Execution example¶
GaN interatomic potential¶
In this section, show you an execution example of HDNNP training
using 1st order differentiation of interatomic potential
(e.g. interatomic forces) of GaN
Data file¶
Prepare a .xyz format file which have some structures with energy and force data.
GaN.xyz
32
Lattice="6.46474316 0.0 0.0 -3.23237159 5.5986318 0.0 0.0 0.0 10.53232454" Properties=species:S:1:pos:R:3:forces:R:3 energy=-194.5164333 tag=CrystalGa16N16 pbc="T T T"
Ga 1.61619000 0.93311000 2.62845000 0.00000300 0.00001200 -0.00570900
Ga 3.23237000 3.73242000 2.62845000 0.00003900 -0.00004700 -0.00571500
Ga 4.84856000 0.93311000 2.62845000 0.00000400 -0.00001100 -0.00563600
Ga -0.00000000 3.73242000 7.89461000 -0.00003800 0.00003200 -0.00564200
Ga 1.61619000 0.93311000 7.89461000 0.00006100 -0.00001800 -0.00571100
Ga 3.23237000 3.73242000 7.89461000 0.00002100 -0.00006400 -0.00572000
Ga 4.84856000 0.93311000 7.89461000 -0.00003200 -0.00002300 -0.00565600
Ga -0.00000000 3.73242000 2.62845000 0.00002100 -0.00002000 -0.00565100
Ga -0.00000000 1.86621000 5.26153000 -0.00006900 0.00005900 -0.00572300
Ga 1.61619000 4.66553000 5.26153000 -0.00002700 0.00008200 -0.00571900
Ga 3.23237000 1.86621000 5.26153000 0.00001800 -0.00001400 -0.00566500
Ga -1.61619000 4.66553000 10.52769000 -0.00002700 -0.00002600 -0.00566900
Ga -0.00000000 1.86621000 10.52769000 -0.00002200 0.00008500 -0.00568700
Ga 1.61619000 4.66553000 10.52769000 0.00000600 -0.00002400 -0.00574300
Ga 3.23237000 1.86621000 10.52769000 0.00000100 0.00007600 -0.00564000
Ga -1.61619000 4.66553000 5.26153000 0.00002200 -0.00000200 -0.00568800
N 1.61619000 0.93311000 4.61253000 0.00005500 -0.00002000 -0.00041000
N 3.23237000 3.73242000 4.61253000 0.00003600 -0.00000900 -0.00037900
N 4.84856000 0.93311000 4.61253000 -0.00004100 0.00000700 -0.00041100
N -0.00000000 3.73242000 9.87869000 -0.00001300 -0.00003500 -0.00042500
N 1.61619000 0.93311000 9.87869000 0.00001200 0.00002900 -0.00040900
N 3.23237000 3.73242000 9.87869000 0.00002700 -0.00006200 -0.00041700
N 4.84856000 0.93311000 9.87869000 -0.00000400 0.00002500 -0.00041500
N -0.00000000 3.73242000 4.61253000 -0.00004500 -0.00000400 -0.00041800
N -0.00000000 1.86621000 1.97945000 0.00000000 -0.00000800 -0.00034400
N 1.61619000 4.66553000 1.97945000 -0.00000200 0.00000500 -0.00033700
N 3.23237000 1.86621000 1.97945000 0.00001700 0.00001600 -0.00036100
N -1.61619000 4.66553000 7.24561000 0.00002800 -0.00002300 -0.00036000
N -0.00000000 1.86621000 7.24561000 -0.00008200 0.00001500 -0.00043200
