Re: [SIESTA-L] Transition bands

[Marty Blaber]

Hi Dahbia,
  This information doesn't get written out (because generally there is a lot
of it).
To make SIESTA write it out, you will have to edit optical.F. The relevant
code is between lines ~590 through to ~640. The bands are numbered ie =
initial band, je = final band. The energy of the transition is stored in
ediff, and the transition probability is T.

Hope this helps,

Regards,
Marty



2009/1/13 Dahbia Ammi 

> Dear SIESTA users,
>
> Is there someone who can tell me how to find the transition bands? For
> example: if I find absorption peak corresponding to a transition from band s
> to band p. In what file, I can find that the transition corresponding to
> these bands?
>
>
> Thanks before
>
>
>
>
>
>

Re: [SIESTA-L] Optical theory

[Marty Blaber]

Hi Julie,

For solids:
There is a paper by Ambrosch-Draxl on calculating the optical
properties of solids (In the FP-LAPW basis). The third and fourth
pages are relevant though:
C. Ambrosh-Draxl, J O. Sofo, "Linear optical properties of solids
within the..." Comp. Phys. Comm. 175 (2006) pg 1-16
There is also a correction that needs to be included to the matrix
elements when calculating the transitions in momentum space because
siesta uses non-local pseudopotentials. The ref for that is:  Read A J
and Needs R J 1991 Phys. Rev. B 44 13071
For a good review of optical calculations in general see:
1.  Onida, G., L. Reining, and A. Rubio, Electronic excitations:
density-functional versus many-body Green's-function approaches.
Reviews of Modern Physics, 2002. 74(2): p. 601-659.


Cheers,
Marty


2008/12/12 Julie Smart :
> Hello all,
>
> Is it possible to introduce a more detailed refrence for the optical
> calculations in ""Siesta""? Pls do not address me to known "solid states"
> books. I want to know what approaches "siesta" uses.
>
> Regards,
> Julie Smart
>
> Caltech University
> www.caltech.edu
>
>
>
>

Re: [SIESTA-L] correct optical calculation

[Marty Blaber]

Hi Julie,

The reason for the wiggles is generally because the integration mesh isn't
fine enough for the broadening you have used. Lower broadening requires
finer mesh. Having said that, if the experimental data looks similar with
the calculation at 0.2 eV, you shouldn't have to go much below that. (Maybe
try 0.1 eV and an optical mesh of 50? just to check)
No need to increase the 1, should be fine as you have no periodicity in this
direction.
Your definition of scissor operator is correct! (Sorry, I should have been
more concise)

