[Pw_forum] Error during examples run.

2010-08-18 Thread Vit
Dear QE users!
I've just compiled QE-4.2.1 with ACML and gfortran on 2*AMD Xenon Dual Core 
server.
Test's were passed with small discrepancy, but running all the examples i've 
got this error:

root at thunder ~/Install/QE/espresso-4.2.1/examples # time ./run_all_examples 
>> 
4_cores
At line 98 of file lambda.f90 (unit = 4, file = 'elph. 0.00. 0.00. 
0.00')
Fortran runtime error: Constant string in input format
(5x,'Gaussian Broadening: ',f7.3,' Ry, ngauss=',i4)
  ^

Here is the make.sys file (ranamed to txt because of google mail). 
What can I do to avoid this error in future?

With best regards, 
Koroteev Victor
Junior researcher NIIC SB RAS
-- next part --
# 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 $<


# 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 

DFLAGS =  -D__GFORTRAN -D__STD_F95 -D__FFTW -D__MPI -D__PARA -D__ACML
FDFLAGS= $(DFLAGS)

# IFLAGS = how to locate directories where files to be included are
# In most cases, IFLAGS = -I../include

IFLAGS = -I../include

# MOD_FLAGS = flag used by f90 compiler to locate modules
# Each Makefile defines the list of needed modules in MODFLAGS

MOD_FLAG  = -I

# Compilers: fortran-90, fortran-77, C
# If a parallel compilation is desired, MPIF90 should be a fortran-90 
# compiler that produces executables for parallel execution using MPI
# (such as for instance mpif90, mpf90, mpxlf90,...);
# otherwise, an ordinary fortran-90 compiler (f90, g95, xlf90, ifort,...)
# If you have a parallel machine but no suitable candidate for MPIF90,
# try to specify the directory containing "mpif.h" in IFLAGS
# and to specify the location of MPI libraries in MPI_LIBS

MPIF90 = mpif90
#F90   = gfortran
CC = cc
F77= gfortran

# C preprocessor and preprocessing flags - for explicit preprocessing, 
# if needed (see the compilation rules above)
# preprocessing flags must include DFLAGS and IFLAGS

CPP= cpp
CPPFLAGS   = -P -traditional $(DFLAGS) $(IFLAGS)

# compiler flags: C, F90, F77
# C flags must include DFLAGS and IFLAGS
# F90 flags must include MODFLAGS, IFLAGS, and FDFLAGS with appropriate syntax

CFLAGS = -O3 $(DFLAGS) $(IFLAGS)
F90FLAGS   = $(FFLAGS) -x f95-cpp-input $(FDFLAGS) $(IFLAGS) $(MODFLAGS)
FFLAGS = -O3 -g

# compiler flags without optimization for fortran-77
# the latter is NEEDED to properly compile dlamch.f, used by lapack

FFLAGS_NOOPT   = -O0 -g

# Linker, linker-specific flags (if any)
# Typically LD coincides with F90 or MPIF90, LD_LIBS is empty

LD = mpif90
LDFLAGS= -g
LD_LIBS= 

# External Libraries (if any) : blas, lapack, fft, MPI

# If you have nothing better, use the local copy :
# BLAS_LIBS = /your/path/to/espresso/BLAS/blas.a
# BLAS_LIBS_SWITCH = internal

BLAS_LIBS  = -L/opt/acml4.4.0/gfortran64/lib -lacml
BLAS_LIBS_SWITCH = external

# If you have nothing better, use the local copy :
# LAPACK_LIBS = /your/path/to/espresso/lapack-3.2/lapack.a
# LAPACK_LIBS_SWITCH = internal
# For IBM machines with essl (-D__ESSL): load essl BEFORE lapack !
# remember that LAPACK_LIBS precedes BLAS_LIBS in loading order

LAPACK_LIBS= -L/opt/acml4.4.0/gfortran64/lib -lacml
LAPACK_LIBS_SWITCH = external

