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Topics - kaypu

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1
General Questions and Answers / Fermi energy location in band diagram for ATK and VASP
« on: November 30, 2020, 15:39 »
Dear Quantumwise staff:
 Hi, i found the Fermi energy in band diagram is different for VASP and ATK. Take MoS2 for example, For VASP, the Fermi energy is near valence band (See VASP.jpg). However, for ATK. the Fermi energy locates about half of valence and conduction (see ATK.jpg). So, i want to know, how to determine Fermi energy in ATK? DOS integration from the lowest energy to Fermi energy=total electron?

2
General Questions and Answers / Warning on calculating FET
« on: June 21, 2020, 03:01 »
Dear Quantumwise staff:
 Hi,
 I want to simulate the MoS2 and WSe2 Van der Waals FET, the electrodes are p-doping. at the beginning of Equivalent Bulk calculation,  ATK shows a warning:
"Not all occupied bands were included in the diagonalization.  The eigenvalues will be re-calculated with an increased number of bands"
i want to know what causes this warning? 
Thanks

3
General Questions and Answers / Question on calculation of Dipole
« on: October 24, 2019, 04:41 »
Dear quantunwise staff：
      Here is the molecule system in the attachment，we calculate the dipole in Gaussian and ATK, respectively.
For atk（GGA-PBE，DZP）：dipole     (e*bohr)    = 5.3662629780200824e-14, -7.290162499260885e-13, -2.6478867127832016e-12
For Gaussian（B3LYP，6-31g*）：dipole     (debye)  9.03655361E-01, -8.41922597E-01, -1.92566377E-02

PS: The structure optimization is performed in Gaussian(B3LYP，6-31g*). Then, put the relaxed molecular configuration to atk and Gaussian for electronic structure calculation.

why such a big different?

4
General Questions and Answers / DFT+MD with electric field
« on: May 15, 2019, 11:34 »
Dear QuantumWise staffs:
Using a 'post-step-hook' hook function,  as shown in https://forum.quantumatk.com/index.php?topic=4696.msg20375#msg20375,  the corresponding script as follows:
*********************************************************************
charges = PartialCharges(bulk_configuration).evaluate()
field = [0.01, 0.0, 0.0]*Volt/Ang
class ElectricFieldHook(object):
   def __init__(self, charges, electric_field):
      # Store the charges and the electric field.
      charges = charges.reshape(-1, 1)
      field = electric_field.reshape(1, 3)
      self.efield_forces = (charges*field).convertTo(eV/Ang)

   def __call__(self, step, time, configuration, forces, stress):
        # Add the electric field forces to the forces vector.
      forces += self.efield_forces

electric_field_hook = ElectricFieldHook(
    charges=partial_charges,
    electric_field=field
)

# -------------------------------------------------------------
# Molecular Dynamics
# -------------------------------------------------------------

initial_velocity = None

method = NVTBerendsen(
    time_step=1*femtoSecond,
    reservoir_temperature=300*Kelvin,
    thermostat_timescale=100*femtoSecond,
    initial_velocity=initial_velocity,
    heating_rate=0*Kelvin/picoSecond,
)

rigid_indices_0 = [203, 204, 205, 206, 207, 208, 209, 210, 211, 212,
                   213, 214, 215, 216, 217, 218, 219, 220, 221, 222,
                   223, 224, 225, 226, 227, 228, 229, 230, 231, 232,
                   233, 234, 235, 236, 237, 238, 239, 240, 241, 242]
rigid_indices_1 = [ 0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11, 12,
                   13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,
                   26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38,
                   39]

constraints = [RigidBody(rigid_indices_0),
               RigidBody(rigid_indices_1)]

md_trajectory = MolecularDynamics(
    bulk_configuration,
    constraints=constraints,
    trajectory_filename='trajectory.nc',
    steps=200,
    log_interval=1,
    post_step_hook=electric_field_hook,
    method=method
)

bulk_configuration = md_trajectory.lastImage()
nlsave('Device-AGNR-Tran1-MDopt.nc', md_trajectory)
*****************************************************************************
it doesn't work,  the error message is "NL.ComputerScienceUtilities.Exceptions.NLTypeError: The LCAOCalculator does not
support calculation of PartialCharges."
how to deal with it? Thanks

5
General Questions and Answers / Question on Transmission Paths
« on: October 9, 2018, 04:34 »
Dear QuantumWise staff:
I have read the paper exploring local currents in molecular juctions. http://www.nature.com/nchem/journal/v2/n3/pdf/nchem.546.pdf

As the author said, the local currents could divide into sigma and pi systems, how could i do the same thing in ATK?

