# Accompanying dataset for article:

David Packwood, James Kermode, Letif Mones, Noam Bernstein, John Woolley Nicholas Gould, Christoph Ortner, and Gabor Csanyi, A universal preconditioner for simulating condensed phase materials, J. Chem. Phys. (2016)

## Required software

- ASE (currently `jameskermode` fork needed, will shortly be merged into ASE trunk):

        git clone https://gitlab.com/jameskermode/ase
        cd ase
        git checkout precon
        python setup.py install

- Jupyter notebook:

        pip install jupyter

- QUIP/quippy (optional, for some of the interatomic potentials):

        git clone https://github.com/libAtoms/QUIP
        cd QUIP
        make config
        make
        make quippy
        make install-quippy

- MatSciPy (optional, for fast neighbour lists):

        git clone https://github.com/libAtoms/matscipy
        cd matscipy
        python setup.py install

- PyAMG (optional, for fast preconditioner inversion/application): 

        pip install pyamg

- Some of the tests also require VASP, CASTEP or CP2K DFT codes
- Some of the notebooks require Julia (v0.4.x)

## General files
    README-dataset.txt - this file
    notebooks/plots.ipynb - Jupyter notebook (Python)

## Data files for Fig. 1
    notebooks/spectra3.ipynb - Jupyter notebook (Julia)

## Data files for Fig. 2
    Si_slab/quip_params.xml - SW force field parameters
    Si_slab/test_precon.xyz - input structure
    Si_slab/results.new.C1_Exp_3.0_Pfrommer_ID.json - results (all cases)
    Si_slab/run.py - Python script

## Data files for Fig. 3
    Si_crack/params.xml - SW force field parameters
    Si_crack/crack.xyz - input structure
    Si_crack/crack.json - results (ID, A=0, A=3 preconditioners)
    Si_crack/crack_Pfrommer.json - results (Pfrommer preconditioner)
    Si_crack/test-crack.ipynb - Jupyter notebook

## Data files for Fig. 4
    notebooks/precon-scaling.ipynb - Jupyter notebook (Python)

## Data files for Fig. 5

PAW setups used are from the vasp 4.6 distribution: regular La and Al, and O_s (soft).

    LaAlO3_crack/LaAlO3_crack.c0.xyz - input structure
    LaAlO3_crack/KPOINTS - VASP kpoint mesh
    LaAlO3_crack/run.py - Python script
    LaAlO3_crack/results.ID.json - results
    LaAlO3_crack/results.C1.json - results
    LaAlO3_crack/results.Exp_3.0.json - results
    LaAlO3_crack/results.Pfrommer.json - results

## Data files for Fig. 6

PAW setups used are from the vasp 4.6 distribution: regular Al, but the conventional O.

    gamma_Al2O3/gamma_Al2O3_Johannes_1.01.c0.xyz 0 input structure
    gamma_Al2O3/INCAR.template - VASP input file
    gamma_Al2O3/run.py - Python script
    gamma_Al2O3/results.C1.json - results
    gamma_Al2O3/results.Exp_3.0.json - results
    gamma_Al2O3/results.ID.json - results
    gamma_Al2O3/results.Pfrommer.json - results

## Data files for Fig. 7

    ice/run/run.py - Python script
    ice/run/common/BASIS_SET - CP2K input
    ice/run/common/cp2k_input_force.template - CP2K input
    ice/run/common/iceVIII.xyz - CP2K input
    ice/run/common/POTENTIAL - CP2K input
    ice/results/dump.json.VIIIbig.geom.new_preconpy_cp2k_force_preconLBFGS_ID_fmax_0.001_armijo - results
    ice/results/dump.json.VIIIbig.geom.new_preconpy_cp2k_force_preconLBFGS_Exp_A_0.0_rcut_2.25_fmax_0.001_armijo - results
    ice/results/dump.json.VIIIbig.geom.new_preconpy_cp2k_force_preconLBFGS_Exp_A_3.0_fmax_0.001_armijo - results
    ice/results/dump.json.VIIIbig.geom.cell.new_preconpy_cp2k_force_stress_preconLBFGS_ID_fmax_0.001_armijo - results
    ice/results/dump.json.VIIIbig.geom.cell.new_preconpy_cp2k_force_stress_preconLBFGS_Exp_A_0.0_rcut_2.25_fmax_0.001_armijo - results
    ice/results/dump.json.VIIIbig.geom.cell.new_preconpy_cp2k_force_stress_preconLBFGS_Exp_A_3.0_fmax_0.001_armijo - results

## Data files for Fig. 8
    notebooks/dimer-fig.ipynb - Jupyter notebook (Julia)