Fortran modules

Currently, the Pencil Code contains 547 Fortran files.

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Main source files (src)

The src directory contains 321 Fortran files.

File	Description	Scientific References
ascalar	This module is used to solve the equation of supersaturation for either the Smoluchowski approach or the swarm model.
bfield	This module directly evolves the magnetic field instead of the vector potential; special care needs to be taken to guarantee the divergence of the field remains zero.
border_profiles
boundcond	Module for boundary conditions. Extracted from (no)mpicomm, since all non-periodic (external) boundary conditions require the same code for serial and parallel runs.
boundcond_alt	Module for boundary conditions. Extracted from (no)mpicomm, since all non-periodic (external) boundary conditions require the same code for serial and parallel runs.
cdata	Global variables are defined in this module.
chemistry	This modules adds chemical species and reactions. The units used in the chem.in files are cm3,mole,sec,kcal and K
chemistry_simple	! This modules addes chemical species and reactions. The units used in the chem.in files are cm3,mole,sec,kcal and K This was found out by comparing the mechanism found in samples/0D/chemistry_H2_ignition_delay with Flow Reactor Studies and Kinetic Modeling of the ReactionH/O22 of A. MUELLER, T. J. KIM, R. A. YETTER, F. L. DRYER
chiral	This modules solves two reactive scalar advection equations This is used for modeling the spatial evolution of left and right handed aminoacids.	Vachaspati & Brandenburg (2025) Brandenburg & Multamäki (2004)
combine_videofiles	Not a module
cosmicray	This modules solves the cosmic ray energy density equation. It follows the description of Hanasz & Lesch (2002,2003) as used in their ZEUS 3D implementation.
cosmicray_nolog	This modules solves the cosmic ray energy density equation. It follows the description of Hanasz & Lesch (2002,2003) as used in their ZEUS 3D implementation.
cosmicrayflux	Module for calculating Cosmic Ray Flux.
cparam	Module containing global parameters (constants).
debug_io_dist	Distributed debug-IO (i.e. each process writes its own file data/procX)
debug_io_hdf5	HDF5 debug-IO module
debug_io_mpi	Parallel debug-IO via MPI2 (i.e. write to a single file in data/allprocs)
density	This module takes care of the continuity equation.
density_bcs
density_methods	11-mar-15/MR: Created to avoid circular dependencies with EquationOfState.
density_stratified
density_stratified_methods	Dummy module for density_stratified, with which all density queries should be done in EquationOfState.
deriv
deriv_10th
deriv_2nd
deriv_2nd_all	This module is a copy of the ‘deriv_2nd’ module, but implements all derivatives, including up to 6th order, with 2nd order accuracy. In ‘deriv_2nd’ the 3rd or higher derivatives are otherwise unavailable. To provide higher derivatives in this module, nghost must be 3.
deriv_4th
deriv_4th_all	This module is a copy of the ‘deriv_4th’ module, but implements all derivatives, including up to 6th order, with 4th order accuracy. In ‘deriv_4th’ the 5th or higher derivatives are otherwise unavailable. To provide higher derivatives in this module, nghost must be 4.
deriv_8th
deriv_alt
detonate	This module searches for gravitationally collapsing sites and detonates them.
diagnostics
diagnostics_outlog
dustdensity	This module takes care of everything related to dust density.
dustvelocity	This module takes care of everything related to dust velocity	Johansen et al. (2004) Haugen et al. (2022)
emulated	Module emulating not universally available intrinsics
entropy	This module takes care of evolving the entropy.
entropy_bcs
entropy_const	This module is for systems with spatially fixed entropy distribution. This implies Ds/Dt=u.grads only, which is used in Ds/Dt=(1/gamma)*Dlnp/Dt-Dlnrho/Dt, for example. This procedure has been used in the context of accretion discs (see von Rekowski et al., 2003, A&A 398, 825). The shock jump relations are modified (see Sect 9.3.6 of Brandenburg 2003, in “Computational aspects…”, ed. Ferriz-Mas & Nunez, Taylor & Francis, or astro-ph/0109497.
entropy_onefluid	This module takes care of entropy (initial condition and time advance) for a fluid consisting of gas and perfectly coupled pressureless dust.
eos_chemistry	Equation of state for an ideal gas without ionization.
eos_chemistry_simple	Equation of state for an ideal gas without ionization.
eos_fixed_ionization	Thermodynamics with Fixed ionization fraction
eos_idealgas	Equation of state for an ideal gas without ionization.
eos_ionization	This modules contains the routines for simulation with simple hydrogen ionization.
eos_temperature_ionization	Routine for ideal gas with variable degree of ionization and hence variable mean molecular weight. Here, the ionization fraction, yH, is allocated as an additional auxiliary array in f.
equ	subroutines in the chosen set of physics modules.
farray	This module allocates and manages indices in the f-array in a controlled way. This includes handling different types of variable that may be stored in the f-array like PDE variables, auxiliaries, communicated auxiliaries and global variables.
farray_alloc	Dynamical allocation of f and df.
fft_nr	Not a module
fftpack	Not a module
file_io_common	This module holds only common standard code for all File-IO modules. It is NOT meant to be used as a replacement for the other File-IO modules!
file_io_dist	This module goes straight and implements distributed file Input/Output. We use here only F95 features and are explicitly not HPC-friendly.
file_io_f2003	This module goes straight and implements distributed file Input/Output. We use here only F2003 features (HPC-friendly).
file_io_f95	This module takes care of massive parallel file Input/Output. We use here only F95 features for HPC-friendly behaviour.
filter	Filters for smoothing, removing trends (like spurious build-up of horizontal momentum) and similar.
fixed_point	Find the fixed points of a field line mapping. Field line mappings are maps of F(x,y) through field lines which trace point at z = z0 to z = z1. Fixed points are such that F(x,y) = (x,y)
forcing	This module contains routines both for delta-correlated and continuous forcing. The fcont pencil is only provided for continuous forcing.
fourier_fft	This module contains FFT wrapper subroutines.
fourier_fftpack	This module contains FFT wrapper subroutines.
general	Module with general utility subroutines.
geometrical_types	Collection of geometrical object types. (Presently only rectangular toroid)
ghost_check	This module tests the ghost zones consistency. For more documentation about the ghost zones, please refer to Mpicomm.f90.
ghostfold_mpicomm	This module folds ghost zones for a multiple processor run.
ghostfold_nompicomm	This module folds ghost zones for a single processor run.
global_pushpars
gpu_astaroth	This module contains GPU related types and functions to be used with the ASTAROTH nucleus.
gravity_r	Radial gravity
gravity_simple	This module takes care of simple types of gravity, i.e. where gx=gx(x) or gy=gy(y) or gz=gz(z) Here the gravity master pencils gravx_xpencil, gravy_ypencil and gravz_zpencil only need to be calculated once, and then these can simply be added to the equations of motion again and again.
grid
hdf5_io_parallel	This module takes care of massive parallel HDF5 file Input/Output. We use here only F95 and MPI features for HPC-friendly behaviour.
hdf5_io_parallel_chunked	This module takes care of massive parallel HDF5 file Input/Output. We use here only F95 and MPI features for HPC-friendly behaviour.
heatflux	This module computes the time depentend heat flux equation. The non-Fourier form is written tau * dq/dt + q = F(T,rho …) The analytical solution for constant F is that q converges exponential to F with a time scale of tau.
hydro	This module takes care of most of the things related to velocity. Pressure, for example, is added in the energy (entropy) module.
