[SIESTA-L] Zinc Pseudopotential error

[RAJAN SINGH]

Dear Siesta Users,

I am trying to simulate a Zinc based system with GGA-PBE approximation and
DZP as basis set. I downloaded the Pseudopotential of Zn from the siesta
website, while using the same I am geting following error:

atom: Called for Zn(Z =  30)

read_vps: Pseudopotential generation method:
read_vps: ATM3  Troullier-Martins
Total valence charge:   12.0

read_vps: Pseudopotential includes a core correction:
read_vps: Pseudo-core for xc-correction

xc_check: Exchange-correlation functional:
xc_check: GGA Perdew, Burke & Ernzerhof 1996
V l=0 = -2*Zval/r beyond r=  2.4566
V l=1 = -2*Zval/r beyond r=  2.4261
V l=2 = -2*Zval/r beyond r=  2.4261
V l=3 = -2*Zval/r beyond r=  2.7837
All V_l potentials equal beyond r=  2.7491
This should be close to max(r_c) in ps generation
All pots = -2*Zval/r beyond r=  2.7837

VLOCAL1: 99.0% of the norm of Vloc inside  5.744 Ry
VLOCAL1: 99.9% of the norm of Vloc inside 13.090 Ry
atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge3.31606
atom: Maximum radius for r*vlocal+2*Zval:2.92640
GHOST: WARNING: Ghost state for L =  0
GHOST: No ghost state for L =  1
GHOST: No ghost state for L =  2
GHOST: No ghost state for L =  3
KBgen: WARNING: Ghost states have been detected
KBgen: WARNING: Some parameter should be changed in the
KBgen: WARNING: pseudopotential generation procedure.
Stopping Program from Node:0

Kindly suggest the possible solutions for the same. Also, if someone has Zn
Pseudopotential then please tell me how to get one.

Thank you so much for your help.

With Regards
Rajan Singh

Re: [SIESTA-L] Eig2DOS parameters

[RAJAN SINGH]

Dear Sir

Actually I try with not providing the values and each time it is taking
smearing as .002 and number of point as 200.

Regards
Riya

On 22-May-2017 1:35 AM, "I. Camps"  wrote:

> Dear Riya,
>
> There aren´t default values for these parameters.
>
> Take in mind that its YOU who is constructing the DOS (a continuum
> function) from the eigenvalues (discrete values).
>
> The idea here is (following your points):
> - the program will add a gaussian or lorentzian function centered in each
> eigenvalue. To draw a gaussian/lorentzian curve, you need two parameters:
> the position where it will be centered (in this case is the eigenvalue) and
> the width of it. You can play with this value: if you put a very small
> value, then your gaussian/lorenztian will look like a line. If you put a
> big value, each gaussian/lorentzian will superpose with its neighbor and
> you will loose the contribution form neighbor eigenvalues (my suggestion is
> that you put a value like 100meV, visualize the graph, if the graph looks
> fine for you, or, if not, change the value, make the graph...). This value
> should be reported in your final work.
> - This is a number of energy values to make the total curve (from the sum
> of gaussians/lorentizans). The greater this number is, better the quality
> of the graph is. If this number is small, you can loose some features of
> the DOS. As in the first point, play with different values: 200, 300, etc.
> - in general, I select the energy window in such a way that the gap is
> inside it. Actually, I made an energy windows always around the Fermi
> level, something like Emin=EFermi-3eV and Emax=EFermi+3eV.
>
> If you do not supply these values you can not produce the DOS.
>
> You have another way to produce the DOS that is using the PDOS directive
> in your FDF input. Then, using a tool like "fmpdos" from prof. Postnikov
> (usually in \siesta-source\Util\Contrib\APostnikov\) you can generate,
> instead the PDOS, the DOS.
>
> Yes, all these values will affect the looks of the plot. But, as your
> conclusion will be based in that look, it would be desired that the look is
> good.
>
>
> []'s,
>
> Camps
>
> On Sat, May 20, 2017 at 3:17 AM, Riya Rogers 
> wrote:
>
>>
>> Dear All
>>
>> What is the default values for the following parameters in Eig2DOS:
>>
>> - peak width (in eV) for broadening (gaussian or lorentzian).
>> - number of points in the energy window
>> - energy window: Emin and Emax (wrt E_F shifted to zero)
>>
>>
>> And what if I dont supply these values in .EIG file?
>>
>> Is my calculation of DOS is wrong?
>>
>> or these values only affect the looks of plot.
>>
>>
>> Thanks
>>
>>
>> Regards
>>
>> Riya
>>
>>
>

[SIESTA-L] Is relaxation is necessary during k-point optimization

[RAJAN SINGH]

Dear Siesta Users

I have a fairly large system of about 50 atoms of graphene ribbon. I want
to optimize the same in terms of k-points and mesh cutoff.

But if I relax my system at each k-point, It will cost too much time.

My question is

Can I skip the relaxation fr each k point??
And plot Energies vs kpoint n evaluate optimized k-point??

Please help me in this.

Thank u so much...

With Regarda
Rajan

Re: [SIESTA-L] Error in parallel siesta 4.1b1

[RAJAN SINGH]

Dear Dr Nick

after this step I have this error

Error: Different types in pointer assignment at (1); attempted assignment
of UNKNOWN to REAL(8)
Fatal Error: Error count reached limit of 25.
make: *** [m_mixing.o] Error 1

kindly give me some directions to remove this one.

Regards
Rajan

[SIESTA-L] NETCDF error

[RAJAN SINGH]

Dear Siesta users

I am facing following errors while trying to install 4.1-b1 in parallel
mode with NETCDF:

Fatal Error: Can't open module file 'netcdf.mod' for reading at (1): No
such file or directory
make[2]: *** [nf_ncdf.o] Error 1
make[2]: Leaving directory
`/home/rajan.singh/siesta-4.1-b1ncdf/Obj/NCDF/src'
make[1]: *** [lib] Error 2
make[1]: Leaving directory `/home/rajan.singh/siesta-4.1-b1ncdf/Obj/NCDF'
make: *** [libncdf.a] Error 2


can anyone tell me what is wrong?
my arch file is attached with mail.

thanking you

regards
Rajan


arch.make
Description: Binary data

Re: [SIESTA-L] Error in installation of Parallel version of Siesta-4.1-b1 on cluster

[RAJAN SINGH]

Dear Roberto

I am facing the same problem, I didnt understand your point. Should I
install openmpi using f95 or by f90?
Can you tell me which versions of libraries to use?
I am really stuck, kindly help me.
Thanking You

Regards
Rajan

On Wed, Nov 9, 2016 at 7:32 AM, RCP  wrote:

> Hi,
> The message is pretty clear: the compiler used in your MPI library is
> different from the one you're using to compile Siesta. That's a nasty
> thing about *.mod files. No cure other than using the same compiler.
> Regards,
> Roberto
>
> PD: Eventualy, you might try to rebuild the MPI package using your
> current fortran compiler.
>
>
> On 11/09/2016 12:03 PM, Rishi Sreedhar wrote:
>
>> Dear team Siesta,
>> Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â
>> We were trying to install the parallel version of siesta 4.1-b1 on our
>> cluster but were facing difficulty due to lack of proficiency in Linux.
>> Hereby attaching the arch.make file and also the list of module
>> libraries installed in the cluster.Â
>>
>> We are getting the following error:
>>
>>
>> /home/r.sreedhar/siesta-4.1-b1/Src/m_matio.F90:26:8:
>>
>> Â Â Â Â  use mpi
>> Â Â Â Â Â Â Â  1
>> Fatal Error: Cannot read module file ‘mpi.mod’ opened at (1),
>> because it was created by a different version of GNU Fortran
>> compilation terminated.
>> make: *** [m_matio.o] Error 1
>>
>>
>> Kindly help us out as we are at our wit's end and have tried everything
>> we know.
>> Thank you for the time.
>>
>> with regards,
>> Rishi Sreedhar.
>>
>
> -
>

[SIESTA-L] INTEL MKL LIBRARIES-11.3.2 version for parallel siesta

[RAJAN SINGH]

Dear Siesta users

I am using INTEL MKL LIBRARIES-11.3.2 version 64 bit linux, I think there
is some problem in installation because I am getting segmentation errors
etc while running the parallel job.

Kindly help me in writing correct arch.make file.

Thanking you

Regards
Rajan

[SIESTA-L] errors in running parallel siesta

[RAJAN SINGH]

Dear Siesta Users

I am getting following errors when I am running a code in parallel siesta
(10 processors):

forrtl: No such file or directory
forrtl: No such file or directory
forrtl: No such file or directory
forrtl: No such file or directory
forrtl: severe (28): CLOSE error, unit 100, file "Unknown"


Kindly give some suggestions.

thanking you

Regards
Rajan

Re: [SIESTA-L] Submit parallel siesta job using SLURM schedular

[RAJAN SINGH]

Dear Dr Nick

Thank u so much...

Regards
Rajan

On 16-Nov-2016 1:52 am, "Nick Papior"  wrote:

> Ask your cluster administrator. I bet there is guidelines you should
> follow.
>
> --
>
> Kind regards Nick Papior
>
> On 15 Nov 2016 8:42 pm, "RAJAN SINGH"  wrote:
>
>> Dear Siesta Users
>>
>> How to submit siesta job into parallel environment using SLURM?
>>
>> Any idea how to write script? Or basic idea to write SLURM script file
>> for siesta?
>>
>> Any suggestions will be helpful.
>>
>> Thanking you
>>
>> Regards
>> Rajan
>>
>

[SIESTA-L] Submit parallel siesta job using SLURM schedular

[RAJAN SINGH]

Dear Siesta Users

How to submit siesta job into parallel environment using SLURM?

Any idea how to write script? Or basic idea to write SLURM script file for
siesta?

Any suggestions will be helpful.

Thanking you

Regards
Rajan

Re: [SIESTA-L] Fwd: parallel siesta 4.1 b1 with intel mkl libraries

[RAJAN SINGH]

Dear Hongyi

Actually i have to use slurm.

Regards
Rajan

On 11-Nov-2016 4:53 pm, "Hongyi Zhao"  wrote:

> 2016-11-11 17:17 GMT+08:00 RAJAN SINGH :
> > Dear Hongyi
> >
> > I successfully compiled arch.make file. But I am not able to submit my
> > simulation as a job in cluster using SLURM schedular. Do you know any
> > possible solution?
>
> I use torque & Maui and both are free.  You can get them from here:
> http://www.adaptivecomputing.com/support/download-center/.
>
> Regards
>
> >
> > thanking you
> >
> > Regards
> > Rajan
> >
> > On Fri, Nov 11, 2016 at 12:11 PM, Hongyi Zhao 
> wrote:
> >>
> >> 2016-11-10 16:34 GMT+08:00 RAJAN SINGH :
> >> > Dear Sir
> >> >
> >> > Can you provide your arch.make file, it would be very helpful.
> >>
> >> Hi,
> >>
> >> Have you compiled successfully with my arch.make or not?
> >>
> >> Regards
> >>
> >> >
> >> > Thanking you
> >> >
> >> > Regards
> >> > Rajan
> >> >
> >> > On Thu, Nov 10, 2016 at 1:50 PM, Hongyi Zhao 
> >> > wrote:
> >> >>
> >> >> 2016-11-10 15:36 GMT+08:00 RAJAN SINGH :
> >> >> > Dear Siesta users
> >> >> >
> >> >> > After some modifications in arch.make file i got following errors:
> >> >> >
> >> >> >
> >> >> >
> >> >> > /cm/shared/apps/intel/compilers_and_libraries/
> current/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.a(mkl_blacs_memory.o):
> >> >> > In function `mkl_blacs_malloc':
> >> >> > mkl_blacs_memory.c:(.text+0x8f): undefined reference to
> >> >> > `mkl_serv_iface_malloc'
> >> >> > mkl_blacs_memory.c:(.text+0xf0): undefined reference to
> >> >> > `mkl_serv_iface_free'
> >> >> >
> >> >> >
> >> >> > /cm/shared/apps/intel/compilers_and_libraries/
> current/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.a(
> bi_f77_get_constants_.o):
> >> >> > In function `bi_f77_get_constants_':
> >> >> > bi_f77_get_constants_.c:(.text+0xf): undefined reference to
> >> >> > `mkl_serv_get_mpi_wrappers'
> >> >> > bi_f77_get_constants_.c:(.text+0x54): undefined reference to
> >> >> > `mkl_serv_get_mpi_wrappers'
> >> >> > bi_f77_get_constants_.c:(.text+0x68): undefined reference to
> >> >> > `mkl_serv_get_mpi_wrappers'
> >> >> > bi_f77_get_constants_.c:(.text+0x7c): undefined reference to
> >> >> > `mkl_serv_get_mpi_wrappers'
> >> >> > bi_f77_get_constants_.c:(.text+0x90): undefined reference to
> >> >> > `mkl_serv_get_mpi_wrappers'
> >> >> >
> >> >> >
> >> >> > /cm/shared/apps/intel/compilers_and_libraries/
> current/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.a(
> bi_f77_get_constants_.o):bi_f77_get_constants_.c:(.text+0xa4):
> >> >> > more undefined references to `mkl_serv_get_mpi_wrappers' follow
> >> >> > collect2: error: ld returned 1 exit status
> >> >> > make: *** [siesta] Error 1
> >> >> >
> >> >> > The new arch.make file is attached with this mail. kindly give me
> >> >> > solution
> >> >> > to this problem.
> >> >>
> >> >> I use the following setting when linking with MKL statically:
> >> >>
> >> >> ##
> >> >> # type of linking with MKL: static
> >> >> ##
> >> >> MKL_LIBS= -Wl,--start-group
> >> >> $(MKLROOT)/lib/intel64/libmkl_scalapack_lp64.a
> >> >> $(MKLROOT)/lib/intel64/libmkl_blacs_intelmpi_lp64.a
> >> >> $(MKLROOT)/lib/intel64/libmkl_intel_lp64.a
> >> >> $(MKLROOT)/lib/intel64/libmkl_sequential.a
> >> >> $(MKLROOT)/lib/intel64/libmkl_core.a -Wl,--end-group -lpthread -lm
> >> >> LIBS=$(MKL_LIBS)
> >> >>
> >> >> Regards
> >> >>
> >> >> >
> >> >> > Thanking you
> >> >> >
> >> >> > regards
> >> >> > Rajan
> >> >> >
> >> >>
> >> >>
> >> >>
> >> >> --
> >> >> Hongyi Zhao 
> >> >> Xinjiang Technical Institute of Physics and Chemistry
> >> >> Chinese Academy of Sciences
> >> >> GnuPG DSA: 0xD108493
> >> >
> >> >
> >>
> >>
> >>
> >> --
> >> Hongyi Zhao 
> >> Xinjiang Technical Institute of Physics and Chemistry
> >> Chinese Academy of Sciences
> >> GnuPG DSA: 0xD108493
> >
> >
>
>
>
> --
> Hongyi Zhao 
> Xinjiang Technical Institute of Physics and Chemistry
> Chinese Academy of Sciences
> GnuPG DSA: 0xD108493
>

Re: [SIESTA-L] Fwd: parallel siesta 4.1 b1 with intel mkl libraries

[RAJAN SINGH]

Dear Hongyi

I successfully compiled arch.make file. But I am not able to submit my
simulation as a job in cluster using SLURM schedular. Do you know any
possible solution?

thanking you

Regards
Rajan

On Fri, Nov 11, 2016 at 12:11 PM, Hongyi Zhao  wrote:

> 2016-11-10 16:34 GMT+08:00 RAJAN SINGH :
> > Dear Sir
> >
> > Can you provide your arch.make file, it would be very helpful.
>
> Hi,
>
> Have you compiled successfully with my arch.make or not?
>
> Regards
>
> >
> > Thanking you
> >
> > Regards
> > Rajan
> >
> > On Thu, Nov 10, 2016 at 1:50 PM, Hongyi Zhao 
> wrote:
> >>
> >> 2016-11-10 15:36 GMT+08:00 RAJAN SINGH :
> >> > Dear Siesta users
> >> >
> >> > After some modifications in arch.make file i got following errors:
> >> >
> >> >
> >> > /cm/shared/apps/intel/compilers_and_libraries/
> current/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.a(mkl_blacs_memory.o):
> >> > In function `mkl_blacs_malloc':
> >> > mkl_blacs_memory.c:(.text+0x8f): undefined reference to
> >> > `mkl_serv_iface_malloc'
> >> > mkl_blacs_memory.c:(.text+0xf0): undefined reference to
> >> > `mkl_serv_iface_free'
> >> >
> >> > /cm/shared/apps/intel/compilers_and_libraries/
> current/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.a(
> bi_f77_get_constants_.o):
> >> > In function `bi_f77_get_constants_':
> >> > bi_f77_get_constants_.c:(.text+0xf): undefined reference to
> >> > `mkl_serv_get_mpi_wrappers'
> >> > bi_f77_get_constants_.c:(.text+0x54): undefined reference to
> >> > `mkl_serv_get_mpi_wrappers'
> >> > bi_f77_get_constants_.c:(.text+0x68): undefined reference to
> >> > `mkl_serv_get_mpi_wrappers'
> >> > bi_f77_get_constants_.c:(.text+0x7c): undefined reference to
> >> > `mkl_serv_get_mpi_wrappers'
> >> > bi_f77_get_constants_.c:(.text+0x90): undefined reference to
> >> > `mkl_serv_get_mpi_wrappers'
> >> >
> >> > /cm/shared/apps/intel/compilers_and_libraries/
> current/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.a(
> bi_f77_get_constants_.o):bi_f77_get_constants_.c:(.text+0xa4):
> >> > more undefined references to `mkl_serv_get_mpi_wrappers' follow
> >> > collect2: error: ld returned 1 exit status
> >> > make: *** [siesta] Error 1
> >> >
> >> > The new arch.make file is attached with this mail. kindly give me
> >> > solution
> >> > to this problem.
> >>
> >> I use the following setting when linking with MKL statically:
> >>
> >> ##
> >> # type of linking with MKL: static
> >> ##
> >> MKL_LIBS= -Wl,--start-group
> >> $(MKLROOT)/lib/intel64/libmkl_scalapack_lp64.a
> >> $(MKLROOT)/lib/intel64/libmkl_blacs_intelmpi_lp64.a
> >> $(MKLROOT)/lib/intel64/libmkl_intel_lp64.a
> >> $(MKLROOT)/lib/intel64/libmkl_sequential.a
> >> $(MKLROOT)/lib/intel64/libmkl_core.a -Wl,--end-group -lpthread -lm
> >> LIBS=$(MKL_LIBS)
> >>
> >> Regards
> >>
> >> >
> >> > Thanking you
> >> >
> >> > regards
> >> > Rajan
> >> >
> >>
> >>
> >>
> >> --
> >> Hongyi Zhao 
> >> Xinjiang Technical Institute of Physics and Chemistry
> >> Chinese Academy of Sciences
> >> GnuPG DSA: 0xD108493
> >
> >
>
>
>
> --
> Hongyi Zhao 
> Xinjiang Technical Institute of Physics and Chemistry
> Chinese Academy of Sciences
> GnuPG DSA: 0xD108493
>

Re: [SIESTA-L] Fwd: parallel siesta 4.1 b1 with intel mkl libraries

[RAJAN SINGH]

Dear Sir

Can you provide your arch.make file, it would be very helpful.

