Messages

1

General Questions and Answers / Re: Interface builder from ATK python

« on: June 27, 2018, 14:16 »

Thank you Daniele and Petr

That pic helped, I managed to create the same interface. But creating the larger interfaces is almost impossible because there are too many possibilities (i.e. blue dots). It would be nice to incorporate some filtering into the VNL interface builder or enable the assembly of interfaces directly through the GeneralizedMatching method.

Fabian

2

General Questions and Answers / Re: Interface builder from ATK python

« on: June 21, 2018, 16:01 »

I disagree, your log-file shows exactly the same numbers. The first three matchings are:

Code

+----------------------------------------------------------------------------------------+
|    A              B        Strain     Atoms    Area    Aspect    Angle    Rotation     |
+----------------------------------------------------------------------------------------+
[ 1  1  1] >-< [ 0  0  1]   0.000050     1750     69.0      1.0      60.0       19.1
[ 1  1  1] >-< [ 0  0  1]   0.000070     1705     69.0      1.0      60.0       19.1
[ 1  1  1] >-< [ 0  0  1]   0.000110      232     69.0      1.0      60.0       19.1

Which have differing numbers of atoms (1750, 1705 and 232) but apparently the same Area (69.0).
I would assume that collumn "Area" shows the area of the cross-section. Is that wrong, what does "Area" refer to?

EDIT:
Is there an easy way of actually assemble this interface? I have not managed to get the same interfaces through the Interface Builder in VNL and the output of GeneralizedLatticeMatch is not sufficient to create it manually.

3

General Questions and Answers / Re: Interface builder from ATK python

« on: June 14, 2018, 13:59 »

I used: atkpython match_au_mose2.py | grep '0  0  1'
With the files:
match_au_mose2.py

Code

configuration_1 = nlread('au.cif',BulkConfiguration)[-1]
configuration_2 = nlread('MoSe2.cif',BulkConfiguration)[-1]

generalized_lattice_match = GeneralizedLatticeMatch(
                            configuration_1,
                            configuration_2,
                            max_strain=0.02,
                            maximum_miller_index=1,
                            longest_surface_lattice_vector=100*Angstrom,
                            max_surface_area=10000.0*Angstrom**2,
                            user_given_miller_index=(1,1,1)
                            )

With au.cif:

Code

data_global
_cell_length_a 2.97513963
_cell_length_b 2.97513963
_cell_length_c 2.97513963
_cell_angle_alpha 60.00000000
_cell_angle_beta 60.00000000
_cell_angle_gamma 60.00000000
_symmetry_space_group_name_H-M 'P -1'
loop_
_symmetry_equiv_pos_as_xyz
  'x,y,z'
loop_
_atom_site_label
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
Au 0.00000000 0.00000000 0.00000000

and MoSe2.cif

Code

data_global
_cell_length_a 3.32910723
_cell_length_b 3.32910723
_cell_length_c 13.06127836
_cell_angle_alpha 90.00000000
_cell_angle_beta 90.00000000
_cell_angle_gamma 120.00000000
_symmetry_space_group_name_H-M 'P -1'
loop_
_symmetry_equiv_pos_as_xyz
  'x,y,z'
loop_
_atom_site_label
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
Mo 0.33333300 0.66666700 0.25000000
Se 0.66666700 0.33333300 0.12100000
Se 0.66666700 0.33333300 0.37900000

4

General Questions and Answers / Re: Interface builder from ATK python

« on: June 13, 2018, 18:09 »

It's giving me weird information though. Looking at two hexagonal cells (111 of the first and 001 of the second material): the area of the interface is constant, even though the number of atoms increases. Is this a bug or intended?

Here is an excerpt of the output:
|     A                     B            Strain     Atoms    Area    Aspect    Angle    Rotation     |
[ 1  1  1] >-< [ 0  0  1]   0.000050     1750     69.0         1.0         60.0          19.1
[ 1  1  1] >-< [ 0  0  1]   0.000070      1705     69.0        1.0         60.0          19.1
[ 1  1  1] >-< [ 0  0  1]   0.000110        232     69.0         1.0         60.0          19.1
[ 1  1  1] >-< [ 0  0  1]   0.000560        151     69.0         1.0         60.0          19.1
[ 1  1  1] >-< [ 0  0  1]   0.000640       142     69.0         1.0         60.0          19.1
[ 1  1  1] >-< [ 0  0  1]   0.001490         88     69.0         1.0         60.0          19.1
[ 1  1  1] >-< [ 0  0  1]   0.007410          29     69.0         1.0         60.0          19.1
[ 1  1  1] >-< [ 0  0  1]   0.011550           16     69.0         1.0         60.0          19.1

I am using the version "Atomistix ToolKit 2017.1 [Build ce08f12] "

5

General Questions and Answers / Re: Interface builder from ATK python

« on: June 13, 2018, 17:24 »

Perfect, that's exactly what I was looking for. Thank you!

6

General Questions and Answers / Interface builder from ATK python

« on: June 13, 2018, 13:34 »

Dear Quantumwise Team

I would like to use the Interface Matching algorithm from a python script. But I could not find any documentation about how to do that.
Is it possible to access these routines from atkpython or do I HAVE to go through the interface?

Kind regards,
Fabian Ducry

7

General Questions and Answers / Re: Exporting DynamicalMatrix with higher precision

« on: May 25, 2017, 13:32 »

Thank you for the reply. I will do as you suggested.

Fabian Ducry

8

General Questions and Answers / Exporting DynamicalMatrix with higher precision

« on: May 24, 2017, 12:10 »

Dear all

I have computed the DynamicalMatrix of a system. Now I would like to export the matrix. Using

Code

 dynamical_matrix.nlprint('dynamical_matrix.txt')

prints the matrix at the available k-point to the file dynamical_matrix.txt. However, it does so only up to two decimals.

Is there a way to increase the precision?
Alternatively, how could I access the data in the object? Then I could write my own print function.

Thanks in advance!

Fabian Ducry

9

General Questions and Answers / Re: Read ReaxFF parameter file

« on: May 18, 2017, 17:01 »

This additional line did the trick. Everything works smoothly now, thank you!

10

General Questions and Answers / Read ReaxFF parameter file

« on: May 17, 2017, 14:54 »

Dear all

I would like to run simulations with the parameter from a certain publication (Atomic origin of ultrafast resistance switching in nanoscale electrometallization cells, doi:10.1038/nmat4221). I do have the set of parameters but loading the file with

Code

potentialSet = TremoloXPotentialSet(name='reaxff_test')
potentialSet.addParticleType(ParticleType(symbol='O',
                                          mass=15.9994*atomic_mass_unit))
potentialSet.addParticleType(ParticleType(symbol='Cu',
                                          mass=63.5*atomic_mass_unit))
potentialSet.addParticleType(ParticleType(symbol='Si',
                                          mass=28*atomic_mass_unit))
potentialSet.addPotential(ReaxFFPotential(file='ffield_CuSiO.txt',
                                          qeq=True,
                                          qeqEps=1.000000e-06,
                                          qeqMaxIter=200,
                                          lgvdw=False,
                                          bond_rcut=5.0*Angstrom,
                                          hbond_rcut=7.5*Angstrom,
                                          thb_bond_rcut=1e-8,
                                          thb_bond_rcutsq=1e-16,
                                          multiwell=False,
                                          strict_bondpairs=True))

fails: RuntimeError: Error in ...reaxff.c line 5402: ReaxFF data file ffield_CuSiO.txt not valid: could not read atom name and its Atomic number

The parameters are in the attached file.

How do I need to format the file to be read, is there an example somewhere?

Thanks in advance
Fabian Ducry