Upload folder using huggingface_hub
Browse files- checkpoints/chemical_system/config.yaml +224 -0
- checkpoints/chemical_system_energy_above_hull/config.yaml +251 -0
- checkpoints/dft_band_gap/config.yaml +224 -0
- checkpoints/dft_mag_density/config.yaml +224 -0
- checkpoints/dft_mag_density_hhi_score/config.yaml +251 -0
- checkpoints/mattergen_base/config.yaml +184 -0
- checkpoints/ml_bulk_modulus/config.yaml +224 -0
- checkpoints/space_group/config.yaml +224 -0
checkpoints/chemical_system/config.yaml
ADDED
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1 |
+
adapter:
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2 |
+
adapter:
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3 |
+
_target_: mattergen.adapter.GemNetTAdapter
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4 |
+
atom_type_diffusion: mask
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5 |
+
denoise_atom_types: true
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6 |
+
gemnet:
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7 |
+
_target_: mattergen.common.gemnet.gemnet_ctrl.GemNetTCtrl
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8 |
+
atom_embedding:
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9 |
+
_target_: mattergen.common.gemnet.layers.embedding_block.AtomEmbedding
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10 |
+
emb_size: 512
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11 |
+
with_mask_type: true
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12 |
+
condition_on_adapt:
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13 |
+
- chemical_system
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14 |
+
cutoff: 7.0
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15 |
+
emb_size_atom: 512
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16 |
+
emb_size_edge: 512
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17 |
+
latent_dim: 512
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18 |
+
max_cell_images_per_dim: 5
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19 |
+
max_neighbors: 50
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20 |
+
num_blocks: 4
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21 |
+
num_targets: 1
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22 |
+
otf_graph: true
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23 |
+
regress_stress: true
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24 |
+
scale_file: /scratch/amlt_code/mattergen/common/gemnet/gemnet-dT.json
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25 |
+
hidden_dim: 512
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26 |
+
property_embeddings: {}
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27 |
+
property_embeddings_adapt:
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28 |
+
chemical_system:
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29 |
+
_target_: mattergen.property_embeddings.PropertyEmbedding
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30 |
+
conditional_embedding_module:
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31 |
+
_target_: mattergen.property_embeddings.ChemicalSystemMultiHotEmbedding
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32 |
+
hidden_dim: 512
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33 |
+
name: chemical_system
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34 |
+
scaler:
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35 |
+
_target_: torch.nn.Identity
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36 |
+
unconditional_embedding_module:
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37 |
+
_target_: mattergen.property_embeddings.EmbeddingVector
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38 |
+
hidden_dim: 512
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39 |
+
full_finetuning: true
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40 |
+
load_epoch: last
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41 |
+
model_path: checkpoints/mattergen_base
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42 |
+
data_module:
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43 |
+
_recursive_: true
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44 |
+
_target_: mattergen.common.data.datamodule.CrystDataModule
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45 |
+
average_density: 0.05771451654022283
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46 |
+
batch_size:
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47 |
+
train: 64
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48 |
+
val: 64
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+
dataset_transforms:
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50 |
+
- _partial_: true
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51 |
+
_target_: mattergen.common.data.dataset_transform.filter_sparse_properties
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52 |
+
max_epochs: 2200
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53 |
+
num_workers:
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54 |
+
train: 0
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55 |
+
val: 0
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56 |
+
properties:
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57 |
+
- chemical_system
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58 |
+
root_dir: datasets/cache/alex_mp_20/
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+
train_dataset:
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60 |
+
_target_: mattergen.common.data.dataset.CrystalDataset.from_cache_path
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61 |
+
cache_path: datasets/cache/alex_mp_20/train
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62 |
+
dataset_transforms:
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63 |
+
- _partial_: true
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64 |
+
_target_: mattergen.common.data.dataset_transform.filter_sparse_properties
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+
properties:
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66 |
+
- chemical_system
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67 |
+
transforms:
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68 |
+
- _partial_: true
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69 |
+
_target_: mattergen.common.data.transform.symmetrize_lattice
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70 |
+
- _partial_: true
|
71 |
+
_target_: mattergen.common.data.transform.set_chemical_system_string
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72 |
+
transforms:
|
73 |
+
- _partial_: true
|
74 |
+
_target_: mattergen.common.data.transform.symmetrize_lattice
|
75 |
+
- _partial_: true
|
76 |
+
_target_: mattergen.common.data.transform.set_chemical_system_string
|
77 |
+
val_dataset:
|
78 |
+
_target_: mattergen.common.data.dataset.CrystalDataset.from_cache_path
|
79 |
+
cache_path: datasets/cache/alex_mp_20/val
|
80 |
+
dataset_transforms:
|
81 |
+
- _partial_: true
|
82 |
+
_target_: mattergen.common.data.dataset_transform.filter_sparse_properties
|
83 |
+
properties:
|
84 |
+
- chemical_system
|
85 |
+
transforms:
|
86 |
+
- _partial_: true
|
87 |
+
_target_: mattergen.common.data.transform.symmetrize_lattice
|
88 |
+
- _partial_: true
|
89 |
+
_target_: mattergen.common.data.transform.set_chemical_system_string
|
90 |
+
lightning_module:
|
91 |
+
_target_: mattergen.diffusion.lightning_module.DiffusionLightningModule
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92 |
+
diffusion_module:
|
93 |
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_target_: mattergen.diffusion.diffusion_module.DiffusionModule
|
94 |
+
corruption:
|
95 |
+
_target_: mattergen.diffusion.corruption.multi_corruption.MultiCorruption
|
96 |
+
discrete_corruptions:
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+
atomic_numbers:
|
98 |
+
_target_: mattergen.diffusion.corruption.d3pm_corruption.D3PMCorruption
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99 |
+
d3pm:
|
100 |
+
_target_: mattergen.diffusion.d3pm.d3pm.MaskDiffusion
|
101 |
+
dim: 101
|
102 |
+
schedule:
|
103 |
+
_target_: mattergen.diffusion.d3pm.d3pm.create_discrete_diffusion_schedule
|
104 |
+
kind: standard
|
105 |
+
num_steps: 1000
|
106 |
+
offset: 1
|
107 |
+
sdes:
|
108 |
+
cell:
|
109 |
+
_target_: mattergen.common.diffusion.corruption.LatticeVPSDE.from_vpsde_config
|
110 |
+
vpsde_config:
|
111 |
+
beta_max: 20
|
112 |
+
beta_min: 0.1
|
113 |
+
limit_density: 0.05771451654022283
|
114 |
+
limit_var_scaling_constant: 0.25
|
115 |
+
pos:
|
116 |
+
_target_: mattergen.common.diffusion.corruption.NumAtomsVarianceAdjustedWrappedVESDE
|
117 |
+
limit_info_key: num_atoms
|
118 |
+
sigma_max: 5.0
|
119 |
+
wrapping_boundary: 1.0
|
120 |
+
loss_fn:
|
121 |
+
_target_: mattergen.common.loss.MaterialsLoss
|
122 |
+