N 1.61619000 4.66553000 7.24561000 -0.00002200 0.00004200 -0.00040100
N 3.23237000 1.86621000 7.24561000 0.00001900 -0.00001200 -0.00039500
N -1.61619000 4.66553000 1.97945000 0.00000400 -0.00001800 -0.00046000
32
Lattice="6.46474316 0.0 0.0 -3.23237159 5.5986318 0.0 0.0 0.0 10.53232454" Properties=species:S:1:pos:R:3:forces:R:3 energy=-169.96635976 tag=CrystalGa16N16 pbc="T T T"
Ga 1.44265000 1.46790000 2.04947000 -0.95595000 -3.56110800 2.54045000
Ga 2.88538000 4.34404000 2.89380000 4.75932000 -2.04809500 -1.43108200
Ga 4.38372000 0.68215000 2.61606000 0.15090500 6.97113700 2.40537400
Ga 0.47836000 3.95213000 7.90284000 -3.31821700 -0.13409600 -0.21437100
Ga 1.82415000 1.43420000 8.18380000 -0.78327100 -2.70531000 -3.50469000
Ga 3.49351000 3.96284000 7.92622000 1.84595600 -0.42627100 -0.16593100
Ga 5.17229000 0.83662000 7.71745000 -0.46937900 1.21688400 1.11923500
Ga -0.04508000 3.95689000 2.71946000 -3.88117900 -1.84159800 0.64959300
Ga -0.96518000 1.98086000 5.22137000 1.12890800 -1.31857500 -0.37168600
Ga 1.18573000 3.20454000 5.22045000 1.58317800 1.58466500 0.77557000
Ga 2.91073000 1.45415000 5.60119000 -0.29420600 -1.79185700 -2.55652100
Ga -0.99634000 4.45389000 0.07004000 -2.39983600 3.43545000 1.27018200
Ga 0.17764000 1.60544000 10.36435000 6.30208700 4.30252400 2.73199900
Ga 2.35420000 4.13573000 0.39168000 -1.28509600 -0.64262000 -3.92936300
...
4
Lattice="3.21629013 0.0 0.0 -1.60814507 2.78538896 0.0 0.0 0.0 5.23996246" Properties=species:S:1:pos:R:3:forces:R:3 energy=-24.3605335 tag=CrystalGa2N2 pbc="T T T"
Ga 1.60815000 0.92846000 2.61537000 0.00057000 -0.00032400 -0.00131800
Ga 0.00000000 1.85693000 5.23535000 -0.00055000 0.00030900 -0.00128000
N 1.60815000 0.92846000 4.58958000 0.00038300 -0.00020300 0.00049500
N 0.00000000 1.85693000 1.96960000 -0.00030900 0.00021200 0.00050600
4
Lattice="3.21629013 0.0 0.0 -1.60814507 2.78538896 0.0 0.0 0.0 5.23996246" Properties=species:S:1:pos:R:3:forces:R:3 energy=-24.04284841 tag=CrystalGa2N2 pbc="T T T"
Ga 1.56998000 1.01961000 2.64712000 0.37879200 -0.65345000 -0.84588100
Ga 0.00233000 1.78610000 5.21359000 1.53422400 0.01126800 0.83092200
N 1.80998000 0.78162000 4.55671000 -1.91098000 0.49960800 -0.07141600
N -0.02338000 1.90257000 1.95274000 0.00855700 0.14604000 0.09234500
4
Lattice="3.21629013 0.0 0.0 -1.60814507 2.78538896 0.0 0.0 0.0 5.23996246" Properties=species:S:1:pos:R:3:forces:R:3 energy=-24.07370026 tag=CrystalGa2N2 pbc="T T T"
Ga 1.68022000 0.78468000 2.59601000 -0.77026300 1.15126700 0.71828100
Ga -0.04831000 1.97869000 0.01593000 -1.05203000 0.42443800 -0.31339000
