Upload evaluated MFI methane 8x512 step-40000 artifacts

Checkpoint, baseline and contact-correction samples/metrics, plotting arrays, resolved configuration, logs, and checksums.

artifacts/mfi_methane/endpoint_independent_8x512_b256_s1_step40000/README.md

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+# MFI methane endpoint-independent 8x512, step 40000
+
+This directory contains the best fully evaluated MFI methane checkpoint as of
+2026-09-05, together with all arrays needed to reproduce the evaluation plots.
+
+## Contents
+
+- `checkpoint/`: Lightning checkpoint at step 40000.
+- `metrics/baseline.json`: scalar metrics at 50 and 100 bar.
+- `samples/baseline.npz`: generated and reference positions, graph offsets,
+  counts, density and occupancy grids, RDFs, pair histograms, and minimum
+  distances at both pressures.
+- `metrics/contact_*` and `samples/contact_*`: Euler-200 sampling-only bounded
+  contact-correction sweep using the same checkpoint.
+- `config/`: resolved Hydra configuration, overrides, and training protocol.
+- `logs/`: compact run and evaluation logs.
+- `manifest.json`: byte sizes and SHA-256 checksums for every uploaded source.
+
+The NPZ position arrays are flattened. The corresponding `*_offsets` arrays
+delimit individual configurations. Positions and histogram radii are in
+angstroms.
+
+## Baseline two-pressure averages
+
+| Count TV | Spatial TV | Occupancy TV | Pair TV | CH4-CH4 overlap | CH4-O overlap | Median CH4-CH4 rmin |
+|---:|---:|---:|---:|---:|---:|---:|
+| 0.052900 | 0.043782 | 0.072493 | 0.018554 | 0.003732 | 0.000225 | 3.1996 A |
+
+## Contact-correction two-pressure averages
+
+| Variant | Spatial TV | Occupancy TV | Pair TV | CH4-CH4 overlap | CH4-O overlap | Median CH4-CH4 rmin |
+|---|---:|---:|---:|---:|---:|---:|
+| low | 0.048662 | 0.084369 | 0.015909 | 0.003190 | 0.000162 | 3.2260 A |
+| mid | 0.061249 | 0.112420 | 0.020002 | 0.002944 | 0.000272 | 3.2226 A |
+| high | 0.078421 | 0.140648 | 0.025108 | 0.004172 | 0.000545 | 3.1981 A |

artifacts/mfi_methane/endpoint_independent_8x512_b256_s1_step40000/checkpoint/epoch=249-step=40000.ckpt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:23d683b3b5481a667b3113b76abd9538c1ffd3dfff0b79c75ce4aae45ba2c6c7
+size 348882433

artifacts/mfi_methane/endpoint_independent_8x512_b256_s1_step40000/config/hydra_config.yaml

