Author Topic: molecular device configration (Read 4179 times)

Maneesh · « **on:** August 20, 2013, 11:20 »

Dear sir,

good noon

when I tried to reproduce the result in the tutorial given on net for the DTB device
I have reproduce the result up to transmission spectrum and densisty of states ,PDDOS,MPSH

but the problem arises when I try to calculate the I-V curve of the device by using the script given in the tutorials
the calculation failed and I am unable to get the I-V curve , I have tried many times.

please guide

thanks

maneesh

Anders Blom · « **Reply #1 on:** August 20, 2013, 14:33 »

More details needed. Error messages?

Maneesh · « **Reply #2 on:** August 24, 2013, 09:48 »

Respected sir,

For DTB device as I have mentioned my previous mail when I try to run the following script (script attached)
and shows the status failed and produce the no output. i.e I-V characteristics . I am struggling with this problem
from last many days. I have seen the form where some other users encounied exactly the same problem and they filed to produce the result .
kindly sort out the problem and help me in reproducing the result .

thank you

maneesh

# -------------------------------------------------------------
# TwoProbe configuration
# -------------------------------------------------------------

# -------------------------------------------------------------
# Left electrode
# -------------------------------------------------------------

# Set up lattice
vector_a = [8.65127469112, -6.75261456523e-33, 0.0]*Angstrom
vector_b = [-4.32563734556, 7.49222365763, 4.09015759516e-16]*Angstrom
vector_c = [0.0, 0.0, 7.06373620597]*Angstrom
left_electrode_lattice = UnitCell(vector_a, vector_b, vector_c)

# Define elements
left_electrode_elements = [Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold, Gold, Gold, Gold]

# Define coordinates
left_electrode_coordinates = [[ 0.72107876, 1.24846289, 1.17728937],
[ 3.60483699, 1.24846289, 1.17728937],
[ 6.48859522, 1.24846289, 1.17728937],
[-0.72080035, 3.74587078, 1.17728937],
[ 5.04671611, 3.74587078, 1.17728937],
[ 2.16295788, 3.74587078, 1.17728937],
[ 3.60483699, 6.24327867, 1.17728937],
[-2.16267947, 6.24327867, 1.17728937],
[ 0.72107876, 6.24327867, 1.17728937],
[ 2.16295788, 2.08093219, 3.5318681 ],
[-0.72080035, 2.08093219, 3.5318681 ],
[ 5.04671611, 2.08093219, 3.5318681 ],
[-3.60455858, 7.07574796, 3.5318681 ],
[-2.16267947, 4.57834008, 3.5318681 ],
[ 2.16295788, 7.07574796, 3.5318681 ],
[ 3.60483699, 4.57834008, 3.5318681 ],
[ 0.72107876, 4.57834008, 3.5318681 ],
[-0.72080035, 7.07574796, 3.5318681 ],
[ 7.93047434, 0.4159936 , 5.88644684],
[ 0.72107876, 2.91340148, 5.88644684],
[ 2.16295788, 5.41080937, 5.88644684],
[-0.72080035, 5.41080937, 5.88644684],
[ 5.04671611, 5.41080937, 5.88644684],
[ 2.16295788, 0.4159936 , 5.88644684],
[ 3.60483699, 2.91340148, 5.88644684],
[ 5.04671611, 0.4159936 , 5.88644684],
[ 6.48859522, 2.91340148, 5.88644684]]*Angstrom

# Set up configuration
left_electrode = BulkConfiguration(
bravais_lattice=left_electrode_lattice,
elements=left_electrode_elements,
cartesian_coordinates=left_electrode_coordinates
)

# -------------------------------------------------------------
# Right electrode
# -------------------------------------------------------------

# Set up lattice
vector_a = [8.65127469112, -6.75261456523e-33, 0.0]*Angstrom
vector_b = [-4.32563734556, 7.49222365763, 4.09015759516e-16]*Angstrom
vector_c = [0.0, 0.0, 7.06373620597]*Angstrom
right_electrode_lattice = UnitCell(vector_a, vector_b, vector_c)

# Define elements
right_electrode_elements = [Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold, Gold, Gold, Gold]

