[Pw_forum] ATOMIC_POSITIONS after 'final coordinates'

[Xijun Wang]

Hi, dear espressors,

I'm new to espresso (switching from CPMD) and I have a simple question
regarding to the output file of a relax calculation.

There is an extra "ATOMIC_POSITIONS" section after the "final
coordinates". It is neither the final coordinates, nor the starting
coordinates, nor cystal coordinates. What's that? See below the output
file. I'd appreciate it if someone can tell me where to find the
explanation to the output file in the manual. I have searched the
maillist and manual online but find no answer.

Xijun Wang
--
Department of Chemistry and Biochemistry, Concordia University
7141 Sherbrooke Ouest, Montreal, QC, Canada (H4B 1R6)
Tel: 514-848-2424-#5835 (Lab) TA office: SP175.23

*** output file of the relaxation calculation ***
-
...
? ? ?Damped Dynamics: convergence achieved in ?11 steps
? ? ?End of damped dynamics calculation
? ? ?Final energy = ? -3499.4924725209 Ry
Begin final coordinates
? ? ?new unit-cell volume = ? 5281.07728 a.u.^3 ( ? 782.57490 Ang^3 )
CELL_PARAMETERS (alat= 19.96079920)
? ?1.0 ? 0.0 ? 0.0
? ?0.0 ? 0.591661302 ? 0.0
? -0.254163181 ? 0.0 ? 1.122317102
ATOMIC_POSITIONS (angstrom)
Zr ? ? ?-0.000121009 ? 0.0 ? 0.48982
Zr ? ? ? 0.050917464 ? 0.0 ? 6.659231281
...
End final coordinates


? ? ?Entering Dynamics: ? ?iteration = ? ?11
? ? ? = ? 0.78384260
ATOMIC_POSITIONS (angstrom)
Zr ? ? ? 0.33474 ? 0.0 ? 0.000130486
Zr ? ? ? 0.050452867 ? 0.0 ? 6.659368418
...

 Writing output data file rx.damp.save
...

[Pw_forum] At line 174 of file paw_gipaw.f90 (unit = 14, file = '')

[Emine Kucukbenli]

Hi Daniel,
are you sure you are using pseudopotentials that hold gipaw information?
if so, send me the pseudo i'll check what is wrong.
thanks
emine kucukbenli, phd student, sissa, italy



   SISSA Webmail https://webmail.sissa.it/
   Powered by Horde http://www.horde.org/

[Pw_forum] At line 174 of file paw_gipaw.f90 (unit = 14, file = '')

[Paolo Giannozzi]

On Sep 6, 2011, at 18:56 , Daniel Lima wrote:

> Thanks in advance and sorry for bad english

bad english is not a problem: it is the norm here.
The problem is that you haven't specified which
version of the code you are talking about. Gipaw,
in particular, has undergone serious changes in
the last versions

P.
---
Paolo Giannozzi, Dept of Chemistry,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222

[Pw_forum] wfc files: heavy I/O, handling for restarts

[S. K. S.]

Dear Prof. Paolo,

Thanks a lot for your reply.

> which QE code and which files are you referring to? <

That is phonon code (ph.x) and the files I mentioned before are given below
in detail.

With the earlier versions up to 4.1.3, phonon code runs fine and  I got
following files
(bold and underlined items are folders) in the tmp directory of a local
disk.
The nodes which are used by the codes are node186, 036, 139.

   node186:/tmpscratch/sksct8/tmp$ ls

> *pbmno.save* _phpbmno.com1_phpbmno.dwf2   _phpbmno.igk3
> _phpbmno.prd3
> pbmno.wfc1 _phpbmno.com2_phpbmno.dwf3   _phpbmno.mixd1
> _phpbmno.recover
> pbmno.wfc2 _phpbmno.com3_phpbmno.ebar1  _phpbmno.mixd2
> _phpbmno.recover2
> pbmno.wfc3 _phpbmno.dvkb31  _phpbmno.ebar2  _phpbmno.mixd3
> _phpbmno.recover3
> _phpbmno.bar1  _phpbmno.dvkb32  _phpbmno.ebar3  *_phpbmno.phsave** * *
> _phpbmno.save*
> _phpbmno.bar2  _phpbmno.dvkb33  _phpbmno.igk_phpbmno.prd1
> _phpbmno.bar3  _phpbmno.dwf1_phpbmno.igk2   _phpbmno.prd2
>

node036:/tmpscratch/sksct8/tmp$ ls
pbmno.wfc4 _phpbmno.dwf4  _phpbmno.mixd4  _phpbmno.recover4
pbmno.wfc5 _phpbmno.dwf5  _phpbmno.mixd5  _phpbmno.recover5
_phpbmno.bar4  _phpbmno.igk4  _phpbmno.prd4   _phpbmno.wfc4
_phpbmno.bar5  _phpbmno.igk5  _phpbmno.prd5   _phpbmno.wfc5

node139:/tmpscratch/sksct8/tmp$ ls
pbmno.wfc6 _phpbmno.bar8  _phpbmno.igk7  _phpbmno.recover6
_phpbmno.wfc8
pbmno.wfc7 _phpbmno.dwf6  _phpbmno.igk8  _phpbmno.recover7
pbmno.wfc8 _phpbmno.dwf7  _phpbmno.prd6  _phpbmno.recover8
_phpbmno.bar6  _phpbmno.dwf8  _phpbmno.prd7  _phpbmno.wfc6
_phpbmno.bar7  _phpbmno.igk6  _phpbmno.prd8  _phpbmno.wfc7

However, with the new version 4.3.1, for the exactly same input files and
job scripts I only get these files and nothing else :

node045:/tmpscratch/sksct84/tmp$ ls
*pbmno.save*  pbmno.wfc1  *_ph0*

node111:/tmpscratch/sksct84/tmp$ ls
pbmno.wfc2  pbmno.wfc3

node092:/tmpscratch/sksct84/tmp$ ls
pbmno.wfc4  pbmno.wfc5

node080:/tmpscratch/sksct84/tmp$ ls
pbmno.wfc6  pbmno.wfc7

node072:/tmpscratch/sksct84/tmp$ ls
pbmno.wfc8

Note that,  the used nodes in this time are  node045, node111, node092,
node080, node072.

