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parameters [2013/08/21 11:21] – update for tabular view danielparameters [2019/08/11 12:11] (current) – daniel
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 |<100% 33% 33% 33%>| |<100% 33% 33% 33%>|
 ^ **config*** | string | (none) | ^ **config*** | string | (none) |
-| file with atomic configurations in force format, see [[Configurations]] |||+| file with atomic configurations in force format, see [[config:main|Configurations]] |||
  
 |<100% 33% 33% 33%>| |<100% 33% 33% 33%>|
 ^ **startpot*** | string | (none) | ^ **startpot*** | string | (none) |
-| file name containing the starting potential, see [[Potential_files|Potential files]] |||+| file name containing the starting potential, see [[potfiles:main|Potential files]] |||
  
 |<100% 33% 33% 33%>| |<100% 33% 33% 33%>|
 ^ **tempfile*** | string | (none) | ^ **tempfile*** | string | (none) |
-| file name for temporary (intermediate) potentials, see [[Tempfile]] |||+| file name for temporary (intermediate) potentials, see [[output:tempfile]] |||
  
 |<100% 33% 33% 33%>| |<100% 33% 33% 33%>|
 ^ **endpot** | string | $startpot_end | ^ **endpot** | string | $startpot_end |
-| file name for final potential, see [[Potential_files|Potential files]] |||+| file name for final potential, see [[potfiles:main|Potential files]] |||
  
 |<100% 33% 33% 33%>| |<100% 33% 33% 33%>|
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 |<100% 33% 33% 33%>| |<100% 33% 33% 33%>|
 ^ **plotfile** | string | (none) | ^ **plotfile** | string | (none) |
-| file name for plotting potential, see [[Plotfile]] |||+| file name for plotting potential, see [[output:plotfile]] |||
  
 |<100% 33% 33% 33%>| |<100% 33% 33% 33%>|
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 |<100% 33% 33% 33%>| |<100% 33% 33% 33%>|
 ^ **write_pair** | boolean | 0 | ^ **write_pair** | boolean | 0 |
-| write radial pair distribution, see [[Pair_distribution|Pair distribution]] |||+| write radial pair distribution, see [[output:pair_distribution|Pair distribution]] |||
  
 |<100% 33% 33% 33%>| |<100% 33% 33% 33%>|
 ^ **write_lammps** | boolean | 0 | ^ **write_lammps** | boolean | 0 |
-| write potential in LAMMPS format, see [[Lammps]] |||+| write potential in LAMMPS format, see [[output:lammps|LAMMPS]] ||| 
 + 
 +|<100% 33% 33% 33%>| 
 +^ **cell_scale** | float | 1.0 | 
 +| rescale all cells, see [[cell_scale]] |||
  
 ====  Minimization options  ==== ====  Minimization options  ====
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 |<100% 33% 33% 33%>| |<100% 33% 33% 33%>|
 ^ **eng_weight*** | float | (none) | ^ **eng_weight*** | float | (none) |
-| weight of energy in minimization, see [[Algorithms]] |||+| weight of energy in minimization, see [[algorithms:main|Algorithms]] |||
  
 |<100% 33% 33% 33%>| |<100% 33% 33% 33%>|
 ^ **stress_weight**  | float | (none) | ^ **stress_weight**  | float | (none) |
-| (* if compiled with ''stress'') weight of [[Stress|stress]] in minimiziation, see [[Algorithms]] |||+| (* if compiled with ''stress'') weight of [[Stress|stress]] in minimiziation, see [[algorithms:main|Algorithms]] |||
  
 |<100% 33% 33% 33%>| |<100% 33% 33% 33%>|
-^ **anneal_temp** | float | 1. | +^ **anneal_temp** | float | 1.0 | 
-| starting temperature for simulated annealing, set to 0 to skip simulated annealing, see [[Simulated Annealing]] |||+| starting temperature for simulated annealing, set to 0 to skip simulated annealing, see [[algorithms:simann|Simulated Annealing]] |||
  
 |<100% 33% 33% 33%>| |<100% 33% 33% 33%>|
-^ **evo_threshold** | float | 1. | +^ **evo_threshold** | float | 1.0 | 
-| stop the evolutionary algorithm if the difference in the population is smaller than this, set to zero to skip evo, see [[Differential Evolution]] |||+| stop the evolutionary algorithm if the difference in the population is smaller than this, set to zero to skip evo, see [[algorithms:diffevo|Differential Evolution]] |||
  