@@ -0,0 +1,448 @@
+representation: pointcloud
+seed: 1
+heads:
+  heads:
+    _target_: grand_canonical_generator.model.layers.heads.MultiHeadModule
+    fuse_parallel_heads: true
+    heads_configs:
+      graph_aggregation: mean
+      node_heads:
+        atom_type_head:
+          input_dim: ${model.head_node_dim}
+          output_dim: ${len:${data.vocab.atom_tokens}}
+          hidden_dim: 128
+        charge_head:
+          input_dim: ${model.head_node_dim}
+          output_dim: ${len:${data.vocab.charge_tokens}}
+          hidden_dim: 128
+        ins_intensity_head:
+          input_dim: ${model.head_node_dim}
+          output_dim: 1
+          hidden_dim: 128
+        do_del_head:
+          input_dim: ${model.head_node_dim}
+          output_dim: 1
+          hidden_dim: 128
+        do_sub_a_head:
+          input_dim: ${model.head_node_dim}
+          output_dim: 1
+          hidden_dim: 128
+  insertion_head:
+    _target_: ${if:${eq:${oc.select:model.insertion_params.head_mode,gmm}, gmm}, grand_canonical_generator.model.layers.heads.EquivariantGMMHead,
+      grand_canonical_generator.model.layers.heads.EquivariantUnimodalInsertionHead}
+    _recursive_: false
+    hidden_dim: ${model.head_node_dim}
+    K: ${model.insertion_params.K}
+    mean_param: ${oc.select:model.insertion_params.mean_param,equivariant}
+    periodic_box_size: ${oc.select:data.periodic_box_size,null}
+    N_a: ${len:${data.vocab.atom_tokens}}
+    N_c: ${len:${data.vocab.charge_tokens}}
+    rbf_embedding_args:
+      _target_: grand_canonical_generator.model.layers.embedding.RBFEmbedding
+      num_rbf: 128
+      rbf_dmax: 3.5
+      out_dim: 64
+      dropout: 0.0
+      trainable: false
+  insertion_coordinate_head:
+    _target_: grand_canonical_generator.model.layers.heads.InsertionCFMCoordinateHead
+    hidden_dim: ${model.head_node_dim}
+    periodic_box_size: ${data.periodic_box_size}
+    num_rbf: 32
+    hidden_layers: 2
+    rbf_max_distance: null
+    interaction_cutoff: null
+    use_geometry_residual: false
+    distance_floor: 0.001
+    steric_aggregation: mean
+    steric_softmin_temperature: 0.15
+  insertion_coordinate_head_sde:
+    _target_: grand_canonical_generator.model.layers.heads.InsertionCFMCoordinateHead
+    hidden_dim: ${model.head_node_dim}
+    periodic_box_size: ${data.periodic_box_size}
+    num_rbf: 32
+    hidden_layers: 1
+    rbf_max_distance: null
+    interaction_cutoff: null
+    predict_score: true
+    use_geometry_residual: false
+    distance_floor: 0.001
+    steric_aggregation: mean
+    steric_softmin_temperature: 0.15
+  interaction_insertion_coordinate_head:
+    _target_: grand_canonical_generator.model.layers.heads.InsertionCFMCoordinateHead
+    hidden_dim: ${model.head_node_dim}
+    periodic_box_size: ${data.periodic_box_size}
+    num_rbf: 32
+    hidden_layers: 2
+    rbf_max_distance: ${oc.eval:"${data.periodic_box_size} / 2.0"}
+    interaction_cutoff: ${oc.eval:"${data.periodic_box_size} / 2.0"}
+    use_geometry_residual: false
+    distance_floor: 0.001
+    steric_aggregation: mean
+    steric_softmin_temperature: 0.15
+  reservoir_insertion_head:
+    _target_: grand_canonical_generator.model.layers.heads.ReservoirInsertionHead
+    input_dim: ${model.head_node_dim}
+    hidden_dim: 128
+    rate_parameterization: softplus
+    max_rate: null
+model:
+  module:
+    optimizer_config:
+      optimizer:
+        lr: 0.002
+        momentum: 0.95
+        weight_decay: 0.0
+      aux_optimizer:
+        lr: 0.01
+        betas:
+        - 0.9
+        - 0.95
+        eps: 1.0e-10
+        weight_decay: 0.0
+      emb_optimizer:
+        lr: 0.01
+      scheduler:
+        _target_: grand_canonical_generator.utils.lr_schedulers.MultiGroupCosineWarmupLR
+        warmup_steps: ${oc.eval:"int(0.1 * ${model.module.optimizer_config.scheduler.total_steps})"}
