Re: [SIESTA-L] psf of Boron

2015-02-27 Por tôpico Jean-Joseph Adjizian 

There are some already available on the website for LDA and GGA.

http://departments.icmab.es/leem/siesta/Databases/Pseudopotentials/periodictable-intro.html

And if you dont want to use these ones, you can generate one using the 
ATOM program.


Cheers,

Jean-Jo

Dr Jean-Joseph Adjizian
jean.adjiz...@uclouvain.be
Téléphone : +32 (0)10 47 85 66
IMCN, Universite Catholique de Louvain
Chemin des Étoiles 8 bte L7.03.01
1348, Louvain-La-Neuve, Belgium

Le 27/02/15 17:52, aouchenni boudjemaa a écrit :

Hi siesta users,

   Is some one has the psf optimised of Boron (B).

thanks in advance
B. Aouchenni

Re: [SIESTA-L] Problem using gnubands

2015-07-23 Por tôpico Jean-Joseph Adjizian 

Hi,

have you opened your arch.make file?
I think what Nick Papior is saying is to change your Fortran compiler. 
Instead of using f95 you should use gfortran.
And surprisingly, if you do a search in your arch.make file there is 
only one match for f95. Maybe if you change it to gfortran?


Cheers,

Jean-Jo

Le 23/07/15 10:43, jv sharma a écrit :

Dear Prof. Nick,

Sorry to bother, attached here my arch.make file. Could you please let 
me know where to make the changes, and also how to proceed after 
making changes in this file?


On Thu, Jul 23, 2015 at 2:06 PM, Nick Papior nickpap...@gmail.com 
mailto:nickpap...@gmail.com wrote:


Ah. Would you please try gfortran instead of f95. Edit your
arch.make file.

[SIESTA-L] Siesta-pexsi

2015-10-14 Por tôpico Jean-Joseph Adjizian 

Dear Users,

I am trying to compile siesta-pexsi.
I have installed all the dependencies necessary to build the the pexsi 
lib. (parmetis, metis, superlu and scotch)
Then I have created the pexsi lib libpexsi_linux.a. I ran the test in 
the example folder.

mpirun -n 1 ./driver_pselinv_complex_(suffix) and it worked fine.

Then I compile siesta-pexsi using an arch.make that I have used and has 
worked in the past for siesta-trunk-462.
I have tried to add a link to the pexsi library in the arch.make by 
extending the line:
LIBS=$(SCALAPACK_LIBS) $(BLACS_LIBS) $(LAPACK_LIBS) $(BLAS_LIBS) 
$(NETCDF_LIBS) $(PEXSI_LIB) $(DSUPERLU_LIB) $(PARMETIS_LIB) $(METIS_LIB)
and giving the path to the new library for $(PEXSI_LIB) $(DSUPERLU_LIB) 
$(PARMETIS_LIB) $(METIS_LIB)
 it compile until the linking is done but at the end of the compilation 
I get this error.
"pexsi/src/libpexsi_linux.a(interface.o): In function 
`ReadDistSparseMatrixFormattedHeadInterface':"


I imagine I dont call the pexsi library correctly. Could anyone help me 
please? Has anyone managed to install siesta-pexsi correctly?


Thank you in advance,

Jean-Jo

--
Dr Jean-Joseph Adjizian
jean.adjiz...@uclouvain.be
Téléphone : +32 (0)10 47 85 66
IMCN, Universite Catholique de Louvain
Chemin des Étoiles 8 bte L7.03.01
1348, Louvain-La-Neuve, Belgium

Re: [SIESTA-L] vim syntax highlighting

2016-04-14 Por tôpico Jean-Joseph Adjizian 

Hi Arthur,

Thanks for the tip. It works just fine now.

Jean-Joseph

Le 14/04/16 12:50, Arthur France-Lanord a écrit :

you can just add “syn case ignore”.




On 14 Apr 2016, at 11:37, Jean-Joseph Adjizian <jean.adjiz...@uclouvain.be> 
wrote:



.