N 1.47544000 1.12447000 4.57171000 1.50854300 -1.32922700 -0.04524600
N 0.01431000 1.77059000 1.98155000 0.31937700 -0.24596800 -0.35639000
4
Lattice="3.21629013 0.0 0.0 -1.60814507 2.78538896 0.0 0.0 0.0 5.23996246" Properties=species:S:1:pos:R:3:forces:R:3 energy=-24.06789171 tag=CrystalGa2N2 pbc="T T T"
Ga 1.55216000 1.03346000 2.59780000 1.76477100 -1.33788800 0.62275500
Ga 0.04645000 1.78043000 0.02483000 -0.39888700 -0.84820500 -0.84426800
N 1.59299000 0.75442000 4.54056000 0.36047300 1.45854900 0.51138400
N 0.06265000 1.88907000 1.95951000 -1.73396900 0.72932900 -0.27762300
4
Lattice="3.21629013 0.0 0.0 -1.60814507 2.78538896 0.0 0.0 0.0 5.23996246" Properties=species:S:1:pos:R:3:forces:R:3 energy=-24.10933618 tag=CrystalGa2N2 pbc="T T T"
Ga 1.62285000 0.92354000 2.56898000 -0.87387700 0.84344000 1.29437700
Ga -0.00655000 1.82730000 0.04373000 0.63633100 1.10065300 -1.07564600
N 1.65007000 1.03662000 4.56438000 -0.83168500 -1.16592600 0.26072300
N -0.08253000 1.92082000 1.98507000 1.07124400 -0.78418500 -0.47994500
4
Lattice="3.21629013 0.0 0.0 -1.60814507 2.78538896 0.0 0.0 0.0 5.23996246" Properties=species:S:1:pos:R:3:forces:R:3 energy=-24.15961153 tag=CrystalGa2N2 pbc="T T T"
Ga 1.61929000 0.86275000 2.60668000 0.91655600 0.12884500 0.02524600
Ga -0.02746000 1.90759000 0.02534000 -0.00425900 0.48361500 -1.32527900
N 1.57325000 1.05930000 4.54898000 0.29235100 -0.94998800 0.25695700
N 0.11613000 1.80106000 1.90435000 -1.21017800 0.33509300 1.05032200
4
Lattice="3.21629013 0.0 0.0 -1.60814507 2.78538896 0.0 0.0 0.0 5.23996246" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.90497111 tag=CrystalGa2N2 pbc="T T T"
Ga 1.57753000 1.01962000 2.53889000 -0.58498700 0.38561600 1.95812800
Ga 0.05221000 1.77667000 0.06084000 -0.50913400 -1.39207300 -1.16507600
N 1.60109000 0.71987000 4.62834000 0.25821000 2.35785600 -0.69708500
N -0.10050000 2.01120000 1.98576000 0.83273600 -1.35617800 -0.10520400
4
Lattice="3.21629013 0.0 0.0 -1.60814507 2.78538896 0.0 0.0 0.0 5.23996246" Properties=species:S:1:pos:R:3:forces:R:3 energy=-24.17936965 tag=CrystalGa2N2 pbc="T T T"
Ga 1.65588000 0.84325000 2.61391000 -0.48280700 0.58352400 -0.06140200
Ga -0.05236000 1.91994000 0.00989000 1.13163900 0.73695700 -0.46324400
N 1.63413000 1.09260000 4.55873000 -1.08709100 -1.30806300 0.05205700
N -0.00295000 1.80336000 1.93549000 0.44154800 -0.01662100 0.47920500
4
Lattice="3.21629013 0.0 0.0 -1.60814507 2.78538896 0.0 0.0 0.0 5.23996246" Properties=species:S:1:pos:R:3:forces:R:3 energy=-23.82707164 tag=CrystalGa2N2 pbc="T T T"
...