+        total_steps: 40000
+        min_lr_fraction: 0.05
+        last_epoch: -1
+      interval: step
+      monitor: null
+      framework_vector_optimizer:
+        lr: 0.0003
+        betas:
+        - 0.9
+        - 0.95
+        eps: 1.0e-10
+        weight_decay: 0.0
+    loss_weights:
+      x: 2.0
+    _target_: grand_canonical_generator.model.lightning.transformer.LightningModuleRatesTransformer
+    insertion_params: ${model.insertion_params}
+    n_atoms_strategy: ${data.n_atoms_strategy}
+    ins_noise_scale: ${data.ins_noise_scale}
+    ema_decay: 0.999
+    enable_ema: false
+    use_ema_for_eval: false
+    use_self_conditioning: false
+    time_dist: ${if:${eq:${model.sample_time_strategy}, log}, ${model.beta_sched},
+      ${model.linear_sched}}
+    integrator: ${model.integrator}
+    vocab: ${data.vocab}
+    use_learnable_loss_weights: false
+    use_time_weights: false
+    position_loss_time_weighting: auto
+    position_loss_time_weight_clamp_max: 100.0
+    velocity_target_remaining_floor: 1.0e-05
+    velocity_target_max_norm: null
+    near_contact_cutoff: 0.0
+    near_contact_power: 2.0
+    near_contact_distance_floor: 0.05
+    near_contact_separation_weight: 0.0
+    near_contact_separation_reduction: graph_pair
+    near_contact_separation_time_max: 1.0
+    near_contact_node_weight_scale: 0.0
+    near_contact_pair_scope: mobile_mobile
+    near_contact_framework_cutoff: null
+    near_contact_framework_atom_types: null
+    position_loss_remaining_power: 0.0
+    sanitize_nonfinite_loss: false
+    thermodynamic_count_model:
+      _target_: grand_canonical_generator.model.thermodynamic_count.EnumeratedThermodynamicCountModel
+      min_count: 0
+      max_count: ${data.max_particles}
+    count_loss_weight: 1.0
+    initialize_count_from_density_of_states: true
+    initialize_graph_intensity_from_mean_count: false
+    learned_gmm_source: null
+    gmm_source_loss_weight: 0.1
+    gmm_source_variance_reg_weight: 0.01
+    gmm_source_coupling: periodic_ot
+    flow_sampling: null
+    path_gradients: null
+    energy_weighted_flow_matching: null
+    periodic_position_loss: true
+    model:
+      _target_: grand_canonical_generator.model.finetune.mfi_context.MfiConditionalDiTBackboneWithHeads
+      _recursive_: false
+      atom_type_embedding_args: ${embeddings.atom_type_embedding}
+      time_embedding_args: ${embeddings.time_embedding}
+      node_count_embedding_args: ${embeddings.node_count_embedding}
+      chemical_potential_embedding_args: null
+      ideal_gas_mu_intensity_skip: false
+      backbone_model_args: ${model.backbone}
+      heads_args: null
+      ins_head_args: null
+      reservoir_insertion_head_args: null
+      insertion_location_head_args: null
+      framework_gate_tanh: false
+      node_gate_init: 0.1
+      framework_context_args:
+        num_atom_types: ${len:${data.vocab.atom_tokens}}
+        host_embedding_dim: 32
+        rbf_dim: 32
+        cutoff: ${oc.eval:"6.0 / ${data.coordinate_std}"}
+        radial_embedding: rff
+        rff_num_features: 128
+        rff_lengthscale: 0.15
+        use_vector_output: false
+        vector_aggregation: mean
+        vector_normalization_epsilon: ${oc.eval:"0.5 / ${data.coordinate_std}"}
+        vector_gate_init: 1.0
+        message_chunk_size: 262144
+      state_condition_dim: 2
+      condition_on_pressure: false
+  insertion_params:
+    K: 10
+    D: 3
+    head_mode: unimodal
+    mean_param: mlp
+    insertion_intensity_mode: per_node
+    graph_intensity_parameterization: pending_count
+    sequential_sibling_conditioning: false
+  rotate: true
+  n_augmentations: 1
+  integrator: ${integrator.integrator}
+  beta_sched:
+    _target_: torch.distributions.Beta
+    concentration1: 2.0
+    concentration0: 1.0
+  linear_sched:
+    _target_: torch.distributions.Uniform
+    low: 0.0
