Exp/mtrsm Mattergen example addition

other/experiments/mtrgn/README.md

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+# Example of using Mattergen to generate a material
+
+## 1. Installation and setup
+
+### 1.0. Clone the repository
+
+```bash
+git clone https://github.com/Exabyte-io/mattergen.git && cd mattergen
+```
+
+### 1.1. Create virtual environment
+
+```bash
+pyenv local 3.10.12
+python -m venv .venv-3.10.12
+source .venv-3.10.12/bin/activate
+```
+
+### 1.2. Install the package
+
+Try this approach first:
+
+```bash
+pip install -e .
+```
+
+In case of issues, try using `uv`:
+
+```bash
+pip install uv
+uv pip install -e .
+```
+
+### 1.3. Fix torch compatibility
+
+In case of compatibility issues with torch and torch-scatter, you can try to reinstall specific versions.
+
+Below are the directives for Apple Silicon, 12.6 OSX:
+
+```bash
+pip install --no-cache-dir --force-reinstall "torch==2.4.1"
+```
+
+In case `torch-scatter` installation fails, try:
+```bash
+pip install --no-cache-dir --force-reinstall  torch-scatter -f https://data.pyg.org/whl/torch-2.4.1.html
+```
+
+### 1.4. Set environment variables
+
+For Apple Silicon devices (M-series chips) set fallback to CPU:
+```bash
+export MATTERGEN_DEVICE=cpu
+export PYTORCH_ENABLE_MPS_FALLBACK=1;
+```
+
+## 2.0. Run example
+
+Set model name and results path:
+```bash
+export MODEL_NAME=chemical_system_energy_above_hull
+export RESULTS_PATH="results/$MODEL_NAME/"
+```
+
+Run generation:
+```bash
+mattergen-generate $RESULTS_PATH --pretrained-name=$MODEL_NAME --batch_size=1 --properties_to_condition_on="{'chemical_system': 'Si-O'}" --diffusion_guidance_factor=2.0
+```
+
+## 3.0. Results
+
+File structure expected to be like:
+```
+results
+  chemical_system_energy_above_hull
+    generated_crystals.extxyz
+    generated_crystals_cif.zip
+    generated_trajectories.zip
+```
+
+Example structural output:
+```
+8
+Lattice="4.810662746429443 0.0 2.003615617752075 2.0573911375230405 4.4635489819590255 1.6285755634307861 0.0 0.0 6.223104953765869" Properties=species:S:1:pos:R:3 pbc="T T T"
+Si       3.19007697       0.64344807       2.15220843
+O        6.29417322       4.25980285       4.64711970
+Si       2.52538380       3.42031925       3.52259767
+O        6.28716089       4.28023109       7.76082322
+O        3.88651095       4.26880406       3.65002186
+O        2.86109621       2.03830726       2.83004283
+O        1.84533000       3.12136774       5.01444792
+O        3.87107245       0.94328279       6.87403968
+```
+
+## 4.0. Run relaxation (optional)
+
+To relax the generated structures, you can use the [Relaxation Notebook](../mtrsm/relax_generated_material.ipynb).
+
+Copy the generated `extxyz` file to the `mtrsm/data/` folder and run the notebook.

other/experiments/mtrgn/results/chemical_system_energy_above_hull/generated_crystals.extxyz

@@ -0,0 +1,10 @@
+8
+Lattice="4.810662746429443 0.0 2.003615617752075 2.0573911375230405 4.4635489819590255 1.6285755634307861 0.0 0.0 6.223104953765869" Properties=species:S:1:pos:R:3 pbc="T T T"
+Si       3.19007697       0.64344807       2.15220843
+O        6.29417322       4.25980285       4.64711970
+Si       2.52538380       3.42031925       3.52259767
+O        6.28716089       4.28023109       7.76082322
+O        3.88651095       4.26880406       3.65002186
+O        2.86109621       2.03830726       2.83004283
+O        1.84533000       3.12136774       5.01444792
+O        3.87107245       0.94328279       6.87403968

other/experiments/mtrsm/data/generated_crystals.extxyz

@@ -0,0 +1,10 @@
+8
+Lattice="4.810662746429443 0.0 2.003615617752075 2.0573911375230405 4.4635489819590255 1.6285755634307861 0.0 0.0 6.223104953765869" Properties=species:S:1:pos:R:3 pbc="T T T"
+Si       3.19007697       0.64344807       2.15220843
+O        6.29417322       4.25980285       4.64711970
+Si       2.52538380       3.42031925       3.52259767
+O        6.28716089       4.28023109       7.76082322
+O        3.88651095       4.26880406       3.65002186
+O        2.86109621       2.03830726       2.83004283
+O        1.84533000       3.12136774       5.01444792
+O        3.87107245       0.94328279       6.87403968