update readme

Author: mlund

README.md

@@ -1,4 +1,22 @@
-# Angular Scan
+<p align="center">
+  <img src="assets/duello-logo.png" alt="crates.io", height="200">
+</p>
+<p align="center">
+    <a href="https://opensource.org/licenses/Apache-2.0">
+        <img src="https://img.shields.io/badge/License-Apache%202.0-blue.svg">
+    </a>
+</p>
+
+-----
+
+<p align = "center">
+<b>Duello</b></br>
+<i>Virial Coefficient and Dissociation Constant Estimation for Rigid Macromolecules</i>
+</p>
+
+-----
+
+# Introduction
 
 This iterates over all intermolecular poses between two rigid molecules.
 For each pose, defined by two quaternions and a mass center separation, the
@@ -11,36 +29,52 @@ the thermally averaged energy, $u(r) = \sum u(r)e^{-\beta u(r)} / Q$.
 
 ![Angular Scan](assets/illustration.png)
 
-## Usage
+# Installation
+
+```console
+pip install duello
+```
+
+# Usage
 
 The command-line tool `duello` does the 6D scanning and calculates
-the potential of mean force, w(r) which
+the potential of mean force, _w(r)_ which
 is used to derive the 2nd virial coefficient and twobody dissociation constant.
-Two input structures are requires (`.xyz` format) and all particle types must
+The two input structures should be in `.xyz` format and all particle names must
 be defined in the topology file.
-The topology files also defines the particular pair-potential to use.
+The topology also defines the particular pair-potential to use.
 Note that currently, a coulomb potential is automatically added and should
-hence not be specified in the topology.
+hence _not_ be specified in the topology.
 
 ```console
-duello scan --icotable -1 cppm-p18.xyz -2 cppm-p00.xyz --rmin 40.5 --rmax 60 --dr 1.0 --top topology.yaml --resolution 0.6 --molarity 0.05
+duello scan \
+    --icotable \
+    --mol1 cppm-p18.xyz \
+    --mol2 cppm-p18.xyz \
+    --rmin 37 --rmax 50 --dr 0.5 \
+    --top topology.yaml \
+    --resolution 0.8 \
+    --cutoff 1000 \
+    --molarity 0.05 \
+    --temperature 298.15
 ```
 
-### Examples
+The program is written in Rust and attempts to use all available CPU cores.
+
+## Examples
 
-See the `examples/` directory for examples; run scripts are provided in the
-`scripts/` directory:
+Ready run scripts examples are provided in the `scripts/` directory:
 
 Command               | Description
 --------------------- | ------------------------------------------------------------
 `scripts/cppm.sh`     | Spherical, multipolar particles using the CPPM model
 `scripts/lysozyme.sh` | Two coarse grained lysozyme molecules w. Calvados3 interactions
 
-## Development
+# Development
 
 This is for development purposes only.
 
-### Create `pip` package using Maturin
+## Create `pip` package using Maturin
 
 ```console
 pip install ziglang pipx