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Revision 1.4 - (hide annotations) (download)
Fri Sep 5 18:30:14 2014 UTC (10 years, 10 months ago) by jmc
Branch: MAIN
CVS Tags: HEAD
Changes since 1.3: +1 -1 lines
updated (new STREAMICE_TIMESTEP)

1 adcroft 1.1 C
2     C Invocation from WRAPPER level...
3 jmc 1.2 C
4 adcroft 1.1 C |
5     C |-THE_MODEL_MAIN :: Primary driver for the MITgcm algorithm
6     C | :: Called from WRAPPER level numerical
7 jmc 1.2 C | :: code invocation routine. On entry
8 adcroft 1.1 C | :: to THE_MODEL_MAIN separate thread and
9     C | :: separate processes will have been established.
10     C | :: Each thread and process will have a unique ID
11     C | :: but as yet it will not be associated with a
12     C | :: specific region in decomposed discrete space.
13     C |
14 jmc 1.2 C |-INITIALISE_FIXED :: Set fixed model arrays such as topography,
15 adcroft 1.1 C | | :: grid, solver matrices etc..
16 jmc 1.2 C | |
17 adcroft 1.1 C | |-INI_PARMS :: Routine to set kernel model parameters.
18 jmc 1.2 C | | :: Kernel parameters are read from file "data"
19     C | | :: in directory in which code executes.
20     C | |
21     C | |-PACKAGES_BOOT :: Start up the optional package environment.
22     C | | :: Runtime selection of active packages.
23 jmc 1.3 C | |-PACKAGES_READPARMS :: read each package input parameter file
24 jmc 1.2 C | | |- ${PKG}_READPARMS
25 adcroft 1.1 C | |
26 jmc 1.2 C | |-SET_PARMS :: Finalise model parameter setting (if fct of pkg usage)
27 adcroft 1.1 C | |
28 jmc 1.3 C | |-INI_MODEL_IO :: Initialise Input/Output setting
29     C | | |-MNC_INIT :: Initialise MITgcm NetCDF interface (MNC)(see pkg/mnc)
30     C | | |-MNC_CW_INIT :: Initialise MNC grid and variable types (see pkg/mnc)
31     C | | |-MON_INIT :: Initialises monitor package ( see pkg/monitor )
32     C | |
33     C | |-INI_GRID :: Control grid array (vert. and horiz.) initialisation.
34     C | | | :: Grid arrays are held and described in GRID.h.
35     C | | |-LOAD_GRID_SPACING :: Load grid spacing (vector) from files
36     C | | |-INI_VERTICAL_GRID :: Set up vertical grid and coordinate
37     C | | |-INI_CARTESIAN_GRID :: Cartesian horiz. grid initialisation
38     C | | | :: (calculate grid from kernel parameters).
39 jmc 1.2 C | | |-INI_SPHERICAL_POLAR_GRID :: Spherical polar horiz. grid setting
40     C | | | :: (calculate grid from kernel parameters).
41 jmc 1.3 C | | |-INI_CURVILINEAR_GRID :: General orthogonal, structured horiz. grid
42     C | | | :: initialisation; input from raw grid files
43     C | | | :: (LONC.bin, LATC.bin, DXF.bin, ... ) or per
44     C | | | :: face file: horizGridFile(.faceXXX.bin)
45     C | | |-INI_CYLINDER_GRID :: Cylindrical horiz. grid setting
46     C | |
47     C | |-LOAD_REF_FILES :: Read-in reference vertical profiles (T,S,Rho)
48     C | |-INI_EOS :: Initialise Equation Of State (EOS) coefficients
49     C | |-SET_REF_STATE :: Set reference pressure/geopotential, reference
50     C | | :: stratification (for implicit IGW), vertical
51     C | | :: velocity scaling factor and anelastic ref. density
52     C | |-SET_GRID_FACTORS :: Set grid factors (fct of k) for deep-atmosphere
53 adcroft 1.1 C | |
54 jmc 1.2 C | |-INI_DEPTHS :: Read (from "bathyFile") or set bathymetry/orography.
