Messages

151

General Questions and Answers / how should i write a script to specify the different initial_scaled_spin

« on: January 14, 2011, 13:34 »

how should i write a script to specify the different initial_scaled_spin for different atoms in differnt region (has some rules)
hi. i have wrote a script including below small code:
for index in range(len(scattering_elements)):
        if (scattering_elements[index]=="Carbon") :
                if (scattering_coordinates[index][2]> 17):
                      scattering_region_initial_scaled_spin[index]=1
                elif  (scattering_coordinates[index][2]< 13):
                       scattering_region_initial_scaled_spin[index]=1
        else:
           scattering_region_initial_scaled_spin[index]=0

this code is used to specify initial_scaled_spin for the atoms in scattering region(obey some rules see the if

language), but there is errror:
Traceback (most recent call last):
  File "two-my-own-scf-ALL-DZP.py", line 143, in ?
    scattering_region_initial_scaled_spin[index]=0
NameError: name 'scattering_region_initial_scaled_spin' is not defined
how should i revised my code, i have a look at the manual ATK(2008)Page 215, the script is similar to mine, but

still can not find a way to solve.
ps: i am a beginner in python.

152

General Questions and Answers / the SPIN-POLARIZED orientiation of GNR electrode

« on: January 14, 2011, 06:21 »

he SPIN-POLARIZED orientiation of GNR electrode

hi, recently, i have saw a paper appl.phys.lett.96.042104 (2010)
and in the artical, the spin orientation of the two GNR leads are set parallel and anti-parallel, only the two case.
my understanding is: left lead: top edge up,low edge up. right lead： top edge up,low edge up.
the anti-parallel is similar. am i right?
however as i know, aslo zh answered in Re: how can we set the value of " initial_scaled_spin", At least, you should consider two cases: i) the parallel spin configuration (i.e., ferromagnetic state) for the two edges of a graphene nanoribbon; ii) the anti-parallel spin configuration (anti-ferromagnetic state) the two edges of a graphene nanoribbon.   
therefore based upon zh answering, i think the spin orientation configure has much more.
for example left lead is top:up,low:up and right lead is top:up,low:down.
left lead is top:up,low:up and right lead is top:down,low:up.
left lead is top:up,low:down and right lead is top:up,low:down.
left lead is top:up,low:down and right lead is top:down,low:down
.........................
why the paper above only consider two of all configures?

153

General Questions and Answers / Re: small question about the ldos parameter:energy

« on: January 13, 2011, 13:29 »

yes, but the ldos are usually stored in vnl file, how i extract  the data information from vnl? or how i strore the data in other format (can read directly)
thanks  a a lot

154

General Questions and Answers / small question about the ldos parameter:energy

« on: January 13, 2011, 09:44 »

i have a small question about the ldos parameter :energy,i.e
 ldos = calculateLocalDensityOfStates(
lih2li_scf,
energy = 0.0*eV,
quantum_number = (0.0,0.0)
i have read the manual, and find we can only calculate the ldos at one energy everytime
now, i want to calculate a energy region such as -0.1ev~0.1ev in siesta program(below) and get a total ldos by summarizing the ldos at every energy point at the energy region. is it possible in atk? 3x!!

%block LocalDensityOfStates
-0.1  0.1 eV
%endblock LocalDensityOfStates

155

General Questions and Answers / four question about mpsh calculation

« on: January 7, 2011, 15:03 »

hi : every one
i have some question about mpsh calculation:
1) if i have many projection_atoms in calculateProjectedHamiltonianEigenstates funtion, beside i wrote one by one such as below, can i write a loop in python language, how to write in script?
2) i have searched the forum, and found MPSH is only suitable molecular in scattering region , not for the nanowire in scattering region? is it true? and why?
3) the mpsh analysis is better for the molecular only  (Zh answer), but others says if the molecular interact with sufacelayer atoms strongly , it should include some surfacelayer atoms.  so i am confusing.
4) i have two quantum _numbers to concern. one is the first one below zero energy. and another is the first one above the zero. (i think, they are related the transport in Ef (no bias condition)? but when i watch the 3D plot of the  mpsh, i thought, it should have two Eigenstates( the two i set above), but i only saw one  Eigenstates. why ?
   
maybe my question is foolish. i would like some idear to clarify.

calculateProjectedHamiltonianEigenstates(
    self_consistent_calculation = scf,
    projection_atoms = (72, 73, 74, 75……), 
    quantum_numbers = (547,548,549,550,551,552,553,554,)

156

General Questions and Answers / Re: how to view the LDOS in VNL clearly

« on: January 5, 2011, 11:10 »

we can see the periodic image of ldos in the picture, the ldos is repeated in x direction . so if i see along x direction, the repeated ldos prevents me seeing clearly the atom slab in yz plane as well as ldos.
my question is is there anty way to  locate  the ldos only in the yz plane where the atoms exsit. not like the first fig, the ldos is spilted by two part because of the periodic condition. as i know, in other softeware, we can determine the position of ldos plotting.   

