updated scripts for mace, updated readme and gitignore

.gitignore

@@ -19,3 +19,11 @@ models/matris/**/*.o
 *.so
 *.o
 *.pdf
+
+__pycache__/
+*.py[cod]
+*$py.class
+
+# Evaluation outputs
+eval_results/
+**/eval_results/

README.md

@@ -14,7 +14,7 @@ size_categories:
 
 ## Repository Structure
 
-Datasets are stored in the `datasets/` directory and are provided in both `.h5` and `.xyz` formats.
+Datasets are stored in the `datasets/` directory and are provided in both `.h5` and `.xyz` formats. The directory also includes the 1000 larger systems dataset. For `.h5` datasets (used with EquiformerV2), the training and validation split is handled automatically during loading. The reaaining models used `.xyz` format.
 
 All model implementations, training code, evaluation code, and checkpoints are located in the `models/` directory. Each model subdirectory contains:
 
@@ -25,4 +25,4 @@ The scripts are configured to be launched from the repository root directory. Fo
 
 ```bash
 ./models/matris/scripts/run_matris.sh
-
+```

models/mace/README.md

@@ -1,5 +0,0 @@
-## Introduction
-
-Running the script can be found in mace/cli/run_train
-
-you can run it from scripts/run_mace.sh. Just speicfy pathways

models/mace/mace/cli/our_files/{run_eval.py → eval_matris.py}

@@ -329,7 +329,9 @@ def main():
     # Build validation set/loader ONCE, using the first model for z_table + r_max
     # (assumes comparable checkpoints; if not, rebuild per model instead)
     # -------------------------------------------------------------------------
-    first_model = torch.load(model_paths[0], map_location="cpu")
+    print("\n")
+    print(model_paths[0])
+    first_model = torch.load(model_paths[0], map_location="cpu", weights_only=False)
     n_params_total = count_params_millions(first_model, trainable_only=False)
     n_params_train = count_params_millions(first_model, trainable_only=True)
 

models/mace/scripts/eval_matris.sh

@@ -0,0 +1,103 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+# ----------------------------
+# Resolve paths
+# ----------------------------
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+MACE_REPO_DIR="$(cd "$SCRIPT_DIR/.." && pwd)"
+REPO_ROOT="$(cd "$SCRIPT_DIR/../../.." && pwd)"
+
+# ----------------------------
+# User settings
+# ----------------------------
+NAME="eval"
+
+VALID_FILE="$REPO_ROOT/datasets/xyz/test.xyz"
+
+OUT_DIR="$MACE_REPO_DIR/eval_results"
+OUT_TXT_FILE="$OUT_DIR/test.txt"
+
+MODEL_PATHS=(
+  "$MACE_REPO_DIR/runs/mace_seed42.model"
+)
+
+BATCH_SIZE="5"
+SEED="42"
+DEVICE="cuda"
+
+# ----------------------------
+# Detect number of visible GPUs
+# ----------------------------
+if command -v nvidia-smi &> /dev/null; then
+  NGPUS="$(nvidia-smi -L | wc -l | tr -d ' ')"
+else
+  NGPUS="1"
+fi
+
+NGPUS="${NGPUS:-1}"
+
+# ----------------------------
+# Sanity checks
+# ----------------------------
+if [ ! -d "$MACE_REPO_DIR/mace" ]; then
+  echo "ERROR: MACE package directory not found:"
+  echo "$MACE_REPO_DIR/mace"
+  exit 1
+fi
+
+if [ ! -f "$VALID_FILE" ]; then
+  echo "ERROR: Validation file not found:"
+  echo "$VALID_FILE"
+  exit 1
+fi
+
+for model_path in "${MODEL_PATHS[@]}"; do
+  if [ ! -f "$model_path" ]; then
+    echo "ERROR: Model checkpoint not found:"
+    echo "$model_path"
+    exit 1
+  fi
+done
+
+mkdir -p "$OUT_DIR"
+
+echo "Using NGPUS=${NGPUS}"
+echo "MACE_REPO_DIR=${MACE_REPO_DIR}"
