tprnfor     = .true.    tstress     = .true./    ibrav= 1,     A=2.8664 
   nat= 2     ntyp= 1    occupations='smearing',    smearing='mp',    
degauss=0.02,    ecutwfc =37    ecutrho =240    nspin   = 2    
starting_magnetization(1) = 0.4/    conv_thr        = 1.0d-8    
mixing_beta      = 0.7/   ion_dynamics = 'bfgs'/   cell_dynamics = 
'bfgs' / ATOMIC_SPECIESFe  55.847  Fe.pbe-n-kjpaw_psl.0.2.4.UPFATOMIC_POSITIONS 
crystal Fe   0.   0.   0. Fe   
0.5001   0.5001   0.5001K_POINTS automatic8 
 8  8  0  0  0
The result: CELL_PARAMETERS (alat=  5.41671099)   0.987418499   0.0   
0.0   0.0   0.987418499   0.0   0.0   
0.0   0.987418499


Gui WeiSchool of Mechanical Engineering，Chongqing University, China
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Re: [QE-users] SCF energy tolerance of GGA+U for Er2O3

[David Foster]

Dear Friends,
With increasing cutoff of ecut and rho, scf converges very good to 0.00056RY, 
but after it, I get error of cdiaghg
 estimated scf accuracy    <  88.51397074 Ry estimated scf accuracy 
   <  83.12113178 Ry
 estimated scf accuracy    <  71.36984815 Ry
 estimated scf accuracy    <  18.56626142 Ry
 estimated scf accuracy    <  16.50426903 Ry
 estimated scf accuracy    <  10.98856402 Ry
 estimated scf accuracy    <   9.29719956 Ry
 estimated scf accuracy    <   9.04328354 Ry
 estimated scf accuracy    <   7.59328356 Ry
 estimated scf accuracy    <   4.30614522 Ry
 estimated scf accuracy    <   2.21579595 Ry
 estimated scf accuracy    <   2.06363848 Ry
 estimated scf accuracy    <   2.06296140 Ry
 estimated scf accuracy    <   1.34208729 Ry
 estimated scf accuracy    <   1.19303974 Ry
 estimated scf accuracy    <   0.77385185 Ry
 estimated scf accuracy    <   0.35651056 Ry
 estimated scf accuracy    <   0.35249019 Ry
 estimated scf accuracy    <   0.33018969 Ry
 estimated scf accuracy    <   0.29144253 Ry
 estimated scf accuracy    <   0.29003126 Ry
 estimated scf accuracy    <   0.15010288 Ry
 estimated scf accuracy    <   0.16890222 Ry
 estimated scf accuracy    <   0.17333274 Ry
 estimated scf accuracy    <   0.20983308 Ry
 estimated scf accuracy    <   0.16568269 Ry
 estimated scf accuracy    <   0.15870553 Ry
 estimated scf accuracy    <   0.15107152 Ry
 estimated scf accuracy    <   0.16370376 Ry
 estimated scf accuracy    <   0.09504571 Ry
 estimated scf accuracy    <   0.07604307 Ry
 estimated scf accuracy    <   0.06449930 Ry
 estimated scf accuracy    <   0.02894336 Ry
 estimated scf accuracy    <   0.02200061 Ry
 estimated scf accuracy    <   0.00853408 Ry
 estimated scf accuracy    <   0.00663002 Ry
 estimated scf accuracy    <   0.00282189 Ry
 estimated scf accuracy    <   0.00240517 Ry
 estimated scf accuracy    <   0.00251009 Ry
 estimated scf accuracy    <   0.00159343 Ry
 estimated scf accuracy    <   0.00129758 Ry
 estimated scf accuracy    <   0.00127796 Ry
 estimated scf accuracy    <   0.00070475 Ry
 estimated scf accuracy    <   0.00056218 Ry
 estimated scf accuracy    <   0.00055564 Ry
 estimated scf accuracy    <   0.00056799 Ry
===
iteration # 47 ecut=   150.00 Ry beta= 0.03
 Davidson diagonalization with overlap

 %%
 Error in routine  cdiaghg (1192):
  problems computing cholesky
 %%

 stopping ...



Here is my input:
===

   title = 'Er2O3'
 calculation = 'scf'
    restart_mode = 'from_scratch'
  outdir = './Er2O3',
  pseudo_dir = './'
  prefix = 'Er2O3'
 disk_io = 'default'
   verbosity = 'default'
   etot_conv_thr=5.0D-5
   forc_conv_thr=1.0D-3
   nstep=1000
   wf_collect=.true.
/
 
   ibrav = 0
   nat = 40
   ntyp = 2
   ecutwfc = 150
   ecutrho = 600
!   starting_magnetization(1)=0.0
   starting_magnetization(2)=0.2
!   starting_magnetization(3)=-0.2
!  tot_magnetization=0.0
   nspin=2
   occupations='smearing'
   degauss=0.003
   smearing='gaussian'
!   occupations='fixed'
   nbnd=350
  lda_plus_u=.true.
   hubbard_u(2)=5.0
!   hubbard_u(3)=1D-40
!   hubbard_alpha(2)=-0.08
!   hubbard_alpha(3)=-0.08
   
/
 
    electron_maxstep = 1
    conv_thr = 1.0D-5
 mixing_mode = 'local-TF'
 mixing_beta = 0.03
 mixing_ndim = 25
 diagonalization = 'davidson'
! diago_thr_init=1.0D-11
! diago_david_ndim=10
!  startingwfc='file'
!  startingpot='file'
/
 
    ion_dynamics = 'bfgs'
/
 
    cell_dynamics = 'bfgs'
/
ATOMIC_SPECIES
   O   15.999   O.revpbe-nl-rrkjus_psl.1.0.0.UPF
   Er   167.259 Er.revpbe-spdfn-rrkjus_psl.1.0.0.UPF
ATOMIC_POSITIONS crystal
O    0.010082090   

Re: [QE-users] SCF energy tolerance of GGA+U for Er2O3

[David Foster]

Dear Lorenzo,My system is an output of optimized experimental primitive 
structure of Er2O3. Since I know it has a gap, I used a small smearing instead 
of occupation=fixed for better convergence of SCF. However, you know that using 
large smearing produces wrong results. I use your comment to change mixing 
mode. I know that SCF convergence in f-series with hubbard parameter is 
difficult. I will post new results.

Regards
 
 David 

On Monday, December 17, 2018, 2:30:14 PM GMT+3:30, Lorenzo Paulatto 
 wrote:  
 
 You're using a very large value of U in a large system, with little symmetry, 
a very small smearing and no initial guess on the final state (starting_ns, 
mixing_fixed_eigenvalues, magnetization,..) it's going to take a lot of sweat, 
tears and possibly blood to converge it. I see no magic solution. Maybe try to 
use a different mixing_mode. Cheers

-- 
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Written on a virtual keyboard with real fingers
On Mon, 17 Dec 2018, 08:41 David Foster https://lists.quantum-espresso.org/mailman/listinfo/users
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[QE-users] SCF energy tolerance of GGA+U for Er2O3

[David Foster]

HiI used revpbe to optimize Er2O3 primitive cell. Everything is OK. Now, I need 
DFT+U for DOS and Band. SCF energy fluctuate as 
follows:=estimated scf accuracy    <  39.48681516 Ry
 estimated scf accuracy    <  62.66497979 Ry
 estimated scf accuracy    <  63.09572639 Ry
 estimated scf accuracy    <  65.51102942 Ry
 estimated scf accuracy    <  38.91981596 Ry
 estimated scf accuracy    <  39.16118677 Ry
 estimated scf accuracy    <  65.24746072 Ry
 estimated scf accuracy    <  81.25768469 Ry
 estimated scf accuracy    <  83.63928837 Ry
 estimated scf accuracy    <  78.22312608 Ry
 estimated scf accuracy    <  70.08066621 Ry
 estimated scf accuracy    <  66.42158960 Ry
 estimated scf accuracy    <  55.83405116 Ry
 estimated scf accuracy    <  54.30262362 Ry
 estimated scf accuracy    <  31.70735190 Ry
 estimated scf accuracy    <  35.65134657 Ry
 estimated scf accuracy    <  38.08212833 Ry
 estimated scf accuracy    <  37.82156916 Ry
 estimated scf accuracy    <   8.30484867 Ry
 estimated scf accuracy    <  17.05143657 Ry
 estimated scf accuracy    <  16.85399058 Ry
 estimated scf accuracy    <  17.27497482 Ry
 estimated scf accuracy    <   7.37306474 Ry
 estimated scf accuracy    <   7.95583285 Ry
 estimated scf accuracy    <   8.03418270 Ry
 estimated scf accuracy    <  15.08314663 Ry
 estimated scf accuracy    <  14.83297715 Ry
 estimated scf accuracy    <  48.43672832 Ry
 estimated scf accuracy    <  52.44897671 Ry
 estimated scf accuracy    <  12.74671487 Ry
 estimated scf accuracy    <  40.31811669 Ry
 estimated scf accuracy    <  19.32262516 Ry
 estimated scf accuracy    <  27.27358109 Ry
 estimated scf accuracy    < 345.44964154 Ry
 estimated scf accuracy    < 123.36609528 Ry
 estimated scf accuracy    < 119.14228290 Ry
 estimated scf accuracy    < 116.83678045 Ry
 estimated scf accuracy    < 117.74401387 Ry
 estimated scf accuracy    < 181.29702486 Ry
 estimated scf accuracy    < 180.04206377 Ry
 estimated scf accuracy    < 151.90818606 Ry
 estimated scf accuracy    < 141.35828132 Ry
 estimated scf accuracy    < 168.85573261 Ry
 estimated scf accuracy    < 135.56334254 Ry
 estimated scf accuracy    <  79.93385392 Ry
 estimated scf accuracy    <  85.33637732 Ry
 estimated scf accuracy    <  95.64968100 Ry
 estimated scf accuracy    <  55.79689175 Ry
 estimated scf accuracy    <  55.26482299 Ry
 estimated scf accuracy    <  54.58782920 Ry
 estimated scf accuracy    < 135.62051557 Ry
 estimated scf accuracy    < 138.39169551 Ry
 estimated scf accuracy    < 166.62307406 Ry
 estimated scf accuracy    < 132.82418933 Ry
 estimated scf accuracy    < 148.82628809 Ry
 estimated scf accuracy    < 114.39893792 Ry
 estimated scf accuracy    <  48.32881238 Ry
 estimated scf accuracy    < 262.66993710 Ry
 estimated scf accuracy    < 176.68031395 Ry
 estimated scf accuracy    < 187.83180834 Ry
 estimated scf accuracy    < 267.53233975 Ry
 estimated scf accuracy    < 265.56657262 Ry
 estimated scf accuracy    <  70.58100989 Ry
 estimated scf accuracy    <  74.04771777 Ry
 estimated scf accuracy    <  72.79391958 Ry
 estimated scf accuracy    <  54.58647026 Ry
 estimated scf accuracy    <  63.99394382 Ry
 estimated scf accuracy    <  53.24009783 Ry
 estimated scf accuracy    <  51.00617518 Ry
 estimated scf accuracy    <  44.50595942 Ry
 estimated scf accuracy    <  38.49013470 Ry
 estimated scf accuracy    <  55.18210929 Ry
 estimated scf accuracy    <  56.64217959 Ry
 estimated scf accuracy    <  56.29693753 Ry
 estimated scf accuracy    <  70.43212315 Ry
 estimated scf accuracy    <  66.94323095 Ry
 estimated scf accuracy    <  63.21746180 Ry
 estimated scf accuracy    <  64.75245613 Ry
 estimated scf accuracy    <  65.45080268 Ry
 estimated scf accuracy    <  62.81184523 Ry
 estimated scf accuracy    <  64.90143507 Ry
 estimated scf accuracy    <  71.61145717 Ry
 estimated scf accuracy    <  64.67931817 Ry
 estimated scf accuracy    <  71.57778462 Ry
 estimated scf accuracy    <  67.13110887 Ry
 estimated scf accuracy    <  68.64481698 Ry
 estimated scf accuracy    <  77.40931903 Ry
 estimated scf accuracy    <  74.95430924 Ry
 estimated scf accuracy    <  71.25096191 Ry
 estimated scf accuracy    <  99.82470246 Ry
 estimated scf accuracy    <  95.68431196 Ry
 estimated scf 

[QE-users] ELPA 2018

[David Foster]

Hi,1- Is there any help/manual for linking elpa 2018 with QE6.3?2- Is it 
possible to link them without GPU? I see that the make command search about 
cuda libraries.
Thanks
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[Pw_forum] VC-relax with HSE

[David Foster]

Dear Users,1- Is it possible to use hybrid method (such as HSE) for VC-Relax 
calculation? I tested version 6.2, but I got error. Any help?
2- Which pseudopotential is suitable for HSE (I think PBE pseudo is good)?

Regards
 
 David___
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[Pw_forum] Error in UPF.F90 in Modules

[David Foster]

Dear Users,Compiling 6.2.1 version with intel cluster studio 2015 I get 
following error:===
mpiifort -O2 -assume byterecl -g -traceback -nomodule -fpp -D__FFTW -D__MPI  
-I/root/qe-6.2.1/include -I/root/qe-6.2.1/FoX/finclude -I../include/ 
-I../iotk/src -I../ELPA/src -I../FFTXlib -I../LAXlib -I../UtilXlib 
-I../KS_Solvers/CG -I/root/qe-6.2.1/include -I/root/qe-6.2.1/FoX/finclude 
-I../include/ -I. -c upf.f90
upf.f90(75): internal error: Please visit 
'http://www.intel.com/software/products/support' for assistance.
   IF (PRESENT(xml_only) ) xml_only_ = xml_only
^
[ Aborting due to internal error. ]
compilation aborted for upf.f90 (code 1)
make[1]: *** [upf.o] Error 1
make[1]: Leaving directory 
`/root/qe-6.2.1/Modules'= 
Any help?
 
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Re: [Pw_forum] SCF Convergence Criteria

[David Foster]

Hi Lorenzo,Yes, I am doing relaxation. Thank you. My system has f-electron, and 
is very hard to be converged. So, I think I should change upscale to 1. Thank 
you again.  


Regards
 
 David 

On Wednesday, December 6, 2017, 9:27:09 PM GMT+3:30, Lorenzo Paulatto 
<paul...@gmail.com> wrote:  
 
 Are you doing a relax calculation? If yes, check the upscale parameter in the 
doc

-- 
Lorenzo Paulatto
Written on a virtual keyboard with real fingers
On Dec 6, 2017 18:28, "David Foster" <davidfoster...@yahoo.com> wrote:

HiI have set "Conv_Thr" to 1.0D-5 in my calculation. As you see follow, the 
estimated scf change is less than 10^(-5) but it has not been converged!!! Is 
there any criteria for SCF convergence in the code which has not been 
documented in the manual?


==total cpu time spent up to now is 8119.0 secs

 total energy  =  -16045.57783278 Ry
 Harris-Foulkes estimate   =  -16045.57783128 Ry
 estimated scf accuracy    <   0.0207 Ry

 total magnetization   =    -0.01 Bohr mag/cell
 absolute magnetization    =    79.80 Bohr mag/cell

 iteration #164 ecut=   140.00 Ry beta=0.01
 Davidson diagonalization with overlap
 ethr =  3.21E-10,  avg # of iterations =  2.0

 total cpu time spent up to now is 8138.3 secs

 total energy  =  -16045.57783497 Ry
 Harris-Foulkes estimate   =  -16045.57783360 Ry
 estimated scf accuracy    <   0.0201 Ry

 total magnetization   =    -0.01 Bohr mag/cell
 absolute magnetization    =    79.80 Bohr mag/cell

 iteration #165 ecut=   140.00 Ry beta=0.01
 Davidson diagonalization with overlap
 ethr =  3.21E-10,  avg # of iterations =  2.0

== ===

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[Pw_forum] SCF Convergence Criteria

[David Foster]

HiI have set "Conv_Thr" to 1.0D-5 in my calculation. As you see follow, the 
estimated scf change is less than 10^(-5) but it has not been converged!!! Is 
there any criteria for SCF convergence in the code which has not been 
documented in the manual?


==total cpu time spent up to now is 8119.0 secs

 total energy  =  -16045.57783278 Ry
 Harris-Foulkes estimate   =  -16045.57783128 Ry
 estimated scf accuracy    <   0.0207 Ry

 total magnetization   =    -0.01 Bohr mag/cell
 absolute magnetization    =    79.80 Bohr mag/cell

 iteration #164 ecut=   140.00 Ry beta=0.01
 Davidson diagonalization with overlap
 ethr =  3.21E-10,  avg # of iterations =  2.0

 total cpu time spent up to now is 8138.3 secs

 total energy  =  -16045.57783497 Ry
 Harris-Foulkes estimate   =  -16045.57783360 Ry
 estimated scf accuracy    <   0.0201 Ry

 total magnetization   =    -0.01 Bohr mag/cell
 absolute magnetization    =    79.80 Bohr mag/cell

 iteration #165 ecut=   140.00 Ry beta=0.01
 Davidson diagonalization with overlap
 ethr =  3.21E-10,  avg # of iterations =  2.0

=

Regards
 
 David___
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[Pw_forum] SCF Convergence Criteria

[David Foster]

HiI have set "Conv_Thr" to 1.0D-5 in my calculation. As you see follow, the 
estimated scf change is less than 10^(-5) but it has not been converged!!! Is 
there any criteria for SCF convergence in the code which has not been 
documented in the manual?


==total cpu time spent up to now is 8119.0 secs

 total energy  =  -16045.57783278 Ry
 Harris-Foulkes estimate   =  -16045.57783128 Ry
 estimated scf accuracy    <   0.0207 Ry

 total magnetization   =    -0.01 Bohr mag/cell
 absolute magnetization    =    79.80 Bohr mag/cell

 iteration #164 ecut=   140.00 Ry beta=0.01
 Davidson diagonalization with overlap
 ethr =  3.21E-10,  avg # of iterations =  2.0

 total cpu time spent up to now is 8138.3 secs

 total energy  =  -16045.57783497 Ry
 Harris-Foulkes estimate   =  -16045.57783360 Ry
 estimated scf accuracy    <   0.0201 Ry

 total magnetization   =    -0.01 Bohr mag/cell
 absolute magnetization    =    79.80 Bohr mag/cell

 iteration #165 ecut=   140.00 Ry beta=0.01
 Davidson diagonalization with overlap
 ethr =  3.21E-10,  avg # of iterations =  2.0

=
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[Pw_forum] SCF Convergence Criteria

[David Foster]

HiI have set "Conv_Thr" to 1.0D-5 in my calculation. As you see follow, the 
estimated scf change is less than 10^(-5) but it has not been converged!!! Is 
there any criteria for SCF convergence in the code which has not been 
documented in the manual?


==total cpu time spent up to now is 8119.0 secs

 total energy  =  -16045.57783278 Ry
 Harris-Foulkes estimate   =  -16045.57783128 Ry
 estimated scf accuracy    <   0.0207 Ry

 total magnetization   =    -0.01 Bohr mag/cell
 absolute magnetization    =    79.80 Bohr mag/cell

 iteration #164 ecut=   140.00 Ry beta=0.01
 Davidson diagonalization with overlap
 ethr =  3.21E-10,  avg # of iterations =  2.0

 total cpu time spent up to now is 8138.3 secs

 total energy  =  -16045.57783497 Ry
 Harris-Foulkes estimate   =  -16045.57783360 Ry
 estimated scf accuracy    <   0.0201 Ry

 total magnetization   =    -0.01 Bohr mag/cell
 absolute magnetization    =    79.80 Bohr mag/cell

 iteration #165 ecut=   140.00 Ry beta=0.01
 Davidson diagonalization with overlap
 ethr =  3.21E-10,  avg # of iterations =  2.0

=
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[Pw_forum] How to fix angles in VC-Relax?

[David Foster]

Dear Users,I am working on a bulk which axes are not orthogonal. I want to 
relax only axes and fix the angels. Which version of "cell_dofree" is proper 
for this issue?

Regards
 
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Re: [Pw_forum] problem in relaxing gold cluster

[David Foster]

Hi I suggest some points for you:
1-You can use ibrav=0 (instead of ibrav=1) and a big box (diameter of your 
cluster+10 A in each direction). place the cluster in the center of the box.2- 
reduce mixing_beta3- leave the mixing_mode to be its default value.


