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MPI-AMRVAC
3.1
The MPI - Adaptive Mesh Refinement - Versatile Advection Code
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| ►Nm_octree_mg_1d | |
| ►Nm_octree_mg_2d | |
| ►Nm_octree_mg_3d | |
| Nmod_advance | Module containing all the time stepping schemes |
| Nmod_afld | Module for including anisotropic flux limited diffusion (AFLD)-approximation in Radiation-hydrodynamics simulations using mod_rhd Based on Turner and stone 2001. See [1]Moens, N., Sundqvist, J. O., El Mellah, I., Poniatowski, L., Teunissen, J., and Keppens, R., “Radiation-hydrodynamics with MPI-AMRVAC . Flux-limited diffusion”, Astronomy and Astrophysics, vol. 657, 2022. doi:10.1051/0004-6361/202141023. For more information |
| Nmod_amr_fct | |
| Nmod_amr_grid | |
| Nmod_amr_neighbors | |
| Nmod_amr_solution_node | |
| Nmod_amrvac | This module contains modules that users could want to have in their mod_usr.t code, so that they don't have to include them individually |
| Nmod_ard | Module activating the advection-reaction-diffusion equation module |
| Nmod_ard_phys | Module containing the physics routines for advection-reaction-diffusion equations |
| Nmod_b0 | |
| Nmod_basic_types | Module with basic data types used in amrvac |
| Nmod_bc_data | Module to set boundary conditions from user data |
| Nmod_boundary_conditions | |
| Nmod_bremsstrahlung | |
| Nmod_cak_force | Module to include CAK radiation line force in (magneto)hydrodynamic models Computes both the force from free electrons and the force from an ensemble of lines (various possibilities for the latter). There is an option to only simulate the pure radial CAK force (with various corrections applied) as well as the full vector CAK force. Depending on the chosen option additional output are the CAK line force component(s) and, when doing a 1-D radial force, the finite disc factor |
| Nmod_cak_opacity | This module reads in CAK line opacities in the Gayley (1995) notation (alpha, Qbar, Q0, kappae) from corresponding tables. Tabulated values assume LTE conditions and are a function of mass density (D) and temperature (T), which are both given in base 10 logarithm. The construction of the tables is outlined in Poniatowski+ (2021), A&A, 667 |
| Nmod_calculate_xw | Handles computations for coordinates and variables in output |
| Nmod_coarsen | |
| Nmod_coarsen_refine | Module to coarsen and refine grids for AMR |
| Nmod_collapse | Collapses D-dimensional output to D-1 view by line-of-sight integration |
| Nmod_comm_lib | |
| Nmod_con2prim_vars | |
| Nmod_config | Module that allows working with a configuration file |
| Nmod_connectivity | This module contains variables that describe the connectivity of the mesh and also data structures for connectivity-related communication |
| Nmod_constants | Module for physical and numeric constants |
| Nmod_constrained_transport | |
| ►Nmod_convert | |
| Nmod_convert_files | |
| Nmod_dipole | Sets up a magnetic dipole in a 3D cartesian box |
| Nmod_dt | |
| Nmod_dust | Module for including dust species, which interact with the gas through a drag force |
| Nmod_errest | |
| Nmod_finite_difference | Module with finite difference methods for fluxes |
| Nmod_finite_volume | Module with finite volume methods for fluxes |
| Nmod_fix_conserve | Module for flux conservation near refinement boundaries |
| Nmod_fld | Nicolas Moens Module for including flux limited diffusion (FLD)-approximation in Radiation-hydrodynamics simulations using mod_rhd Based on Turner and stone 2001. See [1]Moens, N., Sundqvist, J. O., El Mellah, I., Poniatowski, L., Teunissen, J., and Keppens, R., “Radiation-hydrodynamics with MPI-AMRVAC . Flux-limited diffusion”, Astronomy and Astrophysics, vol. 657, 2022. doi:10.1051/0004-6361/202141023. For more information |
| ►Nmod_forest | Module with basic grid data structures |
| Nmod_functions_bfield | |
| Nmod_functions_connectivity | |
| Nmod_functions_forest | |
| Nmod_geometry | Module with geometry-related routines (e.g., divergence, curl) |
| ►Nmod_ghostcells_update | Update ghost cells of all blocks including physical boundaries |
| Nmod_global_parameters | This module contains definitions of global parameters and variables and some generic functions/subroutines used in AMRVAC |