[SIESTA-L] Getting Current in Transiesta 4.1

2016-09-21 Por tôpico Jean-Joseph Adjizian 

Hello everyone,

I have a quick (and maybe silly question) about extracting the value of 
the current at a finite bias in the new version of Tbtrans.


In the previous version, it was quite straightforward as it was printed 
out in the output file.


It seems that is not the case anymore, unless I have not set the 
parameter right.


Could someone could guide me please?


Thanks in advance,


Jean-Jo

Re: [SIESTA-L] Getting Current in Transiesta 4.1

2016-09-21 Por tôpico Jean-Joseph Adjizian 

Thanks a lot for the quick reply.

I guess any NetCDF-4 version would do the trick for tbtrans? as long as 
they are version 4.X.X.


how would you test that siesta is correctly installed with netcdf?

So with netcdf, tbtrans prints out the current by default in the ouptfile ?

Thank a lot in advance?


JJ


Le 21/09/16 à 16:47, Nick Papior a écrit :
The latest tbtrans version will "only" print out the current if one 
has compiled with NetCDF-4. There are many more features enabled by 
using NetCDF-4 and I would HIGHLY recommend you to enable all those 
features.


One may calculate the current easily by numeric integration and the 
fermi-functions.


Again, I would highly advice to enable NetCDF-4 for complete feature set.

2016-09-21 16:17 GMT+02:00 Jean-Joseph Adjizian 
<jean.adjiz...@uclouvain.be <mailto:jean.adjiz...@uclouvain.be>>:


Hello everyone,

I have a quick (and maybe silly question) about extracting the
value of the current at a finite bias in the new version of Tbtrans.

In the previous version, it was quite straightforward as it was
printed out in the output file.

It seems that is not the case anymore, unless I have not set the
parameter right.

Could someone could guide me please?


Thanks in advance,


Jean-Jo






--
Kind regards Nick

Re: [SIESTA-L] << compiling siesta-4.1-b1 with NetCDF >>

2016-09-27 Por tôpico Jean-Joseph Adjizian 

Hello,

Sorry, but it seems that I keep struggling with tbtrans installation.

I have installed netcdf.4.4.1 and netcdf-fortran.

I have used the arch.make given in the previous email.

I compile transiesta with no problem but when I compile tbtrans I get 
the following error when it tries to compile m_tbt_sigma_save.F90.


/"
/

/mpiifort -c -O1 
-I/projects/acad/ucl-naps/software/netcdf_Tbtrans/include 
-I/projects/acad/ucl-naps/software/netcdf_Tbtrans/include -DCDF -DNCDF_4 
-DNCDF_PARALLEL  -DTBTRANS m_tbt_sigma_save.F90 //
//m_tbt_sigma_save.F90(260): error #6404: This name does not have a 
type, and must have an explicit type. [MPI_COMM_WORLD]//

//comm = MPI_COMM_WORLD, &//
//---^//
//compilation aborted for m_tbt_sigma_save.F90 (code 1)//
//make: *** [m_tbt_sigma_save.o] Error 1/

"

I am not really an expert in compilation error, could someone guide me 
please?


Thanks a lot in advance,


Jean-Jo



Le 23/09/16 à 16:25, Nick Papior a écrit :

It should be placed at the end of the arch.make.

Try the attached arch.make file.

2016-09-23 16:15 GMT+02:00 I. Camps >:


Sorry, it didn't work :(


[]'s,

Camps

On Fri, Sep 23, 2016 at 11:09 AM, Nick Papior
> wrote:

Ah, ok. Now I see.

You should (both) do this in your arch.make.

You may track it on launchpad:
https://bugs.launchpad.net/siesta/+bug/1627041


The easy fix is this:

FFLAGS += $(INCFLAGS) $(NETCDF_INCFLAGS)

which should work (disclaimer I haven't tested this).

2016-09-23 15:54 GMT+02:00 I. Camps >:

Yes, I compiled everything with the same intel compiler.


[]'s,

Camps

On Fri, Sep 23, 2016 at 10:51 AM, Nick Papior
> wrote:

Have you compiled the netcdf and hdf5 with the same
intel compiler? That is necessary.

Sadly, this is one of the inconveniences of fortran.