hydro_kinematic	This module supplies a kinematic velocity field. Most of the content of this module was moved with revision r12019 by Dhrubaditya Mitra on 5-nov-09 away from nohydro.f90 To inspect the revision history of the file before that time, check out nohydro.f90 prior to or at revision r12018.
hydro_potential	This module takes care of most of the things related to velocity. Pressure, for example, is added in the energy (entropy) module.
hyperresi_strict_2nd	This module applies a sixth order hyperresistivity to the induction equation (following Brandenburg & Sarson 2002). This hyperresistivity ensures that the energy dissipation rate is positive define everywhere.
hypervisc_strict_2nd	This module applies a sixth order hyperviscosity to the equation of motion (following Haugen & Brandenburg 2004). This hyperviscosity ensures that the energy dissipation rate is positive define everywhere.
hypervisc_strict_fft	This module applies a sixth order hyperviscosity to the equation of motion (following Haugen & Brandenburg 2004). This hyperviscosity ensures that the energy dissipation rate is positive define everywhere.
implicit_diffusion	This module provides general facilities to implicitly solve a diffusion equation.
implicit_physics	This module solves the radiative diffusion implicitly thanks to an Alternate Direction Implicit Scheme (ADI) in a D’Yakonov form lambda_x T(n+1/2) = lambda_x + lambda_z lambda_z T(n+1) = T(n+1/2)
initcond	This module contains code used by the corresponding physics modules to set up various initial conditions (stratitication, perturbations, and other structures). This module is not used during run time (although it is used by the physics modules that are used both during run time and for the initial condition).
interstellar	This modules contains the routines for SNe-driven ISM simulations. Replaces old module relabelled as interstellar_old Jul 15 FAG.
interstellar_old	This modules contains the old routines for SNe-driven ISM simulations. It may be necessary to select this for using old simulation data
io_collect	I/O via MPI root rank by collecting data from all processors. (storing data into one file, e.g. data/allprocs/var.dat)
io_collect_xy	I/O via MPI by collecting data from all processors in the xy-plane. (storing data into files, e.g. data/proc(0,7,15,…)/var.dat)
io_collect_xy_f2003	I/O via MPI by collecting data from all processors in the xy-plane. (storing data into files, e.g. data/proc(0,7,15,…)/var.dat)
io_dist	Distributed IO (i.e. each process writes its own file data/procX)
io_dist_outlog	Distributed IO (i.e. each process writes its own file data/procX)
io_hdf5	I/O via the HDF5 hyperslab-by-chunk IO routines. (storing data into one file, e.g. data/allprocs/VAR#.h5)
io_mpi2	I/O via the MPI v2 standard IO routines. (storing data into one file, e.g. data/allprocs/var.dat)
io_wrapper
lorenz_gauge	Lorenz gauge, dphi/dt = -cphi2*divA, with possibility to add diffusion and advection terms. The difficulty is that first derivatives are applied twice during one loop in the calculation of gauge waves. This leads to wiggles that are difficult to damp.
lsode_for_chemistry	Specific module only used by timestep_LSODE if chemistry is solved with the implicit solver LSODE for stiff ODEs.
magnetic	This modules deals with all aspects of magnetic fields; if no magnetic fields are invoked, a corresponding replacement dummy routine is used instead which absorbs all the calls to the magnetically relevant subroutines listed in here.
messages	This module takes care of code messages.
mpicomm	This module takes care of MPI communication.
neutraldensity	This module is used both for the initial condition and during run time. It contains dlnrhon_dt and init_lnrhon, among other auxiliary routines.
neutralvelocity	This module takes care of everything related to velocity
noascalar	This modules solves the passive scalar advection equation.
noborder_profiles
noboundcond	Module for boundary conditions. Extracted from (no)mpicomm, since all non-periodic (external) boundary conditions require the same code for serial and parallel runs.
nochemistry
nochiral	This modules solves two reactive scalar advection equations This is used for modeling the spatial evolution of left and right handed aminoacids.
nocosmicray	This modules solves the passive scalar advection equation
nocosmicrayflux
nodebug	Not a module
nodensity
nodensity_bcs
nodensity_methods	11-mar-15/MR: Created to avoid circular dependencies with EquationOfState.
noderiv
nodetonate	This module is dummy.
nodustdensity	This module takes care of everything related to dust density.
nodustvelocity	This module takes care of everything related to dust velocity.
noenergy	Dummy module for energy equation.
noenergy_bcs
noentropy	Calculates pressure gradient term for polytropic equation of state $p=text{const}rho^{Gamma}$.
noeos	This module takes care of everything related to equation of state.
nofarray_alloc
nofixed_point
noforcing	This module contains routines both for delta-correlated and continuous forcing. The fcont pencil is only provided for continuous forcing.
nofourier	This module contains FFT wrapper subroutines.
noghostfold
nogpu	This module contains GPU related dummy types and functions.
nogravity
nogrid
nohdf5_io	This module is a dummy module for non-HDF5 IO. 28-Oct-2016/PABoudin: coded
noheatflux
nohydro	no variable $uv$: useful for kinematic dynamo runs.
nohyperresi_strict	This module applies a sixth order hyperresistivity to the induction equation (following Brandenburg & Sarson 2002). This hyperresistivity ensures that the energy dissipation rate is positive define everywhere.
nohypervisc_strict	This module applies a sixth order hyperviscosity to the equation of motion (following Haugen & Brandenburg 2004).
noimplicit_diffusion	Dummy
noimplicit_physics
noinitial_condition	This module provide a way for users to specify custom initial conditions.
nointerstellar	Dummy module.
nolorenz_gauge	Lorenz gauge, dphi/dt = -cphi2*divA
nolsode_for_chemistry	This module calculates the chemistry contribution to df in the case where chemistry is solved separately using the LSODE solver
nomagnetic
nompicomm	Dummy module for MPI communication. This allows the code to run on a single CPU.
noneutraldensity	This module is used both for the initial condition and during run time. It contains dlnrhon_dt and init_lnrhon, among other auxiliary routines.
noneutralvelocity	This module takes care of everything related to neutral velocity
noNSCBC	Module for NSCBC boundary conditions. To be included from boundcond.f90.
noopacity	This module is the dummy for the opacity module(s).
noparticles	This module takes care of everything related to dust particles.
noparticles_adaptation	This modules takes care of adapting the number of particles in a grid cell to a desired value. This module is based on an original idea by Jacob Trier Frederiksen.
noparticles_adsorbed	This module takes care of everything related to particle surface fractions.
noparticles_breakup	Dummy module for particle breakup.
noparticles_caustics	This module writes information about the local state of the gas at the positions of a selected number of particles.
noparticles_chemistry	This module takes care of everything related to particle chemistry
noparticles_coagulation	This modules takes care of instantaneous coagulation, shattering, erosion, and bouncing of superparticles.
noparticles_collisions	This modules takes care of instantaneous collisions between superparticles.
noparticles_condensation	This modules takes care of condensation / evaporation or deposition / sublimation of superparticles
noparticles_density	This module takes care of everything related to the density represented by each (super)particle.
noparticles_diagnos_dv	This modules takes care of instantaneous collisions between superparticles.
noparticles_diagnos_state	This modules takes care of instantaneous collisions between superparticles.
noparticles_drag	This module takes care of drag forces between particles and gas.
noparticles_grad	This module tries to solve for gradient matrix of particle velocities
noparticles_kmeans	Dummy version of k-means vector quantization algorithm using the Forgy initialisation of the codebook.
