[Pw_forum] Units in dynamical matrix files

[Paolo Giannozzi]

On Jul 8, 2009, at 18:09 , Paolo Giannozzi wrote:

> All Q-E codes use atomic Rydberg units

i.e. energy in Ry, lengths in Bohr radii
(or \hbar=1, e^2=2, electron mass m=1/2)

> with the exception of CP that uses atomic Hartree units

i.e. energy in Ha, lengths in Bohr radii
(or \hbar=1, e=1, electron mass m=1)

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] Units in dynamical matrix files

[Paolo Giannozzi]

On Jul 8, 2009, at 16:26 , Cristian Degli Esposti Boschi wrote:

> And what are the typical units used for force constants?

I don't think there are "typical" units for force constants:
one chooses a system of units and uses those. All Q-E
codes use atomic Rydberg units, with the exception of
CP that uses atomic Hartree units

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] Units in dynamical matrix files

[Lorenzo Paulatto]

In data 08 luglio 2009 alle ore 16:55:12, Serge Nakhmanson  
 ha scritto:
> I think the difference here is the same as
> between Ry and Ha energy units, so that in
> the "convention" that QE uses an extra 1/2
> proliferates into the mass units as well.

I does indeed, Rydberg atomic units have a few quirks. The other important  
one in electron_charge = sqrt(2)

If you are interested in more details, have a look at this table I found  
on google where everything is explained clearly:  


best regards


-- 
Lorenzo Paulatto
SISSA  &  DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www:   http://people.sissa.it/~paulatto/

 *** save italian brains ***
  http://saveitalianbrains.wordpress.com/

[Pw_forum] Units in dynamical matrix files

[Cristian Degli Esposti Boschi]

Dear all,

I would like to have some clarifications on the units used in dynamical 
matrix files produced by the ph.x program in the QE suite.

At the beginning of dynamical matrix file the masses are not expressed 
in the same units as in the input files used for pw.x, that is [amu].

It seems to me that in the dynamical matrix file the masses could be in
atomic units, which I would say correspond to electron masses.

So there should be a conversion factor

1 amu = (1.660538782 ? 10^-27 kg / 9.1093826 ? 10^-31 kg) me
   = 1822.8884 me

However there is still a factor 1/2 to include to pass from
the amu values to those reported at the beginning of the dynamical
matrix file.

Am I right? Why the 1/2 factor?

And what are the typical units used for force constants?

Thanks a lot. Cristian
-- 
___
Cristian Degli Esposti Boschi
CNR, CNISM, Unita' di Ricerca di Bologna, c/o
Dipartimento di Fisica, Universita' di Bologna
viale Berti-Pichat, 6/2, 40127, Bologna, Italia
tel. ++39 051 2095114   fax ++39 051 2095113
e-mail: cristian.degliesposti -AT- unibo.it
web:http://www.df.unibo.it/fismat/theory
___

[Pw_forum] Errors in examples of QuantumEspresso

[leila salimi]

Hi every body,
I have been trying to install the code "espresso-4.0.5" on IBM pSeries 575, a 
clustered SMP (Symmetric Multiprocessing) system.
and I used the special make.sys which is matched with our system and then ?make 
pwall? was successful but now I'm getting the following error trying to run the 
examples.
Do you have any idea what is going wrong?

Best Regards,
Leila Salimi.
Isfahan University of Technology, Isfahan, Iran.


 from ewald : error # 1
>  optimal alpha not found

running the scf calculation...STOP 2
Error condition encountered during test: exit status = 2
Aborting
  running the geometry relaxation for CO...STOP 2
Error condition encountered during test: exit status = 2
Aborting

As the following "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 $<


# 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__XLF -D__MASS -D__ESSL -D__LINUX_ESSL
FDFLAGS= -D__XLF,-D__MASS,-D__ESSL,-D__LINUX_ESSL

# IFLAGS = how to locate directories where files to be included are
# In most cases, IFLAGS = -I../include
# If loading an external FFTW library, add the location of FFTW include files