Thanking you

Regards
Rajan

On Thu, Nov 10, 2016 at 1:50 PM, Hongyi Zhao  wrote:

> 2016-11-10 15:36 GMT+08:00 RAJAN SINGH :
> > Dear Siesta users
> >
> > After some modifications in arch.make file i got following errors:
> >
> > /cm/shared/apps/intel/compilers_and_libraries/current/mkl/lib/intel64/
> libmkl_blacs_intelmpi_lp64.a(mkl_blacs_memory.o):
> > In function `mkl_blacs_malloc':
> > mkl_blacs_memory.c:(.text+0x8f): undefined reference to
> > `mkl_serv_iface_malloc'
> > mkl_blacs_memory.c:(.text+0xf0): undefined reference to
> > `mkl_serv_iface_free'
> > /cm/shared/apps/intel/compilers_and_libraries/current/mkl/lib/intel64/
> libmkl_blacs_intelmpi_lp64.a(bi_f77_get_constants_.o):
> > In function `bi_f77_get_constants_':
> > bi_f77_get_constants_.c:(.text+0xf): undefined reference to
> > `mkl_serv_get_mpi_wrappers'
> > bi_f77_get_constants_.c:(.text+0x54): undefined reference to
> > `mkl_serv_get_mpi_wrappers'
> > bi_f77_get_constants_.c:(.text+0x68): undefined reference to
> > `mkl_serv_get_mpi_wrappers'
> > bi_f77_get_constants_.c:(.text+0x7c): undefined reference to
> > `mkl_serv_get_mpi_wrappers'
> > bi_f77_get_constants_.c:(.text+0x90): undefined reference to
> > `mkl_serv_get_mpi_wrappers'
> > /cm/shared/apps/intel/compilers_and_libraries/current/mkl/lib/intel64/
> libmkl_blacs_intelmpi_lp64.a(bi_f77_get_constants_.o):bi_
> f77_get_constants_.c:(.text+0xa4):
> > more undefined references to `mkl_serv_get_mpi_wrappers' follow
> > collect2: error: ld returned 1 exit status
> > make: *** [siesta] Error 1
> >
> > The new arch.make file is attached with this mail. kindly give me
> solution
> > to this problem.
>
> I use the following setting when linking with MKL statically:
>
> ##
> # type of linking with MKL: static
> ##
> MKL_LIBS= -Wl,--start-group
> $(MKLROOT)/lib/intel64/libmkl_scalapack_lp64.a
> $(MKLROOT)/lib/intel64/libmkl_blacs_intelmpi_lp64.a
> $(MKLROOT)/lib/intel64/libmkl_intel_lp64.a
> $(MKLROOT)/lib/intel64/libmkl_sequential.a
> $(MKLROOT)/lib/intel64/libmkl_core.a -Wl,--end-group -lpthread -lm
> LIBS=$(MKL_LIBS)
>
> Regards
>
> >
> > Thanking you
> >
> > regards
> > Rajan
> >
>
>
>
> --
> Hongyi Zhao 
> Xinjiang Technical Institute of Physics and Chemistry
> Chinese Academy of Sciences
> GnuPG DSA: 0xD108493
>

[SIESTA-L] Fwd: parallel siesta 4.1 b1 with intel mkl libraries

[RAJAN SINGH]

Dear Siesta users

After some modifications in arch.make file i got following errors:

/cm/shared/apps/intel/compilers_and_libraries/current/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.a(mkl_blacs_memory.o):
In function `mkl_blacs_malloc':
mkl_blacs_memory.c:(.text+0x8f): undefined reference to
`mkl_serv_iface_malloc'
mkl_blacs_memory.c:(.text+0xf0): undefined reference to
`mkl_serv_iface_free'
/cm/shared/apps/intel/compilers_and_libraries/current/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.a(bi_f77_get_constants_.o):
In function `bi_f77_get_constants_':
bi_f77_get_constants_.c:(.text+0xf): undefined reference to
`mkl_serv_get_mpi_wrappers'
bi_f77_get_constants_.c:(.text+0x54): undefined reference to
`mkl_serv_get_mpi_wrappers'
bi_f77_get_constants_.c:(.text+0x68): undefined reference to
`mkl_serv_get_mpi_wrappers'
bi_f77_get_constants_.c:(.text+0x7c): undefined reference to
`mkl_serv_get_mpi_wrappers'
bi_f77_get_constants_.c:(.text+0x90): undefined reference to
`mkl_serv_get_mpi_wrappers'
/cm/shared/apps/intel/compilers_and_libraries/current/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.a(bi_f77_get_constants_.o):bi_f77_get_constants_.c:(.text+0xa4):
more undefined references to `mkl_serv_get_mpi_wrappers' follow
collect2: error: ld returned 1 exit status
make: *** [siesta] Error 1

The new arch.make file is attached with this mail. kindly give me solution
to this problem.

Thanking you

regards
Rajan


arch.make
Description: Binary data

[SIESTA-L] parallel siesta 4.1 b1 with intel mkl libraries

[RAJAN SINGH]

Dear Siesta users

I tried to compile Siesta-4.1 b-1 with intel mkl libraries but I am getting
following errors:

m_zminim.o: In function `__m_zminim_MOD_calc_densmat':
/home/rajan.singh/siesta-4.1-b1/Src/m_zminim.F90:2566: undefined reference
to `pzgemm_'
/home/rajan.singh/siesta-4.1-b1/Src/m_zminim.F90:2568: undefined reference
to `pzgemm_'
/home/rajan.singh/siesta-4.1-b1/Src/m_zminim.F90:2570: undefined reference
to `pzgemm_'
diagonalizeHk.o: In function `diagonalizehk_':
diagonalizeHk.F90:(.text+0x16b): undefined reference to `numroc_'
m_orderbands.o: In function `__m_orderbands_MOD_order_index':
m_orderbands.F:(.text+0x365): undefined reference to `indxg2p_'
collect2: error: ld returned 1 exit status
make: *** [siesta] Error 1


I am attaching my arch.make file for reference, kindly provide possible
solutions.

Thanking you

regards
Rajan


arch.make
Description: Binary data

[SIESTA-L] Error in parallel siesta 4.1b1

[RAJAN SINGH]

Dear siesta users

I tried to install parallel version of siesta 4.1b1 using gcc open mp
library but i m facing following error:

/home/r.sreedhar/siesta-4.1-b1/Src/m_spin.F90:60.29:
type(tSpin), public :: spin
 1
Error: Object 'spin' at (1) must have the SAVE attribute for default
initialization of a component
make: *** [m_spin.o] Error 1

I am attaching arch.make file for reference. Kindly give me suggestions for
this problem.

Thanking you

Regrads
Rajan


arch.make
Description: Binary data

Re: [SIESTA-L] z coordinates from output differnt from input

[RAJAN SINGH]

I think you are putting old files in the same folder, please check.

On 10-Sep-2016 7:58 pm, "toufik esssakhri"  wrote:

Dear TRansiesta users,


i am getting z coordinates in output file different to those in input file
in the scatternig calculations

and the code prints the following error


Structure of the Left electrode | System electrode:

X (Ang) Y (Ang) Z (Ang) | X (Ang) Y (Ang) Z (Ang)

0.0 0.0 0.0 | 0.0 0.0 0.0

1.49000 1.49000 1.49000 | 1.49000 1.49000 1.49000

0.0 0.0 2.98000 | 0.0 0.0 2.98000

1.49000 1.49000 4.47000 | 0.0 0.0 5.15000

0.0 0.0 5.96000 | 1.49000 1.49000 5.15000

1.49000 1.49000 7.45000 | 0.0 0.0 7.24000

"The electrodes are not situated in the same coordinates. Please correct.
Stopping Program from Node:0"


positions in input file are :

0.00  0.00   0.00

1.49  1.49   1.49

0.00  0.00  2.98

1.49  1.49  4.47

0.00  0.00  5.96

1.49  1.49  7.45

...

any advice?

bests

Re: [SIESTA-L] LDA Basis Set for Fluorine

[RAJAN SINGH]

Dear Dan

I think, I saw papers in which GGA-PBE and DZP is used but better to
confirm once.

Regards
Rajan

On 26-Aug-2016 11:45 pm, "Dan Gil"  wrote:

> Thank you for your reply Rajan.
>
> Can I use the DZP basis set for any species in my system, except titanium
> (Mg, O, F)?
> For the XC.authors option, do I choose CA?
>
> Here is my input.fdf file.
>
> SystemName  2Slabs10Ang
> SystemLabel 2Slabs10Ang
> NumberOfAtoms   108
> NumberOfSpecies 4
>
> %block ChemicalSpeciesLabel
>  1  12 Mg
>  2  9  F
>  3  22 Ti
>  4  8  O
> %endblock ChemicalSpeciesLabel
>
> %block PAO.BasisSizes
> Mg DZP
> F  DZP
> O  DZP
> %endblock PAO.BasisSizes
>
> PAO.BasisTypesplit
> %block PAO.Basis
> Ti5  1.91
>  n=301   E 93.95  5.20
>5.69946662616249
>1.00
>  n=311   E 95.47  5.20
>5.69941339465994
>1.00
>  n=402   E 96.47  5.60
>6.099963989753075.09944363262274
>1.001.00
>  n=322   E 46.05  4.95
>5.943270357846174.70009988294302
>1.001.00
>  n=411   E  0.50  1.77
>3.05365979938936
>1.00
> %endblock PAO.Basis
>
> XC.functional LDA
> XC.authorsCA
> # SaveRho   .true.
>
> # SCF options
> DM.MixingWeight   0.005 # New DM amount for next SCF cycle
> DM.Tolerance  1.d-5 # Tolerance in maximum difference
> SolutionMethoddiagon# OrderN or Diagon
> DM.UseSaveDM  .true.
> MaxSCFIterations  300
> MeshCutoff120 Ry
>
> MD.TypeOfRun  CG
> MD.NumCGsteps 8000
> MD.InitialTemperature 300.0 K
> MD.TargetTemperature  300.0 K
> MD.MaxForceTol0.04 eV/ang
>
> WaveFuncKPointsScale ReciprocalLatticeVectors
>
> %block WaveFuncKPoints
>  0.000 0.000 0.000 from 1 to 5  # Gamma point wavefunction 1 to 5
> %endblock WaveFuncKPoints
>
> DM.PulayOnFile F
> DM.NumberPulay 3
>
> LatticeConstant 1   Ang
>
> %block LatticeVectors
>  9.246000  0.00  0.00
>  0.00  9.246000  0.00
>  0.000000  0.00 80.00
> %endblock LatticeVectors
>
> WarningMinimumAtiomicDistance 1.0 Ang
> AtomicCoordinatesFormat  NotScaledCartesianAng
> %block AtomicCoordinatesAndAtomicSpecies < Coord.fdf
>
> On Fri, Aug 26, 2016 at 2:02 PM, RAJAN SINGH 
> wrote:
>
>> You can use DZP basis set
>>
>> On 26-Aug-2016 11:31 pm, "Dan Gil"  wrote:
>>
>>> Hello,
>>>
>>> I am simulating rutile TiO2 and sellaite MgF2 crystals in slab geometry.
>>> I think that I have to use LDA since Titanium has semicore states.
>>>
>>> I have found Ti, O, and Mg Basis sets and pseudopotentials on the SIESTA
>>> team's website. But with the little experience I have I wish I could find a
>>> Fluorine basis set instead of generating one. Is there one available?
>>>
>>> Best Regards,
>>>
>>> Dan
>>>
>>
>

Re: [SIESTA-L] LDA Basis Set for Fluorine

[RAJAN SINGH]

You can use DZP basis set

On 26-Aug-2016 11:31 pm, "Dan Gil"  wrote:

> Hello,
>
> I am simulating rutile TiO2 and sellaite MgF2 crystals in slab geometry. I
> think that I have to use LDA since Titanium has semicore states.
>
> I have found Ti, O, and Mg Basis sets and pseudopotentials on the SIESTA
> team's website. But with the little experience I have I wish I could find a
> Fluorine basis set instead of generating one. Is there one available?
>
> Best Regards,
>
> Dan
>

[SIESTA-L] Confusion for value of PAO.ENRGYSHIFT for cnt n zgnr

[RAJAN SINGH]

Dear users

I am having a confusion regarding Pao.basis values. Usually papers wont
specify this value.

Can anyone confirm for CNT And ZGNR .02 ie default value is ok??

Please help me with this.

Regards
Rajan

[SIESTA-L] Confusion for value of pao.basis for cnt n zgnr

[RAJAN SINGH]

Dear users

I am having a confusion regarding Pao.basis values. Usually papers wont
specify this value.

Can anyone confirm for CNT And ZGNR .02 ie default value is ok??

Please help me with this.

Regards
Rajan

Re: [SIESTA-L] Band structure for doped ZGNR

[RAJAN SINGH]

Even according to me you should to try all possible combinations and the
combination with the lowes energy is correct.

This is wht is done by researchers.
In dft it is assumed tht everything is done at close to absolute temp. So
entropy is very less.

On 31-Jul-2016 5:25 pm, "Максим Арсентьев"  wrote:

Hi, Camps,
What do you mean "is generated based in disorder and entropy" pls. give a
link. As i know till now to find a place for dopant you should to try all
possible combinations and the combination with the lowes energy is correct.
This i know other researchers do, but your route is unknown for me, explain.

2016-07-31 13:30 GMT+04:00 Riya Rogers :

> Primitive means smallest cell possible so it contains few atoms so your
> doping percentage is higher
>
> On 31-Jul-2016 6:16 am, "I. Camps"  wrote:
>
>> Hello,
>>
>> If you use doping, you can not (or should not) use the primitive cell.
>> This is because you will need to select a % of atoms to substitute that
>> aren't enough in the primitive (or minimal) cell, so you have to use a
>> bigger cell (supercell) with greater number of atoms. Using the primitive
>> cell, will generate a crystal not dopped. A dopped crystal has a "few"
>> extra or substituted atoms.
>>
>> Other problem is how will you select the corresponding atom (or site) for
>> substitution. You have to use a theory to help you with this task. One of
>> them is the use of quase random structures where the "best" structure is
>> generated based in disorder and entropy.
>>
>> On Sat, Jul 30, 2016, 17:51 Максим Арсентьев 
>> wrote:
>>
>>> so you mean because of doping you have a supercell now? Anyway your
>>> system still have symmmetry - for choosing k - points use this paper. It is
>>>  general manner. I did not dealt with supercells but do not think your
>>> problem is critical.
>>>
>>> 2016-07-30 23:00 GMT+04:00 Riya Rogers :
>>>
 Doped means is it replacement of carbon or other molecule in vicinity?