noparticles_lyapunov	This module writes information about the local state of the gas at the positions of a selected number of particles.
noparticles_main	This module contains all the main structure needed for particles.
noparticles_map	This module contains subroutines for mapping particles on the mesh.
noparticles_mass	This module takes care of everything related to the mass of the particles.
noparticles_mpicomm	This module deals with communication of particles between processors.
noparticles_number	This module takes care of everything related to particle number.
noparticles_persistence	This module calculates the probability distribution function the particles that have moved a certain distance away from their initial position.
noparticles_potential	The no module for particles potential
noparticles_radius	This module takes care of everything related to particle radius.
noparticles_selfgravity	This module takes care of everything related to particle self-gravity.
noparticles_sink	This module takes care of everything related to sink particles.
noparticles_spin	This module takes care of everything related to particle spin.
noparticles_stalker	This module writes information about the local state of the gas at the positions of a selected number of particles.
noparticles_stirring	This module takes care of stirring of particles.
noparticles_sub	This module contains subroutines useful for the Particle module.
noparticles_surfspec	This module takes care of everything related to particle surface fractions.
noparticles_temperature	This module takes care of everything related to particle temperature.
noparticles_tetrad
nopointmasses	This module takes care of direct N-body gravity between point masses.
nopoisson	This module solves the Poisson equation.
nopolymer	This modules deals with all aspects of polymers.
nopower_spectrum	reads in full snapshot and calculates power spetrum of u
nopscalar	This modules solves the passive scalar advection equation.
nopython
noradiation
noselfgravity	This module takes care of self gravity.
noSGS_hydro	This module is the dummy for the SGS_hydro module in which e.g the SGS viscous force or viscous heat is computed.
noshear	This modules deals with all aspects of shear; if no shear is invoked, a corresponding replacement dummy routine is used instead which absorbs all the calls to the shear relevant subroutines listed in here.
noshock	This module calculates a divergence of u based shock finding profile used by shock viscosities and diffusion terms. eg. the total voscosity is taken as: nu_total = nu + nu_shock*dx*smooth(max5(-(div u)))) where dx*smooth(max5(-(div u)))) is the profile calculated here in.
nosignal_handling
noslices	This module produces slices for animation purposes.
nosolid_cells	This module add solid (as in no-fluid) cells in the domain. This can be used e.g. in order to simulate a cylinder in a cross flow.
nosolid_cells_mpicomm
nosolid_cells_ogrid_cdata
nosolid_cells_ogrid_chemistry
nosolid_cells_ogrid_sub
nospecial	This module provide a way for users to specify custom (i.e. not in the standard Pencil Code) physics, diagnostics etc.
nostreamlines
nostruct_func
notestfield	This modules deals with all aspects of testfield fields; if no testfield fields are invoked, a corresponding replacement dummy routine is used instead which absorbs all the calls to the testfield relevant subroutines listed in here.
notestflow	This modules deals with all aspects of testfield fields; if no testfield fields are invoked, a corresponding replacement dummy routine is used instead which absorbs all the calls to the testfield relevant subroutines listed in here.
notestperturb	test perturbation method
notestscalar	This modules deals with all aspects of testscalar fields; if no testscalar fields are invoked, a corresponding replacement dummy routine is used instead which absorbs all the calls to the testscalar relevant subroutines listed in here.
notimeavg
notraining
noviscosity	This module is the dummy for the viscosity module in which e.g the viscous force or viscous heat is computed.
noweno_transport	This module take care of WENO (weighted essentially non oscillatory) transport.
noyinyang	This module contains Yin-Yang related dummy types and functions.
noyinyang_mpi	This module contains Yin-Yang related dummy types and functions.
NSCBC	Module for NSCBC (Navier-Stokes Characteristic Boundary Conditions). NSCBC is an alternative way of imposing (time-dependent) boundary conditions through solving differential equations on the boundaries.
param_io	IO of init and run parameters. Subroutines here are ‘at the end of the food chain’, i.e. depend on all physics modules plus possibly others. Using this module is also a compact way of referring to all physics modules at once.
particles_adaptation	This modules takes care of adapting the number of particles in a grid cell to a desired value. This module is based on an original idea by Jacob Trier Frederiksen and was developed by Anders Johansen and Chao-Chin Yang.
particles_adsorbed	This module takes care of the evolution of adsorbed species on the particle surface for reactive particles
particles_breakup	Secondary breakup of Lagrangian liquid parcels.
particles_caustics	This modules solves for the gradient matrix of flow velocities. The gradient matrix Sigma obeys the equation: (d/dt) Sigma = (1/(taup))*(S - Sigma) - Sigma^2 where A is the flow gradient matrix at the position of the particle; and taup is the Stokes time.
particles_cdata	Global particle variables
particles_charged	This module takes care of everything related to inertial particles.
particles_chemistry	This module implements reactive particles.
particles_coagulation	This modules takes care of instantaneous coagulation, shattering, erosion, and bouncing of superparticles.
particles_collisions	This modules takes care of instantaneous collisions between superparticles.
particles_density	This module takes care of everything related to the density represented by each (super)particle.
particles_diagnos_dv	This module bins particle pairs in separation and relative velocity at regular intervals.
particles_diagnos_state	This module tracks the evolution of particles in terms of user defined “states”. Currently the only implemented state is in terms of the local gas velocity.
particles_drag	This module integrates drag forces between particles and gas.
particles_dust	This module takes care of everything related to inertial particles.
particles_dust_blocks	This module takes care of everything related to dust particles.
particles_eikonal	Eikonal solver, “particles” refer here to points on the trajectory.
particles_grad	This module tries to solve for gradient matrix of particle velocities
particles_lagrangian	This module takes care of everything related to inertial particles.
particles_lyapunov	This module writes information about the local state of the gas at the positions of a selected number of particles.
particles_main	This module contains all the main structure needed for particles.
particles_map	This module contains subroutines for mapping particles on the mesh. Different domain decompositions have different versions of this module.
particles_map_blocks	This module contains subroutines useful for mapping particles on the mesh.
particles_map_index	This module contains subroutines for particle-mesh related operations.
particles_mass	This module takes care of everything related to the mass of the particles.
particles_mass_swarm	This module handles the mass of super-particles.
particles_mpicomm	This module deals with communication of particles between processors.
particles_mpicomm_blocks	This module deals with communication of particles between processors.
particles_number	This module takes care of everything related to internal particle number.
particles_persistence	This module calculates the probability distribution function the particles that have moved a certain distance away from their initial position.
particles_potential	This module takes care of everything related to pairwise interaction of particles. It is experimental now (April 2016)
particles_radius	This module takes care of everything related to particle radius.
