gpuma 0.5.0__tar.gz

gpuma-0.5.0/LICENSE.md

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 Niklas Hölter
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

gpuma-0.5.0/MANIFEST.in

@@ -0,0 +1,11 @@
+include LICENSE
+include README.md
+include pyproject.toml
+
+recursive-include examples *.py *.json *.xyz
+
+# Exclude build and cache artifacts
+prune build
+prune dist
+prune .pytest_cache
+prune **/__pycache__

gpuma-0.5.0/PKG-INFO

@@ -0,0 +1,146 @@
+Metadata-Version: 2.4
+Name: gpuma
+Version: 0.5.0
+Summary: GPUMA - Geometry optimization toolkit using Fairchem UMA models and Torch-Sim
+Author-email: Niklas Hölter <niklas.hoelter@uni-muenster.de>
+License-Expression: MIT
+Keywords: chemistry,geometry-optimization,uma,fairchem,ase,mlip,gpuma
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Classifier: Topic :: Scientific/Engineering :: Physics
+Requires-Python: >=3.12
+Description-Content-Type: text/markdown
+License-File: LICENSE.md
+Requires-Dist: ase==3.27.0
+Requires-Dist: torch-sim-atomistic==0.5.1
+Requires-Dist: fairchem-core<2.10,>=2.7
+Requires-Dist: morfeus-ml>=0.7
+Requires-Dist: rdkit>=2022.9.5
+Requires-Dist: tables>=3.10.2
+Requires-Dist: scipy<1.15.0
+Requires-Dist: hf_xet
+Provides-Extra: yaml
+Requires-Dist: pyyaml>=6.0; extra == "yaml"
+Provides-Extra: dev
+Requires-Dist: pytest>=9.0.0; extra == "dev"
+Requires-Dist: build>=1.2.1; extra == "dev"
+Requires-Dist: twine>=5.0.0; extra == "dev"
+Requires-Dist: pip-tools>=7.5.2; extra == "dev"
+Requires-Dist: ruff>=0.14.14; extra == "dev"
+Requires-Dist: mkdocs>=1.6.1; extra == "dev"
+Requires-Dist: mkdocs-material>=9.7.1; extra == "dev"
+Requires-Dist: mkdocstrings[python]>=1.0.2; extra == "dev"
+Dynamic: license-file
+
+# GPUMA
+
+<div align="center">
+  <img src="docs/logo_bg.png" alt="GPUMA Logo"/>
+</div>
+
+---
+
+GPUMA is a minimalist Python toolkit for facile and rapid high-throughput molecular geometry optimization 
+based on the [UMA/OMol25 machine-learning interatomic potential](https://arxiv.org/abs/2505.08762).  
+
+GPUMA is especially designed for batch optimizations of many structures (conformer ensembles, datasets) on GPU,
+ensuring efficient parallelization and maximum GPU utilization by leveraging the [torch-sim library](https://arxiv.org/abs/2508.06628).
+It wraps Fairchem UMA models and torch-sim functionality to provide both a simple command-line 
+interface (CLI) and a small but expressive Python API for single- and multi-structure optimizations.
+
+If conformer sampling is desired, GPUMA can generate conformer ensembles on the fly from SMILES strings 
+using the [morfeus library](https://digital-chemistry-laboratory.github.io/morfeus/). Alternative input formats
+are described in the CLI section below.
+
+Feedback and improvements are always welcome!
+
+## Installation
+
+### Option 1: Install from PyPI (recommended)
+
+```bash
+pip install gpuma
+```
+
+This installs `gpuma` together with its core dependencies. Make sure you are using
+Python 3.12 or newer.
+
+> ⚠️ **Required for UMA models:**</br>
+> To access the UMA models on Hugging Face, **you must provide a token** either via the `HUGGINGFACE_TOKEN` environment variable or via the config (direct token string or path to a file containing the token).
+
+### Option 2: Install from source
+
+```bash
+# clone the repository
+git clone https://github.com/niklashoelter/gpuma.git
