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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "https://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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<title>MPI-AMRVAC: Data Types List</title>
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<div id="projectname">MPI-AMRVAC
 <span id="projectnumber">3.1</span>
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<div id="projectbrief">The MPI - Adaptive Mesh Refinement - Versatile Advection Code (development version)</div>
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<div class="title">Data Types List</div> </div>
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<div class="textblock">Here are the data types with brief descriptions:</div><div class="directory">
<div class="levels">[detail level <span onclick="javascript:toggleLevel(1);">1</span><span onclick="javascript:toggleLevel(2);">2</span>]</div><table class="directory">
<tr id="row_0_" class="even"><td class="entry"><span style="width:0px;display:inline-block;"> </span><span id="arr_0_" class="arrow" onclick="toggleFolder('0_')">►</span><span class="icona"><span class="icon">N</span></span><a class="el" href="namespacem__octree__mg__1d.html" target="_self">m_octree_mg_1d</a></td><td class="desc"></td></tr>
<tr id="row_0_0_" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="structm__octree__mg__1d_1_1mg__lvl__t.html" target="_self">mg_lvl_t</a></td><td class="desc">Lists of blocks per refinement level </td></tr>
<tr id="row_0_1_" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="structm__octree__mg__1d_1_1mg__box__t.html" target="_self">mg_box_t</a></td><td class="desc">Box data structure </td></tr>
<tr id="row_0_2_" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="structm__octree__mg__1d_1_1mg__buf__t.html" target="_self">mg_buf_t</a></td><td class="desc">Buffer type (one is used for each pair of communicating processes) </td></tr>
<tr id="row_0_3_" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="structm__octree__mg__1d_1_1mg__comm__t.html" target="_self">mg_comm_t</a></td><td class="desc"></td></tr>
<tr id="row_0_4_" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="structm__octree__mg__1d_1_1mg__bc__t.html" target="_self">mg_bc_t</a></td><td class="desc"></td></tr>
<tr id="row_0_5_" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="structm__octree__mg__1d_1_1mg__timer__t.html" target="_self">mg_timer_t</a></td><td class="desc"></td></tr>
<tr id="row_0_6_" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="structm__octree__mg__1d_1_1mg__t.html" target="_self">mg_t</a></td><td class="desc"></td></tr>
<tr id="row_0_7_" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacem__octree__mg__1d_1_1mg__subr__bc.html" target="_self">mg_subr_bc</a></td><td class="desc">To fill ghost cells near physical boundaries </td></tr>
<tr id="row_1_"><td class="entry"><span style="width:0px;display:inline-block;"> </span><span id="arr_1_" class="arrow" onclick="toggleFolder('1_')">►</span><span class="icona"><span class="icon">N</span></span><a class="el" href="namespacem__octree__mg__2d.html" target="_self">m_octree_mg_2d</a></td><td class="desc"></td></tr>
<tr id="row_1_0_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="structm__octree__mg__2d_1_1mg__lvl__t.html" target="_self">mg_lvl_t</a></td><td class="desc">Lists of blocks per refinement level </td></tr>
<tr id="row_1_1_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="structm__octree__mg__2d_1_1mg__box__t.html" target="_self">mg_box_t</a></td><td class="desc">Box data structure </td></tr>
<tr id="row_1_2_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="structm__octree__mg__2d_1_1mg__buf__t.html" target="_self">mg_buf_t</a></td><td class="desc">Buffer type (one is used for each pair of communicating processes) </td></tr>
<tr id="row_1_3_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="structm__octree__mg__2d_1_1mg__comm__t.html" target="_self">mg_comm_t</a></td><td class="desc"></td></tr>
<tr id="row_1_4_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="structm__octree__mg__2d_1_1mg__bc__t.html" target="_self">mg_bc_t</a></td><td class="desc"></td></tr>
<tr id="row_1_5_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="structm__octree__mg__2d_1_1mg__timer__t.html" target="_self">mg_timer_t</a></td><td class="desc"></td></tr>
<tr id="row_1_6_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="structm__octree__mg__2d_1_1mg__t.html" target="_self">mg_t</a></td><td class="desc"></td></tr>
<tr id="row_1_7_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacem__octree__mg__2d_1_1mg__subr__bc.html" target="_self">mg_subr_bc</a></td><td class="desc">To fill ghost cells near physical boundaries </td></tr>