particles_selfgravity	This module takes care of everything related to particle self-gravity by inverting the Poisson equation of the particle density mapped on the grid.
particles_sink	This module takes care of everything related to sink particles.
particles_spin	This module takes care of everything related to particle spin including lifting forces. The module maintains a full f-array vorticity field, to be able to interpolate on the flow vorticity.
particles_stalker	This module writes information about the local state of the gas at the positions of a selected number of particles.
particles_stirring	This module takes care of stirring of particles.
particles_sub	This module contains useful subroutines for the particle modules. Subroutines that depend on domain decomposition should be put in the Particles_map module.
particles_surfspec	This module takes care the gas phase species in the immediate vicinity of reactive particles.
particles_temperature	This module takes care of everything related to inertial particles.
particles_tetrad	Follow a particle. For this particle solve for three other particles that that are in the neighbourhood of the particle we were following. These four particles together forms a tetrad.
particles_tracers	This module takes care of everything related to tracer particles.
pencil_check
pencil_emul	Not a module
persist	Module to handle variables whose state should persist between executions of run.x, e.g. the random number seeds and some other forcing state information.
pointmasses	This module takes care of direct N-body gravity between point masses.
poisson	This module solves the Poisson equation (d^2/dx^2 + d^2/dy^2 + d^2/dz^2 - h) f = RHS(x,y,z) [which for h/=0 could also be called inhomogenous nonuniform Helmholtz equation] for the function f(x,y,z).
poisson_logspirals	This module contains (more or less) a replica of poisson.f90, implementing the version of poisson equation solving that I have been building (the method outlined in Clement Baruteau’s thesis).
poisson_multigrid	This module solves the Poisson equation (d^2/dx^2 + d^2/dy^2 + d^2/dz^2 - h) f = RHS(x,y,z) [which for h/=0 could also be called inhomogenous nonuniform Helmholtz equation] for the function f(x,y,z), starting from the second-order accurate 7-point discretization of that equation.
polymer	This modules deals with all aspects of polymers.
polynomialroots	PURPOSE - Solve for the roots of a polynomial equation with real coefficients, up to quartic order. Returns a code indicating the nature of the roots found.
power_spectrum	reads in full snapshot and calculates power spetrum of u
pscalar	This modules solves the passive scalar advection equation.
pscalar_nolog	This modules solves (multiple) passive scalar advection equation(s) Solves for c, not ln(c).
python
radiation_ray	Radiation (solves transfer equation along rays).
read_all_videofiles	Not a module
read_vectorfiles	Not a module
read_videofiles	Not a module
register	A module for setting up the f-array and related variables (‘register’ the velocity, energy, magnetic, etc modules).
run
selfgravity	This module takes care of self gravity by solving the Poisson equation (d^2/dx^2 + d^2/dy^2 + d^2/dz^2)phi = 4*pi*G*rho for the potential phi.
selfgravity_logspirals	This module takes care of self gravity by solving the Poisson equation (d^2/dx^2 + d^2/dy^2 + d^2/dz^2)phi = 4*pi*G*rho for the potential phi.
SGS_hydro	This module is the dummy for the SGS_hydro module in which e.g the SGS force or heat is computed.
shared_variables	This module is an interface to allow modules to register pointers to their internal variables so that other modules may then request them by name.
shear	This modules deals with all aspects of shear; if no shear is invoked, a corresponding replacement dummy routine is used instead which absorbs all the calls to the shear relevant subroutines listed in here.
shock	This modules implements viscous heating and diffusion terms here for shock viscosity nu_total = nu + nu_shock*dx^2*smooth(max5(-(div u))))
shock_highorder	This modules implements viscous heating and diffusion terms here for shock viscosity nu_total = nu + nu_shock*dx^2*smooth(max5(-(div u))))
signal_handling
slices	This module produces slices for animation purposes.
slices_methods	This module provides routines for obtaining slice data.
snapshot	Write snapshot files (variables and power spectra).
solid_cells	This module add solid (as in no-fluid) cells in the domain. This can be used e.g. in order to simulate a cylinder in a cross flow.
solid_cells_ogrid	This module add solid (as in no-fluid) cells in the domain. This can be used e.g. in order to simulate a cylinder in a cross flow.
solid_cells_ogrid_cdata
solid_cells_ogrid_chemistry	This modules addes chemical species and reactions. The units used in the chem.in files are cm3,mole,sec,kcal and K This was found out by comparing the mechanism found in samples/0D/chemistry_H2_ignition_delay with Flow Reactor Studies and Kinetic Modeling of the ReactionH/O22 of A. MUELLER, T. J. KIM, R. A. YETTER, F. L. DRYER
solid_cells_ogrid_mpicomm
solid_cells_ogrid_nompicomm
solid_cells_ogrid_sub
special
start	Not a module
streamlines
struct_func	Calculates 2-point structure functions and/or PDFs and saves them during the run.
sub	This module contains useful subroutines.
syscalls	This module takes care of system calls and provides ANSI-C functionality.
temperature_bcs
temperature_idealgas	This module can replace the energy module by using lnT or T (with ltemperature_nolog=.true.) as dependent variable. For a perfect gas with constant coefficients (no ionization) we have: (1-1/gamma) * cp*T = cs20 * exp( (gamma-1)*ln(rho/rho0)-gamma*s/cp )
temperature_ionization	This module can replace the energy module by using lnT or T (with ltemperature_nolog=.true.) as dependent variable.
testfield_axisym	Test-field module for axisymmetric turbulence. No special settings in cparam.local are needed.
testfield_axisym2	Test-field module for axisymmetric turbulence. No special settings in cparam.local are needed.
testfield_meri
testflow_z	This modules deals with all aspects of testflow fields; if no testflow fields are invoked, a corresponding replacement dummy routine is used instead which absorbs all the calls to the testflow relevant subroutines listed in here.
thermal_energy	This module can replace the energy module by using the thermal energy eth as dependent variable. For a perfect gas we have
timeavg
timestep	Runge-Kutta time advance, accurate to order itorder. At the moment, itorder can be 1, 2, or 3.
timestep_LSODE	Timestepping routine corresponding to the use of LSODE to solve chemistry. The transport equations are solved as usual using RK methods but the chemistry ODEs are separated and solved implicitly using LSODE either following a sequential (1 chemistry step) or symmetric (2 chemistry steps) splitting scheme.
timestep_RKC-10
timestep_RKC-20
timestep_RKC-25
timestep_RKC-40
timestep_rkf
timestep_rkf_1d
timestep_rkf_lowsto	Runge-Kutta-Fehlberg Low-Storage method Christopher A. Kennedy, Mark H. Carpenter, R.Michael Lewis, Low-storage, explicit Runge-Kutta schemes for the compressible Navier-Stokes equations, Applied Numerical Mathematics, Volume 35, Issue 3, 2000, Pages 177-219, ISSN 0168-9274, https://doi.org/10.1016/S0168-9274(99)00141-5.
timestep_stiff	adapted from timestep_rkf, and from numerical recipe stiff algorithm
timestep_strang	Runge-Kutta time advance, accurate to order itorder. At the moment, itorder can be 1, 2, or 3. Split one dt into two dt/2 steps with RK method. Please add documentation on why this is beneficial…
timestep_sts
timestep_subcycle
training_torchfort
viscosity	This modules implements viscous heating and diffusion terms here for cases 1) nu constant, 2) mu = rho.nu 3) constant and
weno_transport	This module take care of WENO (weighted essentially non oscillatory) transport.
write_default_namelists	Not a module
yinyang	This module contains Yin-Yang related types and functions which are incompatible with FORTRAN 95.
yinyang_mpi	This module contains Yin-Yang related types and functions which are incompatible with FORTRAN 95.

