Add README.md
Browse files- EdenGNN-Uni_abacus.ckpt +0 -3
- EdenGNN-Uni_aug.ckpt +0 -3
- EdenGNN-Uni_pseudo.ckpt +0 -3
- ase_sort.dat +0 -9
- config_uni_abacus.yaml +0 -280
- config_uni_aug.yaml +0 -280
- config_uni_density.yaml +0 -280
- twist/mos2.ckpt +0 -3
EdenGNN-Uni_abacus.ckpt
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version https://git-lfs.github.com/spec/v1
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oid sha256:b955929f5808ff11c980e1fd0151ef69bc148946648385e5679f46096424d83f
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size 26543498
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EdenGNN-Uni_aug.ckpt
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version https://git-lfs.github.com/spec/v1
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oid sha256:bf96caf1916787562da607844c5cd297e92d477c7cb19d7534f7d9de1e293316
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size 26560322
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EdenGNN-Uni_pseudo.ckpt
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version https://git-lfs.github.com/spec/v1
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oid sha256:b9ea9e299a575c9260ce3841010803149d9b7bf68dba1871f8e43a153ab4d456
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size 26561290
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ase_sort.dat
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config_uni_abacus.yaml
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# ------------------------------------------------------------------------------
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# EdenGNN Configuration Template
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#
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# Convention:
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# Key: Value # [Tag] Description
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#
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#
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# Tags:
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# [set]: Must be set in your first usage.
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# [check]: Must be checked before running.
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# [check train]: Must be checked in the training stage.
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# [check predict]: Must be checked in the predicting stage.
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# [default]: Works well with default values, modify only if necessary.
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# ------------------------------------------------------------------------------
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run:
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# [default] Global random number seed
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seed: 42
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# [default] Hardware device for computation. Options: "cpu", "cuda:0", etc.
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device: cuda:0
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# [default] Number of GPUs to use for data distributed training. Experimental usage.
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num_gpus: 1
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# [check] "train" or "predict"
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mode: predict
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# [check] Task type. 0: density; 1: augmentation; 2: density & augmentation; 3: hamiltonian. Must match ckpt if any.
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task: 0
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# [check] Wandb project
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project: edengnn
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# [check] Name of work, useful if using wandb online mode.
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name: universal
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# [check] The final result is stored at: `run.save_dir/run.project/timestamp`.
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save_dir:
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# [default] Wandb log mode
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log: offline
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-
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# [check] path to ckpt file. used for prediction or restarting training
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checkpoint: /path/to/EdenGNN-Uni_abacus.ckpt
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# [default]
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resume: False # True only when restarting an interupted training
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# [default]
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dtype: float32
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data:
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# [check]:
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dft_software: "abacus"
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-
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openmx:
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# [set]:
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path_template: absolute/path/to/EdenGNN-main/scripts/openmx/template.dat
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# [default]: Cutoff energy in [Hartree] for specifying the real space grid
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# density. See the scf.energycutoff tag in OpenMX.
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encut: 220
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# [check predict]: number of cpus used for restart OpenMX calculations
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num_proc: 64
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vasp:
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# [check] Should be consistent with the LMAXMIX tag of your VASP calculations
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lmix_max: 6
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# [set]
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path_template: absolute/path/to/EdenGNN-main/scripts/vasp/template.incar
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# [default] in [eV]. will be used in the future to specify the grid shape
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encut: 520
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-
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# [check train] Directory of scf calculations which contain sub directories
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# the name of which are consistent in data.path_train and data.path_val
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dir:
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| 81 |
-
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abacus:
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# [check train] Abacus 'suffix' keywords. used for reading the training directories
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prefix: aiida
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# [default] in [Rydberg]. See Abacus manual.
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ecutwfc: 100
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siesta:
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# [check train] SIESTA 'SystemLabel' keywords. used for reading the training directories
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prefix: aiida
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# [check train] filename of the SIESTA output log
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filename_out: siesta_out
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# [default] in [Rydberg]. See SIESTA manual.
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meshcutoff: 300
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# [check predict] the sampling density (in Ang^{-1}) in the Brillouin zone. N_i = |b_i| / dk. 0.15 is accurate enough.
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dk_bz: 0.15
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# [check predict] the sampling density along high symmetry lines for plotting band structures.
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dk_band: 0.037
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# [check predict] If true, convert to primitive cell.
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plot_band: True
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# [check train]
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path_train: # sacd paths of working directories
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# [check train]
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path_val: # sacd paths of working directories
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# [check predict] txt files storing the input SAD CHGCAR paths for inference
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path_predict:
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# [default]
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num_workers: 4
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# [check train] True if run.task = 1
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use_bin: False
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# [default] Currently EdenGNN only supports batch size = 1. batch > 1 will
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# raise errors.