Regards
 
 David 

On Sunday, December 3, 2017, 2:49:08 PM GMT+3:30, hajar zareyi 
 wrote:  
 
 Dear all,
I am trying to relax gold cluster but the structure is going to break apart. 
there is my input file
  = 'relax' ,restart_mode = 'from_scratch' 
,outdir="./TMP",pseudo_dir ="./",         tprnfor   = .true.tstress = 
.true.prefix = 'AU',/ = 1,celldm(1) = 34.75,nat = 13,ntyp = 
1,ecutwfc = 45 ,ecutrho = 500,                       occupations = 'smearing' 
,degauss= 0.01 ,smearing= 'gaussian',/ _mode = 'local-TF'       
                          mixing_beta = 0.7conv_thr = 1.D-6 , / / 
/ATOMIC_SPECIESAu    196.966657   Au.blyp-d-hgh.UPFATOMIC_POSITIONS 
(angstrom)Au 7.000 10.000 10.000Au 8.360 7.644 10.000Au 
11.080 7.644 10.000Au 12.440 10.000 10.000Au 11.080 
12.356 10.000Au 8.360 12.356 10.000Au 9.720 10.000  
10.000Au 9.7238155 8.4315277  7.777622Au 8.3424810 10.7842271  7.780175Au 
11.0523480 10.8179223  7.78000Au 9.7238155 8.4315277  12.2223780Au 8.3328179 
10.7673656  12.220Au 11.0523480 10.8179223  12.220
K_POINTS gamma
is there any one to help me to correct it
 

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[Pw_forum] Question about fixed magnetization calculation

[David Foster]

Hi
I am studying electronic structure of "A2B3" compound which 'A' is a metal with 
f electrons, and B is oxygen. At first, I did an antiferromagnetic VC-relax 
calculation for my primitive lattice containing 16 A and 24 B. I got total 
magnetization of -0.02 BM/Cell, and absolute magnetization of  79.06 
BM/Cell.Now, I want to do a fixed occupation calculation with 
anti-ferromagnetic property. 
1- What value for starting_magnetization of A1 and A2 should I set in my new 
calculation?

2- Is it logical to use Hubbard U near to its experimental gap (without LR 
method) to calculate its band structure?in some studies I see that some author 
test U parapmeter in the range 1-10 eV to see effect of U.
3- How order in CPU time I will encounter approximately If I use G0W0 comparing 
to normal SCF calculation without it?


Regards
 
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Re: [Pw_forum] Phonon negative Frequency

[David Foster]

Hi1- Use parallel version2- A bad converged structure (with low threshold) may 
give large negative phonons.3- Use very tight SCF convergence


Regards
 
 David 

On Wednesday, November 29, 2017, 10:42:44 AM GMT+3:30, Suresh A 
 wrote:  
 
 Dear All,
 I am ran phonon calculation for anatase previously and got 
negative frequencies. I was install QE-5.2.0 in serial mode and took days to 
finish the calculation in my desktop.

Is there any way to know the negative frequency before the calculation ends? So 
that the time can be saved.
                                 Thank You 
   
 Yours Sincerly,

A.Suresh,
Research Scholar,
School of Physics,
Madurai Kamaraj University,
Madurai.
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Re: [Pw_forum] Vacuum for non-periodic structure

[David Foster]

HiInstead of using "Cell_dofree" for "all" use it only in your periodic 
direction (z for example).


Regards
 
 David 

On Wednesday, November 29, 2017, 10:48:55 AM GMT+3:30, Anik Mondol 
 wrote:  
 
 Dear Users,
I am doing a DFT calculation of GaN nanowires, While designing the nanowire 
(approximately 10 A diameter) , I had added around 10 A of vacuum on x and y 
direction. Now I have performed a vc-relax calculation before band calculation, 
the cell volume has shrunk . The vacuum has decreased . Now to make sure the 
results don't be affected by the identical replicas , at least  how much vacuum 
is needed ? Now, that the vacuum has shrunk, will that impose any effect on 
results in this respects. I mean, How can I be sure this vacuum is enough?

Mondol Anik Kumar 
Bangladesh University of Engineering and Technology 
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[Pw_forum] Graphene doped relaxation

[David Foster]

Dear Users
I have done following steps for optimization of Ni- doped 3*3 graphene 
supercell:

1- I constructed unit cell of graphene monolayer (2 atoms) with large vacuum 
(20A in z direction).
2- I optimized both atoms positions and lattice parameters (except for z). It 
means a,b, alpha,beta, and gamma might be changed during relaxation.
3- Then I constructed 3*3 supercell by optimized data of unit cell
4- After, I substituted one Ni atom in place of one carbon atom.
5-  I optimized again both atoms positions and lattice parameters (except for 
z). It means a,b, alpha, beta, and gamma might be changed during relaxation.

Is this process right? especially for step 5. In other words, do I need to 
relax lattice parameters (except z) in addition to atoms positions or not?

Regards
 
 David Foster
 
 Ph.D. Student of Chemistry
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Re: [Pw_forum] Charge of a supercell with a vacancy

[David Foster]

Dear Mostafa

Thanks for your help.

Regards
 
 David Foster
 



On Thu, 10/27/16, Mostafa Youssef <myous...@mit.edu> wrote:

 Subject: Re: [Pw_forum] Charge of a supercell with a vacancy
 To: "pw_forum@pwscf.org" <pw_forum@pwscf.org>
 Date: Thursday, October 27, 2016, 1:48 AM
 
 
 
  
 
 
 
 Dear
 David,
 
 
 
 In experiments , neutral O2 gas leaves the TiO2 crystal
 causing the creation of oxygen vacancies behind.
  However, these vacancies can have any charge state.
  Neutral in which the two electrons (reminiscent of O2-
 ion) set around the vacancy forming polarons,
  2+ in which the two electrons leaves the vacant site
 and go somewhere else, or 1+ which is intermediate
 between the past two cases. 
 
 
 
 Have a look at the following paper for theoretical
 analysis of the oxygen vacancy in TiO2:
 J. Phys. Chem. C 2010, 114, 21694–21704
 
 
 
 
 
 
 For an experimental point view, have a look at figure
 2.4 (and the associated discussion) in the following
 thesis:
 
 
 
 
https://scholar.google.com.eg/citations?view_op=view_citation=en=1Ga4WncJ=pubdate_for_view=1Ga4WncJ:u-x6o8ySG0sC
 
 
 
 
 
 
 
 
 
 Regards,
 Mostafa
 MIT
 
 
 
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[Pw_forum] Charge of a supercell with a vacancy

[David Foster]

Dear Users

In an Oxygen-Vacancy of a supercell of TiO2, how should I set supercell charge? 
For one O-vacancy is it +2 or neutral?

In experimental works, oxygen separated and goes to the infinity with minus 
charge or it is in neutral radical form?

Regards
 
 David Foster
 
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Re: [Pw_forum] vc-relax problem

[David Foster]

Thanks Mostafa, I got it :-)

Regards
 
 David Foster
 
 Ph.D. Student of Chemistry


On Sun, 3/20/16, Mostafa Youssef <myous...@mit.edu> wrote:

 Subject: Re: [Pw_forum] vc-relax problem
 To: "pw_forum@pwscf.org" <pw_forum@pwscf.org>
 Date: Sunday, March 20, 2016, 1:10 AM
 
 
 
  
 #yiv2696291800 P
 {margin-top:0;margin-bottom:0;}
 
 
 Dear
 David,
 
 
 
 
 
 In principle, starting from a 2D material and applying
 vc_relax should end up with the 3D version of the material.
 That is in the graphene case you should end up with graphite
 upon complete convergence.  I doubt that this
 simulation is your intention here.
 
 
 
 If you would like , instead, to study biaxial strain effect
 on doped graphene, then simple manual changes of the a and b
 of the supercell and relax  calculation should do the
 job. 
 
 
 
 
 
 
 
 
 Best Regards,
 
 Mostafa 
 
 MIT
 
 
 
 
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[Pw_forum] vc-relax problem

[David Foster]

  C   0.6629579286767470   0.9187453484234860   0.000791882000
  C   0.7965538253125150   0.9853722213410399   0.000780264100
  C   0.8632342863818040   0.9186931763034320   0.000763622200
  N   0.4631246241068560   0.1185000696135500   0.000970019900
K_POINTS automatic
4 4 1 0 0 0

=

It seems it is better not to use vc-relax, and instead use relax+changing 
volume by hand :-)
Anybody can help to solve this problem?

Regards
 
 David Foster
 
 Ph.D. Student of Chemistry
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[Pw_forum] Mixing PAW, US, and NC pseudopotentials

[David Foster]

Dear Users and Developers,
 In the last performed comparing DFT solid codes in the site 
"https://molmod.ugent.be/deltacodesdft;, QE is the best pseudopotential code 
with "SSSP-Accuracy" which is a mixture of PAW, US, and NC pseudopotentials.
My question is about this mixture process. Can we use them simultaneously in 
one simulation run? For example, in a calculation of Alcohol+TiO2 surface, Is 
it possible to choose US for carbon, PAW for Ti, and NC for O? (this is only an 
example).

Regards
 
 David Foster
 
 Ph.D. Student of Chemistry
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[Pw_forum] what should be the max errors for neb.x

[David Foster]

Dear NEB Developers,
I am calculating the activation energy for forward and backward reaction of 
"butadiene with ethylene"

I know the code searches for the MEP and reports forces perpendicular to the 
path.

In ideal situation, the errors should be zero, i.e. no forces perpendicular to 
path.

However, this is ideal, and in real situations, we finally get some errors.

But, how much less should be these errors.

I took 20 images with more than 40 iterations. But, the max error is 0.6. Is it 
good?

Unfortunately, the examples and tutorials for this section is low.
Regards

David Foster

Ph.D. Student of Chemistry
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Re: [Pw_forum] error: tcp_peer_recv_connect_ack

[David Foster]

Dear Mahya
I agree with Axel, too. But some points for you:
1- The first thing, you should recognize your crystal symmetry, and choose 
proper ibrav
2- start the input file from PW examples, and change the commands according 
your need.
3- Always, I emphasize, always, check your input file with xcrysden, before you 
run.
4- Use some graphical progrms such as GaussView, VESTA, Materials Studio, ..., 
if you can not recognize the proper position of atoms.
5- Before doing anything, read manuals of the code, run its example, download 
the free tutorials, do the exercises. 

Regards

David Foster

Ph.D. Student of Chemistry


On Fri, 8/7/15, Axel Kohlmeyer <akohl...@gmail.com> wrote:

 Subject: Re: [Pw_forum] error: tcp_peer_recv_connect_ack
 To: "PWSCF Forum" <pw_forum@pwscf.org>
 Date: Friday, August 7, 2015, 10:50 AM
 
 On Fri, Aug 7, 2015 at
 6:08 AM, Mahya Zare <mahyazar...@gmail.com>
 wrote:
 
 please stop flooding
 this mailing list with repeated requests of the
 same kind and particularly stop the extremely
 rude practice of
 hijacking threads on
 completely different topics.
 
 > Dear Users
 > Kindly
 help me how to make Ceo2 nano sheet. I used the lattice
 parameters
 > a=5.411A, C=15.0A, space
 group fm3m (225)
 > and atomic positions
 Ce 0 0 0, and O 1/4 1/4 1/4,O 3/4 3/4 3/4 which are not
 > looks ok. Please help me for makes
 pwscf
 
 your questions are of
 the kind that you should first and foremost
 discuss with your adviser or supervisor. it is
 not the job of a
 mailing list to teach
 people basics of how to do computational
 research and also not to tell you how to do
 your specific research
 project. finding out
 how to do this in both cases are the
 responsibility of yourself and your
 adviser/superviser.
 
 please
 also keep in mind that your violations of common mailing
 list
 courtesy will severely limit your
 chances or getting meaningful help.
 there is
 only a limited pool of people out of all mailing list
 subscribers that answer at all, but your
 behavior will irritate many
 of them and thus
 you should not expect much more help outside of what
 you already got unless you change your ways.
 
 thanks for your understanding
 and cooperation,
 
      
 axel.
 
 
 
 
 >
 >
 Whether the position of atoms in the bulk of nano-sheet
 position of atoms in
 > space is different
 or just by changing the working point in the Brillouin
 > space to aim Rsyd.fayly I send you a
 sample of cerium oxide file is relaxing
 >
 the nano-sheets is it limited to questions can get a full
 mesh? by choosing
 > one of vector network
 as much as 15 angstroms
 >
 > On Fri, Aug 7, 2015 at 1:34 PM, Ludwig,
 Stephan
 > <stephan.lud...@pi1.physik.uni-stuttgart.de>
 wrote:
 >>
 >>
 Hello,
 >>
 >>
 I'm using Quantum-Espresso on a cluster. With
 normconserving
 >> pseudopotentials. I
 don't have any problems.
 >>
 >> With ultrasoft pseudos I also receive
 a result for ecutwfc=60 ecutrho=240
 >>
 (I did it just for test purpuses).
 >>
 >> When I
 enlarge these parameters to more sensible values
 (ecutwfc=80,
 >> ecutrho=800) I receive
 the error message
 >>
 >>
 >>
 [uc1n516:53049] [[53309,1],0] tcp_peer_recv_connect_ack:
 received
 >> different version from
 [[0,62],469762048]: auth/none instead of 1.8.7
 >> I have no idea what that means. Can
 anybody please help me?
 >>
 >>
 >> The
 calculation is interrupted whithin the first scf-step.
 >>
 >> Here is my
 input:
 >>
 >>
 >> 
 >>
 title = 'etot_vs_ecutwfc' ,
 >>
 calculation = 'scf' ,
 >>
 wf_collect = .FALSE.,
 >> restart_mode
 = 'from_scratch',
 >>
 max_seconds = 3.D+5,
 >> outdir =
 './' ,
 >> wfcdir =
 './' ,
 >> pseudo_dir =
 '/home/st/st_st/st_phy72394/pseudo/' ,
 >> prefix =
 'MeDH-TTPetot_vs_ecutwfc' ,
 >>
 /
 >> 
 >> ibrav = -12,
 >>
 A = 32.783 ,
 >> B = 7.995 ,
 >> C = 11.170 ,
 >>
 cosAB = 0 ,
 >> cosAC = -0.132602381688
 ,
 >> cosBC = 0 ,
 >> nat = 236,
 >>
 ntyp = 5,
 >> ecutwfc = 80,
 >> ecutrho = 800,
 >> occupations = 'smearing' ,
 >> degauss = 0.02 ,
 >> smearing = 'gaussian' ,
 >> exxdiv_treatment =
 'gygi-baldereschi' ,
 >> /
 >> 
 >> conv_thr = 1.0D-8
 >> /
 >>
 ATOMIC_SPECIES
 >> H 1.00790
 H.pz-rrkjus_psl.0.1.UPF
 >> C 12.01100
 C.pz-n-rrkjus_psl.0.1.UPF
 >> F
 18.98800 F.pz-n-rrkjus_psl.0.1.UPF
 >>
 S 32.06500 S.pz-n-rrkjus_psl.0.1.UPF
 >> As 74.92200
 As.pz-n-rrkjus_psl.0.2.UPF
 >>
 ATOMIC_POSITIONS angstroms
 >> S
 5.52835 0.29521 2.16999
 >> S 21.91985
 4.29246 2.16999
 >> S 4.78777 7.69929
 7.70567
 >> S 21.17927 3.70204
 7.70567
 

Re: [Pw_forum] keep getting negative frequencies in phonon calculation

[David Foster]

I have encountered such a problem for my studies. Taking care of following 
points may help you:

1- see the stress and pressure for your crystal. its force should be very low.
2- use large cutoff for wfn and rho, even much larger than the converged values 
against energy/atom
or force/atom (1mRy/atom).
3- use very dense k-point grid in scf
4- use very low convergence threshold for scf (10^(-10) for example), and for 
phonon (10^(-14))
5- if after dynmat.x, the acoustic phonons are near to 1cm-1, it is good.
6- taking care of spin-magnetization.

Regards

David Foster

Ph.D. Student of Chemistry


On Sat, 8/8/15, Khalid Ibne Masood Khalid <kimu...@gmail.com> wrote:

 Subject: [Pw_forum] keep getting negative frequencies in phonon calculation
 To: "PWSCF Forum" <pw_forum@pwscf.org>
 Date: Saturday, August 8, 2015, 12:02 AM
 
 Dear
 Researchers,
 I think this is an old problem, but I require your
 advice about how to solve this problem. I am trying to
 calculate the phonon dispersion curve of a 2D insulator
 material, and followed example 02 of phonon program. In the
 ph.x input file I have used:
 
   tr2_ph=1.0d-12,
   ldisp=.true.,
   nq1=2, nq2=2, nq3=1
  
 [increasing nq1 and nq2 will be more complicated]
 
 I have tried almost all types of asr, zero-dim,
 crystal and simple, but yet I am getting negative
 frequencies in the phonon dispersion curve.
 
 Now Sir, what should I do to correct this problem.
 Should ldisp = .false. solve the problem?
 
 Thank you.
 
 Khalid Ibne Masood
 M.Sc student
 BUET
 
 
 
 
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Re: [Pw_forum] Wrong k-string? in nscf+lelfield

[David Foster]

please provide your input file
Regards

David Foster

Ph.D. Student of Chemistry


On Fri, 8/7/15, Mojtaba Mirseraji <quantum.pw...@gmail.com> wrote:

 Subject: [Pw_forum] Wrong k-string? in nscf+lelfield
 To: Pw_forum@pwscf.org
 Date: Friday, August 7, 2015, 9:47 AM
 
 Dear Users
 
 I perform lelfield=.true. option in PWSCF (only in nscf) for
 berry
 calculations of polarization but unfortunately
 " Wrong k-string? "
 error is showed.
 
 I do not know how to solve it
 
 Regards
 
 Mojtaba Mirseraji
 Ph.D. Candidate
 Theoretical Condensed Matter Physics
 Arak Univ.
 IRAN
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[Pw_forum] Q2R code and phonon at gamma

[David Foster]

Dear users,
I calculated phonons at gamma point of a 2*2 supercell of graphene after 
vc-relax>scf.
all frequencies are positive.
Now, I need to use q2r.x code to impose ASR on them.
The ph.x generated one matdyn file which I named it as "graph22G.dyn", 
but q2r.x code searches for graph22G.dyn0. I didn't use grid of q-point, so, I 
only have one dyn file.
I also used the trick of the header of q2r.f90 file, with nr1,nr2,nr3, nfile, 
and filin:
nr1=150, nr2=150, nr3=300
nfile=1
graph22G.dyn
but q2r.x, in this case, shows the error of namelist.

I am not sure that the q2r.x can be used for gamma point only, or it is only 
for grid of q-points.
Should I use phcg.x instead of ph.x for gamma point?
Any guide will be appreciated.



Regards

David Foster

Ph.D. Student of Chemistry
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Re: [Pw_forum] making doc for TDDFPT

[David Foster]

Dear Iurri
thanks, but still two problems
1- I make html for 3 codes (davidson, eels, spectrum), but for lanczos it gives 
error.
2- from makefile in root of QE5.2.0, the doc of TDDFPT are not produced due to 
the 
lack of option doc in TDDFPT/makefile.
Regards

David Foster

Ph.D. Student of Chemistry


On Tue, 8/4/15, Iurii Timrov <itim...@sissa.it> wrote:

 Subject: Re: [Pw_forum] making doc for TDDFPT
 To: "PWSCF Forum" <pw_forum@pwscf.org>
 Cc: "David Foster" <davidfoster...@yahoo.com>
 Date: Tuesday, August 4, 2015, 6:33 AM
 
 Dear David,
 
 On 2015-08-04 09:57, David
 Foster wrote:
 > Dear Developers
 > Please add "doc" option in
 makefile of TDDFPT. It has been forgotten.
 > So, "make doc" doesn't work
 for this directory
 > 
 
 I have added "make doc" and
 "make doc_clean" options in the Makefile of 
 TDDFPT.
 
 >
 For PHONON, "make doc" command only produces
 INPUT_PH and INPUT_D3,
 > but not anything
 for MATDYN and Q2R.
 > 
 > Please add these to the makefile.
 > 
 > 
 > Regards
 > 
 > David Foster
 > 
 > Ph.D. Student of Chemistry
 >
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 Best regards,
 Iurii
 
 -- 
 Dr. Iurii TIMROV
 Postdoctoral
 Researcher
 SISSA - International School for
 Advanced Studies
 Condensed Matter Sector
 Via Bonomea n. 265,
 Trieste
 34151, Italy
 (+39) 04 03 78 74 77
 http://people.sissa.it/~itimrov/
 
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Re: [Pw_forum] problem restarting calculation with hybrid-ultrasoft pseudo potential using QE 5.2

[David Foster]

Dear Behzad

I am not sure I understand correctly your problem. If you mean post-processing 
by "restart" word, then:
You need the former files such as wfn, charge, ... you must insert correctly 
the outdir and prefix in your new input file.

The xml is in outdir/prefix.save.


Regards

David Foster

Ph.D. Student of Chemistry


On Tue, 8/4/15, Behnaz Bagheri <behnaz.bagher...@gmail.com> wrote:

 Subject: [Pw_forum] problem restarting calculation with hybrid-ultrasoft 
pseudo potential using QE 5.2
 To: "PWSCF Forum" <pw_forum@pwscf.org>
 Date: Tuesday, August 4, 2015, 1:31 AM
 
 Dear all, 
 
 I am using the new version of QE 5.2 and I am running
 a "relax" calculation with hybrid xc and ultrasoft
 pseudo potential. The problem is I  cannot restart the
 calculation since It doesn't produce me an *.xml file in
 the output directory. I don't know what is the reason
 for it. Can anybody help me with it?
 
 Best,
 Behnaz
 
 --
 Behnaz Bagheri
 PhD Candidate
 Department
 of Mathematics and Computer Science
 Centre
 for Analysis, Scientific Computing, and Applications
 W
 Technische
 Universiteit Eindhoven
 


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[Pw_forum] making doc for TDDFPT

[David Foster]

Dear Developers
Please add "doc" option in makefile of TDDFPT. It has been forgotten. So, "make 
doc" doesn't work for this directory

For PHONON, "make doc" command only produces INPUT_PH and INPUT_D3, but not 
anything for MATDYN and Q2R.

