Code initialization

Namelists.f90

Description

Read and print the input namelist

Quick access

Variables

runhours, runminutes, runseconds

Routines

defaultnamelists(), readnamelists(), select_tscheme(), writenamelists()

Needed modules

• iso_fortran_env (output_unit())

• precision_mod: This module controls the precision used in MagIC

• constants: module containing constants and parameters used in the code.

• truncation: This module defines the grid points and the truncation

• radial_functions: This module initiates all the radial functions (transport properties, density, temperature, cheb transforms, etc.)

• physical_parameters: Module containing the physical parameters

• num_param: Module containing numerical and control parameters

• torsional_oscillations: This module contains information for TO calculation and output

• init_fields: This module is used to construct the initial solution.

• logic: Module containing the logicals that control the run

• output_data: This module contains the parameters for output control

• parallel_mod: This module contains the blocking information

• special: This module contains all variables for the case of an imposed IC dipole, an imposed external magnetic field and a special boundary forcing to excite inertial modes

• movie_data (movie(), n_movies(), n_movies_max())

• charmanip (capitalize()): This module contains several useful routines to manipule character strings

• probe_mod: Module for artificial sensors to compare time series of physical data with experiments. Probes are located in a radially symmetrical way

• useful (abortrun()): This module contains several useful routines.

• dirk_schemes (type_dirk()): This module defines the type_dirk which inherits from the abstract type_tscheme. It actually implements all the routine required to time-advance an diagonally implicit Runge-Kutta scheme. It makes use

• multistep_schemes (type_multistep()): This module defines the type_multistep which inherits from the abstract type_tscheme. It actually implements all the routine required to time-advance an IMEX multistep scheme such as CN/AB2, SBDF(2,3,4),

• time_schemes (type_tscheme()): This module defines an abstract class type_tscheme which is employed for the time advance of the code.

Variables

• namelists/runhours [integer,private]

• namelists/runminutes [integer,private]

• namelists/runseconds [integer,private]

Subroutines and functions

subroutine namelists/readnamelists(tscheme)

Purpose of this subroutine is to read the input namelists. This program also determins logical parameters that are stored in logic.f90.

Parameters

tscheme [real ]

Called from

magic

Call to

defaultnamelists(), abortrun(), capitalize(), select_tscheme(), initialize_truncation()

subroutine namelists/writenamelists(n_out)

Purpose of this subroutine is to write the namelist to file unit n_out. This file has to be open before calling this routine.

Parameters

n_out [integer ,in]

Called from

magic

subroutine namelists/defaultnamelists()

Purpose of this subroutine is to set default parameters for the namelists.

Called from

readnamelists()

subroutine namelists/select_tscheme(scheme_name, tscheme)

This routine determines which family of time stepper should be initiated depending on the name found in the input namelist.

Parameters

• scheme_name [character(len=72),inout] :: Name of the time scheme

• tscheme [real ]

Called from

readnamelists()

Call to

capitalize()

startFiels.f90

Description

This module is used to set-up the initial starting fields. They can be obtained by reading a starting checkpoint file or by setting some starting conditions.

Quick access

Variables

botcond, botxicond, deltacond, deltaxicond, topcond, topxicond

Routines

getstartfields()

Needed modules

• truncation: This module defines the grid points and the truncation

• precision_mod: This module controls the precision used in MagIC

• parallel_mod: This module contains the blocking information

• radial_data (n_r_cmb(), n_r_icb(), nrstart(), nrstop()): This module defines the MPI decomposition in the radial direction.

• communications (lo2r_one()): This module contains the different MPI communicators used in MagIC.

• radial_functions (rscheme_oc(), r(), or1(), alpha0(), dltemp0(), dlalpha0(), beta(), orho1(), temp0(), rho0(), r_cmb(), otemp1(), ogrun(), dentropy0(), dxicond(), r_icb()): This module initiates all the radial functions (transport properties, density, temperature, cheb transforms, etc.)