d3pm_hybrid_lambda: 0.01
|
123 |
+
include_atomic_numbers: true
|
124 |
+
include_cell: true
|
125 |
+
include_pos: true
|
126 |
+
reduce: sum
|
127 |
+
weights:
|
128 |
+
atomic_numbers: 1.0
|
129 |
+
cell: 1.0
|
130 |
+
pos: 0.1
|
131 |
+
model:
|
132 |
+
_target_: mattergen.adapter.GemNetTAdapter
|
133 |
+
atom_type_diffusion: mask
|
134 |
+
denoise_atom_types: true
|
135 |
+
gemnet:
|
136 |
+
_target_: mattergen.common.gemnet.gemnet_ctrl.GemNetTCtrl
|
137 |
+
atom_embedding:
|
138 |
+
_target_: mattergen.common.gemnet.layers.embedding_block.AtomEmbedding
|
139 |
+
emb_size: 512
|
140 |
+
with_mask_type: true
|
141 |
+
condition_on_adapt:
|
142 |
+
- chemical_system
|
143 |
+
cutoff: 7.0
|
144 |
+
emb_size_atom: 512
|
145 |
+
emb_size_edge: 512
|
146 |
+
latent_dim: 512
|
147 |
+
max_cell_images_per_dim: 5
|
148 |
+
max_neighbors: 50
|
149 |
+
num_blocks: 4
|
150 |
+
num_targets: 1
|
151 |
+
otf_graph: true
|
152 |
+
regress_stress: true
|
153 |
+
scale_file: /scratch/amlt_code/mattergen/common/gemnet/gemnet-dT.json
|
154 |
+
hidden_dim: 512
|
155 |
+
property_embeddings: {}
|
156 |
+
property_embeddings_adapt:
|
157 |
+
chemical_system:
|
158 |
+
_target_: mattergen.property_embeddings.PropertyEmbedding
|
159 |
+
conditional_embedding_module:
|
160 |
+
_target_: mattergen.property_embeddings.ChemicalSystemMultiHotEmbedding
|
161 |
+
hidden_dim: 512
|
162 |
+
name: chemical_system
|
163 |
+
scaler:
|
164 |
+
_target_: torch.nn.Identity
|
165 |
+
unconditional_embedding_module:
|
166 |
+
_target_: mattergen.property_embeddings.EmbeddingVector
|
167 |
+
hidden_dim: 512
|
168 |
+
pre_corruption_fn:
|
169 |
+
_target_: mattergen.property_embeddings.SetEmbeddingType
|
170 |
+
dropout_fields_iid: false
|
171 |
+
p_unconditional: 0.2
|
172 |
+
optimizer_partial:
|
173 |
+
_partial_: true
|
174 |
+
_target_: torch.optim.Adam
|
175 |
+
lr: 5.0e-06
|
176 |
+
scheduler_partials:
|
177 |
+
- frequency: 1
|
178 |
+
interval: epoch
|
179 |
+
monitor: loss_train
|
180 |
+
scheduler:
|
181 |
+
_partial_: true
|
182 |
+
_target_: torch.optim.lr_scheduler.ReduceLROnPlateau
|
183 |
+
factor: 0.6
|
184 |
+
min_lr: 1.0e-06
|
185 |
+
patience: 100
|
186 |
+
verbose: true
|
187 |
+
strict: true
|
188 |
+
trainer:
|
189 |
+
_target_: pytorch_lightning.Trainer
|
190 |
+
accelerator: gpu
|
191 |
+
accumulate_grad_batches: 1
|
192 |
+
callbacks:
|
193 |
+
- _target_: pytorch_lightning.callbacks.LearningRateMonitor
|
194 |
+
log_momentum: false
|
195 |
+
logging_interval: step
|
196 |
+
- _target_: pytorch_lightning.callbacks.ModelCheckpoint
|
197 |
+
every_n_epochs: 1
|
198 |
+
filename: '{epoch}-{loss_val:.2f}'
|
199 |
+
mode: min
|
200 |
+
monitor: loss_val
|
201 |
+
save_last: true
|
202 |
+
save_top_k: 1
|
203 |
+
verbose: false
|
204 |
+
- _target_: pytorch_lightning.callbacks.TQDMProgressBar
|
205 |
+
refresh_rate: 50
|
206 |
+
- _target_: mattergen.common.data.callback.SetPropertyScalers
|
207 |
+
check_val_every_n_epoch: 1
|
208 |
+
devices: 8
|
209 |
+
gradient_clip_algorithm: value
|
210 |
+
gradient_clip_val: 0.5
|
211 |
+
logger:
|
212 |
+
_target_: pytorch_lightning.loggers.WandbLogger
|
213 |
+
job_type: train_finetune
|
214 |
+
project: crystal-generation
|
215 |
+
settings:
|
216 |
+
_save_requirements: false
|
217 |
+
_target_: wandb.Settings
|
218 |
+
start_method: fork
|
219 |
+
max_epochs: 200
|
220 |
+
num_nodes: 1
|
221 |
+
precision: 32
|
222 |
+
strategy:
|
223 |
+
_target_: pytorch_lightning.strategies.ddp.DDPStrategy
|
224 |
+
find_unused_parameters: true
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checkpoints/chemical_system_energy_above_hull/config.yaml
ADDED
@@ -0,0 +1,251 @@
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|
1 |
+
adapter:
|
2 |
+
adapter:
|
3 |
+
_target_: mattergen.adapter.GemNetTAdapter
|
4 |
+
atom_type_diffusion: mask
|
5 |
+
denoise_atom_types: true
|
6 |
+
gemnet:
|
7 |
+
_target_: mattergen.common.gemnet.gemnet_ctrl.GemNetTCtrl
|
8 |
+
atom_embedding:
|
9 |
+
_target_: mattergen.common.gemnet.layers.embedding_block.AtomEmbedding
|
10 |
+
emb_size: 512
|
11 |
+
with_mask_type: true
|
12 |
+
condition_on_adapt:
|
13 |
+
- chemical_system
|
14 |
+
- energy_above_hull
|
15 |
+
cutoff: 7.0
|
16 |
+
emb_size_atom: 512
|
17 |
+
emb_size_edge: 512
|
18 |
+
latent_dim: 512
|
19 |
+
max_cell_images_per_dim: 5
|
20 |
+
max_neighbors: 50
|
21 |
+
num_blocks: 4
|
22 |
+
num_targets: 1
|
23 |
+
otf_graph: true
|
24 |
+
regress_stress: true
|
25 |
+
scale_file: /scratch/amlt_code/mattergen/common/gemnet/gemnet-dT.json
|
26 |
+
hidden_dim: 512
|
27 |
+
property_embeddings: {}
|
28 |
+
property_embeddings_adapt:
|
29 |
+
chemical_system:
|
30 |
+
_target_: mattergen.property_embeddings.PropertyEmbedding
|
31 |
+
conditional_embedding_module:
|
32 |
+
_target_: mattergen.property_embeddings.ChemicalSystemMultiHotEmbedding
|
33 |
+
hidden_dim: 512
|
34 |
+
name: chemical_system
|
35 |
+
scaler:
|
36 |
+
_target_: torch.nn.Identity
|
37 |
+
unconditional_embedding_module:
|
38 |
+
_target_: mattergen.property_embeddings.EmbeddingVector
|
39 |
+
hidden_dim: 512
|
40 |
+
energy_above_hull:
|
41 |
+
_target_: mattergen.property_embeddings.PropertyEmbedding
|
42 |
+
conditional_embedding_module:
|
43 |
+
_target_: mattergen.diffusion.model_utils.NoiseLevelEncoding
|
44 |
+
d_model: 512
|
45 |
+
name: energy_above_hull
|
46 |
+
scaler:
|
47 |
+
_target_: mattergen.common.utils.data_utils.StandardScalerTorch
|
48 |
+
unconditional_embedding_module:
|
49 |
+
_target_: mattergen.property_embeddings.EmbeddingVector
|
50 |
+
hidden_dim: 512
|
51 |
+
full_finetuning: true
|
52 |
+
load_epoch: last
|
53 |
+
model_path: checkpoints/mattergen_base
|
54 |
+
data_module:
|
55 |
+
_recursive_: true
|
56 |
+
_target_: mattergen.common.data.datamodule.CrystDataModule
|
57 |
+
average_density: 0.05771451654022283
|
58 |
+
batch_size:
|
59 |
+
train: 64
|
60 |
+
val: 64
|
61 |
+
dataset_transforms:
|
62 |
+
- _partial_: true
|
63 |
+
_target_: mattergen.common.data.dataset_transform.filter_sparse_properties
|
64 |
+
max_epochs: 2200
|
65 |
+
num_workers:
|
66 |
+
train: 0
|
67 |
+
val: 0
|
68 |
+
properties:
|
69 |
+
- chemical_system
|
70 |
+
- energy_above_hull
|
71 |
+
root_dir: datasets/cache/alex_mp_20
|
72 |
+
train_dataset:
|
73 |
+
_target_: mattergen.common.data.dataset.CrystalDataset.from_cache_path
|
74 |
+
cache_path: datasets/cache/alex_mp_20/train
|
75 |
+
dataset_transforms:
|
76 |
+
- _partial_: true
|
77 |
+
_target_: mattergen.common.data.dataset_transform.filter_sparse_properties
|
78 |
+
properties:
|
79 |
+
- chemical_system
|
80 |
+
- energy_above_hull
|
81 |
+
transforms:
|
82 |
+
- _partial_: true
|
83 |
+
_target_: mattergen.common.data.transform.symmetrize_lattice
|
84 |
+
- _partial_: true
|
85 |
+
_target_: mattergen.common.data.transform.set_chemical_system_string
|
86 |
+
transforms:
|
87 |
+
- _partial_: true
|
88 |
+
_target_: mattergen.common.data.transform.symmetrize_lattice
|
89 |
+
- _partial_: true
|
90 |
+
_target_: mattergen.common.data.transform.set_chemical_system_string
|
91 |
+
val_dataset:
|
92 |
+
_target_: mattergen.common.data.dataset.CrystalDataset.from_cache_path
|
93 |
+
cache_path: datasets/cache/alex_mp_20/val
|
94 |
+
dataset_transforms:
|
95 |
+
- _partial_: true
|
96 |
+
_target_: mattergen.common.data.dataset_transform.filter_sparse_properties
|
97 |
+
properties:
|
98 |
+
- chemical_system
|
99 |
+
- energy_above_hull
|
100 |
+
transforms:
|
101 |
+
- _partial_: true
|
102 |
+
_target_: mattergen.common.data.transform.symmetrize_lattice
|
103 |
+
- _partial_: true
|
104 |
+
_target_: mattergen.common.data.transform.set_chemical_system_string
|
105 |
+
lightning_module:
|
106 |
+
_target_: mattergen.diffusion.lightning_module.DiffusionLightningModule
|
107 |
+
diffusion_module:
|
108 |
+
_target_: mattergen.diffusion.diffusion_module.DiffusionModule
|
109 |
+
corruption:
|
110 |
+
_target_: mattergen.diffusion.corruption.multi_corruption.MultiCorruption
|
111 |
+
discrete_corruptions:
|
112 |
+
atomic_numbers:
|
113 |
+
_target_: mattergen.diffusion.corruption.d3pm_corruption.D3PMCorruption
|
114 |
+
d3pm:
|
115 |
+
_target_: mattergen.diffusion.d3pm.d3pm.MaskDiffusion
|
116 |
+
dim: 101
|
117 |
+
schedule:
|
118 |
+
_target_: mattergen.diffusion.d3pm.d3pm.create_discrete_diffusion_schedule
|
119 |
+
kind: standard
|
120 |
+
num_steps: 1000
|
121 |
+
offset: 1
|
122 |
+
sdes:
|
123 |
+
cell:
|
124 |
+
_target_: mattergen.common.diffusion.corruption.LatticeVPSDE.from_vpsde_config
|
125 |
+
vpsde_config:
|
126 |
+
beta_max: 20
|
127 |
+
beta_min: 0.1
|
128 |
+
limit_density: 0.05771451654022283
|
129 |
+
limit_var_scaling_constant: 0.25
|
130 |
+
pos:
|
131 |
+
_target_: mattergen.common.diffusion.corruption.NumAtomsVarianceAdjustedWrappedVESDE
|
132 |
+
limit_info_key: num_atoms
|
133 |
+
sigma_max: 5.0
|
134 |
+
wrapping_boundary: 1.0
|
135 |
+
loss_fn:
|
136 |
+
_target_: mattergen.common.loss.MaterialsLoss
|
137 |
+
d3pm_hybrid_lambda: 0.01