Please add these to the makefile.


Regards

David Foster

Ph.D. Student of Chemistry
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Re: [Pw_forum] vc-relax calculation

[David Foster]

Dear Elham
For adsorption process, you should follow steps:

1- vc-relax your experimental primitive or conventional cell.

2-cleave your surface by miller indexes, and construct your slab. you must 
provide 15-20 A vacuum
in z-direction.

3- only relax the slab with constrain in z and angles (alpha, beta, gamma).
if you vc-relax the slab, then your z-direction lattice constant will change.
if you model surface, then you must fix position of some 3-5 first layers as a 
bulk.
if you model thin film, then you can relax all atoms, even low layers.

4- take frequencies to be sure that your slab is in local minimum.

5- add you adsorbant on the surface, and repeat steps 3 and 4.

for DOS and BAND you need exact scf and high-k point, respectively.



Regards

David Foster

Ph.D. Student of Chemistry


On Mon, 8/3/15, Elham <e.chemistr...@gmail.com> wrote:

 Subject: Re: [Pw_forum] vc-relax calculation
 To: pw_forum@pwscf.org
 Date: Monday, August 3, 2015, 5:45 AM
 
 Dear David
 Thank
 you very much for  answer my question.
 
 First I vc-relax the
 pure surface (obtain a b c) and then different molecules adsorb on surface do
 vc-relax (a b c) a slightly changed.
 for
 comparison result It is
 problem? Best
 RegardsElhamPh.D. Student of
 Chemistry
 
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Re: [Pw_forum] vc-relax calculation

[David Foster]

Dear Elham,
Relaxation only minimizes ion positions+electronic charges, and not lattice 
constants (a,b,c).
If you initiate from experimental structures, I propose to do VC-RELAX.
During vc-relax, it is possible that a,b,c,alpha,beta, and gamma to be changed.
If you relax a structure, and then change its composition (for example, doped 
one atom inside it), it depends that what you want. For example, if you have a 
slab for which some layers act as bulk, you should not use vc-relax. But if you 
use a sheet such as graphene, you can use vc-relax but with constrain in z axis.
Regards

David Foster

Ph.D. Student of Chemistry


On Sun, 8/2/15, Elham <e.chemistr...@gmail.com> wrote:

 Subject: [Pw_forum] vc-relax calculation
 To: pw_forum@pwscf.org
 Date: Sunday, August 2, 2015, 10:16 PM
 
 Dear PWSCF experts
 and PWSCF users
 Is necessary do vc-relax calculation after the
 relax calculation  for electronic
 calculation (band,dos,..)?
 What is necessary do vc-relax
 calculation?
 Thanks so muchElham
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[Pw_forum] error and negative frequencies in phonons of Fe-doped graphene

[David Foster]

%
 Error in routine write_dfile_star (1):
 this subroutine produces random garbage without symmetry!
 %%

 %%
 Error in routine write_dfile_star (1):
 this subroutine produces random garbage without symmetry!
 %%%%%%

 stopping ...
==
Any help?

   


Regards

David Foster

Ph.D. Student of Chemistry
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Re: [Pw_forum] Magnetization on the Fe atom doped on the graphene

[David Foster]

Dear Pang,

Thank you for your kindness. I will correct the input and report the corrected 
total_magnetization, as soon as possible. 

However, I think total_magnetization should not be changed, due to the approach 
I took in my previous calculation (I have not fixed it, and the correct value 
calculated from SCF). So, output from start_magnetization=0 is equal to 
start_magnetization=0.5 or any other values. 

I have a question about this subject:

In chemistry, we discuss about spin multiplicity for molecules (clusters). But, 
in solid state physics, we discuss about magnetic moment.
What is the relationship between spin multiplicity and magnetic moment, if we 
want to calculate a cluster model with QE?

I am not sure, but, I think, if we take Stot=sigma(Si) as the total spin of 
electrons, the spin multiplicity is 2Stot+1, and the magnetic moment is 2*Stot, 
which is summation of number of spin-up electrons minus summation of number of 
spin-down electrons.

See Stefano de Gironcoli comment:
(http://qe-forge.org/pipermail/pw_forum/2003-March/074663.html)

TM = \int (n_up-n_down) d^3r  (from Stefano, TM is total_magnetization)

Am I right?

For, example, for triplet state (Stot=1) of a molecule, we should take the 
total_magnetization of 2 (which has 2*Stot relationship). For example, see 
following posts:

http://qe-forge.org/pipermail/pw_forum/2013-September/102317.html

http://qe-forge.org/pipermail/pw_forum/2006-May/078792.html


Now, about my run (4*4 graphene sheet+one Fe doped atom), I have 4 unpaired 
electron (d6 from Fe). So, I should get total_magnetization near to 4 
bohr-magneton. Is it right?


=
Regards

David Foster
Ph.D. Student of Chemistry
=

On Fri, 7/17/15, 庞瑞(PANG Rui) <pan...@sustc.edu.cn> wrote:

 Subject: Re: [Pw_forum] Magnetization on the Fe atom doped on the graphene
 To: "PWSCF Forum" <pw_forum@pwscf.org>
 Date: Friday, July 17, 2015, 11:54 PM
 
 Dear David 
 You set
 "starting_magnetization(3)=0.5", but you only have
 two elements. Therefore , the starting_magnetization of Fe
 is actually zero. 
 Best wishes.
 Pang Rui
 
 
 
 
 --庞瑞(PANG Rui)South
 University of Science and Technology of China/Department of
 PhysicsNo.1088,Xueyuan
 Road, Shenzhen,Guangdong
    -- Original ------From:  "David
 Foster"<davidfoster...@yahoo.com>;Date:
  Fri, Jul 17, 2015 08:44 PMTo:
  "pw_forum"<pw_forum@pwscf.org>;
 Subject:
  [Pw_forum] Magnetization on the Fe atom doped on the
 graphene Dear Users
 
 I have doped one Fe atom in
 the supercell of graphene, and used
 "starting_magnetization" keyword (due to the
 electronic configuration of Fe which is 4s2 3d6).
 
 Here it is my input:
 
 =
 
   
 title = 'graph44'
  calculation =
 'vc-relax'
     restart_mode =
 'from_scratch'
  
 outdir = './graph44_relax'
   pseudo_dir =
 './'
  
 prefix = 'graph44'
 
 disk_io = 'default'
    verbosity
 = 'default'
   
 etot_conv_thr=1.0D-6
   
 forc_conv_thr=1.0D-2
   
 nstep=1000
   
 tstress=.true.
   
 tprnfor=.true.
 /
  
   
 ibrav = 4
   
 nat = 32
   
 celldm(1)=18.783876326
   
 celldm(3)=2.004008
  
 ntyp = 2
 
 ecutwfc = 75
 
 ecutrho = 500
   
 starting_magnetization(1)=0.5
   
 starting_magnetization(3)=0.5
  
 nspin=2
  
 occupations='smearing'
  
 degauss=0.02
  
 smearing='mv'
   
 nbnd=160
   
 
 /
  
     electron_maxstep =
 1000
    
 conv_thr = 1.0D-7
  mixing_mode =
 'plain'
  mixing_beta =
 0.5
 
 mixing_ndim = 15
 
 diagonalization = 'david'
 /
  
     ion_dynamics =
 'bfgs'
 /
  
     cell_dynamics =
 'bfgs'
    
 cell_dofree='2Dxy'
 /
 ATOMIC_SPECIES
    C  
 12.0107 C.pbe-n-rrkjus_psl.1.0.0.UPF
    Fe  55.845 
 Fe.pbe-spn-rrkjus_psl.1.0.0.UPF
 
 ATOMIC_POSITIONS crystal
  
 C   0.0827257631375200   0.1654515262750400  
 0. 1 1 0
   C  
 0.1654515262077270   0.0827257630794374  
 0. 1 1 0
   C  
 0.3309030525741389   0.1654515262750400  
 0. 1 1 0
   C  
 0.4136288157449489   0.0827257630794371  
 0. 1 1 0
   C  
 0.5790803421113629   0.1654515262750400  
 0. 1 1 0
   C  
 0.6618061051815698   0.0827257630794374  
 0. 1 1 0
   C  

[Pw_forum] Magnetization on the Fe atom doped on the graphene

[David Foster]

here is 4 unpaired electron). But, I got 0.01 
Bohr-magneton. Any help?


Regards

David Foster

Ph.D. Student of Chemistry

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[Pw_forum] parallel version for Windows

[David Foster]

Dear Axel

Thanks for your effort for providing the windows version. Until now, I ran the 
linux version which had been compiled with ifort, intelmpi, icc on a cluster of 

CentOs6.5. I downloaded windows version last day, and did according your user 
guide (installing mpich2, ...).

 I ran sample input for a SMP system with 16 core. It was interesting and very 
simple. However, I have a question:

Is it possible to use HPC tools to run the program through a windows cluster. 
What should I do? 

Regards

David Foster

Ph.D. Student of Chemistry
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Re: [Pw_forum] Slab optimization with -24kbar stress!!!

[David Foster]

Dear Serge
Thank you for your help. I think the best judge for this issue is experimental 
data for adsorption process, as you noted.

Thank you Nicola, Cyrille, and Serge for your helps.

Regards

David Foster

Ph.D. Student of Chemistry


On Fri, 12/5/14, Serge Nakhmanson <s...@ims.uconn.edu> wrote:

 Subject: Re: [Pw_forum] Slab optimization with -24kbar  stress!!!
 To: "PWSCF Forum" <pw_forum@pwscf.org>
 Date: Friday, December 5, 2014, 7:36 PM
 
 On 12/5/14 10:36 AM,
 David Foster wrote:
 > If I do according
 to the published works, I get large stress, as it was
 discussed in previous long discussion.
 >
 If I do according to Nicola's advice, the stress
 eventually reduces, but the bottom layers positions will not
 be the bulk ones.
 > Which one is
 correct?
 >
 David,
 
 I do not think you are asking
 the right question here.
 
 IMO, the appropriate question is: what elastic
 condition on my system do I want 
 to
 simulate?
 
 If you want to do
 a surface that is rigidly clamped to the bulk, you will get
 
 (correctly!) non-zero residual stress.
 BTW, a 24 kBar stress is not large, unless you
 got a very soft system like a 
 polymer/molecular crystal.
 
 If you want to do a surface that is completely
 relaxed, do a vc-relax on your 
 slab and get
 rid of the stress completely.
 
 Finally, you can also do a partially relaxed
 surface and get a stress that is 
 somewhere
 in between.
 
 I am not an
 expert on CeO, but could imagine that all of these cases may
 be 
 appropriate -- depending on what you
 are after. The latter is for you and your
 advisor (I hope you got one?) to 
 figure
 out. Usually you have to take hint
 from
 experiments, i.e., find out what sort of films and surfaces
 
 experimentalists are dealing with, and
 then
 decide how you can mimic this in your
 simulation.
 
 S.
 
 -- 
 Serge M. Nakhmanson
 Dep-t of Materials Science & Engineering,
 and Institute of Materials Science
 University of Connecticut
 Storrs, CT 06269-3136
 Phone:
 (860) 486-5252
 http://satori.ims.uconn.edu/
 
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Re: [Pw_forum] Slab optimization with -24kbar stress!!!

[David Foster]

Dear Cyrille, Nicola, and Serge
Thanks for your helps.
My main problem comes back to the computational method section in scholarly 
papers.
In adsorption of molecules on surfaces, authors say that they cleave a surface 
from fully optimized (vc-relax) unit cell, enlarge it 2*2 or
3*3 times in u and v directions, and then define 15-20 angstrom vacuum in the z 
direction. 
Then all of them take 2-4 bottom layers fixed to represent bulk, and only relax 
(and not vc-relax) other atoms containing 
adsorbed molecule. 
If I do according to the published works, I get large stress, as it was 
discussed in previous long discussion.
If I do according to Nicola's advice, the stress eventually reduces, but the 
bottom layers positions will not be the bulk ones.
Which one is correct?
Serge, maybe in the links you have provided this issue has been addressed. I 
will read them.

Regards

David Foster

Ph.D. Student of Chemistry


On Fri, 12/5/14, Serge Nakhmanson <s...@ims.uconn.edu> wrote:

 Subject: Re: [Pw_forum] Slab optimization with -24kbar stress!!!
 To: "PWSCF Forum" <pw_forum@pwscf.org>
 Date: Friday, December 5, 2014, 5:24 PM
 
 
 On 12/5/14 5:11 AM,
 David Foster wrote:
 
 
 
   
 1- Cyrille, I fixed both in-plane and z-direction lattice
 constants. I need to fix the 15A vacuum in the z to prevent
 periodic interactions for studying adsorption.
 
 
 
 
 Dear David,
 
 
 
 Just my 2 cents to add to this.
 
 
 
 (a) Residual surface stress is a perfectly
 "legal" quantity. Some
 people hunt for it (as well as for the surface elastic
 constants)
 
 specifically with DFT. You can check it out here:
 
 
 
 http://dx.doi.org/10.1103/PhysRevB.71.094104
 
 
 
 or here
 
 
 
 http://dx.doi.org/10.1016/j.cma.2010.09.007
 
 
 
 It is a lot of fun! :)
 
 
 
 
 
 (b) You have to be *extremely careful* when attaching
 something (a
 molecule?) to your surface, as this will open a
 
 new can of worms. You will need to check if your
 combined system is
 likely to have a dipole moment pointing perpendicularly
 to
 
 the slab -- and it might. Then you may have to keep an
 xy mirror
 plane running through the middle of your slab [adding
 many more
 
 atoms to the calculation] or apply a dipole correction
 [makes
 calculation convergence much slower]
 
 to get rid of it. If you don't, you run a chance of
 having a
 spurious electric field in vacuum due to interaction
 between the
 
 polarized slab and is periodic images.
 
 
 
 There is an old paper that comments on the situation:
 
 
 
 http://dx.doi.org/10.1103/PhysRevB.63.205426
 
 
 
 but much more had been published since then.
 
 
 
 The really graceful way of studying slabs involves using
 a code that
 can do 2D PBC in plane and break periodicity along
 the
 
 perpendicular direction. But then you have to abandon
 the PW basis
 -- i.e., codes like VASP and QE -- and use something
 else.
 
 
 
 HTH,
 
 
 
 Serge
 
 
 
 
 
 
   -- 
 
 Serge M. Nakhmanson 
 
 Dep-t of Materials Science & Engineering, and
 Institute of
 Materials Science 
 
 University of Connecticut 
 
 Storrs, CT 06269-3136 
 
 Phone: (860) 486-5252 
 
 http://satori.ims.uconn.edu/
 
 
 
   
 
   
 -Inline Attachment Follows-
 
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Re: [Pw_forum] Slab optimization with -24kbar stress!!!

[David Foster]

Dear Nicola and Cyrille

Thanks for your help. But:

1- Cyrille, I fixed both in-plane and z-direction lattice constants. I need to 
fix the 15A vacuum in the z to prevent periodic interactions for studying 
adsorption.
As Nicola said, it is possible to relax in-plane lattice constants, but 
what do you mean with this sentence: 
  "you should zero stress in the direction 
perpendicular to the surface" 
Do you mean relaxation in z-direction?!! It is vacuum, and if I do it, the 
vacuum thickness reduces and this is not my purpose.
 
I converged smearing, k-point, wave function energy-cutoff and ... in the 
unit cell with 1mRY of total energy, and then used appropriate k-point
for 2*2 surface slab, i.e., for z-direction I used 1 (due to the vacuum in 
z), and for x and y directions, I used half of the k-points for conventional 
cell
(because of double-sizing "a" and "b" in 2*2 surface slab). Do you mean 
that I should converge them with stress value, too?

2- Nicola, Yes, It seems that I need to use z-constrained vc-relax to minimize 
the in-plane stress. I will do it, and check its stress.
   But for your second comment, I constructed the slab by using fully optimized 
conventional cell (with vc-relax command). I don't think their plane
   are very close. About your final comment, Do you mean I should change the 
atoms positions in the z-direction and repeat z-constrained vc-relax?


   Regards

   David Foster

   Ph.D. Student of Chemistry


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Re: [Pw_forum] Slab optimization with -24kbar stress!!!

[David Foster]

 -0.00032173   0.  0.00-47.33  0.00
  -0.   0.  -0.00010117 -0.00  0.00-14.88


 bfgs converged in  19 scf cycles and  18 bfgs steps
 (criteria: energy <  1.0E-09, force <  1.0E-04)

 End of BFGS Geometry Optimization

 Final energy   =  -12030.2278842492 Ry
Begin final coordinates

ATOMIC_POSITIONS (crystal)
O0.12500   0.0   0.00   0   0
O0.12500   0.0   0.1562436470   0   0
O0.124894956   0.0   0.314126336
O0.37500   0.25000   0.2343654700   0   0
O0.37500   0.25000   0.0781218230   0   0
O0.381640476   0.24895   0.391672517
O0.37500   0.0   0.00   0   0
O0.37500  -0.0   0.1562436470   0   0
O0.375105056   0.0   0.314126337
O0.12500   0.25000   0.2343654700   0   0
O0.12500   0.25000   0.0781218230   0   0
O0.118359527   0.24893   0.391672516
O0.62500  -0.0   0.00   0   0
O0.62500  -0.0   0.1562436470   0   0
O0.624894944  -0.0   0.314126337
O0.87500   0.25000   0.2343654700   0   0
O0.87500   0.25000   0.0781218230   0   0
O0.881640473   0.24893   0.391672516
O0.87500  -0.0   0.00   0   0
O0.87500  -0.0   0.1562436470   0   0
O0.875105044  -0.0   0.314126336
O0.62500   0.25000   0.2343654700   0   0
O0.62500   0.25000   0.0781218230   0   0
O0.618359524   0.24895   0.391672517
O0.12500   0.5   0.00   0   0
O0.12500   0.5   0.1562436470   0   0
O0.124894991   0.5   0.314126379
O0.37500   0.75000   0.2343654700   0   0
O0.37500   0.75000   0.0781218230   0   0
O0.381640476   0.75105   0.391672517
O0.37500   0.5   0.00   0   0
O0.37500   0.5   0.1562436470   0   0
O0.375105021   0.5   0.314126380
O0.12500   0.75000   0.2343654700   0   0
O0.12500   0.75000   0.0781218230   0   0
O0.118359527   0.75107   0.391672516
O0.62500   0.5   0.00   0   0
O0.62500   0.5   0.1562436470   0   0
O0.624894979   0.5   0.314126380
O0.87500   0.75000   0.2343654700   0   0
O0.87500   0.75000   0.0781218230   0   0
O0.881640473   0.75107   0.391672516
O0.87500   0.5   0.00   0   0
O0.87500   0.5   0.1562436470   0   0
O0.875105009   0.5   0.314126379
O0.62500   0.75000   0.2343654700   0   0
O0.62500   0.75000   0.0781218230   0   0
O0.618359524   0.75105   0.391672517
Ce   0.0   0.0   0.0781218230   0   0
Ce   0.0   0.0   0.2343654700   0   0
Ce   0.0  -0.0   0.385984246
Ce   0.25000   0.25000   0.00   0   0
Ce   0.25007   0.24867   0.317491908
Ce   0.25000   0.25000   0.1562436470   0   0
Ce   0.5  -0.0   0.0781218230   0   0
Ce   0.5  -0.0   0.2343654700   0   0
Ce   0.5  -0.0   0.385984250
Ce   0.75000   0.25000   0.00   0   0
Ce   0.74993   0.24867   0.317491908
Ce   0.75000   0.25000   0.1562436470   0   0
Ce   0.0   0.5   0.0781218230   0   0
Ce   0.0   0.5   0.2343654700   0   0
Ce   0.0   0.5   0.385984123
Ce   0.25000   0.75000   0.00   0   0
Ce   0.25007   0.75133   0.317491908
Ce   0.25000   0.75000   0.1562436470   0   0
Ce   0.5   0.5   0.0781218230   0   0
Ce   0.5   0.5   0.2343654700   0   0
Ce   0.5   0.5   0.385984125
Ce   0.75000   0.75000   0.00   0   0
Ce   0.74993   0.75133   0.317491908
Ce   0.75000   0.75000   0.1562436470   0   0
End final coordinates

=====


Regards

David Foster

Ph.D. Student of Chemistry


On Thu, 12/4/14, Paolo Giannozzi <paolo.gianno...@uniud.it> wrote:

 Subject: Re: [Pw_forum] Slab optimization with -24kbar stress!!!
 To: "PWSCF Forum" <pw_forum@pwscf.org>
 Date: Thursday, December 4, 2014, 11:40 PM
 
 On Thu, 2014-12-04 at 10:2

[Pw_forum] Slab optimization with -24kbar stress!!!