Cheers,
Marty


2008/12/8 Julie Smart <[EMAIL PROTECTED]>

> Dear Marty,
>
> Happy to receive your guide. I have put broadening of 0.2 eV, since when I
> consider smaller amounts, the imaginary part of dielectric function goes to
> have alot of ups and downs which changes the results I expect. Should I
> again try to cgange it to smaller amounts?
>
> Also, for 2D structure I have:
>
> %block kgrid_Monkhorst_Pack
>  8   0   0   0.00
>   0  8   0   0.00
>   0   0  1   0.00
> %endblock kgrid_Monkhorst_Pack
>
> So, I have chosen the mesh as:
>
> %block Optical.Mesh
>40 40 1
> %endblock Optical.Mesh
>
> should I still change "1" to higher amounts?
>
> Also, for the Scissor, as far as I got you we will have "optical scissor =
> experimental bandgap - calculated bandgap" ?
>
> Wait for your kind advice.
>
> Best wishes
> Julie Smart
>
> Caltech University
> www.*caltech*.edu <http://www.caltech.edu/>
>
>
>
>
>
>
> --
> *From:* Marty Blaber <[EMAIL PROTECTED]>
> *To:* SIESTA-L@listserv.uam.es
> *Sent:* Monday, December 8, 2008 4:07:18 AM
> *Subject:* Re: [SIESTA-L] correct optical calculation
>
> Hi Julie,
>
> The scissor operator moves all the eigenvalues above the fermi energy
> (chemical potential) up by the value you specify, this is to compensate for
> the underestimation of the band gap. Usually you just choose it so that
> you're band gap matches experiment.
> The Broadening parameter specifies the size of the gaussian convolved with
> the transitions, and as such also defines the number of points that appear
> in the .EPSIMG file.
> As a rule of thumb you should try to keep the broadening reasonably low.
> You can always broaden the data further, but you can't deconvolve the
> gaussian out of the data (because of the correlation between gaussian width
> and number of points).
> I generally use a broadening of 0.02 eV.
> Don't forget that if you're dealing with metals, the plasma frequency
> converges slower than the transitions, so you should use large optical mesh.
> Your optical.Mesh should be the same style as you're monkhorst pack grid,
> but much higher density.
> To get accurate optical calculations, on gold for example, you should use a
> monkhorst pack grid of about 21, but you may have to go as high as 29 if
> you're unit cell is small.
> %block kgrid_Monkhorst_Pack
>   21   0   0   0.00
>0  21   0   0.00
>0   0  21   0.00
> %endblock kgrid_Monkhorst_Pack
>
> And then use a mesh like this:
>
> %block Optical.Mesh
>65 65 65
> %endblock Optical.Mesh
>
> Note that you should test the convergence of these parameters. Also, the
> finer that your broadening is, the more points you need in optical kspace to
> get smooth data.
>
> The real part is more difficult, if you're using metals, you will have to
> guess the relaxation time. And you must check the convergence of the plasma
> frequency with increasing optical mesh.
>
> Cheers,
> MArty
>
>
>
> 2008/12/7 Julie Smart <[EMAIL PROTECTED]>
>
>> Hi all,
>>
>> I have read all mailing archive of Siesta and also all the tutorials and
>> the power points about optical properties. Still I have problem with
>> Optical.Broaden and Optical.Scissor, seems that I have no good idea what
>> they do although forexample I know what gaussian broadening is. To cut it
>> short, I want to know usually what ranges of these two parameters ore
>> suitable for bulk, 1D and 2D structures. Also, when I can get the best shape
>> of imaginary and real part of dielectric function.
>>
>> It would be an honor to receive your advice.
>> Best wishes
>> Julie Smart
>>
>> Caltech University
>> www.*caltech*.edu <http://www.caltech.edu>
>>
>>
>>
>>
>
>

Re: [SIESTA-L] [SUSPECTED-SPAM] Re: [SIESTA-L] ./optical

[Marty Blaber]

Hi Catrina,

The problem with your data file is that it has too many points. (The default
limit is 10 000 points)

I've edited the optical.f file to allow for 25000 points.
you can compile it using
gfortran -O4 optical.f -o optical
the O4 makes the calculation much faster.

The program should have stopped with an error saying "Too many points" but
this doesn't always work

I'll email the result to you personally because I don't think the list
accepts attachments that are very big.

Cheers,
Marty


2008/12/8 catrina desport <[EMAIL PROTECTED]>

> Hello Marty,
>
> Thank you for helping me.
>
> I didn't find Nan's in e2.file, you can see it in the enclosed. I would be
> thankful to see what is going wrong.
>
> Regards,
> Catrina
>
> --
> **
>
>


optical.tar.gz
Description: GNU Zip compressed data

Re: [SIESTA-L] [SUSPECTED-SPAM] Re: [SIESTA-L] ./optical

[Marty Blaber]

Hi Catrina,
 Do you have any strange numbers in e2.dat are there any NaN's or anything?
These should give you an error, but may cause seg fault.
Worst case scenario, could you post the e2.dat here.

Cheers,
Marty


2008/12/7 catrina desport <[EMAIL PROTECTED]>

> Hello,
>
> can you run the regular "siesta" (compiled with gfortran) ?
>
>  yes I can. I also do not receive segfaults while I compile other .f files
> in utility, this has occured only for "optical" what should I change in it
> to get the run?
>
> Regards,
> Catrina
>
> --
> *From:* Sushil Auluck <[EMAIL PROTECTED]>
> *To:* SIESTA-L@listserv.uam.es
> *Sent:* Sunday, December 7, 2008 12:50:24 PM
> *Subject:* Re: [SIESTA-L] [SUSPECTED-SPAM] Re: [SIESTA-L] ./optical
> 
> hi,
> can you run the regular "siesta" (compiled with gfortran) ?
> do you still get segfaults..if yes then your compilation may
> not be correct.
> s.auluck
>
> -- ...
> Prof. Sushil Auluck  Phone:+91-512-6797092/6148
> Department of Physics  +91-512-6798177(Home)
>
> Indian Institute of Technology  Cell :+91-9305548667  Kanpur 208016
> (UP)  Fax  :+91-512-6790914India
> E-mail:[EMAIL PROTECTED]
> FB 480 or 378  [EMAIL PROTECTED]
> http://www.iitk.ac.in/phy/People/phy_facvis.html
> http://www.iitk.ac.in/phy/New01/profile_SA.html
> ...
>
>