 On 30-Jul-2016 10:38 pm, "maryam jamaati"  wrote:

> Dear siesta users,
>
> According to helpful advices of some friends (Nick, Kamaraj,..), I
> reduced geometry to unit cell for calculation of ZGNR band structure.
> Whether we have to use minimal unit cell for doped ZGNR or not?
>
> Kind regards,
>
> Maryam Jamaati
>
>
>>>
>>>
>>> --
>>> Best wishes,
>>> Maxim Arsent'ev, Ph.D. (Chemistry)
>>> Laboratory of research of nanostructures
>>> Institute of Silicate Chemistry of RAS
>>>
>> --
>>
>> []`s
>>
>> Camps
>>
>


-- 
Best wishes,
Maxim Arsent'ev, Ph.D. (Chemistry)
Laboratory of research of nanostructures
Institute of Silicate Chemistry of RAS

Re: [SIESTA-L] what is the meaning of Internal auxiliary supercell

[Rajan Singh]

Dear Dr Nick
Thank you so much for your valuable help.
Regards
Rajan

Sent from my Sony Xperia™ smartphone

Nick Papior  wrote:

>You need not worry about the used supercells (given that you have setup the 
>coordinates and unit cell vectors) in the transiesta calculation. 
>
>The number of supercells are ONLY important in the electrode calculations. 
>
>--
>
>Kind regards Nick Papior
>
>On 4 May 2016 16:01, "Rajan Singh"  wrote:
>
>Dear Dr Nick
>
>During relaxation i got 3 supercells but during transiesta run it is written 
>as naive supercell 1 1 1
>Is this correct?
>
>Thanking you
>
>Regards
>Rajan
>
>Sent from my Sony Xperia™ smartphone
>
>Nick Papior  wrote:
>
>The auxiliary supercell refers to the number of neighbouring cells that the 
>primary unit cell interacts with. Hence H /= 0 within these "auxiliary" 
>supercells and H = 0 outside. 
>
>For transiesta it is important that the electrodes only interact with the 
>neighbouring cells. In the transport direction the auxiliary number of 
>supercells should be 2 or 3.
>
>--
>
>Kind regards Nick Papior
>
>On 4 May 2016 13:16, "RAJAN SINGH"  wrote:
>
>Dear Siesta Users
>
>What is the meaning of Internal auxiliary supercell and how it affect the 
>result?
>
>Please clarify I will be highly obliged.
>
>Thanking you
>
>With Regards
>
>Rajan 
>

Re: [SIESTA-L] what is the meaning of Internal auxiliary supercell

[Rajan Singh]

Dear Dr Nick

During relaxation i got 3 supercells but during transiesta run it is written as 
naive supercell 1 1 1
Is this correct?

Thanking you

Regards
Rajan

Sent from my Sony Xperia™ smartphone

Nick Papior  wrote:

>The auxiliary supercell refers to the number of neighbouring cells that the 
>primary unit cell interacts with. Hence H /= 0 within these "auxiliary" 
>supercells and H = 0 outside. 
>
>For transiesta it is important that the electrodes only interact with the 
>neighbouring cells. In the transport direction the auxiliary number of 
>supercells should be 2 or 3.
>
>--
>
>Kind regards Nick Papior
>
>On 4 May 2016 13:16, "RAJAN SINGH"  wrote:
>
>Dear Siesta Users
>
>What is the meaning of Internal auxiliary supercell and how it affect the 
>result?
>
>Please clarify I will be highly obliged.
>
>Thanking you
>
>With Regards
>
>Rajan 
>

Re: [SIESTA-L] Problem in getting E-k plot of PRB paper(PhysRevB.59.9858)

[RAJAN SINGH]

Dear Dr Nick

I got my results matched but I saw this in the out file:

superc: Internal auxiliary supercell: 1 x 1 x 6  =   6
superc: Number of atoms, orbitals, and projectors: 60684876


I put no of atoms as 10

Is somthing wrong?

Thanking you

With Regards
Rajan

On Fri, Apr 29, 2016 at 6:02 PM, RAJAN SINGH 
wrote:

> Dear Dr Nick thank you I will try to implement this as soon as possible.
>
> With Regards
> Rajan Singh
>
> On Fri, Apr 29, 2016 at 5:27 PM, Nick Papior  wrote:
>
>> Try and reduce your nanoribbon to the smallest unit cell possible.
>> This will prevent you from getting folded bands.
>>
>>
>> 2016-04-29 13:49 GMT+02:00 RAJAN SINGH :
>>
>>> Dear Siesta Users
>>>
>>> I am trying to implement the PRB paper attach with this mail, I am
>>> unable to figure out why my results are not matching.
>>>
>>> My input fdf file as well as output E-k plot file (nanoribbon.dat) both
>>> are attached with this mail.
>>>
>>> Kindly help me with this problem, I will be highly obliged.
>>>
>>> Thanking you
>>>
>>> With regards
>>> Rajan Singh
>>>
>>>
>>>
>>>
>>
>>
>> --
>> Kind regards Nick
>>
>
>

[SIESTA-L] what is the meaning of Internal auxiliary supercell

[RAJAN SINGH]

Dear Siesta Users

What is the meaning of Internal auxiliary supercell and how it affect the
result?

Please clarify I will be highly obliged.

Thanking you

With Regards
Rajan

Re: [SIESTA-L] Problem in getting E-k plot of PRB paper(PhysRevB.59.9858)

[RAJAN SINGH]

Dear Dr Nick thank you I will try to implement this as soon as possible.

With Regards
Rajan Singh

On Fri, Apr 29, 2016 at 5:27 PM, Nick Papior  wrote:

> Try and reduce your nanoribbon to the smallest unit cell possible.
> This will prevent you from getting folded bands.
>
>
> 2016-04-29 13:49 GMT+02:00 RAJAN SINGH :
>
>> Dear Siesta Users
>>
>> I am trying to implement the PRB paper attach with this mail, I am unable
>> to figure out why my results are not matching.
>>
>> My input fdf file as well as output E-k plot file (nanoribbon.dat) both
>> are attached with this mail.
>>
>> Kindly help me with this problem, I will be highly obliged.
>>
>> Thanking you
>>
>> With regards
>> Rajan Singh
>>
>>
>>
>>
>
>
> --
> Kind regards Nick
>

[SIESTA-L] Lattice sizes in z-direction for band structure calculation (system is periodic in z-rection)

[RAJAN SINGH]

Dear Siesta Users

I want to calculate band structure of Hydrogen passivated graphene
nanoribbon, my system has periodicity in z-direction.

In order to avoid the interactions from neighboring cells x and y lattice
sizes should be 10 Ang more than highest x and y coordinates of my system.

I am having a doubt that what should be the lattice size in z-direction?

Should I kept z-direction lattice size such that it is 10 ang higher than
my highest z-coordinate?

or Should I kept z-direction lattice size such that if i repeat my lattice
it forms a bigger lattice?

Kindly give me the possible solution, I will be highly obliged.

Thanking You

With Regards
Rajan Singh

Re: [SIESTA-L] 4-ZGNR transmission spectrum

[RAJAN SINGH]

Dear Riya

This paper is available on researchgate. If you have a account there then
you can see the paper. I think may be you should try once.

Regards
Rajan

On Tue, Mar 29, 2016 at 8:43 AM, Riya Rogers 
wrote:

> Dear Uma
>
> Thank you
>
> Bt i dnt have subscription for this journal can you please send me this
> paper.
>
> Regards
> Riya
>
> On Mon, Mar 28, 2016 at 4:19 AM, Uma Shankar Sharma  > wrote:
>
>> You may validate your results from paper entitled "Electronic Transport
>> Properties of 8AGNR and 4ZGNR" published by
>>  Quantum Matter
>> ,
>> Volume 2, Number 3, June 2013, pp. 225-228(4)
>>
>> On Sat, Mar 26, 2016 at 1:17 PM, Riya Rogers 
>> wrote:
>>
>>>
>>> Dear All
>>>
>>> I was simulating 4-ZGNR transmission spectrum using transisesta.
>>>
>>> Can anyone suggest some good reference paper from which I can validate
>>> my results.
>>>
>>> I was trying to find out but I wont be able to find any suitable as many
>>> write 4-zgnr but their structure is something different as shown in their
>>> paper.
>>>
>>> Please anyone help me.
>>>
>>> Thanking you
>>>
>>> With Regards
>>> Riya
>>>
>>
>>
>

Re: [SIESTA-L] transiesta doesn't converge

[RAJAN SINGH]

Dear Raha

I think atleast one atom of your left electrode's  z-coordinate has to be
zero. other x and y coordinates may not be zero i think

regards
Rajan

On Sun, Mar 27, 2016 at 11:29 AM, Nick Papior  wrote:

> I haven't checked your right electrode, but your input coordinates for the
> left electrode are very wrong...
>
> --
>
> Kind regards Nick Papior
> On 26 Mar 2016 08:20, "Raha khalili"  wrote:
>
>> Dear Transiessta users,
>>
>> I am trying to find transmission of a molecular junction consisting of a
>> single-molecule sandwiched between two gold contacts with Transiesta.
>> Everything is Ok for left and right electrodes but the calculation for
>> whole system get aborted by cluster system after around ten days foe
>> several times. I don't know whether this is a problem related to my input
>> files or not.
>>
>> Here are attached the input file for electrodes and scattering region.
>> Any suggestion will be appreciated.
>>
>> Best wishes,
>> Raha
>>
>> --
>> Khadijeh Khalili
>> Nanotechnology group, Physics department, university of Mazandaran
>> Babolsar, Iran
>>
>

[SIESTA-L] collinear ferromagnetic spin calculations

[RAJAN SINGH]

Dear Siesta Users

I want to perform  collinear ferromagnetic spin calculations and hence want
to obtain a transmission spectrum of ZGNR.

How to perform such calculations?

Please tell me the procedure, I will be highly obliged.

ThankingYou

Regards
Rajan

Re: [SIESTA-L] Fwd: Electronic temperature default value and unit

[Rajan Singh]

Thank u Dr Maxim

But should we kept it near zero Kelvin to get the exact ground state energy of 
system?

Regards
Rajan

Sent from my Sony Xperia™ smartphone

Максим Арсентьев  wrote:

>It is smearing.
>
>When F-D is used, then it is real temperature of your system, if M-V it is not
>
>It is correct, if your system is nonmetalliuc
>
>
>2016-03-20 10:07 GMT+03:00 RAJAN SINGH :
>
>
>Dear Siesta Users
>
>I read the manual where electronic temperature is written as 300 K p-p.
>
>What does that mean? Is is 300 K or something else??
>
>Again How to decide the temp for band structure calculations?
>
>
>Please clarify my doubts.
>
>Thanking you
>
>With Regards
>
>Rajan Singh
>
>
>
>
>
>-- 
>
>Best wishes,
>
>Maxim Arsent'ev, Ph.D. (Chemistry)
>
>Laboratory of research of nanostructures
>
>Institute of Silicate Chemistry of RAS
>

[SIESTA-L] Fwd: Electronic temperature default value and unit

[RAJAN SINGH]

Dear Siesta Users

I read the manual where electronic temperature is written as 300 K p-p.

What does that mean? Is is 300 K or something else??

Again How to decide the temp for band structure calculations?

Please clarify my doubts.

Thanking you

With Regards
Rajan Singh

[SIESTA-L] Electronic temperature default value and unit

[RAJAN SINGH]

Dear Siesta Users

I read the manual where electronic temperature is written as 300 K p-p.

What does that mean? Is is 300 K or something else??

Please clarify my doubts.

Thanking you

With Regards
Rajan Singh

RE: [SIESTA-L] Convergence tests & transmission

[Rajan Singh]

Hii

You should do following steps:

1. Decide your structure 
2. Run structure with different k pts and plot energy vs k pt
See after some k pt energy values nearly same
3. Do same with mesh cuttoff
4. Relax structure with CG steps
5. Then electrode calculation 
And finally tranmission calculations

Regards
Rajan Singh

Sent from my Sony Xperia™ smartphone

j_hek...@uni-muenster.de wrote:

>Dear users,
>
>I am pretty new to Siesta/TranSiesta and I'm currently struggling with the 
>following topic: I want to compute equilibrium transmission of 
>Poly(3-Methylthiophene) with different chain lengths. My current (ideally 
>periodic) _test_ system consists of 100 atoms (a 10mer) of which 2x40 atoms 
>build the electrodes. At the moment I'm doing lots of tests with different 
>parameters like k vectors, box sizes, MeshCutoff and others. The finally 
>important quantity is the transmission. 
>My problem is now that I'm not really seeing a "pattern": I find it hard to 
>understand which physical quantity indicates a good or bad convergence w.r.t. 
>the transmission. I'm observing energies and of course the transmission 
>function. What confuses me most is that the transmission function changes 
>shape very drastically for changes like e.g. increasing or decreasing the 
>kx,ky vectors by 1. Sometimes transmission values de- or increase by up to 6 
>magnitues, in combination with a totally different characteristic. 
>Also, the same calculation yields deviations of up to 15% at for example 
>T(E=Ef) when repeated. Could this be connected to a numerical instability due 
>to a compilation problem or a "defective" math library?
>Literature indicates a transmission T(E=Ef) ~ 0-1 G0. Most of my results range 
>between 0.17 and 0.01 G0 (again: with very different transmission function 
>shapes).
>I'm afraid of having an understanding problem somewhere or missing out 
>something important.
>
>I hope that I can get some advice.
>
>Thanks and best regards,
>JH

[SIESTA-L] Problem in compilation of TbTrans_rep in Siesta-4.0

[RAJAN SINGH]

Dear all

I am facing following error while compiling TbTrans_rep in Siesta-4.0
version:

cdiag.o: In function `cdiag_':
cdiag.F:(.text+0x585): undefined reference to `ilaenv_'
cdiag.F:(.text+0x5c9): undefined reference to `ilaenv_'
cdiag.F:(.text+0x812): undefined reference to `zhegv_'
cdiag.F:(.text+0x88d): undefined reference to `zcopy_'
cdiag.F:(.text+0x9ce): undefined reference to `zhegvx_'
cdiag.F:(.text+0xbb5): undefined reference to `zpotrf_'
cdiag.F:(.text+0xc4a): undefined reference to `zhegst_'
cdiag.F:(.text+0xd15): undefined reference to `zhemm_'
cdiag.F:(.text+0xd9e): undefined reference to `zgemm_'
cdiag.F:(.text+0x1081): undefined reference to `zheevx_'
cdiag.F:(.text+0x12ce): undefined reference to `zgemm_'
cdiag.F:(.text+0x1320): undefined reference to `zcopy_'
cdiag.F:(.text+0x137c): undefined reference to `zcopy_'
cdiag.F:(.text+0x140d): undefined reference to `ztrsm_'
m_ts_aux_rout.o: In function `__m_ts_aux_rout_MOD_csolveg':
m_ts_aux_rout.F:(.text+0x8d1): undefined reference to `zgesv_'
m_ts_electrode.o: In function `__m_ts_electrode_MOD_surface_green':
m_ts_electrode.F90:(.text+0x9f1): undefined reference to `zgemm_'
m_ts_electrode.F90:(.text+0x1384): undefined reference to `zgemm_'
m_ts_electrode.F90:(.text+0x1431): undefined reference to `zgemm_'
m_ts_electrode.F90:(.text+0x158e): undefined reference to `zgemm_'
m_ts_electrode.F90:(.text+0x1641): undefined reference to `zgemm_'
m_ts_electrode.o:m_ts_electrode.F90:(.text+0x16de): more undefined
references to `zgemm_' follow
m_ts_scattering.o: In function `__m_ts_scattering_MOD_getgf':
m_ts_scattering.F:(.text+0x8e9): undefined reference to `zgesv_'
m_ts_scattering.F:(.text+0x9cb): undefined reference to `zgesv_'
m_ts_scattering.F:(.text+0xdc2): undefined reference to `zgemm_'
m_ts_scattering.F:(.text+0xec6): undefined reference to `zgemm_'
m_ts_scattering.F:(.text+0xfa7): undefined reference to `zgemm_'
m_ts_scattering.F:(.text+0x1070): undefined reference to `zgemm_'
m_ts_scattering.F:(.text+0x122e): undefined reference to `zgemm_'
m_ts_scattering.o:m_ts_scattering.F:(.text+0x12ef): more undefined
references to `zgemm_' follow
zheevds.o: In function `zheevds_':
zheevds.F90:(.text+0x65): undefined reference to `lsame_'
zheevds.F90:(.text+0x84): undefined reference to `lsame_'
zheevds.F90:(.text+0x15c): undefined reference to `lsame_'
zheevds.F90:(.text+0x1d6): undefined reference to `lsame_'
zheevds.F90:(.text+0x304): undefined reference to `xerbla_'
zheevds.F90:(.text+0x37b): undefined reference to `dlamch_'
zheevds.F90:(.text+0x395): undefined reference to `dlamch_'
zheevds.F90:(.text+0x402): undefined reference to `zlanhe_'
zheevds.F90:(.text+0x4a0): undefined reference to `zlascl_'
zheevds.F90:(.text+0x555): undefined reference to `zhetrd_'
zheevds.F90:(.text+0x5a7): undefined reference to `dsterf_'
zheevds.F90:(.text+0x662): undefined reference to `zstedc_'
zheevds.F90:(.text+0x6ee): undefined reference to `zunmtr_'
zheevds.F90:(.text+0x77b): undefined reference to `dscal_'
m_lowdin.o: In function `__m_lowdin_MOD_zsqrtm':
m_lowdin.f90:(.text+0x31e): undefined reference to `zhpev_'
m_lowdin.o: In function `__m_lowdin_MOD_zinvsqrtm':
m_lowdin.f90:(.text+0x8f3): undefined reference to `zhpev_'
m_lowdin.o: In function `__m_lowdin_MOD_lowdin_trans':
m_lowdin.f90:(.text+0xd12): undefined reference to `zgemm_'
m_lowdin.f90:(.text+0xd62): undefined reference to `zgemm_'
transmission.o: In function `transmission_':
transmission.f90:(.text+0xd51): undefined reference to `zgemm_'
transmission.f90:(.text+0x1656): undefined reference to `zgemm_'
transmission.f90:(.text+0x1dfc): undefined reference to `zgemm_'
transmission.o:transmission.f90:(.text+0x1e6d): more undefined references
to `zgemm_' follow
tt_eig.o: In function `tt_eig_':
tt_eig.f90:(.text+0x69d): undefined reference to `zgeev_'
atompdos.o: In function `atompdos_':
atompdos.F90:(.text+0x75d): undefined reference to `zgemm_'
atompdos.F90:(.text+0x7cc): undefined reference to `zgemm_'
collect2: ld returned 1 exit status
***Please see top of Makefile