SCALAPACK_LIBS = 

# nothing needed here if the the internal copy of FFTW is compiled
# (needs -D__FFTW in DFLAGS)

FFT_LIBS   = 

# For parallel execution, the correct path to MPI libraries must
# be specified in MPI_LIBS (except for IBM if you use mpxlf)

MPI_LIBS   = 

# IBM-specific: MASS libraries, if available and if -D__MASS is defined in 
FDFLAGS

MASS_LIBS  = 

# pgplot libraries (used by some post-processing tools)

PGPLOT_LIBS= 

# ar command and flags - for most architectures: AR = ar, ARFLAGS = ruv

AR = ar
ARFLAGS= ruv

# ranlib command. If ranlib is not needed (it isn't in most cases) use
# RANLIB = echo

RANLIB = ranlib

# all internal and external libraries - do not modify

FLIB_TARGETS   = all

LIBOBJS= ../flib/ptools.a ../flib/flib.a 

[Pw_forum] Intel MPI

2010-08-18 Thread Paolo Giannozzi

On Aug 18, 2010, at 19:03 , joaquin peralta wrote:

> We use a surface of Al with 81 atoms in 128 cpus using intelMPI and  
> openMPI 1.4

but not in the same way! the first job uses 8 pools of 16 processors,  
the second
1 pool of 128 processors. The first choice seems to be reasonable,  
the second
isn't, since an enormous amount of time is spent in communications  
(look at the
time spent in fft_scatter).

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





[Pw_forum] Intel MPI

2010-08-18 Thread Goranka Bilalbegovic
On Wed, Aug 18, 2010 at 3:16 PM, Paolo Giannozzi wrote:
Can anybody report any experience linking with Intel version of MPI?
---

Intel MPI is installed on the cluster I am using. Several recent versions of
QE (including 4.2.1) are compiling and running without any
problems.

However, I do have problems in running SaX jobs on the same cluster. The
problems with running SaX jobs started last year when this cluster was
changed and several new libraries and compilers were installed at the same
time. Together with the system manager I was trying to detect the problem
with SaX. The frst idea was that this is because of (then new for us) the
Lustre file system, the second was mvapich.  A new version of mvapich was
installed, but it did not help. There is a possibility that SaX jobs do not
run on this cluster (they stayed in the queue forever) because of the
problems with Intel MPI.

Best regards,
-- 
Goranka Bilalbegovic,
Department of Physics, Faculty of Science,
University of Zagreb, Croatia
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[Pw_forum] Graphene Structural Relaxation

2010-08-18 Thread lfhuang
Dear M. Pazoki:
 Your results were so strange to me, who have done some calculation on 
graphene with the PBE-rrkjus PP. I guess there should be something wrong in 
your input file. In addition to Xirainbow's comments, I want to say that 
Ecut=(30,300) Ry is good enough for the optimization of graphitic lattices, 
(35,350) may be better for some other purposes and (40,400) is great!
You'd better supply your input file, then people can tell why your results 
were strange.

Best Wishes!
Yours Sincerely
L. F. Huang

--
==
L.F.Huang(???) DFT and phonon physics
==
Add: Research Laboratory for Computational Materials Sciences,
Instutue of Solid State Physics,the Chinese Academy of Sciences,
P.O.Box 1129, Hefei 230031, P.R.China
Tel: 86-551-5591464-326(office)
Fax: 86-551-5591434
Our group: http://theory.issp.ac.cn
==


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[Pw_forum] the best choice for k-point

2010-08-18 Thread Hanyu
I think (1 1 8) converged very well.