| Nmod_gravity | Module for including gravity in (magneto)hydrodynamics simulations |
| Nmod_hd | Module containing all hydrodynamics |
| Nmod_hd_hllc | Hydrodynamics HLLC module |
| Nmod_hd_phys | Hydrodynamics physics module |
| Nmod_hd_roe | Module with Roe-type Riemann solver for hydrodynamics |
| Nmod_hyperdiffusivity | Subroutines for Roe-type Riemann solver for HD |
| Nmod_init_datafromfile | Module to set (or derive) initial conditions from user data We read in a vtk file that provides values on grid |
| Nmod_initialize | This module handles the initialization of various components of amrvac |
| Nmod_initialize_amr | |
| Nmod_input_output | Module for reading input and writing output |
| Nmod_input_output_helper | |
| Nmod_interpolation | |
| Nmod_ionization_degree | Module ionization degree - get ionization degree for given temperature |
| Nmod_kdv | Module for including kdv source term in simulations adds \(-\delta^2*\sum_i \partial_{iii} \rho \) over dimensions i |
| Nmod_lfff | Program to extrapolate linear force-free fields in 3D Cartesian coordinates, based on exact Green function method (Chiu & Hilton 1977 ApJ 212,873) |
| Nmod_limiter | Module with slope/flux limiters |
| Nmod_load_balance | |
| Nmod_lookup_table | A Fortran 90 module for creating 1D and 2D lookup tables. These tables can be used to efficiently interpolate one or more values |
| Nmod_lu | |
| Nmod_magnetofriction | Module mod_magnetofriction.t Purpose: use magnetofrictional method to relax 3D magnetic field to force-free field 01.04.2016 developed by Chun Xia and Yang Guo 04.10.2017 modulized by Chun Xia Usage: in amrvac.par: &methodlist time_stepper='onestep' ! time marching scheme, or 'twostep','threestep' flux_method=13*'cd4' ! or 'tvdlf', 'fd' limiter= 13*'koren' ! or 'vanleer','cada3','mp5' so on / &meshlist ditregrid=20 ! set iteration interval for adjusting AMR / &mhd_list mhd_magnetofriction=.true. / &mf_list mf_it_max=60000 ! set the maximum iteration number mf_ditsave=20000 ! set iteration interval for data output mf_cc=0.3 ! stability coefficient controls numerical stability mf_cy=0.2 ! frictional velocity coefficient mf_cdivb=0.01 ! divb cleaning coefficient controls diffusion speed of divb / |
| Nmod_mf | |
| Nmod_mf_phys | Magnetofriction module |
| Nmod_mhd | |
| Nmod_mhd_hllc | |
| ►Nmod_mhd_phys | Magneto-hydrodynamics module |
| Nmod_mhd_roe | Subroutines for Roe-type Riemann solver for MHD |
| Nmod_mp5 | Module containing the MP5 (fifth order) flux scheme |
| ►Nmod_multigrid_coupling | Module to couple the octree-mg library to AMRVAC. This file uses the VACPP preprocessor, but its use is kept to a minimum |
| Nmod_nonlinear | Module activating the nonlinear scalar equation module allowing to solve Burgers, nonconvex, and KdV equations |
| Nmod_nonlinear_phys | Module containing the physics routines for scalar nonlinear equation |
| Nmod_nonlinear_roe | Module containing Roe solver for scalar nonlinear equation |
| Nmod_odeint | This module packages odeint from numerical recipes |
| Nmod_oneblock | |
| Nmod_opal_opacity | This module reads in Rosseland-mean opacities from OPAL tables. Table opacity values are given in base 10 logarithm and are a function of mass density (R) and temperature (T), which are also both given in base 10 logarithm |
| Nmod_particle_advect | Tracer for advected particles moving with fluid flows By Jannis Teunissen, Bart Ripperda, Oliver Porth, and Fabio Bacchini (2017-2020) |
| ►Nmod_particle_base | Module with shared functionality for all the particle movers |
| Nmod_particle_gca | Particle mover with Newtonian/relativistic Guiding Center Approximation (GCA) By Jannis Teunissen, Bart Ripperda, Oliver Porth, and Fabio Bacchini (2016-2020) |
| Nmod_particle_lorentz | Particle mover with Newtonian/relativistic Boris scheme for Lorentz dynamics By Jannis Teunissen, Bart Ripperda, Oliver Porth, and Fabio Bacchini (2016-2020) |
| Nmod_particle_sample | Scattered sampling based on fixed- or moving-particle interpolation By Fabio Bacchini (2020) |
| Nmod_particles | Module containing all the particle routines |
| Nmod_pfss | Module mod_pfss.t – potential field source surface model PURPOSE : to extrapolate global potential magnetic field of the sun from synoptic magnetograms 2013.11.04 Developed by S. Moschou and C. Xia 2014.04.01 Allow to change source surface (C. Xia) PRECONDITIONS: |
