Topics

91

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

92

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,)

93

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?

94

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

95

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!

96

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