https://dune-copasi.netlify.app/assets/js/8c955914.ead4e439.js

1"use strict";(self.webpackChunkdune_copasi_docusaurus=self.webpackChunkdune_copasi_docusaurus||[]).push([[6743],{5843:(e,n,t)=>{t.r(n),t.d(n,{assets:()=>m,contentTitle:()=>p,default:()=>v,frontMatter:()=>d,metadata:()=>h,toc:()=>f});var i=t(4848),a=t(8453),r=t(1470),o=t(9365),s=t(1302);const l='#########################################################################\n# HEAT EQUATION:\n#\n# \u2202\u209cu = \u2202\u2093(T\xb7\u2202\u2093u) + \u2202\u1d67(T\xb7\u2202\u1d67u)\n#\n# where u(x,y,t) is the temperature at a time t on the domain for a\n# thermal conductivity T.\n#\n# See: https://en.wikipedia.org/wiki/Heat_equation\n#\n#########################################################################\n\n[grid]\n# extensions of the grid in x and y directions\nextensions = 1 0.1\n# where the grid left-bottom corner starts\norigin = 0.0 0.0\n# number of cells of the initial grid in x and y directions\ncells = 10 1\n# number of times to refine the grid\nrefinement_level = 5\n\n# defines a compartment with the name "domain"\n[compartments.domain]\nexpression = 1\n\n# Define a constant with name "T" to use in the equations\n[parser_context.T]\ntype = constant\nvalue = 0.005\n\n# our model is linear because there is no reaction\n[model]\nis_linear = true\n\n##### Definition of the equation to solve function u(x,y,t) ######\n\n# Declares the compartment where this function is defined\n[model.scalar_field.u]\ncompartment = domain\n\n# Declares that the equation is transient\n[model.scalar_field.u.storage]\nexpression = 1\n\n# Declares the diffusion part on the diffusion-reaction equation\n[model.scalar_field.u.cross_diffusion.u]\nexpression = T\n\n[model.scalar_field.u.initial]\n# Declares the value of the function at the initial time: u(x,y,0)\n# Try changing this to be a function of x and y: use "position_x" and "position_y"\n# to represents its values, for example:\n# "expression = position_x^2"\n# represents the case where u(x,y,0) := x^2\n# ...\n# function for u(x,y,0)\nexpression = 10\n\n# Declares the diffusion part on the diffusion-reaction equation\n# Here we use the following ExprTk syntax to constraint the left and right parts of\n# the compartment: "condition ? if_true : if_false"\n# the "if_true" part contains the values set on the left and right boundaries\n[model.scalar_field.u.constrain.boundary]\nexpression = (position_x <= 0. or position_x >= 1.) ? 0. : no_value\nparser_type = ExprTk\n\n[model.time_step_operator]\n# initial time of the simulation\ntime_begin = 0\n# final time of the simulation\ntime_end = 10\n',c='#########################################################################\n# VOLKA-TERRA EQUATIONS:\n#\n# \u2202\u209cu = \u03b1\xb7u   - \u03b2\xb7u\xb7v\n# \u2202\u209cv = \u03b4\xb7u\xb7v - \u03b3\xb7v\n#\n# See: https://en.wikipedia.org/wiki/Lotka%E2%80%93Volterra_equations\n#\n# Note that there is not derivative on the positions x or y, so the\n# functions are the same on every point in x and y for a given time t.\n# Hence, we do not refine the grid at all.\n#\n#########################################################################\n\n[grid]\n# extensions of the grid in x and y directions\nextensions = 1 1\n# number of cells of the initial grid in x and y directions\ncells = 1 1\n\n# defines a compartment with the name "domain"\n[compartments.domain]\nexpression = 1\n\n# Define constants with name "alpha", "beta", "delta", and "gamma"\n# representing \u03b1, \u03b2, \u03b4, and \u03b3 respectively\n[parser_context.alpha]\ntype = constant\nvalue = 0.666666\n[parser_context.beta]\ntype = constant\nvalue = 1.33333\n[parser_context.delta]\ntype = constant\nvalue = 1\n[parser_context.gamma]\ntype = constant\nvalue = 1\n\n# our model is linear because there is a non-linear reaction part\n[model]\nis_linear = false\n\n##### Definition of the equation to solve function u(x,y,t) ######\n\n# Declares the compartment where this function is defined\n[model.scalar_field.u]\ncompartment = domain\n\n# Declares that the equation is transient\n[model.scalar_field.u.storage]\nexpression = 1\n\n# Declares the reaction part on the diffusion-reaction equation for equation for u\n[model.scalar_field.u.reaction]\nexpression = alpha*u - beta*u*v\n\n# Declares the jacobian of the reaction of u\n[model.scalar_field.u.reaction.jacobian.u]\n# \u2202\u1d64(\u03b1\xb7u - \u03b2\xb7u\xb7v) = \u03b1 - \u03b2\xb7v\nexpression = alpha - beta*v\n[model.scalar_field.u.reaction.jacobian.v]\n# \u2202\u1d65(\u03b1\xb7u - \u03b2\xb7u\xb7v) = - \u03b2\xb7u\nexpression = -beta*u\n\n[model.scalar_field.u.initial]\n# function for u(x,y,0)\nexpression = 1\n\n##### Definition of the equation to solve function v(x,y,t) ######\n\n# Declares the compartment where this function is defined\n[model.scalar_field.v]\ncompartment = domain\n\n# Declares that the equation is transient\n[model.scalar_field.v.storage]\nexpression = 1\n\n# Declares the reaction part on the diffusion-reaction equation for equation for v\n[model.scalar_field.v.reaction]\nexpression = delta*u*v - gamma*v\n\n# Declares the jacobian of the reaction of v\n[model.scalar_field.v.reaction.jacobian.u]\n# \u2202\u1d64(\u03b4\xb7u\xb7v - \u03b3\xb7v) = \u03b4\xb7v\nexpression = delta*v\n[model.scalar_field.v.reaction.jacobian.v]\n# \u2202\u1d65(\u03b4\xb7u\xb7v - \u03b3\xb7v) = \u03b4\xb7u - \u03b3\nexpression = delta*u-gamma\n\n[model.scalar_field.v.initial]\n# function for v(x,y,0)\nexpression = 1\n\n[model.time_step_operator]\n# initial time of the simulation\ntime_begin = 0\n# final time of the simulation\ntime_end = 20\n# limit the maximum time-step\ntime_step_max = 0.25\n',u="#########################################################################\n# GREY-SCOTT EQUATIONS:\n#\n# \u2202\u209cu = 2\xb7D\xb7\u2202\u2093\u2202\u2093u + f\xb7(1-u) - u\xb7v\xb2\n# \u2202\u209cv =   D\xb7\u2202\u2093\u2202\u2093u - (f+k)\xb7v + u\xb7v\xb2\n#\n# See: https://groups.csail.mit.edu/mac/projects/amorphous/GrayScott/\n#\n#########################################################################\n\n[grid]\nextensions = 1 1\ndimension = 2\nrefinement_level = 7\n\n[parser_context.bump]\ntype = function\nexpression = x, y: 0.5*exp(-100*(x^2 + y^2))\nparser_t

