COSMIC-ASCEC User Manual GitHub
Automated configurational sampling and topological screening of molecular clusters • Química Física Teórica • Universidad de Antioquia, Colombia

Simulation Box

Box Suggestion — adjust as needed

Molecule → XYZ Converter

Enter any PubChem identifier (name, SMILES, CAS, InChI) to generate 3D coordinates.
Download .mol from Novoprolabs and drop it on the preview.
Periodic Table

Molecule Preview

⏣

Generate a molecule or drop a .mol file here

Sampling Mode

Annealing Theory Level

Quenching & Box Settings

Geometry Optimization

Geometry Refinement

Energy Refinement

COSMIC Screening

Pipeline Overview

Annealing GFN2-xTB
→
Geometry Optimization GFN2-xTB
→
COSMIC 1 th=auto
→
Geometry Refinement B97-3c
→
COSMIC 2 th=auto
→
Results Final PES

Advanced ASCEC Configuration

Complete control over annealing, optimization, cosmic, and rescue behavior. Use the User Manual for parameter-level details.

Pipeline Overview

Annealing GFN2-xTB
→
Geometry Optimization GFN2-xTB
→
COSMIC 1 th=auto
→
Geometry Refinement B3LYP
→
COSMIC 2 th=auto
→
Results Final PES

Annealing Theory Level

Quenching & Packing

Geometry Optimization

Geometry Optimization Input Preview

Geometry Refinement

Geometry Refinement Input Preview

Energy Refinement

Energy Refinement Input Preview

COSMIC Screening

COSMIC 1 (after optimization)

COSMIC 2 (after refinement)

Recovery Mode

COSMIC Weights

Tolerances

Molecule → XYZ Converter

For complex molecules, download .mol and drop on the viewer.
⏣

Generate a molecule or drop a .mol file here

Simulation Box

Complete .asc File Preview

Protocol Builder

Define the workflow stages. For docs, see the User Manual.

Protocol Preview

⚙️ Installation

One-click install for Linux and Windows. The installer pulls Miniconda (if missing), the py11 environment, and every dependency including standalone xTB, the new default annealing backend.

ASCEC requires Python 3.10+ (3.11 recommended). ORCA is optional — a preliminary run uses standalone xTB and needs no ORCA at all. Install ORCA only if you want DFT-level optimization or refinement stages.

Prerequisites: git — installed automatically if missing (from conda-forge on Linux; winget or conda-forge on Windows), with a source-archive fallback so a git-free install still works. A network connection is needed for the initial download. Administrator rights are not required on either platform.
If you do install ORCA: use ORCA 6.1.1 (Linux). ORCA 6.0 is not supported due to parser limitations. The User Manual includes ORCA installation instructions for Linux.

Option 1: Automatic "One-Click" Installation (Recommended)

What the installer does: 1) installs Miniconda if missing, 2) creates the Python 3.11 py11 environment, 3) installs all dependencies from conda-forge (numpy/scipy/matplotlib, cclib, openbabel, xtb, orca-pi), 4) clones ASCEC + COSMIC, 5) wires up ascec / cosmic launchers on PATH.

🐧 Linux (bash)

Clones into ~/software/ascec04. Aliases go into a fenced # >>> COSMIC ASCEC >>> block in ~/.bashrc (and ~/.zshrc if present) — only that block is rewritten on reinstall, so your own aliases are never touched. Re-running on a checkout with uncommitted edits skips the git pull instead of discarding them.

1. Download the installation script
wget https://raw.githubusercontent.com/manuel2gl/qft-cosmic-ascec/main/install.sh
2. Run the script
bash install.sh
3. Reload your terminal configuration
source ~/.bashrc

🪟 Windows

Clones into %USERPROFILE%\software\ascec04, drops ascec.cmd/cosmic.cmd into %USERPROFILE%\bin, and adds that directory to your user PATH. Git is installed automatically if missing; you can also install Git for Windows yourself beforehand.

1. Download the installer
2. Double-click win_install.bat in File Explorer

Because the file came from the internet, Windows marks it and SmartScreen may show "Windows protected your PC". Choose More info → Run anyway. The installer is plain, readable batch — open it in Notepad first if you want to check exactly what it does.

3. Open a new terminal so the new PATH takes effect
ascec your_input.asc
On Windows, running calculations is fully supported — annealing, preoptimization, clustering and refinement all work. ascec status, Ctrl+D detach and the after <PID> background queue are Linux-only, since they rely on process groups, signals and /proc.
Manual setup: open the User Manual and follow Step-by-Step Conda Installation, or use the environment.yml shipped in the repository (conda env create -f environment.yml).

Examples

Water Hexamer (B97-3c Refinement Theory Level)

Water hexamer most stable motifs
Most stable motifs (top 3)
Water hexamer ensemble
Hexamer ensemble
Open Water Hexamer Folder

Formic Acid (B97-3c Refinement Theory Level)

Formic acid global minimum
Global minimum
Formic acid ensemble
Formic ensemble
Open Formic Folder

ASCEC Workflow Visuals

ASCEC annealing representation
ASCEC annealing representation
COSMIC clustering dendrogram
COSMIC clustering example (H9)