Following filenames are used: sys_conf_state1_solvent1_method1_subset_state2_solvent2_method2_anythingelse_jt.ext, here

• sys – system name, for example
  • OPV5 – PPV oligomer of 5 core repeating units
  • TCNQ-F2 – TCNQ molecule with two hydrogens replaced by fluorines
  • PO4--- – anion of PO4 with charge -3
  • benzeneN2ON2S – benzene molecule with -N-O-N- and -N-S-N- arcs attached instead of hydrogens at the opposite sides
  • G7 – special notation which were used in a publication
• conf – configuration
  • molec – molecule
  • molec-a – lowest energy conformer in case if 'molec' entry is not the lowest (typical situation for high-symmetry conformer)
  • molec-b – second lowest energy conformer
  • molec-s – saddle point
  • molec-p – planar conformer
  • molec-t – twisted conformer
  • molecH – singly protonated
  • molecH2 – doubly protonated
  • molecG – singly deprotonated
  • cluster4 – cluster of 4 atoms (dangling bonds are allowed)
  • molec4 – passivated cluster of 4 atoms
  • cryst – crystal
  • cryst-m – monoclinic polymorph
  • cryst-rr – rhombohedral polymorph in primitive (rhombohedral) unit cell
  • cryst2 – crystal with doubled cell
  • dimer,trimerlayer,bilayer,chain,ring – self-explanatory
  • base – pi-conjugated backbone
  • conf5 – configuration 5
  • stack4p – stack of 4 molecules with PBC
• solvent1 – solvent in which the configuration is obtained or optimized
  • vac – vacuum (normally should be omitted)
  • hpt – heptane
  • tol – toluene
  • clf – chloroform
  • clb – chlorobenzene
  • thf – tetrahydrofuran
  • dcm – dichloromethane
  • dclb – o-dichlorobenzene
  • eth – ethanol
  • acn – acetonitrile
  • dmso – dimethylsulfoxide
  • wat – water
• state1 – electronic state (charge,spin,excitation) at which the configuration is obtained or optimized
  • O=S=S0 – neutral ground state
  • R=S1 – lowest excited singlet
  • S2,S3 – higher excited singlets
  • T=T1 – lowest energy triplet
  • D,Q,Q,X,X – doublet,quartet,quintet,sextet,septet (adjacent multiplicities are distinguished by number of electrons defined by sys)
  • N=N1 – anion (charge -1)
  • N2,N3 – higher energy states with charge -1
  • NN – charge -2
  • P=P1 – positive charge
  • PT – positively charged triplet
  • omit state1 section if the state is guessable (usually if it is 'O')
  • charges are relative, i.e. for PO4--- 'O' means charge -3 whereas neutral state will be encoded as 'PPP'
  • charge state must be at the beginning and excitation number must be at the end
  • excited states are numbered from 1 except for S# and D# notations which are numbered from 0 (so that N2=NS1)
• method1 – method by which the configuration is obtained, can be either "exp" (experiment) or an encoded method
• subset – subset of atoms, use "+" for "and" (e.g. "1+4" for molecule 1 and molecule 4), use "-" for "through", use the following symbols to encode translations:
  • a – [1,0,0], a3 or aaa – [3,0,0]
  • b – [0,1,0]
  • c – [0,0,1]
  • i – [-1,0,0]
  • j – [0,-1,0]
  • k – [0,0,-1]
• solvent2 – solvent for single point calculation, omit if solvent2=solvent1
• state2 – state for single point calculation (charge is relative to system charge not to state1), omit if state2=state1
• method2 – single point calculation method, omit if method2=method1
• anythingelse – see examples
  • new,symmetrized – reserved
  • old – initial geometry for optimization
  • planar – (depreciated, use conf) planarized backbone
  • fly – calculation duplicated by Firefly
  • alt,min1,min2 – (depreciated, use conf) alternative conformations
  • spd2 – saddle point for dihedral 2
• jt – job/calculation type
  • bin – wave-function (ev,evc,s1e files should be moved to "bin" folder)
  • em – geometry optimization (omit after moving to "em" folder)
  • esp – atomic charges (electrostatic, Hirshfield, CM5)
  • exc – excited state calculations
  • exc1 – excited state calculations with density of 1st excited state
  • excS,excT – excited state calculations singlets or triplets
  • excLR,excSS – LR or SS solvation of 1st excited state (for absorption excLR=exc, for emission excLR=exc1)
  • freq – frequencies (frcc file should be moved to "bin" folder)
  • guess – initial guess for wave-function
  • md400K1A10ns – 10 ns molecular dynamics at T=400K, P=1Atm
  • mgf,mo,no – MO/NO visualization (omit after moving to "mgf" folder)
  • nbo,lmo – NBO and LMO analysis
  • nto# – NTO visualization (move to "mgf" folder)
  • polar – polarization
  • sp – trivial single point calculation (usually "sp" should be omitted)

Instead of separator "_" you can use "/", that is use folders.

In MolMod package

• solvents are tabulated in tb_solvents
• states are decoded by DecodeState command
• methods are decoded by DecodeMethod command
• translations are decoded by DecodeTranslation command
• job types for Gaussian are detailed in 'exam_gau' script