1ype = ExprTk\n\n[parser_context.F]\ntype = constant\nvalue = 0.0420\n\n[parser_context.k]\ntype = constant\nvalue = 0.0610\n\n[parser_context.D]\ntype = constant\nvalue = 1e-5\n\n[model]\norder = 1\nparser_type = ExprTk\n\n[model.time_step_operator]\ntime_begin = 0\ntime_end = 10000\ntime_step_initial = 0.1\ntime_step_max = 50\n\n[model.time_step_operator.linear_solver]\ntype = RestartedGMRes\npreconditioner.type = Jacobi\n\n[model.time_step_operator.nonlinear_solver]\ntype = Alexander2\nconvergence_condition.relative_tolerance = 1.00000000000000002e-08\nconvergence_condition.absolute_tolerance = 0\n\n[model.writer.vtk]\npath = vtk\n\n[compartments]\ncompartment.expression = 1\n\n[model.scalar_field.U]\ncompartment = compartment\ninitial.expression = 0.7\nstorage.expression = 1\nreaction.expression = F*(1-U) - U*V^2\nreaction.jacobian.U.expression = -F - V^2\nreaction.jacobian.V.expression = -2*U*V\ncross_diffusion.U.expression = D*2\n\n[model.scalar_field.V]\ncompartment = compartment\ninitial.expression = bump(0.25-position_x, 0.25-position_y) + bump(0.25-position_x, 0.75-position_y) + bump(0.75-position_x, 0.25-position_y) + bump(0.75-position_x, 0.75-position_y)\nstorage.expression = 1\nreaction.expression = -(F+k)*V + U*V^2\nreaction.jacobian.U.expression = V^2\nreaction.jacobian.V.expression = -(F+k) + 2*U*V\ncross_diffusion.V.expression = D\n",d={id:"ini_file",title:"Config File",description:"Syntax of INI file",sidebar_label:"Config File",tags:["API","CLI"]},p=void 0,h={id:"ini_file",title:"Config File",description:"Syntax of INI file",s

1ource:"@site/docs/ini_file.mdx",sourceDirName:".",slug:"/ini_file",permalink:"/docs/next/ini_file",draft:!1,unlisted:!1,editUrl:"https://gitlab.dune-project.org/copasi/dune-copasi/-/edit/master/doc/docusaurus/docs/ini_file.mdx",tags:[{inline:!0,label:"API",permalink:"/docs/next/tags/api"},{inline:!0,label:"CLI",permalink:"/docs/next/tags/cli"}],version:"current",lastUpdatedBy:"Santiago Ospina De Los R\xedos",lastUpdatedAt:1732665958e3,frontMatter:{id:"ini_file",title:"Config File",description:"Syntax of INI file",sidebar_label:"Config File",tags:["API","CLI"]},sidebar:"docs",previous:{title:"Configuration Options",permalink:"/docs/next/config"},next:{title:"Options",permalink:"/docs/next/param_tree"}},m={},f=[];function x(e){const n={a:"a",admonition:"admonition",code:"code",p:"p",pre:"pre",table:"table",tbody:"tbody",td:"td",th:"th",thead:"thead",tr:"tr",...(0,a.R)(),...e.components};return(0,i.jsxs)(i.Fragment,{children:[(0,i.jsx)(n.admonition,{title:"CLI Usage",type:"note",children:(0,i.jsxs)(n.p,{children:["This documentation page is intended for the ",(0,i.jsx)(n.a,{href:"use_cli",children:"Command Line Interface (CLI)"}),". If you're new to DuneCopasi, we recommend starting with our ",(0,i.jsx)(n.a,{href:"/tutorials",children:"Tutorials"}),"."]})}),"\n",(0,i.jsxs)(n.p,{children:["To express different ",(0,i.jsx)(n.a,{href:"/math_model",children:"mathematical problems"})," we typically write a configuration file (with ",(0,i.jsx)(n.code,{children:".ini"})," extension by convention) which entails all the information that is needed for the DuneCopasi solver to construct the problem at hand.\nThe configuration file consists of a parameter tree containing the ",(0,i.jsx)(n.a,{href:"param_tree",children:"simulation options"}),". 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