Re: [Pw_forum] 'd' state pdos for Al

2015-01-10 Thread Paolo Giannozzi 
On Thu, 2015-01-08 at 11:53 -0600, Sai Kumar Ramadugu wrote:
> 
> If I run a pseudopotential generation calculation with iswitch=3, then
> the ld1.wfc prints the 3d but the ld1ps.wfc does not print the 3d
> states and hence the generated UPF does not 3d in  section.
> So how can I add manually the 3d section to the  section? 

you have just 3s and 3p angular momentum channels in your PP.
You may run a "test" calculation like this, for instance:

&input
   atom='Al',
   rel=1,
   iswitch=2,
   config='[Ne] 3s2 3p1 3d0',
   dft='PBE'
 /
 &test
   file_pseudo='Al.pbe-nl-rrkjus_psl.1.0.0.UPF', !File name
   nconf=1,
   configts(1)='3s1 3p1 3d0', !Electronic configuration
 /

Note that the 3d orbital is not bound for the ground state of Al. 
This is why I have removed an electron in the test configuration

P.

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Re: [Pw_forum] Electric field in silicene

2015-01-10 Thread Khalid Ibne Masood Khalid 
Well, this is not an expert opinion, but I faced similar problem when I
tried to simulate the band structure of graphene on BN under external
electric field, and my experience is: startingwfc = 'random' solved the
problem.

Hope it would work for you too.

On Sat, Jan 10, 2015 at 11:41 PM, siham Sadki  wrote:

>
>
> Dear all,
>
> I am wanting to get the Dos of silicene under the effect of an
> external electric field. I have done the scf calculations without
> electric field , then again did the scf calculation with an electric
> field included in the z-direction (with value 0.008ua). But the
> convergence is not achieved and it stopped after 100 iterations and
> giving it this message:
>
> "convergence NOT achieved after 100 iterations: stopping"
>
> You will find below  in file for the scf calculation when an
> electric field is applied:
>  &control
> calculation = 'scf'
> restart_mode='from_scratch',
> prefix='Si11ca00E0.008',
> lelfield=.true.,
> nberrycyc=3
> gdir=3
> pseudo_dir ='/home/siham/Desktop/espresso-5.0.1-GPU/pseudo',
> outdir='/home/siham/Desktop/espresso-5.0.1-GPU/tmp'
>/
>  &system
> ibrav= 4,
> celldm(1)=7.3103,
> celldm(3)= 5,
> nat= 2, ntyp= 1,
> ecutwfc = 50.0,
> ecutrho =370.0
> nbnd = 12,
>   /
>  &electrons
>conv_thr =  1.0d-8
>mixing_beta = 0.2
>efield_cart(1)=0.d0, efield_cart(2)=0.d0, efield_cart(3)=0.008d0
>  /
>  &ions
>   /
> ATOMIC_SPECIES
>  Si 28.086  Si.pbe-rrkj.UPF
> ATOMIC_POSITIONS (Angstrom)
>  Si   0.0   0.0 2.001457804
>  Si   -0.00019   2.233446401   2.447251213
> K_POINTS {automatic}
> 10 10 1 1 1 1
> Thanks in advance
>
>  --
>
>
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[Pw_forum] Electric field in silicene

2015-01-10 Thread siham Sadki 

 

Dear all,

I am wanting to get the Dos of silicene under the effect of an
external electric field. I have done the scf calculations without
electric field , then again did the scf calculation with an electric
field included in the z-direction (with value 0.008ua). But the
convergence is not achieved and it stopped after 100 iterations and
giving it this message:

"convergence NOT achieved after 100 iterations: stopping"

