Faunus

https://faunus.readthedocs.io/en/latest/
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Faunus is a flexible Monte Carlo simulation framework written in C++ with Python bindings, designed...
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### Setup Ashbaugh-Hatch Potential

Source: https://faunus.readthedocs.io/en/latest/_docs/energy.html

Example configuration for the Ashbaugh-Hatch potential within the energy section of a Faunus input file.

```yaml
atomlist:
    - hydrophobic: {sigma: 5.0, eps: 1.0, lambda: 1.0}
    - hydrophilic: {sigma: 5.0, eps: 1.0, lambda: 0.0}
energy:
    - nonbonded:
        default:
            - ashbaugh-hatch: {mixing: LB}
```

--------------------------------

### Electric Potential Configuration Example

Source: https://faunus.readthedocs.io/en/latest/_sources/_docs/analysis.md.txt

Example configuration for the electricpotential analysis module using a random_walk policy to measure potential at target points.

```yaml
- electricpotential:
    nstep: 20
    ncalc: 10
    epsr: 80
    type: plain
    policy: random_walk
    stride: 10   # in angstrom
    structure:
      - [0,0,0]  # defines two target points...
      - [0,0,0]  # ...positions are randomly set
```

--------------------------------

### Open Faunus user manual in browser

Source: https://faunus.readthedocs.io/en/latest/_sources/_docs/docs.md.txt

Launches the Faunus user guide in a web browser.

```bash
faunus-manual
```

--------------------------------

### Faunus analysis configuration example

Source: https://faunus.readthedocs.io/en/latest/_sources/_docs/analysis.md.txt

Example YAML configuration for the `analysis` section, showing how to add multiple analysis functions with their parameters. All analysis methods support `nstep` (sampling interval) and `nskip` (initial steps excluded).

```yaml
analysis:
    - systemenergy: {file: energy.dat.gz, nstep: 500, nskip: 2000}
    - xtcfile: {file: traj.xtc, nstep: 1000}
    - widom:  {molecule: water, ninsert: 20, nstep: 50}
    - molrdf: {name1: water, name2: water, nstep: 100,
               dr: 0.1, dim: 3, file: rdf.dat}
    - ...
```

--------------------------------

### YAML input format example

Source: https://faunus.readthedocs.io/en/latest/_sources/_docs/running.md.txt

Shows the equivalent YAML structure for defining an atom list.

```yaml
atomlist:
    - Na+: { q: 1.0, mw: 22.99 }
```

--------------------------------

### Install pre-commit hook for code formatting

Source: https://faunus.readthedocs.io/en/latest/_sources/_docs/install.md.txt

Installs a git pre-commit hook that automatically styles changes with clang-format, beneficial for contributors.

```bash
cd faunus
./scripts/git-pre-commit-format install
```

--------------------------------

### Build and run Faunus Docker image

Source: https://faunus.readthedocs.io/en/latest/_sources/_docs/install.md.txt

Downloads the Dockerfile from the repository, builds the image, and starts a JupyterLab session on port 8888.

```bash
curl -s https://raw.githubusercontent.com/mlund/faunus/master/scripts/Dockerfile | docker build -t faunuslab -
docker run -it -p 8888:8888 faunuslab # open generated url in a browser
```

--------------------------------

### Restart from state file

Source: https://faunus.readthedocs.io/en/latest/_docs/running.html

Starts a simulation from a previously saved state file using the --state option.

```bash
faunus --input in.json --state state.json

```

--------------------------------

### Cluster move configuration example

Source: https://faunus.readthedocs.io/en/latest/_docs/moves.html

Example configuration for the 'cluster' move, specifying molecules, satellites, a distance threshold matrix, and translational/rotational displacements. The 'analysis' option saves shape properties to 'cluster_shape.dat.gz'.

```yaml
cluster:
   molecules: [protein, cations]
   satellites: [cations]
   threshold:
      protein protein: 25
      protein cations: 15
      cations cations: 0
   dp: 3
   dprot: 1
   analysis: {file: cluster_shape.dat.gz}