<tr id="row_2_" class="even"><td class="entry"><span style="width:0px;display:inline-block;"> </span><span id="arr_2_" class="arrow" onclick="toggleFolder('2_')">►</span><span class="icona"><span class="icon">N</span></span><a class="el" href="namespacem__octree__mg__3d.html" target="_self">m_octree_mg_3d</a></td><td class="desc"></td></tr>
<tr id="row_2_0_" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="structm__octree__mg__3d_1_1mg__lvl__t.html" target="_self">mg_lvl_t</a></td><td class="desc">Lists of blocks per refinement level </td></tr>
<tr id="row_2_1_" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="structm__octree__mg__3d_1_1mg__box__t.html" target="_self">mg_box_t</a></td><td class="desc">Box data structure </td></tr>
<tr id="row_2_2_" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="structm__octree__mg__3d_1_1mg__buf__t.html" target="_self">mg_buf_t</a></td><td class="desc">Buffer type (one is used for each pair of communicating processes) </td></tr>
<tr id="row_2_3_" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="structm__octree__mg__3d_1_1mg__comm__t.html" target="_self">mg_comm_t</a></td><td class="desc"></td></tr>
<tr id="row_2_4_" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="structm__octree__mg__3d_1_1mg__bc__t.html" target="_self">mg_bc_t</a></td><td class="desc"></td></tr>
<tr id="row_2_5_" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="structm__octree__mg__3d_1_1mg__timer__t.html" target="_self">mg_timer_t</a></td><td class="desc"></td></tr>
<tr id="row_2_6_" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="structm__octree__mg__3d_1_1mg__t.html" target="_self">mg_t</a></td><td class="desc"></td></tr>
<tr id="row_2_7_" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacem__octree__mg__3d_1_1mg__subr__bc.html" target="_self">mg_subr_bc</a></td><td class="desc">To fill ghost cells near physical boundaries </td></tr>
<tr id="row_3_"><td class="entry"><span style="width:0px;display:inline-block;"> </span><span id="arr_3_" class="arrow" onclick="toggleFolder('3_')">►</span><span class="icona"><span class="icon">N</span></span><a class="el" href="namespacemod__convert.html" target="_self">mod_convert</a></td><td class="desc"></td></tr>
<tr id="row_3_0_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__convert_1_1sub__convert__vars.html" target="_self">sub_convert_vars</a></td><td class="desc"></td></tr>
<tr id="row_3_1_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="structmod__convert_1_1convert__vars__method.html" target="_self">convert_vars_method</a></td><td class="desc"></td></tr>
<tr id="row_4_" class="even"><td class="entry"><span style="width:0px;display:inline-block;"> </span><span id="arr_4_" class="arrow" onclick="toggleFolder('4_')">►</span><span class="icona"><span class="icon">N</span></span><a class="el" href="namespacemod__forest.html" target="_self">mod_forest</a></td><td class="desc">Module with basic grid data structures </td></tr>
<tr id="row_4_0_" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="structmod__forest_1_1tree__node__ptr.html" target="_self">tree_node_ptr</a></td><td class="desc">Pointer to a <a class="el" href="structmod__forest_1_1tree__node.html" title="The data structure that contains information about a tree node/grid block.">tree_node</a> </td></tr>
<tr id="row_4_1_" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="structmod__forest_1_1tree__node.html" target="_self">tree_node</a></td><td class="desc">The data structure that contains information about a tree node/grid block </td></tr>
<tr id="row_5_"><td class="entry"><span style="width:0px;display:inline-block;"> </span><span id="arr_5_" class="arrow" onclick="toggleFolder('5_')">►</span><span class="icona"><span class="icon">N</span></span><a class="el" href="namespacemod__ghostcells__update.html" target="_self">mod_ghostcells_update</a></td><td class="desc">Update ghost cells of all blocks including physical boundaries </td></tr>
<tr id="row_5_0_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="structmod__ghostcells__update_1_1wbuffer.html" target="_self">wbuffer</a></td><td class="desc"></td></tr>
<tr id="row_6_" class="even"><td class="entry"><span style="width:0px;display:inline-block;"> </span><span id="arr_6_" class="arrow" onclick="toggleFolder('6_')">►</span><span class="icona"><span class="icon">N</span></span><a class="el" href="namespacemod__multigrid__coupling.html" target="_self">mod_multigrid_coupling</a></td><td class="desc">Module to couple the octree-mg library to AMRVAC. This file uses the VACPP preprocessor, but its use is kept to a minimum </td></tr>
<tr id="row_6_0_" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__multigrid__coupling_1_1after__new__tree.html" target="_self">after_new_tree</a></td><td class="desc"></td></tr>
