Difference between revisions of "MD options"

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(Created page with "Molecular dynamics simulations are invoked with the <code>turbogap md</code> command. The most important options in the input file that you need to worry about are: #...")
 
 
(8 intermediate revisions by 2 users not shown)
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# <code>[[md_nsteps]]</code>: the number of time steps to propagate the atomic positions;
 
# <code>[[md_nsteps]]</code>: the number of time steps to propagate the atomic positions;
 
# <code>[[thermostat]]</code>: formalism to keep the temperature constant (or not);
 
# <code>[[thermostat]]</code>: formalism to keep the temperature constant (or not);
 +
## <code>[[thermostat_groupID]]</code>: the group ID of atoms on which thermostat will act;
 
## <code>[[t_beg]]</code>: the initial thermostating temperature if a thermostat is chosen;
 
## <code>[[t_beg]]</code>: the initial thermostating temperature if a thermostat is chosen;
 
## <code>[[t_end]]</code>: the final thermostating temperature if a thermostat is chosen;
 
## <code>[[t_end]]</code>: the final thermostating temperature if a thermostat is chosen;
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## <code>[[gamma_p]]</code>: the inverse compressibility of the system if a thermostat is chosen;
 
## <code>[[gamma_p]]</code>: the inverse compressibility of the system if a thermostat is chosen;
 
## <code>[[barostat_sym]]</code>: selects which degrees of freedom of the simulation box are affected by the barostating;
 
## <code>[[barostat_sym]]</code>: selects which degrees of freedom of the simulation box are affected by the barostating;
−
# <code>[[scale_box]]</code>: determines whether the simulation box is scalend during the simulation;
+
# <code>[[scale_box]]</code>: determines whether the simulation box is scaled during the simulation;
 
# <code>[[box_scaling_factor]]</code>: determines by how much the box will be increased during the simulation;
 
# <code>[[box_scaling_factor]]</code>: determines by how much the box will be increased during the simulation;
 
# <code>[[write_thermo]]</code>: how often to write out thermodynamic information;
 
# <code>[[write_thermo]]</code>: how often to write out thermodynamic information;
 
# <code>[[write_xyz]]</code>: how often to write out detailed trajectory information;
 
# <code>[[write_xyz]]</code>: how often to write out detailed trajectory information;
 
# <code>[[write_lv]]</code>: determines whether the lattice vectors are written together with the thermodynamic information;
 
# <code>[[write_lv]]</code>: determines whether the lattice vectors are written together with the thermodynamic information;
−
# <code>[[neighbors_buffer]]</code>: defines a buffer region beyond the potential's actual cutoff to enable less frequent neighbor list builds.
+
# <code>[[neighbors_buffer]]</code>: defines a buffer region beyond the potential's actual cutoff to enable less frequent neighbor list builds;
 +
# <code>[[make_group]]</code>: 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 ==
 +
 
 +
# <code>[[adaptive_time]]</code>: formalism to perform MD with variable time-steps;
 +
## <code>[[adapt_time_groupID]]</code>: a valid group ID of atoms on which this process will act;
 +
## <code>[[adapt_tstep_interval]]</code>: interval at which the algorithm is called to calculate a new time-step;
 +
## <code>[[adapt_tmin]]</code>: minimum limit of time-step;
 +
## <code>[[adapt_tmax]]</code>: maximum limit of time-step;
 +
## <code>[[adapt_xmax]]</code>: maximum allowed displacement by an atom per time-step;
 +
## <code>[[adapt_emax]]</code>: maximum allowed energy transfer by an atom per time-step;
 +
 
 +
== Electronic stopping ==
 +
 
 +
# <code>[[electronic_stopping]]</code>: formalism(s) to estimate electronic energy loss (EEL) of atoms;
 +
## <code>[[eel_groupID]]</code>: a valid group ID of atoms on which this process will act;
 +
## <code>[[eel_cut]]</code>: lower energy cutoff below which no EEL is to be calculated;
 +
## <code>[[eel_freq_out]]</code>: how often to write the EEL data to file;
 +
## <code>[[estop_filename]]</code>: name of the file containing electronic stopping power data;
 +
## <code>[[eel_md_last_step]]</code>: last step of MD in previous run in case of a restarted simulation;
 +
## <code>[[eel_md_prev_time]]</code>: MD time evolved in previous run in case of a restarted simulation;
 +
## <code>[[eel_E_prev_time]]</code>: last value of cumulative electronic energy loss in previous run in case of a restarted simulation;
 +
 
 +
== Non-adiabatic processes ==
 +
 
 +
# <code>[[nonadiabatic_processes]]</code>: formalism(s) to account for electronic stopping and electron-phonon coupling;
 +
## <code>[[eph_groupID]]</code>: a valid group ID on which this process will act;
 +
## <code>[[eph_fdm_option]]</code>: choice to activate/deactivate updating of electronic temperature;
 +
## <code>[[eph_friction_option]]</code>: choice to activate/deactivate friction forces;
 +
## <code>[[eph_random_option]]</code>: choice to activate/deactivate random forces;
 +
## <code>[[eph_betafile]]</code>: name of file containing electronic stopping coupling parameter data;
 +
## <code>[[eph_Tinfile]]</code>: name of file containing electronic parameters and mesh for finite difference method (FDM);
 +
## <code>[[eph_box_limits]]</code>: lower and higher boundaries on three directions to construct mesh for FDM;
 +
## <code>[[eph_rho_e]]</code>: scaling parameter for FDM mesh;
 +
## <code>[[eph_C_e]]</code>: electronic heat capacity per unit volume;
 +
## <code>[[eph_kappa_e]]</code>: electronic thermal conductivity;
 +
## <code>[[eph_Ti_e]]</code>: initial electronic temperature;
 +
## <code>[[eph_gsx]]</code>: number of grids in x-direction;
 +
## <code>[[eph_gsy]]</code>: number of grids in y-direction;
 +
## <code>[[eph_gsz]]</code>: number of grids in z-direction;
 +
## <code>[[eph_fdm_steps]]</code>: number of steps for integration of heat diffusion equation;
 +
## <code>[[eph_md_last_step]]</code>: last step of MD in previous run in case of restarted run;
 +
## <code>[[eph_md_prev_time]]</code>: MD time evolved in previous run in case of restarted run;
 +
## <code>[[eph_E_prev_time]]</code>: last value of cumulative electronic energy transfer in previous run in case of restarted run;
 +
## <code>[[eph_freq_Tout]]</code>: how often to write out energy transfer and electronic temperature data;
 +
## <code>[[eph_freq_mesh_Tout]]</code>: how often to write out full map of electronic temperatures;
 +
## <code>[[eph_Toutfile]]</code>: name of the file for electronic temperature map;

Latest revision as of 10:11, 29 March 2024

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;
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