• physical_parameters (interior_model(), epss(), imps(), n_r_lcr(), ktopv(), kbotv(), lffac(), imagcon(), thexpnb(), vischeatfac(), impxi()): Module containing the physical parameters

• num_param (dtmax(), alpha()): Module containing numerical and control parameters

• special (lgrenoble()): This module contains all variables for the case of an imposed IC dipole, an imposed external magnetic field and a special boundary forcing to excite inertial modes

• output_data (log_file(), n_log_file()): This module contains the parameters for output control

• blocking (lo_map(), llm(), ulm(), ulmmag(), llmmag()): Module containing blocking information

• logic (l_conv(), l_mag(), l_cond_ic(), l_heat(), l_srma(), l_sric(), l_mag_kin(), l_mag_lf(), l_rot_ic(), l_z10mat(), l_rot_ma(), l_temperature_diff(), l_single_matrix(), l_chemical_conv(), l_anelastic_liquid(), l_save_out(), l_parallel_solve(), l_mag_par_solve(), l_phase_field(), l_onset(), l_non_adia()): Module containing the logicals that control the run

• init_fields (l_start_file(), init_s1(), init_b1(), tops(), pt_cond(), initv(), inits(), initb(), initxi(), ps_cond(), start_file(), init_xi1(), topxi(), xi_cond(), omega_ic1(), omega_ma1(), initphi(), init_phi()): This module is used to construct the initial solution.

• fields: This module contains all the fields used in MagIC in the hybrid (LM,r) space as well as their radial derivatives. It defines both the LM-distributed arrays and the R-distributed arrays….

• fieldslast: This module contains all the work arrays of the previous time-steps needed to time advance the code. They are needed in the time-stepping scheme….

• timing (timer_type()): This module contains functions that are used to measure the time spent.

• constants (zero(), c_lorentz_ma(), c_lorentz_ic(), osq4pi(), one(), two(), sq4pi()): module containing constants and parameters used in the code.

• useful (cc2real(), logwrite()): This module contains several useful routines.

• radial_der (get_dr(), exch_ghosts(), bulk_to_ghost()): Radial derivatives functions

• readcheckpoints (readstartfields_mpi()): This module contains the functions that can help reading and mapping of the restart files

• time_schemes (type_tscheme()): This module defines an abstract class type_tscheme which is employed for the time advance of the code.

• updatewps_mod (get_single_rhs_imp()): This module handles the time advance of the poloidal potential w, the pressure p and the entropy s in one single matrix per degree. It contains the computation of the implicit terms and the linear

• updatewp_mod (get_pol_rhs_imp(), get_pol_rhs_imp_ghost(), w_ghost(), fill_ghosts_w(), p0_ghost()): This module handles the time advance of the poloidal potential w and the pressure p. It contains the computation of the implicit terms and the linear solves.

• updates_mod (get_entropy_rhs_imp(), get_entropy_rhs_imp_ghost(), s_ghost(), fill_ghosts_s()): This module handles the time advance of the entropy s. It contains the computation of the implicit terms and the linear solves….

• updatexi_mod (get_comp_rhs_imp(), get_comp_rhs_imp_ghost(), xi_ghost(), fill_ghosts_xi()): This module handles the time advance of the chemical composition xi. It contains the computation of the implicit terms and the linear solves….

• updatephi_mod (get_phase_rhs_imp(), get_phase_rhs_imp_ghost(), phi_ghost(), fill_ghosts_phi()): This module handles the time advance of the phase field phi. It contains the computation of the implicit terms and the linear solves….

• updatez_mod (get_tor_rhs_imp(), get_tor_rhs_imp_ghost(), z_ghost(), fill_ghosts_z()): This module handles the time advance of the toroidal potential z It contains the computation of the implicit terms and the linear solves….

• updateb_mod (get_mag_rhs_imp(), get_mag_ic_rhs_imp(), b_ghost(), aj_ghost(), get_mag_rhs_imp_ghost(), fill_ghosts_b()): This module handles the time advance of the magnetic field potentials b and aj as well as the inner core counterparts b_ic and aj_ic. It contains the computation of the implicit terms and the linear

Variables

• start_fields/botcond [real,public]

  Conducting heat flux at the inner boundary

• start_fields/botxicond [real,public]

  Conducting mass flux at the inner boundary

• start_fields/deltacond [real,public]

  Temperature or entropy difference between boundaries

• start_fields/deltaxicond [real,public]

  Composition difference between boundaries

• start_fields/topcond [real,public]

  Conducting heat flux at the outer boundary

• start_fields/topxicond [real,public]

  Conducting mass flux at the outer boundary

Subroutines and functions

subroutine start_fields/getstartfields(time, tscheme, n_time_step)

Purpose of this subroutine is to initialize the fields and other auxiliary parameters.

