materialsvirtuallab / snap Goto Github PK
View Code? Open in Web Editor NEWRepository for spectral neighbor analysis potential (SNAP) model development.
License: BSD 3-Clause "New" or "Revised" License
Repository for spectral neighbor analysis potential (SNAP) model development.
License: BSD 3-Clause "New" or "Revised" License
Dear Developers,
Greetings. Last night I watched a demo here, https://www.youtube.com/watch?v=GiebtsjYfgs
This is interesting. I have a very basic query.
Would you kindly help me to know how to extract data from OUTCAR/vasprun.xml file and write a dict contains one structure with data. For multiple structures how can I merge them in a single json file. If you share any script/tool that will be very helpful.
I will wait to hear from you.
Thanks.
Hi,
I am trying to use the SNAP potential for NbMoTaW in LAMMPS (29Oct20). I am getting the following error
ERROR: Incorrect SNAP parameter file (src/SNAP/pair_snap.cpp:732)
If I remove the diagonalstyle 3
from the Ta-W-Nb-Mo.snapparam, it is working.
Is there a workaround for this? Is it safe to omit this line?
Best,
Abu Anand
University of Toronto
Hi, I met some problem reproducing the VASP result for a Ni slab.
The total energy difference is significant. I hope you can help me figuring out what should be changed.
This is the JSON dict, the 4th item of Ni/Surface.json:
{'_id': '59b4ba43ffc31d171c78afbb',
'params': {'pp': {'Ni': 'Ni_pv'},
'env': 'bulk',
'e_cut': 520,
'k_prod': 40,
'bader': False},
'group': 'Ni',
'tags': ['Surface'],
'structure': {'@module': 'pymatgen.core.structure',
'@class': 'Structure',
'lattice': {'matrix': [[2.479787, 0.0, 0.0],
[-1.239893, 2.147558, 0.0],
[0.0, 0.0, 24.294656]],
'a': 2.479787,
'b': 2.479786284100507,
'c': 24.294656,
'alpha': 90.0,
'beta': 90.0,
'gamma': 119.99999621016981,
'volume': 129.38086036717198},
'sites': [{'species': [{'element': 'Ni', 'occu': 1}],
'abc': [0.333334, 0.666668, 0.082544],
'xyz': [3.3333399995783e-07, 1.4317081967440002, 2.005378084864],
'label': 'Ni'},
{'species': [{'element': 'Ni', 'occu': 1}],
'abc': [0.0, 0.0, 0.999689],
'xyz': [0.0, 0.0, 24.287100361984002],
'label': 'Ni'},
{'species': [{'element': 'Ni', 'occu': 1}],
'abc': [0.666666, 0.333332, 0.166332],
'xyz': [1.2398936666659999, 0.7158498032560001, 4.040978721792],
'label': 'Ni'},
{'species': [{'element': 'Ni', 'occu': 1}],
'abc': [0.333334, 0.666668, 0.334122],
'xyz': [3.3333399995783e-07, 1.4317081967440002, 8.117379052032],
'label': 'Ni'},
{'species': [{'element': 'Ni', 'occu': 1}],
'abc': [0.0, 0.0, 0.250335],
'xyz': [0.0, 0.0, 6.081802709759999],
'label': 'Ni'},
{'species': [{'element': 'Ni', 'occu': 1}],
'abc': [0.666666, 0.333332, 0.416978],
'xyz': [1.2398936666659999, 0.7158498032560001, 10.130337069568],
'label': 'Ni'}]},
'num_atoms': 6,
'outputs': {'energy': -33.38981773,
'forces': [[-0.0, -0.0, -0.00470706],
[0.0, 0.0, 0.00549928],
[0.0, -0.0, -0.00421769],
[0.0, 0.0, 0.00470706],
[-0.0, 0.0, 0.00421769],
[-0.0, -0.0, -0.00549928]],
'stress': [-22.25152803, -22.25151688, -14.67323629, -5.18e-06, 0.0, 0.0]}}
Here is my INCAR (generated by pymatgen.io.vasp.sets.MVLSlabSet
):
ALGO = Fast
EDIFF = 0.0001
EDIFFG = -0.02
ENCUT = 520
IBRION = 2
ICHARG = 1
ISIF = 3
ISMEAR = 0
ISPIN = 2
LORBIT = 11
LREAL = Auto
LWAVE = False
MAGMOM = 6*5.0
NELM = 100
NSW = 99
PREC = Accurate
SIGMA = 0.05
Hi,
From your Snap/Mo paper:
In comparison, the corresponding MAEs in the energies, forces, and stress components for the Mo EAM potential of Zhou et al. [32] are 122 meV/atom, 0.41 eV/A° , and 3.48 GPa, respectively
However, I find that the direct total energy MAE (~4 eV/atom) of the absolute EAM/Zhou04 and DFT is far larger than 122 meV/atom.
But the relative total energy MAE is around this value:
y_eam = array_of_eam_energies / array_of_natoms - eam_bulk
y_dft = array_of_dft_energies / array_of_natoms - dft_bulk
print(mean_absolute_error(y_eam, y_dft)
Is my guess correct?
The total energy of the last structure of Mo.surface.json:
dft_energy = -10.3133037725 * 12
The DFT total energy of bulk bcc Mo is around -10.91973776 eV
The EAM/Zhou04 total energy of this structure is just -75.384721 eV
The EAM/Zhou04 total energy of bulk bcc Mo is -6.8100034 eV
y_dft = -123.75964527
dft_ref = -10.91973776
y_eam = -75.384721
eam_ref = -6.8100034
print(y_dft / 12 - dft_ref - (y_eam / 12 - eam_ref)) # 0.07849067083333416
So the direct diff is 4.03124 eV/atom
while the relative diff is 0.078 eV/atom
.
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