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batch_size: 1
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optimize:
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# [check train] loss_train = \sum_i weight_train_i * loss_i
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# loss_val = \sum_i weight_val_i * loss_i
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loss_dict:
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grid_func_out: # charge density
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weight_train: 1.
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weight_val: 1.
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loss: "L1"
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aug_tensor: # augmentation occupancy
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weight_train: 0.
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weight_val: 0.
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loss: "L1"
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# this is deprecated. total charge errors are logged during training
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total_charge:
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#weight_train: 0.0 # deprecated
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weight_val: 0.0
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loss: "L2"
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operator:
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weight_train: 1.0
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weight_val: 1.0
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loss: "L1"
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# [check train]
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lr: 0.005
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task: ${run.task}
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# [default] Freeze the parameters of the MLPs of the RBFs. Experimental usage
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freeze_basis: False
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# [default] Log step of training loss.
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log_every_n_steps: 20
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# [default] used for training universal models
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val_check_interval_steps:
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# [default] Large than 1 means DDP training is on. Experimental usage.
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accumulate_grad_batches: 1
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# [default] Set scheduler.
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scheduler:
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type: ReduceLROnPlateau
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ReduceLROnPlateau:
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factor: 0.5 #
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patience: 10 #
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min_lr: 0.00002
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threshold: 0.00001
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max_epochs: 3000
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max_steps: 1000000
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# [default] Set optimizer.
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optimizer:
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type: AdamW
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AdamW:
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epsilon: 1e-8
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beta1: 0.99
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beta2: 0.999
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# [default] 0 default; 1 for debug. deprecated
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# log_level: 0
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# [default]
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gradient_clip_val: 0.0
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model:
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compile: False
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task: ${run.task}
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lmix_max: ${data.vasp.lmix_max}
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# [check predict] Whether or not predict total charge density. Set True for
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# predict VASP CHGCAR. Otherwise set it False.
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use_sad: False
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# [check train] Maximum number of probe points per training chunk. Should be
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# set close to the OOM value to improve speed.
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# (depends on your GPU, 20,000,000 works for A800 GPU which has 80G VRAM).
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chunk_size_train: 1000000
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# [check] Maximum number of probe points per prediction chunk.
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# (depends on your GPU, 20,000,000 works for A800 GPU which has 80G VRAM).
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chunk_size_predict: 1000000
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atom:
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# [default]
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l_max: 6
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# [default]
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num_types: 100
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edge:
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# [default]
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n_radial_basis: 8
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# [default]
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radial_type: Bessel
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# [default] The maximum distance between neighbor atoms.
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cutoff: 4.0
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conv:
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# [default]
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num_conv_layers: 3
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# [default]
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num_radial_filter_neurons: 64
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# [default]
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num_radial_filter_layers: 2
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# [default] Irreps of node features in the graph convolutions.
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irreps_node_features: 64x0e+64x0o+20x1o+20x1e+16x2o+16x2e+8x3o+8x3e+6x4o+6x4e+5x5e+5x5o+4x6e+4x6o
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probe:
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# [default]
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l_max: 6
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-
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edge:
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# [default]: The radius in [Angstrom] which determines the neighbor grids
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# for atoms.
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cutoff: 3.0
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| 244 |
-
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# [default]
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n_radial_basis: 8
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-
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# [default]
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n_z_embedding_dim: 8
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-
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# [default]
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n_z_embedding_neurons: 20 #
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# [default]
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n_z_embedding_layers: 2
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-
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conv:
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# [default]
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num_radial_filter_neurons: 20
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-
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# [default]
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| 262 |
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num_radial_filter_layers: 2
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| 263 |
-
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# [default] the number of radial basis for each angular quantum number.
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n_channels: 4
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operator:
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basis: [0, 0, 1, 1, 2, 2, 3]
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offsite:
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symmetrize: False
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cutoff: 12.0
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| 271 |
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n_radial_basis: 8
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num_radial_filter_layers: 2
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| 273 |
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num_radial_filter_neurons: 64
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-
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-
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-
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wandb:
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project: ${run.project}
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name: ${run.name}
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mode: ${run.log}
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|
config_uni_aug.yaml
DELETED
|
@@ -1,280 +0,0 @@
|
|
| 1 |
-
# ------------------------------------------------------------------------------
|
| 2 |
-
# EdenGNN Configuration Template
|
| 3 |
-
#
|
| 4 |
-
# Convention:
|
| 5 |
-
# Key: Value # [Tag] Description
|
| 6 |
-
#
|
| 7 |
-
#
|
| 8 |
-
# Tags:
|
| 9 |
-
# [set]: Must be set in your first usage.
|
| 10 |
-
# [check]: Must be checked before running.
|
| 11 |
-
# [check train]: Must be checked in the training stage.
|
| 12 |
-
# [check predict]: Must be checked in the predicting stage.
|
| 13 |
-
# [default]: Works well with default values, modify only if necessary.
|
| 14 |
-
# ------------------------------------------------------------------------------
|
| 15 |
-
|
| 16 |
-
run:
|
| 17 |
-
# [default] Global random number seed
|
| 18 |
-
seed: 42
|
| 19 |
-
|
| 20 |
-
# [default] Hardware device for computation. Options: "cpu", "cuda:0", etc.
|
| 21 |
-
device: cuda:0
|
| 22 |
-
|
| 23 |
-
# [default] Number of GPUs to use for data distributed training. Experimental usage.
|
| 24 |
-
num_gpus: 1
|
| 25 |
-
|
| 26 |
-
# [check] "train" or "predict"
|
| 27 |
-
mode: predict
|
| 28 |
-
|
| 29 |
-
# [check] Task type. 0: density; 1: augmentation; 2: density & augmentation; 3: hamiltonian. Must match ckpt if any.
|
| 30 |
-
task: 1
|
| 31 |
-
|
| 32 |
-
# [check] Wandb project
|
| 33 |
-
project: edengnn
|
| 34 |
-
|
| 35 |
-
# [check] Name of work, useful if using wandb online mode.
|
| 36 |
-
name: universal
|
| 37 |
-
|
| 38 |
-
# [check] The final result is stored at: `run.save_dir/run.project/timestamp`.
|
| 39 |
-
save_dir:
|
| 40 |
-
|
| 41 |
-
# [default] Wandb log mode
|
| 42 |
-
log: offline
|
| 43 |
-
|
| 44 |
-
# [check] path to ckpt file. used for prediction or restarting training
|
| 45 |
-
checkpoint: /path/to/EdenGNN-Uni_aug.ckpt
|
| 46 |
-
|
| 47 |
-
# [default]
|
| 48 |
-
resume: False # True only when restarting an interupted training
|
| 49 |
-
|
| 50 |
-
# [default]
|
| 51 |
-
dtype: float32
|
| 52 |
-
|
| 53 |
-
data:
|
| 54 |
-
# [check]:
|
| 55 |
-
dft_software: "vasp"
|
| 56 |
-
|
| 57 |
-
openmx:
|
| 58 |
-
# [set]:
|
| 59 |
-
path_template: absolute/path/to/EdenGNN-main/scripts/openmx/template.dat
|
| 60 |
-
|
| 61 |
-
# [default]: Cutoff energy in [Hartree] for specifying the real space grid
|
| 62 |
-
# density. See the scf.energycutoff tag in OpenMX.
|
| 63 |
-
encut: 220
|
| 64 |
-
|
| 65 |
-
# [check predict]: number of cpus used for restart OpenMX calculations
|
| 66 |
-
num_proc: 64
|
| 67 |
-
|
| 68 |
-
vasp:
|
| 69 |
-
# [check] Should be consistent with the LMAXMIX tag of your VASP calculations
|
| 70 |
-
lmix_max: 6
|
| 71 |
-
|
| 72 |
-
# [set]
|
| 73 |
-
path_template: absolute/path/to/EdenGNN-main/scripts/vasp/template.incar
|
| 74 |
-
|
| 75 |
-
# [default] in [eV]. will be used in the future to specify the grid shape
|
| 76 |
-
encut: 520
|
| 77 |
-
|
| 78 |
-
# [check train] Directory of scf calculations which contain sub directories
|
| 79 |
-
# the name of which are consistent in data.path_train and data.path_val
|
| 80 |
-
dir:
|
| 81 |
-
|
| 82 |
-
abacus:
|
| 83 |
-
# [check train] Abacus 'suffix' keywords. used for reading the training directories
|
| 84 |
-
prefix: aiida
|
| 85 |
-
|
| 86 |
-
# [default] in [Rydberg]. See Abacus manual.
|
| 87 |
-
ecutwfc: 100
|
| 88 |
-
|
| 89 |
-
siesta:
|
| 90 |
-
# [check train] SIESTA 'SystemLabel' keywords. used for reading the training directories
|
| 91 |
-
prefix: aiida
|
| 92 |
-
|
| 93 |
-
# [check train] filename of the SIESTA output log
|
| 94 |
-
filename_out: siesta_out
|
| 95 |
-
|
| 96 |
-
# [default] in [Rydberg]. See SIESTA manual.
|
| 97 |
-
meshcutoff: 300
|
| 98 |
-
|
| 99 |
-
# [check predict] the sampling density (in Ang^{-1}) in the Brillouin zone. N_i = |b_i| / dk. 0.15 is accurate enough.
|
| 100 |
-
dk_bz: 0.15
|
| 101 |
-
|
| 102 |
-
# [check predict] the sampling density along high symmetry lines for plotting band structures.
|
| 103 |
-
dk_band: 0.037
|
| 104 |
-
|
| 105 |
-
# [check predict] If true, convert to primitive cell.
|
| 106 |
-
plot_band: True
|
| 107 |
-
|
| 108 |
-
# [check train]
|
| 109 |
-
path_train: # sacd paths of working directories
|
| 110 |
-
|
| 111 |
-
# [check train]
|
| 112 |
-
path_val: # sacd paths of working directories
|
| 113 |
-
|
| 114 |
-
# [check predict] txt files storing the input SAD CHGCAR paths for inference
|
| 115 |
-
path_predict:
|
| 116 |
-
|
| 117 |
-
# [default]
|
| 118 |
-
num_workers: 4
|
| 119 |
-
|
| 120 |
-
# [check train] True if run.task = 1
|
| 121 |
-
use_bin: False
|
| 122 |
-
|
| 123 |
-
# [default] Currently EdenGNN only supports batch size = 1. batch > 1 will
|
| 124 |
-
# raise errors.
|
| 125 |
-
batch_size: 1
|
| 126 |
-
|
| 127 |
-
optimize:
|
| 128 |
-
# [check train] loss_train = \sum_i weight_train_i * loss_i
|
| 129 |
-
# loss_val = \sum_i weight_val_i * loss_i
|
| 130 |
-
loss_dict:
|
| 131 |
-
grid_func_out: # charge density
|
| 132 |
-
weight_train: 1.
|
| 133 |
-
weight_val: 1.
|
| 134 |
-
loss: "L1"
|
| 135 |
-
aug_tensor: # augmentation occupancy
|
| 136 |
-
weight_train: 0.
|
| 137 |
-
weight_val: 0.
|
| 138 |
-
loss: "L1"
|
| 139 |
-
# this is deprecated. total charge errors are logged during training
|
| 140 |
-
total_charge:
|
| 141 |
-
#weight_train: 0.0 # deprecated
|
| 142 |
-
weight_val: 0.0
|
| 143 |
-
loss: "L2"
|
| 144 |
-
operator:
|
| 145 |
-
weight_train: 1.0
|
| 146 |
-
weight_val: 1.0
|
| 147 |
-
loss: "L1"
|
| 148 |
-
|
| 149 |
-
# [check train]
|
| 150 |
-
lr: 0.005
|
| 151 |
-
task: ${run.task}
|
| 152 |
-
|
| 153 |
-
# [default] Freeze the parameters of the MLPs of the RBFs. Experimental usage
|
| 154 |
-
freeze_basis: False
|
| 155 |
-
|
| 156 |
-
# [default] Log step of training loss.
|
| 157 |
-
log_every_n_steps: 20
|
| 158 |
-
|
| 159 |
-
# [default] used for training universal models
|
| 160 |
-
val_check_interval_steps:
|
| 161 |
-
|
| 162 |
-
# [default] Large than 1 means DDP training is on. Experimental usage.
|
| 163 |
-
accumulate_grad_batches: 1
|
| 164 |
-
|
| 165 |
-
# [default] Set scheduler.
|
| 166 |
-
scheduler:
|
| 167 |
-
type: ReduceLROnPlateau
|
| 168 |
-
ReduceLROnPlateau:
|
| 169 |
-
factor: 0.5 #
|
| 170 |
-
patience: 10 #
|
| 171 |
-
min_lr: 0.00002
|
| 172 |
-
threshold: 0.00001
|
| 173 |
-
max_epochs: 3000
|
| 174 |
-
max_steps: 1000000
|
| 175 |
-
|
| 176 |
-
# [default] Set optimizer.
|
| 177 |
-
optimizer:
|
| 178 |
-
type: AdamW
|
| 179 |
-
AdamW:
|
| 180 |
-
epsilon: 1e-8
|
| 181 |
-
beta1: 0.99
|
| 182 |
-
beta2: 0.999
|
| 183 |
-
|
| 184 |
-
# [default] 0 default; 1 for debug. deprecated
|
| 185 |
-
# log_level: 0
|
| 186 |
-
|
| 187 |
-
# [default]
|
| 188 |
-
gradient_clip_val: 0.0
|
| 189 |
-
|
| 190 |
-
model:
|
| 191 |
-
compile: False
|
| 192 |
-
task: ${run.task}
|
| 193 |
-
lmix_max: ${data.vasp.lmix_max}
|
| 194 |
-
|
| 195 |
-
# [check predict] Whether or not predict total charge density. Set True for
|
| 196 |
-
# predict VASP CHGCAR. Otherwise set it False.
|
| 197 |
-
use_sad: False
|
| 198 |
-
|
| 199 |
-
# [check train] Maximum number of probe points per training chunk. Should be
|
| 200 |
-
# set close to the OOM value to improve speed.
|
| 201 |
-
# (depends on your GPU, 20,000,000 works for A800 GPU which has 80G VRAM).
|
| 202 |
-
chunk_size_train: 1000000
|
| 203 |
-
|
| 204 |
-
# [check] Maximum number of probe points per prediction chunk.
|
| 205 |
-
# (depends on your GPU, 20,000,000 works for A800 GPU which has 80G VRAM).
|
| 206 |
-
chunk_size_predict: 1000000
|
| 207 |
-
|
| 208 |
-
atom:
|
| 209 |
-
# [default]
|
| 210 |
-
l_max: 6
|
| 211 |
-
|
| 212 |
-
# [default]
|
| 213 |
-
num_types: 100
|
| 214 |
-
|
| 215 |
-
edge:
|
| 216 |
-
# [default]
|
| 217 |
-
n_radial_basis: 8
|
| 218 |
-
|
| 219 |
-
# [default]
|
| 220 |
-
radial_type: Bessel
|
| 221 |
-
|
| 222 |
-
# [default] The maximum distance between neighbor atoms.
|
| 223 |
-
cutoff: 4.0
|
| 224 |
-
conv:
|
| 225 |
-
# [default]
|
| 226 |
-
num_conv_layers: 3
|
| 227 |
-
|
| 228 |
-
# [default]
|
| 229 |
-
num_radial_filter_neurons: 64
|
| 230 |
-
|
| 231 |
-
# [default]
|
| 232 |
-
num_radial_filter_layers: 2
|
| 233 |
-
|
| 234 |
-
# [default] Irreps of node features in the graph convolutions.
|
| 235 |
-
irreps_node_features: 64x0e+64x0o+20x1o+20x1e+16x2o+16x2e+8x3o+8x3e+6x4o+6x4e+5x5e+5x5o+4x6e+4x6o
|
| 236 |
-
probe:
|
| 237 |
-
# [default]
|
| 238 |
-
l_max: 6
|
| 239 |
-
|
| 240 |
-
edge:
|
| 241 |
-
# [default]: The radius in [Angstrom] which determines the neighbor grids
|
| 242 |
-
# for atoms.
|
| 243 |
-
cutoff: 4.0
|
| 244 |
-
|
| 245 |
-
# [default]
|
| 246 |
-
n_radial_basis: 8
|
| 247 |
-
|
| 248 |
-
# [default]
|
| 249 |
-
n_z_embedding_dim: 8
|
| 250 |
-
|
| 251 |
-
# [default]
|
| 252 |
-
n_z_embedding_neurons: 20 #
|
| 253 |
-
|
| 254 |
-
# [default]
|
| 255 |
-
n_z_embedding_layers: 2
|
| 256 |
-
|
| 257 |
-
conv:
|
| 258 |
-
# [default]
|
| 259 |
-
num_radial_filter_neurons: 20
|
| 260 |
-
|
| 261 |
-
# [default]
|
| 262 |
-
num_radial_filter_layers: 2
|
| 263 |
-
|
| 264 |
-
# [default] the number of radial basis for each angular quantum number.
|
| 265 |
-
n_channels: 4
|
| 266 |
-
operator:
|
| 267 |
-
basis: [0, 0, 1, 1, 2, 2, 3]
|
| 268 |
-
offsite:
|
| 269 |
-
symmetrize: False
|
| 270 |
-
cutoff: 12.0
|
| 271 |
-
n_radial_basis: 8
|
| 272 |
-
num_radial_filter_layers: 2
|
| 273 |
-
num_radial_filter_neurons: 64
|
| 274 |
-
|
| 275 |
-
|
| 276 |
-
|
| 277 |
-
wandb:
|
| 278 |
-
project: ${run.project}
|
| 279 |
-
name: ${run.name}
|
| 280 |
-
mode: ${run.log}
|
|
|
|
|
|
|
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|
config_uni_density.yaml
DELETED
|
@@ -1,280 +0,0 @@
|
|
| 1 |
-
# ------------------------------------------------------------------------------
|
| 2 |
-
# EdenGNN Configuration Template
|
| 3 |
-
#
|
| 4 |
-
# Convention:
|
| 5 |
-
# Key: Value # [Tag] Description
|
| 6 |
-
#
|
| 7 |
-
#
|
| 8 |
-
# Tags:
|
| 9 |
-
# [set]: Must be set in your first usage.
|
| 10 |
-
# [check]: Must be checked before running.
|
| 11 |
-
# [check train]: Must be checked in the training stage.
|
| 12 |
-
# [check predict]: Must be checked in the predicting stage.
|
| 13 |
-
# [default]: Works well with default values, modify only if necessary.
|
| 14 |
-
# ------------------------------------------------------------------------------
|
| 15 |
-
|
| 16 |
-
run:
|
| 17 |
-
# [default] Global random number seed
|
| 18 |
-
seed: 42
|
| 19 |
-
|
| 20 |
-
# [default] Hardware device for computation. Options: "cpu", "cuda:0", etc.
|
| 21 |
-
device: cuda:0
|
| 22 |
-
|
| 23 |
-
# [default] Number of GPUs to use for data distributed training. Experimental usage.
|
| 24 |
-
num_gpus: 1
|
| 25 |
-
|
| 26 |
-
# [check] "train" or "predict"
|
| 27 |
-
mode: predict
|
| 28 |
-
|
| 29 |
-
# [check] Task type. 0: density; 1: augmentation; 2: density & augmentation; 3: hamiltonian. Must match ckpt if any.
|
| 30 |
-
task: 0
|
| 31 |
-
|
| 32 |
-
# [check] Wandb project
|
| 33 |
-
project: edengnn
|
| 34 |
-
|
| 35 |
-
# [check] Name of work, useful if using wandb online mode.
|
| 36 |
-
name: universal
|
| 37 |
-
|
| 38 |
-
# [check] The final result is stored at: `run.save_dir/run.project/timestamp`.
|
| 39 |
-
save_dir:
|
| 40 |
-
|
| 41 |
-
# [default] Wandb log mode
|
| 42 |
-
log: offline
|
| 43 |
-
|
| 44 |
-
# [check] path to ckpt file. used for prediction or restarting training
|
| 45 |
-
checkpoint: /path/to/EdenGNN-Uni_density.ckpt
|
| 46 |
-
|
| 47 |
-
# [default]
|
| 48 |
-
resume: False # True only when restarting an interupted training
|
| 49 |
-
|
| 50 |
-
# [default]
|
| 51 |
-
dtype: float32
|
| 52 |
-
|
| 53 |
-
data:
|
| 54 |
-
# [check]:
|
| 55 |
-
dft_software: "vasp"
|
| 56 |
-
|
| 57 |
-
openmx:
|
| 58 |
-
# [set]:
|
| 59 |
-
path_template: absolute/path/to/EdenGNN-main/scripts/openmx/template.dat
|
| 60 |
-
|
| 61 |
-
# [default]: Cutoff energy in [Hartree] for specifying the real space grid
|
| 62 |
-
# density. See the scf.energycutoff tag in OpenMX.
|
| 63 |
-
encut: 220
|
| 64 |
-
|
| 65 |
-
# [check predict]: number of cpus used for restart OpenMX calculations
|
| 66 |
-
num_proc: 64
|
| 67 |
-
|
| 68 |
-
vasp:
|
| 69 |
-
# [check] Should be consistent with the LMAXMIX tag of your VASP calculations
|
| 70 |
-
lmix_max: 6
|
| 71 |
-
|
| 72 |
-
# [set]
|
| 73 |
-
path_template: absolute/path/to/EdenGNN-main/scripts/vasp/template.incar
|
| 74 |
-
|
| 75 |
-
# [default] in [eV]. will be used in the future to specify the grid shape
|
| 76 |
-
encut: 520
|
| 77 |
-
|
| 78 |
-
# [check train] Directory of scf calculations which contain sub directories
|
| 79 |
-
# the name of which are consistent in data.path_train and data.path_val
|
| 80 |
-
dir:
|
| 81 |
-
|
| 82 |
-
abacus:
|
| 83 |
-
# [check train] Abacus 'suffix' keywords. used for reading the training directories
|
| 84 |
-
prefix: aiida
|
| 85 |
-
|
| 86 |
-
# [default] in [Rydberg]. See Abacus manual.
|
| 87 |
-
ecutwfc: 100
|
| 88 |
-
|
| 89 |
-
siesta:
|
| 90 |
-
# [check train] SIESTA 'SystemLabel' keywords. used for reading the training directories
|
| 91 |
-
prefix: aiida
|
| 92 |
-
|
| 93 |
-
# [check train] filename of the SIESTA output log
|
| 94 |
-
filename_out: siesta_out
|
| 95 |
-
|
| 96 |
-
# [default] in [Rydberg]. See SIESTA manual.
|
| 97 |
-
meshcutoff: 300
|
| 98 |
-
|
| 99 |
-
# [check predict] the sampling density (in Ang^{-1}) in the Brillouin zone. N_i = |b_i| / dk. 0.15 is accurate enough.
|
| 100 |
-
dk_bz: 0.15
|
| 101 |
-
|
| 102 |
-
# [check predict] the sampling density along high symmetry lines for plotting band structures.
|
| 103 |
-
dk_band: 0.037
|
| 104 |
-
|
| 105 |
-
# [check predict] If true, convert to primitive cell.
|
| 106 |
-
plot_band: True
|
| 107 |
-
|
| 108 |
-
# [check train]
|
| 109 |
-
path_train: # sacd paths of working directories
|
| 110 |
-
|
| 111 |
-
# [check train]
|
| 112 |
-
path_val: # sacd paths of working directories
|
| 113 |
-
|
| 114 |
-
# [check predict] txt files storing the input SAD CHGCAR paths for inference
|
| 115 |
-
path_predict:
|
| 116 |
-
|
| 117 |
-
# [default]
|
| 118 |
-
num_workers: 4
|
| 119 |
-
|
| 120 |
-
# [check train] True if run.task = 1
|
| 121 |
-
use_bin: False
|
| 122 |
-
|
| 123 |
-
# [default] Currently EdenGNN only supports batch size = 1. batch > 1 will
|
| 124 |
-
# raise errors.
|
| 125 |
-
batch_size: 1
|
| 126 |
-
|
| 127 |
-
optimize:
|
| 128 |
-
# [check train] loss_train = \sum_i weight_train_i * loss_i
|
| 129 |
-
# loss_val = \sum_i weight_val_i * loss_i
|
| 130 |
-
loss_dict:
|
| 131 |
-
grid_func_out: # charge density
|
| 132 |
-
weight_train: 1.
|
| 133 |
-
weight_val: 1.
|
| 134 |
-
loss: "L1"
|
| 135 |
-
aug_tensor: # augmentation occupancy
|
| 136 |
-
weight_train: 0.
|
| 137 |
-
weight_val: 0.
|
| 138 |
-
loss: "L1"
|
| 139 |
-
# this is deprecated. total charge errors are logged during training
|
| 140 |
-
total_charge:
|
| 141 |
-
#weight_train: 0.0 # deprecated
|
| 142 |
-
weight_val: 0.0
|
| 143 |
-
loss: "L2"
|
| 144 |
-
operator:
|
| 145 |
-
weight_train: 1.0
|
| 146 |
-
weight_val: 1.0
|
| 147 |
-
loss: "L1"
|
| 148 |
-
|
| 149 |
-
# [check train]
|
| 150 |
-
lr: 0.005
|
| 151 |
-
task: ${run.task}
|
| 152 |
-
|
| 153 |
-
# [default] Freeze the parameters of the MLPs of the RBFs. Experimental usage
|
| 154 |
-
freeze_basis: False
|
| 155 |
-
|
| 156 |
-
# [default] Log step of training loss.
|
| 157 |
-
log_every_n_steps: 20
|
| 158 |
-
|
| 159 |
-
# [default] used for training universal models
|
| 160 |
-
val_check_interval_steps:
|
| 161 |
-
|
| 162 |
-
# [default] Large than 1 means DDP training is on. Experimental usage.
|
| 163 |
-
accumulate_grad_batches: 1
|
| 164 |
-
|
| 165 |
-
# [default] Set scheduler.
|
| 166 |
-
scheduler:
|
| 167 |
-
type: ReduceLROnPlateau
|
| 168 |
-
ReduceLROnPlateau:
|
| 169 |
-
factor: 0.5 #
|
| 170 |
-
patience: 10 #
|
| 171 |
-
min_lr: 0.00002
|
| 172 |
-
threshold: 0.00001
|
| 173 |
-
max_epochs: 3000
|
| 174 |
-
max_steps: 1000000
|
| 175 |
-
|
| 176 |
-
# [default] Set optimizer.
|
| 177 |
-
optimizer:
|
| 178 |
-
type: AdamW
|
| 179 |
-
AdamW:
|
| 180 |
-
epsilon: 1e-8
|
| 181 |
-
beta1: 0.99
|
| 182 |
-
beta2: 0.999
|
| 183 |
-
|
| 184 |
-
# [default] 0 default; 1 for debug. deprecated
|
| 185 |
-
# log_level: 0
|
| 186 |
-
|
| 187 |
-
# [default]
|
| 188 |
-
gradient_clip_val: 0.0
|
| 189 |
-
|
| 190 |
-
model:
|
| 191 |
-
compile: False
|
| 192 |
-
task: ${run.task}
|
| 193 |
-
lmix_max: ${data.vasp.lmix_max}
|
| 194 |
-
|
| 195 |
-
# [check predict] Whether or not predict total charge density. Set True for
|
| 196 |
-
# predict VASP CHGCAR. Otherwise set it False.
|
| 197 |
-
use_sad: False
|
| 198 |
-
|
| 199 |
-
# [check train] Maximum number of probe points per training chunk. Should be
|
| 200 |
-
# set close to the OOM value to improve speed.
|
| 201 |
-
# (depends on your GPU, 20,000,000 works for A800 GPU which has 80G VRAM).
|
| 202 |
-
chunk_size_train: 1000000
|
| 203 |
-
|
| 204 |
-
# [check] Maximum number of probe points per prediction chunk.
|
| 205 |
-
# (depends on your GPU, 20,000,000 works for A800 GPU which has 80G VRAM).
|
| 206 |
-
chunk_size_predict: 1000000
|
| 207 |
-
|
| 208 |
-
atom:
|
| 209 |
-
# [default]
|
| 210 |
-
l_max: 6
|
| 211 |
-
|
| 212 |
-
# [default]
|
| 213 |
-
num_types: 100
|
| 214 |
-
|
| 215 |
-
edge:
|
| 216 |
-
# [default]
|
| 217 |
-
n_radial_basis: 8
|
| 218 |
-
|
| 219 |
-
# [default]
|
| 220 |
-
radial_type: Bessel
|
| 221 |
-
|
| 222 |
-
# [default] The maximum distance between neighbor atoms.
|
| 223 |
-
cutoff: 4.0
|
| 224 |
-
conv:
|
| 225 |
-
# [default]
|
| 226 |
-
num_conv_layers: 3
|
| 227 |
-
|
| 228 |
-
# [default]
|
| 229 |
-
num_radial_filter_neurons: 64
|
| 230 |
-
|
| 231 |
-
# [default]
|
| 232 |
-
num_radial_filter_layers: 2
|
| 233 |
-
|
| 234 |
-
# [default] Irreps of node features in the graph convolutions.
|
| 235 |
-
irreps_node_features: 64x0e+64x0o+20x1o+20x1e+16x2o+16x2e+8x3o+8x3e+6x4o+6x4e+5x5e+5x5o+4x6e+4x6o
|
| 236 |
-
probe:
|
| 237 |
-
# [default]
|
| 238 |
-
l_max: 6
|
| 239 |
-
|
| 240 |
-
edge:
|
| 241 |
-
# [default]: The radius in [Angstrom] which determines the neighbor grids
|
| 242 |
-
# for atoms.
|
| 243 |
-
cutoff: 4.0
|
| 244 |
-
|
| 245 |
-
# [default]
|
| 246 |
-
n_radial_basis: 8
|
| 247 |
-
|
| 248 |
-
# [default]
|
| 249 |
-
n_z_embedding_dim: 8
|
| 250 |
-
|
| 251 |
-
# [default]
|
| 252 |
-
n_z_embedding_neurons: 20 #
|
| 253 |
-
|
| 254 |
-
# [default]
|
| 255 |
-
n_z_embedding_layers: 2
|
| 256 |
-
|
| 257 |
-
conv:
|
| 258 |
-
# [default]
|
| 259 |
-
num_radial_filter_neurons: 20
|
| 260 |
-
|
| 261 |
-
# [default]
|
| 262 |
-
num_radial_filter_layers: 2
|
| 263 |
-
|
| 264 |
-
# [default] the number of radial basis for each angular quantum number.
|
| 265 |
-
n_channels: 4
|
| 266 |
-
operator:
|
| 267 |
-
basis: [0, 0, 1, 1, 2, 2, 3]
|
| 268 |
-
offsite:
|
| 269 |
-
symmetrize: False
|
| 270 |
-
cutoff: 12.0
|
| 271 |
-
n_radial_basis: 8
|
| 272 |
-
num_radial_filter_layers: 2
|
| 273 |
-
num_radial_filter_neurons: 64
|
| 274 |
-
|
| 275 |
-
|
| 276 |
-
|
| 277 |
-
wandb:
|
| 278 |
-
project: ${run.project}
|
| 279 |
-
name: ${run.name}
|
| 280 |
-
mode: ${run.log}
|
|
|
|
|
|
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twist/mos2.ckpt
DELETED
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@@ -1,3 +0,0 @@
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| 1 |
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version https://git-lfs.github.com/spec/v1
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| 2 |
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oid sha256:b8b7759012f4622cf710f53ba3acc00533abd708c75445e88d388528bc3841e0
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| 3 |
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size 26533682
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