Config file¶
training_config.py
(necessary parts picked up)
c.TrainingApplication.verbose = True
c.DatasetConfig.parameters = {
'type1': [
(5.0,),
],
'type2': [
(5.0, 0.01, 2.0),
(5.0, 0.01, 3.2),
(5.0, 0.01, 3.8),
(5.0, 0.1, 2.0),
(5.0, 0.1, 3.2),
(5.0, 0.1, 3.8),
(5.0, 1.0, 2.0),
(5.0, 1.0, 3.2),
(5.0, 1.0, 3.8),
],
'type4': [
(5.0, 0.01, -1, 1),
(5.0, 0.01, -1, 2),
(5.0, 0.01, -1, 4),
(5.0, 0.01, 1, 1),
(5.0, 0.01, 1, 2),
(5.0, 0.01, 1, 4),
(5.0, 0.1, -1, 1),
(5.0, 0.1, -1, 2),
(5.0, 0.1, -1, 4),
(5.0, 0.1, 1, 1),
(5.0, 0.1, 1, 2),
(5.0, 0.1, 1, 4),
(5.0, 1.0, -1, 1),
(5.0, 1.0, -1, 2),
(5.0, 1.0, -1, 4),
(5.0, 1.0, 1, 1),
(5.0, 1.0, 1, 2),
(5.0, 1.0, 1, 4),
],
}
c.DatasetConfig.preprocesses = [
('pca', (), {}),
]
c.ModelConfig.layers = [
(90, 'tanh'),
(90, 'tanh'),
(1, 'identity'),
]
c.TrainingConfig.batch_size = 100
c.TrainingConfig.data_file = 'data/GaN.xyz'
c.TrainingConfig.epoch = 1000
c.TrainingConfig.interval = 10
c.TrainingConfig.loss_function = (
'first_only',
{}
)
c.TrainingConfig.lr_decay = 1.0e-6
c.TrainingConfig.order = 1
c.TrainingConfig.out_dir = 'output'
c.TrainingConfig.patients = 5
c.TrainingConfig.scatter_plot = True
command line log¶
Once edited configuration file training_config.py, you just do one command hdnnpy trian.
$ hdnnpy train
Construct sub dataset tagged as "CrystalGa16N16"
Successfully loaded & made needed symmetry_function dataset from <workdir>/data/CrystalGa16N16/symmetry_function.npz
Successfully loaded & made needed interatomic_potential dataset from <workdir>/data/CrystalGa16N16/interatomic_potential.npz
Initialized PCA parameters for Ga
Feature dimension: 74 => 74
Cumulative contribution rate = 0.9999999403953552
Initialized PCA parameters for N
Feature dimension: 74 => 74
Cumulative contribution rate = 1.0000001192092896
Construct sub dataset tagged as "CrystalGa2N2"
Successfully loaded & made needed symmetry_function dataset from <workdir>/data/CrystalGa2N2/symmetry_function.npz
Successfully loaded & made needed interatomic_potential dataset from <workdir>/data/CrystalGa2N2/interatomic_potential.npz
Saved PCA parameters to <workdir>/output/preprocess/pca.npz.
early stopping: operator is less
epoch iteration main/RMSE/force main/RMSE/total val/main/RMSE/force val/main/RMSE/total
1 14 1.20575 1.20575 1.21576 1.21576
2 28 1.08758 1.08758 1.06121 1.06121
3 42 0.895798 0.895798 0.865482 0.865482
4 55 0.685623 0.685623 0.694789 0.694789
5 69 0.560702 0.560702 0.603832 0.603832
6 83 0.509542 0.509542 0.570984 0.570984
7 97 0.486743 0.486743 0.552533 0.552533
8 110 0.468966 0.468966 0.540375 0.540375
9 124 0.458917 0.458917 0.531327 0.531327
10 138 0.448132 0.448132 0.524466 0.524466
...
Directory tree¶
After training, directory tree becomes as follows:
workdir
├── data/
│ ├── GaN.xyz
│ ...
├── output/
│ ├── CrystalGa16N16/
│ │ ├── energy.png
│ │ ├── force.png
│ │ └── training.log
│ ├── CrystalGa2N2/
│ │ ├── energy.png
│ │ ├── force.png
│ │ └── training.log
│ ├── master_nnp.npz
│ ├── preprocess/
│ │ └── pca.npz
│ ├── training_config.py
│ └── training_result.yaml
└── training_config.py