<tr id="row_7_"><td class="entry"><span style="width:0px;display:inline-block;"> </span><span id="arr_7_" class="arrow" onclick="toggleFolder('7_')">►</span><span class="icona"><span class="icon">N</span></span><a class="el" href="namespacemod__particle__base.html" target="_self">mod_particle_base</a></td><td class="desc">Module with shared functionality for all the particle movers </td></tr>
<tr id="row_7_0_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="structmod__particle__base_1_1particle__ptr.html" target="_self">particle_ptr</a></td><td class="desc"></td></tr>
<tr id="row_7_1_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="structmod__particle__base_1_1particle__t.html" target="_self">particle_t</a></td><td class="desc"></td></tr>
<tr id="row_7_2_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__particle__base_1_1sub__fill__gridvars.html" target="_self">sub_fill_gridvars</a></td><td class="desc"></td></tr>
<tr id="row_7_3_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__particle__base_1_1sub__define__additional__gridvars.html" target="_self">sub_define_additional_gridvars</a></td><td class="desc"></td></tr>
<tr id="row_7_4_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__particle__base_1_1sub__fill__additional__gridvars.html" target="_self">sub_fill_additional_gridvars</a></td><td class="desc"></td></tr>
<tr id="row_7_5_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__particle__base_1_1sub__integrate.html" target="_self">sub_integrate</a></td><td class="desc"></td></tr>
<tr id="row_7_6_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__particle__base_1_1fun__destroy.html" target="_self">fun_destroy</a></td><td class="desc"></td></tr>
<tr id="row_8_" class="even"><td class="entry"><span style="width:0px;display:inline-block;"> </span><span id="arr_8_" class="arrow" onclick="toggleFolder('8_')">►</span><span class="icona"><span class="icon">N</span></span><a class="el" href="namespacemod__physicaldata.html" target="_self">mod_physicaldata</a></td><td class="desc"></td></tr>
<tr id="row_8_0_" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="structmod__physicaldata_1_1state.html" target="_self">state</a></td><td class="desc"></td></tr>
<tr id="row_8_1_" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="structmod__physicaldata_1_1state__sub.html" target="_self">state_sub</a></td><td class="desc"></td></tr>
<tr id="row_8_2_" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="structmod__physicaldata_1_1grid__field.html" target="_self">grid_field</a></td><td class="desc"></td></tr>
<tr id="row_8_3_" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="structmod__physicaldata_1_1ct__velocity.html" target="_self">ct_velocity</a></td><td class="desc">Velocities store for constrained transport </td></tr>
<tr id="row_9_"><td class="entry"><span style="width:0px;display:inline-block;"> </span><span id="arr_9_" class="arrow" onclick="toggleFolder('9_')">►</span><span class="icona"><span class="icon">N</span></span><a class="el" href="namespacemod__physics.html" target="_self">mod_physics</a></td><td class="desc">This module defines the procedures of a physics module. It contains function pointers for the various supported routines. An actual physics module has to set these pointers to its implementation of these routines </td></tr>
<tr id="row_9_0_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__physics_1_1sub__check__params.html" target="_self">sub_check_params</a></td><td class="desc"></td></tr>
<tr id="row_9_1_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__physics_1_1sub__set__mg__bounds.html" target="_self">sub_set_mg_bounds</a></td><td class="desc"></td></tr>
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<tr id="row_9_18_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__physics_1_1sub__clean__divb.html" target="_self">sub_clean_divb</a></td><td class="desc">Clean initial divb </td></tr>
<tr id="row_9_19_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__physics_1_1sub__set__equi__vars.html" target="_self">sub_set_equi_vars</a></td><td class="desc">Set equilibrium variables other than b0 (e.g. p0 and rho0) </td></tr>
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<tr id="row_10_3_" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__physics__hllc_1_1sub__hllc__init__species.html" target="_self">sub_hllc_init_species</a></td><td class="desc"></td></tr>
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<tr id="row_11_0_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__physics__roe_1_1sub__average.html" target="_self">sub_average</a></td><td class="desc"></td></tr>
<tr id="row_11_1_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__physics__roe_1_1sub__get__eigenjump.html" target="_self">sub_get_eigenjump</a></td><td class="desc"></td></tr>
<tr id="row_11_2_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__physics__roe_1_1sub__rtimes.html" target="_self">sub_rtimes</a></td><td class="desc"></td></tr>