|
138 |
+
include_atomic_numbers: true
|
139 |
+
include_cell: true
|
140 |
+
include_pos: true
|
141 |
+
reduce: sum
|
142 |
+
weights:
|
143 |
+
atomic_numbers: 1.0
|
144 |
+
cell: 1.0
|
145 |
+
pos: 0.1
|
146 |
+
model:
|
147 |
+
_target_: mattergen.adapter.GemNetTAdapter
|
148 |
+
atom_type_diffusion: mask
|
149 |
+
denoise_atom_types: true
|
150 |
+
gemnet:
|
151 |
+
_target_: mattergen.common.gemnet.gemnet_ctrl.GemNetTCtrl
|
152 |
+
atom_embedding:
|
153 |
+
_target_: mattergen.common.gemnet.layers.embedding_block.AtomEmbedding
|
154 |
+
emb_size: 512
|
155 |
+
with_mask_type: true
|
156 |
+
condition_on_adapt:
|
157 |
+
- chemical_system
|
158 |
+
- energy_above_hull
|
159 |
+
cutoff: 7.0
|
160 |
+
emb_size_atom: 512
|
161 |
+
emb_size_edge: 512
|
162 |
+
latent_dim: 512
|
163 |
+
max_cell_images_per_dim: 5
|
164 |
+
max_neighbors: 50
|
165 |
+
num_blocks: 4
|
166 |
+
num_targets: 1
|
167 |
+
otf_graph: true
|
168 |
+
regress_stress: true
|
169 |
+
scale_file: /scratch/amlt_code/mattergen/common/gemnet/gemnet-dT.json
|
170 |
+
hidden_dim: 512
|
171 |
+
property_embeddings: {}
|
172 |
+
property_embeddings_adapt:
|
173 |
+
chemical_system:
|
174 |
+
_target_: mattergen.property_embeddings.PropertyEmbedding
|
175 |
+
conditional_embedding_module:
|
176 |
+
_target_: mattergen.property_embeddings.ChemicalSystemMultiHotEmbedding
|
177 |
+
hidden_dim: 512
|
178 |
+
name: chemical_system
|
179 |
+
scaler:
|
180 |
+
_target_: torch.nn.Identity
|
181 |
+
unconditional_embedding_module:
|
182 |
+
_target_: mattergen.property_embeddings.EmbeddingVector
|
183 |
+
hidden_dim: 512
|
184 |
+
energy_above_hull:
|
185 |
+
_target_: mattergen.property_embeddings.PropertyEmbedding
|
186 |
+
conditional_embedding_module:
|
187 |
+
_target_: mattergen.diffusion.model_utils.NoiseLevelEncoding
|
188 |
+
d_model: 512
|
189 |
+
name: energy_above_hull
|
190 |
+
scaler:
|
191 |
+
_target_: mattergen.common.utils.data_utils.StandardScalerTorch
|
192 |
+
unconditional_embedding_module:
|
193 |
+
_target_: mattergen.property_embeddings.EmbeddingVector
|
194 |
+
hidden_dim: 512
|
195 |
+
pre_corruption_fn:
|
196 |
+
_target_: mattergen.property_embeddings.SetEmbeddingType
|
197 |
+
dropout_fields_iid: false
|
198 |
+
p_unconditional: 0.2
|
199 |
+
optimizer_partial:
|
200 |
+
_partial_: true
|
201 |
+
_target_: torch.optim.Adam
|
202 |
+
lr: 5.0e-06
|
203 |
+
scheduler_partials:
|
204 |
+
- frequency: 1
|
205 |
+
interval: epoch
|
206 |
+
monitor: loss_train
|
207 |
+
scheduler:
|
208 |
+
_partial_: true
|
209 |
+
_target_: torch.optim.lr_scheduler.ReduceLROnPlateau
|
210 |
+
factor: 0.6
|
211 |
+
min_lr: 1.0e-06
|
212 |
+
patience: 100
|
213 |
+
verbose: true
|
214 |
+
strict: true
|
215 |
+
trainer:
|
216 |
+
_target_: pytorch_lightning.Trainer
|
217 |
+
accelerator: gpu
|
218 |
+
accumulate_grad_batches: 1
|
219 |
+
callbacks:
|
220 |
+
- _target_: pytorch_lightning.callbacks.LearningRateMonitor
|
221 |
+
log_momentum: false
|
222 |
+
logging_interval: step
|
223 |
+
- _target_: pytorch_lightning.callbacks.ModelCheckpoint
|
224 |
+
every_n_epochs: 1
|
225 |
+
filename: '{epoch}-{loss_val:.2f}'
|
226 |
+
mode: min
|
227 |
+
monitor: loss_val
|
228 |
+
save_last: true
|
229 |
+
save_top_k: 1
|
230 |
+
verbose: false
|
231 |
+
- _target_: pytorch_lightning.callbacks.TQDMProgressBar
|
232 |
+
refresh_rate: 50
|
233 |
+
- _target_: mattergen.common.data.callback.SetPropertyScalers
|
234 |
+
check_val_every_n_epoch: 5
|
235 |
+
devices: 8
|
236 |
+
gradient_clip_algorithm: value
|
237 |
+
gradient_clip_val: 0.5
|
238 |
+
logger:
|
239 |
+
_target_: pytorch_lightning.loggers.WandbLogger
|
240 |
+
job_type: train_finetune
|
241 |
+
project: crystal-generation
|
242 |
+
settings:
|
243 |
+
_save_requirements: false
|
244 |
+
_target_: wandb.Settings
|
245 |
+
start_method: fork
|
246 |
+
max_epochs: 200
|
247 |
+
num_nodes: 1
|
248 |
+
precision: 32
|
249 |
+
strategy:
|
250 |
+
_target_: pytorch_lightning.strategies.ddp.DDPStrategy
|
251 |
+
find_unused_parameters: true
|
checkpoints/dft_band_gap/config.yaml
ADDED
@@ -0,0 +1,224 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
adapter:
|
2 |
+
adapter:
|
3 |
+
_target_: mattergen.adapter.GemNetTAdapter
|
4 |
+
atom_type_diffusion: mask
|
5 |
+
denoise_atom_types: true
|
6 |
+
gemnet:
|
7 |
+
_target_: mattergen.common.gemnet.gemnet_ctrl.GemNetTCtrl
|
8 |
+
atom_embedding:
|
9 |
+
_target_: mattergen.common.gemnet.layers.embedding_block.AtomEmbedding
|
10 |
+
emb_size: 512
|
11 |
+
with_mask_type: true
|
12 |
+
condition_on_adapt:
|
13 |
+
- dft_band_gap
|
14 |
+
cutoff: 7.0
|
15 |
+
emb_size_atom: 512
|
16 |
+
emb_size_edge: 512
|
17 |
+
latent_dim: 512
|
18 |
+
max_cell_images_per_dim: 5
|
19 |
+
max_neighbors: 50
|
20 |
+
num_blocks: 4
|
21 |
+
num_targets: 1
|
22 |
+
otf_graph: true
|
23 |
+
regress_stress: true
|
24 |
+
scale_file: /scratch/amlt_code/mattergen/common/gemnet/gemnet-dT.json
|
25 |
+
hidden_dim: 512
|
26 |
+
property_embeddings: {}
|
27 |
+
property_embeddings_adapt:
|
28 |
+
dft_band_gap:
|
29 |
+
_target_: mattergen.property_embeddings.PropertyEmbedding
|
30 |
+
conditional_embedding_module:
|
31 |
+
_target_: mattergen.diffusion.model_utils.NoiseLevelEncoding
|
32 |
+
d_model: 512
|
33 |
+
name: dft_band_gap
|
34 |
+
scaler:
|
35 |
+
_target_: mattergen.common.utils.data_utils.StandardScalerTorch
|
36 |
+
unconditional_embedding_module:
|
37 |
+
_target_: mattergen.property_embeddings.EmbeddingVector
|
38 |
+
hidden_dim: 512
|
39 |
+
full_finetuning: true
|
40 |
+
load_epoch: last
|
41 |
+
model_path: checkpoints/mattergen_base
|
42 |
+
data_module:
|
43 |
+
_recursive_: true
|
44 |
+
_target_: mattergen.common.data.datamodule.CrystDataModule
|
45 |
+
average_density: 0.05771451654022283
|
46 |
+
batch_size:
|
47 |
+
train: 64
|
48 |
+
val: 64
|
49 |
+
dataset_transforms:
|
50 |
+
- _partial_: true
|
51 |
+
_target_: mattergen.common.data.dataset_transform.filter_sparse_properties
|
52 |
+
max_epochs: 2200
|
53 |
+
num_workers:
|
54 |
+
train: 0
|
55 |
+
val: 0
|
56 |
+
properties:
|
57 |
+
- dft_band_gap
|
58 |
+
root_dir: datasets/cache/alex_mp_20
|
59 |
+
train_dataset:
|
60 |
+
_target_: mattergen.common.data.dataset.CrystalDataset.from_cache_path
|
61 |
+
cache_path: datasets/cache/alex_mp_20/train
|
62 |
+
dataset_transforms:
|
63 |
+
- _partial_: true
|
64 |
+
_target_: mattergen.common.data.dataset_transform.filter_sparse_properties
|
65 |
+
properties:
|
66 |
+
- dft_band_gap
|
67 |
+
transforms:
|
68 |
+
- _partial_: true
|
69 |
+
_target_: mattergen.common.data.transform.symmetrize_lattice
|
70 |
+
- _partial_: true
|
71 |
+
_target_: mattergen.common.data.transform.set_chemical_system_string
|
72 |
+
transforms:
|
73 |
+
- _partial_: true
|
74 |
+
_target_: mattergen.common.data.transform.symmetrize_lattice
|
75 |
+
- _partial_: true
|
76 |
+
_target_: mattergen.common.data.transform.set_chemical_system_string
|
77 |
+
val_dataset:
|
78 |
+
_target_: mattergen.common.data.dataset.CrystalDataset.from_cache_path
|
79 |
+
cache_path: datasets/cache/alex_mp_20/val
|
80 |
+
dataset_transforms:
|
81 |
+
- _partial_: true
|
82 |
+
_target_: mattergen.common.data.dataset_transform.filter_sparse_properties
|
83 |
+
properties:
|
84 |
+
- dft_band_gap
|
85 |
+
transforms:
|
86 |
+
- _partial_: true
|
87 |
+
_target_: mattergen.common.data.transform.symmetrize_lattice
|
88 |
+
- _partial_: true
|
89 |
+
_target_: mattergen.common.data.transform.set_chemical_system_string
|
90 |
+
lightning_module:
|
91 |
+
_target_: mattergen.diffusion.lightning_module.DiffusionLightningModule
|
92 |
+
diffusion_module:
|
93 |
+
_target_: mattergen.diffusion.diffusion_module.DiffusionModule
|
94 |
+
corruption:
|
95 |
+
_target_: mattergen.diffusion.corruption.multi_corruption.MultiCorruption
|
96 |
+
discrete_corruptions:
|
97 |
+
atomic_numbers:
|
98 |
+
_target_: mattergen.diffusion.corruption.d3pm_corruption.D3PMCorruption
|
99 |
+
d3pm:
|
100 |
+
_target_: mattergen.diffusion.d3pm.d3pm.MaskDiffusion
|
101 |
+
dim: 101
|
102 |
+
schedule:
|
103 |
+
_target_: mattergen.diffusion.d3pm.d3pm.create_discrete_diffusion_schedule
|
104 |
+
kind: standard
|
105 |
+
num_steps: 1000
|
106 |
+
offset: 1
|
107 |
+
sdes:
|
108 |
+
cell:
|
109 |
+
_target_: mattergen.common.diffusion.corruption.LatticeVPSDE.from_vpsde_config
|
110 |
+
vpsde_config:
|
111 |
+
beta_max: 20
|
112 |
+
beta_min: 0.1
|
113 |
+
limit_density: 0.05771451654022283
|
114 |
+
limit_var_scaling_constant: 0.25
|
115 |
+
pos:
|
116 |
+
_target_: mattergen.common.diffusion.corruption.NumAtomsVarianceAdjustedWrappedVESDE
|
117 |
+
limit_info_key: num_atoms
|
118 |
+
sigma_max: 5.0
|
119 |
+
wrapping_boundary: 1.0
|
120 |
+
loss_fn:
|
121 |
+
_target_: mattergen.common.loss.MaterialsLoss
|
122 |
+
d3pm_hybrid_lambda: 0.01
|
123 |
+
include_atomic_numbers: true
|
124 |
+
include_cell: true
|
125 |
+
include_pos: true
|
126 |
+
reduce: sum
|
127 |
+
weights:
|
128 |
+
atomic_numbers: 1.0
|
