# VLMP (Virtual Lab Modeling Platform)
<p align="center">
<img src="https://github.com/PabloIbannez/VLMP/blob/main/docs/_images/logo.png" width="500">
</p>
## Table of Contents
- [Introduction](#introduction)
- [Installation](#installation)
- [Getting Started](#getting-started)
- [Workflow](#workflow)
- [License](#license)
- [Contact](#contact)
## Introduction
VLMP is a Python library designed for running parallelized simulations, specifically optimized for molecular dynamics and other continuous models. Built on the backend technology of UAMMD-structured, it leverages multi-level parallelization to achieve highly efficient simulation runs.
### Features
- **Multi-level Parallelization**: Run multiple simulations concurrently on a single GPU or distribute across multiple GPUs.
- **Optimized for Coarse-grained Models**: Achieve better GPU utilization with small-scale simulations.
- **Highly Configurable**: Easily adaptable for a variety of scientific phenomena.
- **Community Sharing**: Distribute new models as VLMP modules.
## Documentation
[Online Documentation](https://vlmp.readthedocs.io/en/latest/)
## Installation
### Prerequisites
VLMP can be used without any additional program ( but required Python libraries) for generating simulations input files.
For execute these simulations UAMMD-structured must be available in the system. [UAMMD-structured Documentation](https://uammd-structured.readthedocs.io/en/latest/)
### Installing VLMP
Via pip:
```bash
pip install pyVLMP
```
Or clone the GitHub repository:
```bash
git clone https://github.com/PabloIbannez/VLMP.git
cd VLMP
pip install .
```
### Verifying Installation
```python
import VLMP
```
## Getting Started
Here's a minimal example to simulate a set of DNA chains:
```python
import VLMP
from VLMP.utils.units import picosecond2KcalMol_A_time
from numpy import random
# Convert picoseconds to AKMA time unit
ps2AKMA = picosecond2KcalMol_A_time()
# Number of sequences and sequence set size
Nsequence = 10
sequenceSetSize = 10
# Length of each sequence and the basis of DNA
sequenceLength = 100
basis = ['A', 'C', 'G', 'T']
# Generate random sequences
sequences = []
for i in range(Nsequence):
sequences.append(''.join(random.choice(basis, sequenceLength)))
# Populate simulation pool
simulationPool = []
for seq in sequences:
# Configure simulation parameters
simulationPool.append({
"system": [
{"type": "simulationName", "parameters": {"simulationName": seq}},
{"type": "backup", "parameters": {"backupIntervalStep": 100000}}
],
"units": [{"type": "KcalMol_A"}],
"types": [{"type": "basic"}],
"ensemble": [
{"type": "NVT", "parameters": {"box": [2000.0, 2000.0, 2000.0],
"temperature": 300.0}}
],
"integrators": [
{"type": "BBK", "parameters": {"timeStep": 0.02*ps2AKMA,
"frictionConstant": 0.2/ps2AKMA,
"integrationSteps": 1000000}}
],
"models": [
{"type": "MADna", "parameters": {"sequence": seq}}
],
"simulationSteps": [
{"type": "saveState", "parameters": {"intervalStep": 10000,
"outputFilePath": "traj",
"outputFormat": "dcd"}},
{"type": "thermodynamicMeasurement", "parameters": {"intervalStep": 10000,
"outputFilePath": "thermo.dat"}},
{"type": "info", "parameters": {"intervalStep": 10000}}
]
})
# Initialize VLMP and load simulation pool
vlmp = VLMP.VLMP()
vlmp.loadSimulationPool(simulationPool)
# Distribute simulations and set up
vlmp.distributeSimulationPool("size", sequenceSetSize)
vlmp.setUpSimulation("EXAMPLE")
```
Execute the simulations with:
```bash
cd EXAMPLE
python -m VLMP -s VLMPsession.json --local --gpu 0 1
```
## Workflow
1. **Simulation Configuration**: Define simulation parameters.
2. **Simulation Pool Creation**: Prepare multiple configurations for batch execution.
3. **Simulation Distribution**: Distribute simulations across computational resources.
4. **Simulation Execution**: Execute simulations on GPU using UAMMD-structured.