<tr id="row_12_" class="even"><td class="entry"><span style="width:0px;display:inline-block;"> </span><span id="arr_12_" class="arrow" onclick="toggleFolder('12_')">►</span><span class="icona"><span class="icon">N</span></span><a class="el" href="namespacemod__radiative__cooling.html" target="_self">mod_radiative_cooling</a></td><td class="desc">Module radiative cooling – add optically thin radiative cooling for HD and MHD </td></tr>
<tr id="row_12_0_" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__radiative__cooling_1_1get__subr1.html" target="_self">get_subr1</a></td><td class="desc"></td></tr>
<tr id="row_12_1_" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="structmod__radiative__cooling_1_1rc__fluid.html" target="_self">rc_fluid</a></td><td class="desc"></td></tr>
<tr id="row_13_"><td class="entry"><span style="width:0px;display:inline-block;"> </span><span id="arr_13_" class="arrow" onclick="toggleFolder('13_')">►</span><span class="icona"><span class="icon">N</span></span><a class="el" href="namespacemod__supertimestepping.html" target="_self">mod_supertimestepping</a></td><td class="desc">Generic supertimestepping method 1) in amrvac.par in sts_list set the following parameters which have the default values: sts_dtpar=0.9,sts_ncycles=1000,sts_method=1,sourcetype_sts=2 These parametes are general for all the methods added TODO: check if there is any need to have terms implemented with different sets of parameters, and these cannot be general anymore 2) then add programatically in the code a term with the subroutine add_sts_method This method takes as parameters a function which calculated the explicit timestep associated with the term, a subroutine which sets the source term types for the BC and the BC are generated from the variables startVar:endVar flux conservation (fixconserve) is done for the variables specified by ixChangeStart, ixChangeN, ixChangeFixC The following two steps are done in this way as in fortran it is not allowed to pass null function pointers as parameters: 3)in order to to have hooks before_first_cycle, after_last_cycle (e.g. conversion from e_tot to e_int before first sts cycle and back from e_int to e_tot after the last STS cycle for the thermal conductivity module) add them just afterwards with the subroutine set_conversion_methods_to_head 4) to add the hook for error handling (e.g check small values in the thermal conductivity module ) call set_error_handling_to_head which takes as parameter a subroutine the error handling subroutine is called before setting BC </td></tr>
<tr id="row_13_0_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__supertimestepping_1_1subr2.html" target="_self">subr2</a></td><td class="desc">Interface for the function which gets the timestep in dtnew in the derived type </td></tr>
<tr id="row_13_1_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__supertimestepping_1_1subr__e.html" target="_self">subr_e</a></td><td class="desc">Interface for error handling subroutine in the derived type </td></tr>
<tr id="row_13_2_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__supertimestepping_1_1subr5.html" target="_self">subr5</a></td><td class="desc">Interface for the subroutines before_first_cycle and after_last_cycle in the derived type </td></tr>
<tr id="row_13_3_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__supertimestepping_1_1subr3.html" target="_self">subr3</a></td><td class="desc">For the subroutines in this module, which do not depend on the term, but on the parameter sts_method = 1/2 in the parameter file sts_add_source </td></tr>
<tr id="row_14_" class="even"><td class="entry"><span style="width:0px;display:inline-block;"> </span><span id="arr_14_" class="arrow" onclick="toggleFolder('14_')">►</span><span class="icona"><span class="icon">N</span></span><a class="el" href="namespacemod__thermal__conduction.html" target="_self">mod_thermal_conduction</a></td><td class="desc">Thermal conduction for HD and MHD or RHD and RMHD or twofl (plasma-neutral) module Adaptation of <a class="el" href="namespacemod__thermal__conduction.html" title="Thermal conduction for HD and MHD or RHD and RMHD or twofl (plasma-neutral) module Adaptation of mod_...">mod_thermal_conduction</a> for the <a class="el" href="namespacemod__supertimestepping.html" title="Generic supertimestepping method 1) in amrvac.par in sts_list set the following parameters which have...">mod_supertimestepping</a> </td></tr>
<tr id="row_14_0_" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__thermal__conduction_1_1get__var__subr.html" target="_self">get_var_subr</a></td><td class="desc"></td></tr>
<tr id="row_14_1_" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="structmod__thermal__conduction_1_1tc__fluid.html" target="_self">tc_fluid</a></td><td class="desc"></td></tr>
