[Pw_forum] Pw_forum Digest, Vol 25, Issue 10
Dimpy Sharma
dimpy.sharma at tyndall.ie
Wed Jul 8 12:56:13 CEST 2009
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
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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)
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Message: 1
Date: Wed, 8 Jul 2009 02:03:55 -0700 (PDT)
From: ali kazempour <kazempoor2000 at yahoo.com>
Subject: [Pw_forum] vc-relax
To: pw <pw_forum at pwscf.org>
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
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Message: 2
Date: Wed, 8 Jul 2009 11:33:29 +0200 (CEST)
From: "Lorenzo Paulatto" <paulatto at sissa.it>
Subject: Re: [Pw_forum] vc-relax
To: "PWSCF Forum" <pw_forum at pwscf.org>
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/
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Message: 3
Date: Wed, 8 Jul 2009 14:29:38 +0330 (IRST)
From: leila salimi <l.salimi at ph.iut.ac.ir>
Subject: [Pw_forum] Errors in examples of QuantumEspresso
To: pw forum <pw_forum at pwscf.org>
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...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
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Message: 4
Date: Wed, 8 Jul 2009 14:45:02 +0330 (IRST)
From: leila salimi <l.salimi at ph.iut.ac.ir>
Subject: [Pw_forum] Errors in examples of QuantumEspresso
To: pw forum <pw_forum at pwscf.org>, pw <pw_forum-request at pwscf.org>
Message-ID: <13809261.51301247051702751.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.
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 in iotk to produce a dynamical library,
# for Mac OS-X with PowerPC and xlf compiler. In all other cases
# ARFLAGS_DYNAMIC = $(ARFLAGS)
AR = ar
ARFLAGS = ruv
ARFLAGS_DYNAMIC= 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
LIBOBJS = ../flib/ptools.a ../flib/flib.a ../clib/clib.a ../iotk/src/libiotk.a
# Added ESSL
LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FFT_LIBS) $(MPI_LIBS) $(MASS_LIBS) $(ESSL_LIBS) $(PGPLOT_LIBS) $(LD_LIBS)
------------------------------
Message: 5
Date: Wed, 8 Jul 2009 11:20:52 +0100
From: "Dimpy Sharma" <dimpy.sharma at tyndall.ie>
Subject: [Pw_forum] Strain calculation through quantum espresso
To: <pw_forum at pwscf.org>
Message-ID: <D4A761F73683694BBD69D634FF2980153AEAAB at MAIL.tyndall.ie>
Content-Type: text/plain; charset="iso-8859-1"
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
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Message: 6
Date: Wed, 8 Jul 2009 12:34:13 +0200
From: Paolo Giannozzi <giannozz at democritos.it>
Subject: Re: [Pw_forum] Strain calculation through quantum espresso
To: PWSCF Forum <pw_forum at pwscf.org>
Message-ID: <5662B04F-FC35-4CBE-8EE2-D83D29EEE658 at democritos.it>
Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
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
------------------------------
Message: 7
Date: Wed, 8 Jul 2009 12:37:52 +0200
From: Paolo Giannozzi <giannozz at democritos.it>
Subject: Re: [Pw_forum] Errors in examples of QuantumEspresso
To: PWSCF Forum <pw_forum at pwscf.org>
Message-ID: <A2700779-F6D5-4EF9-854D-939C36894326 at democritos.it>
Content-Type: text/plain; charset=US-ASCII; format=flowed
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
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