*I tried to change the following line: #TBTRANS_LINALG=linalg.a # Or maybe
only: zgeev_lapack.a zgesv_lapack.a*

*to only linalg.a*


*and zgeev_lapack.a zgesv_lapack.a*



*in separate installation runs. But TbTrans_rep wont compile.*
*Please suggest me the correct way of installation.*

Thank You

Regards
Rajan Singh

Re: [SIESTA-L] Installation of Siesta-trunk-462

[RAJAN SINGH]

Dear Dr Zhao

I already complied Siesta-4.0 version successfully but I am facing problem
with Siesta-trunk-462 version.
As my project work is in trunk version only I have to install only
trunk-462 version.

thank You

regards
Rajan Singh

On Mon, Feb 8, 2016 at 7:37 PM, Hongyi Zhao  wrote:

> 2016-02-08 20:07 GMT+08:00 RAJAN SINGH :
> > I am also attaching arch.make, config.log, config.status.
>
> I've tried using the self-compiled blas
> + lapack+blacs+scalapack long time before.  The instructions I
> referred is based on the following website:
>
> http://www.vivaolinux.com.br/artigo/Montagem-de-Cluster
> http://www.vivaolinux.com.br/artigo/Montagem-de-Cluster?pagina=7
> http://www.vivaolinux.com.br/artigo/Montagem-de-Cluster?pagina=8
>
> But, this is very tedious and complex way for compiling the siesta.
> Finally, I switched to the method based on the intel's tool chains
> just as I told you in the previous mail.
>
> For you information, I attach a copy of the arch.make file used by me. HTH.
>
> I've used this arch.make to compile the latest siesta-4.0b-485
> successfully.
>
> The versions used for my case of these tools are as follows:
>
> werner@debian-01:~$ which ifort
> /opt/intel/composer_xe_2011_sp1.11.339/bin/intel64/ifort
> werner@debian-01:~$ which mpirun
> /opt/intel/impi/4.1.0.024/intel64/bin/mpirun
> werner@debian-01:~$ echo $LD_LIBRARY_PATH |tr ':' '\n' |egrep
> '/mkl/'|head -1
> /opt/intel/composer_xe_2011_sp1.11.339/mkl/lib/intel64
>
> Regards
>
> >
> > thanking you
> >
> > Regards
> > Rajan
> >
> > On Mon, Feb 8, 2016 at 4:41 PM, RAJAN SINGH 
> > wrote:
> >>
> >> Thank you but since its a newer version it may not that much stable and
> >> some analysis may be different in this version hence I want to use
> >> Siesta-trunk-462 version.
> >>
> >> I already install lapack lib, and siesta-3.2 is easily installed. But I
> am
> >> not able to install trunk version what should I do?
> >>
> >> Thank you
> >>
> >> regards
> >> Rajan
> >>
> >> On Mon, Feb 8, 2016 at 4:05 PM, Alberto Garcia 
> wrote:
> >>>
> >>> Hi,
> >>>
> >>> It is always advisable to install optimized versions of the libraries.
> >>>
> >>> However, you can compile (the *serial* version only) without any
> external
> >>> libraries
> >>> by using the arch.make example in Src/Sys/nolibs.mk, as explained in
> >>> the list link you quote.
> >>>
> >>> But note that this only works for the newer siesta-4.0b version.
> >>>
> >>> There is no point in using trunk-462. You should download siesta-4.0b.
> >>>
> >>>  Alberto
> >>>
> >>>
> >>>
> >>> On 08 Feb 2016, at 10:33, RAJAN SINGH 
> wrote:
> >>>
> >>> > Actually I am getting same errors as one person face when installing
> >>> > Siesta 4.0 version.
> >>> > (http://www.mail-archive.com/siesta-l%40uam.es/msg08520.html)
> >>> >
> >>> > hence I am a bit confused.
> >>> >
> >>> > Regards
> >>> > Rajan
> >>> >
> >>> > On Mon, Feb 8, 2016 at 2:59 PM, RAJAN SINGH <
> singhrajan.i...@gmail.com>
> >>> > wrote:
> >>> > Thank you Dr. Zhao
> >>> >
> >>> > then should I install ifort, mkl, impi?
> >>> >
> >>> > previously I install it on Ubuntu 14.04 then the above software not
> >>> > needed.
> >>> >
> >>> > regards
> >>> > rajan
> >>> >
> >>>
> >>
> >
>
>
>
> --
> Hongyi Zhao 
> Xinjiang Technical Institute of Physics and Chemistry
> Chinese Academy of Sciences
> GnuPG DSA: 0xD108493
>

Re: [SIESTA-L] Installation of Siesta-trunk-462

[RAJAN SINGH]

I am also attaching arch.make, config.log, config.status.

thanking you

Regards
Rajan

On Mon, Feb 8, 2016 at 4:41 PM, RAJAN SINGH 
wrote:

> Thank you but since its a newer version it may not that much stable and
> some analysis may be different in this version hence I want to use
> Siesta-trunk-462 version.
>
> I already install lapack lib, and siesta-3.2 is easily installed. But I am
> not able to install trunk version what should I do?
>
> Thank you
>
> regards
> Rajan
>
> On Mon, Feb 8, 2016 at 4:05 PM, Alberto Garcia  wrote:
>
>> Hi,
>>
>> It is always advisable to install optimized versions of the libraries.
>>
>> However, you can compile (the *serial* version only) without any external
>> libraries
>> by using the arch.make example in Src/Sys/nolibs.mk, as explained in
>> the list link you quote.
>>
>> But note that this only works for the newer siesta-4.0b version.
>>
>> There is no point in using trunk-462. You should download siesta-4.0b.
>>
>>  Alberto
>>
>>
>>
>> On 08 Feb 2016, at 10:33, RAJAN SINGH  wrote:
>>
>> > Actually I am getting same errors as one person face when installing
>> Siesta 4.0 version. (
>> http://www.mail-archive.com/siesta-l%40uam.es/msg08520.html)
>> >
>> > hence I am a bit confused.
>> >
>> > Regards
>> > Rajan
>> >
>> > On Mon, Feb 8, 2016 at 2:59 PM, RAJAN SINGH 
>> wrote:
>> > Thank you Dr. Zhao
>> >
>> > then should I install ifort, mkl, impi?
>> >
>> > previously I install it on Ubuntu 14.04 then the above software not
>> needed.
>> >
>> > regards
>> > rajan
>> >
>>
>>
>


arch.make
Description: Binary data
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.

It was created by siesta configure 2.0, which was
generated by GNU Autoconf 2.59.  Invocation command line was

  $ ../Src/configure 

## - ##
## Platform. ##
## - ##

hostname = NANO-1
uname -m = x86_64
uname -r = 2.6.32-504.el6.x86_64
uname -s = Linux
uname -v = #1 SMP Wed Oct 15 04:27:16 UTC 2014

/usr/bin/uname -p = unknown
/bin/uname -X = unknown

/bin/arch  = x86_64
/usr/bin/arch -k   = unknown
/usr/convex/getsysinfo = unknown
hostinfo   = unknown
/bin/machine   = unknown
/usr/bin/oslevel   = unknown
/bin/universe  = unknown

PATH: /opt/intel/Compiler/11.1/072/bin/intel64
PATH: /opt/openmpi/1.8.7/bin
PATH: /opt/gromacs/5.0.5/bin
PATH: /opt/namd
PATH: /opt/lammps/May15/src
PATH: /usr/lib64/qt-3.3/bin
PATH: /usr/local/bin
PATH: /bin
PATH: /usr/bin
PATH: /usr/local/sbin
PATH: /usr/sbin
PATH: /sbin
PATH: /home/rajan.singh/bin


## --- ##
## Core tests. ##
## --- ##

configure:1348: checking build system type
configure:1366: result: x86_64-unknown-linux-gnu
configure:1374: checking host system type
configure:1388: result: x86_64-unknown-linux-gnu
configure:1466: checking for xlf95
configure:1495: result: no
configure:1466: checking for lf95
configure:1495: result: no
configure:1466: checking for f95
configure:1482: found /usr/bin/f95
configure:1492: result: f95
configure:1507: checking for Fortran compiler version
configure:1510: f95 --version &5
GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11)
Copyright (C) 2010 Free Software Foundation, Inc.

GNU Fortran comes with NO WARRANTY, to the extent permitted by law.
You may redistribute copies of GNU Fortran
under the terms of the GNU General Public License.
For more information about these matters, see the file named COPYING

configure:1513: $? = 0
configure:1515: f95 -v &5
Using built-in specs.
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux
Thread model: posix
gcc version 4.4.7 20120313 (Red Hat 4.4.7-11) (GCC) 
configure:1518: $? = 0
configure:1520: f95 -V &5
f95: '-V' option must have argument
configure:1523: $? = 1
configure:1537: checking for Fortran compiler default output file name
configure:1540: f95conftest.f  >&5
configure:1543: $? = 0
configure:

Re: [SIESTA-L] Installation of Siesta-trunk-462

[RAJAN SINGH]

Thank you but since its a newer version it may not that much stable and
some analysis may be different in this version hence I want to use
Siesta-trunk-462 version.

I already install lapack lib, and siesta-3.2 is easily installed. But I am
not able to install trunk version what should I do?

Thank you

regards
Rajan

On Mon, Feb 8, 2016 at 4:05 PM, Alberto Garcia  wrote:

> Hi,
>
> It is always advisable to install optimized versions of the libraries.
>
> However, you can compile (the *serial* version only) without any external
> libraries
> by using the arch.make example in Src/Sys/nolibs.mk, as explained in
> the list link you quote.
>
> But note that this only works for the newer siesta-4.0b version.
>
> There is no point in using trunk-462. You should download siesta-4.0b.
>
>  Alberto
>
>
>
> On 08 Feb 2016, at 10:33, RAJAN SINGH  wrote:
>
> > Actually I am getting same errors as one person face when installing
> Siesta 4.0 version. (
> http://www.mail-archive.com/siesta-l%40uam.es/msg08520.html)
> >
> > hence I am a bit confused.
> >
> > Regards
> > Rajan
> >
> > On Mon, Feb 8, 2016 at 2:59 PM, RAJAN SINGH 
> wrote:
> > Thank you Dr. Zhao
> >
> > then should I install ifort, mkl, impi?
> >
> > previously I install it on Ubuntu 14.04 then the above software not
> needed.
> >
> > regards
> > rajan
> >
>
>

Re: [SIESTA-L] Installation of Siesta-trunk-462

[RAJAN SINGH]

Actually I am getting same errors as one person face when installing Siesta
4.0 version. (http://www.mail-archive.com/siesta-l%40uam.es/msg08520.html)

hence I am a bit confused.

Regards
Rajan

On Mon, Feb 8, 2016 at 2:59 PM, RAJAN SINGH 
wrote:

> Thank you Dr. Zhao
>
> then should I install ifort, mkl, impi?
>
> previously I install it on Ubuntu 14.04 then the above software not needed.
>
> regards
> rajan
>
> On Mon, Feb 8, 2016 at 2:20 PM, Hongyi Zhao  wrote:
>
>> 2016-02-08 13:57 GMT+08:00 RAJAN SINGH :
>> > Dear Siesta Users
>> >
>> > I am trying to install Siesta-trunk-462 version on Centos-6.6. It is
>> showing
>> > following error:
>> >
>> >
>> >  libSiestaXC.a  \
>> >dc_lapack.a liblapack.a libblas.a  `FoX/FoX-config --libs
>> > --wcml`   dc_lapack.a liblapack.a libblas.a
>> > m_dminim.o: In function `__m_dminim_MOD_minim_cg':
>> > /home/rajan.singh/siesta-trunk-462/Src/m_dminim.F90:890: undefined
>> reference
>> > to `dsytrf_'
>> > /home/rajan.singh/siesta-trunk-462/Src/m_dminim.F90:894: undefined
>> reference
>> > to `dsytri_'
>> > m_dminim.o: In function `__m_dminim_MOD_minim_cg_sparse':
>> > /home/rajan.singh/siesta-trunk-462/Src/m_dminim.F90:1717: undefined
>> > reference to `dsytrf_'
>> > /home/rajan.singh/siesta-trunk-462/Src/m_dminim.F90:1721: undefined
>> > reference to `dsytri_'
>> > m_zminim.o: In function `__m_zminim_MOD_minim_cg':
>> > /home/rajan.singh/siesta-trunk-462/Src/m_zminim.F90:989: undefined
>> reference
>> > to `zhetrf_'
>> > /home/rajan.singh/siesta-trunk-462/Src/m_zminim.F90:993: undefined
>> reference
>> > to `zhetri_'
>> > m_zminim.o: In function `__m_zminim_MOD_minim_cg_sparse':
>> > /home/rajan.singh/siesta-trunk-462/Src/m_zminim.F90:1857: undefined
>> > reference to `zhetrf_'
>> > /home/rajan.singh/siesta-trunk-462/Src/m_zminim.F90:1861: undefined
>> > reference to `zhetri_'
>> > m_svd.o: In function `__m_svd_MOD_solve_with_svd':
>> > /home/rajan.singh/siesta-trunk-462/Src/m_svd.F90:52: undefined
>> reference to
>> > `dgelss_'
>> > collect2: ld returned 1 exit status
>> > make: *** [siesta] Error 1
>> >
>> >
>> > I searched previous mails and find this :
>> > https://www.mail-archive.com/siesta-l%40uam.es/msg00618.html
>> >
>> > hence i do this :
>> >
>> > make zgesv_lapack.a
>> > change arch.make to add zgesv_lapack.a to the LAPACK_LIBS
>> > LAPACK_LIBS=dc_lapack.a liblapack.a zgesv_lapack.a
>> > and then
>> > make
>> >
>> > Then again error is there:
>> >
>> >  dc_lapack.a liblapack.a libblas.a  `FoX/FoX-config --libs --wcml`
>> > dc_lapack.a liblapack.a zgesv_lapack.a libblas.a
>> > m_dminim.o: In function `__m_dminim_MOD_minim_cg':
>> > /home/rajan.singh/siesta-trunk-462/Src/m_dminim.F90:890: undefined
>> reference
>> > to `dsytrf_'
>> > /home/rajan.singh/siesta-trunk-462/Src/m_dminim.F90:894: undefined
>> reference
>> > to `dsytri_'
>> > m_dminim.o: In function `__m_dminim_MOD_minim_cg_sparse':
>> > /home/rajan.singh/siesta-trunk-462/Src/m_dminim.F90:1717: undefined
>> > reference to `dsytrf_'
>> > /home/rajan.singh/siesta-trunk-462/Src/m_dminim.F90:1721: undefined
>> > reference to `dsytri_'
>> > m_zminim.o: In function `__m_zminim_MOD_minim_cg':
>> > /home/rajan.singh/siesta-trunk-462/Src/m_zminim.F90:989: undefined
>> reference
>> > to `zhetrf_'
>> > /home/rajan.singh/siesta-trunk-462/Src/m_zminim.F90:993: undefined
>> reference
>> > to `zhetri_'
>> > m_zminim.o: In function `__m_zminim_MOD_minim_cg_sparse':
>> > /home/rajan.singh/siesta-trunk-462/Src/m_zminim.F90:1857: undefined
>> > reference to `zhetrf_'
>> > /home/rajan.singh/siesta-trunk-462/Src/m_zminim.F90:1861: undefined
>> > reference to `zhetri_'
>> > m_svd.o: In function `__m_svd_MOD_solve_with_svd':
>> > /home/rajan.singh/siesta-trunk-462/Src/m_svd.F90:52: undefined
>> reference to
>> > `dgelss_'
>> > collect2: ld returned 1 exit status
>> > make: *** [siesta] Error 1
>>
>> I can compile it successfully with the intel tool chains, i.e., ifort
>> + mkl + impi + siesta.
>>
>> Regards
>>
>> >
>> > Please help me with this.
>> >
>> > Thanking you
>> >
>> > With Regards
>> > Rajan
>> >
>>
>>
>>
>> --
>> Hongyi Zhao 
>> Xinjiang Technical Institute of Physics and Chemistry
>> Chinese Academy of Sciences
>> GnuPG DSA: 0xD108493
>>
>
>

