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asd-afm

Automated Structure Discovery in Atomic Force Microscopy

asd-stm

Automated Structure Discovery for Scanning Tunneling Microscopy

ash

Atomic Structure Handler - a flexible java tool for building, manipulating and visualising atomic systems.

atom_manipulation_with_rl

Autonomous atom manipulation - in this project, we use deep reinforcement learning algorithms including soft actor-critic, hindsight experience replay, and emphasize recent experience replay to automatize atom manipulation in the Createc scanning tunneling microscope system.

auto-co-afm

Automatic evaluator of the CO-functionalized tips in Atomic Force Microscopy

bader_charges

Simple script that takes charges from a Bader analysis and converts them to effective charges based on the valence electrons in the pseudopotential.

cluskit

cp2k_dft_analysis

Scripts for analyzing output from a CP2K DFT calculation.

cp2k_mtools

This Python package is intended to help running multiple CP2k calculations for the same system or multiple similar systems.

critcatworks

Workflow manager for DFT simulations on nanocluster databases using Fireworks

crystalmap

densitytools

Tools to ease density generation and predictions from MD runs

dft_grid

Contains tools for post processing and visualizing grid based data from DFT calculations (charge density, electric potential) using Python.

dft_gridio

Contains Python modules for efficient reading and writing of file formats containing values on a grid of points used by DFT codes.

dscribe

DScribe is a python package for creating machine learning descriptors for atomistic systems.

ed-afm

Electrostatic Discovery Atomic Force Microscopy

graph-afm

Machine learning molecule graphs from atomic force microscopy images.

kpfm_fem

This Python package is intended to help running finite element method (FEM) calculations related to modeling the macroscopic part of the KPFM probe and storing the results.

kpfm_sim

A set of Python modules for running DFT level KPFM simulations using CP2k and storing the results to a relational database (SQLite).

lammpser

Bottom-up topology maker for LAMMPS

mactravis

This repository is for testing macOS related issues with TravisCI.

matid

MatID is a python package for identifying and analyzing atomistic systems based on their structure. MatID is designed to help researchers in the automated analysis and labeling of atomistic datasets.

mechafm

Mechanical AFM (implementation based on Hapala et al., Phys. Rev. B, 90:085421, 2014)

ml-spm

Machine learning for scanning probe microscopy

molecularui

GUI for designing molecular circuits.

mutualinformation

Mutual Information codes

potential_solver

A Python module for solving electrostatic potential of a distribution of point charges using periodic boundary conditions.

probeparticle_workflow

A workflow for double ProbeParticle method using OpenCL and complex_tip branch of ProbeParticle method

pycp2k

Python Cp2k interface

pysic

Modular package for atomistic simulations based on Python.