55 adcroft 1.1 C | |-INI_MASKS_ETC :: Derive horizontal and vertical cell fractions and
56     C | | :: land masking for solid-fluid boundaries.
57     C | |
58 jmc 1.2 C | |-PACKAGES_INIT_FIXED :: do all packages fixed-initialisation setting
59     C | | |- ${PKG}_INIT_FIXED
60     C | |
61 jmc 1.3 C | |-INI_GLOBAL_DOMAIN :: Initialise domain related (global) quantities.
62     C | |-INI_LINEAR_PHISURF :: Set ref. surface Bo_surf
63 adcroft 1.1 C | |
64     C | |-INI_CORI :: Set coriolis term. zero, f-plane, beta-plane,
65 jmc 1.3 C | | :: sphere options are coded.
66     C | |-INI_CG2D :: 2D conjugate grad solver initialisation.
67     C | |-INI_CG3D :: 3D conjugate grad solver initialisation.
68 jmc 1.2 C | |
69     C | |-CONFIG_SUMMARY :: Provide synopsis of kernel setup. Includes
70     C | | :: annotated table of kernel parameter settings.
71     C | |
72     C | |-PACKAGES_CHECK :: call each package configuration checking S/R
73     C | | |- ${PKG}_CHECK
74 adcroft 1.1 C | |
75 jmc 1.2 C | |-CONFIG_CHECK :: Check config and parameter consistency.
76 adcroft 1.1 C | |
77 jmc 1.3 C | |-WRITE_GRID :: write grid fields to output files
78     C | |-CPL_EXCH_CONFIGS :: exchange config with coupler-interface
79 adcroft 1.1 C |
80 jmc 1.2 C |-CTRL_UNPACK :: Control vector support package. see pkg/ctrl
81 jmc 1.3 C |-COST_DEPENDENT_INIT :: ( see pkg/cost )
82 adcroft 1.1 C |
83     C |-ADTHE_MAIN_LOOP :: Derivative evaluating form of main time stepping loop
84 jmc 1.2 C ! :: Automatically generated by TAMC/TAF.
85 adcroft 1.1 C |
86 jmc 1.2 C |-THE_MAIN_LOOP :: Main timestepping loop routine.
87 adcroft 1.1 C | |
88 jmc 1.3 C | |-INITIALISE_VARIA :: Set the initial conditions for time evolving fields
89 adcroft 1.1 C | | |
90 jmc 1.2 C #ifdef ALLOW_AUTODIFF
91     C | | |-INI_DEPTHS \
92     C | | |-CTRL_DEPTH_INI \
93     C | | |-UPDATE_MASKS_ETC } ALLOW_DEPTH_CONTROL case
94     C | | |-UPDATE_CG2D /
95     C #endif
96     C | | |-INI_NLFS_VARS :: Initialise all Non-Lin Free-Surf arrays (SURFACE.h)
97     C | | |-INI_DYNVARS :: Initialise to zero all DYNVARS.h arrays
98     C | | |-INI_NH_VARS :: Initialise to zero all NH_VARS.h arrays
99 adcroft 1.1 C | | |
100 jmc 1.3 C | | |-INI_FIELDS :: Control initialising model fields to non-zero
101     C | | | |-INI_VEL :: Initialize 3D flow field.
102     C | | | |-INI_THETA :: Set model initial temperature field.
103     C | | | |-INI_SALT :: Set model initial salinity field.
104     C | | | |-INI_PSURF :: Set model initial free-surface height/pressure.
105     C | | | |-READ_PICKUP :: Read in main model pickup files to restart a run.
106 adcroft 1.1 C | | |
107 jmc 1.2 C | | |-INI_MIXING :: Initialise diapycnal diffusivity.
108 adcroft 1.1 C | | |
109 jmc 1.3 C | | |-INI_FORCING :: Set model initial forcing fields, either
110     C | | | | :: set in-line or from file as shown here:
111 adcroft 1.1 C | | | |-READ_FLD_XY_RS(zonalWindFile)
112     C | | | |-READ_FLD_XY_RS(meridWindFile)
113 jmc 1.2 C | | | |-READ_FLD_XY_RS(surfQnetFile)
114 adcroft 1.1 C | | | |-READ_FLD_XY_RS(EmPmRfile)
115     C | | | |-READ_FLD_XY_RS(thetaClimFile)
116     C | | | |-READ_FLD_XY_RS(saltClimFile)
117     C | | | |-READ_FLD_XY_RS(surfQswFile)
118     C | | |
119 jmc 1.3 C | | |-AUTODIFF_INIT_VARIA :: (see pkg/autodiff )