+cd gpuma
+
+# install using (uv) pip
+uv pip install .
+# or, without uv:
+pip install .
+```
+
+## Documentation
+
+Full documentation is available at [https://niklashoelter.github.io/gpuma/](https://niklashoelter.github.io/gpuma/).
+
+For local browsing of the Markdown sources, see in particular:
+- [docs/index.md](docs/index.md) – overview and getting started
+- [docs/install.md](docs/install.md) – installation details
+- [docs/cli.md](docs/cli.md) – CLI options and input formats
+- [docs/config.md](docs/config.md) – configuration file schema and examples
+- [docs/reference.md](docs/reference.md) – API and configuration reference
+
+Using a configuration file is highly recommended for reproducibility and ease of use.
+
+Also check the [examples/](examples) folder in the repository for sample config files and usage examples:
+- [examples/config.json](examples/config.json) – minimal example configuration
+- [examples/example_single_optimization.py](examples/example_single_optimization.py) – single-structure optimization from Python
+- [examples/example_ensemble_optimization.py](examples/example_ensemble_optimization.py) – ensemble/multi-structure optimization from Python
+
+## CLI Usage
+
+The CLI is provided via the command `gpuma`. For best results, create a
+config file (JSON or YAML) and reference it in all CLI calls (see [examples/config.json](examples/config.json) for a minimal example).
+
+### Examples: Batch optimization of multiple XYZ structures
+
+Optimize all XYZ files in a directory (each file containing a single structure):
+
+```bash
+gpuma optimize --config examples/config.json --xyz-dir examples/example_input_xyzs/multi_xyz_dir/
+```
+
+Optimize multiple structures contained in a single multi-XYZ file:
+
+```bash
+gpuma optimize --config examples/config.json --xyz examples/example_input_xyzs/multi_xyz_file.xyz
+```
+
+Refer to the [CLI documentation](docs/cli.md) for details on configuration options, supported input formats (SMILES, XYZ, directories, multi-XYZ files), and additional CLI examples.
+
+## Python API
+
+A minimalistic and high-level Python API is provided for easy integration into custom scripts and workflows.
+
+For example usage, see:
+- [examples/example_single_optimization.py](examples/example_single_optimization.py)
+- [examples/example_ensemble_optimization.py](examples/example_ensemble_optimization.py)
+
+Please refer to the documentation and examples for detailed usage examples and API reference.
+
+## Known limitations
+
+When a run is started from SMILES, an RDKit force field (via the morfeus library) is used to generate an initial structure. Spin is not taken into account during this step, so the initial estimated geometries can be incorrect. When the UMA/Omol25 models are applied subsequently, the structure can sometimes be optimized to a maximum rather than a minimum because the model is not provided with Hessian matrices. This behavior only affects runs originating from SMILES; it does not occur with better starting geometries (e.g., when starting from XYZ files).
+
+## Troubleshooting
+- Missing libraries: install optional dependencies like `pyyaml` if you use YAML configs.
+- Fairchem/UMA: ensure network access for model downloads and optionally set or provide 
+`huggingface_token` (e.g., via a token file) to access the UMA model family.
+
+## License
+MIT License (see LICENSE)