experimental source files (src/experimental)

The src/experimental directory contains 41 Fortran files.

File	Description	Scientific References
analyzers	use EMD, only: analyzer_emd
anelastic	This module solves the Poisson equation for pressure for the linearized density
barneshut	This module implements gas/dust self-gravity using a Barnes-Hut octree algorithm. The main function, do_barneshut, takes the variable ‘phi’ as input, which is the gas/dust density grid from the selfgravity module, and modifies ‘phi’ in place, becoming the gravitational potential.
boussinesq	23-mar-2012/dintrans: coded
conductivity	This module takes care of heat conductivity for the energy equation.
cosmicray_current	Module for calculating Cosmic Ray Flux.
cosmicray_density	This modules solves the cosmic ray energy density equation. It follows the description of Hanasz & Lesch (2002,2003) as used in their ZEUS 3D implementation.
emd
entropy_anelastic	This module takes care of energy (initial condition and time advance)
eos_idealgas_vapor	Equation of state for an ideal gas with variable water vapour.
file_io_f2003	This module takes care of massive parallel file Input/Output. We use here F2003 features for HPC-friendly behaviour.
forcing_cont_sample	This module contains routines both for delta-correlated and continuous forcing. The fcont pencil is only provided for continuous forcing.
gravity_r_radpressure	Radial gravity
hydro_ffreeMHDrel	This module solve the momentum equation for relativistic force-free MHD dS/dt = curlB x B + curlE x E + divE E where E = (BxS)/B^2
magnetic_ffreeMHDrel	Relativistic treatment of force-free magnetic fields. Still quite experimental. This modules deals with all aspects of magnetic fields; if no magnetic fields are invoked, a corresponding replacement dummy routine is used instead which absorbs all the calls to the magnetically relevant subroutines listed in here.
magnetic_shearboxJ	This modules deals with all aspects of magnetic fields; if no magnetic fields are invoked, a corresponding replacement dummy routine is used instead which absorbs all the calls to the magnetically relevant subroutines listed in here.
mpicomm	This module takes care of MPI communication.
neutralvelocity_matchiontemp	This module takes care of everything related to velocity
noconductivity	Dummy module for conductivity.
nompicomm	Dummy module for MPI communication. This allows the code to run on a single CPU.
particles_dust_ajwr	This module takes care of everything related to inertial particles.
particles_dust_brdeplete	This module takes care of everything related to inertial particles.
particles_mpicomm_blocks_partition	This module deals with communication of particles between processors.
particles_nbody_ajwr	This module takes care of direct N-body gravity between particles.
particles_potential	This module takes care of everything related to pairwise interaction of particles. It is experimental now (April 2016)
particles_radius_ajwr	This module takes care of everything related to particle radius.
particles_radius_strubbechiang	This module takes care of everything related to particle radius.
pc_h5collect	Not a module
poisson_cyl	This module solves the Poisson equation in cylindrical coordinates (d^2/dr^2 +1/r*d/dr + 1/r^2*d^2/dy^2 + d^2/dz^2) f = RHS(x,y,z)
poisson_expand	This module solves the Poisson equation (d^2/dx^2 + d^2/dy^2 + d^2/dz^2 - h) f = RHS(x,y,z) [which for h/=0 could also be called inhomogenous nonuniform Helmholtz equation] for the function f(x,y,z). The difference between this and poisson.f90 is that here we solve it in a non-periodic Cartesian grid, expanding the grid to curb the periodicity of the Fourier transforms.
shock_finder
shock_finder_comm_uu
shock_perp	This modules implements viscous heating and diffusion terms here for shock viscosity nu_total = nu + nu_shock*dx^2*smooth(max5(-(div u))))
solid_cells_CGEO	This module add solid (as in no-fluid) cells in the domain. This can be used e.g. in order to simulate a cylinder in a cross flow. Now, apart from the circle geometry, a 2D geometry file similar to STL can be used to represent the solid cells.Details can be found in the paper “A ghost-cell immersed boundary method for the simulations of heat transfer in compressible flows under different boundary conditions Part-II: Complex geometries”
solid_cells_reactive	This module add solid (as in no-fluid) cells in the domain. This can be used e.g. in order to simulate a cylinder in a cross flow.
supernova	This modules contains the routines for SNe-driven ISM simulations. Still in development.
test_chemistry	This modules adds chemical species and reactions. The units used in the chem.in files are cm3,mole,sec,kcal and K
test_eos_chemistry	Equation of state for an ideal gas without ionization.
test_f2003	Not a module
testperturb	test perturbation method
timestep_DufortFrankel	DuFort-Frankel time stepping routine. As is well known, this proceedure has disadvantages, but it is well suited to deal with the time step constrain near the center in spherical polar coordinates.

inactive source files (src/inactive)

The src/inactive directory contains 4 Fortran files.

File	Description	Scientific References
deriv_3sec_insteadof_14min_compiletime
gravitational_waves_hTXk_no_xpara	This module provide a way for users to specify custom (i.e. not in the standard Pencil Code) physics, diagnostics etc.
testfield	This modules deals with all aspects of testfield fields; if no testfield fields are invoked, a corresponding replacement dummy routine is used instead which absorbs all the calls to the testfield relevant subroutines listed in here.
testfield_xz	This modules deals with all aspects of testfield fields; if no testfield fields are invoked, a corresponding replacement dummy routine is used instead which absorbs all the calls to the testfield relevant subroutines listed in here.

initial_condition source files (src/initial_condition)

The src/initial_condition directory contains 67 Fortran files.

