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--- options:main [2018/09/19 17:45] – ↷ Links adapted because of a move operation daniel
+++ options:main [2019/10/08 18:08] (current) – [uq] daniel
@@ Line 5: / Line 5: @@
 //potfit// supports different options to adjust the optimization process to special needs.
 These options need to be specified during the configuration stage.
+^  General options  ^^
+| [[#bindist|bindist]] | Enable writing the binning distribution file |
+| [[#contrib|contrib]] | Enable [[config:bocp|Box of Contributing Particles]] |
+| [[#dsf|dsf]] | Enable the damped shift force approach |
+| [[#evo|evo]] | Enable evolutionary optimization algorithm |
+| [[#fweight|fweight]] | Enable force weight adjustment |
+| [[#mpi|mpi]] | Enable MPI parallelization |
+| [[#nopunish|nopunish]] | Disable punishments for optimization |
+| [[#resc|resc]] | Enable rescaling of tabulated potentials |
+| [[#stress|stress]] | Add stress in optimization target |
+| [[#uq|uq]] | Generate potential ensemble for uncertainty quantification |
+[[#deprecated options|Deprecated options]]
+-----
 ===== General options =====
+==== bindist ====
+Create a [[output:bindistfile|binning distribution file]] from the provided atomic configurations. This feature is only supported for tabulated potentials.
+Use this command line switch during the './waf configure' stage to enable the dist feature:
+<code>--enable-bindist</code>
 ==== contrib ====
@@ Line 14: / Line 37: @@
 Use this command line switch during the './waf configure' stage to enable the contrib feature:
 <code>--enable-contrib</code>
-==== dist ====
-Create a [[:distfile|radial distribution file]] from the provided atomic configurations.
-Use this command line switch during the './waf configure' stage to enable the dist feature:
-<code>--enable-dist</code>
 ==== dsf ====
@@ Line 32: / Line 48: @@
 ==== evo ====
-Use the evolutionary algorithm instead of simulated annealing when performing the coarse optimization.
+Use the [[algorithms:diffevo|evolutionary algorithm]] instead of [[algorithms:simann|simulated annealing]] when performing the coarse optimization.
 Use this command line switch during the './waf configure' stage to enable the evo algorithm:
@@ Line 46: / Line 62: @@
 ==== mpi ====
-Enable [[:mpi|MPI parallelization]] for force calculations.
+Enable [[running:mpi|MPI parallelization]] for force calculations.
 Use this command line switch during the './waf configure' stage to enable the MPI feature:
@@ Line 60: / Line 76: @@
 ==== resc ====
-Enable [[:resc|rescaling]] (use with care!)
+Enable [[:resc|rescaling]] (use with care!). This option is only available for tabulated potentials.
 Use this command line switch during the './waf configure' stage to enable the resc feature:
@@ Line 67: / Line 83: @@
 ==== stress ====
-Include [[:stress]] in fitting process
+Include [[:stress]] in fitting process. If this is not enabled //potfit// will only use forces and energy in the optimization process.
 Use this command line switch during the './waf configure' stage to enable the stress feature:
 <code>--enable-stress</code>
-=====  Deprecated Options in the Compilation Target  =====
+==== uq ====
+Generate potential ensemble for [[uq|uncertainty quantification]].
+Use this command line switch during the './waf configure' stage to enable the uncertainty quantification feature:
+<code>--enable-uq</code>
+-----
+===== Deprecated Options =====
-The following options have been removed from potfit and are no longer supported.
+The following options have been removed from //potfit// and are no longer supported.
   * limit
@@ Line 82: / Line 107: @@
   * wzero
-Short explanations for these options can be found [[:deprecated_options|here]].
+Short explanations for these options can be found [[options:deprecated|here]].