2016-09-23 15:23 GMT+02:00 I. Camps >:

Here is the arch.make:
##
# source
/opt/intel/parallel_studio_xe_2015/psxevars.sh
# source
/opt/intel/parallel_studio_xe_2017.0.035/psxevars.sh
# source
/opt/intel/Compiler/11.0/083/bin/ifortvars.sh intel64
# source /opt/intel/impi_5.0.2/bin64/mpivars.sh
# This file is part of the SIESTA package.
#
# Copyright (c) Fundacion General Universidad
Autonoma de Madrid:
# E.Artacho, J.Gale, A.Garcia, J.Junquera,
P.Ordejon, D.Sanchez-Portal
# and J.M.Soler, 1996- .
#
# Use of this software constitutes agreement with
the full conditions
# given in the SIESTA license, as signed by all
legitimate users.
#
# 
# Description:
# Intel compiler/mkl  V11 on atto
# OpenMPI with support for Intel compiler V11
#  MKL V11 libraries, including a
version of BLACS provided
# by Intel for the
openmpi framework,
# and Intel's own
Scalapack, Lapack, and BLAS.
#
# Execution:
#
# $(OPENMPI_ROOT)/bin in PATH
# $(OPENMPI_ROOT)/lib in LD_LIBRARY_PATH
#
#   mpirun -np NPROCS siesta 
#
SIESTA_ARCH=intel-mpi
#
#
FC=mpiifort
FC_SERIAL=ifort

#
#  You can play with other optimization options
#  I am not sure whether the compiler attempts to
multithread the code
#
FFLAGS= -w  -O2 -mp
FFLAGS_CHECKS=-g -O0 -debug full -traceback -C
FFLAGS_DEBUG= -g
LDFLAGS=
#COMP_LIBS += libncdf.a libfdict.a
RANLIB=echo
#
# You might want to turn off FoX for Intel11
#

Re: [SIESTA-L] Installation of NetCDF with CDF4 support (also installation of HDF5 and zlib)

2016-09-28 Por tôpico Jean-Joseph Adjizian 

Hello Nick,

I should report and say thank you very much for this.
After slightly modifying the script for my configuration, I can say that 
it is all working well.
Sorry for all the emails. Still not sure what was wrong on my side but 
that's a different issue ;)
Again thank you very much and I am sure your script would be useful for 
many people.


Kind regards,

Jean-Jo



Le 27/09/16 à 21:39, Nick Papior a écrit :

Dear list,

Several have asked questions about installation of NetCDF4 successfully.

If you simply download NetCDF and install it using configure without 
any flags you will only get support for CDF-3.
Although you have downloaded NetCDF-4.4.1 it will NOT intrinsically 
install NetCDF with CDF-4 support. I know this is very confusing, and 
it is indeed very unfortunate.
To further complicate the issue, SIESTA requires the Fortran library 
which requires a second installation.


To ease the use of the NetCDF features I have created a script which 
should install NetCDF (source version: 4.4.0) with full CDF4 support.

The script has been tested on Debian.

All you need to do is download these sources to your installation 
directory:

http://zlib.net/zlib-1.2.8.tar.gz
https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.16/src/hdf5-1.8.16.tar.bz2
https://github.com/Unidata/netcdf-c/archive/v4.4.0.tar.gz
https://github.com/Unidata/netcdf-fortran/archive/v4.4.3.tar.gz

Also download the attached install.sh script to your installation 
directory.


The installation script will NOT install the parallel version, but you 
should be able to adapt the script accordingly if you really want this 
feature enabled.


Please run through the script and read the comments to ensure that it 
will do as you requested.
I will probably not be able to help you change the script to your 
liking, but feel free to post any changes that adhere to different 
compilers etc.


Once you have edited the script and read the comments, you may run the 
script:

$> bash ./install.sh

and it will install, first zlib, then hdf5, then netcdf-c and lastly, 
netcdf-fortran.


