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options [2018/09/11 16:54] – danieloptions:main [2019/10/08 18:08] (current) – [uq] daniel
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 ====== Compilation options ====== ====== Compilation options ======
 ---- ----
-In addition to selecting the parallelization method (MPI), various options can be compiled into //potfit//. 
  
-We give here a list of all possible options, and describe what their purpose is and how they are used. +//potfit// supports different options to adjust the optimization process to special needs. 
-Possible Options in the Compilation Target+These options need to be specified during the configuration stage.
  
-|  | [[#adp|adp]] | [[#apot|apot]] | [[#contrib|contrib]] | [[#coulomb|coulomb]] | [[#debug|debug]] | +^  General options  ^^ 
-| [[#dipole|dipole]] | [[#dist|dist]] | [[#eam|eam]] | [[#evo|evo]] | [[#fweight|fweight]] | [[#mpi|mpi]] | +| [[#bindist|bindist]] | Enable writing the binning distribution file | 
-| [[#meam|meam]] | [[#nopunish|nopunish]] | [[#pair|pair]] | [[#prof|prof]] | [[#resc|resc]] | [[#stiweb|stiweb]] | +| [[#contrib|contrib]] | Enable [[config:bocp|Box of Contributing Particles]] | 
-| [[#stress|stress]] | [[#tbeam|tbeam]] | [[#tersoff|tersoff]] | [[#tersoffmod|tersoffmod]] |+| [[#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 =====+===== General options =====
  
-<html><div id="apot"><b>apot</b></div> +==== bindist ====
-&nbsp;&nbsp;&nbsp;Use </html>[[Analytic_potentials|analytic potentials]]+
  
-<html><div id="contrib"><b>contrib</b></div> +Create a [[output:bindistfile|binning distribution file]] from the provided atomic configurations. This feature is only supported for tabulated potentials.
-&nbsp;&nbsp;&nbsp;Enable support for a </html>[[Box of Contributing Particles|box of contributing particles]]+
  
-=====  Interactions  =====+Use this command line switch during the './waf configure' stage to enable the dist feature: 
 +<code>--enable-bindist</code>
  
-<html><div id="pair"><b>pair</b></div> +==== contrib ====
-&nbsp;&nbsp;&nbsp;Use </html>[[interactions:pair_potentials|pair potentials]]+
  
-<html><div id="eam"><b>eam</b></div> +Enable support for [[config:bocp|Box of Contributing Particles]].
-&nbsp;&nbsp;&nbsp;Use </html>[[interactions:eam|Embedded Atom Method]] potentials+
  
-<html><div id="eam"><b>tbeam</b></div> +Use this command line switch during the './waf configure' stage to enable the contrib feature: 
-&nbsp;&nbsp;&nbsp;Use </html>[[interactions:tbeam|Two Band Embedded Atom Method]] potentials+<code>--enable-contrib</code>      
  
-<html><div id="adp"><b>adp</b></div> +==== dsf ====
-&nbsp;&nbsp;&nbsp;Use </html>[[interactions:adp|Angular Dependent Potentials]]+
  
-<html><div id="coulomb"><b>coulomb</b></div> +Use the damped shifted force approach when calculating forces. This feature is only available for  
-&nbsp;&nbsp;&nbsp;Use </html>[[interactions:coulomb|coulomb]] interactions+coulomb-based interactions!
  