+    high: 1.0
+  sample_time_strategy: linear
+  head_node_dim: ${model.backbone.out_node_nf}
+  token_weighting:
+    type_loss_token_weights: uniform
+    weight_alpha: 0.4
+  backbone:
+    _target_: grand_canonical_generator.model.backbones.dit.DiTBackbone
+    _recursive_: false
+    d_input: ${embeddings.atom_type_embedding.out_dim}
+    d_cond: ${oc.eval:"${embeddings.time_embedding.out_dim} + ${embeddings.node_count_embedding.out_dim}"}
+    d_model: 512
+    out_node_nf: 256
+    num_layers: 8
+    nhead: 16
+    mlp_ratio: 4.0
+    periodic_box_size: ${data.periodic_box_size}
+    use_absolute_position_embedding: true
+    position_output_mode: equivariant_displacement
+    equivariant_output_pairs: cutoff
+    use_pair_bias: false
+    mic_message_cutoff: 1.2
+    mic_message_num_layers: 1
+    mic_displacement_aggregation: sqrt_degree
+    mic_displacement_normalization_epsilon: null
+    allow_geometry_blind_attention: false
+    adaln_norm_type: layernorm
+    fuse_adaln_projections: true
+    rbf_embedding_args:
+      _target_: grand_canonical_generator.model.layers.embedding.RandomFourierDistanceEmbedding
+      num_rbf: 128
+      rbf_dmax: 3.5
+      out_dim: 32
+      dropout: 0.0
+      trainable: false
+      num_features: 128
+      lengthscale: 0.15
+      trainable_scale: false
+      seed: 0
+    position_embedding_args:
+      _target_: grand_canonical_generator.model.layers.embedding.TorusFourierPositionEmbedding
+      box_size: ${data.periodic_box_size}
+      max_freq: 16
+      out_dim: ${model.backbone.d_model}
+      dropout: 0.0
+schedule:
+  _target_: grand_canonical_generator.flow_matching.schedules.SmoothstepSchedule
+  shift: 0.8
+trainer:
+  trainer:
+    deterministic: warn
+    devices: 1
+    accelerator: auto
+    strategy: auto
+    precision: bf16-mixed
+    max_epochs: 30000
+    max_steps: 40000
+    accumulate_grad_batches: 1
+    num_sanity_val_steps: 0
+    gradient_clip_val: 10.0
+    gradient_clip_algorithm: norm
+    check_val_every_n_epoch: 100000
+    limit_val_batches: 0
+    limit_predict_batches: 4
+  do_train: true
+  do_validate: false
+  do_predict: false
+  enable_midfit_validation: false
+  checkpoint_path: /lustre/fs1/portfolios/nvr/projects/nvr_qualg_lmbm/users/anburger/grand-canonical-generator/outputs/results/mfi_methane/training/mfi_ep_ind_8x512_nc_baseline_40k_b256_s1_oci-nrt-cs-001_b256_s1_6583017/every_n_epochs/epoch=249-step=40000.ckpt
+  weights_path: null
+callbacks:
+  monitor_metric: val/batch/pair_dist_l1
+  monitor_metric_mode: min
+  progress:
+    interval_seconds: 60
+    every_n_steps: 500
+  model_checkpoints:
+    dirpath: best_checkpoint
+    save_top_k: 1
+    save_last: false
+    verbose: false
+  every_n_epochs_checkpoint:
+    dirpath: every_n_epochs
+    every_n_epochs: 1
+    save_top_k: 1
+    save_last: false
+    verbose: false
+    save_on_train_epoch_end: true
+  step_checkpoint:
+    dirpath: step_checkpoints
+    every_n_train_steps: 500
+    monitor: step
+    mode: max
+    signal_checkpoint: true
+    save_top_k: 2
+    save_last: false
+    verbose: false
+logging:
+  enabled: false
+  project: grand-canonical-generator-mfi-methane
+  name: ${oc.env:GRAND_CANONICAL_GENERATOR_RUN_ID,base}
+  save_dir: .
+  offline: true
+integrator:
+  integrator:
+    _target_: grand_canonical_generator.flow_matching.integration_atomic.RateIntegrator
+    vocab: ${data.vocab}
+    distributions: None
+    insertion_params: ${model.insertion_params}
+    n_atoms_strategy: ${data.n_atoms_strategy}
+    time_strategy: log
+    time_beta_alpha: 2.0
+    time_beta_beta: 1.0
+    num_integration_steps: 100
+    insertion_schedule_integration: analytic_schedule_factor
+    graph_insertion_event_model: bernoulli
+    ins_noise_scale: ${data.ins_noise_scale}
+    renoise_insertions: true
+    use_minimum_image_position_update: null