gpuma-0.5.0/README.md

@@ -0,0 +1,109 @@
+# GPUMA
+
+<div align="center">
+  <img src="docs/logo_bg.png" alt="GPUMA Logo"/>
+</div>
+
+---
+
+GPUMA is a minimalist Python toolkit for facile and rapid high-throughput molecular geometry optimization 
+based on the [UMA/OMol25 machine-learning interatomic potential](https://arxiv.org/abs/2505.08762).  
+
+GPUMA is especially designed for batch optimizations of many structures (conformer ensembles, datasets) on GPU,
+ensuring efficient parallelization and maximum GPU utilization by leveraging the [torch-sim library](https://arxiv.org/abs/2508.06628).
+It wraps Fairchem UMA models and torch-sim functionality to provide both a simple command-line 
+interface (CLI) and a small but expressive Python API for single- and multi-structure optimizations.
+
+If conformer sampling is desired, GPUMA can generate conformer ensembles on the fly from SMILES strings 
+using the [morfeus library](https://digital-chemistry-laboratory.github.io/morfeus/). Alternative input formats
+are described in the CLI section below.
+
+Feedback and improvements are always welcome!
+
+## Installation
+
+### Option 1: Install from PyPI (recommended)
+
+```bash
+pip install gpuma
+```
+
+This installs `gpuma` together with its core dependencies. Make sure you are using
+Python 3.12 or newer.
+
+> ⚠️ **Required for UMA models:**</br>
+> To access the UMA models on Hugging Face, **you must provide a token** either via the `HUGGINGFACE_TOKEN` environment variable or via the config (direct token string or path to a file containing the token).
+
+### Option 2: Install from source
+
+```bash
+# clone the repository
+git clone https://github.com/niklashoelter/gpuma.git
+cd gpuma
+
+# install using (uv) pip
+uv pip install .
+# or, without uv:
+pip install .
+```
+
+## Documentation
+
+Full documentation is available at [https://niklashoelter.github.io/gpuma/](https://niklashoelter.github.io/gpuma/).
+
+For local browsing of the Markdown sources, see in particular:
+- [docs/index.md](docs/index.md) – overview and getting started
+- [docs/install.md](docs/install.md) – installation details
+- [docs/cli.md](docs/cli.md) – CLI options and input formats
+- [docs/config.md](docs/config.md) – configuration file schema and examples
+- [docs/reference.md](docs/reference.md) – API and configuration reference
+
+Using a configuration file is highly recommended for reproducibility and ease of use.
+
+Also check the [examples/](examples) folder in the repository for sample config files and usage examples:
+- [examples/config.json](examples/config.json) – minimal example configuration
+- [examples/example_single_optimization.py](examples/example_single_optimization.py) – single-structure optimization from Python
+- [examples/example_ensemble_optimization.py](examples/example_ensemble_optimization.py) – ensemble/multi-structure optimization from Python
+
+## CLI Usage
+
+The CLI is provided via the command `gpuma`. For best results, create a
+config file (JSON or YAML) and reference it in all CLI calls (see [examples/config.json](examples/config.json) for a minimal example).
+
+### Examples: Batch optimization of multiple XYZ structures
+
+Optimize all XYZ files in a directory (each file containing a single structure):
+
+```bash
+gpuma optimize --config examples/config.json --xyz-dir examples/example_input_xyzs/multi_xyz_dir/
+```
+
+Optimize multiple structures contained in a single multi-XYZ file:
+
+```bash
+gpuma optimize --config examples/config.json --xyz examples/example_input_xyzs/multi_xyz_file.xyz
+```
+
+Refer to the [CLI documentation](docs/cli.md) for details on configuration options, supported input formats (SMILES, XYZ, directories, multi-XYZ files), and additional CLI examples.
+
+## Python API
+
+A minimalistic and high-level Python API is provided for easy integration into custom scripts and workflows.
+
+For example usage, see:
+- [examples/example_single_optimization.py](examples/example_single_optimization.py)
+- [examples/example_ensemble_optimization.py](examples/example_ensemble_optimization.py)
+
+Please refer to the documentation and examples for detailed usage examples and API reference.
+
+## Known limitations
+
+When a run is started from SMILES, an RDKit force field (via the morfeus library) is used to generate an initial structure. Spin is not taken into account during this step, so the initial estimated geometries can be incorrect. When the UMA/Omol25 models are applied subsequently, the structure can sometimes be optimized to a maximum rather than a minimum because the model is not provided with Hessian matrices. This behavior only affects runs originating from SMILES; it does not occur with better starting geometries (e.g., when starting from XYZ files).
+
+## Troubleshooting
+- Missing libraries: install optional dependencies like `pyyaml` if you use YAML configs.
+- Fairchem/UMA: ensure network access for model downloads and optionally set or provide 
+`huggingface_token` (e.g., via a token file) to access the UMA model family.
+
+## License
+MIT License (see LICENSE)