--
Kind regards Nick

[SIESTA-L] TBtrans netcdf

2017-12-15 Por tôpico Jean-Joseph Adjizian 

Dear all,

I am  trying to install TBtrans with NETCDF dependencies using the 
latest version 4.1-b3.
The libraries i am using are intelmpi/2017.3.196/64  and 
mkl/lp64/11.2.4.223.
Any installation (Siesta, transiesta) with these libraries work just 
fine without netcdf.

It is only when I add the netcdf flags in the arch.make.

To install netcdf, I used the script 'install_netcdf4.bash' given in the 
Docs folder.

It seems to work fine since I get this message after execution:

/Completed installing Fortran NetCDF library//
//
//##//
//# Completed installation #//
//#   of NetCDF package    #//
//#  and its dependencies  #//
//##//
//
//
//Please add the following to the BOTTOM of your arch.make file//
//
//INCFLAGS += 
-I/software/netcdf_Tbtrans/for_4.1_b3/build/netcdf/4.4.1.1/include//
//LDFLAGS += -L/software/netcdf_Tbtrans/for_4.1_b3/build/zlib/1.2.11/lib 
-Wl,-rpath=/software/netcdf_Tbtrans/for_4.1_b3/build/zlib/1.2.11/lib//
//LDFLAGS += -L/software/netcdf_Tbtrans/for_4.1_b3/build/hdf5/1.8.16/lib 
-Wl,-rpath=/software/netcdf_Tbtrans/for_4.1_b3/build/hdf5/1.8.16/lib//
//LDFLAGS += 
-Lsoftware//netcdf_Tbtrans/for_4.1_b3/build/netcdf/4.4.1.1/lib 
-Wl,-rpath=/software/netcdf_Tbtrans/for_4.1_b3/build/netcdf/4.4.1.1/lib//

//LIBS += -lnetcdff -lnetcdf -lhdf5_hl -lhdf5 -lz//
//COMP_LIBS += libncdf.a libfdict.a//
//FPPFLAGS += -DCDF -DNCDF -DNCDF_4/


So I add these line in my arch.make. But when I try to compile 
Transiesta and TBtrans I get the following:


/netcdf_ncdf.f90(280): error #7013: This module file was not generated 
by any release of this compiler.   [MPI]//

//    use mpi//
//^//
//netcdf_ncdf.f90(356): error #6580: Name in only-list does not exist.   
[MPI_INFO_NULL]//

//    use mpi, only : MPI_INFO_NULL//
//^//
//netcdf_ncdf.f90(401): error #7013: This module file was not generated 
by any release of this compiler.   [MPI]//

//    use mpi, only : MPI_INFO_NULL//
//^//
//netcdf_ncdf.f90(2966): error #7013: This module file was not generated 
by any release of this compiler.   [MPI]//

//    use mpi//
//^//
//netcdf_ncdf.f90(387): error #6404: This name does not have a type, and 
must have an explicit type.   [MPI_INFO_NULL]//

//    comm = this%comm, info=MPI_INFO_NULL), &//
//---^//
//netcdf_ncdf.f90(433): error #6406: Conflicting attributes or multiple 
declaration of name.   [MPI_INFO_NULL]//

//    comm = this%comm, info=MPI_INFO_NULL), &//
//---^//
//netcdf_ncdf.f90(401): error #6580: Name in only-list does not exist.   
[MPI_INFO_NULL]//

//    use mpi, only : MPI_INFO_NULL//
//^//
//netcdf_ncdf.f90(3054): error #6404: This name does not have a type, 
and must have an explicit type.   [MPI_COMM_WORLD]//

//    call MPI_Comm_Rank(MPI_Comm_World,Node,MPIerror)//
//---^//
//compilation aborted for netcdf_ncdf.f90 (code 1)//
//make[1]: *** [netcdf_ncdf.o] Error 1//
//make[1]: Leaving directory 
`/software/transiesta/4.1_b3_NETCDF/src/Util/TS/TBtrans/ncdf'//

//make: *** [libncdf.a] Error 2

/Please also find the arch.make I am using for this.

Any tip?

Thank you for your kind help.