You will find below  in file for the scf calculation when an
electric field is applied:
 &control
calculation = 'scf'
restart_mode='from_scratch',
prefix='Si11ca00E0.008',
lelfield=.true.,
nberrycyc=3
gdir=3
pseudo_dir ='/home/siham/Desktop/espresso-5.0.1-GPU/pseudo',
outdir='/home/siham/Desktop/espresso-5.0.1-GPU/tmp'
   /
 &system
ibrav= 4,
celldm(1)=7.3103,
celldm(3)= 5,
nat= 2, ntyp= 1,
ecutwfc = 50.0,
ecutrho =370.0
nbnd = 12,
  /
 &electrons
   conv_thr =  1.0d-8
   mixing_beta = 0.2
   efield_cart(1)=0.d0, efield_cart(2)=0.d0, efield_cart(3)=0.008d0
 /
 &ions
  /
ATOMIC_SPECIES
 Si 28.086  Si.pbe-rrkj.UPF
ATOMIC_POSITIONS (Angstrom)
 Si   0.0   0.0 2.001457804
 Si   -0.00019   2.233446401   2.447251213
K_POINTS {automatic}
10 10 1 1 1 1
Thanks in advance





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Re: [Pw_forum] cluster

2015-01-10 Thread raha khalili 
Dear Dr. Paulatto

Thank's a lot for you helping.

Sorry for another question.

I want to use 4 systems (4 separate cases) simultaneously.
I've connected them to a server by a hub switch. After installing fedora 18
and configuring NFS and password-less SSH, then I've installed
(mpich2-1.4.1p1) and (espresso-5.1.1) on all of them (1server and 3
clinets) by this commands:

# ./configure --enable-parallel --with-internal-lapack --with-internal-blas
# make all

Could you please tell me if I am in right way or not?
And which version of QE and MPICH is appropriate for me?

Best regards,
Raha


On Sat, Jan 10, 2015 at 1:35 PM, Lorenzo Paulatto <
lorenzo.paula...@impmc.upmc.fr> wrote:

>
> On 10/01/15 10:30, raha khalili wrote:
> >  This program is part of the open-source Quantum ESPRESSO suite
> >  for quantum simulation of materials; please cite
> >  "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
> >   URL http://www.quantum-espresso.org";,
> >  in publications or presentations arising from this work. More
> > details at
> > http://www.quantum-espresso.org/quote
> >
> >  Serial version
>
> Dear Raha,
> you are using the serial version of the code, please compile the
> parallel version in order to run it in parallel. If you are using the
> pre-packed version of mpich that comes with some linux distributions you
> have to install the development version of the package.
>
> In any case, I *strongly* recommend that you seek the help of some local
> linux expert (i.e. anybody with some exprience will do).
>
> kind regards
>
> --
> Dr. Lorenzo Paulatto
> IdR @ IMPMC -- CNRS & Université Paris 6
> +33 (0)1 44 275 084 / skype: paulatz
> http://www-int.impmc.upmc.fr/~paulatto/
> 23-24/4é16 Boîte courrier 115, 4 place Jussieu 75252 Paris Cédex 05
>
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>



-- 
Khadije Khalili
Ph.D Student of Solid-State Physics
Department of Physics
University of Mazandaran
Babolsar, Iran
kh.khal...@stu.umz.ac.ir
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Re: [Pw_forum] *.save not found

2015-01-10 Thread toufik esssakhri 


> From: paolo.gianno...@uniud.it
> To: pw_forum@pwscf.org
> Date: Sat, 10 Jan 2015 10:05:59 +0100
> Subject: Re: [Pw_forum] *.save not found
> 
> On Fri, 2015-01-09 at 19:35 +0100, toufik esssakhri wrote:
> 
> > i am using qe-5.0.1, after some scf iterations the jobs stops with
> > following error : 
> 
> >  from pp_check_file : error # 2
> >  file /home/./*.save not found
> 
> > what does that means? 
> 
> it means that your file system has some problem, in my opinion
> 
> Paolo
> 
> 
> -- 
> Paolo Giannozzi, Dept. Chemistry&Physics&Environment, 
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222 
> 
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thank Prof. Paolo, 

this problem occurs only when performing calculation for hybrid functionnal
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Re: [Pw_forum] cluster