[David Foster]

:

==
.
.
.
atom   71 type  2   force = 0.0009   -0.0005   -0.0464
 atom   72 type  2   force =-0.00040.01180.00769631

 Total force = 0.43 Total SCF correction = 0.01


 entering subroutine stress ...


 negative rho (up, down):  7.323E-04 7.323E-04
  total   stress  (Ry/bohr**3)   (kbar) P=  -24.51
  -0.7691   0.  -0.-11.31  0.00 -0.00
   0.  -0.00032173   0.  0.00-47.33  0.00
  -0.   0.  -0.00010117 -0.00  0.00-14.88


 bfgs converged in  19 scf cycles and  18 bfgs steps
 (criteria: energy <  1.0E-09, force <  1.0E-04)

 End of BFGS Geometry Optimization
.
.
==

As you see final stress is -24.51 kbar ??!!
As you know, for slab, we don't used "vc-relax", and only optimize ions 
positions. What should I do to reduce the stress on the slab?
 


Regards

David Foster
Ph.D. Student of Chemistry
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[Pw_forum] About BFGS optimized structure

[David Foster]

Dear Users
I have two questions:
1) I use QE5.1, and optimized CeO2 primitive cell. We all know that after 
getting final optimized structure, QE does an extra scf with new cell 
parameters. My last energy (with new cell parameters) and optimized one 
difference is about 0.1RY. Now, do I need a new vc-relax calculation with 
previous parameters as input? 

this is my input cell parameter of vc-relax calculation:
=
 celldm(1)=  10.225308  celldm(2)=   0.00  celldm(3)=   0.00
 celldm(4)=   0.00  celldm(5)=   0.00  celldm(6)=   0.00

crystal axes: (cart. coord. in units of alat)
   a(1) = (  -0.530413   0.25   0.530403 )  
   a(2) = (   0.52   0.530414   0.530414 )  
   a(3) = (  -0.530413   0.530403   0.25 )  


  site n. atom  positions (cryst. coord.)
 1   O   tau(   1) = (  0.290  0.270  0.290  )
 2   O   tau(   2) = ( -0.250 -0.250  0.750  )
 3   Ce  tau(   3) = (  0.000  0.000  0.000  )
=


and this is my optimized vc-relax output:
===
CELL_PARAMETERS (alat= 10.22530811)
  -0.530413331   0.24549   0.530403418
   0.52398   0.530413516   0.530413516
  -0.530413331   0.530403418   0.24549

ATOMIC_POSITIONS (crystal)
O0.263099905   0.256909491   0.263099905
O   -0.236877222  -0.243128052   0.763122778
Ce   0.013777317   0.006218561   0.013777317
End final coordinates
=


My last extra scf force and stress are (with the final optimized cell):
==
Total force = 0.003745 Total SCF correction = 0.00

 entering subroutine stress ...

  total   stress  (Ry/bohr**3)   (kbar) P=   26.51
   0.00017290  -0.0007  -0.0007 25.43 -0.01 -0.01
  -0.0007   0.00018388  -0.0007 -0.01 27.05 -0.01
  -0.0007  -0.0007   0.00018388 -0.01 -0.01 27.05
==

2) I used ibrav=2 in above calculation, and changed the experimental positions 
of one oxygen atom to change the crystal structure from its stable form (I need 
to do this, because with experimental data, I always get the input structure 
after doing vc-relax). Now, I need to change the primitive cell to its 
conventional. I used xcrysden and VESTA, but they only show the primitive 
structure. How can I change the QE output to its conventional cell. 

Regards

David Foster

Ph.D. Student of Chemistry
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[Pw_forum] A "relax" input runs on CPU (pw.x) but not on CPU-GPU (pw-gpu.x)

[David Foster]

Dear Axel
I have some questions in this topic, too. Suppose we use a poor DP floating 
point performance GTX cards for QE-GPU. Does the codes in 
GPU technology of nVIDIA (such as CUDA and ...) change the DP of QE to SP 
automatically?  or program ended with error.
If it changes DP to SP automatically, users might get wrong results without any 
attention.

How about a full SP GPU card for full DP code? Does code run on it?

Regards

David Foster

Ph.D. Student of Chemistry


On Sat, 6/21/14, Axel Kohlmeyer  wrote:

 Subject: Re: [Pw_forum] A "relax" input runs on CPU (pw.x) but not on  CPU-GPU 
(pw-gpu.x)
 To: "PWSCF Forum" 
 Date: Saturday, June 21, 2014, 2:20 AM
 
 On Sat, Jun 21, 2014 at 4:20 AM, Reza
 Behjatmanesh-Ardakani
 
 wrote:
 > Dear Axel
 > This was just a proposal. If I am right, Terachem code
 can use gaming cards for GPU calculations (I saw some of its
 authors' papers).
 
 yes, but terachem was written from ground up with new
 algorithms to
 avoid loss of precision. in quantum mechanics this is
 important, since
 a lot of calculations depend on comparing large numbers of
 equal sign
 and magnitude and looking at the difference. about the only
 part of a
 plane wave DFT calculation that is "conservative" in terms
 of
 precision without a massive redesign are the FFTs. the loss
 of
 precision is fairly small when replacing double precision
 FFTs with
 single precision ones. for the many 3d-FFTs required, this
 is
 particularly beneficial when trying to scale out via MPI, as
 this
 reduces the amount of bytes that need to be sent and copied
 around in
 half and also reduces the strain on memory bandwidth.
 
 > As you know, the main problem of GTX cards comes back
 to two important things. One, single precision, and the
 other lack of ECC.
 
 ECC is a lesser issue. and it is not a problem of single
 precision,
 but lack of performance with double precision due to having
 only a
 fraction of double precision units. another issue is the
 lack of RAM.
 also you have to distinguish between different GTX cards. a
 few of the
 most high-end consumer cards? *do* have the full set of
 double
 precision units and a large amount of RAM.
 
 ECC is mostly relevant for people running a large number of
 GPUs in a
 supercomputer environment.
 
 >
 > It is not necessary to write a stand alone code. We can
 test the QE-GPU with both TESLA and/or GTX and QE (cpu
 only), and compare the outputs.
 
 but it is pointless to run on a hardware that is not
 competitive.
 you'll have a hard time already to get a 2x speedup from
 using a top
 level tesla card vs. an all CPU run on a decent machine.
 what would be
 the point of having the GPU _decelerate_ your calculation?
 
 in general, a lot of the GPU stuff is hype and
 misinformation. the
 following is a bit old, but still worth a read:
 
http://www.hpcwire.com/2011/12/13/ten_ways_to_fool_the_masses_when_giving_performance_results_on_gpus/
 
 as a consequence of a very smart and successful PR strategy,
 there is
 now the impression that *any* kind of GPU will result in a
 *massive*
 speedup. even people with a laptop GPU with 2 SMs, no memory
 bandwidth
 are now expecting 100x speedups and more. however, except
 for a few
 corner cases and applications that are very well represented
 on GPUs
 (not very complex) and badly on a CPU, you will often get
 more like a
 2x-5x speedup in a "best effort" comparison of a well
 equipped host
 with a high-end GPU. in part, this situation has become
 worse with
 some choices made by nvidia hardware and software engineers.
 while 5
 years back, the difference between a consumer and a
 computing GPU was
 small, the consumer models have been systematically
 "downgraded" (via
 removing previously supported management features in the
 driver and
 having consumer cards be based on a simplified design that
 mostly
 makes them mid-level GPUs).
 
 > I tested it for only one case (rutile 3*3*2 supercell),
 and saw that the GTX output is similar to the CPU one.
 >
 > However, It is needed to test for different cases and
 different clusters to be sure that the lack of ECC and
 double precision has no effect on results.
 
 sorry, this statement doesn't make any sense. it looks to
 me, like you
 need to spend some time learning what the technical
 implications of
 ECC and single-vs-double precision are (and the fact that it
 is the
 software that chooses which precision is used, not the
 hardware)..
 
 whether a card has ECC or not. broken memory is broken
 memory. and if
 it works, it works. so there is not much to test. if you
 want to find
 out, whether your GPU has broken or borderline memory, run
 the GPU
 memtest. it is much more effective at finding issues than
 any other
 application.
 
 where ECC helps is for very long running calculations or
 calculations
 across a very large number of GPUs when a single bitfli

[Pw_forum] ibrav7 doesn't show the structure of BaNi2As2 correctly

[David Foster]

Dear Tone
Thank you. It was very helpful.
Regards

David Foster

Ph.D. Student of Chemistry


On Wed, 5/28/14, Tone Kokalj  wrote:

 Subject: Re: [Pw_forum] ibrav7 doesn't show the structure of BaNi2As2 correctly
 To: pw_forum at pwscf.org
 Date: Wednesday, May 28, 2014, 1:25 PM
 
 On Wed, 2014-05-28 at 10:43 -0700,
 David Foster wrote:
 >? Dear Prof. Kokalj
 > 
 > Maybe this question bored you, but it is important for
 me. Sorry for any inconvenience. 
 > 
 > Would you please give me more information that how to
 recognize the difference in the lattice definition. 
 > If I am right in both softwares (QE and MS) A=B 
 > So, how did you recognize the difference? 
 
 Actually I didn't (at least initially). But from experience
 I know that
 such kinds of problems are typically due to mismatches in
 lattice
 definitions. Your reference to A=Bhttp://www.gnu.org/philosophy/no-word-attachments.html
 
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[Pw_forum] ibrav7 doesn't show the structure of BaNi2As2 correctly

[David Foster]

 Dear Prof. Kokalj

Maybe this question bored you, but it is important for me. Sorry for any 
inconvenience. 

Would you please give me more information that how to recognize the difference 
in the lattice definition. If I am right in both softwares (QE and MS) A=B wrote:

 Subject: Re: [Pw_forum] ibrav7 doesn't show the structure of BaNi2As2 correctly
 To: pw_forum at pwscf.org
 Date: Wednesday, May 28, 2014, 9:25 AM
 
 On Wed, 2014-05-28 at 08:51 -0700,
 David Foster wrote:
 > Dear Prof. Kokalj
 > Thank you very much for your kindness. I checked the
 positions that I gathered from MS Visualizer to prepare
 ibrav=7 input. 
 
 Don't know what is MS Visualizer. Anyway I took a closer
 look and
 realized that the problem is the lattice definition, which
 is different
 in the two cases (MS Visualizer vs QE). All you need to do
 is to swap
 the columns, i.e., this will work for ibrav=7:
 
 ATOMIC_POSITIONS crystal
 ? Ba? ? 0.0? ?
 0.0???0.0
 ? As? ? 0.0? ?
 0.34710???0.34710
 ? As? ? 0.0? ?
 0.65290???0.65290
 ? Ni? ? 0.5? ?
 0.75000???0.25000
 ? Ni? ? 0.5? ?
 0.25000???0.75000
 
 
 Regards, Tone
 -- 
 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 mailing list
 Pw_forum at pwscf.org
 http://pwscf.org/mailman/listinfo/pw_forum
 

[Pw_forum] ibrav7 doesn't show the structure of BaNi2As2 correctly

[David Foster]

Dear Prof. Kokalj

Thank you for your help. The problem is solved with your help.

Thanks again.

Regards

David Foster

Ph.D. Student of Chemistry


On Wed, 5/28/14, Tone Kokalj  wrote:

 Subject: Re: [Pw_forum] ibrav7 doesn't show the structure of BaNi2As2 correctly
 To: pw_forum at pwscf.org
 Date: Wednesday, May 28, 2014, 9:25 AM
 
 On Wed, 2014-05-28 at 08:51 -0700,
 David Foster wrote:
 > Dear Prof. Kokalj
 > Thank you very much for your kindness. I checked the
 positions that I gathered from MS Visualizer to prepare
 ibrav=7 input. 
 
 Don't know what is MS Visualizer. Anyway I took a closer
 look and
 realized that the problem is the lattice definition, which
 is different
 in the two cases (MS Visualizer vs QE). All you need to do
 is to swap
 the columns, i.e., this will work for ibrav=7:
 
 ATOMIC_POSITIONS crystal
 ? Ba? ? 0.0? ?
 0.0???0.0
 ? As? ? 0.0? ?
 0.34710???0.34710
 ? As? ? 0.0? ?
 0.65290???0.65290
 ? Ni? ? 0.5? ?
 0.75000???0.25000
 ? Ni? ? 0.5? ?
 0.25000???0.75000
 
 
 Regards, Tone
 -- 
 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 mailing list
 Pw_forum at pwscf.org
 http://pwscf.org/mailman/listinfo/pw_forum
 

[Pw_forum] ibrav7 doesn't show the structure of BaNi2As2 correctly

[David Foster]

Dear Prof. Kokalj
Please change .bin extensions to .cif to see the files.
Regards

David Foster

Ph.D. Student of Chemistry


On Tue, 5/27/14, Tone Kokalj  wrote:

 Subject: Re: [Pw_forum] ibrav7 doesn't show the structure of BaNi2As2 correctly
 To: pw_forum at pwscf.org
 Date: Tuesday, May 27, 2014, 11:56 PM
 
 On Tue, 2014-05-27 at 10:50 -0700,
 David Foster wrote:
 > Dear Prof. Kokalj
 > Thank you again for your guide. I usually use it, but
 introducing 0<ibrav<14 in cases which there are
 symmetry, increases speed of calculations.
 
 In this case, one way to convert is this: first convert
 from
 "crystal-conventional" coordinates to Cartesian and then
 from Cartesian
 to "crystal-primitive". This involves a bit of matrix
 algebra and
 "octave" program comes very handy in this respect.
 
 Regards.
 -- 
 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 mailing list
 Pw_forum at pwscf.org
 http://pwscf.org/mailman/listinfo/pw_forum
 

[Pw_forum] ibrav7 doesn't show the structure of BaNi2As2 correctly

[David Foster]

Dear Prof. Kokalj
Thank you very much for your kindness. I checked the positions that I gathered 
from MS Visualizer to prepare ibrav=7 input. I have attached two cif files, one 
belonging to primitive_p1, and the other belonging to conventional_p1 (here p1 
means no symmetry or all atoms). Both files I generated from MS. You can see 
that the lattice parameters that have been used for crystal positions of atoms 
(from primitive_p1.cif) all belong to the primitive. Please check the files.
If the files areopened with other programs such as Vesta, you can see the 
positions of file primitive_p1.cif are relative to primitive translational 
vectors.
It will be appreciated if you help.
PS: I generated nanotube (ibrav=12) by this method and everything is OK. If it 
is necessary, I can send it too.
Thanks again, and sorry for delay. 

Regards

David Foster

Ph.D. Student of Chemistry


On Tue, 5/27/14, Tone Kokalj  wrote:

 Subject: Re: [Pw_forum] ibrav7 doesn't show the structure of BaNi2As2 correctly
 To: pw_forum at pwscf.org
 Date: Tuesday, May 27, 2014, 11:56 PM
 
 On Tue, 2014-05-27 at 10:50 -0700,
 David Foster wrote:
 > Dear Prof. Kokalj
 > Thank you again for your guide. I usually use it, but
 introducing 0<ibrav<14 in cases which there are
 symmetry, increases speed of calculations.
 
 In this case, one way to convert is this: first convert
 from
 "crystal-conventional" coordinates to Cartesian and then
 from Cartesian
 to "crystal-primitive". This involves a bit of matrix
 algebra and
 "octave" program comes very handy in this respect.
 
 Regards.
 -- 
 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 mailing list
 Pw_forum at pwscf.org
 http://pwscf.org/mailman/listinfo/pw_forum
-- next part --
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[Pw_forum] ibrav7 doesn't show the structure of BaNi2As2 correctly

[David Foster]

Dear Prof. Kokalj
Thank you again for your guide. I usually use it, but introducing 0<ibrav<14 in 
cases which there are symmetry, increases speed of calculations.

So, I need a way to change the output of MS Visualizer primitive atoms 
positions to be usable for QE.

Thanks again
 
Regards

David Foster

Ph.D. Student of Chemistry


On Tue, 5/27/14, Tone Kokalj  wrote:

 Subject: Re: [Pw_forum] ibrav7 doesn't show the structure of BaNi2As2 correctly
 To: pw_forum at pwscf.org
 Date: Tuesday, May 27, 2014, 8:39 AM
 
 On Tue, 2014-05-27 at 08:21 -0700,
 David Foster wrote:
 > Dear Tone and Giovanni
 > 
 > thank you for your helps. So, how can I correct crystal
 positions by using v1, v2, and v3?
 
 My advice is the following: given the fact that ibrav>0
 cases always
 depend on the definition of the hard-coded lattices and
 conventions, I
 almost always use ibrav=0 + CELL_PARAMETERS. This way the
 user
 controls/specifies the structure the way he/she sees fit.
 
 Regards,
 -- 
 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 mailing list
 Pw_forum at pwscf.org
 http://pwscf.org/mailman/listinfo/pw_forum
 

[Pw_forum] ibrav7 doesn't show the structure of BaNi2As2 correctly

[David Foster]

Dear Tone and Giovanni

thank you for your helps. So, how can I correct crystal positions by using v1, 
v2, and v3?
Regards

David Foster

Ph.D. Student of Chemistry


On Tue, 5/27/14, Giovanni Pizzi  wrote:

 Subject: Re: [Pw_forum] ibrav7 doesn't show the structure of BaNi2As2 correctly
 To: "PWSCF Forum" 
 Date: Tuesday, May 27, 2014, 7:28 AM
 
 
   
 
 
   
   
 Dear David,
 
   I think that the relative (crystal) coordinates that
 you write for
   the 5-atom cell are still expressed in terms of the
 conventional
   cell (the one with vectors (a,0,0), (0,a,0), (0,0,c).
 This is the
   cell used in the case ibrav=14, reason for which you
 get the
   correct structure.
 
   
 
   Instead, the cell used in ibrav=7 is the primitive one
 - the docs
   say:
 
   
 
   v1=(a/2)(1,-1,c/a),? v2=(a/2)(1,1,c/a),?
 v3=(a/2)(-1,-1,c/a)
 
   
 
   Therefore you have to express the relative (crystal)
 coordinates
   with respect to this basis set, and not in terms of
 the lattice
   vectors of the conventional cell.
 
   
 
   Best,
 
   
 
   Giovanni Pizzi
 
   
 
   
 
   
 
   On 05/27/2014 03:48 PM, David Foster wrote:
 
 
 
   Dear users
 
 The atomic positions for BaNi2As2 crystal with space group
 of I4/mmm (139) are:
 
 Ba (2a): 0, 0,   0 
 As (4e): 0, 0,   0.3471 
 Ni(4d):   0, 0.5, 0.25
 
 I used MS Visualizer to build the conventional tetragonal
 cell (a = b = 4.1474  c = 11.619).
 
 After seeing the structure with MS, I convert it to
 primitive and finding all atoms positions. Only 5 atoms
 there are in primitive (If I am right):
 
 Ba 0.00 0.00  0.00
 As 0.347100 0.347100  0.00
 As 0.652900 0.652900  0.00
 Ni 0.75 0.25  0.50
 Ni 0.25 0.75  0.50
 
 I prepared two input file for QE5.0.3, one with ibrav=7 and
 5 atoms, and the other with ibrav=14 and all atoms in
 conventional cell instead of its primitive:
 with P1 symmetry, the cell has 10 atoms:
 Ba 0. 0.  0.
 Ba 0.5000 0.5000  0.5000
 As 0.000 0.000  0.3471
 As 0.5000 0.5000  0.8471
 As 0.000 0.000  0.6529
 As 0.5000 0.5000  0.1529
 Ni 0.000 0.5000  0.25000
 Ni 0.500 0.  0.25
 Ni 0.000 0.5000  0.75000
 Ni 0.500 0.  0.75
 
 I have attached two inputs and two pictures that xcrysden
 shows. While ibrav=14 shows the crystal correctly, ibrav=7
 has a problem and doesn't show the crystal properly. I
 am confused!!
 Any help will be appreciated.
 
 
 
 Then, I 
  
 Regards
 
 David Foster
 
 Ph.D. Student of Chemistry
   
 
   
   
 
   ___
 Pw_forum mailing list
 Pw_forum at pwscf.org
 http://pwscf.org/mailman/listinfo/pw_forum
 
 
 
 
 
 -- 
 Giovanni Pizzi
 Post-doctoral Research Scientist
 EPFL STI IMX THEOS
 MXC 340 (B?timent MXC)
 Station 12
 CH-1015 Lausanne (Switzerland)
 Phone: +41 21 69 31124
   
 
 
 -Inline Attachment Follows-
 
 ___
 Pw_forum mailing list
 Pw_forum at pwscf.org
 http://pwscf.org/mailman/listinfo/pw_forum

[Pw_forum] ibrav7 doesn't show the structure of BaNi2As2 correctly

[David Foster]

Dear Tone and Giovanni

thank you for your helps. So, how can I correct crystal positions by using v1, 
v2, and v3?
Regards

David Foster

Ph.D. Student of Chemistry


On Tue, 5/27/14, Giovanni Pizzi  wrote:

 Subject: Re: [Pw_forum] ibrav7 doesn't show the structure of BaNi2As2 correctly
 To: "PWSCF Forum" 
 Date: Tuesday, May 27, 2014, 7:28 AM
 
 
   
 
 
   
   
 Dear David,
 
   I think that the relative (crystal) coordinates that
 you write for
   the 5-atom cell are still expressed in terms of the
 conventional
   cell (the one with vectors (a,0,0), (0,a,0), (0,0,c).
 This is the
   cell used in the case ibrav=14, reason for which you
 get the
   correct structure.
 