129 |
+
cell: 1.0
|
130 |
+
pos: 0.1
|
131 |
+
model:
|
132 |
+
_target_: mattergen.adapter.GemNetTAdapter
|
133 |
+
atom_type_diffusion: mask
|
134 |
+
denoise_atom_types: true
|
135 |
+
gemnet:
|
136 |
+
_target_: mattergen.common.gemnet.gemnet_ctrl.GemNetTCtrl
|
137 |
+
atom_embedding:
|
138 |
+
_target_: mattergen.common.gemnet.layers.embedding_block.AtomEmbedding
|
139 |
+
emb_size: 512
|
140 |
+
with_mask_type: true
|
141 |
+
condition_on_adapt:
|
142 |
+
- dft_band_gap
|
143 |
+
cutoff: 7.0
|
144 |
+
emb_size_atom: 512
|
145 |
+
emb_size_edge: 512
|
146 |
+
latent_dim: 512
|
147 |
+
max_cell_images_per_dim: 5
|
148 |
+
max_neighbors: 50
|
149 |
+
num_blocks: 4
|
150 |
+
num_targets: 1
|
151 |
+
otf_graph: true
|
152 |
+
regress_stress: true
|
153 |
+
scale_file: /scratch/amlt_code/mattergen/common/gemnet/gemnet-dT.json
|
154 |
+
hidden_dim: 512
|
155 |
+
property_embeddings: {}
|
156 |
+
property_embeddings_adapt:
|
157 |
+
dft_band_gap:
|
158 |
+
_target_: mattergen.property_embeddings.PropertyEmbedding
|
159 |
+
conditional_embedding_module:
|
160 |
+
_target_: mattergen.diffusion.model_utils.NoiseLevelEncoding
|
161 |
+
d_model: 512
|
162 |
+
name: dft_band_gap
|
163 |
+
scaler:
|
164 |
+
_target_: mattergen.common.utils.data_utils.StandardScalerTorch
|
165 |
+
unconditional_embedding_module:
|
166 |
+
_target_: mattergen.property_embeddings.EmbeddingVector
|
167 |
+
hidden_dim: 512
|
168 |
+
pre_corruption_fn:
|
169 |
+
_target_: mattergen.property_embeddings.SetEmbeddingType
|
170 |
+
dropout_fields_iid: false
|
171 |
+
p_unconditional: 0.2
|
172 |
+
optimizer_partial:
|
173 |
+
_partial_: true
|
174 |
+
_target_: torch.optim.Adam
|
175 |
+
lr: 5.0e-06
|
176 |
+
scheduler_partials:
|
177 |
+
- frequency: 1
|
178 |
+
interval: epoch
|
179 |
+
monitor: loss_train
|
180 |
+
scheduler:
|
181 |
+
_partial_: true
|
182 |
+
_target_: torch.optim.lr_scheduler.ReduceLROnPlateau
|
183 |
+
factor: 0.6
|
184 |
+
min_lr: 1.0e-06
|
185 |
+
patience: 100
|
186 |
+
verbose: true
|
187 |
+
strict: true
|
188 |
+
trainer:
|
189 |
+
_target_: pytorch_lightning.Trainer
|
190 |
+
accelerator: gpu
|
191 |
+
accumulate_grad_batches: 1
|
192 |
+
callbacks:
|
193 |
+
- _target_: pytorch_lightning.callbacks.LearningRateMonitor
|
194 |
+
log_momentum: false
|
195 |
+
logging_interval: step
|
196 |
+
- _target_: pytorch_lightning.callbacks.ModelCheckpoint
|
197 |
+
every_n_epochs: 1
|
198 |
+
filename: '{epoch}-{loss_val:.2f}'
|
199 |
+
mode: min
|
200 |
+
monitor: loss_val
|
201 |
+
save_last: true
|
202 |
+
save_top_k: 1
|
203 |
+
verbose: false
|
204 |
+
- _target_: pytorch_lightning.callbacks.TQDMProgressBar
|
205 |
+
refresh_rate: 50
|
206 |
+
- _target_: mattergen.common.data.callback.SetPropertyScalers
|
207 |
+
check_val_every_n_epoch: 5
|
208 |
+
devices: 8
|
209 |
+
gradient_clip_algorithm: value
|
210 |
+
gradient_clip_val: 0.5
|
211 |
+
logger:
|
212 |
+
_target_: pytorch_lightning.loggers.WandbLogger
|
213 |
+
job_type: train_finetune
|
214 |
+
project: crystal-generation
|
215 |
+
settings:
|
216 |
+
_save_requirements: false
|
217 |
+
_target_: wandb.Settings
|
218 |
+
start_method: fork
|
219 |
+
max_epochs: 200
|
220 |
+
num_nodes: 1
|
221 |
+
precision: 32
|
222 |
+
strategy:
|
223 |
+
_target_: pytorch_lightning.strategies.ddp.DDPStrategy
|
224 |
+
find_unused_parameters: true
|
checkpoints/dft_mag_density/config.yaml
ADDED
@@ -0,0 +1,224 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
adapter:
|
2 |
+
adapter:
|
3 |
+
_target_: mattergen.adapter.GemNetTAdapter
|
4 |
+
atom_type_diffusion: mask
|
5 |
+
denoise_atom_types: true
|
6 |
+
gemnet:
|
7 |
+
_target_: mattergen.common.gemnet.gemnet_ctrl.GemNetTCtrl
|
8 |
+
atom_embedding:
|
9 |
+
_target_: mattergen.common.gemnet.layers.embedding_block.AtomEmbedding
|
10 |
+
emb_size: 512
|
11 |
+
with_mask_type: true
|
12 |
+
condition_on_adapt:
|
13 |
+
- dft_mag_density
|
14 |
+
cutoff: 7.0
|
15 |
+
emb_size_atom: 512
|
16 |
+
emb_size_edge: 512
|
17 |
+
latent_dim: 512
|
18 |
+
max_cell_images_per_dim: 5
|
19 |
+
max_neighbors: 50
|
20 |
+
num_blocks: 4
|
21 |
+
num_targets: 1
|
22 |
+
otf_graph: true
|
23 |
+
regress_stress: true
|
24 |
+
scale_file: /scratch/amlt_code/mattergen/common/gemnet/gemnet-dT.json
|
25 |
+
hidden_dim: 512
|
26 |
+
property_embeddings: {}
|
27 |
+
property_embeddings_adapt:
|
28 |
+
dft_mag_density:
|
29 |
+
_target_: mattergen.property_embeddings.PropertyEmbedding
|
30 |
+
conditional_embedding_module:
|
31 |
+
_target_: mattergen.diffusion.model_utils.NoiseLevelEncoding
|
32 |
+
d_model: 512
|
33 |
+
name: dft_mag_density
|
34 |
+
scaler:
|
35 |
+
_target_: mattergen.common.utils.data_utils.StandardScalerTorch
|
36 |
+
unconditional_embedding_module:
|
37 |
+
_target_: mattergen.property_embeddings.EmbeddingVector
|
38 |
+
hidden_dim: 512
|
39 |
+
full_finetuning: true
|
40 |
+
load_epoch: last
|
41 |
+
model_path: checkpoints/mattergen_base
|
42 |
+
data_module:
|
43 |
+
_recursive_: true
|
44 |
+
_target_: mattergen.common.data.datamodule.CrystDataModule
|
45 |
+
average_density: 0.05771451654022283
|
46 |
+
batch_size:
|
47 |
+
train: 64
|
48 |
+
val: 64
|
49 |
+
dataset_transforms:
|
50 |
+
- _partial_: true
|
51 |
+
_target_: mattergen.common.data.dataset_transform.filter_sparse_properties
|
52 |
+
max_epochs: 2200
|
53 |
+
num_workers:
|
54 |
+
train: 0
|
55 |
+
val: 0
|
56 |
+
properties:
|
57 |
+
- dft_mag_density
|
58 |
+
root_dir: datasets/cache/alex_mp_20
|
59 |
+
train_dataset:
|
60 |
+
_target_: mattergen.common.data.dataset.CrystalDataset.from_cache_path
|
61 |
+
cache_path: datasets/cache/alex_mp_20/train
|
62 |
+
dataset_transforms:
|
63 |
+
- _partial_: true
|
64 |
+
_target_: mattergen.common.data.dataset_transform.filter_sparse_properties
|
65 |
+
properties:
|
66 |
+
- dft_mag_density
|
67 |
+
transforms:
|
68 |
+
- _partial_: true
|
69 |
+
_target_: mattergen.common.data.transform.symmetrize_lattice
|
70 |
+
- _partial_: true
|
71 |
+
_target_: mattergen.common.data.transform.set_chemical_system_string
|
72 |
+
transforms:
|
73 |
+
- _partial_: true
|
74 |
+
_target_: mattergen.common.data.transform.symmetrize_lattice
|
75 |
+
- _partial_: true
|
76 |
+
_target_: mattergen.common.data.transform.set_chemical_system_string
|
77 |
+
val_dataset:
|
78 |
+
_target_: mattergen.common.data.dataset.CrystalDataset.from_cache_path
|
79 |
+
cache_path: datasets/cache/alex_mp_20/val
|
80 |
+
dataset_transforms:
|
81 |
+
- _partial_: true
|
82 |
+
_target_: mattergen.common.data.dataset_transform.filter_sparse_properties
|
83 |
+
properties:
|
84 |
+
- dft_mag_density
|
85 |
+
transforms:
|
86 |
+
- _partial_: true
|
87 |
+
_target_: mattergen.common.data.transform.symmetrize_lattice
|
88 |
+
- _partial_: true
|
89 |
+
_target_: mattergen.common.data.transform.set_chemical_system_string
|
90 |
+
lightning_module:
|
91 |
+
_target_: mattergen.diffusion.lightning_module.DiffusionLightningModule
|
92 |
+
diffusion_module:
|
93 |
+
_target_: mattergen.diffusion.diffusion_module.DiffusionModule
|
94 |
+
corruption:
|
95 |
+
_target_: mattergen.diffusion.corruption.multi_corruption.MultiCorruption
|
96 |
+
discrete_corruptions:
|
97 |
+
atomic_numbers:
|
98 |
+
_target_: mattergen.diffusion.corruption.d3pm_corruption.D3PMCorruption
|
99 |
+
d3pm:
|
100 |
+
_target_: mattergen.diffusion.d3pm.d3pm.MaskDiffusion
|
101 |
+
dim: 101
|
102 |
+
schedule:
|
103 |
+
_target_: mattergen.diffusion.d3pm.d3pm.create_discrete_diffusion_schedule
|
104 |
+
kind: standard
|
105 |
+
num_steps: 1000
|
106 |
+
offset: 1
|
107 |
+
sdes:
|
108 |
+
cell:
|
109 |
+
_target_: mattergen.common.diffusion.corruption.LatticeVPSDE.from_vpsde_config
|
110 |
+
vpsde_config:
|
111 |
+
beta_max: 20
|
112 |
+
beta_min: 0.1
|
113 |
+
limit_density: 0.05771451654022283
|
114 |
+
limit_var_scaling_constant: 0.25
|
115 |
+
pos:
|
116 |
+
_target_: mattergen.common.diffusion.corruption.NumAtomsVarianceAdjustedWrappedVESDE
|
117 |
+
limit_info_key: num_atoms
|
118 |
+
sigma_max: 5.0
|
119 |
+
wrapping_boundary: 1.0
|
120 |
+
loss_fn:
|
121 |
+
_target_: mattergen.common.loss.MaterialsLoss
|
122 |
+
d3pm_hybrid_lambda: 0.01
|
123 |
+
include_atomic_numbers: true
|
124 |
+
include_cell: true
|
125 |
+
include_pos: true
|
126 |
+
reduce: sum
|
127 |
+
weights:
|
128 |
+
atomic_numbers: 1.0
|
129 |
+
cell: 1.0
|
130 |
+
pos: 0.1
|
131 |
+
model:
|
132 |
+
_target_: mattergen.adapter.GemNetTAdapter
|
133 |
+
atom_type_diffusion: mask
|
134 |
+
denoise_atom_types: true
|
135 |
+
gemnet:
|
136 |
+
_target_: mattergen.common.gemnet.gemnet_ctrl.GemNetTCtrl
|
137 |
+
atom_embedding:
|
138 |
+
_target_: mattergen.common.gemnet.layers.embedding_block.AtomEmbedding
|
139 |
+
emb_size: 512
|
140 |
+
with_mask_type: true
|
141 |
+
condition_on_adapt:
|
142 |
+
- dft_mag_density
|
143 |
+
cutoff: 7.0
|
144 |
+
emb_size_atom: 512
|
145 |
+
emb_size_edge: 512
|
146 |
+
latent_dim: 512
|
147 |
+
max_cell_images_per_dim: 5
|
148 |
+
max_neighbors: 50
|
149 |
+
