MD options

Molecular dynamics simulations are invoked with the turbogap md command. The most important options in the input file that you need to worry about are:

1. md_step: the time step for velocity Verlet integration;
2. md_nsteps: the number of time steps to propagate the atomic positions;
3. thermostat: formalism to keep the temperature constant (or not);
   1. thermostat_groupID: the group ID of atoms on which thermostat will act;
   2. t_beg: the initial thermostating temperature if a thermostat is chosen;
   3. t_end: the final thermostating temperature if a thermostat is chosen;
   4. tau_t: the time constant for the thermostat, if chosen;
4. barostat: formalism to keep the pressure constant (or not);
   1. p_beg: the initial barostating pressure if a barostat is chosen;
   2. p_end: the final barostating pressure if a barostat is chosen;
   3. tau_p: the time constant of the barostat, if chosen;
   4. gamma_p: the inverse compressibility of the system if a thermostat is chosen;
   5. barostat_sym: selects which degrees of freedom of the simulation box are affected by the barostating;
5. scale_box: determines whether the simulation box is scaled during the simulation;
6. box_scaling_factor: determines by how much the box will be increased during the simulation;
7. write_thermo: how often to write out thermodynamic information;
8. write_xyz: how often to write out detailed trajectory information;
9. write_lv: determines whether the lattice vectors are written together with the thermodynamic information;
10. neighbors_buffer: defines a buffer region beyond the potential's actual cutoff to enable less frequent neighbor list builds;
11. make_group: to make a group of atoms by a definite style in the simulation system.

There are also various additional features which can be invoked through different input options. A number of useful features are also currently being developed. These features will suite specific purposes.

Adaptive time

1. adaptive_time: formalism to perform MD with variable time-steps;
   1. adapt_time_groupID: a valid group ID of atoms on which this process will act;
   2. adapt_tstep_interval: interval at which the algorithm is called to calculate a new time-step;
   3. adapt_tmin: minimum limit of time-step;
   4. adapt_tmax: maximum limit of time-step;
   5. adapt_xmax: maximum allowed displacement by an atom per time-step;
   6. adapt_emax: maximum allowed energy transfer by an atom per time-step;

Electronic stopping

1. electronic_stopping: formalism(s) to estimate electronic energy loss (EEL) of atoms;
   1. eel_groupID: a valid group ID of atoms on which this process will act;
   2. eel_cut: lower energy cutoff below which no EEL is to be calculated;
   3. eel_freq_out: how often to write the EEL data to file;
   4. estop_filename: name of the file containing electronic stopping power data;
   5. eel_md_last_step: last step of MD in previous run in case of a restarted simulation;
   6. eel_md_prev_time: MD time evolved in previous run in case of a restarted simulation;
   7. eel_E_prev_time: last value of cumulative electronic energy loss in previous run in case of a restarted simulation;

Non-adiabatic processes

1. nonadiabatic_processes: formalism(s) to account for electronic stopping and electron-phonon coupling;
   1. eph_groupID: a valid group ID on which this process will act;
   2. eph_fdm_option: choice to activate/deactivate updating of electronic temperature;
   3. eph_friction_option: choice to activate/deactivate friction forces;
   4. eph_random_option: choice to activate/deactivate random forces;
   5. eph_betafile: name of file containing electronic stopping coupling parameter data;
   6. eph_Tinfile: name of file containing electronic parameters and mesh for finite difference method (FDM);
   7. eph_box_limits: lower and higher boundaries on three directions to construct mesh for FDM;
   8. eph_rho_e: scaling parameter for FDM mesh;
   9. eph_C_e: electronic heat capacity per unit volume;
   10. eph_kappa_e: electronic thermal conductivity;
   11. eph_Ti_e: initial electronic temperature;
   12. eph_gsx: number of grids in x-direction;
   13. eph_gsy: number of grids in y-direction;
   14. eph_gsz: number of grids in z-direction;
   15. eph_fdm_steps: number of steps for integration of heat diffusion equation;
   16. eph_md_last_step: last step of MD in previous run in case of restarted run;
   17. eph_md_prev_time: MD time evolved in previous run in case of restarted run;
   18. eph_E_prev_time: last value of cumulative electronic energy transfer in previous run in case of restarted run;
   19. eph_freq_Tout: how often to write out energy transfer and electronic temperature data;
   20. eph_freq_mesh_Tout: how often to write out full map of electronic temperatures;
   21. eph_Toutfile: name of the file for electronic temperature map;