   
 
   Instead, the cell used in ibrav=7 is the primitive one
 - the docs
   say:
 
   
 
   v1=(a/2)(1,-1,c/a),? v2=(a/2)(1,1,c/a),?
 v3=(a/2)(-1,-1,c/a)
 
   
 
   Therefore you have to express the relative (crystal)
 coordinates
   with respect to this basis set, and not in terms of
 the lattice
   vectors of the conventional cell.
 
   
 
   Best,
 
   
 
   Giovanni Pizzi
 
   
 
   
 
   
 
   On 05/27/2014 03:48 PM, David Foster wrote:
 
 
 
   Dear users
 
 The atomic positions for BaNi2As2 crystal with space group
 of I4/mmm (139) are:
 
 Ba (2a): 0, 0,   0 
 As (4e): 0, 0,   0.3471 
 Ni(4d):   0, 0.5, 0.25
 
 I used MS Visualizer to build the conventional tetragonal
 cell (a = b = 4.1474  c = 11.619).
 
 After seeing the structure with MS, I convert it to
 primitive and finding all atoms positions. Only 5 atoms
 there are in primitive (If I am right):
 
 Ba 0.00 0.00  0.00
 As 0.347100 0.347100  0.00
 As 0.652900 0.652900  0.00
 Ni 0.75 0.25  0.50
 Ni 0.25 0.75  0.50
 
 I prepared two input file for QE5.0.3, one with ibrav=7 and
 5 atoms, and the other with ibrav=14 and all atoms in
 conventional cell instead of its primitive:
 with P1 symmetry, the cell has 10 atoms:
 Ba 0. 0.  0.
 Ba 0.5000 0.5000  0.5000
 As 0.000 0.000  0.3471
 As 0.5000 0.5000  0.8471
 As 0.000 0.000  0.6529
 As 0.5000 0.5000  0.1529
 Ni 0.000 0.5000  0.25000
 Ni 0.500 0.  0.25
 Ni 0.000 0.5000  0.75000
 Ni 0.500 0.  0.75
 
 I have attached two inputs and two pictures that xcrysden
 shows. While ibrav=14 shows the crystal correctly, ibrav=7
 has a problem and doesn't show the crystal properly. I
 am confused!!
 Any help will be appreciated.
 
 
 
 Then, I 
  
 Regards
 
 David Foster
 
 Ph.D. Student of Chemistry
   
 
   
   
 
   ___
 Pw_forum mailing list
 Pw_forum at pwscf.org
 http://pwscf.org/mailman/listinfo/pw_forum
 
 
 
 
 
 -- 
 Giovanni Pizzi
 Post-doctoral Research Scientist
 EPFL STI IMX THEOS
 MXC 340 (B?timent MXC)
 Station 12
 CH-1015 Lausanne (Switzerland)
 Phone: +41 21 69 31124
   
 
 
 -Inline Attachment Follows-
 
 ___
 Pw_forum mailing list
 Pw_forum at pwscf.org
 http://pwscf.org/mailman/listinfo/pw_forum

[Pw_forum] ibrav7 doesn't show the structure of BaNi2As2 correctly

[David Foster]

Dear Tone and Giovanni

thank you for your helps. So, how can I correct crystal positions by using v1, 
v2, and v3?
Regards

David Foster

Ph.D. Student of Chemistry


On Tue, 5/27/14, Giovanni Pizzi  wrote:

 Subject: Re: [Pw_forum] ibrav7 doesn't show the structure of BaNi2As2 correctly
 To: "PWSCF Forum" 
 Date: Tuesday, May 27, 2014, 7:28 AM
 
 
   
 
 
   
   
 Dear David,
 
   I think that the relative (crystal) coordinates that
 you write for
   the 5-atom cell are still expressed in terms of the
 conventional
   cell (the one with vectors (a,0,0), (0,a,0), (0,0,c).
 This is the
   cell used in the case ibrav=14, reason for which you
 get the
   correct structure.
 
   
 
   Instead, the cell used in ibrav=7 is the primitive one
 - the docs
   say:
 
   
 
   v1=(a/2)(1,-1,c/a),? v2=(a/2)(1,1,c/a),?
 v3=(a/2)(-1,-1,c/a)
 
   
 
   Therefore you have to express the relative (crystal)
 coordinates
   with respect to this basis set, and not in terms of
 the lattice
   vectors of the conventional cell.
 
   
 
   Best,
 
   
 
   Giovanni Pizzi
 
   
 
   
 
   
 
   On 05/27/2014 03:48 PM, David Foster wrote:
 
 
 
   Dear users
 
 The atomic positions for BaNi2As2 crystal with space group
 of I4/mmm (139) are:
 
 Ba (2a): 0, 0,   0 
 As (4e): 0, 0,   0.3471 
 Ni(4d):   0, 0.5, 0.25
 
 I used MS Visualizer to build the conventional tetragonal
 cell (a = b = 4.1474  c = 11.619).
 
 After seeing the structure with MS, I convert it to
 primitive and finding all atoms positions. Only 5 atoms
 there are in primitive (If I am right):
 
 Ba 0.00 0.00  0.00
 As 0.347100 0.347100  0.00
 As 0.652900 0.652900  0.00
 Ni 0.75 0.25  0.50
 Ni 0.25 0.75  0.50
 
 I prepared two input file for QE5.0.3, one with ibrav=7 and
 5 atoms, and the other with ibrav=14 and all atoms in
 conventional cell instead of its primitive:
 with P1 symmetry, the cell has 10 atoms:
 Ba 0. 0.  0.
 Ba 0.5000 0.5000  0.5000
 As 0.000 0.000  0.3471
 As 0.5000 0.5000  0.8471
 As 0.000 0.000  0.6529
 As 0.5000 0.5000  0.1529
 Ni 0.000 0.5000  0.25000
 Ni 0.500 0.  0.25
 Ni 0.000 0.5000  0.75000
 Ni 0.500 0.  0.75
 
 I have attached two inputs and two pictures that xcrysden
 shows. While ibrav=14 shows the crystal correctly, ibrav=7
 has a problem and doesn't show the crystal properly. I
 am confused!!
 Any help will be appreciated.
 
 
 
 Then, I 
  
 Regards
 
 David Foster
 
 Ph.D. Student of Chemistry
   
 
   
   
 
   ___
 Pw_forum mailing list
 Pw_forum at pwscf.org
 http://pwscf.org/mailman/listinfo/pw_forum
 
 
 
 
 
 -- 
 Giovanni Pizzi
 Post-doctoral Research Scientist
 EPFL STI IMX THEOS
 MXC 340 (B?timent MXC)
 Station 12
 CH-1015 Lausanne (Switzerland)
 Phone: +41 21 69 31124
   
 
 
 -Inline Attachment Follows-
 
 ___
 Pw_forum mailing list
 Pw_forum at pwscf.org
 http://pwscf.org/mailman/listinfo/pw_forum

[Pw_forum] ibrav7 doesn't show the structure of BaNi2As2 correctly

[David Foster]

Dear users

The atomic positions for BaNi2As2 crystal with space group of I4/mmm (139) are:

Ba (2a): 0, 0,   0 
As (4e): 0, 0,   0.3471 
Ni(4d):   0, 0.5, 0.25

I used MS Visualizer to build the conventional tetragonal cell (a = b = 4.1474  
c = 11.619).

After seeing the structure with MS, I convert it to primitive and finding all 
atoms positions. Only 5 atoms there are in primitive (If I am right):

Ba 0.00 0.00  0.00
As 0.347100 0.347100  0.00
As 0.652900 0.652900  0.00
Ni 0.75 0.25  0.50
Ni 0.25 0.75  0.50

I prepared two input file for QE5.0.3, one with ibrav=7 and 5 atoms, and the 
other with ibrav=14 and all atoms in conventional cell instead of its primitive:
with P1 symmetry, the cell has 10 atoms:
Ba 0. 0.  0.
Ba 0.5000 0.5000  0.5000
As 0.000 0.000  0.3471
As 0.5000 0.5000  0.8471
As 0.000 0.000  0.6529
As 0.5000 0.5000  0.1529
Ni 0.000 0.5000  0.25000
Ni 0.500 0.  0.25
Ni 0.000 0.5000  0.75000
Ni 0.500 0.  0.75

I have attached two inputs and two pictures that xcrysden shows. While ibrav=14 
shows the crystal correctly, ibrav=7 has a problem and doesn't show the crystal 
properly. I am confused!!
Any help will be appreciated.



Then, I 
 
Regards

David Foster

Ph.D. Student of Chemistry
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[Pw_forum] fluctuation in SCF energies of CO adsorbed on Pd110

[David Foster]

Dear Prof. Giannozzi

Thank you for your comments. I will correct the inputs according to your ideas.


Regards

David Foster

Ph.D. Student of Chemistry


On Wed, 4/23/14, Paolo Giannozzi  wrote:

 Subject: Re: [Pw_forum] fluctuation in SCF energies of CO adsorbed on Pd110
 To: "PWSCF Forum" 
 Date: Wednesday, April 23, 2014, 7:18 PM
 
 I would increase degauss by at least
 a factor 10.
 The kind of behavior you have is typical of metals
 that are not treated as such. degauss=0.001 is
 very small and it may not have enough effect.
 
 For a Gamma-only calculation, K_POINTS gamma is 
 faster (allows the usage of memory- and cpu-saving 
 tricks). 1000 bands (instead of 1300) should be 
 sufficient. For a first test you should use smaller
 cutoffs.
 
 Paolo
 
 On Sun, 2014-04-20 at 09:20 -0700, David Foster wrote:
 > Dear users
 > 
 > I have prepared an input for interaction between CO and
 Pd(110). I optimized 3*3*3 supercell of Pd bulk, and then
 cleaved a 110 surface and constructed a slab. I inserted CO
 molecule which has been optimized with QE5.0.2 in it. Now, I
 try to optimize this mixed system (CO+Pd(110)).
 > 
 > My main problem is that in scf I see the fluctuation in
 energies. My input and output has been attached. In all
 calculations I used QE5.0.2 and the same USPP. I used PBE
 DFT in the PP. I used nspin=2 due to the presence of oxygen
 atom. I introduced start_magnetization for all species. I
 fixed three bottom layers in the cell. I used ibrav=14 to
 optimize bulk phase of Pd, and didn't change it in all
 computation.
 > I used degauss=0.001RY. In addition I used smearing
 technique for both bulk and slab.
 > 
 > The run is continuing, but I think finally, I will
 encounter with problem.
 > 
 > Any idea for rapid convergence and solve the issue in
 fluctuation energy is appreciated.
 > 
 > 
 > 
 > 
 > Regards
 > 
 > David Foster
 > 
 > Ph.D. Student of Chemistry
 > ___
 Pw_forum mailing list Pw_forum at pwscf.org
 http://pwscf.org/mailman/listinfo/pw_forum
 
 -- 
 Paolo Giannozzi, Dept.
 Chemistry, 
 Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
 Phone +39-0432-558216, fax +39-0432-558222 
 
 ___
 Pw_forum mailing list
 Pw_forum at pwscf.org
 http://pwscf.org/mailman/listinfo/pw_forum
 

[Pw_forum] Fwd: au111 surface

[David Foster]

Dear Raha
Sorry, I only used Windows version, and didn't install on linux.
Regards

David Foster

Ph.D. Student of Chemistry


On Mon, 4/21/14, raha khalili  wrote:

 Subject: Re: [Pw_forum] Fwd: au111 surface
 To: "PWSCF Forum" 
 Date: Monday, April 21, 2014, 5:20 AM
 
 Dear David?
 Very thanks for your?suggestion. I
 downloaded?avogadro-1.1.1.?First I
 have installed cmake and gt4.8. But I get this error when
 installing:
 
 steps as INSTALL file in avogadro
 directory:
 cd?avogadro-1.1.1mkdir buildcd buildcmake
 ../
 
 
 -- The C compiler identification is GNU
 4.7.2-- The CXX compiler identification is GNU
 4.7.2-- Check for working C compiler:
 /usr/lib64/ccache/cc-- Check for working C
 compiler: /usr/lib64/ccache/cc -- works
 -- Detecting C compiler ABI info-- Detecting
 C compiler ABI info - done-- Check for working
 CXX compiler: /usr/lib64/ccache/c++-- Check for
 working CXX compiler: /usr/lib64/ccache/c++ -- works
 -- Detecting CXX compiler ABI info--
 Detecting CXX compiler ABI info - done-- The
 build type is Release-- Performing Test
 HAVE_NO_RTTI-- Performing Test HAVE_NO_RTTI -
 Success
 -- Performing Test HAVE_RTTI-- Performing
 Test HAVE_RTTI - Success-- Performing Test
 HAVE_GCC_VISIBILITY-- Performing Test
 HAVE_GCC_VISIBILITY - Success-- Performing Test
 COMPILES_WITHOUT_FPERMISSIVE
 -- Performing Test COMPILES_WITHOUT_FPERMISSIVE -
 FailedCMake Error at
 /usr/share/cmake/Modules/FindQt4.cmake:1368
 (message):? Found unsuitable Qt version
 "" from NOTFOUND, this code requires Qt 4.x
 Call Stack (most recent call first):?
 CMakeLists.txt:226 (find_package)
 Could you tell me please what the
 problem is?
 Best Regards
 Raha
 
 
 On Sun, Apr 20, 2014 at
 9:16 PM, David Foster 
 wrote:
 
 Dear
 Raha
 
 You can use Avogadro for constructing it. The code is free.
 In addition, you can search the web to find its cif file and
 use it in Avogadro, if you don't want to do it by hand.
 
 
 
 
 
 
 
 
 
 Regards
 
 
 
 David Foster
 
 
 
 Ph.D. Student of Chemistry
 
 
 
 
 
 On Sat, 4/19/14, raha khalili 
 wrote:
 
 
 
 ?Subject: [Pw_forum] Fwd: au111 surface
 
 ?To: "PWSCF Forum" 
 
 ?Date: Saturday, April 19, 2014, 3:45 AM
 
 
 
 ?Dear QE users
 
 
 
 ?I want to?construct?Au111 surfaces. But my
 
 ?output file seems to be incorrect. Could you help me for
 
 ?it?
 
 
 
 ?Input:? ?
 
 ?calculation = 'relax'? ?
 
 ?restart_mode='from_scratch',? ?
 
 ?prefix='au',? ? tprnfor =
 
 ?.true.? ? pseudo_dir =
 
 ?'/home/khalili/espresso-5.0.2/pseudo',
 
 ?? ?
 
 ?outdir='./'?/??
 
 ?? ibrav= 0, celldm(1)=6.0, celldm(2)=1,
 
 ?celldm(3)=0.222460766,? ? nat= 13, ntyp=
 
 ?1,? ? noncolin=.true.,? ?
 
 ?lspinorb=.true.,
 
 ?? ? starting_magnetization(1)=0.0,? ?
 
 ?ecutwfc = 27.0,? ? ecutrho =
 
 ?391.0,? ?
 
 ?occupations='smearing',? ?
 
 ?smearing='fd',? ?
 
 ?degauss=0.001
 
 ??/?? ?
 
 ?diagonalization='david'? ?
 
 ?electron_maxstep = 500,? ? mixing_mode =
 
 ?'plain'? ? mixing_beta =
 
 ?0.7? ? conv_thr = ?1.0d-6
 
 ??/? ? ? ? ? ?
 
 ?ion_dynamics =
 
 ?'bfgs'/ATOMIC_SPECIES?Au
 
 ??196.966 ?
 
 ?Au.rel-pz-dn-rrkjus_psl.0.1.UPFATOMIC_POSITIONS?Au
 
 ?? ? ? 2.949785413 ?
 3.672551581 ? 0.719332431
 
 ?Au ? ? ? 2.742687251 ? 2.86557 ?
 
 ?0.719332431Au ? ? ? 3.563230179 ? 3.098796549
 
 ?? 0.719332431Au ? ? ? 3.356132017 ?
 
 ?2.291817190 ? 0.719332431Au ? ? ? 3.534436578
 
 ?? 1.470557957 ? 0.051950134
 
 ?Au ? ? ? 3.732270300 ? 2.268356755 ?
 
 ?0.051950134Au ? ? ? 3.928237209 ? 3.069472551
 
 ?? 0.051950134Au ? ? ? 2.912648680 ?
 
 ?2.043258658 ? 0.051950134Au ? ? ? 3.119592323
 
 ?? 2.850332820 ? 0.051950134
 
 ?Au ? ? ? 3.343806277 ? 3.659523280 ?
 
 ?0.051950134Au ? ? ? 2.299120168 ? 2.617060049
 
 ?? 0.051950134Au ? ? ? 2.523263349 ?
 
 ?3.426298953 ? 0.051950134Au ? ? ? 2.730361511
 
 ?? 4.233278312 ? 0.051950134
 
 ?CELL_PARAMETERS6.0 0.0 0.00.0 6.0
 
 ?0.00.0 0.0 1.334764594K_POINTS
 
 ?{Automatic}?1 1 4 1 1 1
 
 ?output:?
 
 ?ATOMIC_POSITIONS (alat)Au ? ? ?
 
 ?2.937386209 ? 3.582923161 ? 0.719330203Au ? ?
 
 ?? 2.593545725 ? 2.740963547 ? 0.719333040Au ?
 
 ?? ? 3.670168686 ? 3.044796914 ? 0.719331555Au
 
 ?? ? ? 3.326200204 ? 2.202685361 ? 0.719334648
 
 ?Au ? ? ? 3.478788201 ? 1.670372948 ?
 
 ?0.051951374Au ? ? ? 3.865644556 ? 2.412608619
 
 ?? 0.051953914Au ? ? ? 4.175978091 ?
 
 ?3.185452798 ? 0.051947555Au ? ? ? 2.759515725
 
 ?? 2.097309245 ? 0.051954205
 
 ?Au ? ? ? 3.133871517 ? 2.883011335 ?
 
 ?0.051949504Au ? ? ? 3.504225226 ? 3.675472063
 
 ?? 0.051948273Au ? ? ? 2.091449270 ?
 
 ?2.593809644 ? 0.051950705Au ? ? ? 2.407897276
 
 ?? 3.365285757 ? 0.051948060
 
 ?Au ? ? ? 2.790900569 ? 4.112185484 ?
 
 ?0.051947893End final
 
 ?coordinates
 
 ?Any help will be appreciated.?--?
 
 
 
 ?Khadije KhaliliPh.D
 
 ?Student of Solid-State PhysicsDepartment of
 
 ?PhysicsUniversity of
 
 ?MazandaranBabolsar, Irankh.khalili at stu.umz.ac.ir
 
 ??
 
 
 
 
 
 ?

[Pw_forum] fluctuation in SCF energies of CO adsorbed on Pd110

[David Foster]

Thank you again Axel. It was very helpful for me.


Regards

David Foster

Ph.D. Student of Chemistry


On Mon, 4/21/14, Axel Kohlmeyer  wrote:

 Subject: Re: [Pw_forum] fluctuation in SCF energies of CO adsorbed on Pd110
 To: "PWSCF Forum" 
 Date: Monday, April 21, 2014, 4:59 AM
 
 On Mon, Apr 21, 2014 at 6:28 AM,
 David Foster 
 wrote:
 > Thanks Axel
 > Yes, in chemistry wee see always the MOs. But in many
 unknown cases, we should calculate the MOs by computations.
 To use the codes, we need to define 2S+1. In quantum
 chemistry codes we use different spin-multiplicity, and we
 choose each one that give smaller energy. What about
 plane-wave methods?
 
 where in the schoedinger equation does it say it only works
 for
 atom-centric basis sets?
 
 > Why choosing spin-polarization causes that the energy
 fluctuate so much?
 
 i think you are jumping to conclusions here. have you run
 the slab
 configuration without the CO molecule. charge sloshing can
 happen for
 all kinds of reasons, and usually it is affected by the
 amount of
 mixing used and not so much by doing LSDA, but using LSDA
 does offer
 additional degrees of freedom for the electronic system to
 evolve and
 thus can emphasize problems like charge sloshing.
 
 > If I compare these two calculations (one with
 spin-polarization and one without it), I should get the same
 energy. Is it right?
 
 only if there is no magnetization.
 
 axel.
 