num_blocks: 4
|
150 |
+
num_targets: 1
|
151 |
+
otf_graph: true
|
152 |
+
regress_stress: true
|
153 |
+
scale_file: /scratch/amlt_code/mattergen/common/gemnet/gemnet-dT.json
|
154 |
+
hidden_dim: 512
|
155 |
+
property_embeddings: {}
|
156 |
+
property_embeddings_adapt:
|
157 |
+
dft_mag_density:
|
158 |
+
_target_: mattergen.property_embeddings.PropertyEmbedding
|
159 |
+
conditional_embedding_module:
|
160 |
+
_target_: mattergen.diffusion.model_utils.NoiseLevelEncoding
|
161 |
+
d_model: 512
|
162 |
+
name: dft_mag_density
|
163 |
+
scaler:
|
164 |
+
_target_: mattergen.common.utils.data_utils.StandardScalerTorch
|
165 |
+
unconditional_embedding_module:
|
166 |
+
_target_: mattergen.property_embeddings.EmbeddingVector
|
167 |
+
hidden_dim: 512
|
168 |
+
pre_corruption_fn:
|
169 |
+
_target_: mattergen.property_embeddings.SetEmbeddingType
|
170 |
+
dropout_fields_iid: false
|
171 |
+
p_unconditional: 0.2
|
172 |
+
optimizer_partial:
|
173 |
+
_partial_: true
|
174 |
+
_target_: torch.optim.Adam
|
175 |
+
lr: 5.0e-06
|
176 |
+
scheduler_partials:
|
177 |
+
- frequency: 1
|
178 |
+
interval: epoch
|
179 |
+
monitor: loss_train
|
180 |
+
scheduler:
|
181 |
+
_partial_: true
|
182 |
+
_target_: torch.optim.lr_scheduler.ReduceLROnPlateau
|
183 |
+
factor: 0.6
|
184 |
+
min_lr: 1.0e-06
|
185 |
+
patience: 100
|
186 |
+
verbose: true
|
187 |
+
strict: true
|
188 |
+
trainer:
|
189 |
+
_target_: pytorch_lightning.Trainer
|
190 |
+
accelerator: gpu
|
191 |
+
accumulate_grad_batches: 1
|
192 |
+
callbacks:
|
193 |
+
- _target_: pytorch_lightning.callbacks.LearningRateMonitor
|
194 |
+
log_momentum: false
|
195 |
+
logging_interval: step
|
196 |
+
- _target_: pytorch_lightning.callbacks.ModelCheckpoint
|
197 |
+
every_n_epochs: 1
|
198 |
+
filename: '{epoch}-{loss_val:.2f}'
|
199 |
+
mode: min
|
200 |
+
monitor: loss_val
|
201 |
+
save_last: true
|
202 |
+
save_top_k: 1
|
203 |
+
verbose: false
|
204 |
+
- _target_: pytorch_lightning.callbacks.TQDMProgressBar
|
205 |
+
refresh_rate: 50
|
206 |
+
- _target_: mattergen.common.data.callback.SetPropertyScalers
|
207 |
+
check_val_every_n_epoch: 1
|
208 |
+
devices: 8
|
209 |
+
gradient_clip_algorithm: value
|
210 |
+
gradient_clip_val: 0.5
|
211 |
+
logger:
|
212 |
+
_target_: pytorch_lightning.loggers.WandbLogger
|
213 |
+
job_type: train_finetune
|
214 |
+
project: crystal-generation
|
215 |
+
settings:
|
216 |
+
_save_requirements: false
|
217 |
+
_target_: wandb.Settings
|
218 |
+
start_method: fork
|
219 |
+
max_epochs: 200
|
220 |
+
num_nodes: 1
|
221 |
+
precision: 32
|
222 |
+
strategy:
|
223 |
+
_target_: pytorch_lightning.strategies.ddp.DDPStrategy
|
224 |
+
find_unused_parameters: true
|
checkpoints/dft_mag_density_hhi_score/config.yaml
ADDED
@@ -0,0 +1,251 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
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|
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|
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|
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|
|
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|
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|
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|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
adapter:
|
2 |
+
adapter:
|
3 |
+
_target_: mattergen.adapter.GemNetTAdapter
|
4 |
+
atom_type_diffusion: mask
|
5 |
+
denoise_atom_types: true
|
6 |
+
gemnet:
|
7 |
+
_target_: mattergen.common.gemnet.gemnet_ctrl.GemNetTCtrl
|
8 |
+
atom_embedding:
|
9 |
+
_target_: mattergen.common.gemnet.layers.embedding_block.AtomEmbedding
|
10 |
+
emb_size: 512
|
11 |
+
with_mask_type: true
|
12 |
+
condition_on_adapt:
|
13 |
+
- dft_mag_density
|
14 |
+
- hhi_score
|
15 |
+
cutoff: 7.0
|
16 |
+
emb_size_atom: 512
|
17 |
+
emb_size_edge: 512
|
18 |
+
latent_dim: 512
|
19 |
+
max_cell_images_per_dim: 5
|
20 |
+
max_neighbors: 50
|
21 |
+
num_blocks: 4
|
22 |
+
num_targets: 1
|
23 |
+
otf_graph: true
|
24 |
+
regress_stress: true
|
25 |
+
scale_file: /scratch/amlt_code/mattergen/common/gemnet/gemnet-dT.json
|
26 |
+
hidden_dim: 512
|
27 |
+
property_embeddings: {}
|
28 |
+
property_embeddings_adapt:
|
29 |
+
dft_mag_density:
|
30 |
+
_target_: mattergen.property_embeddings.PropertyEmbedding
|
31 |
+
conditional_embedding_module:
|
32 |
+
_target_: mattergen.diffusion.model_utils.NoiseLevelEncoding
|
33 |
+
d_model: 512
|
34 |
+
name: dft_mag_density
|
35 |
+
scaler:
|
36 |
+
_target_: mattergen.common.utils.data_utils.StandardScalerTorch
|
37 |
+
unconditional_embedding_module:
|
38 |
+
_target_: mattergen.property_embeddings.EmbeddingVector
|
39 |
+
hidden_dim: 512
|
40 |
+
hhi_score:
|
41 |
+
_target_: mattergen.property_embeddings.PropertyEmbedding
|
42 |
+
conditional_embedding_module:
|
43 |
+
_target_: mattergen.diffusion.model_utils.NoiseLevelEncoding
|
44 |
+
d_model: 512
|
45 |
+
name: hhi_score
|
46 |
+
scaler:
|
47 |
+
_target_: mattergen.common.utils.data_utils.StandardScalerTorch
|
48 |
+
unconditional_embedding_module:
|
49 |
+
_target_: mattergen.property_embeddings.EmbeddingVector
|
50 |
+
hidden_dim: 512
|
51 |
+
full_finetuning: true
|
52 |
+
load_epoch: last
|
53 |
+
model_path: checkpoints/mattergen_base
|
54 |
+
data_module:
|
55 |
+
_recursive_: true
|
56 |
+
_target_: mattergen.common.data.datamodule.CrystDataModule
|
57 |
+
average_density: 0.05771451654022283
|
58 |
+
batch_size:
|
59 |
+
train: 64
|
60 |
+
val: 64
|
61 |
+
dataset_transforms:
|
62 |
+
- _partial_: true
|
63 |
+
_target_: mattergen.common.data.dataset_transform.filter_sparse_properties
|
64 |
+
max_epochs: 2200
|
65 |
+
num_workers:
|
66 |
+
train: 0
|
67 |
+
val: 0
|
68 |
+
properties:
|
69 |
+
- dft_mag_density
|
70 |
+
- hhi_score
|
71 |
+
root_dir: datasets/cache/alex_mp_20
|
72 |
+
train_dataset:
|
73 |
+
_target_: mattergen.common.data.dataset.CrystalDataset.from_cache_path
|
74 |
+
cache_path: datasets/cache/alex_mp_20/train
|
75 |
+
dataset_transforms:
|
76 |
+
- _partial_: true
|
77 |
+
_target_: mattergen.common.data.dataset_transform.filter_sparse_properties
|
78 |
+
properties:
|
79 |
+
- dft_mag_density
|
80 |
+
- hhi_score
|
81 |
+
transforms:
|
82 |
+
- _partial_: true
|
83 |
+
_target_: mattergen.common.data.transform.symmetrize_lattice
|
84 |
+
- _partial_: true
|
85 |
+
_target_: mattergen.common.data.transform.set_chemical_system_string
|
86 |
+
transforms:
|
87 |
+
- _partial_: true
|
88 |
+
_target_: mattergen.common.data.transform.symmetrize_lattice
|
89 |
+
- _partial_: true
|
90 |
+
_target_: mattergen.common.data.transform.set_chemical_system_string
|
91 |
+
val_dataset:
|
92 |
+
_target_: mattergen.common.data.dataset.CrystalDataset.from_cache_path
|
93 |
+
cache_path: datasets/cache/alex_mp_20/val
|
94 |
+
dataset_transforms:
|
95 |
+
- _partial_: true
|
96 |
+
_target_: mattergen.common.data.dataset_transform.filter_sparse_properties
|
97 |
+
properties:
|
98 |
+
- dft_mag_density
|
99 |
+
- hhi_score
|
100 |
+
transforms:
|
101 |
+
- _partial_: true
|
102 |
+
_target_: mattergen.common.data.transform.symmetrize_lattice
|
103 |
+
- _partial_: true
|
104 |
+
_target_: mattergen.common.data.transform.set_chemical_system_string
|
105 |
+
lightning_module:
|
106 |
+
_target_: mattergen.diffusion.lightning_module.DiffusionLightningModule
|
107 |
+
diffusion_module:
|
108 |
+
_target_: mattergen.diffusion.diffusion_module.DiffusionModule
|
109 |
+
corruption:
|
110 |
+
_target_: mattergen.diffusion.corruption.multi_corruption.MultiCorruption
|
111 |
+
discrete_corruptions:
|
112 |
+
atomic_numbers:
|
113 |
+
_target_: mattergen.diffusion.corruption.d3pm_corruption.D3PMCorruption
|
114 |
+
d3pm:
|
115 |
+
_target_: mattergen.diffusion.d3pm.d3pm.MaskDiffusion
|
116 |
+
dim: 101
|
117 |
+
schedule:
|
118 |
+
_target_: mattergen.diffusion.d3pm.d3pm.create_discrete_diffusion_schedule
|
119 |
+
kind: standard
|
120 |
+
num_steps: 1000
|
121 |
+
offset: 1
|
122 |
+
sdes:
|
123 |
+
cell:
|
124 |
+
_target_: mattergen.common.diffusion.corruption.LatticeVPSDE.from_vpsde_config
|
125 |
+
vpsde_config:
|
126 |
+
beta_max: 20
|
127 |
+
beta_min: 0.1
|
128 |
+
limit_density: 0.05771451654022283
|
129 |
+
limit_var_scaling_constant: 0.25
|
130 |
+
pos:
|
131 |
+
_target_: mattergen.common.diffusion.corruption.NumAtomsVarianceAdjustedWrappedVESDE
|
132 |
+
limit_info_key: num_atoms
|
133 |
+
sigma_max: 5.0
|
134 |
+
wrapping_boundary: 1.0
|
135 |
+
loss_fn:
|
136 |
+
_target_: mattergen.common.loss.MaterialsLoss
|
137 |
+
d3pm_hybrid_lambda: 0.01
|
138 |
+
include_atomic_numbers: true
|
139 |
+
include_cell: true
|
140 |
+
include_pos: true
|
141 |
+
reduce: sum
|
142 |
+
weights:
|
143 |
+
atomic_numbers: 1.0
|
144 |
+
cell: 1.0
|
145 |
+
pos: 0.1
|
146 |
+
model:
|
147 |
+
_target_: mattergen.adapter.GemNetTAdapter
|
148 |
+
atom_type_diffusion: mask
|
149 |
+
denoise_atom_types: true
|
150 |
+
gemnet:
|
151 |
+
_target_: mattergen.common.gemnet.gemnet_ctrl.GemNetTCtrl
|
152 |
+
atom_embedding:
|
153 |
+