On Sat, Aug 14, 2010 at 10:41 PM, Farzad Molani wrote:

>   hello QE users,
> I'm going to achieve the best kpoint and cut-off for my system. I got
> results but I do'nt know, What is the best choice for K-point?
> please help me,
> thanks in advance.?
>  energy(Ry)k-point
> -270.57530321   1 1 3
> -270.58540932   1 1 4
> -270.58749209   1 1 5
> -270.58517276   1 1 6
> -270.58547581   1 1 7
> -270.58556388   1 1 8
> -270.58553867   1 1 9
> -270.58554333   1 1 10
>
> Farzad Molani,
> Ph.D Student,
> Department of Theoretical Physical Chemistry,
> K. N. Toosi University of Technology,
> Tehran, Iran.
> Tel.:  009891 4442 3308
> Tel.:  009821 2306 4280
> Fax: 009821 2285 3650
> Web: 
> http://www.chem.kntu.ac.ir/~sjalili:/<http://www.chem.kntu.ac.ir/%7Esjalili:/>
>
>
> ___
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>
>


-- 
-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=**=-=**=-=**=-=*=-=*=-=*=-=*=-=*=-
 Hanyu Liu(???),
 State key  Laboratory of Superhard Materials, Jilin University, China
 Email: liuhanyu08 at mails.jlu.edu.cn or ouuing at gmail.com
 skype: ouuing
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[Pw_forum] Error during examples run.

2010-08-18 Thread Paolo Giannozzi

On Aug 18, 2010, at 15:33 , Vit wrote:

>   Fortran runtime error: Constant  
> string in input format
> (5x,'Gaussian Broadening: ',f7.3,' Ry, ngauss=',i4)

it looks like your compiler doesn't like the format in

 read (iuelph,9000) degauss1, ngauss1
9000 format(5x,'Gaussian Broadening: ',f7.3,' Ry, ngauss=',i4)

Not sure what the standard says. Ignore it if you do not need to
calculate electron-phonon coefficients. Otherwise, replace with:

9000 format(26x,f7.3,12x,i4)

and the like for all other formats.

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





[Pw_forum] Super Cell

2010-08-18 Thread Stefano Baroni
Sure you can! Who else should determine the atomic positions?
Can you explain a little better what the problem is? 
SB

On Aug 17, 2010, at 8:03 PM, Vin?cius Bertuzzo Lima wrote:

> Please, it is possible to do this:
> 
> I was wondering how to proceed the calculus by considering a cell where I 
> determine the exact place where the atoms are located.
> I want to determine by myself the coordinates for each atom in the lattice.
> 
> Vin?cius Bertuzzo Lima
> Student of chemical in "Universidade Estadual Paulista - Unesp - FC" Brazil-SP
> ___
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---
Stefano Baroni - SISSA  &  DEMOCRITOS National Simulation Center - Trieste
http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni 
(skype)

La morale est une logique de l'action comme la logique est une morale de la 
pens?e - Jean Piaget

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[Pw_forum] Intel MPI

2010-08-18 Thread Paolo Giannozzi
Can anybody report any experience linking with Intel
version of MPI?

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





[Pw_forum] Speeding up the calculations

2010-08-18 Thread Paolo Giannozzi

On Aug 16, 2010, at 12:12 , Bipul Rakshit wrote:

> 1. in GRID_examples, its in 4.2 version examples only.
> But I  think its just a script, and it will work with older  
> versions of espresso's also.

I don't think so: some minor changes were made to the input and the  
logic of
the phonon code

> 2. With your personal experience, is libraries like scalapack, FFTW  
> increase
> the calculation speed  (the phonon calculation especially)

my personal experience is a) reported in the user guide, b) of little  
importance
anyway, since the actual performances of a code depend upon a large  
number
of factors

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





[Pw_forum] Intel MPI

2010-08-18 Thread joaquin peralta
Me and Claudia

are using intelmpi 4.0 in http://cystorm.ece.iastate.edu with a very good
performance .. but we are not sure now ... let me explain :

We use a surface of Al with 81 in 128 cpus using intelMPI and openMPI 1.4

The compilations options (make.sys), input file and output files are in this
page (sorry for use my page but was the more fast) :

http://www.lpmd.cl/jperalta/index.php?n=Site.QE-Cystorm

Probably is not a good test, because we detect after that the cluster
schedule manager (torque) was not work properly with intelMPI and was very
probably that some external works are using process in the open-mpi running.
Look this thread about schedule-manager and intelMPI
http://software.intel.com/en-us/forums/showthread.php?t=76537

Right now the cluster is under a upgrade, sure when we can do more test we
shared that.