2015-01-10 Thread Lorenzo Paulatto 

On 10/01/15 10:30, raha khalili wrote:
>  This program is part of the open-source Quantum ESPRESSO suite
>  for quantum simulation of materials; please cite
>  "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
>   URL http://www.quantum-espresso.org";,
>  in publications or presentations arising from this work. More 
> details at
> http://www.quantum-espresso.org/quote
>
>  Serial version

Dear Raha,
you are using the serial version of the code, please compile the 
parallel version in order to run it in parallel. If you are using the 
pre-packed version of mpich that comes with some linux distributions you 
have to install the development version of the package.

In any case, I *strongly* recommend that you seek the help of some local 
linux expert (i.e. anybody with some exprience will do).

kind regards

-- 
Dr. Lorenzo Paulatto
IdR @ IMPMC -- CNRS & Université Paris 6
+33 (0)1 44 275 084 / skype: paulatz
http://www-int.impmc.upmc.fr/~paulatto/
23-24/4é16 Boîte courrier 115, 4 place Jussieu 75252 Paris Cédex 05

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Re: [Pw_forum] *.save not found

2015-01-10 Thread Paolo Giannozzi 
On Fri, 2015-01-09 at 19:35 +0100, toufik esssakhri wrote:

> i am using qe-5.0.1, after some scf iterations the jobs stops with
> following error : 

>  from pp_check_file : error # 2
>  file /home/./*.save not found

> what does that means? 

it means that your file system has some problem, in my opinion

Paolo


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

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[Pw_forum] cluster

2015-01-10 Thread raha khalili 
Dear all,

I am trying to do a scf calculation in a QE compiled with mpich.
Could you kindly help me?

Best,
Raha

*# mpirun -np 6 --host 192.168.196.1,192.168.196.2
/home/khalili/espresso-5.1.1/bin/pw.x -in mw.scf.in  |
tee mw.scf.out*

output: Program PWSCF v.5.1.1 starts on 10Jan2015 at 12:54:34

 This program is part of the open-source Quantum ESPRESSO suite
 for quantum simulation of materials; please cite
 "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
  URL http://www.quantum-espresso.org";,
 in publications or presentations arising from this work. More details
at
 http://www.quantum-espresso.org/quote

 Serial version
 Reading input from mw.scf.in
 Message from routine read_cards :
 DEPRECATED: no units specified in CELL_PARAMETERS card

 Current dimensions of program PWSCF are:
 Max number of different atomic species (ntypx) = 10
 Max number of k-points (npk) =  4
 Max angular momentum in pseudopotentials (lmaxx) =  3

 Program PWSCF v.5.1.1 starts on 10Jan2015 at 12:54:34

 This program is part of the open-source Quantum ESPRESSO suite
 for quantum simulation of materials; please cite
 "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
  URL http://www.quantum-espresso.org";,
 in publications or presentations arising from this work. More details
at
 http://www.quantum-espresso.org/quote

 Serial version
 Reading input from mw.scf.in
 Message from routine read_cards :
 DEPRECATED: no units specified in CELL_PARAMETERS card

 Current dimensions of program PWSCF are:
 Max number of different atomic species (ntypx) = 10
 Max number of k-points (npk) =  4
 Max angular momentum in pseudopotentials (lmaxx) =  3

 Program PWSCF v.5.1.1 starts on 10Jan2015 at 12:54:34

 This program is part of the open-source Quantum ESPRESSO suite
 for quantum simulation of materials; please cite
 "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
  URL http://www.quantum-espresso.org";,
 in publications or presentations arising from this work. More details
at
 http://www.quantum-espresso.org/quote

 Serial version
 Reading input from mw.scf.in
 Message from routine read_cards :
 DEPRECATED: no units specified in CELL_PARAMETERS card