157

General Questions and Answers / how to view the LDOS in VNL clearly

« on: January 5, 2011, 06:17 »

hi ,everyone here
i want to have a look at the LDOS in VNL, but the picture has some problem. my structure is a slab and in  yz plane, there the ldos was plot like that (see my attached),the ldos was plot in cell, therefore, for a atom in yz plane, its ldos is slit two part, one is around yz plane,another is in the other side of the unit cell(the period condition in x direction). so it is not convenient for me to see.  i repeat the ldos in x direction( see also my attached ), i can get a full ldos around yz plane, but if i see perpendicular to the yz( i think it is the best angle) ,the image of ldos does exit, so would you tell me how to solve this problem?

158

General Questions and Answers / the restart script in ATK manual does not work

« on: December 27, 2010, 08:57 »

hi: everyone :
i am testing the restart script written in ATK mamual(2008,10,page 451,  it does not work(the script is wrong?)
 so i want to know the proper script for me to restart a relax job from a *.nc file. is the nc file the only needed file for restart? is the initial  structure information file VNL needed(i.e. 'atomic_configuration')?

the script is :

# Import the KohnSham module from ATK
from ATK.KohnSham import *
# Read self consistent calculation from NetCDF file
scf = restoreSelfConsistentCalculation('h2.nc')
# Set the force tolerance
opt = geometricOptimizationParameters(
force_tolerance=0.00001*electronVolt/Angstrom
)
# Set name of check point file
params = runtimeParameters(
verbosity_level=10
)
# Calculate the optimized atomic geometry
h2_opt = calculateOptimizedAtomicGeometry(
self_consistent_calculation=scf,
optimization_parameters=opt,
runtime_parameters=params
)
# Print the coordinates of the individual atoms
print '\nAtom coordinates\n---------------------------'
for coord in h2_opt.cartesianCoordinates():
 for c in coord:
  print '%7.4f' % (c.inUnitsOf(Angstrom)),




the out is :
raceback (most recent call last):
  File "relax-continue.py", line 17, in ?
    runtime_parameters=params
NLArgumentNameError: When the parameters, ['runtime_parameters'], are specified, the parameters, ['atomic_configuration', 'method', 'runtime_parameters'], must also be specified

159

General Questions and Answers / energyContourIntegralParameters

« on: December 16, 2010, 13:04 »

when i calculated the the transmission spectra,.
I used SZP basis for H and C, the results consist well with the results published in a paper(also ATK calculation)
later, i used DZP for C and SZP for H, it does not convergence at all.
i have tuned parameters such as mixing parameters, but they does not  work.
until i tuned below papameter, it works (according to the ATK forum hints)
 energy_contour_integral_parameters =energyContourIntegralParameters(
    circle_points = 50,
    integral_lower_bound = 4*Rydberg,however, the transmission spectra has rather differences with the SZP calculation as well as the publised work.

So, would you please tell me have you faced the similar question?  why different integral_lower_bound inflence the result so much.
if yes, would you give me some hints? Anyway, i feel the scf convergence is a tricky work.
 
THANKS ALOT!

160

General Questions and Answers / Re: ATKError: Exceeded maximum number of self-consistent iterations.

« on: November 17, 2010, 12:35 »

thank you very much .
i will read it

161

General Questions and Answers / Re: ATKError: Exceeded maximum number of self-consistent iterations.

« on: November 11, 2010, 09:18 »

my scprit is *.vnl in attachment, you can access my structure. and
scf script as well as the reference is J. AM. CHEM. SOC. 2010, 132, 11481–11486. in their paper, they said:
We focus only on the charge transport property in this work
since the spin-polarized calculation produces similar results for
the oscillatory conductance.

162

General Questions and Answers / Re: ATKError: Exceeded maximum number of self-consistent iterations.

« on: November 10, 2010, 05:44 »

Your atoms are outside the unit cell, that's never a good idea.

i have move the atoms in the unit cell. but still it can not convengence.

it seems a serious probblem from the DRHO, it has no trend to reduce at all.

where is?......., i just want to reproduce others work, they mentiond they took a non-spin-polarized calculation. so, i think it is not the spin issues.