Re: [SIESTA-L] correct optical calculation

[Marty Blaber]

Hi Julie,

The scissor operator moves all the eigenvalues above the fermi energy
(chemical potential) up by the value you specify, this is to compensate for
the underestimation of the band gap. Usually you just choose it so that
you're band gap matches experiment.
The Broadening parameter specifies the size of the gaussian convolved with
the transitions, and as such also defines the number of points that appear
in the .EPSIMG file.
As a rule of thumb you should try to keep the broadening reasonably low. You
can always broaden the data further, but you can't deconvolve the gaussian
out of the data (because of the correlation between gaussian width and
number of points).
I generally use a broadening of 0.02 eV.
Don't forget that if you're dealing with metals, the plasma frequency
converges slower than the transitions, so you should use large optical mesh.
Your optical.Mesh should be the same style as you're monkhorst pack grid,
but much higher density.
To get accurate optical calculations, on gold for example, you should use a
monkhorst pack grid of about 21, but you may have to go as high as 29 if
you're unit cell is small.
%block kgrid_Monkhorst_Pack
  21   0   0   0.00
   0  21   0   0.00
   0   0  21   0.00
%endblock kgrid_Monkhorst_Pack

And then use a mesh like this:

%block Optical.Mesh
   65 65 65
%endblock Optical.Mesh

Note that you should test the convergence of these parameters. Also, the
finer that your broadening is, the more points you need in optical kspace to
get smooth data.

The real part is more difficult, if you're using metals, you will have to
guess the relaxation time. And you must check the convergence of the plasma
frequency with increasing optical mesh.

Cheers,
MArty



2008/12/7 Julie Smart <[EMAIL PROTECTED]>

> Hi all,
>
> I have read all mailing archive of Siesta and also all the tutorials and
> the power points about optical properties. Still I have problem with
> Optical.Broaden and Optical.Scissor, seems that I have no good idea what
> they do although forexample I know what gaussian broadening is. To cut it
> short, I want to know usually what ranges of these two parameters ore
> suitable for bulk, 1D and 2D structures. Also, when I can get the best shape
> of imaginary and real part of dielectric function.
>
> It would be an honor to receive your advice.
> Best wishes
> Julie Smart
>
> Caltech University
> www.*caltech*.edu
>
>
>
>

Re: [SIESTA-L] ./optical

[Marty Blaber]

Hi Catrina,

Once you have run input:
./*input* < SysLabel.EPSIMG

you need only run *optical* without the redirect arrow:
./*optical*

This will automatically read the e2.dat file and provide you with the real
permittivity and other such things.

If you're performing a calculation on metals and you want to add the
intraband component of the dielectric function, you can use the following to
convert from relaxation time (in seconds ) into hartree's

H=6.626068E-34;
Elec=1.60217646E-19;
PI=3.14159265;
eV=((1/$1)*H)/(2*PI*Elec);
Har=eV/27.2113845;


Cheers,
Marty


2008/12/7 catrina desport <[EMAIL PROTECTED]>

> To all respected siesta users,
>
> I have compiled siesta with gfortran. After compiling optical from
> "utility" when I write ./optical 
> What's the reason for that.
>
> Quick responce is really needed.
>
> Regards,
> Catrina
>
>

Re: [SIESTA-L] Problem with optical calculation

[Marty Blaber]

Dear Arun,

Try including the ampersand & when redirecting your output:
siesta & outputfile
Although this is probably not very helpful; try running the calculation with
a copy of siesta that does not include MPI at all.