Parameters

• time [real ,out] :: Time of the restart

• tscheme [real ]

• n_time_step [integer ,out] :: Number of past iterations

Called from

magic

Call to

pt_cond(), ps_cond(), xi_cond(), readstartfields_old(), readstartfields_mpi(), logwrite(), initb(), initv(), inits(), initxi(), initphi(), bulk_to_ghost(), exch_ghosts(), fill_ghosts_xi(), get_comp_rhs_imp_ghost(), get_comp_rhs_imp(), fill_ghosts_phi(), get_phase_rhs_imp_ghost(), get_phase_rhs_imp(), get_single_rhs_imp(), fill_ghosts_s(), get_entropy_rhs_imp_ghost(), get_entropy_rhs_imp(), fill_ghosts_w(), get_pol_rhs_imp_ghost(), get_pol_rhs_imp(), fill_ghosts_z(), get_tor_rhs_imp_ghost(), get_tor_rhs_imp(), fill_ghosts_b(), get_mag_rhs_imp_ghost(), get_mag_rhs_imp(), get_mag_ic_rhs_imp(), cc2real()

init_fields.f90

Description

This module is used to construct the initial solution.

Quick access

Variables

amp_b1, amp_s1, amp_s2, amp_v1, amp_xi1, amp_xi2, bots, botxi, bpeakbot, bpeaktop, inform, init_b1, init_phi, init_s1, init_s2, init_v1, init_xi1, init_xi2, l_reset_t, l_start_file, n_s_bounds, n_xi_bounds, nrotic, nrotma, omega_ic1, omega_ic2, omega_ma1, omega_ma2, omegaosz_ic1, omegaosz_ic2, omegaosz_ma1, omegaosz_ma2, phi_bot, phi_top, s_bot, s_top, scale_b, scale_s, scale_v, scale_xi, start_file, tipdipole, tomega_ic1, tomega_ic2, tomega_ma1, tomega_ma2, tops, topxi, tshift_ic1, tshift_ic2, tshift_ma1, tshift_ma2, xi_bot, xi_top

Routines

finalize_init_fields(), initb(), initialize_init_fields(), initphi(), inits(), initv(), initxi(), j_cond(), ps_cond(), pt_cond(), xi_cond()

Needed modules

• precision_mod: This module controls the precision used in MagIC

• iso_fortran_env (output_unit())

• parallel_mod: This module contains the blocking information

• mpi_ptop_mod (type_mpiptop()): This module contains the implementation of MPI_Isend/MPI_Irecv global transpose

• mpi_transp_mod (type_mpitransp()): This is an abstract class that will be used to define MPI transposers The actual implementation is deferred to either point-to-point (MPI_Isend and MPI_IRecv) communications or all-to-all (MPI_AlltoAll)

• truncation (n_r_max(), n_r_maxmag(), n_r_ic_max(), m_min(), l_max(), n_phi_max(), n_theta_max(), n_r_tot(), m_max(), minc(), n_cheb_ic_max(), lm_max(), nlat_padded()): This module defines the grid points and the truncation

• mem_alloc (bytes_allocated()): This little module is used to estimate the global memory allocation used in MagIC

• blocking (lo_map(), st_map(), llm(), ulm(), llmmag(), ulmmag()): Module containing blocking information

• horizontal_data (sintheta(), dlh(), dtheta1s(), dtheta1a(), phi(), costheta(), hdif_b()): Module containing functions depending on longitude and latitude plus help arrays depending on degree and order

• logic (l_rot_ic(), l_rot_ma(), l_sric(), l_srma(), l_cond_ic(), l_temperature_diff(), l_chemical_conv(), l_onset(), l_anelastic_liquid(), l_non_adia(), l_finite_diff()): Module containing the logicals that control the run

• radial_functions (r_icb(), r(), r_cmb(), r_ic(), or1(), jvarcon(), lambda(), or2(), dllambda(), or3(), cheb_ic(), dcheb_ic(), d2cheb_ic(), cheb_norm_ic(), orho1(), chebt_ic(), temp0(), dltemp0(), kappa(), dlkappa(), beta(), dbeta(), epscprof(), ddltemp0(), ddlalpha0(), rgrav(), rho0(), dlalpha0(), alpha0(), otemp1(), ogrun(), rscheme_oc(), o_r_ic()): This module initiates all the radial functions (transport properties, density, temperature, cheb transforms, etc.)

• radial_data (n_r_icb(), n_r_cmb(), nrstart(), nrstop()): This module defines the MPI decomposition in the radial direction.

• constants (pi(), y10_norm(), c_z10_omega_ic(), c_z10_omega_ma(), osq4pi(), zero(), one(), two(), three(), four(), third(), half(), sq4pi()): module containing constants and parameters used in the code.

• useful (abortrun()): This module contains several useful routines.