Re: [SIESTA-L] Installation of Siesta-trunk-462

[RAJAN SINGH]

Thank you Dr. Zhao

then should I install ifort, mkl, impi?

previously I install it on Ubuntu 14.04 then the above software not needed.

regards
rajan

On Mon, Feb 8, 2016 at 2:20 PM, Hongyi Zhao  wrote:

> 2016-02-08 13:57 GMT+08:00 RAJAN SINGH :
> > Dear Siesta Users
> >
> > I am trying to install Siesta-trunk-462 version on Centos-6.6. It is
> showing
> > following error:
> >
> >
> >  libSiestaXC.a  \
> >dc_lapack.a liblapack.a libblas.a  `FoX/FoX-config --libs
> > --wcml`   dc_lapack.a liblapack.a libblas.a
> > m_dminim.o: In function `__m_dminim_MOD_minim_cg':
> > /home/rajan.singh/siesta-trunk-462/Src/m_dminim.F90:890: undefined
> reference
> > to `dsytrf_'
> > /home/rajan.singh/siesta-trunk-462/Src/m_dminim.F90:894: undefined
> reference
> > to `dsytri_'
> > m_dminim.o: In function `__m_dminim_MOD_minim_cg_sparse':
> > /home/rajan.singh/siesta-trunk-462/Src/m_dminim.F90:1717: undefined
> > reference to `dsytrf_'
> > /home/rajan.singh/siesta-trunk-462/Src/m_dminim.F90:1721: undefined
> > reference to `dsytri_'
> > m_zminim.o: In function `__m_zminim_MOD_minim_cg':
> > /home/rajan.singh/siesta-trunk-462/Src/m_zminim.F90:989: undefined
> reference
> > to `zhetrf_'
> > /home/rajan.singh/siesta-trunk-462/Src/m_zminim.F90:993: undefined
> reference
> > to `zhetri_'
> > m_zminim.o: In function `__m_zminim_MOD_minim_cg_sparse':
> > /home/rajan.singh/siesta-trunk-462/Src/m_zminim.F90:1857: undefined
> > reference to `zhetrf_'
> > /home/rajan.singh/siesta-trunk-462/Src/m_zminim.F90:1861: undefined
> > reference to `zhetri_'
> > m_svd.o: In function `__m_svd_MOD_solve_with_svd':
> > /home/rajan.singh/siesta-trunk-462/Src/m_svd.F90:52: undefined reference
> to
> > `dgelss_'
> > collect2: ld returned 1 exit status
> > make: *** [siesta] Error 1
> >
> >
> > I searched previous mails and find this :
> > https://www.mail-archive.com/siesta-l%40uam.es/msg00618.html
> >
> > hence i do this :
> >
> > make zgesv_lapack.a
> > change arch.make to add zgesv_lapack.a to the LAPACK_LIBS
> > LAPACK_LIBS=dc_lapack.a liblapack.a zgesv_lapack.a
> > and then
> > make
> >
> > Then again error is there:
> >
> >  dc_lapack.a liblapack.a libblas.a  `FoX/FoX-config --libs --wcml`
> > dc_lapack.a liblapack.a zgesv_lapack.a libblas.a
> > m_dminim.o: In function `__m_dminim_MOD_minim_cg':
> > /home/rajan.singh/siesta-trunk-462/Src/m_dminim.F90:890: undefined
> reference
> > to `dsytrf_'
> > /home/rajan.singh/siesta-trunk-462/Src/m_dminim.F90:894: undefined
> reference
> > to `dsytri_'
> > m_dminim.o: In function `__m_dminim_MOD_minim_cg_sparse':
> > /home/rajan.singh/siesta-trunk-462/Src/m_dminim.F90:1717: undefined
> > reference to `dsytrf_'
> > /home/rajan.singh/siesta-trunk-462/Src/m_dminim.F90:1721: undefined
> > reference to `dsytri_'
> > m_zminim.o: In function `__m_zminim_MOD_minim_cg':
> > /home/rajan.singh/siesta-trunk-462/Src/m_zminim.F90:989: undefined
> reference
> > to `zhetrf_'
> > /home/rajan.singh/siesta-trunk-462/Src/m_zminim.F90:993: undefined
> reference
> > to `zhetri_'
> > m_zminim.o: In function `__m_zminim_MOD_minim_cg_sparse':
> > /home/rajan.singh/siesta-trunk-462/Src/m_zminim.F90:1857: undefined
> > reference to `zhetrf_'
> > /home/rajan.singh/siesta-trunk-462/Src/m_zminim.F90:1861: undefined
> > reference to `zhetri_'
> > m_svd.o: In function `__m_svd_MOD_solve_with_svd':
> > /home/rajan.singh/siesta-trunk-462/Src/m_svd.F90:52: undefined reference
> to
> > `dgelss_'
> > collect2: ld returned 1 exit status
> > make: *** [siesta] Error 1
>
> I can compile it successfully with the intel tool chains, i.e., ifort
> + mkl + impi + siesta.
>
> Regards
>
> >
> > Please help me with this.
> >
> > Thanking you
> >
> > With Regards
> > Rajan
> >
>
>
>
> --
> Hongyi Zhao 
> Xinjiang Technical Institute of Physics and Chemistry
> Chinese Academy of Sciences
> GnuPG DSA: 0xD108493
>

Re: [SIESTA-L] [POSSIBLE SPAM][R] Compilation problems

[RAJAN SINGH]

I am getting same problem with Siesta -trunk-462 installation.


Error is :

 dc_lapack.a liblapack.a libblas.a  `FoX/FoX-config --libs --wcml`
dc_lapack.a liblapack.a zgesv_lapack.a libblas.a
m_dminim.o: In function `__m_dminim_MOD_minim_cg':
/home/rajan.singh/siesta-trunk-462/Src/m_dminim.F90:890: undefined
reference to `dsytrf_'
/home/rajan.singh/siesta-trunk-462/Src/m_dminim.F90:894: undefined
reference to `dsytri_'
m_dminim.o: In function `__m_dminim_MOD_minim_cg_sparse':
/home/rajan.singh/siesta-trunk-462/Src/m_dminim.F90:1717: undefined
reference to `dsytrf_'
/home/rajan.singh/siesta-trunk-462/Src/m_dminim.F90:1721: undefined
reference to `dsytri_'
m_zminim.o: In function `__m_zminim_MOD_minim_cg':
/home/rajan.singh/siesta-trunk-462/Src/m_zminim.F90:989: undefined
reference to `zhetrf_'
/home/rajan.singh/siesta-trunk-462/Src/m_zminim.F90:993: undefined
reference to `zhetri_'
m_zminim.o: In function `__m_zminim_MOD_minim_cg_sparse':
/home/rajan.singh/siesta-trunk-462/Src/m_zminim.F90:1857: undefined
reference to `zhetrf_'
/home/rajan.singh/siesta-trunk-462/Src/m_zminim.F90:1861: undefined
reference to `zhetri_'
m_svd.o: In function `__m_svd_MOD_solve_with_svd':
/home/rajan.singh/siesta-trunk-462/Src/m_svd.F90:52: undefined reference to
`dgelss_'
collect2: ld returned 1 exit status
make: *** [siesta] Error 1

even if I compile zgesv_lapack.a and make corrections in arch.make then
also it is showing same error.
Please tell me what shpuld i do.

Thank You

regards
Rajan

On Thu, Feb 4, 2016 at 6:17 PM, Zaw Myo Win 
wrote:

> Dear Alberto,
>Thanks alot for your kind help. That really works.
> I can use siesta 4.0 now.
>
> On Thu, Feb 4, 2016 at 7:59 PM, Alberto Garcia  wrote:
>
>> Hi,
>>
>> 1. Please copy Src/Sys/nolibs.make to Obj/arch.make.
>> 2. Change the name of your compiler if needed in arch.make.
>> 3. In Obj, type "make clean" and then "make"
>>
>>   Regards,
>>
>>   Alberto
>>
>> On 04 Feb 2016, at 10:50, Zaw Myo Win 
>> wrote:
>>
>> > Dear Alberto,
>> >I am not using external lapack+blas library, I added
>> COMP_LIBS=linalg.a to arch.make file in the  Src folder . The error is
>> different. Please kindly see below.
>> > Please tell me how I should I solve this problem in details. Thank you
>> for your time.
>> >
>> >
>> > make[1]: Leaving directory
>> `/nfs/disk1/nwzaw2/softwares/SIESTA/siesta-4.0b-485/Obj/SiestaXC'
>> > make: *** No rule to make target `COMP_LIBS=linalg.a', needed by
>> `siesta'.  Stop.
>> >
>> >
>> > On Thu, Feb 4, 2016 at 5:32 PM, Alberto Garcia 
>> wrote:
>> > If you are not using an external lapack+blas library, you should use
>> >
>> > COMP_LIBS=linalg.a
>> >
>> > in the arch.make file to compile all the linear-algebra code in
>> Src/Libs. Version 4.0 needs extra code that is not in the file
>> Src/Libs/lapack.f.
>> >
>> > See Src/Sys/nolibs.make.
>> >
>> >  Regards,
>> >
>> >   Alberto
>> >
>> >
>> > On 04 Feb 2016, at 10:25, Zaw Myo Win 
>> wrote:
>> >
>> > > Dear Siesta Users,
>> > >When I compiled siesta-4.0b, I got the
>> following errors. I could compile and use siesta-3.2 easily in the past.
>> Right now, I can not compile and use siesta 4.0. Please kindly help me on
>> this.
>> > >
>> > >
>> > >
>> > >  siesta.o libfdf.a  libxmlparser.a \
>> > >libSiestaXC.a  \
>> > >dc_lapack.a liblapack.a libblas.a  `FoX/FoX-config
>> --libs --wcml`   dc_lapack.a liblapack.a libblas.a
>> > > m_dminim.o: In function `__m_dminim_MOD_minim_cg':
>> > >
>> /nfs/disk1/nwzaw2/softwares/SIESTA/siesta-4.0b-485/Src/m_dminim.F90:890:
>> undefined reference to `dsytrf_'
>> > >
>> /nfs/disk1/nwzaw2/softwares/SIESTA/siesta-4.0b-485/Src/m_dminim.F90:894:
>> undefined reference to `dsytri_'
>> > > m_dminim.o: In function `__m_dminim_MOD_minim_cg_sparse':
>> > >
>> /nfs/disk1/nwzaw2/softwares/SIESTA/siesta-4.0b-485/Src/m_dminim.F90:1717:
>> undefined reference to `dsytrf_'
>> > >
>> /nfs/disk1/nwzaw2/softwares/SIESTA/siesta-4.0b-485/Src/m_dminim.F90:1721:
>> undefined reference to `dsytri_'
>> > > m_zminim.o: In function `__m_zminim_MOD_minim_cg':
>> > >
>> /nfs/disk1/nwzaw2/softwares/SIESTA/siesta-4.0b-485/Src/m_zminim.F90:989:
>> undefined reference to `zhetrf_'
>> > >
>> /nfs/disk1/nwzaw2/softwares/SIESTA/siesta-4.0b-485/Src/m_zminim.F90:993:
>> undefined reference to `zhetri_'
>> > > m_zminim.o: In function `__m_zminim_MOD_minim_cg_sparse':
>> > >
>> /nfs/disk1/nwzaw2/softwares/SIESTA/siesta-4.0b-485/Src/m_zminim.F90:1857:
>> undefined reference to `zhetrf_'
>> > >
>> /nfs/disk1/nwzaw2/softwares/SIESTA/siesta-4.0b-485/Src/m_zminim.F90:1861:
>> undefined reference to `zhetri_'
>> > > m_svd.o: In function `__m_svd_MOD_solve_with_svd':
>> > > /nfs/disk1/nwzaw2/softwares/SIESTA/siesta-4.0b-485/Src/m_svd.F90:52:
>> undefined reference to `dgelss_'
>> > > collect2: ld returned 1 exit status
>> > > make: *** [siesta] Error 1
>> > >
>> > >
>> > > --
>> > > With Best Regards,
>> > > Mr.Zaw Myo

[SIESTA-L] Installation of Siesta-trunk-462

[RAJAN SINGH]

Dear Siesta Users

I am trying to install Siesta-trunk-462 version on Centos-6.6. It is
showing following error:


 libSiestaXC.a  \
   dc_lapack.a liblapack.a libblas.a  `FoX/FoX-config --libs
--wcml`   dc_lapack.a liblapack.a libblas.a
m_dminim.o: In function `__m_dminim_MOD_minim_cg':
/home/rajan.singh/siesta-trunk-462/Src/m_dminim.F90:890: undefined
reference to `dsytrf_'
/home/rajan.singh/siesta-trunk-462/Src/m_dminim.F90:894: undefined
reference to `dsytri_'
m_dminim.o: In function `__m_dminim_MOD_minim_cg_sparse':
/home/rajan.singh/siesta-trunk-462/Src/m_dminim.F90:1717: undefined
reference to `dsytrf_'
/home/rajan.singh/siesta-trunk-462/Src/m_dminim.F90:1721: undefined
reference to `dsytri_'
m_zminim.o: In function `__m_zminim_MOD_minim_cg':
/home/rajan.singh/siesta-trunk-462/Src/m_zminim.F90:989: undefined
reference to `zhetrf_'
/home/rajan.singh/siesta-trunk-462/Src/m_zminim.F90:993: undefined
reference to `zhetri_'
m_zminim.o: In function `__m_zminim_MOD_minim_cg_sparse':
/home/rajan.singh/siesta-trunk-462/Src/m_zminim.F90:1857: undefined
reference to `zhetrf_'
/home/rajan.singh/siesta-trunk-462/Src/m_zminim.F90:1861: undefined
reference to `zhetri_'
m_svd.o: In function `__m_svd_MOD_solve_with_svd':
/home/rajan.singh/siesta-trunk-462/Src/m_svd.F90:52: undefined reference to
`dgelss_'
collect2: ld returned 1 exit status
make: *** [siesta] Error 1


I searched previous mails and find this :
https://www.mail-archive.com/siesta-l%40uam.es/msg00618.html

hence i do this :

make zgesv_lapack.a
change arch.make to add zgesv_lapack.a to the LAPACK_LIBS
LAPACK_LIBS=dc_lapack.a liblapack.a zgesv_lapack.a
and then
make

Then again error is there:

 dc_lapack.a liblapack.a libblas.a  `FoX/FoX-config --libs --wcml`
dc_lapack.a liblapack.a zgesv_lapack.a libblas.a
m_dminim.o: In function `__m_dminim_MOD_minim_cg':
/home/rajan.singh/siesta-trunk-462/Src/m_dminim.F90:890: undefined
reference to `dsytrf_'
/home/rajan.singh/siesta-trunk-462/Src/m_dminim.F90:894: undefined
reference to `dsytri_'
m_dminim.o: In function `__m_dminim_MOD_minim_cg_sparse':
/home/rajan.singh/siesta-trunk-462/Src/m_dminim.F90:1717: undefined
reference to `dsytrf_'
/home/rajan.singh/siesta-trunk-462/Src/m_dminim.F90:1721: undefined
reference to `dsytri_'
m_zminim.o: In function `__m_zminim_MOD_minim_cg':
/home/rajan.singh/siesta-trunk-462/Src/m_zminim.F90:989: undefined
reference to `zhetrf_'
/home/rajan.singh/siesta-trunk-462/Src/m_zminim.F90:993: undefined
reference to `zhetri_'
m_zminim.o: In function `__m_zminim_MOD_minim_cg_sparse':
/home/rajan.singh/siesta-trunk-462/Src/m_zminim.F90:1857: undefined
reference to `zhetrf_'
/home/rajan.singh/siesta-trunk-462/Src/m_zminim.F90:1861: undefined
reference to `zhetri_'
m_svd.o: In function `__m_svd_MOD_solve_with_svd':
/home/rajan.singh/siesta-trunk-462/Src/m_svd.F90:52: undefined reference to
`dgelss_'
collect2: ld returned 1 exit status
make: *** [siesta] Error 1

Please help me with this.