_target_: mattergen.common.gemnet.layers.embedding_block.AtomEmbedding
|
154 |
+
emb_size: 512
|
155 |
+
with_mask_type: true
|
156 |
+
condition_on_adapt:
|
157 |
+
- dft_mag_density
|
158 |
+
- hhi_score
|
159 |
+
cutoff: 7.0
|
160 |
+
emb_size_atom: 512
|
161 |
+
emb_size_edge: 512
|
162 |
+
latent_dim: 512
|
163 |
+
max_cell_images_per_dim: 5
|
164 |
+
max_neighbors: 50
|
165 |
+
num_blocks: 4
|
166 |
+
num_targets: 1
|
167 |
+
otf_graph: true
|
168 |
+
regress_stress: true
|
169 |
+
scale_file: /scratch/amlt_code/mattergen/common/gemnet/gemnet-dT.json
|
170 |
+
hidden_dim: 512
|
171 |
+
property_embeddings: {}
|
172 |
+
property_embeddings_adapt:
|
173 |
+
dft_mag_density:
|
174 |
+
_target_: mattergen.property_embeddings.PropertyEmbedding
|
175 |
+
conditional_embedding_module:
|
176 |
+
_target_: mattergen.diffusion.model_utils.NoiseLevelEncoding
|
177 |
+
d_model: 512
|
178 |
+
name: dft_mag_density
|
179 |
+
scaler:
|
180 |
+
_target_: mattergen.common.utils.data_utils.StandardScalerTorch
|
181 |
+
unconditional_embedding_module:
|
182 |
+
_target_: mattergen.property_embeddings.EmbeddingVector
|
183 |
+
hidden_dim: 512
|
184 |
+
hhi_score:
|
185 |
+
_target_: mattergen.property_embeddings.PropertyEmbedding
|
186 |
+
conditional_embedding_module:
|
187 |
+
_target_: mattergen.diffusion.model_utils.NoiseLevelEncoding
|
188 |
+
d_model: 512
|
189 |
+
name: hhi_score
|
190 |
+
scaler:
|
191 |
+
_target_: mattergen.common.utils.data_utils.StandardScalerTorch
|
192 |
+
unconditional_embedding_module:
|
193 |
+
_target_: mattergen.property_embeddings.EmbeddingVector
|
194 |
+
hidden_dim: 512
|
195 |
+
pre_corruption_fn:
|
196 |
+
_target_: mattergen.property_embeddings.SetEmbeddingType
|
197 |
+
dropout_fields_iid: false
|
198 |
+
p_unconditional: 0.2
|
199 |
+
optimizer_partial:
|
200 |
+
_partial_: true
|
201 |
+
_target_: torch.optim.Adam
|
202 |
+
lr: 5.0e-06
|
203 |
+
scheduler_partials:
|
204 |
+
- frequency: 1
|
205 |
+
interval: epoch
|
206 |
+
monitor: loss_train
|
207 |
+
scheduler:
|
208 |
+
_partial_: true
|
209 |
+
_target_: torch.optim.lr_scheduler.ReduceLROnPlateau
|
210 |
+
factor: 0.6
|
211 |
+
min_lr: 1.0e-06
|
212 |
+
patience: 100
|
213 |
+
verbose: true
|
214 |
+
strict: true
|
215 |
+
trainer:
|
216 |
+
_target_: pytorch_lightning.Trainer
|
217 |
+
accelerator: gpu
|
218 |
+
accumulate_grad_batches: 1
|
219 |
+
callbacks:
|
220 |
+
- _target_: pytorch_lightning.callbacks.LearningRateMonitor
|
221 |
+
log_momentum: false
|
222 |
+
logging_interval: step
|
223 |
+
- _target_: pytorch_lightning.callbacks.ModelCheckpoint
|
224 |
+
every_n_epochs: 1
|
225 |
+
filename: '{epoch}-{loss_val:.2f}'
|
226 |
+
mode: min
|
227 |
+
monitor: loss_val
|
228 |
+
save_last: true
|
229 |
+
save_top_k: 1
|
230 |
+
verbose: false
|
231 |
+
- _target_: pytorch_lightning.callbacks.TQDMProgressBar
|
232 |
+
refresh_rate: 50
|
233 |
+
- _target_: mattergen.common.data.callback.SetPropertyScalers
|
234 |
+
check_val_every_n_epoch: 5
|
235 |
+
devices: 8
|
236 |
+
gradient_clip_algorithm: value
|
237 |
+
gradient_clip_val: 0.5
|
238 |
+
logger:
|
239 |
+
_target_: pytorch_lightning.loggers.WandbLogger
|
240 |
+
job_type: train_finetune
|
241 |
+
project: crystal-generation
|
242 |
+
settings:
|
243 |
+
_save_requirements: false
|
244 |
+
_target_: wandb.Settings
|
245 |
+
start_method: fork
|
246 |
+
max_epochs: 200
|
247 |
+
num_nodes: 1
|
248 |
+
precision: 32
|
249 |
+
strategy:
|
250 |
+
_target_: pytorch_lightning.strategies.ddp.DDPStrategy
|
251 |
+
find_unused_parameters: true
|
checkpoints/mattergen_base/config.yaml
ADDED
@@ -0,0 +1,184 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
auto_resume: true
|
2 |
+
checkpoint_path: null
|
3 |
+
data_module:
|
4 |
+
_recursive_: true
|
5 |
+
_target_: mattergen.common.data.datamodule.CrystDataModule
|
6 |
+
average_density: 0.05771451654022283
|
7 |
+
batch_size:
|
8 |
+
train: 32
|
9 |
+
val: 32
|
10 |
+
max_epochs: 2200
|
11 |
+
num_workers:
|
12 |
+
train: 0
|
13 |
+
val: 0
|
14 |
+
properties:
|
15 |
+
- dft_bulk_modulus
|
16 |
+
- dft_band_gap
|
17 |
+
- dft_mag_density
|
18 |
+
- ml_bulk_modulus
|
19 |
+
- hhi_score
|
20 |
+
- space_group
|
21 |
+
- energy_above_hull
|
22 |
+
root_dir: datasets/cache/alex_mp_20/
|
23 |
+
train_dataset:
|
24 |
+
_target_: mattergen.common.data.dataset.CrystalDataset.from_cache_path
|
25 |
+
cache_path: datasets/cache/alex_mp_20/train
|
26 |
+
properties:
|
27 |
+
- dft_bulk_modulus
|
28 |
+
- dft_band_gap
|
29 |
+
- dft_mag_density
|
30 |
+
- ml_bulk_modulus
|
31 |
+
- hhi_score
|
32 |
+
- space_group
|
33 |
+
- energy_above_hull
|
34 |
+
transforms:
|
35 |
+
- _partial_: true
|
36 |
+
_target_: mattergen.common.data.transform.symmetrize_lattice
|
37 |
+
- _partial_: true
|
38 |
+
_target_: mattergen.common.data.transform.set_chemical_system_string
|
39 |
+
transforms:
|
40 |
+
- _partial_: true
|
41 |
+
_target_: mattergen.common.data.transform.symmetrize_lattice
|
42 |
+
- _partial_: true
|
43 |
+
_target_: mattergen.common.data.transform.set_chemical_system_string
|
44 |
+
val_dataset:
|
45 |
+
_target_: mattergen.common.data.dataset.CrystalDataset.from_cache_path
|
46 |
+
cache_path: datasets/cache/alex_mp_20/val
|
47 |
+
properties:
|
48 |
+
- dft_bulk_modulus
|
49 |
+
- dft_band_gap
|
50 |
+
- dft_mag_density
|
51 |
+
- ml_bulk_modulus
|
52 |
+
- hhi_score
|
53 |
+
- space_group
|
54 |
+
- energy_above_hull
|
55 |
+
transforms:
|
56 |
+
- _partial_: true
|
57 |
+
_target_: mattergen.common.data.transform.symmetrize_lattice
|
58 |
+
- _partial_: true
|
59 |
+
_target_: mattergen.common.data.transform.set_chemical_system_string
|
60 |
+
lightning_module:
|
61 |
+
_target_: mattergen.diffusion.lightning_module.DiffusionLightningModule
|
62 |
+
diffusion_module:
|
63 |
+
_target_: mattergen.diffusion.diffusion_module.DiffusionModule
|
64 |
+
corruption:
|
65 |
+
_target_: mattergen.diffusion.corruption.multi_corruption.MultiCorruption
|
66 |
+
discrete_corruptions:
|
67 |
+
atomic_numbers:
|
68 |
+
_target_: mattergen.diffusion.corruption.d3pm_corruption.D3PMCorruption
|
69 |
+
d3pm:
|
70 |
+
_target_: mattergen.diffusion.d3pm.d3pm.MaskDiffusion
|
71 |
+
dim: 101
|
72 |
+
schedule:
|
73 |
+
_target_: mattergen.diffusion.d3pm.d3pm.create_discrete_diffusion_schedule
|
74 |
+
kind: standard
|
75 |
+
num_steps: 1000
|
76 |
+
offset: 1
|
77 |
+
sdes:
|
78 |
+
cell:
|
79 |
+
_target_: mattergen.common.diffusion.corruption.LatticeVPSDE.from_vpsde_config
|
80 |
+
vpsde_config:
|
81 |
+
beta_max: 20
|
82 |
+
beta_min: 0.1
|
83 |
+
limit_density: 0.05771451654022283
|
84 |
+
limit_var_scaling_constant: 0.25
|
85 |
+
pos:
|
86 |
+
_target_: mattergen.common.diffusion.corruption.NumAtomsVarianceAdjustedWrappedVESDE
|
87 |
+
limit_info_key: num_atoms
|
88 |
+
sigma_max: 5.0
|
89 |
+
wrapping_boundary: 1.0
|
90 |
+
loss_fn:
|
91 |
+
_target_: mattergen.common.loss.MaterialsLoss
|
92 |
+
d3pm_hybrid_lambda: 0.01
|
93 |
+
include_atomic_numbers: true
|
94 |
+
include_cell: true
|
95 |
+
include_pos: true
|
96 |
+
reduce: sum
|
97 |
+
weights:
|
98 |
+
atomic_numbers: 1.0
|
99 |
+
cell: 1.0
|
100 |
+
pos: 0.1
|
101 |
+
model:
|
102 |
+
_target_: mattergen.denoiser.GemNetTDenoiser
|
103 |
+
atom_type_diffusion: mask
|
104 |
+
denoise_atom_types: true
|
105 |
+
gemnet:
|
106 |
+
_target_: mattergen.common.gemnet.gemnet.GemNetT
|
107 |
+
atom_embedding:
|
108 |
+
_target_: mattergen.common.gemnet.layers.embedding_block.AtomEmbedding
|
109 |
+
emb_size: 512
|
110 |
+
with_mask_type: true
|
111 |
+
cutoff: 7.0
|
112 |
+
emb_size_atom: 512
|
113 |
+
emb_size_edge: 512
|
114 |
+
latent_dim: 512
|
115 |
+
max_cell_images_per_dim: 5
|
116 |
+
max_neighbors: 50
|
117 |
+
num_blocks: 4
|
118 |
+
num_targets: 1
|
119 |
+
otf_graph: true
|
120 |
+
regress_stress: true
|
121 |
+
scale_file: /scratch/amlt_code/mattergen/common/gemnet/gemnet-dT.json
|
122 |
+
hidden_dim: 512
|
123 |
+
property_embeddings: {}
|
124 |
+
property_embeddings_adapt: {}
|
125 |
+
pre_corruption_fn:
|
126 |
+
_target_: mattergen.property_embeddings.SetEmbeddingType
|
127 |
+
dropout_fields_iid: false
|
128 |
+
p_unconditional: 0.2
|
129 |
+
optimizer_partial:
|
130 |
+
_partial_: true
|
131 |
+
_target_: torch.optim.Adam
|
132 |
+
lr: 0.0001
|
133 |
+
scheduler_partials:
|
134 |
+
- frequency: 1
|
135 |
+
interval: epoch
|
136 |
+
monitor: loss_train
|
137 |
+
scheduler:
|
138 |
+
_partial_: true
|
139 |
+
_target_: torch.optim.lr_scheduler.ReduceLROnPlateau
|
140 |
+
factor: 0.6
|
141 |
+
min_lr: 1.0e-06
|
142 |
+
patience: 100
|
143 |
+
verbose: true
|
144 |
+
strict: true
|
145 |
+
load_original: false
|
146 |
+
params: {}
|
147 |
+
train: true
|
148 |
+
trainer:
|
149 |
+
_target_: pytorch_lightning.Trainer
|
150 |
+
accelerator: gpu
|
151 |
+
accumulate_grad_batches: 1
|
152 |
+
callbacks:
|
153 |
+
- _target_: pytorch_lightning.callbacks.LearningRateMonitor
|
154 |
+
log_momentum: false
|
155 |
+
logging_interval: step
|
156 |
+