Cheers,
Marty



2008/10/21 Arun Kumar Manna <[EMAIL PROTECTED]>

>
>  Dear Marty,
>  Yes, I am using MPI.
>  And I am using the command for redirecting my output file as follows:
>  siesta  outputfile
>  Regards,
>  Arun
>
>
>  Arun,
> >
> > Two questions, 1. Are you using MPI? and 2. Are you running the code with
> > stderr redirected to your output file? i.e:
> > siesta & logfile
> >
> > Regards,
> > Marty
> >
> >
> > 2008/10/21 Arun Kumar Manna <[EMAIL PROTECTED]>
> >
> >>  Dear All,
> >>  I am facing problem with Optical Conductivity calculation using
> >>  siesta2.0 package. After scf calculation, the programme suddenly stops.
> >>  And also, I am not getting any error message. My input file structure
> >> is
> >>  as follows:
> >>
> >>  opticalcalculation .true.
> >>  optical.Broaden 0.05 eV
> >>  optical.EnergyMinimum   0eV
> >>  Optical.EnergyMaximum   150eV
> >>  optical.polarizationtypeunpolarized
> >>  %block optical.vector
> >>  0.000  1.000  0.000
> >>  %endblock optical.vector
> >>
> >>  And programme stops by writing the following last few lines in output
> >> file:
> >>  siesta: Stress tensor (static) (eV/Ang**3):
> >>  siesta:-0.0045910.001509   -0.003361
> >>  siesta: 0.001509   -0.004573   -0.003421
> >>  siesta:-0.003361   -0.003421   -0.007421
> >>
> >>  siesta: Cell volume =   3742.787580 Ang**3
> >>
> >>  siesta: Pressure (static):
> >>  siesta:SolidMolecule  Units
> >>  siesta:   0.6021 -0.0053  Ry/Bohr**3
> >>  siesta:   0.00552868 -0.4848  eV/Ang**3
> >>  siesta:   8.85801365 -0.07766841  kBar
> >>
> >>  siesta: Total spin polarization (Qup-Qdown) =0.008491
> >>
> >>  siesta: Electric dipole (a.u.)  =   -2.8620470.002.393311
> >>  siesta: Electric dipole (Debye) =   -7.2746020.006.083193
> >>
> >>  Could anybody please help me by having a look at my input/output file?
> >>
> >>  Thanks
> >>  Arun
> >>
> >>
> >>
> >>
> >> --
> >> PhD Student
> >> JNCASR, Bangalore-560064
> >> India
> >>
> >
>
>
> --
> PhD Student
> JNCASR, Bangalore-560064
> India
>

Re: [SIESTA-L] Problem with optical calculation

[Marty Blaber]

Arun,

Two questions, 1. Are you using MPI? and 2. Are you running the code with
stderr redirected to your output file? i.e:
siesta & logfile

Regards,
Marty


2008/10/21 Arun Kumar Manna <[EMAIL PROTECTED]>

>  Dear All,
>  I am facing problem with Optical Conductivity calculation using
>  siesta2.0 package. After scf calculation, the programme suddenly stops.
>  And also, I am not getting any error message. My input file structure is
>  as follows:
>
>  opticalcalculation .true.
>  optical.Broaden 0.05 eV
>  optical.EnergyMinimum   0eV
>  Optical.EnergyMaximum   150eV
>  optical.polarizationtypeunpolarized
>  %block optical.vector
>  0.000  1.000  0.000
>  %endblock optical.vector
>
>  And programme stops by writing the following last few lines in output
> file:
>  siesta: Stress tensor (static) (eV/Ang**3):
>  siesta:-0.0045910.001509   -0.003361
>  siesta: 0.001509   -0.004573   -0.003421
>  siesta:-0.003361   -0.003421   -0.007421
>
>  siesta: Cell volume =   3742.787580 Ang**3
>
>  siesta: Pressure (static):
>  siesta:SolidMolecule  Units
>  siesta:   0.6021 -0.0053  Ry/Bohr**3
>  siesta:   0.00552868 -0.4848  eV/Ang**3
>  siesta:   8.85801365 -0.07766841  kBar
>
>  siesta: Total spin polarization (Qup-Qdown) =0.008491
>
>  siesta: Electric dipole (a.u.)  =   -2.8620470.002.393311
>  siesta: Electric dipole (Debye) =   -7.2746020.006.083193
>
>  Could anybody please help me by having a look at my input/output file?
>
>  Thanks
>  Arun
>
>
>
>
> --
> PhD Student
> JNCASR, Bangalore-560064
> India
>

Re: [SIESTA-L] Posible SPAM: how to introduce space group in phonon calculation

[Marty Blaber]

Hi Vikas,
Judging by Marcel's comments, I may have misunderstood you. Sorry.

Cheers,
Marty

On Wed, Jun 11, 2008 at 2:57 PM, vikas sharma <[EMAIL PROTECTED]>
wrote:

>
>
> Dear all,
>
> I want to perform the phonon calculation in a crystal. But I could not
> understand where and how to introduce the irreducible symmetry in the input
> fdf file.
>
> Kindly help.
>
> Vikas Sharma,
> Research Scholar,
> Physics Department,
> IIT Delhi, New Delhi-16, India.
>
> --
> From Chandigarh to Chennai - find friends all over India. Click 
> here.