<tr id="row_15_"><td class="entry"><span style="width:0px;display:inline-block;"> </span><span id="arr_15_" class="arrow" onclick="toggleFolder('15_')">►</span><span class="icona"><span class="icon">N</span></span><a class="el" href="namespacemod__thermal__emission.html" target="_self">mod_thermal_emission</a></td><td class="desc"></td></tr>
<tr id="row_15_0_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__thermal__emission_1_1get__subr1.html" target="_self">get_subr1</a></td><td class="desc"></td></tr>
<tr id="row_15_1_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="structmod__thermal__emission_1_1te__fluid.html" target="_self">te_fluid</a></td><td class="desc"></td></tr>
<tr id="row_16_" class="even"><td class="entry"><span style="width:0px;display:inline-block;"> </span><span id="arr_16_" class="arrow" onclick="toggleFolder('16_')">►</span><span class="icona"><span class="icon">N</span></span><a class="el" href="namespacemod__twofl__phys.html" target="_self">mod_twofl_phys</a></td><td class="desc">Magneto-hydrodynamics module </td></tr>
<tr id="row_16_0_" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__twofl__phys_1_1mask__subroutine2.html" target="_self">mask_subroutine2</a></td><td class="desc"></td></tr>
<tr id="row_17_"><td class="entry"><span style="width:0px;display:inline-block;"> </span><span id="arr_17_" class="arrow" onclick="toggleFolder('17_')">►</span><span class="icona"><span class="icon">N</span></span><a class="el" href="namespacemod__usr__methods.html" target="_self">mod_usr_methods</a></td><td class="desc">Module with all the methods that users can customize in AMRVAC </td></tr>
<tr id="row_17_0_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__usr__methods_1_1p__no__args.html" target="_self">p_no_args</a></td><td class="desc"></td></tr>
<tr id="row_17_1_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__usr__methods_1_1init__one__grid.html" target="_self">init_one_grid</a></td><td class="desc">Initialize one grid </td></tr>
<tr id="row_17_2_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__usr__methods_1_1special__bc.html" target="_self">special_bc</a></td><td class="desc">Special boundary types, users must assign conservative variables in boundaries </td></tr>
<tr id="row_17_3_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__usr__methods_1_1special__mg__bc.html" target="_self">special_mg_bc</a></td><td class="desc">Special boundary type for radiation hydrodynamics module, only used to set the boundary conditions for the radiation energy </td></tr>
<tr id="row_17_4_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__usr__methods_1_1internal__bc.html" target="_self">internal_bc</a></td><td class="desc">Internal boundary, user defined This subroutine can be used to artificially overwrite ALL conservative variables in a user-selected region of the mesh, and thereby act as an internal boundary region. It is called just before external (ghost cell) boundary regions will be set by the BC selection. Here, you could e.g. want to introduce an extra variable (nwextra, to be distinguished from nwaux) which can be used to identify the internal boundary region location. Its effect should always be local as it acts on the mesh </td></tr>
<tr id="row_17_5_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__usr__methods_1_1process__grid.html" target="_self">process_grid</a></td><td class="desc">This subroutine is ONLY to be used for computing auxiliary variables which happen to be non-local (like div v), and are in no way used for flux computations. As auxiliaries, they are also not advanced </td></tr>
<tr id="row_17_6_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__usr__methods_1_1sub__modify__io.html" target="_self">sub_modify_io</a></td><td class="desc">If defined, this routine is called before writing output, and it can set/modify the variables in the w array </td></tr>
<tr id="row_17_7_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__usr__methods_1_1process__global.html" target="_self">process_global</a></td><td class="desc">This subroutine is called at the beginning of each time step by each processor. No communication is specified, so the user has to implement MPI routines if information has to be shared </td></tr>
<tr id="row_17_8_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__usr__methods_1_1process__adv__grid.html" target="_self">process_adv_grid</a></td><td class="desc">For processing after the advance (PIC-MHD, e.g.) </td></tr>
<tr id="row_17_9_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__usr__methods_1_1process__adv__global.html" target="_self">process_adv_global</a></td><td class="desc">For processing after the advance (PIC-MHD, e.g.) </td></tr>
<tr id="row_17_10_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__usr__methods_1_1aux__output.html" target="_self">aux_output</a></td><td class="desc">This subroutine can be used in convert, to add auxiliary variables to the converted output file, for further analysis using tecplot, paraview, .... these auxiliary values need to be stored in the nw+1:nw+nwauxio slots </td></tr>