• sht (scal_to_sh())

• physical_parameters (imps(), n_imps_max(), n_imps(), phis(), thetas(), peaks(), widths(), radratio(), imagcon(), opm(), sigma_ratio(), o_sr(), kbots(), ktops(), opr(), epsc(), vischeatfac(), thexpnb(), tmelt(), impxi(), n_impxi_max(), n_impxi(), phixi(), thetaxi(), peakxi(), widthxi(), osc(), epscxi(), kbotxi(), ktopxi(), buofac(), ktopp(), oek(), epsphase()): Module containing the physical parameters

• algebra (prepare_mat(), solve_mat())

• cosine_transform_odd: This module contains the built-in type I discrete Cosine Transforms. This implementation is based on Numerical Recipes and FFTPACK. This only works for n_r_max-1 = 2**a 3**b 5**c, with a,b,c integers….

• dense_matrices

• real_matrices

• band_matrices

Variables

• init_fields/amp_b1 [real,public]

• init_fields/amp_s1 [real,public]

• init_fields/amp_s2 [real,public]

• init_fields/amp_v1 [real,public]

• init_fields/amp_xi1 [real,public]

• init_fields/amp_xi2 [real,public]

• init_fields/bots (*,*) [complex,allocatable/public]

• init_fields/botxi (*,*) [complex,allocatable/public]

• init_fields/bpeakbot [real,public]

• init_fields/bpeaktop [real,public]

• init_fields/inform [integer,public]

  format of start_file

• init_fields/init_b1 [integer,public]

• init_fields/init_phi [integer,public]

  An integer to specify phase field initial configuration

• init_fields/init_s1 [integer,public]

• init_fields/init_s2 [integer,public]

• init_fields/init_v1 [integer,public]

• init_fields/init_xi1 [integer,public]

• init_fields/init_xi2 [integer,public]

• init_fields/l_reset_t [logical,public]

  reset time from startfile ?

• init_fields/l_start_file [logical,public]

  taking fields from startfile ?

• init_fields/n_s_bounds [integer,parameter=20]

• init_fields/n_xi_bounds [integer,parameter=20]

• init_fields/nrotic [integer,public]

• init_fields/nrotma [integer,public]

• init_fields/omega_ic1 [real,public]

• init_fields/omega_ic2 [real,public]

• init_fields/omega_ma1 [real,public]

• init_fields/omega_ma2 [real,public]

• init_fields/omegaosz_ic1 [real,public]

• init_fields/omegaosz_ic2 [real,public]

• init_fields/omegaosz_ma1 [real,public]

• init_fields/omegaosz_ma2 [real,public]

• init_fields/phi_bot [real,public]

  Phase field value at the inner boundary

• init_fields/phi_top [real,public]

  Phase field value at the outer boundary

• init_fields/s_bot (80) [real,public]

  input variables for tops,bots

• init_fields/s_top (80) [real,public]

• init_fields/scale_b [real,public]

• init_fields/scale_s [real,public]

• init_fields/scale_v [real,public]

• init_fields/scale_xi [real,public]

• init_fields/start_file [character(len=72),public]

  name of start_file

• init_fields/tipdipole [real,public]

  adding to symetric field

• init_fields/tomega_ic1 [real,public]

• init_fields/tomega_ic2 [real,public]

• init_fields/tomega_ma1 [real,public]

• init_fields/tomega_ma2 [real,public]

• init_fields/tops (*,*) [complex,allocatable/public]

• init_fields/topxi (*,*) [complex,allocatable/public]

• init_fields/tshift_ic1 [real,public]

• init_fields/tshift_ic2 [real,public]

• init_fields/tshift_ma1 [real,public]

• init_fields/tshift_ma2 [real,public]

• init_fields/xi_bot (80) [real,public]

  input variables for topxi,botxi

• init_fields/xi_top (80) [real,public]

Subroutines and functions

subroutine init_fields/initialize_init_fields()

Memory allocation

Called from

magic

subroutine init_fields/finalize_init_fields()

Memory deallocation

Called from

magic

subroutine init_fields/initv(w, z, omega_ic, omega_ma)

Purpose of this subroutine is to initialize the velocity field So far it is only rudimentary and will be expanded later. Because s is needed for dwdt init_s has to be called before.

Parameters

• w (ulm-(llm)+1,n_r_max) [complex ,inout]

• z (ulm-(llm)+1,n_r_max) [complex ,inout]

• omega_ic [real ,out]

• omega_ma [real ,out]

Called from

getstartfields()

Call to

scal_to_sh()

subroutine init_fields/inits(s, p)

Purpose of this subroutine is to initialize the entropy field according to the input control parameters.