Re: [SIESTA-L] Posible SPAM: how to introduce space group in phonon calculation

[Marty Blaber]

Hi Vikas,
Judging by Marcel's comments, I may have misunderstood you. Sorry.

Cheers,
Marty

On Thu, Jun 12, 2008 at 9:02 AM, Marty Blaber <[EMAIL PROTECTED]> wrote:

> Hi Vikas,
>
> Siesta does not support symmetry.
> You can use the CCMS crystal website to find the crystal you want:
> http://cst-www.nrl.navy.mil/lattice/index.html
> And then use the primitive vectors to build your cell:
> %block LatticeVectors
>  ax ay az
>  bx by bz
>  cx cy cz
> %endblock LatticeVectors
> And then use the Basis Vectors to describe the atomic positions:
> AtomicCoordinatesFormat Fractional
> NumberOfAtoms4
> %block AtomicCoordinatesAndAtomicSpecies
>   0.00  0.00  0.00  3
>  -0.50  0.50  0.50  1
>  -0.25 -0.25 -0.25  2
>   0.25  0.25  0.25  2
> %endblock AtomicCoordinatesAndAtomicSpecies
>
> Hope it works out for you.
>
> Cheers,
> Marty
>
>
>
>
> On Wed, Jun 11, 2008 at 2:57 PM, vikas sharma <[EMAIL PROTECTED]>
> wrote:
>
>>
>>
>> Dear all,
>>
>> I want to perform the phonon calculation in a crystal. But I could not
>> understand where and how to introduce the irreducible symmetry in the input
>> fdf file.
>>
>> Kindly help.
>>
>> Vikas Sharma,
>> Research Scholar,
>> Physics Department,
>> IIT Delhi, New Delhi-16, India.
>>
>> --
>> From Chandigarh to Chennai - find friends all over India. Click 
>> here.<http://in.rd.yahoo.com/tagline_groups_10/*http://in.promos.yahoo..com/groups/citygroups/>
>
>
>

Re: [SIESTA-L] Posible SPAM: how to introduce space group in phonon calculation

[Marty Blaber]

Hi Vikas,

Siesta does not support symmetry.
You can use the CCMS crystal website to find the crystal you want:
http://cst-www.nrl.navy.mil/lattice/index.html
And then use the primitive vectors to build your cell:
%block LatticeVectors
 ax ay az
 bx by bz
 cx cy cz
%endblock LatticeVectors
And then use the Basis Vectors to describe the atomic positions:
AtomicCoordinatesFormat Fractional
NumberOfAtoms4
%block AtomicCoordinatesAndAtomicSpecies
  0.00  0.00  0.00  3
 -0.50  0.50  0.50  1
 -0.25 -0.25 -0.25  2
  0.25  0.25  0.25  2
%endblock AtomicCoordinatesAndAtomicSpecies

Hope it works out for you.

Cheers,
Marty



On Wed, Jun 11, 2008 at 2:57 PM, vikas sharma <[EMAIL PROTECTED]>
wrote:

>
>
> Dear all,
>
> I want to perform the phonon calculation in a crystal. But I could not
> understand where and how to introduce the irreducible symmetry in the input
> fdf file.
>
> Kindly help.
>
> Vikas Sharma,
> Research Scholar,
> Physics Department,
> IIT Delhi, New Delhi-16, India.
>
> --
> From Chandigarh to Chennai - find friends all over India. Click 
> here.

Re: [SIESTA-L] Calculation of Si bulk properties

[Marty Blaber]

Hi Sophia,

I am by no means an expert, but I would try increasing the Mesh Cutoff. I
usually use 300 Ry, but your system is quite large. Try 150 Ry and see what
happens.

Cheers,
Marty




On Tue, Apr 1, 2008 at 9:19 AM, Sophia Nishad <[EMAIL PROTECTED]>
wrote:

> Thanks a lot for outstanding support and help from the group.
>
>
> On Sun, Mar 30, 2008 at 10:22 PM, Sophia Nishad <[EMAIL PROTECTED]>
> wrote:
>
> > Hi,
> >
> > I am a new user of SIESTA. I have been trying to reproduce the results
> > for Si as mention in Soler et. al 2002 paper, before I go for my actual
> > calculations.
> >
> > I have used the DZP Basis mentioned at
> > http://www.uam.es/departamentos/ciencias/fismateriac/siesta/
> > Pseudopotential at
> > http://www.uam.es/departamentos/ciencias/fismateriac/siesta/
> >
> > My calculation for 64-atoms:
> > 1) Lattice Constant: I changed the lattice parameter and find the energy
> > and plotting that I find 5.45 Ang, instead of 5.40 as reported in the
> > paper. Why this so different?
> >
> > 2) Bulk modulus: With B = V*Curvature = V*2c3 = 15 MPa, which is far
> > less than 98.6 MPa? Why? Here, c3 is defined as E =C1 + c2*V + c3*V^2,
> > curve fit to the E vs V curve.
> >
> > 3) Cohesive Energy: I find energy per atom 107.759eV in the bulk. Now to
> > calculate energy per atom I tried to use the suggestions given at
> > http://www.mail-archive.com/siesta-l@listserv.uam.es/msg03118.html
> > I get -7.49eV/atom as pseudopotential calculation, and -576.38eV/atom as
> > ae. So, which one is the energy of the free atom. None is a good one for
> > comparing with the energy I got from bulk to find the cohesive energy.
> >
> > I really tried to search the archive and find solutions to these. I
> > could not find any explicit answers. I am not sure what I am missing. *Some
> > expert's simple directions can solve the problem right away*. I really
> > need this help.
> >
> >
> > Thanks in advance,
> > Sophia
> > Univ. of California - Berkeley
> >
> > Attached fdf file
> >
> > 
> >
> > #
> > -
> > # FDF for a cubic c-Si supercell with 64 atoms
> > #
> > # E. Artacho, April 1999
> > #
> > -
> >
> > SystemName  64-atom Si
> > SystemLabel Si
> >
> > NumberOfAtoms   64
> > NumberOfSpecies 1
> >
> > %block ChemicalSpeciesLabel
> >  1  14  Si
> > %endblock ChemicalSpeciesLabel
> >
> > PAO.BasisSize   DZP
> > PAO.EnergyShift 20 meV
> >
> > %Block PAO.Basis
> > Si   3 -0.46385
> >  n=3   0   2   E15.42551 4.96988
> >  7.0 4.37722
> >  1.0 1.0
> >  n=3   1   2   E 4.69636 3.83128
> >  7.0 4.09123
> >  1.0 1.0
> >  n=3   2   1   E11.96912 0.03131
> >  4.55426
> >  1.0
> > %EndBlock PAO.Basis
> >
> >
> > LatticeConstant 5.430 Ang
> > %block LatticeVectors
> >   2.000  0.000  0.000
> >   0.000  2.000  0.000
> >   0.000  0.000  2.000
> > %endblock LatticeVectors
> >
> > %block kgrid_Monkhorst_Pack
> > 2  0  0 0.0
> > 0  2  0 0.0
> > 0  0  2 0.0
> > %endblock kgrid_Monkhorst_Pack
> >
> >
> > MeshCutoff  40.0 Ry
> >
> > MaxSCFIterations 100
> > DM.MixingWeight  0.3
> > DM.NumberPulay   3
> > DM.Tolerance 1.d-3
> > DM.UseSaveDM
> > XC.functional   LDA
> > XC.authors  CA
> >
> >
> > SolutionMethod   diagon
> > ElectronicTemperature  25 meV
> >
> > WriteForces   true
> > WriteCoorStep true
> >
> > MD.TypeOfRun cg
> > MD.NumCGsteps 0
> > MD.MaxCGDispl 0.1  Ang
> > MD.MaxForceTol0.01 eV/Ang  # earler 0.04
> > SaveRho   true
> >
> > AtomicCoordinatesFormat  ScaledCartesian
> > %block AtomicCoordinatesAndAtomicSpecies
> >0.0   0.0   0.0 1
> >0.0   0.5   0.5 1
> >0.25000   0.25000   0.75000 1
> >0.25000   0.75000   0.25000 1
> >0.5   0.0   0.5 1
> >0.5   0.5   0.0 1
> >0.75000   0.25000   0.25000 1
> >0.75000   0.75000   0.75000 1
> >0.0   0.0   1.0 1
> >0.0   0.5   1.5 1
> >0.25000   0.25000   1.75000 1
> >0.25000   0.75000   1.25000 1
> >0.5   0.0   1.5 1
> >0.5   0.5   1.0 1
> >0.75000   0.25000   1.25000 1
> >0.75000   0.75000   1.75000 1
> >0.0   1.0   0.0 1
> >0.0   1.5   0.5 1
> >0.25000   1.25000   0.75000 1
> >0.25000   1.75000   0.25000 1
> >0.5   1.0   0.50