<tr id="row_17_11_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__usr__methods_1_1add__aux__names.html" target="_self">add_aux_names</a></td><td class="desc">Add names for the auxiliary variables </td></tr>
<tr id="row_17_12_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__usr__methods_1_1source.html" target="_self">source</a></td><td class="desc">Calculate w(iw)=w(iw)+qdt*SOURCE[wCT,qtC,x] within ixO for all indices iw=iwmin...iwmax. wCT is at time qCT </td></tr>
<tr id="row_17_13_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__usr__methods_1_1get__dt.html" target="_self">get_dt</a></td><td class="desc">Limit "dt" further if necessary, e.g. due to the special source terms. The getdt_courant (CFL condition) and the getdt subroutine in the AMRVACPHYS module have already been called </td></tr>
<tr id="row_17_14_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__usr__methods_1_1phys__gravity.html" target="_self">phys_gravity</a></td><td class="desc">Calculate gravitational acceleration in each dimension </td></tr>
<tr id="row_17_15_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__usr__methods_1_1phys__dust__get__3d__dragforce.html" target="_self">phys_dust_get_3d_dragforce</a></td><td class="desc">Calculate the 3d drag force of gas onto dust </td></tr>
<tr id="row_17_16_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__usr__methods_1_1phys__dust__get__dt.html" target="_self">phys_dust_get_dt</a></td><td class="desc">Calculate the time step associated with the usr drag force </td></tr>
<tr id="row_17_17_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__usr__methods_1_1phys__visco.html" target="_self">phys_visco</a></td><td class="desc">Calculation anormal viscosity depending on space </td></tr>
<tr id="row_17_18_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__usr__methods_1_1hd__pthermal.html" target="_self">hd_pthermal</a></td><td class="desc">Calculation anormal pressure for hd & energy=.False </td></tr>
<tr id="row_17_19_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__usr__methods_1_1Rfactor.html" target="_self">Rfactor</a></td><td class="desc">Calculation R factor for ideal gas law with partial ionization </td></tr>
<tr id="row_17_20_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__usr__methods_1_1special__resistivity.html" target="_self">special_resistivity</a></td><td class="desc">Set the "eta" array for resistive MHD based on w or the "current" variable which has components between idirmin and 3 </td></tr>
<tr id="row_17_21_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__usr__methods_1_1special__opacity.html" target="_self">special_opacity</a></td><td class="desc">Set user defined opacity for use in diffusion coeff, heating and cooling, and radiation force </td></tr>
<tr id="row_17_22_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__usr__methods_1_1special__aniso__opacity.html" target="_self">special_aniso_opacity</a></td><td class="desc">Set user defined, anisotropic opacity for use in diffusion coeff, heating and cooling, and radiation force </td></tr>
<tr id="row_17_23_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__usr__methods_1_1special__opacity__qdot.html" target="_self">special_opacity_qdot</a></td><td class="desc">Set user defined opacity for use in diffusion coeff, heating and cooling, and radiation force. Overwrites <a class="el" href="interfacemod__usr__methods_1_1special__opacity.html" title="Set user defined opacity for use in diffusion coeff, heating and cooling, and radiation force.">special_opacity</a> </td></tr>
<tr id="row_17_24_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__usr__methods_1_1special__fluxlimiter.html" target="_self">special_fluxlimiter</a></td><td class="desc">Set user defined FLD flux limiter, lambda </td></tr>
<tr id="row_17_25_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__usr__methods_1_1special__diffcoef.html" target="_self">special_diffcoef</a></td><td class="desc">Set user defined FLD diffusion coefficient </td></tr>
<tr id="row_17_26_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__usr__methods_1_1refine__grid.html" target="_self">refine_grid</a></td><td class="desc">Enforce additional refinement or coarsening One can use the coordinate info in x and/or time qt=t_n and w(t_n) values w. you must set consistent values for integers refine/coarsen: refine = -1 enforce to not refine refine = 0 doesn't enforce anything refine = 1 enforce refinement coarsen = -1 enforce to not coarsen coarsen = 0 doesn't enforce anything coarsen = 1 enforce coarsen e.g. refine for negative first coordinate x < 0 as if (any(x(ix^S,1) < zero)) refine=1 </td></tr>