gpuma-0.5.0/examples/config.json

@@ -0,0 +1,25 @@
+{
+  "optimization": {
+
+    "batch_optimization_mode": "batch",
+    "batch_optimizer": "fire",
+    "max_num_conformers": 20,
+    "conformer_seed": 42,
+
+    "charge": 0,
+    "multiplicity": 1,
+
+    "force_convergence_criterion": 5e-2,
+    "energy_convergence_criterion": null,
+
+    "model_name": "uma-s-1p1",
+    "model_path": null,
+    "model_cache_dir": "/mnt/share/models/cache",
+    "device": "cuda",
+
+    "huggingface_token": null,
+    "huggingface_token_file": null,
+
+    "logging_level": "DEBUG"
+  }
+}

gpuma-0.5.0/examples/example_ensemble_optimization.py

@@ -0,0 +1,99 @@
+#!/usr/bin/env python3
+"""Example: Ensemble and Batch Optimization with GPUMA.
+
+This example demonstrates how to optimize SMILES-generated conformer ensembles
+and how to batch-optimize general structures from multi-XYZ files or directories
+using the GPUMA API.
+"""
+
+import os
+import sys
+
+sys.path.insert(0, os.path.join(os.path.dirname(__file__), "..", "src"))
+
+import gpuma
+from gpuma.config import default_config, load_config_from_file
+
+OUTPUT_DIR = os.path.join(os.path.dirname(__file__), "example_output")
+os.makedirs(OUTPUT_DIR, exist_ok=True)
+
+
+def example_ensemble_from_smiles():
+    """Example 1: Generate and optimize a conformer ensemble from SMILES."""
+    print("=== Example 1: Ensemble optimization from SMILES ===")
+
+    smiles = "CCC(CC)CCOOC(CC)CCOC"  # Example SMILES
+    config = default_config
+    config.optimization.max_num_conformers = 50
+    config.optimization.force_convergence_criterion = 5e-1
+    print(f"Generating conformers for {smiles} and optimizing...")
+
+    output_file = os.path.join(OUTPUT_DIR, "python_ensemble_from_smiles_optimized.xyz")
+
+    results = gpuma.optimize_ensemble_smiles(
+        smiles=smiles,
+        output_file=output_file,
+        config=config
+    )
+
+    print("✓ Ensemble optimization successful!")
+    print(f"  Generated conformers: {len(results)}")
+    for i, s in enumerate(results):
+        print(f"  Conformer {i + 1}: {s.energy:.6f} eV")
+    print(f"  Output saved to: {output_file}")
+
+
+def example_batch_from_multi_xyz():
+    """Example 2: Batch optimize structures from a multi-structure XYZ file."""
+    print("\n=== Example 2: Batch optimization from multi-XYZ file ===")
+
+    input_file = "example_input_xyzs/butene_triplet_multi.xyz"
+    output_file = os.path.join(OUTPUT_DIR, "python_batch_from_multi_xyz_optimized.xyz")
+
+    config = load_config_from_file("config.json")
+    config.optimization.multiplicity = 3
+    results = gpuma.optimize_batch_multi_xyz_file(
+        input_file=input_file,
+        output_file=output_file,
+        config=config
+    )
+
+    print("✓ Batch optimization successful!")
+    print(f"  Successfully optimized: {len(results)}")
+    for i, s in enumerate(results):
+        print(f"  Structure {i + 1}: {s.energy:.6f} eV")
+    print(f"  Output saved to: {output_file}")
+
+
+def example_batch_from_xyz_directory():
+    """Example 3: Batch optimize structures from a directory of XYZ files."""
+    print("\n=== Example 3: Batch optimization from XYZ directory ===")
+
+    input_dir = "example_input_xyzs/multi_xyz_dir"
+    output_file = os.path.join(OUTPUT_DIR, "python_batch_from_directory_optimized.xyz")
+
+    results = gpuma.optimize_batch_xyz_directory(
+        input_directory=input_dir,
+        output_file=output_file
+    )
+
+    comments = [f"Optimized structure {i + 1} from directory" for i in range(len(results))]
+    gpuma.save_multi_xyz(results, output_file, comments)
+
+    print("✓ Batch optimization successful!")
+    print(f"  Successfully optimized: {len(results)}")
+    for i, s in enumerate(results):
+        print(f"  Structure {i + 1}: {s.energy:.6f} eV")
+    print(f"  Output saved to: {output_file}")
+
+
+if __name__ == "__main__":
+    print("GPUMA - Ensemble and Batch Optimization Examples")
+    print("=" * 70)
+
+    example_ensemble_from_smiles()
+    example_batch_from_multi_xyz()
+    example_batch_from_xyz_directory()
+
+    print("\n" + "=" * 70)
+    print("Examples completed! Check the generated XYZ files.")