All the best,

Jean-Jo

ps: Apologies for any inconvenience.
//
##
# CURIE BullX#
##
# load modules:  #
#   fortran/intel/12.1.7.256 #
#   mkl/12.1.7.256   #
#   bullxmpi/1.1.16.5#
##
# 
# This file is part of the SIESTA package.
#
# Copyright (c) Fundacion General Universidad Autonoma de Madrid:
# E.Artacho, J.Gale, A.Garcia, J.Junquera, P.Ordejon, D.Sanchez-Portal
# and J.M.Soler, 1996- .
# 
# Use of this software constitutes agreement with the full conditions
# given in the SIESTA license, as signed by all legitimate users.
#
.SUFFIXES:
.SUFFIXES: .f .F .o .a .f90 .F90

SIESTA_ARCH=x86_64-unknown-linux-gnu--unknown

FPP=
FPP_OUTPUT= 
FC=mpif90
RANLIB=ranlib

SYS=nag

SP_KIND=4
DP_KIND=8
KINDS=$(SP_KIND) $(DP_KIND)

FFLAGS=-O1
FPPFLAGS= -DMPI -DFC_HAVE_FLUSH -DFC_HAVE_ABORT
LDFLAGS=

ARFLAGS_EXTRA=

FCFLAGS_fixed_f=
FCFLAGS_free_f90=
FPPFLAGS_fixed_F=
FPPFLAGS_free_F90=

BLAS_LIBS=
LAPACK_LIBS=
BLACS_LIBS=
SCALAPACK_LIBS=

MKL_LIBS=${MKLROOT}/lib/intel64/libmkl_blas95_lp64.a 
${MKLROOT}/lib/intel64/libmkl_lapack95_lp64.a -L${MKLROOT}/lib/intel64 
-lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_core -lmkl_sequential 
-lmkl_blacs_intelmpi_lp64 -lpthread -lm -ldl


COMP_LIBS=libsiestaLAPACK.a 

NETCDF_LIBS=
NETCDF_INTERFACE=

LIBS=$(MKL_LIBS) 

INCFLAGS += 
-I/projects/acad/ucl-naps/software/netcdf_Tbtrans/for_4.1_b3/build/netcdf/4.4.1.1/include
LDFLAGS += 
-L/projects/acad/ucl-naps/software/netcdf_Tbtrans/for_4.1_b3/build/zlib/1.2.11/lib
 
-Wl,-rpath=/projects/acad/ucl-naps/software/netcdf_Tbtrans/for_4.1_b3/build/zlib/1.2.11/lib
LDFLAGS +=

Re: [SIESTA-L] TBtrans netcdf

2017-12-22 Por tôpico Jean-Joseph Adjizian 

Dear Nick,

Thank you for your response,

I made corrections to my arch.make according to your suggestions.

The error was due to mpif90 for some reason in my arch.make. I tried to 
use mpiifort instead and that just compiled with no error.


Is there a specific reason why mpif90 caused a problem? (Sorry if the 
question is dumb ;-))


Thank you for your help and I wish you a very good Christmas.

Jean-Jo

Le 18/12/2017 à 16:57, Nick Papior a écrit :

Dear jean-jo

When using intel compilers you should add this to your arch.make:

# The atom.f code is very vulnerable. Particularly the Intel compiler
# will make an erroneous compilation of atom.f with high optimization
# levels.
atom.o: atom.F
        $(FC) -c $(FFLAGS_DEBUG) $(INCFLAGS) $(FPPFLAGS) 
$(FPPFLAGS_fixed_F) $<

state_analysis.o: state_analysis.F
        $(FC) -c $(FFLAGS_DEBUG) $(INCFLAGS) $(FPPFLAGS) 
$(FPPFLAGS_fixed_F) $<



Also,
1) add .c to the .SUFFIXES list
2) Do not use libsiestaLAPACK when you have MKL available, these 
lapack/blas are *only* for testing purposes (they are very slow).


On a side-note, are you sure your bullxmpi works 
with -lmkl_blacs_intelmpi_lp64? As far as I can see bullxmpi is an 
OpenMPI variant which means you need to use -lmkl_blacs_openmpi_lp64 
instead.


Lastly, the errors you see are probably because you haven't done a 
make clean?