IFLAGS = -I../include

# MODFLAGS = flag used by f90 compiler to locate modules
# You need to search for modules in ./, in ../iotk/src, in ../Modules
# Some applications also need modules in ../PW and ../PH

MODFLAGS   = -I./  -I../Modules  -I../iotk/src \
 -I../PW  -I../PH

# 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 = mpfort
#F90   = xlf90_r
CC = mpcc
F77= xlf_r

# 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   = $(FFLAGS) -qfree=f90 -WF,$(FDFLAGS) $(IFLAGS) $(MODFLAGS)
FFLAGS = -O4 -qsuffix=cpp=f90 -qdpc -qalias=nointptr -Q

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

FFLAGS_NOOPT   = -O0

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

LD = mpfort
LDFLAGS=
LD_LIBS=

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

# If you have nothing better, use the local copy : ../flib/blas.a

BLAS_LIBS  = /sara/sw/blas/1.0/lib/libblas.a

# The following lapack libraries will be available in flib/ :
# ../flib/lapack.a : contains all needed routines
# ../flib/lapack_atlas.a: only routines not present in the Atlas library
# For IBM machines with essl (-D__ESSL): load essl BEFORE lapack !
# remember that LAPACK_LIBS precedes BLAS_LIBS in loading order

LAPACK_LIBS= /sara/sw/lapack/3.1.1/lib/liblapack.a

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

FFT_LIBS   = /sara/sw/fftw3/3.1.2/lib/libfftw3f.a

# 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  =  -lmassvp6_64 -lmass_64
# ESSL added by Arieh tal 25-6-09
ESSL_LIBS  =  -lessl


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

PGPLOT_LIBS=

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

[Pw_forum] Errors in examples of QuantumEspresso

[leila salimi]

Hi every body,
I have been trying to install the code "espresso-4.0.5" on IBM pSeries 575, a 
clustered SMP (Symmetric Multiprocessing) system.
and I used the special make.sys which is matched with our system and then ?make 
pwall? was successful but now I'm getting the following error trying to run the 
examples.
I will attach "make.sys" and "environment_variables" to this mail.
Do you have any idea what is going wrong?

Best Regards,
Leila Salimi.
Isfahan University of Technology, Isfahan, Iran.


?from ewald : error # ? ? ? ? 1
> ? ? ?optimal alpha not found 

running the scf calculation...STOP 2
Error condition encountered during test: exit status = 2
Aborting
??running the geometry relaxation for CO...STOP 2
Error condition encountered during test: exit status = 2
Aborting
-- next part --
A non-text attachment was scrubbed...
Name: make.sys
Type: application/octet-stream
Size: 4805 bytes
Desc: not available
Url : 
http://www.democritos.it/pipermail/pw_forum/attachments/20090708/bb7764cf/attachment.obj
 
-- next part --
A non-text attachment was scrubbed...
Name: environment_variables
Type: application/octet-stream
Size: 1560 bytes
Desc: not available
Url : 
http://www.democritos.it/pipermail/pw_forum/attachments/20090708/bb7764cf/attachment-0001.obj
 

[Pw_forum] Strain calculation through quantum espresso

[Giovanni Cantele]

Dimpy Sharma wrote:
> Hi Paolo,
>
>  I want to know about calculating strain from Q.E , 
I cannot well understand your question. If I'm not wrong, strain is a 
measure of the deformation of a material,
the stress is the corresponding "load" applied to the material and 
producing the strain. So, if you apply a deformation ("strain") to your 
material,
let's say a cubic material with lattice constant A0 with strain along 
the x direction, you are changing the lattice constant
along x from the equilibrium value A0 to some value A. The strain will 
be measured as (A - A0) / A0.

> howver from stress also we can calculate stress,
?

