AI coding assistants: Claude Code & Codex

AI coding assistants: Claude Code & Codex#

An AI coding assistant is a program that lives in your terminal (or editor), reads the files in your project, and helps you by conversation: you describe what you want in plain language, and it explains code, writes and edits files, and can even run commands — all under your review. For a newcomer to qc-rs this is a gentle on-ramp: you can ask “what does this script do?”, “write a script that optimizes this molecule and prints its Mulliken charges”, or “why did this calculation fail?” and get a concrete, project-aware answer.

This chapter introduces two popular assistants — Claude Code (Anthropic) and Codex CLI (OpenAI). They are optional tools; qc-rs does not require them. (This very manual was drafted with Claude Code — you will see Co-Authored-By: Claude in the git history.)

Note

Accounts and cost Both tools need an account and are paid services (a subscription or metered API usage). Check the current pricing and the official setup docs — links are below — before you rely on them.

What they can do for a qc-rs beginner#

  • Explain code and errors — paste a traceback or point at a file and ask what it means.

  • Write small scripts — “build a water molecule, run B3LYP, and print the dipole moment.”

  • Navigate the codebase — “where is the SCF convergence tolerance set?” across a large repository.

  • Draft tests and docs — a first version you then review and refine.

They are assistants, not oracles: always read what they produce, and keep your work under git so you can undo anything.

How they work#

Both tools run an agentic loop in your terminal: they read your request, look at the relevant files, propose an action (answer, an edit, or a shell command), and — with your permission — carry it out, then repeat. Two things are worth knowing:

  • They read the project’s own instructions. This repository ships an AGENTS.md (and a CLAUDE.md) with coding conventions and a docs/user/CLAUDE.md for the manual; the assistants load these automatically, so their suggestions already follow the project’s rules.

  • They ask before acting. By default an assistant asks for confirmation before it edits a file or runs a command; you approve, edit, or decline. You can loosen or tighten this (permission modes) — but as a beginner, keep confirmations on and read each proposed action.

A typical session#

Working in the repo, a short exchange might look like:

$ claude
> Write a script that computes the HOMO–LUMO gap of benzene with B3LYP/def2-SVP and prints it in eV.

  (the assistant proposes a new file gap.py, and asks to create it)   [y] approve

> Run it.

  (it runs `python gap.py`, shows the output, and explains the number)

> The value looks too large — is that expected for Hartree–Fock vs B3LYP?

  (it explains why HF over-estimates gaps, and offers to switch functionals)

You stay in control the whole time: you approve the file, approve the run, and judge the science.

Claude Code#

Install — the native installer is simplest; it needs no Node.js and auto-updates itself:

curl -fsSL https://claude.ai/install.sh | bash      # macOS / Linux / WSL

(You can also install it from npm — npm install -g @anthropic-ai/claude-code, which needs Node.js 18+ — but the native installer avoids that. Don’t run npm install with sudo; use a per-user Node manager like nvm if you hit permission errors.) The official Claude Code setup docs cover Windows and other options.

Run it from inside your qc-rs checkout:

cd ~/path/to/qc_rs
claude

The first run walks you through authentication (a Claude subscription or an Anthropic API key). After that, just type what you want. A few qc-rs-flavoured prompts:

> Explain what the quickstart in docs/user does, step by step.
> Write a script that optimizes benzene with B3LYP/def2-SVP and reports the C–C bond length.
> This SCF didn't converge — what convergence options can I try?

Claude Code can run shell commands and edit files; it asks for confirmation on actions, and you review each change.

Codex CLI#

OpenAI’s Codex CLI is similar. Install — the native installer (macOS/Linux) again needs no Node.js:

curl -fsSL https://chatgpt.com/codex/install.sh | sh

(Or from npm: npm install -g @openai/codex, Node.js 18+.)

Run and authenticate from your checkout:

cd ~/path/to/qc_rs
codex           # sign in with a ChatGPT account, or set an OpenAI API key

See the official Codex CLI docs for current setup details.

Using them well#

  • Work in a git branch. So you can inspect the diff and discard anything you do not want (see the contributor workflow in the project docs).

  • Review before you run. These tools can execute shell commands and modify files — read the proposed action first, especially anything that deletes, installs, or pushes.

  • Be specific. “Compute the HOMO–LUMO gap of pyridine with ωB97X-D/def2-TZVP and print it in eV” beats “do some chemistry.” Point at files and functions by name.

  • Verify the science. An assistant can write a qc-rs script for you, but you are responsible for the chemistry — check that the method, basis, and result make sense (the rest of this manual is how you learn to).

Let the assistant set up qc-rs#

Because these tools can run commands, an excellent first use is the build itself. Building qc-rs on a new machine means running make setup and make install and getting the environment-specific details right — exactly the fiddly chore an assistant handles well. Once the prerequisites are installed — git, uv + a Python, Rust, a BLAS/LAPACK, and MPI if you need it (the next chapter covers these) — clone the repo, open it in the assistant, and ask:

Build qc-rs with make setup and make install, and save the build configuration to a profile for this machine.

It will detect your machine, run make setup (generating the profile plus the .vscode and build config), run make install (the maturin build), and check import qc. This is often the easiest way to get qc-rs built — but note the assumption in bold: the prerequisites (uv, Python, Rust, BLAS, MPI) must already be installed — the assistant builds qc-rs, not the system toolchain.

Next, get qc-rs installed — by hand or with the assistant — in Installation & the build.

Sources for the install commands: Claude Code setup · Codex CLI. Tooling changes fast — prefer the official docs for the current method.