- _target_: pytorch_lightning.callbacks.ModelCheckpoint
|
157 |
+
every_n_epochs: 1
|
158 |
+
filename: '{epoch}-{loss_val:.2f}'
|
159 |
+
mode: min
|
160 |
+
monitor: loss_val
|
161 |
+
save_last: true
|
162 |
+
save_top_k: 1
|
163 |
+
verbose: false
|
164 |
+
- _target_: pytorch_lightning.callbacks.TQDMProgressBar
|
165 |
+
refresh_rate: 50
|
166 |
+
- _target_: mattergen.common.data.callback.SetPropertyScalers
|
167 |
+
check_val_every_n_epoch: 5
|
168 |
+
devices: 8
|
169 |
+
gradient_clip_algorithm: value
|
170 |
+
gradient_clip_val: 0.5
|
171 |
+
logger:
|
172 |
+
_target_: pytorch_lightning.loggers.WandbLogger
|
173 |
+
job_type: train
|
174 |
+
project: crystal-generation
|
175 |
+
settings:
|
176 |
+
_save_requirements: false
|
177 |
+
_target_: wandb.Settings
|
178 |
+
start_method: fork
|
179 |
+
max_epochs: 2200
|
180 |
+
num_nodes: 2
|
181 |
+
precision: 32
|
182 |
+
strategy:
|
183 |
+
_target_: pytorch_lightning.strategies.ddp.DDPStrategy
|
184 |
+
find_unused_parameters: true
|
checkpoints/ml_bulk_modulus/config.yaml
ADDED
@@ -0,0 +1,224 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
adapter:
|
2 |
+
adapter:
|
3 |
+
_target_: mattergen.adapter.GemNetTAdapter
|
4 |
+
atom_type_diffusion: mask
|
5 |
+
denoise_atom_types: true
|
6 |
+
gemnet:
|
7 |
+
_target_: mattergen.common.gemnet.gemnet_ctrl.GemNetTCtrl
|
8 |
+
atom_embedding:
|
9 |
+
_target_: mattergen.common.gemnet.layers.embedding_block.AtomEmbedding
|
10 |
+
emb_size: 512
|
11 |
+
with_mask_type: true
|
12 |
+
condition_on_adapt:
|
13 |
+
- ml_bulk_modulus
|
14 |
+
cutoff: 7.0
|
15 |
+
emb_size_atom: 512
|
16 |
+
emb_size_edge: 512
|
17 |
+
latent_dim: 512
|
18 |
+
max_cell_images_per_dim: 5
|
19 |
+
max_neighbors: 50
|
20 |
+
num_blocks: 4
|
21 |
+
num_targets: 1
|
22 |
+
otf_graph: true
|
23 |
+
regress_stress: true
|
24 |
+
scale_file: /scratch/amlt_code/mattergen/common/gemnet/gemnet-dT.json
|
25 |
+
hidden_dim: 512
|
26 |
+
property_embeddings: {}
|
27 |
+
property_embeddings_adapt:
|
28 |
+
ml_bulk_modulus:
|
29 |
+
_target_: mattergen.property_embeddings.PropertyEmbedding
|
30 |
+
conditional_embedding_module:
|
31 |
+
_target_: mattergen.diffusion.model_utils.NoiseLevelEncoding
|
32 |
+
d_model: 512
|
33 |
+
name: ml_bulk_modulus
|
34 |
+
scaler:
|
35 |
+
_target_: mattergen.common.utils.data_utils.StandardScalerTorch
|
36 |
+
unconditional_embedding_module:
|
37 |
+
_target_: mattergen.property_embeddings.EmbeddingVector
|
38 |
+
hidden_dim: 512
|
39 |
+
full_finetuning: true
|
40 |
+
load_epoch: last
|
41 |
+
model_path: checkpoints/mattergen_base
|
42 |
+
data_module:
|
43 |
+
_recursive_: true
|
44 |
+
_target_: mattergen.common.data.datamodule.CrystDataModule
|
45 |
+
average_density: 0.05771451654022283
|
46 |
+
batch_size:
|
47 |
+
train: 64
|
48 |
+
val: 64
|
49 |
+
dataset_transforms:
|
50 |
+
- _partial_: true
|
51 |
+
_target_: mattergen.common.data.dataset_transform.filter_sparse_properties
|
52 |
+
max_epochs: 2200
|
53 |
+
num_workers:
|
54 |
+
train: 0
|
55 |
+
val: 0
|
56 |
+
properties:
|
57 |
+
- ml_bulk_modulus
|
58 |
+
root_dir: datasets/cache/alex_mp_20
|
59 |
+
train_dataset:
|
60 |
+
_target_: mattergen.common.data.dataset.CrystalDataset.from_cache_path
|
61 |
+
cache_path: datasets/cache/alex_mp_20/train
|
62 |
+
dataset_transforms:
|
63 |
+
- _partial_: true
|
64 |
+
_target_: mattergen.common.data.dataset_transform.filter_sparse_properties
|
65 |
+
properties:
|
66 |
+
- ml_bulk_modulus
|
67 |
+
transforms:
|
68 |
+
- _partial_: true
|
69 |
+
_target_: mattergen.common.data.transform.symmetrize_lattice
|
70 |
+
- _partial_: true
|
71 |
+
_target_: mattergen.common.data.transform.set_chemical_system_string
|
72 |
+
transforms:
|
73 |
+
- _partial_: true
|
74 |
+
_target_: mattergen.common.data.transform.symmetrize_lattice
|
75 |
+
- _partial_: true
|
76 |
+
_target_: mattergen.common.data.transform.set_chemical_system_string
|
77 |
+
val_dataset:
|
78 |
+
_target_: mattergen.common.data.dataset.CrystalDataset.from_cache_path
|
79 |
+
cache_path: datasets/cache/alex_mp_20/val
|
80 |
+
dataset_transforms:
|
81 |
+
- _partial_: true
|
82 |
+
_target_: mattergen.common.data.dataset_transform.filter_sparse_properties
|
83 |
+
properties:
|
84 |
+
- ml_bulk_modulus
|
85 |
+
transforms:
|
86 |
+
- _partial_: true
|
87 |
+
_target_: mattergen.common.data.transform.symmetrize_lattice
|
88 |
+
- _partial_: true
|
89 |
+
_target_: mattergen.common.data.transform.set_chemical_system_string
|
90 |
+
lightning_module:
|
91 |
+
_target_: mattergen.diffusion.lightning_module.DiffusionLightningModule
|
92 |
+
diffusion_module:
|
93 |
+
_target_: mattergen.diffusion.diffusion_module.DiffusionModule
|
94 |
+
corruption:
|
95 |
+
_target_: mattergen.diffusion.corruption.multi_corruption.MultiCorruption
|
96 |
+
discrete_corruptions:
|
97 |
+
atomic_numbers:
|
98 |
+
_target_: mattergen.diffusion.corruption.d3pm_corruption.D3PMCorruption
|
99 |
+
d3pm:
|
100 |
+
_target_: mattergen.diffusion.d3pm.d3pm.MaskDiffusion
|
101 |
+
dim: 101
|
102 |
+
schedule:
|
103 |
+
_target_: mattergen.diffusion.d3pm.d3pm.create_discrete_diffusion_schedule
|
104 |
+
kind: standard
|
105 |
+
num_steps: 1000
|
106 |
+
offset: 1
|
107 |
+
sdes:
|
108 |
+
cell:
|
109 |
+
_target_: mattergen.common.diffusion.corruption.LatticeVPSDE.from_vpsde_config
|
110 |
+
vpsde_config:
|
111 |
+
beta_max: 20
|
112 |
+
beta_min: 0.1
|
113 |
+
limit_density: 0.05771451654022283
|
114 |
+
limit_var_scaling_constant: 0.25
|
115 |
+
pos:
|
116 |
+
_target_: mattergen.common.diffusion.corruption.NumAtomsVarianceAdjustedWrappedVESDE
|
117 |
+
limit_info_key: num_atoms
|
118 |
+
sigma_max: 5.0
|
119 |
+
wrapping_boundary: 1.0
|
120 |
+
loss_fn:
|
121 |
+
_target_: mattergen.common.loss.MaterialsLoss
|
122 |
+
d3pm_hybrid_lambda: 0.01
|
123 |
+
include_atomic_numbers: true
|
124 |
+
include_cell: true
|
125 |
+
include_pos: true
|
126 |
+
reduce: sum
|
127 |
+
weights:
|
128 |
+
atomic_numbers: 1.0
|
129 |
+
cell: 1.0
|
130 |
+
pos: 0.1
|
131 |
+
model:
|
132 |
+
_target_: mattergen.adapter.GemNetTAdapter
|
133 |
+
atom_type_diffusion: mask
|
134 |
+
denoise_atom_types: true
|
135 |
+
gemnet:
|
136 |
+
_target_: mattergen.common.gemnet.gemnet_ctrl.GemNetTCtrl
|
137 |
+
atom_embedding:
|
138 |
+
_target_: mattergen.common.gemnet.layers.embedding_block.AtomEmbedding
|
139 |
+
emb_size: 512
|
140 |
+
with_mask_type: true
|
141 |
+
condition_on_adapt:
|
142 |
+
- ml_bulk_modulus
|
143 |
+
cutoff: 7.0
|
144 |
+
emb_size_atom: 512
|
145 |
+
emb_size_edge: 512
|
146 |
+
latent_dim: 512
|
147 |
+
max_cell_images_per_dim: 5
|
148 |
+
max_neighbors: 50
|
149 |
+
num_blocks: 4
|
150 |
+
num_targets: 1
|
151 |
+
otf_graph: true
|
152 |
+
regress_stress: true
|
153 |
+
scale_file: /scratch/amlt_code/mattergen/common/gemnet/gemnet-dT.json
|
154 |
+
hidden_dim: 512
|
155 |
+
property_embeddings: {}
|
156 |
+
property_embeddings_adapt:
|
157 |
+
ml_bulk_modulus:
|
158 |
+
_target_: mattergen.property_embeddings.PropertyEmbedding
|
159 |
+
conditional_embedding_module:
|
160 |
+
_target_: mattergen.diffusion.model_utils.NoiseLevelEncoding
|
161 |
+
d_model: 512
|
162 |
+
name: ml_bulk_modulus
|
163 |
+
scaler:
|
164 |
+
_target_: mattergen.common.utils.data_utils.StandardScalerTorch
|
165 |
+
unconditional_embedding_module:
|
166 |
+
_target_: mattergen.property_embeddings.EmbeddingVector
|
167 |
+
hidden_dim: 512
|
168 |
+
pre_corruption_fn:
|
169 |
+
_target_: mattergen.property_embeddings.SetEmbeddingType
|
170 |
+
dropout_fields_iid: false
|
171 |
+
p_unconditional: 0.2
|
172 |
+
optimizer_partial:
|
173 |
+
_partial_: true
|
174 |
+
_target_: torch.optim.Adam
|
175 |
+
lr: 5.0e-06
|
176 |
+
scheduler_partials:
|
177 |
+
- frequency: 1
|
178 |
+
interval: epoch
|
179 |
+
monitor: loss_train
|
180 |
+
scheduler:
|
181 |
+
_partial_: true
|
182 |
+
_target_: torch.optim.lr_scheduler.ReduceLROnPlateau
|
183 |
+
factor: 0.6
|
184 |
+
min_lr: 1.0e-06
|
185 |
+
patience: 100
|
186 |
+
verbose: true
|
187 |
+
strict: true
|
188 |
+
trainer:
|
189 |
+
_target_: pytorch_lightning.Trainer
|
190 |
+
accelerator: gpu
|
191 |
+
accumulate_grad_batches: 1
|
192 |
+
callbacks:
|
193 |
+
- _target_: pytorch_lightning.callbacks.LearningRateMonitor
|
194 |
+
log_momentum: false
|
195 |
+
logging_interval: step
|
196 |
+
- _target_: pytorch_lightning.callbacks.ModelCheckpoint
|
197 |
+
every_n_epochs: 1
|
198 |
+
filename: '{epoch}-{loss_val:.2f}'
|
199 |
+
mode: min
|
200 |
+
monitor: loss_val
|
201 |
+
save_last: true
|
202 |
+
save_top_k: 1
|
203 |
+
verbose: false
|
204 |
+
- _target_: pytorch_lightning.callbacks.TQDMProgressBar
|
205 |
+
refresh_rate: 50
|
206 |
+
- _target_: mattergen.common.data.callback.SetPropertyScalers
|
207 |
+
check_val_every_n_epoch: 1
|
208 |
+
devices: 8
|
209 |
+
gradient_clip_algorithm: value
|
210 |
+
gradient_clip_val: 0.5
|
211 |
+
logger:
|
212 |
+
_target_: pytorch_lightning.loggers.WandbLogger
|
213 |
+
job_type: train_finetune
|
214 |
+