 > Thanks again
 > Any help will be appreciated.
 >
 > Regards
 >
 > David Foster
 >
 > Ph.D. Student of Chemistry
 >
 > 
 > On Mon, 4/21/14, Axel Kohlmeyer 
 wrote:
 >
 >? Subject: Re: [Pw_forum] fluctuation in SCF
 energies of CO adsorbed on Pd110
 >? To: "PWSCF Forum" 
 >? Date: Monday, April 21, 2014, 1:17 AM
 >
 >? On Mon, Apr 21, 2014 at 12:03 AM,
 >? David Foster 
 >? wrote:
 >? > Dear Yun
 >? > Thanks for your rapid answer. Considering
 your answer,
 >? I have two more questions:
 >? >
 >? > 1- In the system I have carbon monoxide.
 carbon atom
 >? has 4 electron in its valance. between O and C
 there is a
 >? triple bond. So, carbon may have one unpaired
 electron that
 >? needs spin-polarization defined. Is it right?
 >
 >? wrong. electrons cannot be "assigned" to
 individual atoms,
 >? they occupy
 >? "molecular" orbitals. please help yourself to a
 little
 >? quantum
 >? chemistry refresher.
 >
 >? > 2- Surface of metals due to the charge
 density near to
 >? the surface needs spin-polarization. Is it
 right?
 >
 >? wrong. you need spin polarization only if you
 have unpaired
 >? electrons..
 >
 >? > One more point. I have prepared input with
 one
 >? graphical program. When I see the input file with
 XCrysDen,
 >? in the primitive form everything is OK, but in
 conventional
 >? form, three to four Pd atoms in the edge of cell
 seems to be
 >? missing
 >
 >? that is just visualization. probably your initial
 geometry
 >? has some
 >? rounding errors in the positions.
 >
 >? axel.
 >
 >? > Regards
 >? >
 >? > David Foster
 >? >
 >? > Ph.D. Student of Chemistry
 >? >
 >? >
 
 >? > On Sun, 4/20/14, Yun Wang 
 >? wrote:
 >? >
 >? >? Subject: Re: [Pw_forum] fluctuation in
 SCF
 >? energies of CO adsorbed on Pd110
 >? >? To: "PWSCF Forum" 
 >? >? Date: Sunday, April 20, 2014, 2:41 PM
 >? >
 >? >? Hi David,I think
 >? >? you need not consider the spin
 polarization for
 >? this system,
 >? >? which will accelerate the
 >? >? convergancy.Cheers,Yun
 >? >
 >? >
 >? >
 >? >
 >? >
 >? >? On Mon, Apr 21, 2014
 >? >? at 2:20 AM, David Foster 
 >? >? wrote:
 >? >
 >? >
 >? >? Dear users
 >? >
 >? >
 >? >
 >? >? I have prepared an input for
 interaction between
 >? CO and
 >? >? Pd(110). I optimized 3*3*3 supercell
 of Pd bulk,
 >? and then
 >? >? cleaved a 110 surface and constructed
 a slab. I
 >? inserted CO
 >? >? molecule which has been optimized with
 QE5.0.2 in
 >? it. Now, I
 >? >? try to optimize this mixed system
 (CO+Pd(110)).
 >? >
 >? >
 >? >
 >? >
 >? >
 >? >? My main problem is that in scf I see
 the
 >? fluctuation in
 >? >? energies. My input and output has been
 attached.
 >? In all
 >? >? calculations I used QE5.0.2 and the
 same USPP. I
 >? used PBE
 >? >? DFT in the PP. I used nspin=2 due to
 the presence
 >? of oxygen
 >? >? atom. I introduced start_magnetiza

[Pw_forum] fluctuation in SCF energies of CO adsorbed on Pd110

[David Foster]

Thanks Axel
Yes, in chemistry wee see always the MOs. But in many unknown cases, we should 
calculate the MOs by computations. To use the codes, we need to define 2S+1. In 
quantum chemistry codes we use different spin-multiplicity, and we choose each 
one that give smaller energy. What about plane-wave methods? 
Why choosing spin-polarization causes that the energy fluctuate so much?
If I compare these two calculations (one with spin-polarization and one without 
it), I should get the same energy. Is it right?

Thanks again
Any help will be appreciated. 

Regards

David Foster

Ph.D. Student of Chemistry


On Mon, 4/21/14, Axel Kohlmeyer  wrote:

 Subject: Re: [Pw_forum] fluctuation in SCF energies of CO adsorbed on Pd110
 To: "PWSCF Forum" 
 Date: Monday, April 21, 2014, 1:17 AM
 
 On Mon, Apr 21, 2014 at 12:03 AM,
 David Foster 
 wrote:
 > Dear Yun
 > Thanks for your rapid answer. Considering your answer,
 I have two more questions:
 >
 > 1- In the system I have carbon monoxide. carbon atom
 has 4 electron in its valance. between O and C there is a
 triple bond. So, carbon may have one unpaired electron that
 needs spin-polarization defined. Is it right?
 
 wrong. electrons cannot be "assigned" to individual atoms,
 they occupy
 "molecular" orbitals. please help yourself to a little
 quantum
 chemistry refresher.
 
 > 2- Surface of metals due to the charge density near to
 the surface needs spin-polarization. Is it right?
 
 wrong. you need spin polarization only if you have unpaired
 electrons..
 
 > One more point. I have prepared input with one
 graphical program. When I see the input file with XCrysDen,
 in the primitive form everything is OK, but in conventional
 form, three to four Pd atoms in the edge of cell seems to be
 missing
 
 that is just visualization. probably your initial geometry
 has some
 rounding errors in the positions.
 
 axel.
 
 > Regards
 >
 > David Foster
 >
 > Ph.D. Student of Chemistry
 >
 > 
 > On Sun, 4/20/14, Yun Wang 
 wrote:
 >
 >? Subject: Re: [Pw_forum] fluctuation in SCF
 energies of CO adsorbed on Pd110
 >? To: "PWSCF Forum" 
 >? Date: Sunday, April 20, 2014, 2:41 PM
 >
 >? Hi David,I think
 >? you need not consider the spin polarization for
 this system,
 >? which will accelerate the
 >? convergancy.Cheers,Yun
 >
 >
 >
 >
 >
 >? On Mon, Apr 21, 2014
 >? at 2:20 AM, David Foster 
 >? wrote:
 >
 >
 >? Dear users
 >
 >
 >
 >? I have prepared an input for interaction between
 CO and
 >? Pd(110). I optimized 3*3*3 supercell of Pd bulk,
 and then
 >? cleaved a 110 surface and constructed a slab. I
 inserted CO
 >? molecule which has been optimized with QE5.0.2 in
 it. Now, I
 >? try to optimize this mixed system (CO+Pd(110)).
 >
 >
 >
 >
 >
 >? My main problem is that in scf I see the
 fluctuation in
 >? energies. My input and output has been attached.
 In all
 >? calculations I used QE5.0.2 and the same USPP. I
 used PBE
 >? DFT in the PP. I used nspin=2 due to the presence
 of oxygen
 >? atom. I introduced start_magnetization for all
 species. I
 >? fixed three bottom layers in the cell. I used
 ibrav=14 to
 >? optimize bulk phase of Pd, and didn't change it
 in all
 >? computation.
 >
 >
 >
 >? I used degauss=0.001RY. In addition I used
 smearing
 >? technique for both bulk and slab.
 >
 >
 >
 >? The run is continuing, but I think finally, I
 will encounter
 >? with problem.
 >
 >
 >
 >? Any idea for rapid convergence and solve the
 issue in
 >? fluctuation energy is appreciated.
 >
 >
 >
 >
 >
 >
 >
 >
 >
 >? Regards
 >
 >
 >
 >? David Foster
 >
 >
 >
 >? Ph.D. Student of Chemistry
 >? ___
 >
 >? Pw_forum mailing list
 >
 >? Pw_forum at pwscf.org
 >
 >? http://pwscf.org/mailman/listinfo/pw_forum
 >
 >
 >
 >? --
 >
 >? Dr. Yun Wang
 >? Research Fellow
 >? Centre for Clean Environment and Energy
 >? Griffith School of Environment
 >? Gold Coast Campus, Griffith University
 >? QLD 4222, Australia
 >? Tel:(61-7) 5552 8456
 >? Fax:(61-7) 5552 8067
 >
 >
 >
 >
 >? -Inline Attachment Follows-
 >
 >? ___
 >? Pw_forum mailing list
 >? Pw_forum at pwscf.org
 >? http://pwscf.org/mailman/listinfo/pw_forum
 > ___
 > Pw_forum mailing list
 > Pw_forum at pwscf.org
 > http://pwscf.org/mailman/listinfo/pw_forum
 
 
 
 -- 
 Dr. Axel Kohlmeyer? akohlmey at gmail.com?
 http://goo.gl/1wk0
 College of Science & Technology, Temple University,
 Philadelphia PA, USA
 International Centre for Theoretical Physics, Trieste.
 Italy.
 ___
 Pw_forum mailing list
 Pw_forum at pwscf.org
 http://pwscf.org/mailman/listinfo/pw_forum
 

[Pw_forum] fluctuation in SCF energies of CO adsorbed on Pd110

[David Foster]

Dear Yun
Thanks for your rapid answer. Considering your answer, I have two more 
questions:

1- In the system I have carbon monoxide. carbon atom has 4 electron in its 
valance. between O and C there is a triple bond. So, carbon may have one 
unpaired electron that needs spin-polarization defined. Is it right?

2- Surface of metals due to the charge density near to the surface needs 
spin-polarization. Is it right?

One more point. I have prepared input with one graphical program. When I see 
the input file with XCrysDen, in the primitive form everything is OK, but in 
conventional form, three to four Pd atoms in the edge of cell seems to be 
missing
Regards

David Foster

Ph.D. Student of Chemistry


On Sun, 4/20/14, Yun Wang  wrote:

 Subject: Re: [Pw_forum] fluctuation in SCF energies of CO adsorbed on Pd110
 To: "PWSCF Forum" 
 Date: Sunday, April 20, 2014, 2:41 PM
 
 Hi David,I think
 you need not consider the spin polarization for this system,
 which will accelerate the
 convergancy.Cheers,Yun
 
 
 
 
 
 On Mon, Apr 21, 2014
 at 2:20 AM, David Foster 
 wrote:
 
 
 Dear users
 
 
 
 I have prepared an input for interaction between CO and
 Pd(110). I optimized 3*3*3 supercell of Pd bulk, and then
 cleaved a 110 surface and constructed a slab. I inserted CO
 molecule which has been optimized with QE5.0.2 in it. Now, I
 try to optimize this mixed system (CO+Pd(110)).
 
 
 
 
 
 My main problem is that in scf I see the fluctuation in
 energies. My input and output has been attached. In all
 calculations I used QE5.0.2 and the same USPP. I used PBE
 DFT in the PP. I used nspin=2 due to the presence of oxygen
 atom. I introduced start_magnetization for all species. I
 fixed three bottom layers in the cell. I used ibrav=14 to
 optimize bulk phase of Pd, and didn't change it in all
 computation.
 
 
 
 I used degauss=0.001RY. In addition I used smearing
 technique for both bulk and slab.
 
 
 
 The run is continuing, but I think finally, I will encounter
 with problem.
 
 
 
 Any idea for rapid convergence and solve the issue in
 fluctuation energy is appreciated.
 
 
 
 
 
 
 
 
 
 Regards
 
 
 
 David Foster
 
 
 
 Ph.D. Student of Chemistry
 ___
 
 Pw_forum mailing list
 
 Pw_forum at pwscf.org
 
 http://pwscf.org/mailman/listinfo/pw_forum
 
 
 
 -- 
 
 Dr. Yun Wang
 Research Fellow
 Centre for Clean Environment and Energy
 Griffith School of Environment
 Gold Coast Campus, Griffith University
 QLD 4222, Australia
 Tel:(61-7) 5552 8456
 Fax:(61-7) 5552 8067
 
 
 
 
 -Inline Attachment Follows-
 
 ___
 Pw_forum mailing list
 Pw_forum at pwscf.org
 http://pwscf.org/mailman/listinfo/pw_forum

[Pw_forum] Fwd: au111 surface

[David Foster]

Dear Raha
You can use Avogadro for constructing it. The code is free. In addition, you 
can search the web to find its cif file and use it in Avogadro, if you don't 
want to do it by hand.




Regards

David Foster

Ph.D. Student of Chemistry


On Sat, 4/19/14, raha khalili  wrote:

 Subject: [Pw_forum] Fwd: au111 surface
 To: "PWSCF Forum" 
 Date: Saturday, April 19, 2014, 3:45 AM
 
 Dear QE users
 
 I want to?construct?Au111 surfaces. But my
 output file seems to be incorrect. Could you help me for
 it?
 
 Input:? ?
 calculation = 'relax'? ?
 restart_mode='from_scratch',? ?
 prefix='au',? ? tprnfor =
 .true.? ? pseudo_dir =
 '/home/khalili/espresso-5.0.2/pseudo',
 ? ?
 outdir='./'?/??
 ? ibrav= 0, celldm(1)=6.0, celldm(2)=1,
 celldm(3)=0.222460766,? ? nat= 13, ntyp=
 1,? ? noncolin=.true.,? ?
 lspinorb=.true.,
 ? ? starting_magnetization(1)=0.0,? ?
 ecutwfc = 27.0,? ? ecutrho =
 391.0,? ?
 occupations='smearing',? ?
 smearing='fd',? ?
 degauss=0.001
 ?/?? ?
 diagonalization='david'? ?
 electron_maxstep = 500,? ? mixing_mode =
 'plain'? ? mixing_beta =
 0.7? ? conv_thr = ?1.0d-6
 ?/? ? ? ? ? ?
 ion_dynamics =
 'bfgs'/ATOMIC_SPECIES?Au
 ?196.966 ?
 Au.rel-pz-dn-rrkjus_psl.0.1.UPFATOMIC_POSITIONS?Au
 ? ? ? 2.949785413 ? 3.672551581 ? 0.719332431
 Au ? ? ? 2.742687251 ? 2.86557 ?
 0.719332431Au ? ? ? 3.563230179 ? 3.098796549
 ? 0.719332431Au ? ? ? 3.356132017 ?
 2.291817190 ? 0.719332431Au ? ? ? 3.534436578
 ? 1.470557957 ? 0.051950134
 Au ? ? ? 3.732270300 ? 2.268356755 ?
 0.051950134Au ? ? ? 3.928237209 ? 3.069472551
 ? 0.051950134Au ? ? ? 2.912648680 ?
 2.043258658 ? 0.051950134Au ? ? ? 3.119592323
 ? 2.850332820 ? 0.051950134
 Au ? ? ? 3.343806277 ? 3.659523280 ?
 0.051950134Au ? ? ? 2.299120168 ? 2.617060049
 ? 0.051950134Au ? ? ? 2.523263349 ?
 3.426298953 ? 0.051950134Au ? ? ? 2.730361511
 ? 4.233278312 ? 0.051950134
 CELL_PARAMETERS6.0 0.0 0.00.0 6.0
 0.00.0 0.0 1.334764594K_POINTS
 {Automatic}?1 1 4 1 1 1
 output:?
 ATOMIC_POSITIONS (alat)Au ? ? ?
 2.937386209 ? 3.582923161 ? 0.719330203Au ? ?
 ? 2.593545725 ? 2.740963547 ? 0.719333040Au ?
 ? ? 3.670168686 ? 3.044796914 ? 0.719331555Au
 ? ? ? 3.326200204 ? 2.202685361 ? 0.719334648
 Au ? ? ? 3.478788201 ? 1.670372948 ?
 0.051951374Au ? ? ? 3.865644556 ? 2.412608619
 ? 0.051953914Au ? ? ? 4.175978091 ?
 3.185452798 ? 0.051947555Au ? ? ? 2.759515725
 ? 2.097309245 ? 0.051954205
 Au ? ? ? 3.133871517 ? 2.883011335 ?
 0.051949504Au ? ? ? 3.504225226 ? 3.675472063
 ? 0.051948273Au ? ? ? 2.091449270 ?
 2.593809644 ? 0.051950705Au ? ? ? 2.407897276
 ? 3.365285757 ? 0.051948060
 Au ? ? ? 2.790900569 ? 4.112185484 ?
 0.051947893End final
 coordinates
 Any help will be appreciated.?--?
 
 Khadije KhaliliPh.D
 Student of Solid-State PhysicsDepartment of
 PhysicsUniversity of
 MazandaranBabolsar, Irankh.khalili at stu.umz.ac.ir
 ?
 
 
 -Inline Attachment Follows-
 
 ___
 Pw_forum mailing list
 Pw_forum at pwscf.org
 http://pwscf.org/mailman/listinfo/pw_forum

[Pw_forum] fluctuation in SCF energies of CO adsorbed on Pd110

[David Foster]

Dear users

I have prepared an input for interaction between CO and Pd(110). I optimized 
3*3*3 supercell of Pd bulk, and then cleaved a 110 surface and constructed a 
slab. I inserted CO molecule which has been optimized with QE5.0.2 in it. Now, 
I try to optimize this mixed system (CO+Pd(110)).

My main problem is that in scf I see the fluctuation in energies. My input and 
output has been attached. In all calculations I used QE5.0.2 and the same USPP. 
I used PBE DFT in the PP. I used nspin=2 due to the presence of oxygen atom. I 
introduced start_magnetization for all species. I fixed three bottom layers in 
the cell. I used ibrav=14 to optimize bulk phase of Pd, and didn't change it in 
all computation.
I used degauss=0.001RY. In addition I used smearing technique for both bulk and 
slab.

The run is continuing, but I think finally, I will encounter with problem.

Any idea for rapid convergence and solve the issue in fluctuation energy is 
appreciated.




Regards

David Foster

Ph.D. Student of Chemistry
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[Pw_forum] supercell and k-point

[David Foster]

Dear users

I have read in some papers that investigate adsorption of some molecules in the 
gas phase

on the solid surface, the authors use only gamma point for the supercell of the 
catalyst (for example 

for 3*3*3 supercells). But in another ones, I see that they use some k-point 
even for supercells.

This subject confuse me. Is there any rule for this? Any help will be 
appreciated.


 
Regards

David Foster

Ph.D. Student of Chemistry

[Pw_forum] metal optimization tricks and constraining in slab

[David Foster]

Thank you Paolo and Axel

I would appreciate it if anybody could guide me about my questions.


Regards

David Foster

Ph.D. Student of Chemistry


On Fri, 4/11/14, Paolo Giannozzi  wrote:

 Subject: Re: [Pw_forum] metal optimization tricks and constraining in slab
 To: "PWSCF Forum" 
 Date: Friday, April 11, 2014, 12:16 PM
 
 On Fri, 2014-04-11 at 09:36 -0700,
 David Foster wrote:
 
 > I have emailed this message two times former (...) but
 
 > I didn't received them in my mail box, so, I think it 
 > has not been sent to any member. 
 
 think twice ... I received both
 
 P.
 
 > I repeat it again, and sorry for inconvenience.
 > 
 > 
 >? 
 > 
 > Dear Users and supporters
 > 
 > "Thank you for your quick answers"
 > 
 > I have two questions:
 > 
 > 1- I prepared 3*3*3 bulk Pd super-cell, and used
 "vc-relax". The relaxation needed
 > 
 >? ? more than 200 iteration. I finally relaxed
 it with restarting command. Please help
 >? ? 
 >? ? me in setting following parameters for
 fast relaxation for metals:
 >? ? 
 >? ? a- degauss (I think increasing it helps
 for fast coarse optimization, but after it
 >? ? 
 >? ? ???needs more fine
 optimization.
 >? ? ???with increasing it, does
 it need more "nbnd"?)
 > 
 >? ? b-mixing beta ( in my calculation, I set
 it to 0.3, but I got very fluctuation in optimization.
 > 
 >? ? ? does increasing it helps
 optimization speed?)
 > 
 >???c- I prepared input by a program that
 saves the structure in cif format. I used the coordination
 > 
 >? ? ? with "crystal" card. is it true?
 > 
 > 2- I prepared 5 layers Pd slab and should fix two
 layers' coordination, but I don't know how.
 >? ???I read input style help but
 confused.
 > 
 > Thanks again
 > 
 > 
 > 
 > 
 > Regards
 > 
 > David Foster
 > 
 > Ph.D. Student of Chemistry
 > ___
 > Pw_forum mailing list
 > Pw_forum at pwscf.org
 > http://pwscf.org/mailman/listinfo/pw_forum
 
 -- 
 Paolo Giannozzi, Dept.
 Chemistry, 
 Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
 Phone +39-0432-558216, fax +39-0432-558222 
 
 ___
 Pw_forum mailing list
 Pw_forum at pwscf.org
 http://pwscf.org/mailman/listinfo/pw_forum
 

[Pw_forum] metal optimization tricks and constraining in slab

[David Foster]

Hi,

I have emailed this message two times former (Thu Apr 10 19:46:20 CEST 2014 and 
Fri Apr 11 
16:05:26 CEST 2014) but I didn't received them in my mail box, so, I think it 
has not been sent
to any member. I repeat it again, and sorry for inconvenience.


 

Dear Users and supporters

"Thank you for your quick answers"

I have two questions:

1- I prepared 3*3*3 bulk Pd super-cell, and used "vc-relax". The relaxation 
needed

   more than 200 iteration. I finally relaxed it with restarting command. 
Please help
   
   me in setting following parameters for fast relaxation for metals:
   
   a- degauss (I think increasing it helps for fast coarse optimization, but 
after it
   
  needs more fine optimization.
  with increasing it, does it need more "nbnd"?)

   b-mixing beta ( in my calculation, I set it to 0.3, but I got very 
fluctuation in optimization.

 does increasing it helps optimization speed?)

  c- I prepared input by a program that saves the structure in cif format. I 
used the coordination

 with "crystal" card. is it true?

2- I prepared 5 layers Pd slab and should fix two layers' coordination, but I 
don't know how.
I read input style help but confused.