Thanking you

With Regards
Rajan

[SIESTA-L] confusion in convergence test of siesta

[RAJAN SINGH]

Dear Siesta Users

During convergence test of k-point, should I relax every time ? (as I
change k-point again I have to relax with new k-point then plot Energy vs
k-point)

Also should I do the same for mesh cut-off? (as I change mesh cut-off again
I have to relax with new mesh cut-off then plot Energy vs mesh cut-off)

please help me with this confusion.

Thank You

Regards
Rajan Singh

Re: [SIESTA-L] What should be the solution method?

[RAJAN SINGH]

For k-point convergence should i relax structure with different k-points?

On Mon, Feb 1, 2016 at 10:30 PM, RAJAN SINGH 
wrote:

> Dear Rafi
>
> Thanks a lot
>
> Regards
> Rajan Singh
>
> On Mon, Feb 1, 2016 at 7:56 AM, Rafi Ullah  wrote:
>
>> For ground state calculations (relaxation run, convergence tests for
>> k-points, and convergence for mesh cut off) the most used and probably
>> efficient method is 'diagon' method. Unless you are simulating some very
>> big system. Transiesta is for transport calculations. If you remove this
>> statement Siesta by default uses diagon method.
>>
>> On Mon, Feb 1, 2016 at 4:12 PM, RAJAN SINGH 
>> wrote:
>>
>>> Dear Siesta Users
>>>
>>> I am a bot confused with the si\olution methods for different kind of
>>> simulation runs.
>>>
>>> What should be the solution method for:
>>>
>>> 1. Relaxation Run
>>> 2. Convergence test for k point
>>> 3. Convergence test for mesh cut off
>>>
>>> Should I use this command line (solution method diagon/transiesta) while
>>> doing above simulations or simple remove this statement and continue with
>>> ./siesta filename.fdf
>>>
>>> please help
>>>
>>> Thank you
>>>
>>> With Regards
>>> Rajan Singh
>>>
>>>
>>
>>
>>
>> --
>> --
>> Ph.D. Student
>> Theory Group
>>
>> CIC nanoGUNE,
>> Tolosa Hiribidea, 76
>> E-20018 Donostia-San Sebastian
>> Spain
>>
>> +34 943 574 063
>> r.ul...@nanogune.eu
>> www.nanogune.eu
>> --
>>
>
>

Re: [SIESTA-L] What should be the solution method?

[RAJAN SINGH]

Dear Rafi

Thanks a lot

Regards
Rajan Singh

On Mon, Feb 1, 2016 at 7:56 AM, Rafi Ullah  wrote:

> For ground state calculations (relaxation run, convergence tests for
> k-points, and convergence for mesh cut off) the most used and probably
> efficient method is 'diagon' method. Unless you are simulating some very
> big system. Transiesta is for transport calculations. If you remove this
> statement Siesta by default uses diagon method.
>
> On Mon, Feb 1, 2016 at 4:12 PM, RAJAN SINGH 
> wrote:
>
>> Dear Siesta Users
>>
>> I am a bot confused with the si\olution methods for different kind of
>> simulation runs.
>>
>> What should be the solution method for:
>>
>> 1. Relaxation Run
>> 2. Convergence test for k point
>> 3. Convergence test for mesh cut off
>>
>> Should I use this command line (solution method diagon/transiesta) while
>> doing above simulations or simple remove this statement and continue with
>> ./siesta filename.fdf
>>
>> please help
>>
>> Thank you
>>
>> With Regards
>> Rajan Singh
>>
>>
>
>
>
> --
> --
> Ph.D. Student
> Theory Group
>
> CIC nanoGUNE,
> Tolosa Hiribidea, 76
> E-20018 Donostia-San Sebastian
> Spain
>
> +34 943 574 063
> r.ul...@nanogune.eu
> www.nanogune.eu
> --
>

[SIESTA-L] What should be the solution method?

[RAJAN SINGH]

Dear Siesta Users

I am a bot confused with the si\olution methods for different kind of
simulation runs.

What should be the solution method for:

1. Relaxation Run
2. Convergence test for k point
3. Convergence test for mesh cut off

Should I use this command line (solution method diagon/transiesta) while
doing above simulations or simple remove this statement and continue with
./siesta filename.fdf

please help

Thank you

With Regards
Rajan Singh

Re: [SIESTA-L] Need advice on correct way of relaxation then transiesta run (Please help me)

[RAJAN SINGH]

Dear Dr. Nick

Actually it is a bit confusing from this link :
http://www.mail-archive.com/siesta-l%40uam.es/msg08286.html).
But my configuration is

left electrode 30 atoms
right electrode 30 atoms
device region 30atom

after relaxation then putting the electrodes when i am running transiesta
Qt and Qt0 didnt match and I am not getting the convergence.

Any suggestions for this problem

Thank You

Regards
Rajan Singh


On Wed, Jan 20, 2016 at 7:12 PM, Nick Papior  wrote:

> You can't use repetition for a graphene nanoribbon electrode.
> Please re-read the manual about its meaning.
>
> 2016-01-20 14:35 GMT+01:00 RAJAN SINGH :
>
>> Dear Dr. Nick
>>
>> I read the mailing list (
>> http://www.mail-archive.com/siesta-l%40uam.es/msg08286.html).
>>
>> As I am using Zigzag Graphene nanoribbon (30+30+30) so I made a electrode
>> of 10 atom and using TS.ReplicateA2Left/Right 3.
>>
>> But it is showing that my electrodes are not situated on same place. I
>> double checked the coordinates but I am not able to figure out what is
>> wrong.
>>
>> I am attaching my electrode and scattering .fdf files.
>>
>> Please help me with this I am doing this for several hours.
>>
>> Thank You
>>
>> Regards
>> Rajan Singh
>>
>> On Wed, Jan 20, 2016 at 1:47 PM, Nick Papior 
>> wrote:
>>
>>> Search the mailing list, this question has been raised many times before.
>>>
>>> 2016-01-20 7:10 GMT+01:00 Riya Rogers :
>>>
>>>> Thanks a lot for your valuable comments Dr Nick
>>>>
>>>> But as Rajan pointed out, I am facing the same problem of transiesta
>>>> convergence.
>>>>
>>>> Should I use : TS.ReplicateA2Left/Right   to increase my electrode size
>>>> and may cause in convergence?
>>>>
>>>> Please comment.
>>>>
>>>> With Regards
>>>> Riya
>>>>
>>>> On Wed, Jan 20, 2016 at 10:33 AM, RAJAN SINGH <
>>>> singhrajan.i...@gmail.com> wrote:
>>>>
>>>>> Thank you Dr Nick
>>>>>
>>>>> After doing relaxation from siesta when I am running my transiesta it
>>>>> wont converge. The Qto and Qt values are not same. How to achieve that?
>>>>>
>>>>> Efermi from SIESTA   :-3.47054
>>>>> Total charge  [Qt0]  :   414.0
>>>>> Charge in update region   [Qc]   :   133.70127
>>>>> Charge outside update region  [Qcn]  :   280.29873
>>>>> Left electrode[L]:   133.72936
>>>>> Left electrode/device [L-C]  : 3.91751
>>>>> Device[C]:   133.70127
>>>>> Device/right electrode[C-R]  : 4.65178
>>>>> Right electrode   [R]:   133.34561
>>>>> Other [O]: 4.65448
>>>>>
>>>>>  Reading GF file, with title:
>>>>>nanoribbon.TSGFL
>>>>>  Title: 'Generated GF file'
>>>>>
>>>>>  Reading GF file, with title:
>>>>>nanoribbon.TSGFR
>>>>>  Title: 'Generated GF file'
>>>>>
>>>>> ts-charge:OL  L-CC  C-RR
>>>>> Qt
>>>>> ts-charge:4.654  133.7293.918  329.5484.652  133.346
>>>>> 609.847
>>>>>
>>>>>
>>>>> With Regards
>>>>> Rajan
>>>>>
>>>>> On Wed, Jan 20, 2016 at 12:06 AM, Nick Papior 
>>>>> wrote:
>>>>>
>>>>>> Please re-read the slides _carefully_. You should probably not relax
>>>>>> the entire device region.
>>>>>>
>>>>>> This is slightly touched in the slides.
>>>>>>
>>>>>> 2016-01-19 19:33 GMT+01:00 RAJAN SINGH :
>>>>>>
>>>>>>> Thank You Prof. Nick.
>>>>>>>
>>>>>>> I read the slides according to them the steps should be :
>>>>>>>
>>>>>>> 1. Relax the Device atoms using siesta run (CG run)
>>>>>>> 2. After relaxation attach the electrodes.
>>>>>>> 3. Again perform the Siesta relaxation (CG run) but this time put a
>>>>>>> geometry constraints on electrode atoms.
>>>>>>> 4. after step 3 relaxation go for Transiesta Run

Re: [SIESTA-L] Need advice on correct way of relaxation then transiesta run (Please help me)

[RAJAN SINGH]

Dear Dr. Nick

I read the mailing list (
http://www.mail-archive.com/siesta-l%40uam.es/msg08286.html).

As I am using Zigzag Graphene nanoribbon (30+30+30) so I made a electrode
of 10 atom and using TS.ReplicateA2Left/Right 3.

But it is showing that my electrodes are not situated on same place. I
double checked the coordinates but I am not able to figure out what is
wrong.

I am attaching my electrode and scattering .fdf files.

Please help me with this I am doing this for several hours.

Thank You

Regards
Rajan Singh

On Wed, Jan 20, 2016 at 1:47 PM, Nick Papior  wrote:

> Search the mailing list, this question has been raised many times before.
>
> 2016-01-20 7:10 GMT+01:00 Riya Rogers :
>
>> Thanks a lot for your valuable comments Dr Nick
>>
>> But as Rajan pointed out, I am facing the same problem of transiesta
>> convergence.
>>
>> Should I use : TS.ReplicateA2Left/Right   to increase my electrode size
>> and may cause in convergence?
>>
>> Please comment.
>>
>> With Regards
>> Riya
>>
>> On Wed, Jan 20, 2016 at 10:33 AM, RAJAN SINGH 
>> wrote:
>>
>>> Thank you Dr Nick
>>>
>>> After doing relaxation from siesta when I am running my transiesta it
>>> wont converge. The Qto and Qt values are not same. How to achieve that?
>>>
>>> Efermi from SIESTA   :-3.47054
>>> Total charge  [Qt0]  :   414.0
>>> Charge in update region   [Qc]   :   133.70127
>>> Charge outside update region  [Qcn]  :   280.29873
>>> Left electrode[L]:   133.72936
>>> Left electrode/device [L-C]  : 3.91751
>>> Device[C]:   133.70127
>>> Device/right electrode[C-R]  : 4.65178
>>> Right electrode   [R]:   133.34561
>>> Other [O]: 4.65448
>>>
>>>  Reading GF file, with title:
>>>nanoribbon.TSGFL
>>>  Title: 'Generated GF file'
>>>
>>>  Reading GF file, with title:
>>>nanoribbon.TSGFR
>>>  Title: 'Generated GF file'
>>>
>>> ts-charge:OL  L-CC  C-RR   Qt
>>> ts-charge:4.654  133.7293.918  329.5484.652  133.346  609.847
>>>
>>>
>>> With Regards
>>> Rajan
>>>
>>> On Wed, Jan 20, 2016 at 12:06 AM, Nick Papior 
>>> wrote:
>>>
>>>> Please re-read the slides _carefully_. You should probably not relax
>>>> the entire device region.
>>>>
>>>> This is slightly touched in the slides.
>>>>
>>>> 2016-01-19 19:33 GMT+01:00 RAJAN SINGH :
>>>>
>>>>> Thank You Prof. Nick.
>>>>>
>>>>> I read the slides according to them the steps should be :
>>>>>
>>>>> 1. Relax the Device atoms using siesta run (CG run)
>>>>> 2. After relaxation attach the electrodes.
>>>>> 3. Again perform the Siesta relaxation (CG run) but this time put a
>>>>> geometry constraints on electrode atoms.
>>>>> 4. after step 3 relaxation go for Transiesta Run.
>>>>>
>>>>> Is that right?
>>>>>
>>>>> Please help me.
>>>>>
>>>>> With Regards
>>>>> Rajan
>>>>>
>>>>> On Tue, Jan 19, 2016 at 11:49 PM, Nick Papior 
>>>>> wrote:
>>>>>
>>>>>> Check these slides, and see if they will help you (they are a guiding
>>>>>> example!):
>>>>>>
>>>>>> http://departments.icmab.es/leem/siesta/tlv14/slides12.pdf
>>>>>>
>>>>>>
>>>>>> 2016-01-19 19:04 GMT+01:00 RAJAN SINGH :
>>>>>>
>>>>>>> Dear Siesta Users
>>>>>>>
>>>>>>> Kindly give me advice on the following:
>>>>>>>
>>>>>>> In order to perform the transiesta calculation on relaxed device
>>>>>>> structure the procedure which I am performing is:
>>>>>>>
>>>>>>> 1. First I write a .fdf file (left electrode + Device + right
>>>>>>> electrode).
>>>>>>> 2. then I remove my electrode atoms from file (KEEPING THE LATTICE
>>>>>>> VECTORS AS SAME)
>>>>>>> 3. Then perform a CG relaxation run.
>>>>>>> 4. Once the run completed then I modify my .fdf file
>>>>>>> (left electrode + RELAXED Device + right electrode)
>>>>>>> 5. Then perfom the transiesta run.
>>>>>>>
>>>>>>>
>>>>>>> Please tell me whether the above process is appropriate and correct
>>>>>>> or not. I am really a bit confuse in this step. I really need help in 
>>>>>>> this
>>>>>>> please help me.
>>>>>>>
>>>>>>> Thank You
>>>>>>>
>>>>>>> With Regards
>>>>>>> Rajan Singh
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Kind regards Nick
>>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> Kind regards Nick
>>>>
>>>
>>>
>>
>
>
> --
> Kind regards Nick
>


electrode.fdf
Description: Binary data


scattering.fdf
Description: Binary data

Re: [SIESTA-L] Need advice on correct way of relaxation then transiesta run (Please help me)

[RAJAN SINGH]

Thank you Dr Nick

After doing relaxation from siesta when I am running my transiesta it wont
converge. The Qto and Qt values are not same. How to achieve that?

Efermi from SIESTA   :-3.47054
Total charge  [Qt0]  :   414.0
Charge in update region   [Qc]   :   133.70127
Charge outside update region  [Qcn]  :   280.29873
Left electrode[L]:   133.72936
Left electrode/device [L-C]  : 3.91751
Device[C]:   133.70127
Device/right electrode[C-R]  : 4.65178
Right electrode   [R]:   133.34561
Other [O]: 4.65448

 Reading GF file, with title:
   nanoribbon.TSGFL
 Title: 'Generated GF file'

 Reading GF file, with title:
   nanoribbon.TSGFR
 Title: 'Generated GF file'

ts-charge:OL  L-CC  C-RR   Qt
ts-charge:4.654  133.7293.918  329.5484.652  133.346  609.847


With Regards
Rajan

On Wed, Jan 20, 2016 at 12:06 AM, Nick Papior  wrote:

> Please re-read the slides _carefully_. You should probably not relax the
> entire device region.
>
> This is slightly touched in the slides.
>
> 2016-01-19 19:33 GMT+01:00 RAJAN SINGH :
>
>> Thank You Prof. Nick.
>>
>> I read the slides according to them the steps should be :
>>
>> 1. Relax the Device atoms using siesta run (CG run)
>> 2. After relaxation attach the electrodes.
>> 3. Again perform the Siesta relaxation (CG run) but this time put a
>> geometry constraints on electrode atoms.
>> 4. after step 3 relaxation go for Transiesta Run.
>>
>> Is that right?
>>
>> Please help me.
>>
>> With Regards
>> Rajan
>>
>> On Tue, Jan 19, 2016 at 11:49 PM, Nick Papior 
>> wrote:
>>
>>> Check these slides, and see if they will help you (they are a guiding
>>> example!):
>>>
>>> http://departments.icmab.es/leem/siesta/tlv14/slides12.pdf
>>>
>>>
>>> 2016-01-19 19:04 GMT+01:00 RAJAN SINGH :
>>>
>>>> Dear Siesta Users
>>>>
>>>> Kindly give me advice on the following:
>>>>
>>>> In order to perform the transiesta calculation on relaxed device
>>>> structure the procedure which I am performing is:
>>>>
>>>> 1. First I write a .fdf file (left electrode + Device + right
>>>> electrode).
>>>> 2. then I remove my electrode atoms from file (KEEPING THE LATTICE
>>>> VECTORS AS SAME)
>>>> 3. Then perform a CG relaxation run.
>>>> 4. Once the run completed then I modify my .fdf file
>>>> (left electrode + RELAXED Device + right electrode)
>>>> 5. Then perfom the transiesta run.
>>>>
>>>>
>>>> Please tell me whether the above process is appropriate and correct or
>>>> not. I am really a bit confuse in this step. I really need help in this
>>>> please help me.
>>>>
>>>> Thank You
>>>>
>>>> With Regards
>>>> Rajan Singh
>>>>
>>>
>>>
>>>
>>> --
>>> Kind regards Nick
>>>
>>
>>
>
>
> --
> Kind regards Nick
>

[SIESTA-L] transiesta convergence Qt and Qt0 not same

[RAJAN SINGH]

Dear Siesta users

After relaxation of nanoribbon when I am running my transiesta
calculations, Qt0 and Qt values are not same. And my transiesta didnt
converge what should I do?

