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parameters [2013/03/01 08:01] – danielparameters [2019/08/11 12:11] (current) – daniel
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 Following is a complete list of all //potfit// parameters, together with a short description of their meaning, and indications when they are needed.  Following is a complete list of all //potfit// parameters, together with a short description of their meaning, and indications when they are needed. 
 Floating point numbers should be given in decimal notation. Vectors are given as a list of components, separated by spaces or tabs (all on one line).  Floating point numbers should be given in decimal notation. Vectors are given as a list of components, separated by spaces or tabs (all on one line). 
-An asterisk marks required parameters. 
  
-The first column contains the name of the parameter, the second the type of the parameter and the third one the initial value (if there is one). The second line is a short explanation for the parameter+An asterisk (*****) marks required parameters. 
 + 
 +|<100% 33% 33% 33%>| 
 +^ parameter name | parameter type | default value | 
 +| short explanation |||
  
 ====  main parameters  ==== ====  main parameters  ====
-;ntypes* - integer - (none) + 
->number of atom types (types vary in [[0,..,ntypes-1]]) +|<100% 33% 33% 33%>| 
 +^ **ntypes*** | integer | (none) | 
 +| number of atom types (types vary in [0,..,ntypes-1]) |||
  
 ====  file names  ==== ====  file names  ====
-;config* - string - (none) + 
->file with atom configuration in force format, see [[Configurations]] +|<100% 33% 33% 33%>| 
-;startpot* - string - (none) +^ **config*** | string | (none) | 
->file name for starting potential, see [[Potential_files]] +| file with atomic configurations in force format, see [[config:main|Configurations]] ||| 
-;tempfile* - string - (none) + 
->file name for temporary (intermediate) potential, see [[Tempfile]] +|<100% 33% 33% 33%>| 
-;endpot - string - $startpot_end +^ **startpot*** | string | (none) | 
->file name for final potential, see [[Potential_files]] +| file name containing the starting potential, see [[potfiles:main|Potential files]] ||| 
-;imdpot - string - (none) + 
->file name prefix for imd potentials, see [[IMD]] +|<100% 33% 33% 33%>| 
-;plotfile - string - (none) +^ **tempfile*** | string | (none) | 
->file name for plotting potential, see [[Plotfile]] +| file name for temporary (intermediate) potentials, see [[output:tempfile]] ||| 
-;flagfile - string - (none) + 
->file whose presence terminates fit, see [[Flagfile]]+|<100% 33% 33% 33%>| 
 +^ **endpot** | string | $startpot_end | 
 +| file name for final potential, see [[potfiles:main|Potential files]] ||| 
 + 
 +|<100% 33% 33% 33%>| 
 +^ **imdpot** | string | (none) | 
 +| file name prefix for imd potentials, see [[IMD]] ||| 
 + 
 +|<100% 33% 33% 33%>| 
 +^ **plotfile** | string | (none) | 
 +| file name for plotting potential, see [[output:plotfile]] ||| 
 + 
 +|<100% 33% 33% 33%>| 
 +^ **flagfile** | string | (none) | 
 +| file, whose presence terminates the current fit, see [[Flagfile]] |||
  
 ====  general options  ==== ====  general options  ====
-;write_pair - boolean - 0 + 
->write radial pair distribution, see [[Pair_distribution]] +|<100% 33% 33% 33%>| 
-;write_lammps - boolean - 0 +^ **write_pair** | boolean | 0 | 
->write potential in LAMMPS format, see [[Lammps]]+| write radial pair distribution, see [[output:pair_distribution|Pair distribution]] ||| 
 + 
 +|<100% 33% 33% 33%>| 
 +^ **write_lammps** | boolean | 0 | 
 +| 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  ====
-;opt - boolean - 0 + 
->whether or not to perform an optimization +|<100% 33% 33% 33%>| 
-;eng_weight* - float - (none) +^ **opt** | boolean | 0 | 
->weight of energy in minimization, see [[:Category:Algorithms|Algorithms]] +| whether or not to perform an optimization ||| 
-;stress_weight (* if compiled with <tt>stress</tt>) - float - (none) + 
->weight of [[Stress|stress]] in minimiziation, see [[:Category:Algorithms|Algorithms]] +|<100% 33% 33% 33%>| 
-;anneal_temp - float - 1. +^ **eng_weight*** | float | (none) | 
->starting temperature for simulated annealing, set to 0 to skip simulated annealing, see [[Simulated|Annealing]] +| weight of energy in minimization, see [[algorithms:main|Algorithms]] ||| 
-;evo_threshold - float - 1. + 
->stop the evolutionary algorithm if the difference in the population is smaller than this, set to zero to skip evo, see [[Differential|Evolution]] +|<100% 33% 33% 33%>| 
-;d_eps - float - 0.0 +^ **stress_weight**  | float | (none) | 
->error margin for powell minimization - if the improvement is smaller, the optimization is stopped, see [[Method|of Least Squares]] +| (* if compiled with ''stress'') weight of [[Stress|stress]] in minimiziation, see [[algorithms:main|Algorithms]] ||| 
-;seed - integer - 4 + 
->seed for random number generator +|<100% 33% 33% 33%>| 
-;apot_punish - float - 0. +^ **anneal_temp** | float | 1.0 | 
->scaling factor for apot punishments, this does not affect out-of-bounds punishment, see [[Analytic|potentials/Punishments]]+| starting temperature for simulated annealing, set to 0 to skip simulated annealing, see [[algorithms:simann|Simulated Annealing]] ||| 
 + 
 +|<100% 33% 33% 33%>| 
 +^ **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 [[algorithms:diffevo|Differential Evolution]] ||| 
 + 
 +|<100% 33% 33% 33%>| 
 +^ **d_eps** | float | 0.0 | 
 +|error margin for powell minimization - if the improvement is smaller, the optimization is stopped, see [[algorithms:lsq]] ||| 
 + 
 +|<100% 33% 33% 33%>| 
 +^ **seed** | integer | 4 | 
 +|seed for random number generator||| 
 + 
 +|<100% 33% 33% 33%>| 
 +^ **apot_punish** | float | 0.0 | 
 +|scaling factor for apot punishments, this does not affect out-of-bounds punishment, see [[Analytic potentials/Punishments]]|||
  