Thanks again




Regards

David Foster

Ph.D. Student of Chemistry

[Pw_forum] metal optimization tricks and constraining in slab

[David Foster]

Dear Users and supporters

"Thank you for your quick answers"

I have two questions:

1- I prepared 3*3*3 bulk Pd super-cell, and used "vc-relax". The relaxation 
needed

   more than 200 iteration. I finally relaxed it with restarting command. 
Please help
   
   me in setting following parameters for fast relaxation for metals:
   
   a- degauss (I think increasing it helps for fast coarse optimization, but 
after it
   
  needs more fine optimization.
  with increasing it, does it need more "nbnd"?)

   b-mixing beta ( in my calculation, I set it to 0.3, but I got very 
fluctuation in optimization.

 does increasing it helps optimization speed?)

  c- I prepared input by a program that saves the structure in cif format. I 
used the coordination

 with "crystal" card. is it true?

2- I prepared 5 layers Pd slab and should fix two layers' coordination, but I 
don't know how.
I read input style help but confused.

Thanks again



Regards

David Foster

Ph.D. Student of Chemistry

[Pw_forum] metal optimization tricks and constraining atomic position in a slab

[David Foster]

Dear Users and supporters

"Thank you for your quick answers"

I have two questions:

1- I prepared 3*3*3 bulk Pd super cell, and used "vc-relax". The relaxation 
needed 

   more than 200 iteration. I finally relaxed it with restarting command. 
Please help
   
   me in setting following parameters for fast relaxation for metals:
   
   a- degauss (I think increasing it helps for fast coarse optimization, but 
after it
   
  needs more fine optimization.
  with increasing it, does it need more "nbnd"?)

   b-mixing beta ( in my calculation, I set it to 0.3, but I got very 
fluctuation in optimization.
 
 does increasing it helps optimization speed?)

  c- I prepared input by a program that saves the structure in cif format. I 
used the coordination

 with "crystal" card. is it true?

2- I prepared 5 layers Pd slab and should fix two layers' coordination, but I 
don't know how.
I read input style help but confused.

Thanks again 
Regards

David Foster

Ph.D. Student of Chemistry

[Pw_forum] Error in a vc_relax calculation

[David Foster]

Dear Users,
I have relaxed a bulk of Pd with "calculation=relax", but I get error when I 
change it with

"calculation=vc-relax". I added the card needed to the input. I have attached 
input and

its output containing the error.

It will be appreciated if anyone help.


Regards

David Foster

Ph.D. Student of Chemistry
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[Pw_forum] choosing k-point in slab calculations

[David Foster]

Dear Users

Suppose, we have constructed a metallic surface and a vacuum slab with some 
thickness.

Normally, these super-cells have no symmetry. My main question is that how we 
should 

choose the k-point? Only in the surface or we can choose some points in the 
inner layers

or even vacuum near to the surface?



PS: I have calculated band structure for the plane parallel to the surface but 
in the middle 

point of the vacuum (far from the surface). I expected that I didn't get any 
band graphs; however,

I got some. Can anybody tell me why? 



Regards

David Foster

Ph.D. Student of Chemistry

[Pw_forum] ibrav for orthorhombic space group

[David Foster]

Very thanks
Regards

David Foster

Ph.D. Student of Chemistry


On Fri, 1/10/14, xirainbow  wrote:

 Subject: Re: [Pw_forum] ibrav for orthorhombic space group
 To: "PWSCF Forum" 
 Date: Friday, January 10, 2014, 6:42 AM
 
 Dear David Foster:
 ? ? ? ? ? Orthorhombic P = composed
 of P.
 ? ? ? ? ? Orthorhombic
 base-centered(bco) = C and A.
 ? ? ? ? ? Orthorhombic
 face-centered = F
 ? ? ? ? ? Orthorhombic
 body-centered? = I.
 ? ? ? ? ? You can find more
 information at here if you can read Chinese.
 http://blog.sina.com.cn/s/blog_5f15ead20100wmjl.html
 
 
 On Fri, Jan 10, 2014 at 2:41 PM, David Foster 
 wrote:
 > Hi everybody
 >
 > Orthorhombic space group (Numbered from 16 to 74) has
 five different kinds of classes starting
 >
 > with "P" "C"? "A"? "F"? "I".
 >
 > P such as 56.Pccn? ? ? ? or?
 57.Pbcm
 >
 > C such as 36.Cmc21? or???37.Ccc2
 >
 > A such as 40.Ama2???or? ?
 41.Aba2
 >
 > F such as 42.Fmm2? ? ? ?
 ???or? ???43.Fdd2
 >
 > I such as 44.Imm2? ? ? ? ?
 or? ? 45.Iba2
 >
 > My question is about ibrav assignment to above space
 groups.
 >
 >
 > in manual we have:
 >
 > 
 >? 8? ? ? ? ? Orthorhombic
 P? ? ? ? ? ? ? ?
 ? celldm(2)=b/a
 >? ? ? ? ? ? ? ?
 ? ? ? ? ? ? ? ?
 ? ? ? ? ? ? ?
 celldm(3)=c/a
 >? ? ???v1 = (a,0,0),? v2 =
 (0,b,0), v3 = (0,0,c)
 >
 >???9? ? ? ? ?
 Orthorhombic base-centered(bco) celldm(2)=b/a
 >? ? ? ? ? ? ? ?
 ? ? ? ? ? ? ? ?
 ? ? ? ? ? ? ?
 celldm(3)=c/a
 >? ? ???v1 = (a/2, b/2,0),?
 v2 = (-a/2,b/2,0),? v3 = (0,0,c)
 >? -9? ? ? ? ? as 9,
 alternate description
 >? ? ???v1 = (a/2,-b/2,0),?
 v2 = (a/2,-b/2,0),? v3 = (0,0,c)
 >
 >? 10? ? ? ? ? Orthorhombic
 face-centered? ? ? celldm(2)=b/a
 >? ? ? ? ? ? ? ?
 ? ? ? ? ? ? ? ?
 ? ? ? ? ? ? ?
 celldm(3)=c/a
 >? ? ???v1 = (a/2,0,c/2),?
 v2 = (a/2,b/2,0),? v3 = (0,b/2,c/2)
 >
 >? 11? ? ? ? ? Orthorhombic
 body-centered? ? ? celldm(2)=b/a
 >? ? ? ? ? ? ? ?
 ? ? ? ? ? ? ? ?
 ? ? ? ? ? ? ?
 celldm(3)=c/a
 >? ? ???v1=(a/2,b/2,c/2),?
 v2=(-a/2,b/2,c/2),? v3=(-a/2,-b/2,c/2)
 > =======
 >
 > so, it is clear that ibrav for "P" is 8, for "I" is 11
 (I am not sure), for "F" is 10.
 >
 > What about "C" and "A"?
 >
 >
 >
 >
 > Regards
 >
 > David Foster
 >
 > Ph.D. Student of Chemistry
 > ___
 > Pw_forum mailing list
 > Pw_forum at pwscf.org
 > http://pwscf.org/mailman/listinfo/pw_forum
 
 
 
 -- 
 
 Hui Wang
 School of physics, Henan University of Science and
 Technology, Henan, China
 ___
 Pw_forum mailing list
 Pw_forum at pwscf.org
 http://pwscf.org/mailman/listinfo/pw_forum
 

[Pw_forum] ibrav for orthorhombic space group

[David Foster]

Hi everybody

Orthorhombic space group (Numbered from 16 to 74) has five different kinds of 
classes starting

with "P" "C"  "A"  "F"  "I".

P such as 56.Pccnor  57.Pbcm   

C such as 36.Cmc21  or   37.Ccc2

A such as 40.Ama2   or41.Aba2

F such as 42.Fmm2   or 43.Fdd2

I such as 44.Imm2  or45.Iba2

My question is about ibrav assignment to above space groups.


in manual we have:


 8  Orthorhombic P  celldm(2)=b/a
 celldm(3)=c/a
  v1 = (a,0,0),  v2 = (0,b,0), v3 = (0,0,c)

  9  Orthorhombic base-centered(bco) celldm(2)=b/a
 celldm(3)=c/a
  v1 = (a/2, b/2,0),  v2 = (-a/2,b/2,0),  v3 = (0,0,c)
 -9  as 9, alternate description
  v1 = (a/2,-b/2,0),  v2 = (a/2,-b/2,0),  v3 = (0,0,c)

 10  Orthorhombic face-centered  celldm(2)=b/a
 celldm(3)=c/a
  v1 = (a/2,0,c/2),  v2 = (a/2,b/2,0),  v3 = (0,b/2,c/2)

 11  Orthorhombic body-centered  celldm(2)=b/a
 celldm(3)=c/a
  v1=(a/2,b/2,c/2),  v2=(-a/2,b/2,c/2),  v3=(-a/2,-b/2,c/2)
===

so, it is clear that ibrav for "P" is 8, for "I" is 11 (I am not sure), for "F" 
is 10.

What about "C" and "A"?




Regards

David Foster

Ph.D. Student of Chemistry

[Pw_forum] Error in converting CIF to QE by "cif2qe.sh"

[David Foster]

Sorry, but I have new problems. I have numbered the output to clearly

talk about it:


1
2   title = 'rutile1'
3 calculation = 'relax'
4restart_mode = 'from_scratch'
5  outdir = './1'
6  pseudo_dir = '../PP/atompaw'
7  prefix = 'rutile1'
8 disk_io = 'none'
9   verbosity = 'default'
10   etot_conv_thr = 0.1
11  forc_conv_thr = 0.0001
12   nstep = 680
13 tstress = .true.
14 tprnfor = .true.
15 /
16 
17   ibrav = 0
18 nat = 0
19ntyp = 1
20 ecutwfc = 60
21 ecutrho = 600
22!  london = .true.
23 /
24 
25electron_maxstep = 200
26conv_thr = 1.0D-7
27  diago_thr_init = 1e-4
28 startingpot = 'atomic'
29 startingwfc = 'atomic'
30 mixing_mode = 'plain'
31 mixing_beta = 0.5
32 mixing_ndim = 8
33 diagonalization = 'david'
34 /
35
36ion_dynamics = 'bfgs'
37 /
38
39
40 ATOMIC_SPECIES
41 0.00  .pbe-van_ak.UPF
42
43 ATOMIC_POSITIONS crystal
44
45 K_POINTS automatic
46 5  5  8   0 0 0
47
48
49 CELL_PARAMETERS
508.680891628420765 0.000 0.000
510.001 8.680891628420765 0.000
520.000 0.000 5.590036668211679


1- at line 41 atomic symbols have not been shown (similar to lorenzo's
   output)

2- at line 44, positions have not been printed (contrary to lorenzo's
   output)

3- I think in rutile, we should have 6 atoms in cell, but lorenzo's
   output has 4 atoms without symbols.



Regards

David Foster

Ph.D. Student of Chemistry


On Wed, 1/8/14, Carlo Nervi  wrote:

 Subject: Re: [Pw_forum] Error in converting CIF to QE by "cif2qe.sh"
 To: pw_forum at pwscf.org
 Date: Wednesday, January 8, 2014, 3:44 AM
 
 Hi David,
 it seems that in the line containing
 _Symmetry_equiv_pos_as_xyz it does 
 not recognize the three necessary parameters.
 Have a look of the original .cif file and if there is only
 spaces after 
 _Symmetry_equiv_pos_as_xyz just delete the line.
 
 In any cases, Lorenzo succeed in using the conversion, so
 maybe it is 
 again a problem related with your version og awk.
 Preferabily please use 
 gawk (gnu awk).
 
 Regards,
 ??? Carlo
 
 Il 08/01/2014 8.56, David Foster ha scritto:
 > Dear Paolo
 >
 > Thank you for reply. I upgrade the file to 5th
 version.
 >
 > I installed gawk 4. Now, I recieve this error:
 >
 >
 > Error in _Symmetry_equiv_pos_as_xyz. Number of fields
 !=3: [1]= [2]= [3]=
 > D:
 >
 >
 >
 > Regards
 >
 > David Foster
 >
 > Ph.D. Student of Chemistry
 >
 > 
 > On Tue, 1/7/14, Paolo Giannozzi 
 wrote:
 >
 >???Subject: Re: [Pw_forum] Error in
 converting CIF to QE by "cif2qe.sh"
 >???To: pw_forum at pwscf.org
 >???Date: Tuesday, January 7, 2014, 2:11
 PM
 >
 >???This is the header of the last
 >???version. Note the fourth line:
 >???---
 >???#? Version 0.5? Date:
 02-Oct-2013
 >???#? Version 0.4? Date: 12 Jun
 2013
 >???#? Version 0.3? Date: 15 Nov
 2012
 >???# tested with GNU awk v.4 - may not
 work with earlier
 >???versions
 >???---
 >
 >???P.
 >???On Tue, 2014-01-07 at 07:08 -0800,
 David Foster wrote:
 >
 >???> I will download new version and
 try.
 >???>
 >???> I work on Debian 7.0 which "mwak"
 has been installed on
 >???it. Do I need to install "gawk" on
 it.
 >???>
 >???>
 >???> Regards
 >???>
 >???> David Foster
 >???>
 >???> Ph.D. Student of Chemistry
 >???>
 >???>
 
 >???> On Tue, 1/7/14, Lorenzo Paulatto
 
 >???wrote:
 >???>
 >???>? Subject: Re: [Pw_forum]
 Error in converting CIF
 >???to QE by "cif2qe.sh"
 >???>? To: "PWSCF Forum" 
 >???>? Date: Tuesday, January 7,
 2014, 5:45 AM
 >???>
 >???>? On 01/07/2014 01:18 PM,
 David Foster
 >???>? wrote:> Dear Users,
 >???>? > I used cif2qe.sh shell
 in PW/tools directory
 >???to convert
 >???>? rutile.cif to
 >???>
 >???>? It works for me, I get the
 following output.
 >???>
 >???>? How do you run the code,
 and which version of
 >???bash and awk
 >???>? do you have? Did you change
 anything in the
 >???script?
 >???>
 >???>
 >???>? best regards
 >???>
 >???>? 
 >???>
 >
 >???>? ? ?
 ???titl

[Pw_forum] Error in converting CIF to QE by "cif2qe.sh"

[David Foster]

Thank you very much, Carlo.

I delete the line

The problem solved.

Thank you very much.


Regards

David Foster

Ph.D. Student of Chemistry


On Wed, 1/8/14, Carlo Nervi  wrote:

 Subject: Re: [Pw_forum] Error in converting CIF to QE by "cif2qe.sh"
 To: pw_forum at pwscf.org
 Date: Wednesday, January 8, 2014, 3:44 AM
 
 Hi David,
 it seems that in the line containing
 _Symmetry_equiv_pos_as_xyz it does 
 not recognize the three necessary parameters.
 Have a look of the original .cif file and if there is only
 spaces after 
 _Symmetry_equiv_pos_as_xyz just delete the line.
 
 In any cases, Lorenzo succeed in using the conversion, so
 maybe it is 
 again a problem related with your version og awk.
 Preferabily please use 
 gawk (gnu awk).
 
 Regards,
 ??? Carlo
 
 Il 08/01/2014 8.56, David Foster ha scritto:
 > Dear Paolo
 >
 > Thank you for reply. I upgrade the file to 5th
 version.
 >
 > I installed gawk 4. Now, I recieve this error:
 >
 >
 > Error in _Symmetry_equiv_pos_as_xyz. Number of fields
 !=3: [1]= [2]= [3]=
 > D:
 >
 >
 >
 > Regards
 >
 > David Foster
 >
 > Ph.D. Student of Chemistry
 >
 > 
 > On Tue, 1/7/14, Paolo Giannozzi 
 wrote:
 >
 >???Subject: Re: [Pw_forum] Error in
 converting CIF to QE by "cif2qe.sh"
 >???To: pw_forum at pwscf.org
 >???Date: Tuesday, January 7, 2014, 2:11
 PM
 >
 >???This is the header of the last
 >???version. Note the fourth line:
 >???---
 >???#? Version 0.5? Date:
 02-Oct-2013
 >???#? Version 0.4? Date: 12 Jun
 2013
 >???#? Version 0.3? Date: 15 Nov
 2012
 >???# tested with GNU awk v.4 - may not
 work with earlier
 >???versions
 >???---
 >
 >???P.
 >???On Tue, 2014-01-07 at 07:08 -0800,
 David Foster wrote:
 >
 >???> I will download new version and
 try.
 >???>
 >???> I work on Debian 7.0 which "mwak"
 has been installed on
 >???it. Do I need to install "gawk" on
 it.
 >???>
 >???>
 >???> Regards
 >???>
 >???> David Foster
 >???>
 >???> Ph.D. Student of Chemistry
 >???>
 >???>
 
 >???> On Tue, 1/7/14, Lorenzo Paulatto
 
 >???wrote:
 >???>
 >???>? Subject: Re: [Pw_forum]
 Error in converting CIF
 >???to QE by "cif2qe.sh"
 >???>? To: "PWSCF Forum" 
 >???>? Date: Tuesday, January 7,
 2014, 5:45 AM
 >???>
 >???>? On 01/07/2014 01:18 PM,
 David Foster
 >???>? wrote:> Dear Users,
 >???>? > I used cif2qe.sh shell
 in PW/tools directory
 >???to convert
 >???>? rutile.cif to
 >???>
 >???>? It works for me, I get the
 following output.
 >???>
 >???>? How do you run the code,
 and which version of
 >???bash and awk
 >???>? do you have? Did you change
 anything in the
 >???script?
 >???>
 >???>
 >???>? best regards
 >???>
 >???>? 
 >???>
 >
 >???>? ? ?
 ???title = 'rutile'
 >???>
 >
 >???>?
 ???calculation = 'relax'
 >???>
 >
 >???>? restart_mode =
 'from_scratch'
 >???>
 >
 >???>? ? ? ? outdir
 = './1'
 >???>
 >
 >???>? ? pseudo_dir =
 '../PP/atompaw'
 >???>
 >
 >???>? ? ? ? prefix
 = 'caz'
 >???>
 >
 >???>? ?
 ???disk_io = 'none'
 >???>
 >
 >???>? ???verbosity
 = 'default'
 >???>
 >???>?
 ???etot_conv_thr = 0.1
 >???>
 >???>?
 ???forc_conv_thr = 0.0001
 >???>
 >
 >???>? ? ?
 ???nstep = 680
 >???>
 >
 >???>? ?
 ???tstress = .true.
 >???>
 >
 >???>? ?
 ???tprnfor = .true.
 >???>???/
 >???>???
 >???>
 >
 >???>? ? ?
 ???ibrav = 0
 >???>
 >
 >???>? ? ? ?
 ???nat = 4
 >???>
 >
 >???>? ? ? ? ?
 ntyp = 1
 >???>
 >
 >???>? ?
 ???ecutwfc = 60
 >???>
 >
 >???>? ?
 ???ecutrho = 600
 >???>? !
 >
 >???>? ? ? ? london
 = .true.
 >???>???/
 >???>???
 >???>
 >???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'
 >???>???/
 >???>? 
 >???>
 >
 >???>? ion_dynamics = 'bfgs'
 >???>???/
 >???>
 >???>
 >???>? ATOMIC_SPECIES
 >???>
 >? ? ? 0.00
 >???>? .pbe-van_a

[Pw_forum] Error in converting CIF to QE by "cif2qe.sh"

[David Foster]

Dear Paolo

Thank you for reply. I upgrade the file to 5th version.

