Configuration

MDFactory uses INI files for global settings and YAML files for simulation-specific parameters.

Managing configuration with the CLI

The mdfactory config command group provides tools to manage your configuration:

mdfactory config init   # interactive setup wizard
mdfactory config show   # display active configuration
mdfactory config path   # print config file path
mdfactory config edit   # open config in $EDITOR

Running mdfactory config init walks you through selecting a database backend and setting paths interactively.

Global configuration

The main config file lives at ~/.config/mdfactory/config.ini (or the platform-appropriate location determined by platformdirs).

You can always print the active path with:

mdfactory config path

Database settings

[database]
TYPE = sqlite

[databases]
USE_RUN_DB = true
USE_ANALYSIS_DB = true

[sqlite]
RUN_DB_PATH = <platform data dir>/runs.db
ANALYSIS_DB_PATH = <platform data dir>/analysis.db

[database]
TYPE = csv

[databases]
USE_RUN_DB = true
USE_ANALYSIS_DB = true

[csv]
RUN_DB_PATH = <platform data dir>/runs.csv
ANALYSIS_DB_PATH = <platform data dir>/analysis

[database]
TYPE = foundry

[databases]
USE_RUN_DB = true
USE_ANALYSIS_DB = true

[foundry]
BASE_PATH = /Group Functions/mdfactory
ANALYSIS_NAME = analysis
RUN_DB_PATH = /Group Functions/mdfactory/runs
ANALYSIS_DB_PATH = /Group Functions/mdfactory/analysis
ARTIFACT_DB_PATH = /Group Functions/mdfactory/artifacts

Config wizard details (mdfactory config init)

The interactive wizard performs this flow in the current code:

1. Optional CGenFF prompt: Do you use CGenFF (SILCSBIO)? if yes, asks for SILCSBIODIR.
2. Parameter store prompt: Parameter store directory:
3. Backend selection: Database backend: with choices sqlite, csv, foundry.
4. Backend-specific prompts (below).
5. Writes config to the user config path (mdfactory config path).
6. Optional initialization: Initialize databases now?

SQLite prompt details

When sqlite is selected, the wizard asks:

• RUN_DATABASE path:
• ANALYSIS_DATABASE path:

Both are normalized to absolute local paths.

CSV prompt details

When csv is selected, the wizard asks:

• RUN_DATABASE CSV path:
• ANALYSIS_DATABASE directory (for per-table CSV files):

For CSV mode, analyses/artifacts are stored as per-table CSV files in the analysis directory.

Foundry prompt details

When foundry is selected, the wizard:

1. Runs fdt config and exits on failure.
2. Verifies Foundry connectivity with FoundryContext().multipass.get_user_info().
3. Asks:
   • Foundry base directory (must already exist in Foundry):
   • Analysis directory name:
4. Derives:
   • ANALYSIS_DB_PATH = <base>/<analysis_name>
   • RUN_DB_PATH = <base>/runs
   • ARTIFACT_DB_PATH = <base>/artifacts
5. Prompts Use these paths? and optionally allows manual overrides.

Validation rules:

• Base path must be absolute (start with /).
• Analysis directory name must not contain / and must not start with ..

Initialization defaults

Initialize databases now? defaults to:

• true for sqlite and csv
• false for foundry

If enabled, it initializes:

• systems backend storage
• analysis backend storage
• artifact backend storage

Simulation input schemas

Simulation YAML/CSV structure is documented here:

• YAML Format
• System Types
• CSV Format
• Parametrization

Run schedules

MDFactory uses run_schedules.yaml to define simulation protocols. This file specifies:

• Minimization steps
• Equilibration stages (NVT, NPT)
• Production run length
• Output frequencies

Find templates in config_templates/run_schedules.yaml.

Environment variables

Override config paths with environment variables:

export MDFACTORY_CONFIG=/path/to/config.ini      # use a specific config file
export MDFACTORY_CONFIG_DIR=/path/to/config/dir   # override config directory
export MDFACTORY_DATA_DIR=/path/to/data           # override data directory

Configuration precedence

Settings are loaded in this order (later values override earlier):

1. Default values (computed at runtime, including platform-appropriate data paths)
2. User config file (~/.config/mdfactory/config.ini)
3. Config file specified via MDFACTORY_CONFIG environment variable