project: crystal-generation
|
215 |
+
settings:
|
216 |
+
_save_requirements: false
|
217 |
+
_target_: wandb.Settings
|
218 |
+
start_method: fork
|
219 |
+
max_epochs: 200
|
220 |
+
num_nodes: 1
|
221 |
+
precision: 32
|
222 |
+
strategy:
|
223 |
+
_target_: pytorch_lightning.strategies.ddp.DDPStrategy
|
224 |
+
find_unused_parameters: true
|
checkpoints/space_group/config.yaml
ADDED
@@ -0,0 +1,224 @@
|
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|
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|
|
|
|
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|
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|
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|
|
|
|
|
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|
|
|
|
|
|
|
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|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
adapter:
|
2 |
+
adapter:
|
3 |
+
_target_: mattergen.adapter.GemNetTAdapter
|
4 |
+
atom_type_diffusion: mask
|
5 |
+
denoise_atom_types: true
|
6 |
+
gemnet:
|
7 |
+
_target_: mattergen.common.gemnet.gemnet_ctrl.GemNetTCtrl
|
8 |
+
atom_embedding:
|
9 |
+
_target_: mattergen.common.gemnet.layers.embedding_block.AtomEmbedding
|
10 |
+
emb_size: 512
|
11 |
+
with_mask_type: true
|
12 |
+
condition_on_adapt:
|
13 |
+
- space_group
|
14 |
+
cutoff: 7.0
|
15 |
+
emb_size_atom: 512
|
16 |
+
emb_size_edge: 512
|
17 |
+
latent_dim: 512
|
18 |
+
max_cell_images_per_dim: 5
|
19 |
+
max_neighbors: 50
|
20 |
+
num_blocks: 4
|
21 |
+
num_targets: 1
|
22 |
+
otf_graph: true
|
23 |
+
regress_stress: true
|
24 |
+
scale_file: /scratch/amlt_code/mattergen/common/gemnet/gemnet-dT.json
|
25 |
+
hidden_dim: 512
|
26 |
+
property_embeddings: {}
|
27 |
+
property_embeddings_adapt:
|
28 |
+
space_group:
|
29 |
+
_target_: mattergen.property_embeddings.PropertyEmbedding
|
30 |
+
conditional_embedding_module:
|
31 |
+
_target_: mattergen.property_embeddings.SpaceGroupEmbeddingVector
|
32 |
+
hidden_dim: 512
|
33 |
+
name: space_group
|
34 |
+
scaler:
|
35 |
+
_target_: torch.nn.Identity
|
36 |
+
unconditional_embedding_module:
|
37 |
+
_target_: mattergen.property_embeddings.EmbeddingVector
|
38 |
+
hidden_dim: 512
|
39 |
+
full_finetuning: true
|
40 |
+
load_epoch: last
|
41 |
+
model_path: checkpoints/mattergen_base
|
42 |
+
data_module:
|
43 |
+
_recursive_: true
|
44 |
+
_target_: mattergen.common.data.datamodule.CrystDataModule
|
45 |
+
average_density: 0.05771451654022283
|
46 |
+
batch_size:
|
47 |
+
train: 64
|
48 |
+
val: 64
|
49 |
+
dataset_transforms:
|
50 |
+
- _partial_: true
|
51 |
+
_target_: mattergen.common.data.dataset_transform.filter_sparse_properties
|
52 |
+
max_epochs: 2200
|
53 |
+
num_workers:
|
54 |
+
train: 0
|
55 |
+
val: 0
|
56 |
+
properties:
|
57 |
+
- space_group
|
58 |
+
root_dir: datasets/cache/alex_mp_20
|
59 |
+
train_dataset:
|
60 |
+
_target_: mattergen.common.data.dataset.CrystalDataset.from_cache_path
|
61 |
+
cache_path: datasets/cache/alex_mp_20/train
|
62 |
+
dataset_transforms:
|
63 |
+
- _partial_: true
|
64 |
+
_target_: mattergen.common.data.dataset_transform.filter_sparse_properties
|
65 |
+
properties:
|
66 |
+
- space_group
|
67 |
+
transforms:
|
68 |
+
- _partial_: true
|
69 |
+
_target_: mattergen.common.data.transform.symmetrize_lattice
|
70 |
+
- _partial_: true
|
71 |
+
_target_: mattergen.common.data.transform.set_chemical_system_string
|
72 |
+
transforms:
|
73 |
+
- _partial_: true
|
74 |
+
_target_: mattergen.common.data.transform.symmetrize_lattice
|
75 |
+
- _partial_: true
|
76 |
+
_target_: mattergen.common.data.transform.set_chemical_system_string
|
77 |
+
val_dataset:
|
78 |
+
_target_: mattergen.common.data.dataset.CrystalDataset.from_cache_path
|
79 |
+
cache_path: datasets/cache/alex_mp_20/val
|
80 |
+
dataset_transforms:
|
81 |
+
- _partial_: true
|
82 |
+
_target_: mattergen.common.data.dataset_transform.filter_sparse_properties
|
83 |
+
properties:
|
84 |
+
- space_group
|
85 |
+
transforms:
|
86 |
+
- _partial_: true
|
87 |
+
_target_: mattergen.common.data.transform.symmetrize_lattice
|
88 |
+
- _partial_: true
|
89 |
+
_target_: mattergen.common.data.transform.set_chemical_system_string
|
90 |
+
lightning_module:
|
91 |
+
_target_: mattergen.diffusion.lightning_module.DiffusionLightningModule
|
92 |
+
diffusion_module:
|
93 |
+
_target_: mattergen.diffusion.diffusion_module.DiffusionModule
|
94 |
+
corruption:
|
95 |
+
_target_: mattergen.diffusion.corruption.multi_corruption.MultiCorruption
|
96 |
+
discrete_corruptions:
|
97 |
+
atomic_numbers:
|
98 |
+
_target_: mattergen.diffusion.corruption.d3pm_corruption.D3PMCorruption
|
99 |
+
d3pm:
|
100 |
+
_target_: mattergen.diffusion.d3pm.d3pm.MaskDiffusion
|
101 |
+
dim: 101
|
102 |
+
schedule:
|
103 |
+
_target_: mattergen.diffusion.d3pm.d3pm.create_discrete_diffusion_schedule
|
104 |
+
kind: standard
|
105 |
+
num_steps: 1000
|
106 |
+
offset: 1
|
107 |
+
sdes:
|
108 |
+
cell:
|
109 |
+
_target_: mattergen.common.diffusion.corruption.LatticeVPSDE.from_vpsde_config
|
110 |
+
vpsde_config:
|
111 |
+
beta_max: 20
|
112 |
+
beta_min: 0.1
|
113 |
+
limit_density: 0.05771451654022283
|
114 |
+
limit_var_scaling_constant: 0.25
|
115 |
+
pos:
|
116 |
+
_target_: mattergen.common.diffusion.corruption.NumAtomsVarianceAdjustedWrappedVESDE
|
117 |
+
limit_info_key: num_atoms
|
118 |
+
sigma_max: 5.0
|
119 |
+
wrapping_boundary: 1.0
|
120 |
+
loss_fn:
|
121 |
+
_target_: mattergen.common.loss.MaterialsLoss
|
122 |
+
d3pm_hybrid_lambda: 0.01
|
123 |
+
include_atomic_numbers: true
|
124 |
+
include_cell: true
|
125 |
+
include_pos: true
|
126 |
+
reduce: sum
|
127 |
+
weights:
|
128 |
+
atomic_numbers: 1.0
|
129 |
+
cell: 1.0
|
130 |
+
pos: 0.1
|
131 |
+
model:
|
132 |
+
_target_: mattergen.adapter.GemNetTAdapter
|
133 |
+
atom_type_diffusion: mask
|
134 |
+
denoise_atom_types: true
|
135 |
+
gemnet:
|
136 |
+
_target_: mattergen.common.gemnet.gemnet_ctrl.GemNetTCtrl
|
137 |
+
atom_embedding:
|
138 |
+
_target_: mattergen.common.gemnet.layers.embedding_block.AtomEmbedding
|
139 |
+
emb_size: 512
|
140 |
+
with_mask_type: true
|
141 |
+
condition_on_adapt:
|
142 |
+
- space_group
|
143 |
+
cutoff: 7.0
|
144 |
+
emb_size_atom: 512
|
145 |
+
emb_size_edge: 512
|
146 |
+
latent_dim: 512
|
147 |
+
max_cell_images_per_dim: 5
|
148 |
+
max_neighbors: 50
|
149 |
+
num_blocks: 4
|
150 |
+
num_targets: 1
|
151 |
+
otf_graph: true
|
152 |
+
regress_stress: true
|
153 |
+
scale_file: /scratch/amlt_code/mattergen/common/gemnet/gemnet-dT.json
|
154 |
+
hidden_dim: 512
|
155 |
+
property_embeddings: {}
|
156 |
+
property_embeddings_adapt:
|
157 |
+
space_group:
|
158 |
+
_target_: mattergen.property_embeddings.PropertyEmbedding
|
159 |
+
conditional_embedding_module:
|
160 |
+
_target_: mattergen.property_embeddings.SpaceGroupEmbeddingVector
|
161 |
+
hidden_dim: 512
|
162 |
+
name: space_group
|
163 |
+
scaler:
|
164 |
+
_target_: torch.nn.Identity
|
165 |
+
unconditional_embedding_module:
|
166 |
+
_target_: mattergen.property_embeddings.EmbeddingVector
|
167 |
+
hidden_dim: 512
|
168 |
+
pre_corruption_fn:
|
169 |
+
_target_: mattergen.property_embeddings.SetEmbeddingType
|
170 |
+
dropout_fields_iid: false
|
171 |
+
p_unconditional: 0.2
|
172 |
+
optimizer_partial:
|
173 |
+
_partial_: true
|
174 |
+
_target_: torch.optim.Adam
|
175 |
+
lr: 5.0e-06
|
176 |
+
scheduler_partials:
|
177 |
+
- frequency: 1
|
178 |
+
interval: epoch
|
179 |
+
monitor: loss_train
|
180 |
+
scheduler:
|
181 |
+
_partial_: true
|
182 |
+
_target_: torch.optim.lr_scheduler.ReduceLROnPlateau
|
183 |
+
factor: 0.6
|
184 |
+
min_lr: 1.0e-06
|
185 |
+
patience: 100
|
186 |
+
verbose: true
|
187 |
+
strict: true
|
188 |
+
trainer:
|
189 |
+
_target_: pytorch_lightning.Trainer
|
190 |
+
accelerator: gpu
|
191 |
+
accumulate_grad_batches: 1
|
192 |
+
callbacks:
|
193 |
+
- _target_: pytorch_lightning.callbacks.LearningRateMonitor
|
194 |
+
log_momentum: false
|
195 |
+
logging_interval: step
|
196 |
+
- _target_: pytorch_lightning.callbacks.ModelCheckpoint
|
197 |
+
every_n_epochs: 1
|
198 |
+
filename: '{epoch}-{loss_val:.2f}'
|
199 |
+
mode: min
|
200 |
+
monitor: loss_val
|
201 |
+
save_last: true
|
202 |
+
save_top_k: 1
|
203 |
+
verbose: false
|
204 |
+
- _target_: pytorch_lightning.callbacks.TQDMProgressBar
|
205 |
+
refresh_rate: 50
|
206 |
+
- _target_: mattergen.common.data.callback.SetPropertyScalers
|
207 |
+
check_val_every_n_epoch: 1
|
208 |
+
devices: 8
|
209 |
+
gradient_clip_algorithm: value
|
210 |
+
gradient_clip_val: 0.5
|
211 |
+
logger:
|
212 |
+
_target_: pytorch_lightning.loggers.WandbLogger
|
213 |
+
job_type: train_finetune
|
214 |
+
project: crystal-generation
|
215 |
+
settings:
|
216 |
+
_save_requirements: false
|
217 |
+
_target_: wandb.Settings
|
218 |
+
start_method: fork
|
219 |
+
max_epochs: 200
|
220 |
+
num_nodes: 1
|
221 |
+
precision: 32
|
222 |
+
strategy:
|
223 |
+
_target_: pytorch_lightning.strategies.ddp.DDPStrategy
|
224 |
+
find_unused_parameters: true
|