+    position_flow_mode: learned
+    position_parameterization: endpoint
+    position_process: ode
+    position_sde_gamma: 0.0
+    position_sde_exact_time_variance: false
+    del_schedule: ${data.interpolator.del_schedule}
+    ins_schedule: ${data.interpolator.ins_schedule}
+    sub_schedule: ${data.interpolator.sub_schedule}
+data:
+  root_path: ${oc.env:PROJECT_ROOT}/data/grand_canonical_mfi_methane
+  split_scheme: pressure_heldout_v2
+  require_archive: true
+  temperature_K: 298.0
+  box_lengths_A:
+  - 40.044
+  - 39.798
+  - 26.766
+  coordinate_std: 10.086414337158203
+  periodic_box_size:
+  - 3.970092535018921
+  - 3.9457035064697266
+  - 2.6536686420440674
+  max_particles: 160
+  use_pbc: true
+  allow_charged: false
+  prior_coordinate_family: uniform
+  n_atoms_strategy: fixed
+  optimal_transport: independent
+  prior_coupling: sampled
+  ins_noise_scale: 0.0
+  move_noise_scale: 0.0
+  move_noise_schedule: quadratic_peak
+  preprocessing:
+    _target_: grand_canonical_generator.dataset.conditional.mfi_methane.MfiMethanePreprocessing
+    root: ${data.root_path}
+    split_scheme: ${data.split_scheme}
+    max_particles: ${data.max_particles}
+    prior_coordinate_family: ${data.prior_coordinate_family}
+    use_pbc: ${data.use_pbc}
+    wham_max_iterations: 50000
+    wham_tolerance: 1.0e-08
+  vocab: null
+  interpolator:
+    _target_: grand_canonical_generator.flow_matching.interpolation_atomic.Interpolator
+    vocab: ${data.vocab}
+    distributions: null
+    n_atoms_strategy: ${data.n_atoms_strategy}
+    optimal_transport: ${data.optimal_transport}
+    ins_noise_scale: ${data.ins_noise_scale}
+    move_noise_scale: ${data.move_noise_scale}
+    move_noise_schedule: ${data.move_noise_schedule}
+    pre_align_iters: 0
+    c_move: 1.0
+    c_sub: 0.0
+    c_ins: 1000000.0
+    c_del: 1000000.0
+    del_schedule: ${schedule}
+    ins_schedule: ${schedule}
+    sub_schedule: ${schedule}
+  datamodule:
+    _target_: grand_canonical_generator.dataset.conditional.mfi_methane_datamodule.MfiMethaneLightningDataModule
+    vocab: ${data.vocab}
+    distributions: null
+    representation: ${representation}
+    datasets:
+      train:
+        _target_: grand_canonical_generator.dataset.conditional.mfi_methane.MfiMethaneFlowDataset
+        root: ${data.root_path}
+        split_scheme: ${data.split_scheme}
+      val:
+      - _target_: grand_canonical_generator.dataset.conditional.mfi_methane.MfiMethaneFlowDataset
+        root: ${data.root_path}
+        split_scheme: ${data.split_scheme}
+      test:
+      - _target_: grand_canonical_generator.dataset.conditional.mfi_methane.MfiMethaneFlowDataset
+        root: ${data.root_path}
+        split_scheme: ${data.split_scheme}
+    interpolator: ${data.interpolator}
+    rotate: false
+    n_augmentations: 1
+    augmentation_mode: none
+    num_workers:
+      train: 8
+      val: 8
+      test: 8
+    prefetch_factor: 4
+    batch_size:
+      train: 256
+      val: 128
+      test: 128
+    balance_batch_counts: true
+    count_balance_buckets: 8
+    n_atoms_strategy: ${data.n_atoms_strategy}
+    optimal_transport: ${data.optimal_transport}
+    prior_coupling: ${data.prior_coupling}
+    time_dist: ${model.module.time_dist}
+embeddings:
+  atom_type_embedding:
+    _target_: grand_canonical_generator.model.layers.embedding.Embedding
+    num_embeddings: ${len:${data.vocab.atom_tokens}}
+    embedding_dim: 32
+    out_dim: 64
+  time_embedding:
+    _target_: grand_canonical_generator.model.layers.embedding.TimeEmbedding
+    embedding_dim: 64
+    out_dim: 64
+  node_count_embedding:
+    _target_: grand_canonical_generator.model.layers.embedding.ExtrapolatableCountEmbedding
+    embedding_dim: 32
+    out_dim: 64
+    min_period: 16.0
+    max_period: 512.0
+    max_count: ${data.max_particles}
+  chemical_potential_embedding: null