 |<100% 33% 33% 33%>| |<100% 33% 33% 33%>|
 ^ **d_eps** | float | 0.0 | ^ **d_eps** | float | 0.0 |
-|error margin for powell minimization - if the improvement is smaller, the optimization is stopped, see [[Method of Least Squares]] |||+|error margin for powell minimization - if the improvement is smaller, the optimization is stopped, see [[algorithms:lsq]] |||
  
 |<100% 33% 33% 33%>| |<100% 33% 33% 33%>|
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 |<100% 33% 33% 33%>| |<100% 33% 33% 33%>|
-^ **apot_punish** | float | 0. |+^ **apot_punish** | float | 0.0 |
 |scaling factor for apot punishments, this does not affect out-of-bounds punishment, see [[Analytic potentials/Punishments]]||| |scaling factor for apot punishments, this does not affect out-of-bounds punishment, see [[Analytic potentials/Punishments]]|||
  
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 |<100% 33% 33% 33%>| |<100% 33% 33% 33%>|
 ^ **plotpointfile*** | string | (none) | ^ **plotpointfile*** | string | (none) |
-| file name for plotting the sampling points, see [[Plotpointfile]] |||+| file name for plotting the sampling points, see [[output:plotpointfile]] |||
  
 |<100% 33% 33% 33%>| |<100% 33% 33% 33%>|
 ^ **distfile** | string | (none) | ^ **distfile** | string | (none) |
-| file name for distribution file (* with compile option 'dist'), see [[Distfile]] |||+| file name for distribution file (* with compile option 'dist'), see [[output:bindistfile]] |||
  
 |<100% 33% 33% 33%>| |<100% 33% 33% 33%>|
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 |<100% 33% 33% 33%>| |<100% 33% 33% 33%>|
 ^ **plotmin** | float | 0.0 | ^ **plotmin** | float | 0.0 |
-| starting point for plotting potentials, see [[Plotfile]] |||+| starting point for plotting potentials, see [[output:plotfile]] |||
  
 |<100% 33% 33% 33%>| |<100% 33% 33% 33%>|
 ^ **enable_cp** | boolean | 0 | ^ **enable_cp** | boolean | 0 |
-| whether or not to include chemical potentials, see [[Pair Potentials]] |||+| whether or not to include chemical potentials, see [[interactions:pair_potentials]] |||
  
 ====  options for output  ==== ====  options for output  ====
  
 |<100% 33% 33% 33%>| |<100% 33% 33% 33%>|
-^ **imdpotsteps** | integer | 1000 | +^ **imdpotsteps** | integer | 500 | 
-| number of points in each function in imd and lammps potential files, see [[IMD]] / [[Lammps]] |||+| number of sampling points in each function in imd potential files, see [[IMD]] |||
  
 |<100% 33% 33% 33%>| |<100% 33% 33% 33%>|
 ^ **output_prefix** | string | (none) | ^ **output_prefix** | string | (none) |
-| prefix for various output files, see [[Output]] |||+| prefix for various output files, see [[output:main|Output]] |||
  
 |<100% 33% 33% 33%>| |<100% 33% 33% 33%>|
-^ **extend** | float | 2. |+^ **extend** | float | 2.0 |
 | how many steps should the imd potentials be extrapolated, see [[IMD]] ||| | how many steps should the imd potentials be extrapolated, see [[IMD]] |||
 +
 +
 +|<100% 33% 33% 33%>|
 +^ **lammpspotsteps** | integer | 500 |
 +| number of sampling points in each funcation in LAMMPS potential files, see [[output:lammps|LAMMPS]] |||
  
 ====  parameter for option coulomb  ==== ====  parameter for option coulomb  ====
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 | mixing parameter for dipole convergence during iteration. ||| | mixing parameter for dipole convergence during iteration. |||
  
 +====  parameters for OpenKIM potentials  ====
 +
 +The options for OpenKIM potentials are described in more detail on the [[models:openkim|OpenKIM]] page.
 +
 +|<100% 33% 33% 33%>|
 +^ **kim_model_name** | string | (none) |
 +| KIM model indentifier |||
 +
 +|<100% 33% 33% 33%>|
 +^ **kim_model_params** | string | (none) |
 +| Special parameter option, see [[models:openkim|OpenKIM]] page for details |||
 +
 +|<100% 33% 33% 33%>|
 +^ **kim_model_output_directory** | string | (none) |
 +| Output directory for the optimized KIM model |||
 +
 +|<100% 33% 33% 33%>|
 +^ **kim_model_output_name** | string | (none) |
 +| Name for the optimized KIM model |||
parameters.1377076893.txt.gz · Last modified: 2013/08/21 11:21 by daniel