gpuma-0.5.0/examples/example_input_xyzs/butene_singlet.xyz

@@ -0,0 +1,14 @@
+12
+Optimized from SMILES: CC=CC | Energy: -4273.493688 eV | Charge: 0 | Multiplicity: 3
+C -1.900595 0.450216 -0.639234
+C -0.526495 0.530608 -0.103370
+C 0.528262 -0.527150 -0.461806
+C 1.900195 -0.451000 0.080194
+H -2.657543 0.379571 0.153486
+H -2.016685 -0.421879 -1.284155
+H -2.169206 1.336974 -1.229126
+H -0.235907 1.334041 0.559052
+H 0.235625 -1.334592 -1.118427
+H 2.168355 -1.336798 0.671650
+H 2.016868 0.422236 0.723465
+H 2.657128 -0.382228 -0.712767

gpuma-0.5.0/examples/example_input_xyzs/butene_triplet.xyz

@@ -0,0 +1,14 @@
+12
+Optimized from SMILES: CC=CC | Energy: -4273.493688 eV | Charge: 0 | Multiplicity: 3
+C     -1.9005950000    0.4502160000   -0.6392340000
+C     -0.5264950000    0.5306080000   -0.1033700000
+C      0.4954239479   -0.7881417480   -0.2154229594
+C      1.9308878903   -0.4499872239   -0.2982345951
+H     -2.6575430000    0.3795710000    0.1534860000
+H     -2.0166850000   -0.4218790000   -1.2841550000
+H     -2.1692060000    1.3369740000   -1.2291260000
+H     -0.2359070000    1.3340410000    0.5590520000
+H      0.0942915852   -1.2946010127    0.6513768880
+H      2.2566221436    0.2044912910    0.5214745924
+H      2.1576011119    0.0590031239   -1.2360411962
+H      2.5716063212   -1.3402964303   -0.2408437298