-<html><div id="dipole"><b>dipole</b></div> +Use this command line switch during the './waf configure' stage to enable the dsf feature: 
-&nbsp;&nbsp;&nbsp;Enable </html>[[interactions:dipole|dipole]] interactions+<code>--enable-dsf</code> 
 +   
 +==== evo ====
  
-<html><div id="meam"><b>meam</b></div> +Use the [[algorithms:diffevo|evolutionary algorithm]] instead of [[algorithms:simann|simulated annealing]] when performing the coarse optimization.
-&nbsp;&nbsp;&nbsp;Enable </html>[[interactions:meam|Modified Embedded Atom Method]] potentials+
  
-<html><div id="stiweb"><b>stiweb</b></div> +Use this command line switch during the './waf configure' stage to enable the evo algorithm: 
-&nbsp;&nbsp;&nbsp;Enable </html>[[interactions:stiweb|Stillinger-Weber]] potentials+<code>--enable-evo</code> 
 +    
 +==== fweight ====
  
-<html><div id="tersoff"><b>tersoff</b></div> +Use [[:fweight|modified weights]] for the forces when calculating the error sum.
-&nbsp;&nbsp;&nbsp;Enable </html>[[interactions:tersoff|Tersoff]] potentials+
  
-<html><div id="tersoff"><b>tersoffmod</b></div> +Use this command line switch during the './waf configure' stage to enable the fweight feature: 
-&nbsp;&nbsp;&nbsp;Enable </html>[[interactions:tersoffmod|modified Tersoff]] potentials+<code>--enable-fweight</code>                               
  
-===== Miscellaneous =====+==== mpi ====
  
-<html><div id="resc"><b>resc</b></div> +Enable [[running:mpi|MPI parallelization]] for force calculations.
-&nbsp;&nbsp;&nbsp;Rescale the potentials if possible. See </html> [[resc]].+
  
-=====  Optimization  =====+Use this command line switch during the './waf configure' stage to enable the MPI feature: 
 +<code>--enable-mpi</code>   
  
-<html><div id="evo"><b>evo</b></div> +==== nopunish ====
-&nbsp;&nbsp;&nbsp;Use </html>[[algorithms:diffevo|evolutionary algorithm]] instead of [[algorithms:simann|simulated annealing]].+
  
-<html><div id="fweight"><b>fweight</b></div> +Disable punishments when calculating the error sum. [[:nopunish]]
-&nbsp;&nbsp;&nbsp;Use modified weights for the forces. See </html> [[fweight]].+
  
-<html><div id="nopunish"><b>nopunish</b></div> +Use this command line switch during the './waf configure' stage to enable the nopunish feature: 
-&nbsp;&nbsp;&nbsp;Disable the punishments in the optimization run. See </html> [[nopunish]].+<code>--enable-nopunish</code>   
  
-<html><div id="stress"><b>stress</b></div> +==== resc ====
-&nbsp;&nbsp;&nbsp;Enables the computation of the stress or pressure tensor and its usage in minimization. See  </html> [[stress]].+
  
-=====  Output  =====+Enable [[:resc|rescaling]] (use with care!). This option is only available for tabulated potentials.
  
-<html><div id="dist"><b>dist</b></div> +Use this command line switch during the './waf configure' stage to enable the resc feature: 
-&nbsp;&nbsp;&nbsp;Creates a </html> [[distfile]]+<code>--enable-resc</code>   
  
-=====  Technical  =====+==== stress ====
  
-<html><div id="debug"><b>debug</b></div> +Include [[:stress]] in fitting process. If this is not enabled //potfit// will only use forces and energy in the optimization process.
-&nbsp;&nbsp;&nbsp;Compile with debug flags. See </html> [[debug]].+
  
-<html><div id="mpi"><b>mpi</b></div> +Use this command line switch during the './waf configure' stage to enable the stress feature: 
-&nbsp;&nbsp;&nbsp;Enable MPI parallelization. See </html> [[MPI]].+<code>--enable-stress</code>   
  
-<html><div id="prof"><b>prof</b></div> +==== uq ==== 
-&nbsp;&nbsp;&nbsp;Include profiling information in the binary, see </html> [[debug]].+ 
 +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 in the Compilation Target  =====+===== 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   * limit
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   * wzero   * wzero
  
-Short explanations for these options can be found [[Deprecated Options|here]].+Short explanations for these options can be found [[options:deprecated|here]].
options/main.1536677661.txt.gz · Last modified: 2018/09/11 16:54 by daniel