Best Regards
Joaquin and Claudia.


On Wed, Aug 18, 2010 at 8:16 AM, Paolo Giannozzi wrote:

> Can anybody report any experience linking with Intel
> version of MPI?
>
> P.
> ---
> Paolo Giannozzi, Dept of Physics, University of 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://www.democritos.it/mailman/listinfo/pw_forum
>



-- 

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http://www.gnm.cl

Joaqu?n Andr?s Peralta Camposano

http://zeth.ciencias.uchile.cl/~jperalta<http://zeth.ciencias.uchile.cl/%7Ejperalta>

In a world without frontiers,
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[Pw_forum] Additional informations about XSpectra

2010-08-18 Thread Matteo Calandra
Dear Christian,

  here the answers to your questions:

 > (1) is the energy range (xemin,xemax) referred to the Fermi energy
 > of the preliminar scf calculation?

No, it is referred to the Fermi level given in input  in the xspectra 
file (input variable ef_r in the input_xspectra namelist. This means 
that if you do not specify the Fermi level then ef_r=0.0 and
they are referred to the energy zero of the preliminary scf run.


 > (1) is there a special convention for the components of the wavevector
 > and of the polarization vector? The defaults are (1,0,0) and (0,1,0);
 > shouldn't they be orthogonal?

This depends on the variable xcoordcrys. If the variable xcoordcrys=.true.
then xkvec and xepsilon are the crystalline components of the wavevector
and the polarization vector with respect to the direct lattice vectors 
as chosen by QE. On the contrary, if xcoordcrys=.false. then they are 
the components with respect to the cartesian axes (in direct space).
Note that also the xkvec components are in direct space as this is
customary in the XAS community.
xkvec and xepsilon should of course be orthogonal. If they are not, then 
the code gives you a warning in output but it does not stop.
The reason is that if you do a dipolar calculation only, then xkvec is
irrelevant.

 > (3) last line of input, after the $cut_occ section
 > (question already posted on past 2/7 in this forum)

it is the number of k-point necessary to calculate the
XANES cross section. In practice you can chose to calculate
the charge density with a given number of k-points and then
the XANES with a larger one. Generally the convergence
of the xanes cross section with respect to k-points is slower
thant that of the charge density.
This is similar to what you do
with a density of states calculation, namely you first calculate
the charge density with Nk k points and then the dos
with a much larger Nk' grid.

All the best, M.

M.


-- 
* * * *
Matteo Calandra, Charge de Recherche (CR1)
Institut de Min?ralogie et de Physique des Milieux Condens?s de Paris
Universit? Pierre et Marie Curie, tour 16, case 115
4 Place Jussieu, 75252 Paris Cedex 05 France
Tel: +33-1-44 27 52 16   Fax: +33-1-44 27 37 85
http://www.impmc.jussieu.fr/~calandra


[Pw_forum] Ni.pbe-sp-mt_gipaw.UPF: one pseudopotential for two, oxidation states? (Merlin Meheut)

2010-08-18 Thread Matteo Calandra
Dear Merlin,

   the pseudopotential Ni.pbe-sp-mt_gipaw.UPF includes 3s and 3p 
semicore states as Paolo giannozzi suggested and it is a norm conseving 
pseudopotential. As far as I remember it was also tested on bulk Ni
and the agreement with the experimental pressure was fine.
Of course, being a Norm conseving with semicore states, it will require
a cutoff of at least of 150 Ryd and not of 27.0 Ryd as your input file 
seems to suggest.