File	Description	Scientific References
1D_loop_init
2d_accretion_disk	21-feb-23/hongzhe: adapted from initial_condition/centrifugal_balance.f90
aerosol_init	This module provide a way for users to specify custom initial conditions.
alfven_wave	This module sets up an Alfven wave of amplitude init_amp0 with wave vector init_k0 and an optional phase init_phase0.
assimilate
baroclinic_init
binarycomparison	This module provide a way for users to specify custom initial conditions.
blobs_domes	Initial condition (density, magnetic field, velocity) for a particular configuration of a braided magnetic field with magnetic domes with nulls.
bonnor_ebert_sphere	Initial condition for a Bonnor-Ebert sphere
borromean_rings	Initial condition (density, magnetic field, velocity) for a particular configuration of magnetic tubes.
braids	Initial condition (density, magnetic field, velocity) for a particular configuration of a braided magnetic field.
bubbles_init	Initial condition for bubbles in a stratified medium. Set bubble size, bubble density, surrounding medium density, temperatures, stratification and magnetic field.
centrifugal_balance	This module provide a way for users to specify custom initial conditions.
centrifugal_balance_neutrals	This module provide a way for users to specify custom initial conditions.
cig_dynamo_benchmark	Set the initial conditions for the CIG Community Accuracy & Performance Benchmark: http://geodynamics.org/cig/community/workinggroups/geodyn/benchmark/ following Christensen et al. Physics of the Earth and Planetary Interiors, 128, 25-34 (2001).
circumplanetary	This module provide a way for users to specify custom initial conditions.
coronae_init
cylindrical_energy	Initial condition (density, magnetic field, velocity) for magnetohydrostatical equilibrium in a global accretion disk in a cylindrically symmetric profile in spherical coordinates. with a polytropic equation of state including entropy equation
disk+corona	This module provide a way for users to specify custom initial conditions.
dust-equilibrium	This module provide a way for users to specify custom initial conditions.
fieldloop	This module provide a way for users to specify custom initial conditions.
fluxring_cylindrical	Initial condition (density, magnetic field, velocity) for magnetohydrostatical equilibrium in a global accretion disk with an imposed (cylindrically symmetric) sound speed profile in spherical coordinates.
fluxrings	Magnetic flux rings. Constructed from a canonical ring which is the rotated and translated; see Pencil Code manual, Section C.3.
hill_vortex	Initial condition (density, magnetic field, velocity) for magnetohydrostatical equilibrium in a global accretion disk with an imposed (cylindrically symmetric) sound speed profile in spherical coordinates.
hor-fluxlayer-By	Horizontal flux layer in B_y, with tanh profiles switching on (off) at z0 (z1) Density and entropy also set appropriately. To reproduce initial condition in Catteneo & Hughes, JFM, v. 196, p. 323, 1988
hs_equilibrium_ism	This module provide a way for users to specify custom initial conditions.
hydrostat-pload
ice_shell	This module provide a way for users to specify custom initial conditions.
import	Initial condition (density, magnetic field, velocity) for a field created externally in pencil code format. The file must be in an appropriate format with the right order of indices and match with start.in. USE WITH CAUTION!
import_glemur	Initial condition (density, magnetic field, velocity) for a field from the code GLEMuR.
iucaa_logo	Initial condition (density, magnetic field, velocity) for a particular configuration of a magnetic tube.
kelvin_helmholtz	This module provide a way for users to specify custom initial conditions.
kelvin_helmholtz_Lecoanet_etal16	Kelvin-Helmholtz initial condition from Lecoanet et al. (2016, MNRAS 455, 4274)
linked_tori_twisted	Initial condition (density, magnetic field, velocity) for a particular configuration of magnetic tubes.
magnetic_carpet	Initial condition (density, magnetic field, velocity) for a particular configuration of magnetic carpets.
mhs_equilibrium	Initial condition (density, magnetic field, velocity) for magnetohydrostatical equilibrium in a global accretion disk with an imposed (cylindrically symmetric) sound speed profile in spherical coordinates.
MRI_2D_Test	Initial condition (density, magnetic field, velocity) for magnetohydrostatical equilibrium in a global accretion disk with an imposed (cylindrically symmetric) sound speed profile in spherical coordinates.
mri_cycle	Initial condition (magnetic field, velocity) for the MRI cycle described in
mri_nonlinear	This module provide a way for users to specify custom initial conditions.
multi_rings	Initial condition (density, magnetic field, velocity) for a particular configuration of magnetic tubes.
nfoil	Initial condition (density, magnetic field, velocity) for a particular configuration of a magnetic tube.
novertical_shear	Initial condition for run without vertical shear using the (unphysical) modified gravity profile of Klahr et al. (2023)
Orszag_Tang_Vortex	Initial condition (density, magnetic field, velocity) for magnetohydrostatical equilibrium in a global accretion disk with an imposed (cylindrically symmetric) sound speed profile in spherical coordinates.
parker_wind	Initial condition for the parker wind in spherical coordinates.
pressure_bump_global	This module provide a way for users to specify custom initial conditions.
random_helical
Rayleigh-Taylor
reflect
rti
shallow_water_init
shock_cloud	Shock-Cloud Initial Condition sets up a 2D version similar to The Magnetohydrodynamics of Shock-Cloud Interaction in Three Dimensions Min-Su Shin, James M Stone, and Gregory F Snyder http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2008ApJ…680..336S&link_type=ABSTRACT
shocktube	This module provide a way for users to specify custom initial conditions.
solar_atmosphere_Omega_bfield	Initial condition for a stably tratified solar atmosphere from the convection zone to the corona, with a Omega shaped magnetic field loop.
spherical_convection	Isentropic initial condition (density, entropy) for convection in spherical coordinates. Produces an isentropic stratification with given surface gravity and surface temperature, and a heat conduction profile proportional to r^-15. The setup was originally introduced in Astron. Nachr., 332, 883.
star_box_layers	31-oct-2011/dintrans: coded (moved here my two subroutines from the entropy module after discussions during the 2011 PC meeting in Toulouse). This module initializes the star-in-a-box setup with a central heating.
star_in_a_box_poly	Piecewise polytopic initial condition for star-in-a-box models	Dobler et al. (2006)
streaming_instability	This module sets up nonlinear streaming instability with multiple particle species.
tabulated	This module loads an existing snapshot and interpolates it to the current grid as the initial condition. The snapshot should be saved as a global snapshot in a single file (default name: tabulated.dat) under the run directory. The user should specify its dimensions using nxtab, nytab, and nztab. The number of variables in the snapshot must be consistent with the current mfarray.
ths1D_equilibrium_ism	This module provides a 1D profile of density and temperature for the initial conditions to be applied for supernova driven turbulence simulations in the interstellar medium. After the 1D profile converges to an equilibrium state save the profiles of rho and tt to init_ism.dat, which will be imported by initial_condition/ths_equilibrium_ism.f90 for 3D simulations
ths_equilibrium_ism	Initial conditions for 3D equilibrium supernova driven turbulence simulations. First run 1D simulation using identical z grid with initial_condition/ths1D_equilibrium_ism.f90. This module will load the converged 1D profiles derived and saved to init_ism.dat (now init_ism.in).
trefoil	Initial condition (density, magnetic field, velocity) for a particular configuration of magnetic flux rings.
twisted_tubes	Initial condition (density, magnetic field, velocity) for a particular configuration of a twsited magnetic field tube(s).
twistedtiltedtoros	17-jul-12/piyali: adapted from fluxrings.f90 but for spherical geometry. Also some major changes, hence a new initial condition
viscous_ring	Initial condition for spherical viscous ring, according to the test of Frederic Masset,
vortex_braids	Initial condition (density, magnetic field, velocity) for a particular configuration of a braided vortex field.
wave_Bx	Initial condition for sin(kz) or cos(kz) magnetic field.
whitehead_link	Initial condition (density, magnetic field, velocity) for a particular configuration of magnetic tubes.