So it is clear from the above example that somehow in the new version
4.3.1,  _phpbmno.save and
_phpbmno.phsave goes inside the directory "_ph0" ;

And the same phonon calculation,  which was running fine with the earlier
version, now stops like this way (a bit
abruptly and rudely, with out much informations or error messages) :


Electric field:
 Dielectric constant
 Born effective charges in two ways


 Atomic displacements:
 There are   5 irreducible representations

 Representation 1  3 modes -T_1u G_15  G_4- To be done

 Representation 2  3 modes -T_1u G_15  G_4- To be done

 Representation 3  3 modes -T_1u G_15  G_4- To be done

 Representation 4  3 modes -T_1u G_15  G_4- To be done

 Representation 5  3 modes -T_2u G_25  G_5- To be done



simply with this error :
--
MPI_ABORT was invoked on rank 2 in communicator MPI_COMM_WORLD
with errorcode 0.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--
--
mpirun has exited due to process rank 2 with PID 8791 on
node node111.cvos.cluster exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
--
[node045:11580] 6 more processes have sent help message help-mpi-api.txt /
mpi-abort
[node045:11580] Set MCA parameter "orte_base_help_aggregate" to 0 to see all
help / error messages


Hope this email explains much better.

Thanks and Regards,
Saha SK
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[Pw_forum] At line 174 of file paw_gipaw.f90 (unit = 14, file = '')

[Eugenio Furtado]

you sure you doing the right thing? Did you choose the correct pseudop? your 
compilation ran perfectly? The system were correctly relaxed? 
Can you send the pseudos and the input for checks? 

Eugenio Furtado de Souza 
Laboratorio de Modelagem Molecular-LABMMOL 
Universidade Federal do Rio de Janeiro 
Av. Athos da Silveira Ramos No 149, CT, Bloco A, sala 609 
tel: (21) 2562-7132 
Cidade Universit?ria, Ilha do Fund?o, Rio de Janeiro-RJ, CEP 21941-90 
- Mensagem original - 
De: "Emine Kucukbenli"  
Para: "pw forum"  
Enviadas: Ter?a-feira, 6 de Setembro de 2011 14:11:41 
Assunto: Re: [Pw_forum] At line 174 of file paw_gipaw.f90 (unit = 14, file = 
'') 


Hi Daniel, 
are you sure you are using pseudopotentials that hold gipaw information? 
if so, send me the pseudo i'll check what is wrong. 
thanks 
emine kucukbenli, phd student, sissa, italy 


 
SISSA Webmail https://webmail.sissa.it/ 
Powered by Horde http://www.horde.org/ 


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-- 
Eugenio Furtado de Souza 
Laboratorio de Modelagem Molecular-LABMMOL 
Universidade Federal do Rio de Janeiro 
Av. Athos da Silveira Ramos No 149, CT, Bloco A, sala 609 
tel: (21) 2562-7132 
Cidade Universit?ria, Ilha do Fund?o, Rio de Janeiro-RJ, CEP 21941-90 
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[Pw_forum] At line 174 of file paw_gipaw.f90 (unit = 14, file = '')

[Daniel Lima]

Hi, 
My name is Daniel Aguiar, and I'm a beginner in Theoretical Calculations. 
I'm having some troubles with the gipaw.x calculations . 
The pw.x was sucessed (JOB DONE!!). 
But in gipaw.x the following mensage appear: 

At line 174 of file paw_gipaw.f90 (unit = 14, file = '') 
Fortran runtime error: File '' does not exist 


I verified in paw_gipaw.f90 and the line is: 

OPEN ( 14, FILE = filerec_sp ) 

What's wrong? 

My nmr input is following below: 

 
job = 'nmr' 
prefix = 'ADAMANTANE-rev-PBE-vdW-nmr' 
tmp_dir = '/home/daniel/Softwares/espresso-4.3/tmp/' 
isolve = 0 
iverbosity = 1 
q_gipaw = 0.01 
spline_ps = .true. 
use_nmr_macroscopic_shape = .false. 
/ 


Thanks in advance and sorry for bad english 
-- 
Daniel Lima Marques de Aguiar 
Universidade Federal do Rio de Janeiro / Centro de Tecnologia 
Instituto de Qu?mica 
Programa de P?s Gradua??o em Qu?mica 
Laborat?rio de Resson?ncia Magn?tica Nuclear - Salas 605/608/614 
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[Pw_forum] wfc files: heavy I/O, handling for restarts

[Paolo Giannozzi]

On Sep 5, 2011, at 21:05 , S. K. S. wrote:

> In the version before QE4.2, the QE codes used to replicate
> the same necessary files to the distributed local disks of all
> the nodes.

which QE code and which files are you referring to?

P.
---
Paolo Giannozzi, Dept of Chemistry,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222

[Pw_forum] heat capacity

[Nafise Rezaei]

Dear Prof. Eyvaz Isaev,

I want to calculate heat capacity for the Rhombohedral lattice (ibrav= 5).
When I try to use QHA package, I have encountered with this message
"Trigonal R: not implemented yet".
I have seen similar question in mailing list and your reply. But yet  I
don't know what should be done?

Thanks in advance,
Nafise

---
Nafise Rezaei
Dept of Physics, Isfahan University of Technology
Isfahan, Iran
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