artifacts/mfi_methane/endpoint_independent_8x512_b256_s1_step40000/config/hydra_overrides.yaml

@@ -0,0 +1,9 @@
+- defaults=mfi_methane_endpoint_independent
+- model_size=8x512
+- seed=1
+- trainer.trainer.max_steps=40000
+- model.module.optimizer_config.scheduler.total_steps=40000
+- data.datamodule.batch_size.train=256
+- model.module.near_contact_separation_weight=0.0
+- model.module.near_contact_node_weight_scale=0.0
+- trainer.checkpoint_path='/lustre/fs1/portfolios/nvr/projects/nvr_qualg_lmbm/users/anburger/grand-canonical-generator/outputs/results/mfi_methane/training/mfi_ep_ind_8x512_nc_baseline_40k_b256_s1_oci-nrt-cs-001_b256_s1_6583017/every_n_epochs/epoch=249-step=40000.ckpt'

artifacts/mfi_methane/endpoint_independent_8x512_b256_s1_step40000/config/hydra_runtime.yaml

@@ -0,0 +1,177 @@
+hydra:
+  run:
+    dir: ${oc.env:GRAND_CANONICAL_GENERATOR_RUN_ROOT,${hydra:runtime.cwd}/outputs/results}/${oc.env:GRAND_CANONICAL_GENERATOR_SYSTEM,${hydra:runtime.choices.data}}/${oc.env:GRAND_CANONICAL_GENERATOR_TASK_TYPE,training}/${oc.env:GRAND_CANONICAL_GENERATOR_RUN_ID}
+  sweep:
+    dir: multirun/${now:%Y-%m-%d}/${now:%H-%M-%S}
+    subdir: ${hydra.job.num}
+  launcher:
+    _target_: hydra._internal.core_plugins.basic_launcher.BasicLauncher
+  sweeper:
+    _target_: hydra._internal.core_plugins.basic_sweeper.BasicSweeper
+    max_batch_size: null
+    params: null
+  help:
+    app_name: ${hydra.job.name}
+    header: '${hydra.help.app_name} is powered by Hydra.
+
+      '
+    footer: 'Powered by Hydra (https://hydra.cc)
+
+      Use --hydra-help to view Hydra specific help
+
+      '
+    template: '${hydra.help.header}
+
+      == Configuration groups ==
+
+      Compose your configuration from those groups (group=option)
+
+
+      $APP_CONFIG_GROUPS
+
+
+      == Config ==
+
+      Override anything in the config (foo.bar=value)
+
+
+      $CONFIG
+
+
+      ${hydra.help.footer}
+
+      '
+  hydra_help:
+    template: 'Hydra (${hydra.runtime.version})
+
+      See https://hydra.cc for more info.
+
+
+      == Flags ==
+
+      $FLAGS_HELP
+
+
+      == Configuration groups ==
+
+      Compose your configuration from those groups (For example, append hydra/job_logging=disabled
+      to command line)
+
+
+      $HYDRA_CONFIG_GROUPS
+
+
+      Use ''--cfg hydra'' to Show the Hydra config.
+
+      '
+    hydra_help: ???
+  hydra_logging:
+    version: 1
+    formatters:
+      simple:
+        format: '[%(asctime)s][HYDRA] %(message)s'
+    handlers:
+      console:
+        class: logging.StreamHandler
+        formatter: simple
+        stream: ext://sys.stdout
+    root:
+      level: INFO
+      handlers:
+      - console
+    loggers:
+      logging_example:
+        level: DEBUG
+    disable_existing_loggers: false
+  job_logging:
+    version: 1
+    formatters:
+      simple:
+        format: '[%(asctime)s][%(name)s][%(levelname)s] - %(message)s'
+    handlers:
+      console:
+        class: logging.StreamHandler
+        formatter: simple
+        stream: ext://sys.stdout
+      file:
+        class: logging.FileHandler
+        formatter: simple
+        filename: ${hydra.runtime.output_dir}/${hydra.job.name}.log