Thanks

6
General Questions and Answers / VibrationalMode of molecule
« on: March 8, 2017, 14:23 »
Dear QuantumWise staff:

     The ATK can do VibrationalMode and PhononDensityofState of an isolate molecule,  whether the energy in phonon density of state corresponds to the vibration frequencies of the molecule (plus hbar)? Or, the vibrationalMode is the vibration frequencies of molecule?

7
General Questions and Answers / How to calculate the enthalpy of reaction in ATK?
« on: March 3, 2017, 08:22 »
Dear QuantumWise staff:
      In the process of gas adsorption, A stands for pristine adsorbate (such as graphene), B is gas molecule (for example CO), and C is the adsorbate with an absorbed gas molecule (graphene+CO). the adsorption process can be represent as A+B=C, the adsorption energy is defined as: Eads=EC-EA-EB. We can calculate the Total energy of A, B, and C respectively by ATK, and get adsorption energy. how to calculate enthalpy in the adsorption process by ATK?

8
General Questions and Answers / How to set spin multiplicity in ATK？
« on: March 3, 2017, 07:30 »
Dear QuantumWise staff:

    How to set spin multiplicity in ATK? For example, the spin state of O2 molecule is triplet, using Dmol3 or Gaussian, we can use spin unrestricted and the mulitiplicity is chosen Triplet. Now, for ATK, how to set?

9
General Questions and Answers / Calculate the electron density for a specific band-by atk 14.3
« on: November 9, 2015, 08:29 »
Dear Quantumwise staff:

according to the page from http://quantumwise.com/forum/index.php?topic=2203.msg10537#msg10537
i try to do it using atk 14.3, but something wrong with it. the script as follows:
**********************************************
from NanoLanguage import *
import NLEngine

def makeGridValues(datagrid, cell, origin, unit):

    n0, n1, n2 = datagrid.shape
    gA, gB, gC = cell
    u0 = NLEngine.Cartesian3D(gA[0],gA[1],gA[2])
    u1 = NLEngine.Cartesian3D(gB[0],gB[1],gB[2])
    u2 = NLEngine.Cartesian3D(gC[0],gC[1],gC[2])
    cell_origin = NLEngine.Cartesian3D(origin[0],origin[1],origin[2])

    grid_descriptor = NLEngine.GridDescriptor(n0,n1,n2,
                                              NLEngine.UnitCell(u0,u1,u2,cell_origin))
    grid3d = NLEngine.RealGrid3D(grid_descriptor,
                                 NLEngine.doubleSequenceToRealVector(datagrid.flatten()),True)

    return GridValues(grid3d,unit)

bulk_configuration = nlread("C:\Users\kaypu\Desktop/zigzag12-band.nc", BulkConfiguration)[0]
conf = nlread("C:\Users\kaypu\Desktop/zigzag12-band.nc", BulkConfiguration, read_state=False)[0]

dm = bulk_configuration.calculator()._densityMatrixCalculator()
number_of_electrons = int(dm.fermiDistribution().numberOfElectrons())