| ►Nmod_physicaldata | |
| ►Nmod_physics | 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 |
| ►Nmod_physics_hllc | |
| ►Nmod_physics_roe | |
| Nmod_point_searching | |
| Nmod_ppm | |
| ►Nmod_radiative_cooling | Module radiative cooling – add optically thin radiative cooling for HD and MHD |
| Nmod_random | Module for pseudo random number generation. The internal pseudo random generator is the xoroshiro128plus method |
| Nmod_random_heating | |
| Nmod_rbsl | To get a RBSL magnetic flux rope in 3D (Titov 2018 ApJL 852, L21) |
| Nmod_rd | Module containing all routines for reaction-diffusion |
| Nmod_rd_phys | Reaction-diffusion module (physics routines) |
| Nmod_refine | |
| Nmod_rhd | Module containing all hydrodynamics |
| Nmod_rhd_hllc | Hydrodynamics HLLC module |
| Nmod_rhd_phys | Radiation-Hydrodynamics physics module Module aims at solving the Hydrodynamic equations toghether with the zeroth moment of the radiative transfer equation. A closure is provided by the flux limited diffusion (FLD)-approximation in the mod_fld.t module. See [1]Moens, N., Sundqvist, J. O., El Mellah, I., Poniatowski, L., Teunissen, J., and Keppens, R., “Radiation-hydrodynamics with MPI-AMRVAC . Flux-limited diffusion”, Astronomy and Astrophysics, vol. 657, 2022. doi:10.1051/0004-6361/202141023. For more information. Another possible closure in the works is the anisotropic flux limited diffusion approximation (AFLD) described in mod_afld.t |
| Nmod_rhd_roe | Module with Roe-type Riemann solver for hydrodynamics |
| Nmod_rho | Module containing all routines for scalar advection |
| Nmod_rho_phys | Module containing the physics routines for scalar advection |
| Nmod_rho_roe | Module containing Roe solver for scalar advection |
| Nmod_rotating_frame | Module for including rotating frame in (magneto)hydrodynamics simulations The rotation vector is assumed to be along z direction (both in cylindrical and spherical) |
| Nmod_selectgrids | |
| Nmod_slice | Writes D-1 slice, can do so in various formats, depending on slice_type |
| Nmod_small_values | Module for handling problematic values in simulations, such as negative pressures |
| Nmod_solar_atmosphere | User can use subroutine get_atm_para to generate 1D solar stmosphere. User should provide heights (h), number density at h=0, number of points (nh), and the gravity (grav) at each point. User can select temperature profile. This subroutine will return density and pressure at each point |
| Nmod_source | Module for handling split source terms (split from the fluxes) |
| Nmod_space_filling_curve | |
| Nmod_srhd | Module containing all special relativistic hydrodynamics (with EOS) |
| Nmod_srhd_phys | Special Relativistic Hydrodynamics (with EOS) physics module |
| ►Nmod_supertimestepping | 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 |
| Nmod_tdfluxrope | |
| ►Nmod_thermal_conduction | Thermal conduction for HD and MHD Adaptation of mod_thermal_conduction for the mod_supertimestepping In order to use it set use_mhd_tc=1 (for the mhd impl) or 2 (for the hd impl) in mhd_list (for the mhd module both hd and mhd impl can be used) or use_new_hd_tc in hd_list parameters to true (for the hd module, hd implementation has to be used) The TC is set by calling one tc_init_hd_for_total_energy and tc_init_mhd_for_total_energy might The second argument: ixArray has to be [rho_,e_,mag(1)] for mhd (Be aware that the other components of the mag field are assumed consecutive) and [rho_,e_] for hd additionally when internal energy equation is solved, an additional element of this array is eaux_: the index of the internal energy variable |
| ►Nmod_thermal_emission | |
| Nmod_timing | |
| Nmod_trac | |
| Nmod_trace_field | |
| Nmod_tvd | Subroutines for TVD-MUSCL schemes |
| Nmod_twofl | |
| Nmod_twofl_hllc | |
| ►Nmod_twofl_phys | Magneto-hydrodynamics module |
| Nmod_twofl_roe | Subroutines for Roe-type Riemann solver for HD |
| ►Nmod_usr_methods | Module with all the methods that users can customize in AMRVAC |
| Nmod_variables | |
| Nmod_venk | |
| Nmod_viscosity | The module add viscous source terms and check time step |
| Nmod_weno |
1.9.1