+echo "REPO_ROOT=${REPO_ROOT}"
+echo "Validation file=${VALID_FILE}"
+echo "Output file=${OUT_TXT_FILE}"
+echo "Evaluating models:"
+for m in "${MODEL_PATHS[@]}"; do
+  echo "  - $m"
+done
+
+# ----------------------------
+# Go to MACE repo root and expose it to Python
+# ----------------------------
+cd "$MACE_REPO_DIR"
+export PYTHONPATH="$MACE_REPO_DIR:${PYTHONPATH:-}"
+
+unset SLURM_JOB_NODELIST \
+      SLURM_NTASKS \
+      SLURM_NTASKS_PER_NODE \
+      SLURM_NNODES \
+      SLURM_LOCALID \
+      SLURM_PROCID \
+      SLURM_NODEID \
+      SLURM_JOB_ID
+
+# ----------------------------
+# Launch evaluation
+# ----------------------------
+torchrun --standalone --nproc_per_node="$NGPUS" -m mace.cli.our_files.eval_matris \
+  --name "$NAME" \
+  --seed "$SEED" \
+  --valid_file "$VALID_FILE" \
+  --batch_size "$BATCH_SIZE" \
+  --valid_batch_size "$BATCH_SIZE" \
+  --device "$DEVICE" \
+  --energy_key "energy" \
+  --forces_key "forces" \
+  --out_txt "$OUT_TXT_FILE" \
+  --model_paths "${MODEL_PATHS[@]}"

models/mace/scripts/run_mace.sh

@@ -1,33 +1,29 @@
 #!/usr/bin/env bash
 set -euo pipefail
 
-
-
 # ----------------------------
-# User settings (edit these)
+# Resolve paths
 # ----------------------------
-MACE_REPO_DIR=""   # repo root (contains "mace/" folder)
-NAME="new_testing"
-CHECKPOINT_DIR="new_models/"
-
-TRAIN_FILE=""
-VALID_FILE=""
-TEST_FILE=""
-
-# If you want a fixed validation set instead of valid_fraction, replace VALID_FRACTION with VALID_FILE below.
-VALID_FRACTION="0.5"
-# VALID_FILE="valid.xyz"   # uncomment and use this instead of --valid_fraction if desired
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+MACE_REPO_DIR="$(cd "$SCRIPT_DIR/.." && pwd)"
+REPO_ROOT="$(cd "$SCRIPT_DIR/../../.." && pwd)"
 
+# ----------------------------
+# User settings
+# ----------------------------
+NAME="mace"
 
+TRAIN_FILE="$REPO_ROOT/datasets/xyz/train.xyz"
+VALID_FILE="$REPO_ROOT/datasets/xyz/val.xyz"
+TEST_FILE="$REPO_ROOT/datasets/xyz/test.xyz"
 
+CHECKPOINT_DIR="$MACE_REPO_DIR/checkpoints_mace"
 
 # From the docs screenshot:
 CONFIG_TYPE_WEIGHTS='{"Default":1.0}'
 
-# IMPORTANT: Replace these example E0s with your actual values if needed.
-# The screenshot shows a dict with element keys; keep as a single-quoted string.
+# Replace these E0s if needed.
 E0S='{1: 2.467478445, 6: 8.0273263225, 8: 3.334308855, 22: 4.879036065}'
-#E0S='{1: 1.0, 6: 1.0, 8: 1.0, 22: 1.0}'
 ATOMIC_NUMBERS='[1,6,8,22]'
 
 MODEL="MACE"
@@ -42,6 +38,8 @@ SEED="11"
 DEVICE="cuda"
 MAX_NUM_EPOCHS="10"
 
+WAND_PROJECT="mace"
+
 # ----------------------------
 # Detect number of visible GPUs
 # ----------------------------
@@ -50,19 +48,58 @@ if command -v nvidia-smi &> /dev/null; then
 else
   NGPUS="1"
 fi
+
 NGPUS="${NGPUS:-1}"
 
+# ----------------------------
+# Sanity checks
+# ----------------------------
+if [ ! -d "$MACE_REPO_DIR/mace" ]; then
+  echo "ERROR: MACE package directory not found:"
+  echo "$MACE_REPO_DIR/mace"
+  exit 1
+fi
+
+if [ ! -f "$TRAIN_FILE" ]; then
+  echo "ERROR: Training file not found:"
+  echo "$TRAIN_FILE"
+  exit 1
+fi
+
+if [ ! -f "$VALID_FILE" ]; then
+  echo "ERROR: Validation file not found:"
+  echo "$VALID_FILE"
+  exit 1
+fi
+
+if [ ! -f "$TEST_FILE" ]; then
+  echo "ERROR: Test file not found:"
+  echo "$TEST_FILE"
+  exit 1
+fi
+
 echo "Using NGPUS=${NGPUS}"