gpuma-0.5.0/examples/example_input_xyzs/butene_triplet_multi.xyz

@@ -0,0 +1,56 @@
+12
+Optimized from SMILES: CC=CC | Energy: -4273.493688 eV | Charge: 0 | Multiplicity: 3
+C     -1.9005950000    0.4502160000   -0.6392340000
+C     -0.5264950000    0.5306080000   -0.1033700000
+C      0.4954239479   -0.7881417480   -0.2154229594
+C      1.9308878903   -0.4499872239   -0.2982345951
+H     -2.6575430000    0.3795710000    0.1534860000
+H     -2.0166850000   -0.4218790000   -1.2841550000
+H     -2.1692060000    1.3369740000   -1.2291260000
+H     -0.2359070000    1.3340410000    0.5590520000
+H      0.0942915852   -1.2946010127    0.6513768880
+H      2.2566221436    0.2044912910    0.5214745924
+H      2.1576011119    0.0590031239   -1.2360411962
+H      2.5716063212   -1.3402964303   -0.2408437298
+12
+Optimized from SMILES: CC=CC | Energy: -4273.493688 eV | Charge: 0 | Multiplicity: 3
+C     -1.9005950000    0.4502160000   -0.6392340000
+C     -0.5264950000    0.5306080000   -0.1033700000
+C      0.4954239479   -0.7881417480   -0.2154229594
+C      1.9308878903   -0.4499872239   -0.2982345951
+H     -2.6575430000    0.3795710000    0.1534860000
+H     -2.0166850000   -0.4218790000   -1.2841550000
+H     -2.1692060000    1.3369740000   -1.2291260000
+H     -0.2359070000    1.3340410000    0.5590520000
+H      0.0942915852   -1.2946010127    0.6513768880
+H      2.2566221436    0.2044912910    0.5214745924
+H      2.1576011119    0.0590031239   -1.2360411962
+H      2.5716063212   -1.3402964303   -0.2408437298
+12
+Optimized from SMILES: CC=CC | Energy: -4273.493688 eV | Charge: 0 | Multiplicity: 3
+C     -1.9005950000    0.4502160000   -0.6392340000
+C     -0.5264950000    0.5306080000   -0.1033700000
+C      0.4954239479   -0.7881417480   -0.2154229594
+C      1.9308878903   -0.4499872239   -0.2982345951
+H     -2.6575430000    0.3795710000    0.1534860000
+H     -2.0166850000   -0.4218790000   -1.2841550000
+H     -2.1692060000    1.3369740000   -1.2291260000
+H     -0.2359070000    1.3340410000    0.5590520000
+H      0.0942915852   -1.2946010127    0.6513768880
+H      2.2566221436    0.2044912910    0.5214745924
+H      2.1576011119    0.0590031239   -1.2360411962
+H      2.5716063212   -1.3402964303   -0.2408437298
+12
+Optimized from SMILES: CC=CC | Energy: -4273.493688 eV | Charge: 0 | Multiplicity: 3
+C     -1.9005950000    0.4502160000   -0.6392340000
+C     -0.5264950000    0.5306080000   -0.1033700000
+C      0.4954239479   -0.7881417480   -0.2154229594
+C      1.9308878903   -0.4499872239   -0.2982345951
+H     -2.6575430000    0.3795710000    0.1534860000
+H     -2.0166850000   -0.4218790000   -1.2841550000
+H     -2.1692060000    1.3369740000   -1.2291260000
+H     -0.2359070000    1.3340410000    0.5590520000
+H      0.0942915852   -1.2946010127    0.6513768880
+H      2.2566221436    0.2044912910    0.5214745924
+H      2.1576011119    0.0590031239   -1.2360411962
+H      2.5716063212   -1.3402964303   -0.2408437298

gpuma-0.5.0/examples/example_input_xyzs/multi_xyz_dir/input (1).xyz

@@ -0,0 +1,20 @@
+18
+Coordinates from ORCA-job input E -364.551519736116
+  C          -2.66062083976099      0.42178070263873      0.32320893307161
+  C          -2.23790785032690     -0.55578771434406     -0.57736610844602
+  C          -0.89063200209219     -0.90649968387654     -0.64549222422337
+  C           0.04788273649760     -0.28481048538367      0.18408020593902
+  C           1.49357028286238     -0.64248526930580      0.07660951215001
+  C           2.51842509141474      0.37149980061321     -0.30242372300699
+  N           2.39888606370255     -0.08899217739450      1.06586985302084
+  C          -0.38198105382051      0.68986026096678      1.09029681299470
+  C          -1.72898631302756      1.04137213098080      1.15676712471904
+  H          -3.71509091084008      0.69647925279893      0.37859486963206
+  H          -2.96136977963007     -1.04925615954480     -1.22850937344232
+  H          -0.56166161680450     -1.67385694172772     -1.35051262268228
+  H           1.68272827957072     -1.66153503648733     -0.27798776877240
+  H           2.19384707878237      1.40118316770369     -0.47720027470562
+  H           3.36733429498554      0.04026932471951     -0.90748331382187
+  H           3.13295275865208     -0.75092606284559      1.30632320005423
+  H           0.35815188608546      1.15089287293532      1.74672078785138
+  H          -2.05552910110378      1.80081203342835      1.86932411243042