Efermi from SIESTA   :-3.47054
Total charge  [Qt0]  :   414.0
Charge in update region   [Qc]   :   133.70127
Charge outside update region  [Qcn]  :   280.29873
Left electrode[L]:   133.72936
Left electrode/device [L-C]  : 3.91751
Device[C]:   133.70127
Device/right electrode[C-R]  : 4.65178
Right electrode   [R]:   133.34561
Other [O]: 4.65448

 Reading GF file, with title:
   nanoribbon.TSGFL
 Title: 'Generated GF file'

 Reading GF file, with title:
   nanoribbon.TSGFR
 Title: 'Generated GF file'

ts-charge:OL  L-CC  C-RR   Qt
ts-charge:4.654  133.7293.918  329.5484.652  133.346  609.847

Thank You

With Regards
Rajan

Re: [SIESTA-L] Need advice on correct way of relaxation then transiesta run (Please help me)

[RAJAN SINGH]

Thank You Prof. Nick.

I read the slides according to them the steps should be :

1. Relax the Device atoms using siesta run (CG run)
2. After relaxation attach the electrodes.
3. Again perform the Siesta relaxation (CG run) but this time put a
geometry constraints on electrode atoms.
4. after step 3 relaxation go for Transiesta Run.

Is that right?

Please help me.

With Regards
Rajan

On Tue, Jan 19, 2016 at 11:49 PM, Nick Papior  wrote:

> Check these slides, and see if they will help you (they are a guiding
> example!):
>
> http://departments.icmab.es/leem/siesta/tlv14/slides12.pdf
>
>
> 2016-01-19 19:04 GMT+01:00 RAJAN SINGH :
>
>> Dear Siesta Users
>>
>> Kindly give me advice on the following:
>>
>> In order to perform the transiesta calculation on relaxed device
>> structure the procedure which I am performing is:
>>
>> 1. First I write a .fdf file (left electrode + Device + right electrode).
>> 2. then I remove my electrode atoms from file (KEEPING THE LATTICE
>> VECTORS AS SAME)
>> 3. Then perform a CG relaxation run.
>> 4. Once the run completed then I modify my .fdf file
>> (left electrode + RELAXED Device + right electrode)
>> 5. Then perfom the transiesta run.
>>
>>
>> Please tell me whether the above process is appropriate and correct or
>> not. I am really a bit confuse in this step. I really need help in this
>> please help me.
>>
>> Thank You
>>
>> With Regards
>> Rajan Singh
>>
>
>
>
> --
> Kind regards Nick
>

[SIESTA-L] Need advice on correct way of relaxation then transiesta run (Please help me)

[RAJAN SINGH]

Dear Siesta Users

Kindly give me advice on the following:

In order to perform the transiesta calculation on relaxed device structure
the procedure which I am performing is:

1. First I write a .fdf file (left electrode + Device + right electrode).
2. then I remove my electrode atoms from file (KEEPING THE LATTICE VECTORS
AS SAME)
3. Then perform a CG relaxation run.
4. Once the run completed then I modify my .fdf file
(left electrode + RELAXED Device + right electrode)
5. Then perfom the transiesta run.


Please tell me whether the above process is appropriate and correct or not.
I am really a bit confuse in this step. I really need help in this please
help me.

Thank You

With Regards
Rajan Singh

Re: [SIESTA-L] transiesta spectrum

[RAJAN SINGH]

Dear Azar

Please look at the z-direction electrode length.

Regards
Rajan

On Tue, Dec 22, 2015 at 1:43 AM, Nick Papior  wrote:

> It really is hard to say what you have done wrong.
>
> 1. Start by doing your electrode calculations,
> 2. Assert that the electrodes actually has the properties that you expect
> (check band-structure etc)
> 3. Check that your electrode is not too long and not too short in the semi
> infinite direction.
> 4. Then, and only then, can you start by creating your device.
> 5. A pristine system can ALWAYS be created by extending an electrode 3
> times, 1 left, 1 device and 1 right. If this is not immediately clear, I
> would highly suggest you to read how the surface self energies are
> calculated, re-read the Brandbyge paper and find the references for the
> self energy calculations.
>
> 2015-12-22 10:35 GMT+01:00 azar ostovan :
>
>> Dear transiesta users
>> I studied on the transport properties of the zigzag nano ribbons as
>> recognized as electrode in and Benzothiadiazole as device.
>> Here we decide to determine the correct numbers of nano ribbons that must
>> be include in the scattering zone, but I couldn’t see any converges in the
>> spectral properties.
>> I consider the 20 atoms electrodes, the scattering zones have 43, 63 and
>> 83 atoms, respectively.
>> I attached the spectrum of the three types of calculations and the input
>> files.
>> The calculations differ just in the number of layers that include in the
>> scattering region.
>> generally how i could find the spectrum of pristine system.
>> thank you in advance
>> Azar
>>
>>
>
>
> --
> Kind regards Nick
>

[SIESTA-L] Relaxation of Graphene Nanoribbon

[RAJAN SINGH]

Dear Siesta Users

I am trying to relax graphene nanoribbon using siesta, but each time when
it converges it change 2-D structure to 3-D.

I am attaching my fdf files for reference.

Please help me with this.

Thank You

Regards
Rajan Singh


nanoribbon.fdf
Description: Binary data

[SIESTA-L] Monkhorst pack

[RAJAN SINGH]

Dear Siesta Users

I am confused how to select 0.0 and 0.5 value in monkhorst pack?

I am doing relaxation, band structure then transmission calculations in
zigzag graphene nanoribbon.

Any one suggest something please.

Thank You

Regards
Rajan

Re: [SIESTA-L] Flag associated with proper electrode length

[RAJAN SINGH]

Thank you so much Dr Nick.

Regards
Rajan Singh

On Wed, Dec 2, 2015 at 6:05 PM, Nick Papior  wrote:

> Please read these two papers to understand the principle of an electrode
> size:
> DOI: 10.1088/0305-4608/15/4/009
> DOI: 10.1088/0305-4608/14/5/016
>
> 2015-12-02 13:24 GMT+01:00 RAJAN SINGH :
>
>> thank you so much Dr. Nick
>>
>> Actually I searched in the mail archive about this and found the
>> following:
>>
>> http://www.mail-archive.com/siesta-l%40uam.es/msg04344.html
>>
>> I am trying the following example:
>>
>>
>> http://dipc.ehu.es/frederiksen/tstutorial/index.php/Zig-zag_graphene_nanoribbon
>>
>> In this example i am not able to understand how they select the electrode
>> length.
>>
>> Please help me with this.
>>
>> Thank You
>>
>> Regards
>> Rajan Singh
>>
>> On Wed, Dec 2, 2015 at 5:41 PM, Nick Papior  wrote:
>>
>>> There is no flag to ensure this.
>>> This question has been posted several times on the mailing list, please
>>> search the mailing list.
>>> It is also addressed in the manual. Please re-read the manual as well.
>>>
>>> 2015-12-02 13:05 GMT+01:00 RAJAN SINGH :
>>>
>>>>
>>>> Dear Siesta Users
>>>>
>>>> How to ensure the electrode length which i have taken for my electrode
>>>> calculation is proper?
>>>>
>>>> Is there any flag associated with it in Siesta-trunk-462 version?
>>>>
>>>> Please enlighten me.
>>>>
>>>> Thank You
>>>>
>>>> With Regards
>>>> Rajan Singh
>>>>
>>>
>>>
>>>
>>> --
>>> Kind regards Nick
>>>
>>
>>
>
>
> --
> Kind regards Nick
>

Re: [SIESTA-L] Flag associated with proper electrode length

[RAJAN SINGH]

thank you so much Dr. Nick

Actually I searched in the mail archive about this and found the following:

http://www.mail-archive.com/siesta-l%40uam.es/msg04344.html

I am trying the following example:

http://dipc.ehu.es/frederiksen/tstutorial/index.php/Zig-zag_graphene_nanoribbon

In this example i am not able to understand how they select the electrode
length.

Please help me with this.

Thank You

Regards
Rajan Singh

On Wed, Dec 2, 2015 at 5:41 PM, Nick Papior  wrote:

> There is no flag to ensure this.
> This question has been posted several times on the mailing list, please
> search the mailing list.
> It is also addressed in the manual. Please re-read the manual as well.
>
> 2015-12-02 13:05 GMT+01:00 RAJAN SINGH :
>
>>
>> Dear Siesta Users
>>
>> How to ensure the electrode length which i have taken for my electrode
>> calculation is proper?
>>
>> Is there any flag associated with it in Siesta-trunk-462 version?
>>
>> Please enlighten me.
>>
>> Thank You
>>
>> With Regards
>> Rajan Singh
>>
>
>
>
> --
> Kind regards Nick
>

[SIESTA-L] Flag associated with proper electrode length

[RAJAN SINGH]

Dear Siesta Users

How to ensure the electrode length which i have taken for my electrode
calculation is proper?

Is there any flag associated with it in Siesta-trunk-462 version?

Please enlighten me.

Thank You

With Regards
Rajan Singh

[SIESTA-L] Electrode warning in Siesta-Trunk-462 version

[RAJAN SINGH]

Dear Siesta Users

I have a doubt in determining the size of electrode cell. while going
through manuals i found the following:

The electrode must be oriented along the z-axis and the unit cell along the
z-direction must be large enough so that orbitals within the unit cell only
interact with a single nearest neighbor cell (the size of the unit cell can
thus be derived from the range of support for the orbital basis functions).
TranSiesta will warn if this is not enforced.

What kind of warning will Transiesta displayed? and how can I ensure that
my cell sizes are correct?

Any kind of help will be highly appreciated.

Thank You.

With Regards
Rajan Singh

Re: [SIESTA-L] Doubt in Electrode setup

[RAJAN SINGH]

Actually when I run for 8 atoms in Electrode region and 32 atom in
Scattering (a total of 48 atom) then it displayed no error. But each one
with 16 atoms (again a total of 48 atom) then only it displayed a error.
Thats why I am not able to understand what you said.

Regards
Rajan Singh


On Sun, Nov 15, 2015 at 1:46 PM, RAJAN SINGH 
wrote:

> Thank you for your response.
>
> But is that mean minimum number of atoms (summation of both electrodes and
> scattering region) should always be higher than 48?
>
> please enlighten a bit more.
>
> Thank you again
>
> Regards
> Rajan Singh
>
> On Sun, Nov 15, 2015 at 1:40 PM, Nick Papior  wrote:
>
>> You can't. A transiesta calculation is created by a left electrode plus
>> the device plus the right  electrode. Hence for the system in question 48
>> atoms is the minimal number of atoms allowed.
>>
>> This is exactly what the error message tells you.
>>
>> --
>>
>> Kind regards Nick Papior
>> On 15 Nov 2015 08:57, "RAJAN SINGH"  wrote:
>>
>>>
>>> Dear Siesta Users
>>>
>>> I have a doubt regarding setting up the electrode. I am going through
>>> the example of Graphene Nanoribbon of the following site:
>>>
>>>
>>> http://dipc.ehu.es/frederiksen/tstutorial/index.php/Zig-zag_graphene_nanoribbon
>>>
>>> In the above example:
>>>
>>> Scattering region has 48 atoms and 16 atoms in electrode region.
>>>
>>> But if I try to simulate the same example with 16 atoms in both
>>> Sacttering and Electrode region then following error displayed:
>>>
>>>   
>>>   *   TRANSIESTA BEGIN   *
>>>   
>>> The contact region size is &  smaller than the
>>> electrode size. Please correct.
>>> Stopping Program from Node:0
>>>
>>> Program aborted. Backtrace:
>>> The contact region size is &  smaller than the
>>> electrode size. Please correct.
>>> Stopping Program from Node:0
>>> #0  0x7F74F92A3777
>>> #1  0x7F74F92A4EC2
>>> #2  0x7F74F9371B58
>>> #3  0x5D0AAA in pxfabort_ at pxf.F90:86
>>> #4  0x5F3E28 in __m_ts_in_siesta_MOD_transiesta at m_ts_in_siesta.F:414
>>> #5  0x4908FB in __m_compute_dm_MOD_compute_dm at compute_dm.F:124
>>> #6  0x4AD0B5 in __m_siesta_forces_MOD_siesta_forces at
>>> siesta_forces.F:115
>>> #7  0x404189 in siesta at siesta.F:23
>>> #8  0x7F74F89CAEC4
>>>
>>> Please tell me how to simulate the same. I am attaching fdf file with
>>> the mail.
>>>
>>> Thank You
>>>
>>> Regards
>>> Rajan Singh
>>>
>>>
>

Re: [SIESTA-L] Doubt in Electrode setup

[RAJAN SINGH]

Thank you for your response.

But is that mean minimum number of atoms (summation of both electrodes and
scattering region) should always be higher than 48?

please enlighten a bit more.

Thank you again

Regards
Rajan Singh

On Sun, Nov 15, 2015 at 1:40 PM, Nick Papior  wrote:

> You can't. A transiesta calculation is created by a left electrode plus
> the device plus the right  electrode. Hence for the system in question 48
> atoms is the minimal number of atoms allowed.
>
> This is exactly what the error message tells you.
>
> --
>
> Kind regards Nick Papior
> On 15 Nov 2015 08:57, "RAJAN SINGH"  wrote:
>
>>
>> Dear Siesta Users
>>
>> I have a doubt regarding setting up the electrode. I am going through the
>> example of Graphene Nanoribbon of the following site:
>>
>>
>> http://dipc.ehu.es/frederiksen/tstutorial/index.php/Zig-zag_graphene_nanoribbon
>>
>> In the above example:
>>
>> Scattering region has 48 atoms and 16 atoms in electrode region.
>>
>> But if I try to simulate the same example with 16 atoms in both
>> Sacttering and Electrode region then following error displayed:
>>
>>   
>>   *   TRANSIESTA BEGIN   *
>>   
>> The contact region size is &  smaller than the
>> electrode size. Please correct.
>> Stopping Program from Node:0
>>
>> Program aborted. Backtrace:
>> The contact region size is &  smaller than the
>> electrode size. Please correct.
>> Stopping Program from Node:0
>> #0  0x7F74F92A3777
>> #1  0x7F74F92A4EC2
>> #2  0x7F74F9371B58
>> #3  0x5D0AAA in pxfabort_ at pxf.F90:86
>> #4  0x5F3E28 in __m_ts_in_siesta_MOD_transiesta at m_ts_in_siesta.F:414
>> #5  0x4908FB in __m_compute_dm_MOD_compute_dm at compute_dm.F:124
>> #6  0x4AD0B5 in __m_siesta_forces_MOD_siesta_forces at siesta_forces.F:115
>> #7  0x404189 in siesta at siesta.F:23
>> #8  0x7F74F89CAEC4
>>
>> Please tell me how to simulate the same. I am attaching fdf file with the
>> mail.
>>
>> Thank You
>>
>> Regards
>> Rajan Singh
>>
>>

[SIESTA-L] Doubt in Electrode setup

[RAJAN SINGH]

Dear Siesta Users

I have a doubt regarding setting up the electrode. I am going through the
example of Graphene Nanoribbon of the following site:

http://dipc.ehu.es/frederiksen/tstutorial/index.php/Zig-zag_graphene_nanoribbon

In the above example:

Scattering region has 48 atoms and 16 atoms in electrode region.

But if I try to simulate the same example with 16 atoms in both Sacttering
and Electrode region then following error displayed:

  
  *   TRANSIESTA BEGIN   *
  
The contact region size is &  smaller than the
electrode size. Please correct.
Stopping Program from Node:0

Program aborted. Backtrace:
The contact region size is &  smaller than the
electrode size. Please correct.
Stopping Program from Node:0
#0  0x7F74F92A3777
#1  0x7F74F92A4EC2
#2  0x7F74F9371B58
#3  0x5D0AAA in pxfabort_ at pxf.F90:86
#4  0x5F3E28 in __m_ts_in_siesta_MOD_transiesta at m_ts_in_siesta.F:414
#5  0x4908FB in __m_compute_dm_MOD_compute_dm at compute_dm.F:124
#6  0x4AD0B5 in __m_siesta_forces_MOD_siesta_forces at siesta_forces.F:115
#7  0x404189 in siesta at siesta.F:23
#8  0x7F74F89CAEC4

Please tell me how to simulate the same. I am attaching fdf file with the
mail.