magnetic source files (src/magnetic)

The src/magnetic directory contains 5 Fortran files.

File	Description	Scientific References
maxwell	This module provide a way for users to specify custom (i.e. not in the standard Pencil Code) physics, diagnostics etc.
meanfield	This modules solves mean-field contributions to both the induction and the momentum equations.
meanfield_demfdt	This modules solves mean-field contributions to both the induction and the momentum equations.
nomeanfield	This modules solves mean-field contributions to both the induction and the momentum equations.
nomeanfield_demfdt	Dummy module for mean-field contributions

obsolete source files (src/obsolete)

The src/obsolete directory contains 16 Fortran files.

File	Description	Scientific References
density_anelastic	This module takes care of the continuity equation.
global_gg_bext	A module container and access functions (‘methods’) for additional variables which are globally needed — here this is the gravity field gg, and an external magnetic field (such that B=curl(A)+B_ext_pot)
localshock	This module fetchs the position of the massive n-body particles and applies extra shock dissipation around them. This allows for less shock dissipation to be used elsewhere in the quiescent regions of the simulation box.
magnetic_axisym	This modules deals with all aspects of magnetic fields; if no magnetic fields are invoked, a corresponding replacement dummy routine is used instead which absorbs all the calls to the magnetically relevant subroutines listed in here.
magnetic_old	This modules deals with all aspects of magnetic fields; if no magnetic fields are invoked, a corresponding replacement dummy routine is used instead which absorbs all the calls to the magnetically relevant subroutines listed in here.
nohydro_file
nosyscalls	This module takes care of system calls and provides ANSI-C functionality.
particles_nbody	This module takes care of direct N-body gravity between particles.
radiation_fld	Radiation in the fluxlimited-diffusion approximation. Doesn’t work convincingly (and maybe never will). Look at the (still experimental) module radiation_ray.f90 for a more sophisticated approach.
radiation_nongrey
radiation_ray_periodic	Radiation (solves transfer equation along rays) The direction of the ray is given by the vector (lrad,mrad,nrad), and the parameters radx0,rady0,radz0 gives the maximum number of steps of the direction vector in the corresponding direction.
temperature	This module replaces the entropy module by using lnT as dependent variable. For a perfect gas with constant coefficients (no ionization) we have (1-1/gamma) * cp*T = cs02 * exp( (gamma-1)*ln(rho/rho0)-gamma*s/cp ) At a later point we may want to rename the module Entropy into Energy
temperature_TT	This module can replace the entropy module by using _T_ as dependent variable. For a perfect gas with constant coefficients (no ionization) we have (1-1/gamma) * cp*T = cs02 * exp( (gamma-1)*ln(rho/rho0)-gamma*s/cp )
visc_hyper	This modules implements viscous heating and diffusion terms here for third order hyper viscosity
visc_smagorinsky	This modules implements viscous heating and diffusion terms here smagorinsky viscosity
visc_var	This modules implements viscous heating and diffusion terms here for cases 1) nu constant, 2) mu = rho.nu 3) constant and

pre_and_post_processing source files (src/pre_and_post_processing)

The src/pre_and_post_processing directory contains 11 Fortran files.

File	Description	Scientific References
pc_collect	Not a module
pc_collect_exp	Not a module
pc_collect_pvar	Not a module
pc_configtest	Not a module
pc_distribute	Not a module
pc_distribute_z	Not a module
pc_extract	Not a module
pc_reduce	Not a module
pc_tecplot	Not a module
pc_tecplot_solid	Not a module
read_xyaver_alpha	Not a module

special source files (src/special)

The src/special directory contains 71 Fortran files.