gpuma-0.5.0/examples/example_input_xyzs/multi_xyz_dir/input (10).xyz

@@ -0,0 +1,20 @@
+18
+Coordinates from ORCA-job input E -364.549730217798
+  C          -2.60252439229563      0.34816901517186      0.31130410379019
+  C          -1.81619706753138      0.36723383006089     -0.84114176363625
+  C          -0.43478749993316      0.21906194158022     -0.74950221699111
+  C           0.18764857468375      0.04868482301169      0.49432764325631
+  C           1.66623135860957     -0.11688012674397      0.61764186318717
+  C           2.40988884007991     -0.91234874642310     -0.39886011249545
+  N           2.56875388667993      0.52302365233375     -0.32437463832906
+  C          -0.61034880946021      0.03520063670998      1.64275835222599
+  C          -1.99391513445871      0.18140408768218      1.55381410761823
+  H          -3.68461744559101      0.46515525510861      0.23967462232967
+  H          -2.28212452724624      0.49817783645742     -1.81904425493374
+  H           0.16268086528061      0.23424811117128     -1.66550812031091
+  H           2.02913183524751     -0.12599094610884      1.64979348744112
+  H           1.81109302291314     -1.34774044945859     -1.20534339501041
+  H           3.28248345818731     -1.50017932433231     -0.10225722946821
+  H           2.04234073038285      1.00325231660204     -1.05321533919576
+  H          -0.13688412948152     -0.08887918008010      2.61894454473068
+  H          -2.59885456621162      0.16840726196522      2.46180833267868

gpuma-0.5.0/examples/example_input_xyzs/multi_xyz_dir/input (11).xyz

@@ -0,0 +1,20 @@
+18
+Coordinates from ORCA-job input E -364.549730217798
+  C          -2.60252439229563      0.34816901517186      0.31130410379019
+  C          -1.81619706753138      0.36723383006089     -0.84114176363625
+  C          -0.43478749993316      0.21906194158022     -0.74950221699111
+  C           0.18764857468375      0.04868482301169      0.49432764325631
+  C           1.66623135860957     -0.11688012674397      0.61764186318717
+  C           2.40988884007991     -0.91234874642310     -0.39886011249545
+  N           2.56875388667993      0.52302365233375     -0.32437463832906
+  C          -0.61034880946021      0.03520063670998      1.64275835222599
+  C          -1.99391513445871      0.18140408768218      1.55381410761823
+  H          -3.68461744559101      0.46515525510861      0.23967462232967
+  H          -2.28212452724624      0.49817783645742     -1.81904425493374
+  H           0.16268086528061      0.23424811117128     -1.66550812031091
+  H           2.02913183524751     -0.12599094610884      1.64979348744112
+  H           1.81109302291314     -1.34774044945859     -1.20534339501041
+  H           3.28248345818731     -1.50017932433231     -0.10225722946821
+  H           2.04234073038285      1.00325231660204     -1.05321533919576
+  H          -0.13688412948152     -0.08887918008010      2.61894454473068
+  H          -2.59885456621162      0.16840726196522      2.46180833267868

gpuma-0.5.0/examples/example_input_xyzs/multi_xyz_dir/input (12).xyz

@@ -0,0 +1,20 @@
+18
+Coordinates from ORCA-job input E -364.549730217798
+  C          -2.60252439229563      0.34816901517186      0.31130410379019
+  C          -1.81619706753138      0.36723383006089     -0.84114176363625
+  C          -0.43478749993316      0.21906194158022     -0.74950221699111
+  C           0.18764857468375      0.04868482301169      0.49432764325631
+  C           1.66623135860957     -0.11688012674397      0.61764186318717
+  C           2.40988884007991     -0.91234874642310     -0.39886011249545
+  N           2.56875388667993      0.52302365233375     -0.32437463832906
+  C          -0.61034880946021      0.03520063670998      1.64275835222599
+  C          -1.99391513445871      0.18140408768218      1.55381410761823
+  H          -3.68461744559101      0.46515525510861      0.23967462232967
+  H          -2.28212452724624      0.49817783645742     -1.81904425493374
+  H           0.16268086528061      0.23424811117128     -1.66550812031091
+  H           2.02913183524751     -0.12599094610884      1.64979348744112
+  H           1.81109302291314     -1.34774044945859     -1.20534339501041
+  H           3.28248345818731     -1.50017932433231     -0.10225722946821
+  H           2.04234073038285      1.00325231660204     -1.05321533919576
+  H          -0.13688412948152     -0.08887918008010      2.61894454473068
+  H          -2.59885456621162      0.16840726196522      2.46180833267868