# Define coordinates
right_electrode_coordinates = [[ 0.72080035, 4.57882217, 1.17728937],
[-0.72107876, 7.07623006, 1.17728937],
[ 2.16267947, 7.07623006, 1.17728937],
[-2.16295788, 4.57882217, 1.17728937],
[-0.72107876, 2.08141429, 1.17728937],
[ 3.60455858, 4.57882217, 1.17728937],
[-3.60483699, 7.07623006, 1.17728937],
[ 5.0464377 , 2.08141429, 1.17728937],
[ 2.16267947, 2.08141429, 1.17728937],
[ 7.93019593, 0.4164757 , 3.5318681 ],
[ 3.60455858, 2.91388358, 3.5318681 ],
[ 6.48831681, 2.91388358, 3.5318681 ],
[ 2.16267947, 5.41129147, 3.5318681 ],
[ 5.0464377 , 0.4164757 , 3.5318681 ],
[ 5.0464377 , 5.41129147, 3.5318681 ],
[-0.72107876, 5.41129147, 3.5318681 ],
[ 0.72080035, 2.91388358, 3.5318681 ],
[ 2.16267947, 0.4164757 , 3.5318681 ],
[ 2.16267947, 3.74635288, 5.88644684],
[-2.16295788, 6.24376076, 5.88644684],
[ 0.72080035, 6.24376076, 5.88644684],
[-0.72107876, 3.74635288, 5.88644684],
[ 6.48831681, 1.24894499, 5.88644684],
[ 0.72080035, 1.24894499, 5.88644684],
[ 5.0464377 , 3.74635288, 5.88644684],
[ 3.60455858, 1.24894499, 5.88644684],
[ 3.60455858, 6.24376076, 5.88644684]]*Angstrom

# Set up configuration
right_electrode = BulkConfiguration(
bravais_lattice=right_electrode_lattice,
elements=right_electrode_elements,
cartesian_coordinates=right_electrode_coordinates
)

# -------------------------------------------------------------
# Central region
# -------------------------------------------------------------

# Set up lattice
vector_a = [8.65127469112, -6.75261456523e-33, 0.0]*Angstrom
vector_b = [-4.32563734556, 7.49222365763, 4.09015759516e-16]*Angstrom
vector_c = [0.0, 0.0, 21.4923367139]*Angstrom
central_region_lattice = UnitCell(vector_a, vector_b, vector_c)

# Define elements
central_region_elements = [Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold, Gold, Gold, Gold, Sulfur, Carbon,
Hydrogen, Hydrogen, Carbon, Carbon, Carbon, Carbon, Hydrogen,
Hydrogen, Carbon, Sulfur, Gold, Gold, Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold,
Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold,
Gold]

# Define coordinates
central_region_coordinates = [[ 0.72107876, 1.24846289, 1.17728937],
[ 3.60483699, 1.24846289, 1.17728937],
[ 6.48859522, 1.24846289, 1.17728937],
[ -0.72080035, 3.74587078, 1.17728937],
[ 5.04671611, 3.74587078, 1.17728937],
[ 2.16295788, 3.74587078, 1.17728937],
[ 3.60483699, 6.24327867, 1.17728937],
[ -2.16267947, 6.24327867, 1.17728937],
[ 0.72107876, 6.24327867, 1.17728937],
[ 2.16295788, 2.08093219, 3.5318681 ],
[ -0.72080035, 2.08093219, 3.5318681 ],
[ 5.04671611, 2.08093219, 3.5318681 ],
[ -3.60455858, 7.07574796, 3.5318681 ],
[ -2.16267947, 4.57834008, 3.5318681 ],
[ 2.16295788, 7.07574796, 3.5318681 ],
[ 3.60483699, 4.57834008, 3.5318681 ],
[ 0.72107876, 4.57834008, 3.5318681 ],
[ -0.72080035, 7.07574796, 3.5318681 ],
[ 7.93047434, 0.4159936 , 5.88644684],
[ 0.72107876, 2.91340148, 5.88644684],
[ 2.16295788, 5.41080937, 5.88644684],
[ -0.72080035, 5.41080937, 5.88644684],
[ 5.04671611, 5.41080937, 5.88644684],
[ 2.16295788, 0.4159936 , 5.88644684],
[ 3.60483699, 2.91340148, 5.88644684],
[ 5.04671611, 0.4159936 , 5.88644684],
[ 6.48859522, 2.91340148, 5.88644684],
[ 2.16295788, 3.74587078, 7.59644684],
[ 2.16295788, 3.74587078, 9.34644649],
[ 1.07984884, 5.62136998, 9.49557904],
[ 3.24594854, 1.87057656, 9.49607409],
[ 1.55660877, 4.79581794, 10.04613074],
[ 2.76904869, 2.69637089, 10.04634658],
[ 1.55658866, 4.79585277, 11.44599014],
[ 2.76902857, 2.69640571, 11.44620598],
[ 1.0796888 , 5.6216471 , 11.99626262],
[ 3.24578851, 1.87085367, 11.99675768],
[ 2.16267947, 3.74635288, 12.14589023],
[ 2.16267947, 3.74635288, 13.89588988],
[ 0.72080035, 4.57882217, 15.60588988],
[ -0.72107876, 7.07623006, 15.60588988],
[ 2.16267947, 7.07623006, 15.60588988],
[ -2.16295788, 4.57882217, 15.60588988],
[ -0.72107876, 2.08141429, 15.60588988],
[ 3.60455858, 4.57882217, 15.60588988],
[ -3.60483699, 7.07623006, 15.60588988],
[ 5.0464377 , 2.08141429, 15.60588988],
[ 2.16267947, 2.08141429, 15.60588988],
[ 7.93019593, 0.4164757 , 17.96046861],
[ 3.60455858, 2.91388358, 17.96046861],
[ 6.48831681, 2.91388358, 17.96046861],
[ 2.16267947, 5.41129147, 17.96046861],
[ 5.0464377 , 0.4164757 , 17.96046861],
[ 5.0464377 , 5.41129147, 17.96046861],
[ -0.72107876, 5.41129147, 17.96046861],
[ 0.72080035, 2.91388358, 17.96046861],
[ 2.16267947, 0.4164757 , 17.96046861],
[ 2.16267947, 3.74635288, 20.31504735],
[ -2.16295788, 6.24376076, 20.31504735],
[ 0.72080035, 6.24376076, 20.31504735],
[ -0.72107876, 3.74635288, 20.31504735],
[ 6.48831681, 1.24894499, 20.31504735],
[ 0.72080035, 1.24894499, 20.31504735],
[ 5.0464377 , 3.74635288, 20.31504735],
[ 3.60455858, 1.24894499, 20.31504735],
[ 3.60455858, 6.24376076, 20.31504735]]*Angstrom