```

--------------------------------

### JSON input format example

Source: https://faunus.readthedocs.io/en/latest/_sources/_docs/running.md.txt

Shows the native JSON structure for defining an atom list.

```json
{ "atomlist": [
        { "Na+": { "q": 1.0, "mw": 22.99 } }
    ]
}
```

--------------------------------

### Install Faunus with Conda

Source: https://faunus.readthedocs.io/en/latest/_sources/_docs/install.md.txt

Adds the conda-forge channel and installs the faunus package. This also installs examples in share/faunus and Python bindings.

```bash
conda config --add channels conda-forge
conda install faunus
```

--------------------------------

### Penalty Function YAML Setup

Source: https://faunus.readthedocs.io/en/latest/_docs/energy.html

Example configuration for the penalty energy term, penalizing the x and y positions of atom 0 to achieve uniform sampling. Options include f0 (penalty increment), scale (scaling factor), update (interval), file (saved/loaded penalty function), and coords (array of one or two coordinates).

```yaml
energy:
- penalty:
    f0: 0.5
    scale: 0.9
    update: 1000
    file: penalty.dat
    coords:
    - atom: {index: 0, property: "x", range: [-2.0,2.0], resolution: 0.1}
    - atom: {index: 0, property: "y", range: [-2.0,2.0], resolution: 0.1}

```

--------------------------------

### Build HTML manual with make manual_html

Source: https://faunus.readthedocs.io/en/latest/_sources/_docs/install.md.txt

Builds the HTML manual using Pandoc.

```bash
make manual_html
```

--------------------------------

### Install a local conda package

Source: https://faunus.readthedocs.io/en/latest/_sources/_docs/install.md.txt

Command to install the built package locally instead of uploading it to anaconda.org.

```bash
conda install -c USER faunus --use-local
```

--------------------------------

### moleculelist YAML example with salt, water, and carbon dioxide

Source: https://faunus.readthedocs.io/en/latest/_sources/_docs/topology.md.txt

Example of a moleculelist definition in YAML, showing salt, water, and carbon dioxide molecules with their properties. The carbon dioxide example includes a structure, harmonic bonds, a harmonic torsion, and an exclusionlist generated by excluded_neighbours.

```yaml
moleculelist:
  - salt: {atoms: [Na,Cl], atomic: true}
  - water:
      structure: water.xyz
      bondlist:
        - harmonic: {index: [0,1], k: 100, req: 1.5}
        - ...
  - carbon_dioxide:
      structure:
        - O: [-1.162,0,0]
        - C: [0,0,0]
        - O: [1.162,0,0]
      bondlist:
        - harmonic: {index: [1,0], k: 8443, req: 1.162}
        - harmonic: {index: [1,2], k: 8443, req: 1.162}
        - harmonic_torsion: {index: [0,1,2], k: 451.9, aeq: 180}
      excluded_neighbours: 2 # generates an exclusionlist as shown below
      exclusionlist: [ [0,1], [1,2], [0,2] ] # redundant in this topology
  - ...
```

--------------------------------

### faunus input from stdin and file I/O

Source: https://faunus.readthedocs.io/en/latest/_docs/running.html

Shows how to run faunus with input from stdin or from a JSON file, with options for file input/output and quiet mode.

```bash
faunus < input.json              # input from stdin
faunus -i in.json -o out.json -q # file input/output and be quiet

```

--------------------------------

### Force ZLIB location with CMake

Source: https://faunus.readthedocs.io/en/latest/_sources/_docs/install.md.txt

Specifies the ZLIB installation directory when multiple ZLIB installations cause CMake conflicts; must be run in a clean build directory.

```bash
cmake -DZLIB_ROOT=...
```

--------------------------------

### insertmolecules configuration example

Source: https://faunus.readthedocs.io/en/latest/_sources/_docs/topology.md.txt

Example of the insertmolecules section in a Faunus input file. It inserts salt to a molarity of 0.1 and 256 water molecules, with 2 water molecules set as inactive.

```yaml
insertmolecules:
  - salt:  { molarity: 0.1 }
  - water: { N: 256, inactive: 2 }

```
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