M.

   
 >> ibrav=2, celldm(1) =6.65, nat=  1, ntyp= 1,
 >> nspin=2,
 >> starting_magnetization(1)=0.5,
 >> degauss=0.02,
 >> smearing='mp',
 >> occupations='smearing',
 >> ecutwfc =27.0
 >> ecutrho =300.0
 >>  /
-- 
* * * *
Matteo Calandra, Charge de Recherche (CR1)
Institut de Min?ralogie et de Physique des Milieux Condens?s de Paris
Universit? Pierre et Marie Curie, tour 16, case 115
4 Place Jussieu, 75252 Paris Cedex 05 France
Tel: +33-1-44 27 52 16   Fax: +33-1-44 27 37 85
http://www.impmc.jussieu.fr/~calandra


[Pw_forum] Intel MPI

2010-08-18 Thread Lazaro Calderin
We have been using mpiifort and mpiicc without major issues. If my
memory serves me well they use the intel mpi libs while
mpif90 and the rest of the gnu compilers provided by intel use mpich.
Regards, L.

On Wed, 2010-08-18 at 15:16 +0200, Paolo Giannozzi wrote:
> Can anybody report any experience linking with Intel
> version of MPI?
> 
> P.
> ---
> Paolo Giannozzi, Dept of Physics, University of Udine
> via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
> 
> 
> 
> ___
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> 
-- 
Lazaro Calderin
Department of Physics
Queen's University
Kingston, Ontario
Canada



[Pw_forum] (no subject)

2010-08-18 Thread Gabriele Sclauzero
Just an additional remark: please specify a meaningful subject in your 
next posts.

Thanks,

GS

On 08/18/2010 12:06 AM, ?lvaro Alves wrote:
>
> Dear all, how do I get the SOMO (Singly Occupied Molecular Orbital) in 
> PWscf?
>
> Regards,
>
> A. S. Santos
>
> Universidade Federal Fluminense
> Niter?i - Rio de Janeiro - Brasil
>
>
>
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-- 

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PH H2 462, Station 3, CH-1015 Lausanne

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[Pw_forum] (no subject)

2010-08-18 Thread Gabriele Sclauzero
Dear Alvaro,

if you are doing a calculation for an isolated molecule (with a 
single k-point), then the code should print the HOMO and the LUMO levels 
at the end of the SCF loop. If I understand well, the SOMO is a singly 
occupied HOMO, hence your molecule is magnetic. If you fix the total 
magnetization then your calculation should converge without using the 
broadening of occupations and the code will still print HOMO and LUMO 
levels.
Once you have identified the band index corresponding to your SOMO you 
can plot the KS eigenstate through the pp.x utility (please see related 
documentation and examples).

HTH

GS


On 08/18/2010 12:06 AM, ?lvaro Alves wrote:
>
> Dear all, how do I get the SOMO (Singly Occupied Molecular Orbital) in 
> PWscf?
>
> Regards,
>
> A. S. Santos
>
> Universidade Federal Fluminense
> Niter?i - Rio de Janeiro - Brasil
>
>
>
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PH H2 462, Station 3, CH-1015 Lausanne

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[Pw_forum] Graphene Structural Relaxation