File	Description	Scientific References
1D_loop
advective_gauge	Advecto-resistive gauge, dLamRA/dt = -u.gradLamRA - U.A_resistive + eta*del2A_resistive A_advecto-resistive=A_resistive+grad(LamRA)
alphadisk	This module solves for a viscously diffusive disk according to the alpha-formalism, also adding photoevaporation. It is a one-dimensional evolutionary model, that evolves the disk over its multimillion year lifetime.
ascale_collapse	This module provide a way for users to specify custom (i.e. not in the standard Pencil Code) physics, diagnostics etc.	Brandenburg & Ntormousi (2025)
atmosphere	This module incorporates all the modules used for Natalia’s aerosol simulations
axionSU2back	Solve the lucky droplet model for many realizations. The different realizations correspond to “meshpoints”. To add the contributions for each step, we use the usual time step in the Pencil Code, so t is just the step, and the accumulated collision times (after 125 steps or so) for all realizations at the same time are the values in the f-array.
axionU1back	Solve axion-U(1) inflation model for many wavenumber values. The different wavenumber correspond to 1D “meshpoints”.
backreact_infl	This module provide a way for users to specify custom (i.e. not in the standard Pencil Code) physics, diagnostics etc.
baroclinic_run
bc_strat	This module sets the open boundary conditions for density in the vertical direction, scaled by stratificaiton.
beta_plane	Add Coriolis force in the beta plane approximation to the hydro equation. The x-axis is in the direction of increasing colatitude, while the z-axis is the radial direction.
boussinesq	This module provide a way for users to specify custom (i.e. not in the standard Pencil Code) physics, diagnostics etc.
chem_stream	This module incorporates all the modules used for Natalia’s neutron star – disk coupling simulations (referred to as nstar)
chiral_mhd	This module provide a way for users to specify custom (i.e. not in the standard Pencil Code) physics, diagnostics etc.
collapse	This module provide a way for users to specify custom (i.e. not in the standard Pencil Code) physics, diagnostics etc.
coronae
dampuu	Special module that damps the velocity field outside a user-specified cuboid. Useful in cases where you do not want waves reflected from the boundary to interfere with the interior of the domain.
disp_current	Electric field, dE/dt = curlB-mu0*J, originally only for the special case of no fluid induction, but now fluid motions are also included.
dynamical_resistivity
electroweaksu2	Dynamical equations for electroweak SU(2) non-Abelian gauge fields
flowaroundsphere	This module provide a way for users to specify custom (i.e. not in the standard Pencil Code) physics, diagnostics etc.
flux_limdiff
footpoints
gravitational_waves	This module provide a way for users to specify custom (i.e. not in the standard Pencil Code) physics, diagnostics etc.
gravitational_waves_hij6	This module provide a way for users to specify custom (i.e. not in the standard Pencil Code) physics, diagnostics etc.
gravitational_waves_hTXk	This module provide a way for users to specify custom (i.e. not in the standard Pencil Code) physics, diagnostics etc.	Roper Pol et al. (2020a) Roper Pol et al. (2020b)
gross_pitaevskii	This module provide a way for users to specify custom (i.e. not in the standard Pencil Code) physics, diagnostics etc.
internal_flow
jet
klein_gordon	This module provide a way for users to specify custom (i.e. not in the standard Pencil Code) physics, diagnostics etc.
Lambda_CDM	This module provide a way for users to specify custom (i.e. not in the standard Pencil Code) physics, diagnostics etc.
lorenz_gauge	Lorenz gauge, dphi/dt = -cphi2*divA
lucky_droplet	Solve the lucky droplet model for many realizations. The different realizations correspond to “meshpoints”. To add the contributions for each step, we use the usual time step in the Pencil Code, so t is just the step, and the accumulated collision times (after 125 steps or so) for all realizations at the same time are the values in the f-array.
magneticspiral
meanfield_alpm	This module serves as a sample for a special_XXX module that introduces additional primitive variables. Use this as a basis for your own special_ module if you need one.
meanfield_alpm_alternate	This module serves as a sample for a special_XXX module that introduces additional primitive variables. Use this as a basis for your own special_ module if you need one.
meanfield_alpm_etat	This module serves as a sample for a special_XXX module that introduces additional primitive variables. Use this as a basis for your own special_ module if you need one.
meanfield_dynamo_z	Mean field dynamo equation
meanfield_e_tensor	This special module will contribute a mean electromotive force to the vector potential differential equation.
multisp_drag_eq	This module handles diagnostics that are related with dust-gas velocities in drag equilibrium, computed by initial_condition/streaming_instability.f90.
neutron_star	This module incorporates all the modules used for Natalia’s neutron star – disk coupling simulations (referred to as nstar)
newton_cooling
NS_polecap
oscillation_0D	Solve for a set of two ODEs, used to test time step
oscillation_0D_Lorenz	Solve for a set of two ODEs, used to test time step
oscillation_3D	This module provide a way for users to specify custom (i.e. not in the standard Pencil Code) physics, diagnostics etc.
param_instab	Parametric instability with a time-dependent forcing
photoelectric_dust
planet_atmosphere	This module includes physics related to planet atmospheres.
pressure_bump	Thie module addes pressure bumps to your simulations. They are needed e.g. when simulating the effects of a pressure bump on particle drift, particle trapping and planetesimal formation via gravitational fragmentation.
radial_dist_func	Calculate the radial distribution function based on a pre-generated input file. This input file is generated by first reading the stored data into IDL by the routine: f90/pencil-christer/isoth_expwave/idl/pvar.pro then the input file is generated with an adapted version of the following routine: f90/pencil-christer/isoth_expwave/idl/rnp256.pro Finally you can then run start.csh with something like the following start.in file:
reaction_0D	Solve for a set of two ODEs, used to test time step
rel_1d	This module provide a way for users to specify custom (i.e. not in the standard Pencil Code) physics, diagnostics etc.
rtime_phiavg	This module calculates a number of outputs and removes a mean (phi-averaged) emf from the simulations with net vertical fields on global accretion disks
schur_triple_decomp	This module provide a way for users to specify custom (i.e. not in the standard Pencil Code) physics, diagnostics etc.
set_gravity
shallow_water
shell	Runs a shell model (only GOY implemented) for turbulence Copied from Dhruba’s code Uses a slaved, Adams-Bashforth scheme run in parallel with the PC time stepping
solar_corona
spiegel	This module is currently fairly much obsolete. This module incorporates all the modules used for Natalia’s neutron star – disk coupling simulations (referred to as nstar)
stellartide
streamfunction	This module solves for a streamfunction for the 2D velocity field.
streamfunction_dimensional	This module solves for a streamfunction for the 2D velocity field.
streamfunction_direct	This module solves for a streamfunction for the 2D velocity field.
streamfunction_fullmultigrid	This module solves for a streamfunction for the 2D velocity field.
streamfunction_multigrid	This module solves for a streamfunction for the 2D velocity field.
symbreak	Solve for a set of two ODEs, used to test time step
turbpotential
twist_inject	This module provide a way for users to specify custom (i.e. not in the standard Pencil Code) physics, diagnostics etc.
twist_inject_delta	This module provide a way for users to specify custom (i.e. not in the standard Pencil Code) physics, diagnostics etc.
van_der_pol	Solve the Van der Pol oscillator equations

test_methods source files (src/test_methods)

The src/test_methods directory contains 11 Fortran files.

File	Description	Scientific References
testfield_axisym4	Test-field module for axisymmetric turbulence. No special settings in cparam.local are needed.
testfield_compress_z	This modules deals with all aspects of testfield fields; if no testfield fields are invoked, a corresponding replacement dummy routine is used instead which absorbs all the calls to the testfield relevant subroutines listed in here.
testfield_general
testfield_nonlin_z	This modules deals with all aspects of testfield fields; if no testfield fields are invoked, a corresponding replacement dummy routine is used instead which absorbs all the calls to the testfield relevant subroutines listed in here.
testfield_x	This modules deals with all aspects of testfield fields; if no testfield fields are invoked, a corresponding replacement dummy routine is used instead which absorbs all the calls to the testfield relevant subroutines listed in here.
testfield_xy	This modules deals with all aspects of testfield fields; if no testfield fields are invoked, a corresponding replacement dummy routine is used instead which absorbs all the calls to the testfield relevant subroutines listed in here.	Brandenburg et al. (2008a)
testfield_xz	This modules deals with all aspects of testfield fields; if no testfield fields are invoked, a corresponding replacement dummy routine is used instead which absorbs all the calls to the testfield relevant subroutines listed in here.
testfield_z	This modules deals with all aspects of testfield fields; if no testfield fields are invoked, a corresponding replacement dummy routine is used instead which absorbs all the calls to the testfield relevant subroutines listed in here.
testscalar	This modules deals with all aspects of testscalar fields; if no testscalar fields are invoked, a corresponding replacement dummy routine is used instead which absorbs all the calls to the testscalar relevant subroutines listed in here.
testscalar_axisym	This modules deals with testscalar fields for axisymmetric turbulence testscalar fields are invoked, a corresponding replacement dummy routine is used instead which absorbs all the calls to the testscalar relevant subroutines listed in here.
testscalar_simple	This modules deals with all aspects of testscalar fields; if no testscalar fields are invoked, a corresponding replacement dummy routine is used instead which absorbs all the calls to the testscalar relevant subroutines listed in here.