gpuma-0.5.0/examples/example_input_xyzs/multi_xyz_dir/input (13).xyz

@@ -0,0 +1,20 @@
+18
+Coordinates from ORCA-job input E -364.549730217798
+  C          -2.60252439229563      0.34816901517186      0.31130410379019
+  C          -1.81619706753138      0.36723383006089     -0.84114176363625
+  C          -0.43478749993316      0.21906194158022     -0.74950221699111
+  C           0.18764857468375      0.04868482301169      0.49432764325631
+  C           1.66623135860957     -0.11688012674397      0.61764186318717
+  C           2.40988884007991     -0.91234874642310     -0.39886011249545
+  N           2.56875388667993      0.52302365233375     -0.32437463832906
+  C          -0.61034880946021      0.03520063670998      1.64275835222599
+  C          -1.99391513445871      0.18140408768218      1.55381410761823
+  H          -3.68461744559101      0.46515525510861      0.23967462232967
+  H          -2.28212452724624      0.49817783645742     -1.81904425493374
+  H           0.16268086528061      0.23424811117128     -1.66550812031091
+  H           2.02913183524751     -0.12599094610884      1.64979348744112
+  H           1.81109302291314     -1.34774044945859     -1.20534339501041
+  H           3.28248345818731     -1.50017932433231     -0.10225722946821
+  H           2.04234073038285      1.00325231660204     -1.05321533919576
+  H          -0.13688412948152     -0.08887918008010      2.61894454473068
+  H          -2.59885456621162      0.16840726196522      2.46180833267868

gpuma-0.5.0/examples/example_input_xyzs/multi_xyz_dir/input (14).xyz

@@ -0,0 +1,20 @@
+18
+Coordinates from ORCA-job input E -364.549730217798
+  C          -2.60252439229563      0.34816901517186      0.31130410379019
+  C          -1.81619706753138      0.36723383006089     -0.84114176363625
+  C          -0.43478749993316      0.21906194158022     -0.74950221699111
+  C           0.18764857468375      0.04868482301169      0.49432764325631
+  C           1.66623135860957     -0.11688012674397      0.61764186318717
+  C           2.40988884007991     -0.91234874642310     -0.39886011249545
+  N           2.56875388667993      0.52302365233375     -0.32437463832906
+  C          -0.61034880946021      0.03520063670998      1.64275835222599
+  C          -1.99391513445871      0.18140408768218      1.55381410761823
+  H          -3.68461744559101      0.46515525510861      0.23967462232967
+  H          -2.28212452724624      0.49817783645742     -1.81904425493374
+  H           0.16268086528061      0.23424811117128     -1.66550812031091
+  H           2.02913183524751     -0.12599094610884      1.64979348744112
+  H           1.81109302291314     -1.34774044945859     -1.20534339501041
+  H           3.28248345818731     -1.50017932433231     -0.10225722946821
+  H           2.04234073038285      1.00325231660204     -1.05321533919576
+  H          -0.13688412948152     -0.08887918008010      2.61894454473068
+  H          -2.59885456621162      0.16840726196522      2.46180833267868

gpuma-0.5.0/examples/example_input_xyzs/multi_xyz_dir/input (15).xyz

@@ -0,0 +1,20 @@
+18
+Coordinates from ORCA-job input E -364.547402520645
+  C          -2.60115214273393      0.33276863076483      0.36743375216779
+  C          -1.96251600704807      0.91187680185847     -0.73064256981145
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+  N           2.32663079419270     -0.57872950994346     -0.92518842388708
+  C          -0.44977584535880     -0.27629392403882      1.28477159064398
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