2017-12-15 15:57 GMT+01:00 Jean-Joseph Adjizian 
<jean.adjiz...@uclouvain.be <mailto:jean.adjiz...@uclouvain.be>>:


Dear all,

I am  trying to install TBtrans with NETCDF dependencies using the
latest version 4.1-b3.
The libraries i am using are intelmpi/2017.3.196/64  and
mkl/lp64/11.2.4.223 <http://11.2.4.223>.
Any installation (Siesta, transiesta) with these libraries work
just fine without netcdf.
It is only when I add the netcdf flags in the arch.make.

To install netcdf, I used the script 'install_netcdf4.bash' given
in the Docs folder.
It seems to work fine since I get this message after execution:

/Completed installing Fortran NetCDF library//
//
//##//
//# Completed installation #//
//#   of NetCDF package    #//
//#  and its dependencies  #//
//##//
//
//
//Please add the following to the BOTTOM of your arch.make file//
//
//INCFLAGS +=
-I/software/netcdf_Tbtrans/for_4.1_b3/build/netcdf/4.4.1.1/include
<http://4.4.1.1/include>//
//LDFLAGS +=
-L/software/netcdf_Tbtrans/for_4.1_b3/build/zlib/1.2.11/lib
-Wl,-rpath=/software/netcdf_Tbtrans/for_4.1_b3/build/zlib/1.2.11/lib//
//LDFLAGS +=
-L/software/netcdf_Tbtrans/for_4.1_b3/build/hdf5/1.8.16/lib
-Wl,-rpath=/software/netcdf_Tbtrans/for_4.1_b3/build/hdf5/1.8.16/lib//
//LDFLAGS +=
-Lsoftware//netcdf_Tbtrans/for_4.1_b3/build/netcdf/4.4.1.1/lib
-Wl,-rpath=/software/netcdf_Tbtrans/for_4.1_b3/build/netcdf/4.4.1.1/lib

<http://4.4.1.1/lib-Wl,-rpath=/software/netcdf_Tbtrans/for_4.1_b3/build/netcdf/4.4.1.1/lib>//
//LIBS += -lnetcdff -lnetcdf -lhdf5_hl -lhdf5 -lz//
//COMP_LIBS += libncdf.a libfdict.a//
//FPPFLAGS += -DCDF -DNCDF -DNCDF_4/


So I add these line in my arch.make. But when I try to compile
Transiesta and TBtrans I get the following:

/netcdf_ncdf.f90(280): error #7013: This module file was not
generated by any release of this compiler.   [MPI]//
//    use mpi//
//^//
//netcdf_ncdf.f90(356): error #6580: Name in only-list does not
exist.   [MPI_INFO_NULL]//
//    use mpi, only : MPI_INFO_NULL//
//^//
//netcdf_ncdf.f90(401): error #7013: This module file was not
generated by any release of this compiler. [MPI]//
//    use mpi, only : MPI_INFO_NULL//
//^//
//netcdf_ncdf.f90(2966): error #7013: This module file was not
generated by any release of this compiler.   [MPI]//
//    use mpi//
//^//
//netcdf_ncdf.f90(387): error #6404: This name does not have a
type, and must have an explicit type. [MPI_INFO_NULL]//
//    comm = this%comm, info=MPI_INFO_NULL), &//
//---^//
//netcdf_ncdf.f90(433): error #6406: Conflicting attributes or
multiple declaration of name. [MPI_INFO_NULL]//
//    comm = this%comm, info=MPI_INFO_NULL), &//
//---^//
//netcdf_ncdf.f90(401): error #6580: Name in only-list does not
exist.   [MPI_INFO_NULL]//
//    use mpi, only : MPI_INFO_NULL//
//^//
//netcdf_ncdf.f90(3054): error #6404: This name does not have a
type, and must have an explicit type. [MPI_COMM_WORLD]//
//    call MPI_Comm_Rank(MPI_Comm_World,Node,MPIerror)//
//---^//
//compilation aborted for netcdf_ncdf.f90 (code 1)//
//make[1]: *** [netcdf_ncdf.o] Error 1//
//make[1]: Leaving directory