 ====  options only for tabulated potentials  ==== ====  options only for tabulated potentials  ====
-;plotpointfile* - string - (none) + 
->file name for plotting the sampling points, see [[Plotpointfile]] +|<100% 33% 33% 33%>| 
-;distfile - string - (none) +^ **plotpointfile*** | string | (none) | 
->file name for distribution file (* with compile option 'dist'), see [[Distfile]] +| file name for plotting the sampling points, see [[output:plotpointfile]] ||| 
-;maxchfile - string - (none) + 
->file with maximal permissible changes for each parameter, see [[Maxchfile]]+|<100% 33% 33% 33%>| 
 +^ **distfile** | string | (none) | 
 +| file name for distribution file (* with compile option 'dist'), see [[output:bindistfile]] ||| 
 + 
 +|<100% 33% 33% 33%>| 
 +^ **maxchfile** | string | (none) | 
 +| file with maximal permissible changes for each parameter, see [[Maxchfile]] |||
  
 ====  options only for analytic potentials  ==== ====  options only for analytic potentials  ====
-;plotmin - float - 0.0 + 
->starting point for plotting potentials, see [[Plotfile]] +|<100% 33% 33% 33%>| 
-;enable_cp - boolean - 0 +^ **plotmin** | float | 0.0 | 
->whether or not to include chemical potentials, see [[Pair|Potentials]]+| starting point for plotting potentials, see [[output:plotfile]] ||| 
 + 
 +|<100% 33% 33% 33%>| 
 +^ **enable_cp** | boolean | 0 | 
 +| whether or not to include chemical potentials, see [[interactions:pair_potentials]] |||
  
 ====  options for output  ==== ====  options for output  ====
-;imdpotsteps - integer - 1000 
->number of points in each function in imd and lammps potential files, see [[IMD]] / [[Lammps]] 
-;output_prefix - string - (none) 
->prefix for various output files, see [[:Category:Output|Output]] 
-;extend - float - 2. 
->how many steps should the imd potentials be extrapolated, see [[IMD]] 
  
-====  parameter for option [[Coulomb|coulomb]]  ==== +|<100% 33% 33% 33%>| 
-;dp_cut - float - 10  +^ **imdpotsteps** | integer | 500 | 
->cutoff-radius for electrostatic interactions, doesn't depend on other pair-function-radii.+| number of sampling points in each function in imd potential files, see [[IMD]] ||| 
 + 
 +|<100% 33% 33% 33%>| 
 +^ **output_prefix** | string | (none) | 
 +| prefix for various output files, see [[output:main|Output]] ||| 
 + 
 +|<100% 33% 33% 33%>| 
 +^ **extend** | float | 2.0 | 
 +| 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  ==== 
 + 
 +|<100% 33% 33% 33%>| 
 +^ **dp_cut** | float | 10 | 
 +| cutoff-radius for electrostatic interactions, doesn't depend on other pair-function-radii. ||| 
 + 
 +====  parameters for option dipole  ==== 
 + 
 +|<100% 33% 33% 33%>| 
 +^ **dp_tol** | float | 1.e-7 | 
 +| dipole iteration precision. ||| 
 + 
 +|<100% 33% 33% 33%>| 
 +^ **dp_mix** | float | 0.2 | 
 +| 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 |||
  
-====  parameters for option [[Dipole|dipole]]  ==== +|<100% 33% 33% 33%>| 
-;dp_tol - float - 1.e-7 +^ **kim_model_output_directory** | string | (none) | 
->dipole iteration precision. +| Output directory for the optimized KIM model |||
-;dp_mix - float - 0.2 +
->mixing parameter for dipole convergence during iteration.+
  
 +|<100% 33% 33% 33%>|
 +^ **kim_model_output_name** | string | (none) |
 +| Name for the optimized KIM model |||
parameters.1362121280.txt.gz · Last modified: 2013/03/01 08:01 by daniel