LUMO = number_of_electrons/2
LLUMO = LUMO+1

# Which state to compute?
spin = Spin.Up
state = LUMO
filename = "bloch_z12_LUMO_up.nc"

# Number of points to sample from G to Z
Nk = 100

density = None
for kz in numpy.linspace(0.2,0.5,Nk):
    b = BlochState(bulk_configuration, quantum_number=state, k_point=[0,0,kz], spin=spin)
    psi = b.toArray()
    if density == None:
        density = (psi*psi.conj()).real
    else:
        density += (psi*psi.conj()).real

cell = conf.bravaisLattice().primitiveVectors().inUnitsOf(Bohr)
origin = conf.bravaisLattice().origin().inUnitsOf(Bohr)
grid = makeGridValues(density,cell,origin,unit = eV/eV)

nlsave(filename, grid)
nlsave(filename, conf)
******************************************************
the wrong message shows as follows:

Traceback (most recent call last):
  File "c:\users\kaypu\appdata\local\temp\1676064135181985.py", line 52, in <module>
    grid = makeGridValues(density,cell,origin,unit = eV/eV)
  File "c:\users\kaypu\appdata\local\temp\1676064135181985.py", line 12, in makeGridValues
    u0 = NLEngine.Cartesian3D(gA[0],gA[1],gA[2])
AttributeError: 'module' object has no attribute 'Cartesian3D'

what's wrong with it, i use 2014.3

10
General Questions and Answers / Question on antiresonance in transmission
« on: May 8, 2015, 05:33 »
Dear QuantumWise staff

Following your advice(http://quantumwise.com/forum/index.php?topic=3385.0), I increase the scattering region and recalculate the s-PDOS. The negative s-PDOS is gone. thank you

in the attachment, there is a dip in the Fermi energy, is that QI or numerical artifact?
near -1.8eV, is there Fano resonance? how to explain it?

thank you

11
General Questions and Answers / Question on negative s-PDOS
« on: May 4, 2015, 08:57 »
Dear QuantumWise staff:

In the attachment, the device is composed of carbon nanotube(m=n=4) and anthracene (certral molecule). all the device has been optmized using LBFGS(z vetor is not fixed).The corresponding script is also in the attachment. The self-energy is chosen recursionself energy to avoid negative transmission appearing. Integral lower bound is set to 4.0 hartree to  eliminate charge missing problem.

but there are still some problem...

in the s-PDOS.jpg, near -1 eV, the PDOS of s state is negative, is that right? could  you help me to figure out this problem?

                                             Thanks

12
General Questions and Answers / Question on PDOS
« on: April 29, 2015, 08:52 »
Dear QuantumWise staff
Whether it is possible for ATK(2014.2) to calculate PDOS and project the density to s, px, py, pz of certain atom? if it is, how to compile  the script,
 thank you

13
General Questions and Answers / How the left/right electrodes are modeled?
« on: March 7, 2015, 13:15 »
Dear QuantumWise staff:
    How the left/right electrodes are modeled? it is done through a self-energy(Recursion self-energy)? And i want to know which model is used for it (wide band approximation, absorbing potential, etc.) in ATK

Thanks

14
General Questions and Answers / Questions on Energy dependent LDOS
« on: November 9, 2014, 14:16 »
hi:
 i use this py(in the attachment) to plot the Energy dependent LDOS at bias of 0.4V. the LDOS in the different energy(-1eV~1eV) are saved to LDOS1-LDOS4. but it doesn't work.
*******************
File "LDOS-plot.py", line 25, in <module>
    X, Y = numpy.meshgrid(z, energies)
  File "./build/lib/python2.7/site-packages/numpy/lib/function_base.py", line 3379, in meshgrid
  File "./zipdir/NL/CommonConcepts/PhysicalQuantity.py", line 456, in __mul__
  File "./zipdir/NL/CommonConcepts/PhysicalQuantity.py", line 249, in unit
AttributeError: 'PhysicalQuantity' object has no attribute '_PhysicalQuantity__unit'
*******************
atk version 2014.1

what's wrong? need to modify the py?

thanks

15
General Questions and Answers / Question about Electrostatic Potential and Electrostatic Difference Potential
« on: December 19, 2013, 08:49 »
Dear QuantumWise staff
             
      What does the Electrostatic Potential consist of when the bias is applied? Does it equal to the Hartree energy?  or equal to the sum of Hartree energy and the electro-static external potential (bias potential)?

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