+    root:
+      level: INFO
+      handlers:
+      - console
+      - file
+    disable_existing_loggers: false
+  env: {}
+  mode: RUN
+  searchpath: []
+  callbacks: {}
+  output_subdir: .hydra
+  overrides:
+    hydra:
+    - hydra.mode=RUN
+    task:
+    - defaults=mfi_methane_endpoint_independent
+    - model_size=8x512
+    - seed=1
+    - trainer.trainer.max_steps=40000
+    - model.module.optimizer_config.scheduler.total_steps=40000
+    - data.datamodule.batch_size.train=256
+    - model.module.near_contact_separation_weight=0.0
+    - model.module.near_contact_node_weight_scale=0.0
+    - trainer.checkpoint_path='/lustre/fs1/portfolios/nvr/projects/nvr_qualg_lmbm/users/anburger/grand-canonical-generator/outputs/results/mfi_methane/training/mfi_ep_ind_8x512_nc_baseline_40k_b256_s1_oci-nrt-cs-001_b256_s1_6583017/every_n_epochs/epoch=249-step=40000.ckpt'
+  job:
+    name: run
+    chdir: null
+    override_dirname: data.datamodule.batch_size.train=256,defaults=mfi_methane_endpoint_independent,model.module.near_contact_node_weight_scale=0.0,model.module.near_contact_separation_weight=0.0,model.module.optimizer_config.scheduler.total_steps=40000,model_size=8x512,seed=1,trainer.checkpoint_path='/lustre/fs1/portfolios/nvr/projects/nvr_qualg_lmbm/users/anburger/grand-canonical-generator/outputs/results/mfi_methane/training/mfi_ep_ind_8x512_nc_baseline_40k_b256_s1_oci-nrt-cs-001_b256_s1_6583017/every_n_epochs/epoch=249-step=40000.ckpt',trainer.trainer.max_steps=40000
+    id: ???
+    num: ???
+    config_name: default
+    env_set: {}
+    env_copy: []
+    config:
+      override_dirname:
+        kv_sep: '='
+        item_sep: ','
+        exclude_keys: []
+  runtime:
+    version: 1.3.2
+    version_base: '1.1'
+    cwd: /lustre/fs1/portfolios/nvr/projects/nvr_qualg_lmbm/users/anburger/grand-canonical-generator
+    config_sources:
+    - path: hydra.conf
+      schema: pkg
+      provider: hydra
+    - path: /lustre/fs1/portfolios/nvr/projects/nvr_qualg_lmbm/users/anburger/grand-canonical-generator/configs
+      schema: file
+      provider: main
+    - path: ''
+      schema: structured
+      provider: schema
+    output_dir: /lustre/fs1/portfolios/nvr/projects/nvr_qualg_lmbm/users/anburger/grand-canonical-generator/outputs/results/mfi_methane/training/mfi_ep_ind_8x512_nc_baseline_40k_b256_s1_oci-nrt-cs-001_b256_s1_6583017
+    choices:
+      train_recipe: none
+      defaults: mfi_methane_endpoint_independent
+      embeddings: mfi_methane
+      data: mfi_methane
+      integrator: integrator
+      logging: wandb_logger
+      callbacks: callbacks
+      trainer: trainer
+      schedule: smoothstep
+      model_size: 8x512
+      model: dit_gc_mfi_factorized
+      loss_weights@model.loss_weights: factorized
+      optimizer@model.optimizer: muon_aux_adam
+      heads: heads
+      hydra/env: default
+      hydra/callbacks: null
+      hydra/job_logging: default
+      hydra/hydra_logging: default
+      hydra/hydra_help: default
+      hydra/help: default
+      hydra/sweeper: basic
+      hydra/launcher: basic
+      hydra/output: default
+  verbose: false