## License
[GPLv3](./LICENSE.txt)
## Contact
For issues and contributions, please contact: [GitHub Issues](https://github.com/PabloIbannez/VLMP/issues)
Raw data
{
"_id": null,
"home_page": "https://github.com/PabloIbannez/pyGrained",
"name": "pyVLMP",
"maintainer": null,
"docs_url": null,
"requires_python": ">=3.7",
"maintainer_email": null,
"keywords": null,
"author": null,
"author_email": "Pablo Ib\u00e1\u00f1ez-Freire <p.ibanez.fre@gmail.com>",
"download_url": "https://files.pythonhosted.org/packages/d0/45/1b98d053045cc5ea2c9b928c85d8940c153857ac9b7980339ee79ed71a44/pyvlmp-1.0.71.tar.gz",
"platform": null,
"description": "# VLMP (Virtual Lab Modeling Platform)\n\n<p align=\"center\">\n <img src=\"https://github.com/PabloIbannez/VLMP/blob/main/docs/_images/logo.png\" width=\"500\">\n</p>\n\n## Table of Contents\n\n- [Introduction](#introduction)\n- [Installation](#installation)\n- [Getting Started](#getting-started)\n- [Workflow](#workflow)\n- [License](#license)\n- [Contact](#contact)\n\n## Introduction\n\nVLMP is a Python library designed for running parallelized simulations, specifically optimized for molecular dynamics and other continuous models. Built on the backend technology of UAMMD-structured, it leverages multi-level parallelization to achieve highly efficient simulation runs.\n\n### Features\n\n- **Multi-level Parallelization**: Run multiple simulations concurrently on a single GPU or distribute across multiple GPUs.\n- **Optimized for Coarse-grained Models**: Achieve better GPU utilization with small-scale simulations.\n- **Highly Configurable**: Easily adaptable for a variety of scientific phenomena.\n- **Community Sharing**: Distribute new models as VLMP modules.\n\n## Documentation\n\n[Online Documentation](https://vlmp.readthedocs.io/en/latest/)\n\n## Installation\n\n### Prerequisites\n\nVLMP can be used without any additional program ( but required Python libraries) for generating simulations input files.\nFor execute these simulations UAMMD-structured must be available in the system. [UAMMD-structured Documentation](https://uammd-structured.readthedocs.io/en/latest/)\n\n### Installing VLMP\n\nVia pip:\n```bash\npip install pyVLMP\n```\n\nOr clone the GitHub repository:\n\n```bash\ngit clone https://github.com/PabloIbannez/VLMP.git\ncd VLMP\npip install .\n```\n\n### Verifying Installation\n\n```python\nimport VLMP\n```\n\n## Getting Started\n\nHere's a minimal example to simulate a set of DNA chains:\n\n```python\n\n import VLMP\n from VLMP.utils.units import picosecond2KcalMol_A_time\n from numpy import random\n\n # Convert picoseconds to AKMA time unit\n ps2AKMA = picosecond2KcalMol_A_time()\n\n # Number of sequences and sequence set size\n Nsequence = 10\n sequenceSetSize = 10\n\n # Length of each sequence and the basis of DNA\n sequenceLength = 100\n basis = ['A', 'C', 'G', 'T']\n\n # Generate random sequences\n sequences = []\n for i in range(Nsequence):\n sequences.append(''.join(random.choice(basis, sequenceLength)))\n\n # Populate simulation pool\n simulationPool = []\n for seq in sequences:\n # Configure simulation parameters\n simulationPool.append({\n \"system\": [\n {\"type\": \"simulationName\", \"parameters\": {\"simulationName\": seq}},\n {\"type\": \"backup\", \"parameters\": {\"backupIntervalStep\": 100000}}\n ],\n \"units\": [{\"type\": \"KcalMol_A\"}],\n \"types\": [{\"type\": \"basic\"}],\n \"ensemble\": [\n {\"type\": \"NVT\", \"parameters\": {\"box\": [2000.0, 2000.0, 2000.0],\n \"temperature\": 300.0}}\n ],\n \"integrators\": [\n {\"type\": \"BBK\", \"parameters\": {\"timeStep\": 0.02*ps2AKMA,\n \"frictionConstant\": 0.2/ps2AKMA,\n \"integrationSteps\": 1000000}}\n ],\n \"models\": [\n {\"type\": \"MADna\", \"parameters\": {\"sequence\": seq}}\n ],\n \"simulationSteps\": [\n {\"type\": \"saveState\", \"parameters\": {\"intervalStep\": 10000,\n \"outputFilePath\": \"traj\",\n \"outputFormat\": \"dcd\"}},\n {\"type\": \"thermodynamicMeasurement\", \"parameters\": {\"intervalStep\": 10000,\n \"outputFilePath\": \"thermo.dat\"}},\n {\"type\": \"info\", \"parameters\": {\"intervalStep\": 10000}}\n ]\n })\n\n # Initialize VLMP and load simulation pool\n vlmp = VLMP.VLMP()\n vlmp.loadSimulationPool(simulationPool)\n\n # Distribute simulations and set up\n vlmp.distributeSimulationPool(\"size\", sequenceSetSize)\n vlmp.setUpSimulation(\"EXAMPLE\")\n```\n\nExecute the simulations with:\n\n```bash\ncd EXAMPLE\npython -m VLMP -s VLMPsession.json --local --gpu 0 1\n```\n\n## Workflow\n\n1. **Simulation Configuration**: Define simulation parameters.\n2. **Simulation Pool Creation**: Prepare multiple configurations for batch execution.\n3. **Simulation Distribution**: Distribute simulations across computational resources.\n4. **Simulation Execution**: Execute simulations on GPU using UAMMD-structured.\n\n## License\n\n[GPLv3](./LICENSE.txt)\n\n## Contact\n\nFor issues and contributions, please contact: [GitHub Issues](https://github.com/PabloIbannez/VLMP/issues)\n\n",
"bugtrack_url": null,
"license": "GPLv3",
"summary": "Virtual Lab Modeling Platform",
"version": "1.0.71",
"project_urls": {
"Homepage": "https://github.com/PabloIbannez/pyGrained"
},
"split_keywords": [],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "7a092ad1821ebfda9aac423412a47c8400ff40de001eafc405d867679fc6f783",
"md5": "520963fc6de4ffb86e2fc2d9f10a9d04",
"sha256": "8a425ad54e190d1a75815fbf20d262ceb8099ad9f024496ec4260c12eff460c4"
},
"downloads": -1,
"filename": "pyVLMP-1.0.71-py3-none-any.whl",
"has_sig": false,
"md5_digest": "520963fc6de4ffb86e2fc2d9f10a9d04",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": ">=3.7",
"size": 202562,
"upload_time": "2024-08-31T20:28:51",
"upload_time_iso_8601": "2024-08-31T20:28:51.074880Z",
"url": "https://files.pythonhosted.org/packages/7a/09/2ad1821ebfda9aac423412a47c8400ff40de001eafc405d867679fc6f783/pyVLMP-1.0.71-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "d0451b98d053045cc5ea2c9b928c85d8940c153857ac9b7980339ee79ed71a44",
"md5": "3041c1d2d2e61d61ab9a2b8cccf98f36",
"sha256": "b115018a6518b6fd94905f7dafd352cb41688f1e44bcc1edf712ebdf79879ea2"
},
"downloads": -1,
"filename": "pyvlmp-1.0.71.tar.gz",
"has_sig": false,
"md5_digest": "3041c1d2d2e61d61ab9a2b8cccf98f36",
"packagetype": "sdist",
"python_version": "source",
"requires_python": ">=3.7",
"size": 133883,
"upload_time": "2024-08-31T20:28:54",
"upload_time_iso_8601": "2024-08-31T20:28:54.077866Z",
"url": "https://files.pythonhosted.org/packages/d0/45/1b98d053045cc5ea2c9b928c85d8940c153857ac9b7980339ee79ed71a44/pyvlmp-1.0.71.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2024-08-31 20:28:54",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "PabloIbannez",
"github_project": "pyGrained",
"travis_ci": false,
"coveralls": false,
"github_actions": false,
"lcname": "pyvlmp"
}
JSON