Input	value
init_s1 < 100:	random noise initialized the noise spectrum decays as l ^ (init_s1-1) with peak amplitude amp_s1 for l=1
init_s1 >=100:	a specific harmonic mode initialized with amplitude amp_s1. init_s1 is interpreted as number llmm where ll: harmonic degree, mm: harmonic order.
init_s2 >100 :	a second harmonic mode initialized with amplitude amp_s2. init_s2 is again interpreted as number llmm where ll: harmonic degree, mm: harmonic order.

Parameters

• s (ulm-(llm)+1,n_r_max) [complex ,inout]

• p (ulm-(llm)+1,n_r_max) [complex ,inout]

Called from

getstartfields()

Call to

pt_cond(), ps_cond(), abortrun(), scal_to_sh(), prepare_mat()

subroutine init_fields/initxi(xi)

Purpose of this subroutine is to initialize the chemical composition according to the input control parameters.

Input	value
init_xi1 < 100:	random noise initialized the noise spectrum decays as l^ (init_xi1-1) with peak amplitude amp_xi1 for l=1
init_xi1 >=100:	a specific harmonic mode initialized with amplitude amp_xi1. init_xi1 is interpreted as number llmm where ll: harmonic degree, mm: harmonic order.
init_xi2 >100 :	a second harmonic mode initialized with amplitude amp_xi2. init_xi2 is again interpreted as number llmm where ll: harmonic degree, mm: harmonic order.

Parameters

xi (ulm-(llm)+1,n_r_max) [complex ,inout]

Called from

getstartfields()

Call to

xi_cond(), abortrun(), scal_to_sh(), prepare_mat()

subroutine init_fields/initb(b, aj, b_ic, aj_ic)

Purpose of this subroutine is to initialize the magnetic field according to the control parameters imagcon and init_b1/2. In addition CMB and ICB peak values are calculated for magneto convection.

Parameters

• b (ulmmag-(llmmag)+1,n_r_maxmag) [complex ,inout]

• aj (ulmmag-(llmmag)+1,n_r_maxmag) [complex ,inout]

• b_ic (ulmmag-(llmmag)+1,n_r_ic_max) [complex ,inout]

• aj_ic (ulmmag-(llmmag)+1,n_r_ic_max) [complex ,inout]

Called from

getstartfields()

Call to

j_cond(), abortrun()

subroutine init_fields/initphi(s, phi)

This subroutine sets the initial phase field distribution. It follows a tanh function with a width of size epsPhase

Parameters

• s (ulm-(llm)+1,n_r_max) [complex ,inout] :: Entropy/Temperature

• phi (ulm-(llm)+1,n_r_max) [complex ,inout] :: Phase field

Called from

getstartfields()

subroutine init_fields/j_cond(lm0, aj0, aj0_ic)

Purpose of this subroutine is to solve the diffusion equation for an initial toroidal magnetic field.

Parameters

• lm0 [integer ,in]

• aj0 (*) [complex ,out] :: aj(l=0,m=0) in the outer core

• aj0_ic (*) [complex ,out] :: aj(l=0,m=0) in the inner core

Called from

initb()

Call to

prepare_mat(), abortrun()

subroutine init_fields/xi_cond(xi0)

Purpose of this subroutine is to solve the chemical composition equation for an the conductive (l=0,m=0)-mode. Output is the radial dependence of the solution in s0.

Parameters

xi0 (*) [real ,out] :: spherically-symmetric part

Called from

initxi(), getstartfields()

Call to

abortrun()

subroutine init_fields/pt_cond(t0, p0)

Purpose of this subroutine is to solve the entropy equation for an the conductive (l=0,m=0)-mode. Output is the radial dependence of the solution in t0 and p0.

Parameters

• t0 (*) [real ,out] :: spherically-symmetric temperature

• p0 (*) [real ,out] :: spherically-symmetric pressure

Called from

inits(), getstartfields()

Call to

prepare_mat(), abortrun()

subroutine init_fields/ps_cond(s0, p0)

Purpose of this subroutine is to solve the entropy equation for an the conductive (l=0,m=0)-mode. Output is the radial dependence of the solution in s0 and p0.

Parameters

• s0 (*) [real ,out] :: spherically-symmetric part

• p0 (*) [real ,out] :: spherically-symmetric part

Called from

inits(), getstartfields()

Call to

prepare_mat(), abortrun()