> as we can relate stress and strain .
>
>   
The QE calc. will give you the corresponding stress tensor if you set 
tstress=.true., *even though* you are using
calculation='scf', 'relax', 

stress in QE:
http://www.quantum-espresso.org/wiki/index.php/Methodological_Background#Stress



Giovanni

 

-- 



Dr. Giovanni Cantele
Coherentia CNR-INFM and Dipartimento di Scienze Fisiche
Universita' di Napoli "Federico II"
Complesso Universitario di Monte S. Angelo - Ed. 6
Via Cintia, I-80126, Napoli, Italy
Phone: +39 081 676910
Fax:   +39 081 676346
E-mail: giovanni.cantele at cnr.it
giovanni.cantele at na.infn.it
Web: http://people.na.infn.it/~cantele
Research Group: http://www.nanomat.unina.it
Skype contact: giocan74

[Pw_forum] Errors in examples of QuantumEspresso

[Paolo Giannozzi]

On Jul 8, 2009, at 13:15 , leila salimi wrote:

>  from ewald : error # 1
>  optimal alpha not found

wasn't it explained a few days ago by LP? newer IBM
compilers have made a mess with the error function
(erf, erfc)

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] Strain calculation through quantum espresso

[Paolo Giannozzi]

On Jul 8, 2009, at 12:20 , Dimpy Sharma wrote:
> Could anyone please tell me how to calculate strain of a supercell  
> through quantum espresso, as in the manual it has not been  
> mentioned properly.
>
could you please explain why you think that there should be anything  
special
in stress calculations for supercells?

---
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] Pw_forum Digest, Vol 25, Issue 10

[Dimpy Sharma]

Hi Paolo,

 I want to know about calculating strain from Q.E , howver from stress also we 
can calculate stress,as we can relate stress and strain .

DS
-Original Message-
From: pw_forum-bounces at pwscf.org on behalf of pw_forum-requ...@pwscf.org
Sent: Wed 7/8/2009 11:38 AM
To: pw_forum at pwscf.org
Subject: Pw_forum Digest, Vol 25, Issue 10
 
Send Pw_forum mailing list submissions to
pw_forum at pwscf.org

To subscribe or unsubscribe via the World Wide Web, visit
http://www.democritos.it/mailman/listinfo/pw_forum
or, via email, send a message with subject or body 'help' to
pw_forum-request at pwscf.org

You can reach the person managing the list at
pw_forum-owner at pwscf.org

When replying, please edit your Subject line so it is more specific
than "Re: Contents of Pw_forum digest..."


Today's Topics:

   1. vc-relax (ali kazempour)
   2. Re: vc-relax (Lorenzo Paulatto)
   3. Errors in examples of QuantumEspresso (leila salimi)
   4. Errors in examples of QuantumEspresso (leila salimi)
   5. Strain calculation through quantum espresso (Dimpy Sharma)
   6. Re: Strain calculation through quantum espresso (Paolo Giannozzi)
   7. Re: Errors in examples of QuantumEspresso (Paolo Giannozzi)


--

Message: 1
Date: Wed, 8 Jul 2009 02:03:55 -0700 (PDT)
From: ali kazempour 
Subject: [Pw_forum] vc-relax
To: pw 
Message-ID: <511270.21408.qm at web112502.mail.gq1.yahoo.com>
Content-Type: text/plain; charset="us-ascii"

Can I use vc-relax to optimize the value of lattice constant in ZnO wurtzite 
structure?Because the lattice constant change and also atomic positions either. 
After finishing the run, Which atomic position shoud be used in next 
calculation(relaxed position or initial positions)? How can I optimize the 
value of u that is ideally equal to 3/8?
thanks a lot

Ali Kazempour

Physics department, Isfahan University of Technology

84156 Isfahan, Iran.Tel-1:  +98 311 391 3733

Fax: +98 311 391 2376  Tel-2:  +98 311 391 2375


  
-- next part --
An HTML attachment was scrubbed...
URL: 
http://www.democritos.it/pipermail/pw_forum/attachments/20090708/7b0b1a07/attachment-0001.htm
 

--

Message: 2
Date: Wed, 8 Jul 2009 11:33:29 +0200 (CEST)
From: "Lorenzo Paulatto" 
Subject: Re: [Pw_forum] vc-relax
To: "PWSCF Forum" 
Message-ID: <42848.78.12.162.251.1247045609.squirrel at webmail.sissa.it>
Content-Type: text/plain;charset=iso-8859-1


On Wed, July 8, 2009 11:03, ali kazempour wrote:
>  Can I use vc-relax to optimize the value of lattice constant in ZnO
>  wurtzite structure?