# Set up configuration
central_region = BulkConfiguration(
bravais_lattice=central_region_lattice,
elements=central_region_elements,
cartesian_coordinates=central_region_coordinates
)

device_configuration = DeviceConfiguration(
central_region,
[left_electrode, right_electrode]
)

device_configuration = nlread('C:/Users/Md Mudassir/au_dtb_au.nc', object_id='gID000')[0]
calculator = device_configuration.calculator()
# Define bias voltages
voltage_list= 0.1 *numpy.arange(1,15)*Volt
#make loop
for voltage in voltage_list:
# Set new calculator with modified electrode voltages on the configuration
# use the self consistent state of the old calculation as starting input.
device_configuration.setCalculator(
calculator(electrode_voltages=(-0.5*voltage, 0.5*voltage)),
initial_state=device_configuration)

# Calculate the transmission spectrum
transmission_spectrum = TransmissionSpectrum(
configuration=device_configuration,
energies=numpy.linspace(-5,5,301)*eV,
kpoints=MonkhorstPackGrid(3,3),
)

#save the results
nlsave('au_dtb_au.nc', device_configuration)
nlsave('au_dtb_au.nc', transmission_spectrum)

but job manager script run after that script is finished

+------------------------------------------------------------------------------+
| NanoLanguageScript execution started |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| |
| Atomistix ToolKit 12.2.2 [Build 144eba5] |
| |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| |
| Device DFT Calculation [Started Sat Aug 24 11:03:45 2013] |
| |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| |
| Device DFT Calculation [Started Sat Aug 24 11:04:01 2013] |
| |
+------------------------------------------------------------------------------+
| Checkpoint Handler |
| Filename : c:\users\mdmuda~1\appdata\local\temp\checkpoint37514305.nc |
| Interval : 0.5 h |
+------------------------------------------------------------------------------+
| Left electrode chemical potential = -1.615082 eV |
| Right electrode chemical potential = -1.715082 eV |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| NanoLanguageScript execution finished |
+------------------------------------------------------------------------------+

and give status result failed why

Anders Blom · « **Reply #3 on:** August 25, 2013, 00:26 »

My best guess is that you do not have enough memory on the computer to run this job. It needs about 2-4 GB to run (the exact amount depends quite a bit on the parameters, like k-point sampling and basis set, which I cannot see in your post).

Maneesh · « **Reply #4 on:** August 25, 2013, 07:28 »

Dear sir,

thanks for your mail

as suggested by you that the memory my p.c is 4 GB which is on the higher side required for running the script .
could you please suggest some more parameter e.g k sampling, basis set etc which may serve the purpose.

thanks

maneesh

kstokbro · « **Reply #5 on:** August 26, 2013, 11:39 »

You may try the latest 13.8beta which use slightly less memory. You can also reduce the memory requirements for different parts of the calculation see
http://www.quantumwise.com/documents/tutorials/latest/MemoryUsage/index.html/

QuantumATK Forum

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Author Topic: molecular device configration (Read 4179 times)

Maneesh

molecular device configration

Anders Blom

Re: molecular device configration

Maneesh

Re: molecular device configration

Anders Blom

Re: molecular device configration

Maneesh

Re: molecular device configration

kstokbro

Re: molecular device configration