Frame 3DD: structural frame analysis

Opensees: analysis of structures under seismic excitation

LAMMPS (Molecular Dynamics simulations)

Quantum ESPRESSO, SIESTA (ab initio calculations)

OVITO, VMD

SciLab (Similar to Matlab)

Octave (Similar to Matlab)

SMath Studio (Similar to MathCad)

WxMaxima (symbolic calulation like Mathematica)

GNU plot (for plotting)

QtiPlot (similar to Origin pro)

Paraview (GUI for own FE code)

Libre Office Suite (Like words)

Mendely (Reference manager)