 Current dimensions of program PWSCF are:
 Max number of different atomic species (ntypx) = 10
 Max number of k-points (npk) =  4
 Max angular momentum in pseudopotentials (lmaxx) =  3
   file C.pz-rrkjus.UPF: wavefunction(s)  2S renormalized
   file H.pz-rrkjus.UPF: wavefunction(s)  1S renormalized
   file C.pz-rrkjus.UPF: wavefunction(s)  2S renormalized
   file C.pz-rrkjus.UPF: wavefunction(s)  2S renormalized
   file H.pz-rrkjus.UPF: wavefunction(s)  1S renormalized
   file H.pz-rrkjus.UPF: wavefunction(s)  1S renormalized
   file N.pz-rrkjus.UPF: wavefunction(s)  2S renormalized
   file N.pz-rrkjus.UPF: wavefunction(s)  2S renormalized
   file N.pz-rrkjus.UPF: wavefunction(s)  2S renormalized
[mpie...@master.cluster.umz] control_cb (./pm/pmiserv/pmiserv_cb.c:202):
assert (!closed) failed
[mpie...@master.cluster.umz] HYDT_dmxu_poll_wait_for_event
(./tools/demux/demux_poll.c:77): callback returned error status
[mpie...@master.cluster.umz] HYD_pmci_wait_for_completion
(./pm/pmiserv/pmiserv_pmci.c:197): error waiting for event
[mpie...@master.cluster.umz] main (./ui/mpich/mpiexec.c:331): process
manager error waiting for completion.


 *Make.sys*

# make.sys.  Generated from make.sys.in by configure.

# compilation rules

.SUFFIXES :
.SUFFIXES : .o .c .f .f90

# most fortran compilers can directly preprocess c-like directives: use
# $(MPIF90) $(F90FLAGS) -c $<
# if explicit preprocessing by the C preprocessor is needed, use:
# $(CPP) $(CPPFLAGS) $< -o $*.F90
#$(MPIF90) $(F90FLAGS) -c $*.F90 -o $*.o
# remember the tabulator in the first column !!!

.f90.o:
$(MPIF90) $(F90FLAGS) -c $<

# .f.o and .c.o: do not modify

.f.o:
$(F77) $(FFLAGS) -c $<

.c.o:
$(CC) $(CFLAGS)  -c $<



# topdir for linking espresso libs with plugins
TOPDIR = /home/khalili/espresso-5.1.1

# DFLAGS  = precompilation options (possible arguments to -D and -U)
#   used by the C compiler and preprocessor
# FDFLAGS = as DFLAGS, for the f90 compiler
# See include/defs.h.README for a list of options and their meaning
# With the exception of IBM xlf, FDFLAGS = $(DFLAGS)
# For IBM xlf, FDFLAGS is the same as DFLAGS with separating commas

# MANUAL_DFLAGS  = additional precompilation option(s), if desired
#  You may use this instead of tweaking DFLAGS and FDFLAGS
#  BEWARE: will not work for IBM xlf! Manually edit FDFLAGS
MANUAL_DFLAGS  =
DFLAGS =  -D__GFORTRAN -D__STD_F95 -D_

Re: [Pw_forum] How to improve the precision of phonon calculation?

2015-01-10 Thread Uri Argaman 
Dear Yu Hailin

In questions like this you should show the SCF input that you use. The
negative frequencies show that the crystal is unstable or your calculations
are not converged. It can be the numerical parameters of the SCF
calculation or the numerical parameters of the phonon calculation. As far
as I know, the only numerical parameter used in the phonon calculation is
tr2_ph.

If your calculation is converged than the negative (imaginary) frequencies
show that the structure is unstable. You must do relaxation (probably to
zero pressure) before the SCF to ensure that the structure is on the
minimum of the energy surface (at list local minimum).

Best regards

Uri Argaman

Ben-Gurion University

Israel
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