 echo "MACE_REPO_DIR=${MACE_REPO_DIR}"
-echo "Train=${TRAIN_FILE}  Test=${TEST_FILE}"
+echo "REPO_ROOT=${REPO_ROOT}"
+echo "Train=${TRAIN_FILE}"
+echo "Valid=${VALID_FILE}"
+echo "Test=${TEST_FILE}"
 echo "Checkpoint_dir=${CHECKPOINT_DIR}"
 
 # ----------------------------
-# Go to repo root and expose it to Python
-cd "${MACE_REPO_DIR}"
-export PYTHONPATH="$(pwd):${PYTHONPATH:-}"
-
-unset SLURM_JOB_NODELIST SLURM_NTASKS SLURM_NTASKS_PER_NODE SLURM_NNODES SLURM_LOCALID SLURM_PROCID SLURM_NODEID SLURM_JOB_ID
+# Go to MACE repo root and expose it to Python
+# ----------------------------
+cd "$MACE_REPO_DIR"
+export PYTHONPATH="$MACE_REPO_DIR:${PYTHONPATH:-}"
+
+unset SLURM_JOB_NODELIST \
+      SLURM_NTASKS \
+      SLURM_NTASKS_PER_NODE \
+      SLURM_NNODES \
+      SLURM_LOCALID \
+      SLURM_PROCID \
+      SLURM_NODEID \
+      SLURM_JOB_ID
 
 # ----------------------------
 # Per-run output folders
@@ -77,67 +114,57 @@ RUN_LOGS_DIR="${RUN_DIR}/logs"
 RUN_WANDB_DIR="${RUN_DIR}/wandb"
 
 mkdir -p \
-  "${RUN_CHECKPOINTS_DIR}" \
-  "${RUN_MODELS_DIR}" \
-  "${RUN_RESULTS_DIR}" \
-  "${RUN_LOGS_DIR}" \
-  "${RUN_WANDB_DIR}"
+  "$RUN_CHECKPOINTS_DIR" \
+  "$RUN_MODELS_DIR" \
+  "$RUN_RESULTS_DIR" \
+  "$RUN_LOGS_DIR" \
+  "$RUN_WANDB_DIR"
 
 echo "RUN_DIR=${RUN_DIR}"
 
-WAND_PROJECT="testing_mace_wandb"
-
 # ----------------------------
 # Launch training
 # ----------------------------
-torchrun --standalone --nproc_per_node=$NGPUS -m mace.cli.run_train \
-  --name="${NAME}" \
-  --seed="${SEED}" \
-  --checkpoints_dir="${RUN_CHECKPOINTS_DIR}" \
-  --model_dir="${RUN_MODELS_DIR}" \
-  --results_dir="${RUN_RESULTS_DIR}" \
-  --log_dir="${RUN_LOGS_DIR}" \
+torchrun --standalone --nproc_per_node="$NGPUS" -m mace.cli.run_train \
+  --name="$NAME" \
+  --seed="$SEED" \
+  --checkpoints_dir="$RUN_CHECKPOINTS_DIR" \
+  --model_dir="$RUN_MODELS_DIR" \
+  --results_dir="$RUN_RESULTS_DIR" \
+  --log_dir="$RUN_LOGS_DIR" \
   \
+  --max_num_epochs="$MAX_NUM_EPOCHS" \
+  --train_file="$TRAIN_FILE" \
+  --valid_file="$VALID_FILE" \
+  --test_file="$TEST_FILE" \
   \
-  --max_num_epochs="${MAX_NUM_EPOCHS}" \
-  --train_file="${TRAIN_FILE}" \
-  --valid_file="${VALID_FILE}" \
-  --test_file="${TEST_FILE}" \
+  --hidden_irreps="$HIDDEN_IRREPS" \
+  --config_type_weights="$CONFIG_TYPE_WEIGHTS" \
+  --E0s="$E0S" \
+  --model="$MODEL" \
+  --r_max="$R_MAX" \
   \
-  \
-  --hidden_irreps="${HIDDEN_IRREPS}" \
-  --config_type_weights="${CONFIG_TYPE_WEIGHTS}" \
-  --E0s="${E0S}" \
-  --model="${MODEL}" \
-  --r_max="${R_MAX}" \
-  \
-  \
-  --batch_size="${BATCH_SIZE}" \
-  --valid_batch_size="${VALID_BATCH_SIZE}" \
+  --batch_size="$BATCH_SIZE" \
+  --valid_batch_size="$VALID_BATCH_SIZE" \
   --ema \
-  --ema_decay="${EMA_DECAY}" \
+  --ema_decay="$EMA_DECAY" \
   --amsgrad \
-  --device="${DEVICE}" \
-  --atomic_numbers "${ATOMIC_NUMBERS}" \
-  \
+  --device="$DEVICE" \
+  --atomic_numbers "$ATOMIC_NUMBERS" \
   \
   --energy_key "energy" \
   --forces_key "forces" \
   \
-  \
   --loss "ours_mae" \
   --forces_weight 1.0 \
   --energy_weight 1.0 \
   --default_dtype "float32" \
   \
-  \
   --distributed \
   \
-  \
   --wandb \
-  --wandb_dir "${RUN_WANDB_DIR}" \
-  --wandb_project "${WAND_PROJECT}" \
-  --wandb_name "${NAME}" \
+  --wandb_dir "$RUN_WANDB_DIR" \
+  --wandb_project "$WAND_PROJECT" \
+  --wandb_name "$NAME" \
   \
-  --swa \
-  
+  #--swa