120 jmc 1.2 C | | |
121     C | | |-PACKAGES_INIT_VARIABLES :: Does initialisation of time evolving
122     C | | | | ${PKG}_INIT_VARIA :: package data.
123     C | | |
124 jmc 1.3 C | | |-COST_INIT_VARIA :: ( see pkg/cost )
125     C | | |-CONVECTIVE_ADJUSTMENT_INI :: Apply conv. adjustment to initial state
126 jmc 1.2 C | | |
127     C | | |-CALC_R_STAR :: Calculate the new level thickness factor (r* coord)
128     C | | |-UPDATE_R_STAR :: Update the level thickness fraction (r* coord).
129     C | | |-UPDATE_SIGMA :: Update the level thickness fraction (sigma-coord).
130 adcroft 1.1 C | | |-CALC_SURF_DR :: Calculate the new surface level thickness.
131     C | | |-UPDATE_SURF_DR :: Update the surface-level thickness fraction.
132 jmc 1.2 C | | |
133 jmc 1.3 C | | |-UPDATE_CG2D :: Update 2D conjugate grad. for Free-Surf.
134 jmc 1.2 C | | |
135 jmc 1.3 C | | |-INTEGR_CONTINUITY :: Integrate the continuity Equation
136 jmc 1.2 C | | | |-INTEGRATE_FOR_W :: Integrate for vertical velocity
137     C | | | |-OBCS_APPLY_W :: Open boundary package (see pkg/obcs).
138     C | | | |-UPDATE_ETAH :: Update Surface height/pressure
139     C | | |
140     C | | |-CALC_R_STAR :: Calculate the new level thickness factor (r* coord)
141     C | | |-CALC_SURF_DR :: Calculate the new surface level thickness.
142     C | | |
143     C | | |-STATE_SUMMARY :: Summarise model prognostic variables.
144     C | | |
145     C | | |-MONITOR :: Monitor state (see pkg/monitor)
146     C | | |
147     C | | |-DO_STATEVARS_TAVE :: Time averaging package ( see pkg/timeave ).
148 jmc 1.3 C | | | |-TIMEAVE_STATVARS :: Accumulate main model state variables
149     C | | | |-PTRACERS_TIMEAVE :: Accumulate passive tracers variables
150 jmc 1.2 C | | |
151     C | | |-DO_THE_MODEL_IO :: Controlling routine for IO
152     C | | | |-WRITE_STATE :: Write model state variables.
153     C | | | |-TIMEAVE_STATV_WRITE :: Write Time averaged output (see pkg/timeave)
154 jmc 1.3 C | | | |-FIZHI_WRITE_STATE :: Write Fizhi pkg output (see pkg/fizhi)
155     C | | | |-AIM_WRITE_TAVE :: Write AIM pkg output (see pkg/aim_v23)
156     C | | | |-LAND_OUTPUT :: Write Land pkg output (see pkg/land)
157     C | | | |-OBCS_OUTPUT :: Write OBCS pkg output (see pkg/obcs)
158     C | | | |-GMREDI_OUTPUT :: Write GM-Redi pkg output (see pkg/gmredi)
159     C | | | |-KPP_OUTPUT :: Write KPP pkg output (see pkg/kpp)
160     C | | | |-PP81_OUTPUT :: Write PP81 pkg output (see pkg/pp81)
161     C | | | |-KL10_OUTPUT :: Write KL10 pkg output (see pkg/kl10)
162     C | | | |-MY82_OUTPUT :: Write MY82 pkg output (see pkg/my82)
163     C | | | |-OPPS_OUTPUT :: Write OPPS pkg output (see pkg/opps)
164     C | | | |-GGL90_OUTPUT :: Write GGL90 pkg output (see pkg/ggl90)
165     C | | | |-SBO_CALC :: Compute SBO diagnostics (see pkg/sbo)
166     C | | | |-SBO_OUTPUT :: Write SBO pkg output (see pkg/sbo)
167     C | | | |-SEAICE_OUTPUT :: Write SeaIce pkg output (see pkg/seaice)