I installed gawk 4. Now, I recieve this error:


Error in _Symmetry_equiv_pos_as_xyz. Number of fields !=3: [1]= [2]= [3]=
D:



Regards

David Foster

Ph.D. Student of Chemistry


On Tue, 1/7/14, Paolo Giannozzi  wrote:

 Subject: Re: [Pw_forum] Error in converting CIF to QE by "cif2qe.sh"
 To: pw_forum at pwscf.org
 Date: Tuesday, January 7, 2014, 2:11 PM
 
 This is the header of the last
 version. Note the fourth line:
 ---
 #? Version 0.5? Date: 02-Oct-2013
 #? Version 0.4? Date: 12 Jun 2013
 #? Version 0.3? Date: 15 Nov 2012
 # tested with GNU awk v.4 - may not work with earlier
 versions
 ---
 
 P.
 On Tue, 2014-01-07 at 07:08 -0800, David Foster wrote:
 
 > I will download new version and try.
 > 
 > I work on Debian 7.0 which "mwak" has been installed on
 it. Do I need to install "gawk" on it.
 > 
 > 
 > Regards
 > 
 > David Foster
 > 
 > Ph.D. Student of Chemistry
 > 
 > 
 > On Tue, 1/7/14, Lorenzo Paulatto 
 wrote:
 > 
 >? Subject: Re: [Pw_forum] Error in converting CIF
 to QE by "cif2qe.sh"
 >? To: "PWSCF Forum" 
 >? Date: Tuesday, January 7, 2014, 5:45 AM
 >? 
 >? On 01/07/2014 01:18 PM, David Foster
 >? wrote:> Dear Users,
 >? > I used cif2qe.sh shell in PW/tools directory
 to convert
 >? rutile.cif to
 >? 
 >? It works for me, I get the following output.
 >? 
 >? How do you run the code, and which version of
 bash and awk
 >? do you have? Did you change anything in the
 script?
 >? 
 > 
 >? best regards
 >? 
 >? 
 >? ? ? ? ? ? ?
 ???
 >? ? ? ???title = 'rutile'
 >? ? ? ? ? ?
 ???
 >? ???calculation = 'relax'
 >? ? ? ? ? ? ?
 ???
 >? restart_mode = 'from_scratch'
 >? ? ? ? ? ? ?
 ???
 >? ? ? ? outdir = './1'
 >? ? ? ? ? ? ?
 ???
 >? ? pseudo_dir = '../PP/atompaw'
 >? ? ? ? ? ? ?
 ???
 >? ? ? ? prefix = 'caz'
 >? ? ? ? ? ? ?
 ???
 >? ? ???disk_io = 'none'
 >? ? ? ? ? ? ?
 ???
 >? ???verbosity = 'default'
 >? ? ? ? ? ???
 >? ???etot_conv_thr = 0.1
 >? ? ? ? ? ???
 >? ???forc_conv_thr = 0.0001
 >? ? ? ? ? ? ?
 ???
 >? ? ? ???nstep = 680
 >? ? ? ? ? ? ?
 ???
 >? ? ???tstress = .true.
 >? ? ? ? ? ? ?
 ???
 >? ? ???tprnfor = .true.
 >???/
 >???
 >? ? ? ? ? ? ?
 ???
 >? ? ? ???ibrav = 0
 >? ? ? ? ? ? ?
 ???
 >? ? ? ? ???nat = 4
 >? ? ? ? ? ? ?
 ???
 >? ? ? ? ? ntyp = 1
 >? ? ? ? ? ? ?
 ???
 >? ? ???ecutwfc = 60
 >? ? ? ? ? ? ?
 ???
 >? ? ???ecutrho = 600
 >? !? ? ? ? ? ?
 ???
 >? ? ? ? london = .true.
 >???/
 >???
 >? ? ? ? ? ? ?
 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'
 >???/
 >? 
 >? ? ? ? ? ? ?
 ???
 >? ion_dynamics = 'bfgs'
 >???/
 >? 
 > 
 >? ATOMIC_SPECIES
 >? ? ? ?
 ???0.00 
 >? .pbe-van_ak.UPF
 >? 
 >? ATOMIC_POSITIONS crystal
 >? ? ? ???0.000
 
 >? ???0.000 
 >? ???0.000
 >? ? ? ???0.3053000
 
 >? ???0.3053000 
 >? ???0.000
 >? ? ? ???0.500
 
 >? ???0.500 
 >? ???0.500
 >? ? ? ???0.8053000
 
 >? ???0.1947000 
 >? ???0.500
 >? 
 >? K_POINTS automatic
 >? 5? 5? 8???0 0 0
 >? 
 > 
 >? CELL_PARAMETERS
 >? ? ? 8.680891628420765 
 >? ???0.000 
 >? ???0.000
 >? ? ? 0.001 
 >? ???8.680891628420765 
 >? ???0.000
 >? ? ? 0.000 
 >? ???0.000 
 >? ???5.590036668211679
 >? 
 > 
 > 
 > 
 >? -- Dr. Lorenzo Paulatto
 >? IdR @ IMPMC -- CNRS & Universit? Paris 6
 >? +33 (0)1 44 275 084 / skype: paulatz
 >? http://www-int.impmc.upmc.fr/~paulatto/
 >? 23-24/4?16 Bo?te courrier 115, 4 place Jussieu
 75252 Paris
 >? C?dex 05
 >? 
 > 
 >? -Inline Attachment Follows-
 >? 
 >? ___
 >? Pw_forum mailing list
 >? Pw_forum at pwscf.org
 >? http://pwscf.org/mailman/listinfo/pw_forum
 > 
 > ___
 > Pw_forum mailing list
 > Pw_forum at pwscf.org
 > http://pwscf.org/mailman/listinfo/pw_forum
 
 -- 
 Paolo Giannozzi, Dept.
 Chemistry, 
 Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
 Phone +39-0432-558216, fax +39-0432-558222 
 
 ___
 Pw_forum mailing list
 Pw_forum at pwscf.org
 http://pwscf.org/mailman/listinfo/pw_forum

[Pw_forum] Error in converting CIF to QE by "cif2qe.sh"

[David Foster]

And I run as follows:

./cif2qe.sh rutile

without .cif


Regards

David Foster

Ph.D. Student of Chemistry


On Tue, 1/7/14, Lorenzo Paulatto  wrote:

 Subject: Re: [Pw_forum] Error in converting CIF to QE by "cif2qe.sh"
 To: "PWSCF Forum" 
 Date: Tuesday, January 7, 2014, 5:45 AM
 
 On 01/07/2014 01:18 PM, David Foster
 wrote:> Dear Users,
 > I used cif2qe.sh shell in PW/tools directory to convert
 rutile.cif to
 
 It works for me, I get the following output.
 
 How do you run the code, and which version of bash and awk
 do you have? Did you change anything in the script?
 
 
 best regards
 
 
 ? ? ? ? ? ? ? ?
 ? ? ???title = 'rutile'
 ? ? ? ? ? ? ?
 ???calculation = 'relax'
 ? ? ? ? ? ? ? ?
 restart_mode = 'from_scratch'
 ? ? ? ? ? ? ? ?
 ? ? ? outdir = './1'
 ? ? ? ? ? ? ? ?
 ? pseudo_dir = '../PP/atompaw'
 ? ? ? ? ? ? ? ?
 ? ? ? prefix = 'caz'
 ? ? ? ? ? ? ? ?
 ? ???disk_io = 'none'
 ? ? ? ? ? ? ? ?
 ???verbosity = 'default'
 ? ? ? ? ? ?
 ???etot_conv_thr = 0.1
 ? ? ? ? ? ?
 ???forc_conv_thr = 0.0001
 ? ? ? ? ? ? ? ?
 ? ? ???nstep = 680
 ? ? ? ? ? ? ? ?
 ? ???tstress = .true.
 ? ? ? ? ? ? ? ?
 ? ???tprnfor = .true.
  /
  
 ? ? ? ? ? ? ? ?
 ? ? ???ibrav = 0
 ? ? ? ? ? ? ? ?
 ? ? ? ???nat = 4
 ? ? ? ? ? ? ? ?
 ? ? ? ? ntyp = 1
 ? ? ? ? ? ? ? ?
 ? ???ecutwfc = 60
 ? ? ? ? ? ? ? ?
 ? ???ecutrho = 600
 !? ? ? ? ? ? ? ?
 ? ? ? london = .true.
  /
  
 ? ? ? ? ? ? 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'
  /
 
 ? ? ? ? ? ? ? ?
 ion_dynamics = 'bfgs'
  /
 
 
 ATOMIC_SPECIES
 ? ? ? ???0.00?
 .pbe-van_ak.UPF
 
 ATOMIC_POSITIONS crystal
 ? ? ???0.000?
 ???0.000?
 ???0.000
 ? ? ???0.3053000?
 ???0.3053000?
 ???0.000
 ? ? ???0.500?
 ???0.500?
 ???0.500
 ? ? ???0.8053000?
 ???0.1947000?
 ???0.500
 
 K_POINTS automatic
 5? 5? 8???0 0 0
 
 
 CELL_PARAMETERS
 ? ? 8.680891628420765?
 ???0.000?
 ???0.000
 ? ? 0.001?
 ???8.680891628420765?
 ???0.000
 ? ? 0.000?
 ???0.000?
 ???5.590036668211679
 
 
 
 
 -- Dr. Lorenzo Paulatto
 IdR @ IMPMC -- CNRS & Universit? Paris 6
 +33 (0)1 44 275 084 / skype: paulatz
 http://www-int.impmc.upmc.fr/~paulatto/
 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris
 C?dex 05
 
 
 -Inline Attachment Follows-
 
 ___
 Pw_forum mailing list
 Pw_forum at pwscf.org
 http://pwscf.org/mailman/listinfo/pw_forum

[Pw_forum] Error in converting CIF to QE by "cif2qe.sh"

[David Foster]

Dear Lorenzo

Thank you for your reply. I used 5.0.2 version of QE. I didn't change anything. 
I will download new version and try.

I work on Debian 7.0 which "mwak" has been installed on it. Do I need to 
install "gawk" on it.


Regards

David Foster

Ph.D. Student of Chemistry


On Tue, 1/7/14, Lorenzo Paulatto  wrote:

 Subject: Re: [Pw_forum] Error in converting CIF to QE by "cif2qe.sh"
 To: "PWSCF Forum" 
 Date: Tuesday, January 7, 2014, 5:45 AM
 
 On 01/07/2014 01:18 PM, David Foster
 wrote:> Dear Users,
 > I used cif2qe.sh shell in PW/tools directory to convert
 rutile.cif to
 
 It works for me, I get the following output.
 
 How do you run the code, and which version of bash and awk
 do you have? Did you change anything in the script?
 
 
 best regards
 
 
 ? ? ? ? ? ? ? ?
 ? ? ???title = 'rutile'
 ? ? ? ? ? ? ?
 ???calculation = 'relax'
 ? ? ? ? ? ? ? ?
 restart_mode = 'from_scratch'
 ? ? ? ? ? ? ? ?
 ? ? ? outdir = './1'
 ? ? ? ? ? ? ? ?
 ? pseudo_dir = '../PP/atompaw'
 ? ? ? ? ? ? ? ?
 ? ? ? prefix = 'caz'
 ? ? ? ? ? ? ? ?
 ? ???disk_io = 'none'
 ? ? ? ? ? ? ? ?
 ???verbosity = 'default'
 ? ? ? ? ? ?
 ???etot_conv_thr = 0.1
 ? ? ? ? ? ?
 ???forc_conv_thr = 0.0001
 ? ? ? ? ? ? ? ?
 ? ? ???nstep = 680
 ? ? ? ? ? ? ? ?
 ? ???tstress = .true.
 ? ? ? ? ? ? ? ?
 ? ???tprnfor = .true.
  /
  
 ? ? ? ? ? ? ? ?
 ? ? ???ibrav = 0
 ? ? ? ? ? ? ? ?
 ? ? ? ???nat = 4
 ? ? ? ? ? ? ? ?
 ? ? ? ? ntyp = 1
 ? ? ? ? ? ? ? ?
 ? ???ecutwfc = 60
 ? ? ? ? ? ? ? ?
 ? ???ecutrho = 600
 !? ? ? ? ? ? ? ?
 ? ? ? london = .true.
  /
  
 ? ? ? ? ? ? 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'
  /
 
 ? ? ? ? ? ? ? ?
 ion_dynamics = 'bfgs'
  /
 
 
 ATOMIC_SPECIES
 ? ? ? ???0.00?
 .pbe-van_ak.UPF
 
 ATOMIC_POSITIONS crystal
 ? ? ???0.000?
 ???0.000?
 ???0.000
 ? ? ???0.3053000?
 ???0.3053000?
 ???0.000
 ? ? ???0.500?
 ???0.500?
 ???0.500
 ? ? ???0.8053000?
 ???0.1947000?
 ???0.500
 
 K_POINTS automatic
 5? 5? 8???0 0 0
 
 
 CELL_PARAMETERS
 ? ? 8.680891628420765?
 ???0.000?
 ???0.000
 ? ? 0.001?
 ???8.680891628420765?
 ???0.000
 ? ? 0.000?
 ???0.000?
 ???5.590036668211679
 
 
 
 
 -- Dr. Lorenzo Paulatto
 IdR @ IMPMC -- CNRS & Universit? Paris 6
 +33 (0)1 44 275 084 / skype: paulatz
 http://www-int.impmc.upmc.fr/~paulatto/
 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris
 C?dex 05
 
 
 -Inline Attachment Follows-
 
 ___
 Pw_forum mailing list
 Pw_forum at pwscf.org
 http://pwscf.org/mailman/listinfo/pw_forum

[Pw_forum] Error in converting CIF to QE by "cif2qe.sh"

[David Foster]

Dear Users,
I used cif2qe.sh shell in PW/tools directory to convert rutile.cif to

QE input. I got following errors:

awk: 29: unexpected character '&'
awk: line 75: syntax error at or near [
awk: line 99: syntax error at or near [
awk: line 101: syntax error at or near [
awk: line 105: syntax error at or near [

===
This is rutile cif:


# Part of the Crystallography Open Database
# All data on this site have been placed in the public domain by the
# contributors.
#--
#$Date: 2010-06-10 15:11:07 + (Thu, 10 Jun 2010) $
#$Revision: 1210 $
#$URL: svn://cod.ibt.lt/cod/cif/9/9009083.cif $
#--
#
# This file is available in the Crystallography Open Database (COD),
# http://www.crystallography.net/. The original data for this entry
# were provided the American Mineralogist Crystal Structure Database,
# http://rruff.geo.arizona.edu/AMS/amcsd.php
#
# The file may be used within the scientific community so long as
# proper attribution is given to the journal article from which the
# data were obtained.
#
data_9009083
loop_
_publ_author_name
'Wyckoff, R. W. G.'
_publ_section_title
;
 Second edition. Interscience Publishers, New York, New York
;
_journal_name_full   'Crystal Structures'
_journal_page_first  239
_journal_page_last   444
_journal_volume  1
_journal_year1963
_chemical_formula_sum'O2 Ti'
_chemical_name_mineral   Rutile
_space_group_IT_number   136
_symmetry_space_group_name_Hall  '-P 4n 2n'
_symmetry_space_group_name_H-M   'P 42/m n m'
_cell_angle_alpha90
_cell_angle_beta 90
_cell_angle_gamma90
_cell_length_a   4.59373
_cell_length_b   4.59373
_cell_length_c   2.95812
_cell_volume 62.423
_exptl_crystal_density_diffrn4.250
_[local]_cod_chemical_formula_sum_orig 'Ti O2'
_cod_database_code   9009083
_amcsd_database_code AMCSD#0011415
loop_
_symmetry_equiv_pos_as_xyz
x,y,z
-y,-x,z
y,x,-z
1/2+y,1/2-x,1/2-z
1/2-y,1/2+x,1/2+z
1/2+x,1/2-y,1/2+z
1/2-x,1/2+y,1/2-z
x,y,-z
-x,-y,z
y,x,z
-y,-x,-z
1/2-y,1/2+x,1/2-z
1/2+y,1/2-x,1/2+z
1/2-x,1/2+y,1/2+z
1/2+x,1/2-y,1/2-z
-x,-y,-z
loop_
_atom_site_label
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
Ti 0.0 0.0 0.0
O 0.30530 0.30530 0.0

anybody can help?

Regards

David Foster

Ph.D. Student of Chemistry

[Pw_forum] 6 symmetry operators not found in MgCl2

[david Foster]

Thanks Paolo. Does this subject (ignoring some symmetry operations) changes 
final energy.


Regards

David Foster

Ph.D. Student of Chemistry


On Mon, 12/23/13, Paolo Giannozzi  wrote:

 Subject: Re: [Pw_forum] 6 symmetry operators not found in MgCl2
 To: pw_forum at pwscf.org
 Date: Monday, December 23, 2013, 4:02 AM
 
 On Mon, 2013-12-23 at 02:23 -0800,
 david Foster wrote:
 
 > the program report "this is supercell, fractional 
 > translations are ignored".
 > 
 > How can force the program to use them.
 
 you cannot. More exactly: you have to find a way to choose
 fractional translations in such a way that the group of
 symmetry operations is a group in the mathematical sense
 of the term; then implement it. I have never found a safe
 and simple way to do that.
 
 P.
 -- 
 Paolo Giannozzi, Dept.
 Chemistry, 
 Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
 Phone +39-0432-558216, fax +39-0432-558222 
 
 ___
 Pw_forum mailing list
 Pw_forum at pwscf.org
 http://pwscf.org/mailman/listinfo/pw_forum
 

[Pw_forum] 6 symmetry operators not found in MgCl2

[david Foster]

Thank you Reza. The problem is solved.


another problem:

In some cases (such as Al2O3 unit cell calculation), the program report "this 
is supercell, fractional 

translations are ignored".

How can force the program to use them. I used "use_all_frac=.true." and set 
nr1=120, nr2=120,nr3=120

nr1s=60, nr2s=60, nr3s=60, but the problem exist. 

For Al2O3 I get 6+inversion=12 symmetry operator, while it has 36 symm. op.



Regards

David Foster

Ph.D. Student of Chemistry

[Pw_forum] 6 symmetry operators not found in MgCl2

[david Foster]

(Ry/au):

 atom1 type  1   force = 0.0.   -0.1948
 atom2 type  2   force =-0.0.0.1948

 Total force = 0.28 Total SCF correction = 0.39
 SCF correction compared to forces is large: reduce conv_thr to get better 
values


 entering subroutine stress ...

  total   stress  (Ry/bohr**3)   (kbar) P=   59.87
   0.00063777   0.   0. 93.82  0.00  0.00
   0.   0.00063777  -0.  0.00 93.82 -0.00
   0.  -0.  -0.5455  0.00 -0.00 -8.02


 bfgs converged in   7 scf cycles and   6 bfgs steps
 (criteria: energy < 0.10E-05, force < 0.10E-03)

 End of BFGS Geometry Optimization

 Final energy   = -31.6080654560 Ry
Begin final coordinates

ATOMIC_POSITIONS (angstrom)
Mg   0.0  -0.0  -0.088986292
Cl   0.0   2.102133000   1.452196292
End final coordinates
.
.
.
.
.
 
=--=
   JOB DONE.
=------=



Regards

David Foster

Ph.D. Student of Chemistry

[Pw_forum] error in relaxation Fe supercell

[david Foster]

Dear Giuseppe

Very thanks


Regards

David Foster

Ph.D. Student of Chemistry

[Pw_forum] error in relaxation Fe supercell

[david Foster]

Dear Axel

Very Thanks.

Regards

David Foster

Ph.D. Student of Chemistry

[Pw_forum] error in relaxation Fe supercell

[david Foster]

Hi all

One more question: In which subroutine/module overlap of atoms are checked?


Regards

David Foster

Ph.D. Student of Chemistry


On Thu, 12/19/13, david  wrote:

 Subject: [Pw_forum] error in relaxation Fe supercell
 To: pw_forum at pwscf.org
 Date: Thursday, December 19, 2013, 1:03 AM
 
 Hi Dear All
 
 I have prepared a 2*2*2 supercell, and tried to optimized
 its coordinations with relax command.
 
 But I have gotten following error in pw.x output (I used
 5.0.2 version, parallel, mpich3.1.4, ifort 13, icc13, and
 icpc) :
 
 
 ==
  Error in routine cdiaghg (176):
 ? ???S matrix not positive definite
  ==
 
 ? ???stopping ...
 
 I have attached both input and output. I will appreciate any
 help.
 
 
 
 
 
 Regards
 
 David Foster
 
 Ph.D. Student of Chemistry
 -Inline Attachment Follows-
 
 ___
 Pw_forum mailing list
 Pw_forum at pwscf.org
 http://pwscf.org/mailman/listinfo/pw_forum

[Pw_forum] error in relaxation Fe supercell

[david Foster]

Sorry. I have corrected my input ( change alat to angstrom). The first error 
was solved, but

New error I got:


===

 Error in routine check_atoms (1):
 atoms #   1 and #  15 overlap!
 
 stopping ...

 
 Error in routine check_atoms (1):
 atoms #   1 and #  15 overlap!

 
 Error in routine check_atoms (1):
 atoms #   1 and #  15 overlap!
 
 stopping ...

 
 Error in routine check_atoms (1):
 atoms #   1 and #  15 overlap!
 

 stopping ...

 
 Error in routine check_atoms (1):
 atoms #   1 and #  15 overlap!
 

 stopping ...

 
 Error in routine check_atoms (1):
 atoms #   1 and #  15 overlap!


 stopping ...

 
 Error in routine check_atoms (1):
 atoms #   1 and #  15 overlap!
 
 stopping ...


 Error in routine check_atoms (1):
 atoms #   1 and #  15 overlap!
 

 stopping ...


 Error in routine check_atoms (1):
 atoms #   1 and #  15 overlap!


 stopping ...

 
 Error in routine check_atoms (1):
 atoms #   1 and #  15 overlap!
 ...




I have attached them.




Regards

David Foster

Ph.D. Student of Chemistry


On Thu, 12/19/13, david  wrote:

 Subject: [Pw_forum] error in relaxation Fe supercell
 To: pw_forum at pwscf.org
 Date: Thursday, December 19, 2013, 1:03 AM
 
 Hi Dear All
 
 I have prepared a 2*2*2 supercell, and tried to optimized
 its coordinations with relax command.
 
 But I have gotten following error in pw.x output (I used
 5.0.2 version, parallel, mpich3.1.4, ifort 13, icc13, and
 icpc) :
 
 
 ==
  Error in routine cdiaghg (176):
 ? ???S matrix not positive definite
  ==
 
 ? ???stopping ...
 
 I have attached both input and output. I will appreciate any
 help.
 
 
 
 
 
 Regards
 
 David Foster
 
 Ph.D. Student of Chemistry
 -Inline Attachment Follows-
 
 ___
 Pw_forum mailing list
 Pw_forum at pwscf.org
 http://pwscf.org/mailman/listinfo/pw_forum
-- next part --
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[Pw_forum] fermi energy

[david foster]

Hi
I need help

I have calculated Fermi energy of iron. It is near to 14 as one of espresso 
example. But recalculation with castep (material studio) give me near to zero.
\
For metals what should be the Fermi energy, typically?
Regards

D. Foster

Ph.D. Student of Chemistry