artifacts/mfi_methane/endpoint_independent_8x512_b256_s1_step40000/config/protocol.txt

@@ -0,0 +1,8 @@
+defaults=mfi_methane_endpoint_independent
+train_recipe=<config default>
+run_id=mfi_ep_ind_8x512_nc_baseline_40k_b256_s1_oci-nrt-cs-001_b256_s1_6583017
+seed=1
+total_steps=40000
+batch_size=256
+muon_lr=<config default>
+hydra_overrides=defaults=mfi_methane_endpoint_independent model_size=8x512 seed=1 trainer.trainer.max_steps=40000 model.module.optimizer_config.scheduler.total_steps=40000 data.datamodule.batch_size.train=256 model.module.near_contact_separation_weight=0.0 model.module.near_contact_node_weight_scale=0.0

artifacts/mfi_methane/endpoint_independent_8x512_b256_s1_step40000/logs/evaluation.log

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+/lustre/fs1/portfolios/nvr/projects/nvr_qualg_lmbm/users/anburger/grand-canonical-generator/src/grand_canonical_generator/dataset/conditional/mfi_methane.py:107: SyntaxWarning: invalid escape sequence '\('
+  the tabulated range use linear interpolation in \(P\). Pressures above the
+/lustre/fs1/portfolios/nvr/projects/nvr_qualg_lmbm/users/anburger/grand-canonical-generator/src/grand_canonical_generator/flow_matching/interpolation_atomic.py:338: SyntaxWarning: invalid escape sequence '\('
+  """Fixed-N geometry interpolant: matching, \(x_t\), and the position target.
+[rank: 0] Seed set to 0
+[rank: 0] Seed set to 1
+Using embedded checkpoint configuration
+{
+  "checkpoint": "epoch=249-step=40000.ckpt",
+  "source": "uniform",
+  "integration_steps": 200,
+  "device": "cuda",
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+  "energy_note": "Disabled for MFI: the available estimate is not RASPA-compatible.",
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+  "ch4_ch4_overlap_A": 3.0,
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+}

artifacts/mfi_methane/endpoint_independent_8x512_b256_s1_step40000/logs/run.log

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+[2026-09-04 16:25:51,414][hydra.utils][INFO] - Instantiating preprocessing...
+[2026-09-04 16:25:54,240][hydra.utils][INFO] - Preprocessing complete.
+Found 3 atom tokens: ['CH4', 'Si', 'O']
+Found 1 charge tokens: ['0']
+[2026-09-04 16:25:54,241][hydra.utils][INFO] - Distributions computed from training dataset.
+[2026-09-04 16:25:54,241][hydra.utils][INFO] - Instantiating <grand_canonical_generator.dataset.conditional.mfi_methane_datamodule.MfiMethaneLightningDataModule>
+[2026-09-04 16:25:55,978][hydra.utils][INFO] - Instantiating <grand_canonical_generator.model.lightning.transformer.LightningModuleRatesTransformer>
+[2026-09-04 16:25:57,139][hydra.utils][INFO] - Skipping val-monitored <ModelCheckpoint>: mid-fit validation is off
+[2026-09-04 16:25:57,140][hydra.utils][INFO] - Adding callback <ModelCheckpoint> for every 1 epochs
+[2026-09-04 16:25:57,140][hydra.utils][INFO] - Adding callback <ModelCheckpoint> for every 500 training steps
+[2026-09-04 16:25:57,141][hydra.utils][INFO] - Adding callback <PeriodicProgressPrinter> every 60 seconds / 500 steps
+[2026-09-04 18:21:09,431][hydra.utils][INFO] - Instantiating preprocessing...
+[2026-09-04 18:21:12,468][hydra.utils][INFO] - Preprocessing complete.
+Found 3 atom tokens: ['CH4', 'Si', 'O']
+Found 1 charge tokens: ['0']
+[2026-09-04 18:21:12,468][hydra.utils][INFO] - Distributions computed from training dataset.
+[2026-09-04 18:21:12,468][hydra.utils][INFO] - Instantiating <grand_canonical_generator.dataset.conditional.mfi_methane_datamodule.MfiMethaneLightningDataModule>
+[2026-09-04 18:21:14,287][hydra.utils][INFO] - Instantiating <grand_canonical_generator.model.lightning.transformer.LightningModuleRatesTransformer>
+[2026-09-04 18:21:15,517][hydra.utils][INFO] - Skipping val-monitored <ModelCheckpoint>: mid-fit validation is off
+[2026-09-04 18:21:15,517][hydra.utils][INFO] - Adding callback <ModelCheckpoint> for every 1 epochs
+[2026-09-04 18:21:15,518][hydra.utils][INFO] - Adding callback <ModelCheckpoint> for every 500 training steps
+[2026-09-04 18:21:15,518][hydra.utils][INFO] - Adding callback <PeriodicProgressPrinter> every 60 seconds / 500 steps

artifacts/mfi_methane/endpoint_independent_8x512_b256_s1_step40000/manifest.json

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+  "seed": 1,
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+}

artifacts/mfi_methane/endpoint_independent_8x512_b256_s1_step40000/metrics/baseline.json

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