Dear ali,
of course you can!


> Because the lattice constant change and also atomic
>  positions either.

You can nail the atoms to their position by adding " 0 0 0" after the
atomic coordinates (see manual for detail), although it only make sense
for crystal and possibly alat coordinates, when you are doing vc-relax.

> After finishing the run, Which atomic position shoud be
>  used in next calculation(relaxed position or initial positions)?

The optimized ones, if not, why would you do the optimization?

>  How can I
>  optimize the value of u that is ideally equal to 3/8?

Doing vc-relax, I don't see the problem )I asume you are using this
notation: http://cst-www.nrl.navy.mil/lattice/struk/b4.html). If you want
the Zn atoms to stay in z=0 you can fix their position as explained above;
nevertheless "u" is just the difference in the z coordinate of Zn and O
atoms.

>  thanks a lot

you are welcome, best regards


-- 
Lorenzo Paulatto
SISSA  &  DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www:   http://people.sissa.it/~paulatto/




  SISSA Webmail https://webmail.sissa.it/
  Powered by SquirrelMail http://www.squirrelmail.org/



--

Message: 3
Date: Wed, 8 Jul 2009 14:29:38 +0330 (IRST)
From: leila salimi 
Subject: [Pw_forum] Errors in examples of QuantumEspresso
To: pw forum 
Message-ID: <2112806.51091247050778893.JavaMail.root at mta.iut.ac.ir>
Content-Type: text/plain; charset="utf-8"

Hi every body,
I have been trying to install the code "espresso-4.0.5" on IBM pSeries 575, a 
clustered SMP (Symmetric Multiprocessing) system.
and I used the special make.sys which is matched with our system and then ?make 
pwall? was successful but now I'm getting the following error trying to run the 
examples.
I will attach "make.sys" and "environment_variables" to this mail.
Do you have any idea what is going wrong?

Best Regards,
Leila Salimi.
Isfahan University of Technology, Isfahan, Iran.


?from ewald : error # ? ? ? ? 1
> ? ? ?optimal alpha not found 

running the scf calculation.

[Pw_forum] vc-relax

[Lorenzo Paulatto]

On Wed, July 8, 2009 11:03, ali kazempour wrote:
>  Can I use vc-relax to optimize the value of lattice constant in ZnO
>  wurtzite structure?

Dear ali,
of course you can!


> Because the lattice constant change and also atomic
>  positions either.

You can nail the atoms to their position by adding " 0 0 0" after the
atomic coordinates (see manual for detail), although it only make sense
for crystal and possibly alat coordinates, when you are doing vc-relax.

> After finishing the run, Which atomic position shoud be
>  used in next calculation(relaxed position or initial positions)?

The optimized ones, if not, why would you do the optimization?

>  How can I
>  optimize the value of u that is ideally equal to 3/8?

Doing vc-relax, I don't see the problem )I asume you are using this
notation: http://cst-www.nrl.navy.mil/lattice/struk/b4.html). If you want
the Zn atoms to stay in z=0 you can fix their position as explained above;
nevertheless "u" is just the difference in the z coordinate of Zn and O
atoms.

>  thanks a lot

you are welcome, best regards


-- 
Lorenzo Paulatto
SISSA  &  DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www:   http://people.sissa.it/~paulatto/




  SISSA Webmail https://webmail.sissa.it/
  Powered by SquirrelMail http://www.squirrelmail.org/

[Pw_forum] Strain calculation through quantum espresso

[Dimpy Sharma]

Hi Quantum espresso users,

Could anyone please tell me how to calculate strain of a supercell through 
quantum espresso, as in the manual it has not been mentioned properly.

