Description of file formats =========================== atomlist -------- atomic symbol for each atom, splitted by line breaks. atommass -------- atomic mass for each atom (in atomic mass units), splitted by line breaks. atomnums -------- atomic charge number Z for each atom (integer), splitted by line breaks. atompos -------- position coordinate of each atom in the order: x, y, z in atomic units, splitted by line breaks (one float per line). atomvel -------- velocity of each atom in the order: x, y, z in atomic units, splitted by line breaks (one float per line). R.log ----- * First column: time in atomic units * Further columns (3 * number of atoms): coordinates for each atom (x, y, z) in atomic units V.log ----- * First column: time in atomic units * Further columns (3 * number of atoms): velocities for each atom (x, y, z) in atomic units E.log ----- * First column: Time in atomic units * Second column: Kinetic energy in atomic units * Third column: Potential energy in atomic units * Fourth column: Total energy in atomic units V_ad.log -------- * First column: Time in atomic units * Further columns: For each considered adiabatic state the potential energy V_cross.log ----------- * First column: Time in atomic units * Further columns: For each considered adiabatic state the potential energy, but reshuffled according to the trivial-crossing-detection scheme S.log -------- * First column: Time in atomic units * Second column: State index of current active state P.log -------- * First column: Time in atomic units * Further column: For each considered adiabatic state the state probability P C.log -------- * First column: Time in atomic units * Further columns: For each considered adiabatic state the state coefficient real part and imaginary part, respectively Switch.log ---------- * First column: '-' (no hop) or '+' (hop) or '*' (attempted hop) * Second column: Time in fs * Third column: Random number * Fourth column: Old state index * 5th column: New state index * 6th column: 'True' or 'False' whether hopping occurred without electric field * 7th column: 'True' or 'False' whether hopping occurred due to electric field NAC.log -------- * First column: State index * Second column: State index * Third column: Time in atomic units * Fourth column: Coupling matrix element between states (real part) * Fith column: Coupling matrix element between states (imaginary part) trivialCrossings.log -------------------- Logs detected trivial crossings. * First column: Time in atomic units * Second column: state index * Third column: state index field.log --------- * First column: Time in atomic units * Second column: Electric field in atomic units * Third column: Pulse envelope in atomic units seed.log -------- contains an integer number that was used to initiated the random number generator occupation.log -------------- * First column: Time in atomic units * Second column: current electronic configuration charge.log -------------- * First column: Time in atomic units * Second column: current total charge partial.log -------------- * First column: Time in atomic units * Further column: For each atom, current partial charge (Mulliken charge) pulse.log --------- * First column: Time in atomic units * Second column: Pulse envelope (normalized) event.log --------- * First column: Time in atomic units * Second column: Event type ('P': Photoionization, 'A': Auger decay, 'F': Fluorescence decay) * Third column: electronic configuration take * Fourth column: rate in atomic units * Fifth column: energy of involved photoelectron/ Auger electron/ Fluorescence photon (binned to eV) in eV topol ----- For each atom a description for the force field in form of a string, splited by a line break. Each atom is described by a unique identifier for the molecule and a atom identifier for the molecule separated by ``_``. The molecule identifier consists of a string and a unique number counting the molecule, e.g., ``1SOL``. The atom indentifier must match the identifier in the force field definition in the ForceField class. The full string for the oxygen atom of the first water molecule could be, e.g., ``1SOL_OW``.