<tr id="row_17_27_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__usr__methods_1_1var__for__errest.html" target="_self">var_for_errest</a></td><td class="desc">This is the place to compute a local auxiliary variable to be used as refinement criterion for the Lohner error estimator only -->it is then requiring and iflag>nw note that ixO=ixI=ixG, hence the term local (gradients need special attention!) </td></tr>
<tr id="row_17_28_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__usr__methods_1_1set__B0.html" target="_self">set_B0</a></td><td class="desc">Here one can add a steady (time-independent) potential background field </td></tr>
<tr id="row_17_29_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__usr__methods_1_1set__J0.html" target="_self">set_J0</a></td><td class="desc">Here one can add a time-independent background current density </td></tr>
<tr id="row_17_30_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__usr__methods_1_1set__equi__vars.html" target="_self">set_equi_vars</a></td><td class="desc">Here one can add a steady (time-independent) equi vars </td></tr>
<tr id="row_17_31_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__usr__methods_1_1transform__w.html" target="_self">transform_w</a></td><td class="desc">Adjust w when restart from dat file with different w variables </td></tr>
<tr id="row_17_32_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__usr__methods_1_1a__refine__threshold.html" target="_self">a_refine_threshold</a></td><td class="desc">Use different threshold in special regions for AMR to reduce/increase resolution there where nothing/something interesting happens </td></tr>
<tr id="row_17_33_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__usr__methods_1_1special__convert.html" target="_self">special_convert</a></td><td class="desc">Allow user to use their own data-postprocessing procedures </td></tr>
<tr id="row_17_34_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__usr__methods_1_1flag__grid.html" target="_self">flag_grid</a></td><td class="desc">Flag=-1 : Treat all cells active, omit deactivation (onentry, default) flag=0 : Treat as normal domain flag=1 : Treat as passive, but reduce by safety belt flag=2 : Always treat as passive </td></tr>
<tr id="row_17_35_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__usr__methods_1_1update__payload.html" target="_self">update_payload</a></td><td class="desc">Update payload of particles </td></tr>
<tr id="row_17_36_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__usr__methods_1_1create__particles.html" target="_self">create_particles</a></td><td class="desc">Create particles </td></tr>
<tr id="row_17_37_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__usr__methods_1_1check__particle.html" target="_self">check_particle</a></td><td class="desc">Check arbitrary particle conditions or modifications </td></tr>
<tr id="row_17_38_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__usr__methods_1_1particle__fields.html" target="_self">particle_fields</a></td><td class="desc">Associate fields to particle </td></tr>
<tr id="row_17_39_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__usr__methods_1_1particle__analytic.html" target="_self">particle_analytic</a></td><td class="desc"></td></tr>
<tr id="row_17_40_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__usr__methods_1_1particle__position.html" target="_self">particle_position</a></td><td class="desc">User-defined particle movement </td></tr>
<tr id="row_17_41_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__usr__methods_1_1after__refine.html" target="_self">after_refine</a></td><td class="desc"></td></tr>
<tr id="row_17_42_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__usr__methods_1_1init__vector__potential.html" target="_self">init_vector_potential</a></td><td class="desc">Initialize vector potential on cell edges for magnetic field </td></tr>
<tr id="row_17_43_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__usr__methods_1_1set__electric__field.html" target="_self">set_electric_field</a></td><td class="desc"></td></tr>
<tr id="row_17_44_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__usr__methods_1_1set__wLR.html" target="_self">set_wLR</a></td><td class="desc">Allow user to specify 'variables' left and right state at physical boundaries to control flux through the boundary surface </td></tr>
<tr id="row_17_45_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__usr__methods_1_1set__surface.html" target="_self">set_surface</a></td><td class="desc"></td></tr>
<tr id="row_17_46_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__usr__methods_1_1set__field__w.html" target="_self">set_field_w</a></td><td class="desc"></td></tr>
<tr id="row_17_47_" class="even" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="interfacemod__usr__methods_1_1set__field.html" target="_self">set_field</a></td><td class="desc"></td></tr>
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