Computational materials science protocols
Molecular crystal CIF refinement
Molecular crystal geometry optimization
- Start with refined CIF converted to XYZ. Each disorder group require separate optimization.
- Use PBE-D3/PAW as optimal trade-off between accuracy and complexity.
- Use fast SCF iterators like ALGO=F or VF.
- If initial geometry is problematic preoptimize at fixed cell.
- Optimize cell+coordinates with k-spacing=0.2 iAo, ECUT=900 eV, and PREC=Accurate.
- MBD and highly dispersive bands might require k-spacing=0.15 iAo.
- Accuracy can be increased gradually in the following order: 1) increase ECUT from 400;
2) increase PREC from normal to accurate; 3) increase k-grid from minimal reasonable
(such as GAMMA-point only, adding more points for highly dispersive directions).
- If feasible, get final geometry by 5-point volume scan at ECUT=600
(keep number of iterations below 40-60, restart if needed).
Otherwise reoptimize atomic positions at ECUT=400 (minimum for organics).
- Decrease k-spacing to 0.06-0.1 to calculate final total energy and eDOS.
- Check consistency of all calculations by volume scan plot and EoS fit (especially K0').
- Symmetrize or at least check symmetry at each run. Check that CIF is not corrupted. Check supersymmetry and symmetry breaking.
- If feasible calculate GAMMA-point phonons and elastic tensor to check the stability.
Determination of molecular crystal geometry from MD snapshot of a large supercell
- It is assumed that all molecules are connected.
- Group molecules into translationally invariant sets.
- Determine cell translations using a reference atom and then fold cells.
- Superimpose molecules to inspect conformational disorder. It is assumed that the conjugated backbone is not conformationally disordered.
- Determine disorder groups for side chains:
1) Determine disordered part of side chains and type of disorder using both cartesian and internal coordinates.
2) Analyze disorder by histograms in proper coordinates.
3) Use cluster analysis (density-based such as DBSCAN and Gaussian distribution-based) to determine disorder groups.
4) Discard nonessential groups.
- Fix a disorder group and calculate average molecule.
Identify atoms whose average position is meaningless and determine their mean positions in internal coordinates.
In particular aliphatic side chains often can be defined only by fixing C-C-C-C dihedrals to their most probable value
consistent with average position of the chain in cartesian coordinates.
- Check intramolecular symmetry and symmetrize.
- Determine unit cell origin, check crystal symmetry, and symmetrize.
- Optimize geometry with any light but accurate method to redetermine the space group.
Electronic coarse-graining of insulators
- PBC are supported only at Gamma point (supercell approach).
- Fragmentize system, identify repeating fragments (monomers), and save to file following quantities:
1) fragments as
2) bonds between fragments as
3) terminal bonds as
T=list([atom#,atom#]) with the 1st atom belonging to a fragment;
4) fragments to monomers map as
5) monomers to fragments map as
6) reference fragment for each monomer as
7) optionally monomer names as
8) optionally symmetry information (translation period, asymmetric unit).
- Calculate MOs and save out,evl,evc,S (or evr)
- Select subspace of MOs for coarse-graining as accurate as possible,
though small number of irrelevant MOs can be discarded later during orbital localization.
- Prelocalize by geometry or other methods such as NBO or spatial localization,
so that you will get a list of pre-LMOs.
- Localize by projection onto pre-LMOs, filter out redundant MOs and pre-LMOs,
iterate until convergence (usually the second iteration is either final or meaningless).
Correct LMO signs by a sign function, or by reference orbitals, or manually, or applying a combination of these methods.
Save the obtained LMOs as evc,evr,h1e (optionally s1e) binary files and plain-text records containing:
1) copy of fragmentation information (see above);
2) basis set fragmentation as
3) LMOs to fragments map as
4) fragments to LMOs map as
5) list of coarse-grained MOs
6) localization method as
Calculation of coarse-grained electronic Hamiltonian for molecular crystal in multimer approximation
- Make sure that the crystal structure file contains information about symmetry and partitioning of the crystal into molecules:
- At the accuracy level of dimer approximation, it is usually enough to consider hydrogen-passivated pi-conjugated backbones instead of entire molecules.
- Load crystal structure and fragmentize molecules if needed,
then rationalize site positions and initialize FGS subpackage of FiniteGroups package.
- Step 1: Determine nearest neighbors (for molecules, not fragments) and save all symmetry unique dimers in xyz-file.
Normally only pi-conjugated atoms should be considered.
The cutoff distance of about 5~Ao can be used to screen out negligible wave-function overlaps (not for Forster energy transfer).
Find a proper supercell size iteratively.
- Step 2: Perform required single point calculations (MOs or excited states)
for all translationally unique molecules, symmetry unique dimers,
and optionally multimers (list of multimers should be provided by user).
For each calculation save out,evc,evr,evl files for frontier orbitals (let say, 8 MOs per band per monomer + 2 extra orbitals).
- Step 3: Fragmentize basis if needed (for each molecule) and save it as evc,evr,h1e files.
You will need reference calculations to correct wave-function sign for each LMO.
- Step 4: Calculate transfer integrals and save Hamiltonian.
For charges, a CG-basis is initialized either pre-calculated or as molecular HOMO/LUMO.
In the latter case the wave-function sign is corrected at this point.
The CG Hamiltonian is calculated by projection on CG-basis for all available multimers.
Then either mean (default) or most appropriate (user-defined) value is selected for evaluation of transfer integrals.
Small transfer integrals are discarded for noncontact pairs.
Finally, unfold dimers and save the Hamiltonian in dat-file.
- Step 5: Print transfer integrals, calculate hopping amplitudes and band structure.
The report is saved to txt-file.