Thank You

Regards
Rajan Singh


electrode_16atom.fdf
Description: Binary data


scat_16atom.fdf
Description: Binary data


scat_48atom.fdf
Description: Binary data

[SIESTA-L] Transiesta Electrode Error

[RAJAN SINGH]

Dear Siesta users

I am trying to simulate a structure in two probe configuration but i am
getting following errors:

The contact region size is &  smaller than the
electrode size. Please correct.
The contact region size is &  smaller than the
electrode size. Please correct.
Stopping Program from Node:0

Program aborted. Backtrace:
Stopping Program from Node:0
#0  0x7F137293C777
#1  0x7F137293DEC2
#2  0x7F1372A0AB58
#3  0x5D0AAA in pxfabort_ at pxf.F90:86
#4  0x5F3E28 in __m_ts_in_siesta_MOD_transiesta at m_ts_in_siesta.F:414
#5  0x4908FB in __m_compute_dm_MOD_compute_dm at compute_dm.F:124
#6  0x4AD0B5 in __m_siesta_forces_MOD_siesta_forces at siesta_forces.F:115
#7  0x404189 in siesta at siesta.F:23
#8  0x7F1372063EC4

Please suggest some solution.

Thank You

Regards
Rajan Singh

Re: [SIESTA-L] Tbtrans error

[RAJAN SINGH]

Dear Nick

I used the TBTrans_rep code and it worked fine.
Thanks a lot for your valuable responses.

With Regards
Rajan Singh

On Fri, Oct 9, 2015 at 2:43 PM, Nick Papior  wrote:

> Use the trunk version and the TBTrans_rep code (those examples where
> created for the updated tbtrans code).
>
> 2015-10-09 11:06 GMT+02:00 RAJAN SINGH :
>
>>
>> Dear Siesta Users
>>
>> I am trying to run simple transiesta example given @
>> http://departments.icmab.es/leem/siesta/tlv14/
>>
>> While running the carbon chain example, tbtrans give the following error
>>
>> ERROR: Unexpected no. orbs. in L elec.
>> Stopping Program from Node:0
>>
>> Program aborted. Backtrace:
>>  ERROR: lastoL,NGL2   0  52
>> ERROR: Unexpected no. orbs. in L elec.
>> Stopping Program from Node:0
>> #0  0x7FEC88DA
>> #1  0x7FEC88DA8EC2
>> #2  0x7FEC88E75B58
>> #3  0x41205A in pxfabort_ at pxf.F90:86
>> #4  0x42842A in tbtrans at tbtrans.F:479
>>
>> I am using default values of basis set and my left and right electrode
>> are same. Please provide me the appropriate solution, any response will be
>> highly appreciated.
>>
>> Thank You in advance.
>>
>> With Regards
>> Rajan Singh
>>
>
>
>
> --
> Kind regards Nick
>

[SIESTA-L] Fwd: Tbtrans error

[RAJAN SINGH]

Dear Siesta Users

I am trying to run simple transiesta example given @
http://departments.icmab.es/leem/siesta/tlv14/

While running the carbon chain example, tbtrans give the following error

ERROR: Unexpected no. orbs. in L elec.
Stopping Program from Node:0

Program aborted. Backtrace:
 ERROR: lastoL,NGL2   0  52
ERROR: Unexpected no. orbs. in L elec.
Stopping Program from Node:0
#0  0x7FEC88DA
#1  0x7FEC88DA8EC2
#2  0x7FEC88E75B58
#3  0x41205A in pxfabort_ at pxf.F90:86
#4  0x42842A in tbtrans at tbtrans.F:479

I am using default values of basis set and my left and right electrode are
same (Attached electrode file : elec.fdf  and carbon atom chain :
chain.fdf).
Please provide me the appropriate solution, any response will be highly
appreciated.

Thank You in advance.

With Regards
Rajan Singh


elec.fdf
Description: Binary data


chain.fdf
Description: Binary data

[SIESTA-L] Tbtrans error

[RAJAN SINGH]

Dear Siesta Users

I am trying to run simple transiesta example given @
http://departments.icmab.es/leem/siesta/tlv14/

While running the carbon chain example, tbtrans give the following error

ERROR: Unexpected no. orbs. in L elec.
Stopping Program from Node:0

Program aborted. Backtrace:
 ERROR: lastoL,NGL2   0  52
ERROR: Unexpected no. orbs. in L elec.
Stopping Program from Node:0
#0  0x7FEC88DA
#1  0x7FEC88DA8EC2
#2  0x7FEC88E75B58
#3  0x41205A in pxfabort_ at pxf.F90:86
#4  0x42842A in tbtrans at tbtrans.F:479

I am using default values of basis set and my left and right electrode are
same. Please provide me the appropriate solution, any response will be
highly appreciated.

Thank You in advance.

With Regards
Rajan Singh

Re: [SIESTA-L] Transiesta : Wrong solution method error

[RAJAN SINGH]

Dear Nick

I already complied the transiesta and it worked for electrode section. One
thing I noticed that this error encountered when I use Siesta-3.2-pl-5
version but if i use Trunk - 462 version then it worked fine.

Thank you

With regards
Rajan Singh

On Fri, Oct 9, 2015 at 1:27 PM, Nick Papior  wrote:

> you have not compiled transiesta (I guess).
> Do
> cd Obj
> make clean
> make transiesta
>
> rerun using the transiesta executable.
>
> 2015-10-09 9:40 GMT+02:00 RAJAN SINGH :
>
>>
>> Dear Siesta Users
>>
>> While running the transiesta example of simple chain of atoms, I am
>> getting error:
>>
>> siesta: ERROR: wrong solution method
>> ERROR STOP from Node:0
>>
>> Program aborted. Backtrace:
>> siesta: ERROR: wrong solution method
>> ERROR STOP from Node:0
>> #0  0x7F9A957DB777
>> #1  0x7F9A957DCEC2
>> #2  0x7F9A958A9B58
>> #3  0x57551A in pxfabort_ at pxf.F90:80
>> #4  0x4A9FC3 in __m_compute_dm_MOD_compute_dm at compute_dm.F:97
>> #5  0x4C3339 in __m_siesta_forces_MOD_siesta_forces at siesta_forces.F:102
>> #6  0x4021C9 in siesta at siesta.F:23
>> #7  0x7F9A94F02EC4
>>
>> Can anyone help me with this type of errors?
>>
>> Thank You
>>
>> Regards
>> Rajan Singh
>>
>
>
>
> --
> Kind regards Nick
>

[SIESTA-L] Transiesta : Wrong solution method error

[RAJAN SINGH]

Dear Siesta Users

While running the transiesta example of simple chain of atoms, I am getting
error:

siesta: ERROR: wrong solution method
ERROR STOP from Node:0

Program aborted. Backtrace:
siesta: ERROR: wrong solution method
ERROR STOP from Node:0
#0  0x7F9A957DB777
#1  0x7F9A957DCEC2
#2  0x7F9A958A9B58
#3  0x57551A in pxfabort_ at pxf.F90:80
#4  0x4A9FC3 in __m_compute_dm_MOD_compute_dm at compute_dm.F:97
#5  0x4C3339 in __m_siesta_forces_MOD_siesta_forces at siesta_forces.F:102
#6  0x4021C9 in siesta at siesta.F:23
#7  0x7F9A94F02EC4

Can anyone help me with this type of errors?

Thank You

Regards
Rajan Singh

Re: [SIESTA-L] Transiesta compilation error

[RAJAN SINGH]

Thank You

With regards
Rajan Singh


On Sat, Oct 3, 2015 at 8:25 PM, Nick Papior  wrote:

> You are missing the zgesv routine (defined in liblapack.a).
>
> Please search the mailing list, it has been asked before.
>
> 2015-10-01 18:27 GMT+00:00 RAJAN SINGH :
>
>>
>> Dear Siesta Users
>>
>> While doing the installation of siesta-3.2 (path level 5) version after
>> generation of "arch.make" file using command "../Src/configure" , when I am
>> typing "make transiesta" command it displays the following error:
>>
>> dc_lapack.a liblapack.a libblas.a  `FoX/FoX-config --libs --wcml`
>> dc_lapack.a liblapack.a libblas.a
>> m_ts_aux_rout.o: In function `__m_ts_aux_rout_MOD_csolveg':
>> /home/rajansingh/siesta-3.2-pl-5/Src/m_ts_aux_rout.F:347: undefined
>> reference to `zgesv_'
>> m_ts_aux_rout.o: In function `csolveg':
>> /home/rajansingh/siesta-3.2-pl-5/Src/m_ts_aux_rout.F:347: undefined
>> reference to `zgesv_'
>> /home/rajansingh/siesta-3.2-pl-5/Src/m_ts_aux_rout.F:347: undefined
>> reference to `zgesv_'
>> collect2: error: ld returned 1 exit status
>> make: *** [transiesta] Error 1
>>
>> Can anyone help me resolving this issue.
>>
>> Thank You
>>
>> Regards
>> Rajan Singh
>>
>
>
>
> --
> Kind regards Nick
>

[SIESTA-L] Transiesta compilation error

[RAJAN SINGH]

Dear Siesta Users

While doing the installation of siesta-3.2 (path level 5) version after
generation of "arch.make" file using command "../Src/configure" , when I am
typing "make transiesta" command it displays the following error:

dc_lapack.a liblapack.a libblas.a  `FoX/FoX-config --libs --wcml`
dc_lapack.a liblapack.a libblas.a
m_ts_aux_rout.o: In function `__m_ts_aux_rout_MOD_csolveg':
/home/rajansingh/siesta-3.2-pl-5/Src/m_ts_aux_rout.F:347: undefined
reference to `zgesv_'
m_ts_aux_rout.o: In function `csolveg':
/home/rajansingh/siesta-3.2-pl-5/Src/m_ts_aux_rout.F:347: undefined
reference to `zgesv_'
/home/rajansingh/siesta-3.2-pl-5/Src/m_ts_aux_rout.F:347: undefined
reference to `zgesv_'
collect2: error: ld returned 1 exit status
make: *** [transiesta] Error 1

Can anyone help me resolving this issue.

Thank You

Regards
Rajan Singh

Re: [SIESTA-L] ISSUE IN INSTALLATION SIESTA-3.2

[RAJAN SINGH]

Thank you once again.

Regards
Rajan Singh

On Sun, Sep 27, 2015 at 4:15 PM, Morteza Roshankar 
wrote:

> ​I wish this would help you​
>
> On Sun, Sep 27, 2015 at 2:00 PM, RAJAN SINGH 
> wrote:
>
>> Dear Siesta Users
>>
>> While doing the installation of siesta-3.2 (path level 5) version after
>> generation of "arch.make" file using command "../Src/configure" , when I am
>> typing "make" command it displays the following error:
>>
>> "make: *** No targets specified and no makefile found.  Stop."
>>
>> Can anyone help me resolving this issue.
>>
>> Thank You
>>
>> Regards
>> Rajan Singh
>>
>
>

[SIESTA-L] ISSUE IN INSTALLATION SIESTA-3.2

[RAJAN SINGH]

Dear Siesta Users

While doing the installation of siesta-3.2 (path level 5) version after
generation of "arch.make" file using command "../Src/configure" , when I am
typing "make" command it displays the following error:

"make: *** No targets specified and no makefile found.  Stop."

Can anyone help me resolving this issue.

Thank You

Regards
Rajan Singh


arch.make
Description: Binary data
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.

It was created by siesta configure 2.0, which was
generated by GNU Autoconf 2.59.  Invocation command line was

  $ ../Src/configure 

## - ##
## Platform. ##
## - ##

hostname = rajansingh
uname -m = x86_64
uname -r = 3.13.0-46-generic
uname -s = Linux
uname -v = #79-Ubuntu SMP Tue Mar 10 20:06:50 UTC 2015

/usr/bin/uname -p = unknown
/bin/uname -X = unknown

/bin/arch  = unknown
/usr/bin/arch -k   = unknown
/usr/convex/getsysinfo = unknown
hostinfo   = unknown
/bin/machine   = unknown
/usr/bin/oslevel   = unknown
/bin/universe  = unknown

PATH: /usr/local/sbin
PATH: /usr/local/bin
PATH: /usr/sbin
PATH: /usr/bin
PATH: /sbin
PATH: /bin
PATH: /usr/games
PATH: /usr/local/games


## --- ##
## Core tests. ##
## --- ##

configure:1348: checking build system type
configure:1366: result: x86_64-unknown-linux-gnu
configure:1374: checking host system type
configure:1388: result: x86_64-unknown-linux-gnu
configure:1466: checking for xlf95
configure:1495: result: no
configure:1466: checking for lf95
configure:1495: result: no
configure:1466: checking for f95
configure:1482: found /usr/bin/f95
configure:1492: result: f95
configure:1507: checking for Fortran compiler version
configure:1510: f95 --version &5
GNU Fortran (Ubuntu 4.8.4-2ubuntu1~14.04) 4.8.4
Copyright (C) 2013 Free Software Foundation, Inc.

GNU Fortran comes with NO WARRANTY, to the extent permitted by law.
You may redistribute copies of GNU Fortran
under the terms of the GNU General Public License.
For more information about these matters, see the file named COPYING

configure:1513: $? = 0
configure:1515: f95 -v &5
Using built-in specs.
COLLECT_GCC=f95
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/4.8/lto-wrapper
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 4.8.4-2ubuntu1~14.04' --with-bugurl=file:///usr/share/doc/gcc-4.8/README.Bugs --enable-languages=c,c++,java,go,d,fortran,objc,obj-c++ --prefix=/usr --program-suffix=-4.8 --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.8 --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --enable-gnu-unique-object --disable-libmudflap --enable-plugin --with-system-zlib --disable-browser-plugin --enable-java-awt=gtk --enable-gtk-cairo --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-4.8-amd64/jre --enable-java-home --with-jvm-root-dir=/usr/lib/jvm/java-1.5.0-gcj-4.8-amd64 --with-jvm-jar-dir=/usr/lib/jvm-exports/java-1.5.0-gcj-4.8-amd64 --with-arch-directory=amd64 --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --enable-objc-gc --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --with-tune=generic --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 4.8.4 (Ubuntu 4.8.4-2ubuntu1~14.04) 
configure:1518: $? = 0
configure:1520: f95 -V &5
f95: error: unrecognized command line option '-V'
f95: fatal error: no input files
compilation terminated.
configure:1523: $? = 4
configure:1537: checking for Fortran compiler default output file name
configure:1540: f95conftest.f  >&5
configure:1543: $? = 0
configure:1589: result: a.out
configure:1594: checking whether the Fortran compiler works
configure:1600: ./a.out
configure:1603: $? = 0
configure:1620: result: yes
configure:1627: checking whether we are cross compiling
configure:1629: result: no
configure:1632: checking for suffix of executables
configure:1634: f95 -o conftestconftest.f  >&5
configure:1637: $? = 0
configure:1662: result: 
configure:1668: checking for suffix of object files
configure:1679: f95 -c   conftest.f >&5
configure:1682: $? = 0
configure:1704: result: o
configure:1712: checking whether we are using the GNU Fortran compiler
configure:1726: f95 -c   conftest.F >&5
configure:1732: $? = 0
configure:1736: test -z 
			 || test ! -s conftest.err
configure:1739: $? = 0
configure:1742: test -s conftest.o
configure:1745: $? = 0
configure:1758: result: yes
configure:1764: checking whether f95 accepts -g
configure:1776: f95 -c -g  conftest.f >&5
configure:1782: $? = 0
configure:1786: test -z 
			 || test ! -s c

[SIESTA-L] I-V characteristics of Graphene nanoribbon in two probe configuration in SIESTA

[RAJAN SINGH]

Dear Siesta users

Is there any tutorial for obtaining I-V characteristics of Graphene
nanoribbon in two probe configuration? also tell me which version of siesta
is best for simulating the same.

Thank you

With Regards
Rajan Singh

Re: [SIESTA-L] How to extract the Hamiltonian and Overlap matrix from HSX file?

[RAJAN SINGH]

hi
If I want hamiltonian of a structure of different atoms arranged in space
with some kind of repetitive geometry then how should i proceed? Is there
any tutorial for such problem?
Thank You

Regards
Rajan

On Sun, Sep 20, 2015 at 12:32 PM, Nick Papior  wrote:

> In the trunk version you can check the file Src/m_hs_matrix.F90, while you
> can check the io routines that reads the HSX file on how to
> retrieve the sparse matrix in the HSX files.
>
> 2015-09-20 2:10 GMT+00:00 peter :
>
>> Hi,
>> I need to get the Hamiltonian and Overlap matrix from the HSX file. My
>> questions are divided into two parts:
>> 1. Is there any existing code that can extract the Hamiltonian and
>> Overlap matrix from HSX file? I guess that these matrices may be in sparse
>> format, but I indeed need these matrices in the full format.
>> 2. If there is no code written for this purpose, is there useful hints
>> helping me to write one?
>>
>> best,
>> Yun-Peng
>>
>
>
>
> --
> Kind regards Nick
>

[SIESTA-L] Graphene based study using Siesta

[RAJAN SINGH]

Dear Sir/Madam

I want to use Siesta for my research work. I want to use it for study the
Graphene and its interface with different materials. Can you suggest me
some tutorials regarding that. I also want to know what are the limitations
of using Siesta for Graphene interface study?

Please enlighten me with your comments.

Thank You.