2010-08-18 Thread Gabriele Sclauzero
On 08/18/2010 12:54 AM, meysam pazoki wrote:
>
>
> -- Forwarded message --
> From: *meysam pazoki*  <mailto:meysam.pazoki at gmail.com>>
> Date: Tue, Jul 20, 2010 at 11:46 PM
> Subject: Graphene Structural Relaxation
> To: pw_forum-request at pwscf.org <mailto:pw_forum-request at pwscf.org>
>
>
> Dear PWSCF users
> I have a problem in relaxation of grahene super cell with 24 atoms. In 
> relaxation procedure ,graphene hooney-comb structure completely 
> destroys and atoms have no regular ordering after relaxation 
> procedure.I use pbe-rrkjus psudopotential,4 3 3 kpoint grid,30 rydberg 
> cutff energy,300 rydberg ecutrho.
> I use both ion_damps & bfgs algorithms and get similar results.
> If i change the ecutrho to 100, atoms have an irregular positions in 3 
> dimension,but when ecut rho set to 300 atoms have irregular position 
> in-plane.
> furthermore if i set 
> :trust_radius_ini=.1D0,trust_radius_max=.3D0,bfgs_ndim = 3,
> I have the honeycomb structure but some of c atoms exprience great 
> forces like:
>
> atom 19 type 1 force = 11948.08469282 -219.69802882 0.
>
> atom 20 type 1 force = 11782.00343549 12.01959200 0.
>
> atom 21 type 1 force = 11748.09287051 115.25218004 0.
>
> atom 22 type 1 force = 11241.09464255 -222.56999757 0.
>
> atom 23 type 1 force = -0.50941109 0.26861287 0.
>
> atom 24 type 1 force = 11905.77649683 -91.34763119 0.
>

These forces are simply crazy... I mean, if the units are those used by 
PWscf (Ry/Bohr) the forces that you are reporting are huge! If you have 
used the PP on the QE website, then the atomic positions and/or the cell 
dimensions that you have supplied to PWscf  must be far off the 
equilibrium ones. Please provide an input file.

GS

> My question is what is wrong in my structure relaxation procedure that 
> result in such non-physical data.
>
> It would appreciated if anyone can help me in this problem
> Thanks in advance
> meysam pazoki
> Ph.D student of physics
> Sharif university of technology
>
>
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[Pw_forum] Graphene Structural Relaxation

2010-08-18 Thread xirainbow
Dear meysam pazoki:
Why you choose (4 3 3) kpoint grid.
If you are dealing with monolayer graphene, I think you should change it to
(1 x x).
Furthermore, I do not think (x=3) is enough for graphene.
Maybe you can increase (x) and have a try:)

On Wed, Aug 18, 2010 at 6:54 AM, meysam pazoki
wrote:

>
>
> -- Forwarded message --
> From: meysam pazoki 
> Date: Tue, Jul 20, 2010 at 11:46 PM
> Subject: Graphene Structural Relaxation
> To: pw_forum-request at pwscf.org
>
>
> Dear PWSCF users
>
> I have a problem in relaxation of grahene super cell with 24 atoms. In
> relaxation procedure ,graphene hooney-comb structure completely destroys and
> atoms have no regular ordering after relaxation procedure.I use pbe-rrkjus
> psudopotential,4 3 3 kpoint grid,30 rydberg cutff energy,300 rydberg
> ecutrho.
> I use both ion_damps & bfgs algorithms and get similar results.
> If i change the ecutrho to 100, atoms have an irregular positions in 3
> dimension,but when ecut rho set to 300 atoms have irregular position
> in-plane.
> furthermore if i set :trust_radius_ini=.1D0,trust_radius_max=.3D0,bfgs_ndim
> = 3,
> I have the honeycomb structure but some of c atoms exprience great forces
> like:
>
> atom 19 type 1 force = 11948.08469282 -219.69802882 0.
>
> atom 20 type 1 force = 11782.00343549 12.01959200 0.
>
> atom 21 type 1 force = 11748.09287051 115.25218004 0.
>
> atom 22 type 1 force = 11241.09464255 -222.56999757 0.
>
> atom 23 type 1 force = -0.50941109 0.26861287 0.
>
> atom 24 type 1 force = 11905.77649683 -91.34763119 0.
>
> My question is what is wrong in my structure relaxation procedure that
> result in such non-physical data.
>
> It would appreciated if anyone can help me in this problem
>
> Thanks in advance
>
> meysam pazoki
> Ph.D student of physics
> Sharif university of technology
>
>
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>


-- 

Hui Wang
School of physics, Nankai University, Tianjin, China
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