General rules:

• Any file must be accessible by the following path "/container/systemfolder/folder/.../file", e.g. "/Molecules/benzene/bm/molec_P/wat_B3LYPp2p_freq.out".
• All calculations for a single system should be kept in one system folder.
• Containers allows to separate data by materials class, project, user, access etc.
• The standard structure of folders and key auxiliary files are given by "_template" system folder.
• Only dat and fig folders are backed-up, all other folders should be recomputable.

The following folders can be scanned for information (their names are reserved):

• arc/ – input files and other archived files
• bin/ – binary files
• bm/ – benchmarking folder
• chk/ – critical checkpoint files (noncritical ones shuld be kept elsewhere)
• dat/ – all textual data generated manually or as high-level postprocessing of standard calculations
• em/ – geometry relaxation files
• fig/ – figures
• md/ – molecular dynamics trajectories and snapshots
• mgf/ – mgf files
• scans/ – PES, conformational, and other scans
• tmp/ – self-explanatory

The following files can be scanned for information:

• dat/main.dat – contains machine-readable key parameters of the system in the format key=value:
  • name,name2 – name and alternative names of the system
  • pubchem – PubChem identifier
  • SMILES – useful if pubchem ID is undefined
  • Q – default charge (if appropriate it should correspond to the singlet spin state)
  • SG – symmetry group (maximum reasonable symmetry)
  • CO – definition of canonic orientation of molecule or crystal
  • base – π-conjugated backbone as list of atom numbers
  • frags,frags2 – fragmentations
  • perm_other – map atom ordering perm_other[other]=this_folder_files (ordering of atom coordinates must identical within this data folder)
  • d0,d1,d2 – definitions of named flexible dihedrals (as [i,j,k,l])
  • ds – definition of all flexible dihedrals (as list of lists)
  • sds – the same for side chains to separate them out of ds
  • tds1,tds2 – definitions of named terminal dihedrals (as [i_terminal,i_dihedral,i_tobereplaced])
  • tds – definition of all terminal dihedrals
  • boxsize – size of simulation box
• dat/molec.xyz – contains most relevant geometry, optionally topology, and also SG and CO records to overwrite 'main.dat' settings
• dat/cryst.xyz – the same for crystal