Thanks

Dimpy

-- next part --
An HTML attachment was scrubbed...
URL: 
http://www.democritos.it/pipermail/pw_forum/attachments/20090708/f7bb5b4b/attachment.htm
 

[Pw_forum] Units in dynamical matrix files

[Serge Nakhmanson]

I had to ponder this question some time ago.

I think the difference here is the same as
between Ry and Ha energy units, so that in
the "convention" that QE uses an extra 1/2
proliferates into the mass units as well.

But this is my guess, which may not be the
ultimate truth. Actually, considering how
many times I get my butt handed back to me
in this forum, I could be totally wrong
about it.

Cheers,

S.

Cristian Degli Esposti Boschi wrote:
> 
> Am I right? Why the 1/2 factor?
> 
> And what are the typical units used for force constants?


-- 
*
  Serge M. Nakhmanson   phone: (630) 252-5205
  Assistant Scientist fax: (630) 252-4798
  MSD-212, Rm. C-224
  Argonne National Laboratory
  9700 S. Cass Ave.
  Argonne, IL 60439
*

[Pw_forum] Strain calculation through quantum espresso (Giovanni Cantele)

[Eduardo Ariel Menendez Proupin]

Hi DS

Strain is a geometrical property. If you want a fast calculation, just use
the Bilbao Crystallographic Server.
http://www.cryst.ehu.es/cryst/strain.html
there you may input two sets of lattice parameters and get the strain
relating both lattices.

Take a look at Fast et al, PRB 51, 17431 (1995). In equations (1) and (2)
are explained the relation between lattice vectors and strain. In  Kittel's
textbook it is explained too, but I am not sure if in all the editions. In
the article of Fast it explains what you can do with Q-E and similar codes.

In Q-E you input the lattice parameters or the lattice vectors, and all the
other stuff, and get the stress tensor as explained in previous posts.

Maybe what you need is to find the strain of a crystal under an specified
stress tensor. As far as I know, with Q-E you cand do it only in the case of
hydrostatic stress (when the stress tensor is the pressure times the
identity matrix), using calculation='vc-relax'  and setting the variable
press. E.g.
 &control
calculation = 'vc-relax'
..
&CELL
cell_dynamics='damp-pr',
press = 35.0, (the value of pressure in kbars)
cell_dofree='all',


For a non-hydrostatic stress, you may need to find the elastic constants (as
in Fasts's paper) first and then solve the equations of elasticity. If the
stress is big, you may need an iterative process.

If you need the strain under a fully specified stress tensor, i.e., the six
independent components of the tensor, you may device a minimization
algorithm implemented in a shell or python script, that run pw.x  to get the
energies and stress.
An alternative is  to find the elastic constants (as in Fasts's paper) first
and then solve the equations of elasticity. If the stress is big, you may
need an iterative process to find the elastic constants under a stress that
is close to your derired stress.

In simple cases, such as uniaxial stress and orthorombic lattices, you do
cell relaxations with constraints (cell_dofree='x' ) keeping one lattice
vector fixed, and by trial and error you can obtain the lattice that produce
the desired component of the stress.




-- 
Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez
-- next part --
An HTML attachment was scrubbed...
URL: 
http://www.democritos.it/pipermail/pw_forum/attachments/20090708/4abbc09b/attachment.htm
 

[Pw_forum] vc-relax

[ali kazempour]

Can I use vc-relax to optimize the value of lattice constant in ZnO wurtzite 
structure?Because the lattice constant change and also atomic positions either. 
After finishing the run, Which atomic position shoud be used in next 
calculation(relaxed position or initial positions)? How can I optimize the 
value of u that is ideally equal to 3/8?
thanks a lot

Ali Kazempour

Physics department, Isfahan University of Technology

84156 Isfahan, Iran.Tel-1:  +98 311 391 3733

Fax: +98 311 391 2376  Tel-2:  +98 311 391 2375


  
-- next part --
An HTML attachment was scrubbed...
URL: 
http://www.democritos.it/pipermail/pw_forum/attachments/20090708/7b0b1a07/attachment.htm