163

General Questions and Answers / ATKError: Exceeded maximum number of self-consistent iterations.

« on: November 9, 2010, 05:33 »

I want to calculate the transport spetrum of graphene nanoribbon--c-atom--graphene nanoribbon, but the scf does not convergence.
i have searched the forum, and found some hints, but i am not sure where is my problem. so i wish someone could help me. 3x!

 # TwoProbe Calculation
# ----------------------------------------------------------------
........

# sc 481 : q =  252.11354 e  dRho =  1.0295E+02
# sc 482 : q =  254.01931 e  dRho =  9.4704E+02
# sc 483 : q =  250.41971 e  dRho =  1.0058E+03
# sc 484 : q =  252.76199 e  dRho =  6.1260E+02
# sc 485 : q =  255.75515 e  dRho =  5.3518E+02
# sc 486 : q =  251.57264 e  dRho =  2.4662E+02
# sc 487 : q =  251.12636 e  dRho =  4.2365E+02
# sc 488 : q =  252.31944 e  dRho =  4.2701E+02
# sc 489 : q =  251.69348 e  dRho =  9.0235E+01
# sc 490 : q =  252.34374 e  dRho =  6.3624E+01
# sc 491 : q =  253.15964 e  dRho =  2.9300E+02
# sc 492 : q =  250.92071 e  dRho =  2.0976E+02
# sc 493 : q =  255.20466 e  dRho =  3.3770E+02
# sc 494 : q =  252.40583 e  dRho =  3.7540E+02
# sc 495 : q =  251.49326 e  dRho =  6.8605E+02
# sc 496 : q =  249.82777 e  dRho =  6.8713E+02
# sc 497 : q =  252.42359 e  dRho =  2.2527E+02
# sc 498 : q =  249.17996 e  dRho =  3.0114E+02
# sc 499 : q =  250.88531 e  dRho =  2.9827E+02
# sc 500 : q =  251.38814 e  dRho =  1.8827E+02
Traceback (most recent call last):
  File "<string>", line 27, in ?
ATKError: Exceeded maximum number of self-consistent iterations.
Traceback (most recent call last):
  File "<string>", line 27, in ?
ATKError: Exceeded maximum number of self-consistent iterations.
Traceback (most recent call last):
  File "<string>", line 27, in ?Traceback (most recent call last):
  File "<string>", line 27, in ?
ATKError: Exceeded maximum number of self-consistent iterations.
Traceback (most recent call last):
  File "<string>", line 27, in ?
ATKError: Exceeded maximum number of self-consistent iterations.
Traceback (most recent call last):
  File "<string>", line 27, in ?
ATKError: Exceeded maximum number of self-consistent iterations.
Traceback (most recent call last):
  File "<string>", line 27, in ?
ATKError: Exceeded maximum number of self-consistent iterations.
Traceback (most recent call last):
  File "<string>", line 27, in ?
ATKError: Exceeded maximum number of self-consistent iterations.
Traceback (most recent call last):
  File "<string>", line 27, in ?
ATKError: Exceeded maximum number of self-consistent iterations.
                                            

ATKError: Exceeded maximum number of self-consistent iterations.

my input file :
from ATK.TwoProbe import *
# Read the atomic configuration from a VNL file
vnl_file = VNLFile("GNR-three-C-GNR-opt.vnl")
configurations = vnl_file.readAtomicConfigurations()
two_probe_conf = configurations["GNR-three-C-GNR-opt"]
# Setting the electrode parameters
bz_int_param = brillouinZoneIntegrationParameters( (1,1,100) )
electrode_parameters = ElectrodeParameters(
brillouin_zone_integration_parameters= bz_int_param
)
# Creating the TwoProbeMethod
ele_den_para = electronDensityParameters(mesh_cutoff=150*Units.Ry)
twoprobe_method = TwoProbeMethod(
(electrode_parameters,electrode_parameters),
electron_density_parameters=ele_den_para,
basis_set_parameters=basisSetParameters(
type=DoubleZetaDoublePolarized),
iteration_control_parameters = iterationControlParameters(
tolerance = 1e-4,
max_steps=500)
)
# Execute the Self Consistent Field
scf = executeSelfConsistentCalculation(
two_probe_conf,
twoprobe_method,
runtime_parameters=runtimeParameters(verbosity_level=1,
checkpoint_filename='GNR-three-C-GNR-opt.nc'))
 and GNR-three-C-GNR-opt.vnl is in attatachment