168     C | | | |-SHELFICE_OUTPUT :: Write ShelfIce pkg output (see pkg/shelfice)
169     C | | | |-BULKF_OUTPUT :: Write Bulk-Force output (see pkg/bulK_force)
170     C | | | |-THSICE_OUTPUT :: Write ThSIce pkg output (see pkg/thsice)
171     C | | | |-PTRACERS_OUTPUT :: Write pTracers pkg output (see pkg/ptracers)
172     C | | | |-MATRIX_OUTPUT :: Write Matrix pkg output (see pkg/matrix)
173     C | | | |-GCHEM_OUTPUT :: Write Geochemistry pkg output (see pkg/gchem)
174     C | | | |-CPL_OUTPUT :: Write Coupler-Interface output (see
175     C | | | | :: pkg/atm_compon_interf, pkg/ocn_compon_interf)
176     C | | | |-LAYERS_CALC :: Calculate layers diagnostics (see pkg/layers)
177     C | | | |-LAYERS_OUTPUT :: Write Layers pkg output (see pkg/layers)
178 jmc 1.2 C | | | |-DIAGNOSTICS_WRITE :: Write pkg/diagnostics output
179     C | | |
180 adcroft 1.1 C====|>| ****************************
181     C====|>| BEGIN MAIN TIMESTEPPING LOOP
182     C====|>| ****************************
183 jmc 1.2 C | |-COST_AVERAGESFIELDS :: time-averaged Cost function terms (see pkg/cost)
184 jmc 1.3 C | |-PROFILES_INLOOP :: ( see pkg/profiles )
185 jmc 1.2 C | /
186     C | |-MAIN_DO_LOOP :: Open-AD case: Main timestepping loop routine
187     C | \ otherwise: just call FORWARD_STEP
188     C | |
189     C/\ | |-FORWARD_STEP :: Step forward a time-step ( AT LAST !!! )
190     C/\ | | |
191 jmc 1.3 C/\ | | |-AUTODIFF_INADMODE_UNSET :: Set/reset some adjoint flags
192     C/\ | | |-RESET_NLFS_VARS :: Reset some Non-Lin Free-Surf vars (Adjoint)
193     C/\ | | |-UPDATE_R_STAR :: Reset r-star factor variables (Adjoint)
194     C/\ | | |-UPDATE_SURF_DR :: Reset NLFS surface thickness vars (Adjoint)
195     C/\ | | |
196     C/\ | | |-PTRACERS_SWITCH_ONOFF :: Set/reset pTracers time-stepping switch
197     C/\ | | |-DIAGNOSTICS_SWITCH_ONOFF :: Activate/de-activate diagnostics
198     C/\ | | |-DO_STATEVARS_DIAGS ( 0 ) :: fill-up state variable diagnostics
199     C/\ | | |
200     C/\ | | |-NEST_CHILD_SETMEMO :: Nesting interface
201     C/\ | | |-NEST_PARENT_IO_1 :: Nesting interface
202     C/\ | | |
203     C/\ | | |-LOAD_FIELDS_DRIVER :: Control loading of input fields from files
204 jmc 1.2 C/\ | | |
205 jmc 1.3 C/\ | | |-BULKF_FORCING :: Calculate surface forcing (see pkg/bulk_force)
206     C/\ | | |-CHEAPAML :: Cheap AML driver ( see pkg/cheapaml )
207 jmc 1.2 C/\ | | |-CTRL_MAP_FORCING :: Control vector support package. (see pkg/ctrl)
208 jmc 1.3 C/\ | | |-DUMMY_IN_STEPPING :: Autodiff package ( pkg/autodiff ).
209 adcroft 1.1 C/\ | | |
210 jmc 1.2 C/\ | | |-CPL_EXPORT_MY_DATA :: Send coupling fields to coupler
211     C/\ | | |-CPL_IMPORT_EXTERNAL_DATA :: Receive coupling fields from coupler
212 adcroft 1.1 C/\ | | |
213 jmc 1.3 C/\ | | |-OASIS_PUT :: Oasis coupler interface
214     C/\ | | |-OASIS_GET :: Oasis coupler interface
215     C/\ | | |
216     C/\ | | |-EBM_DRIVER :: Calculate EBM type atmospheric forcing (see pkg/ebm)
217     C/\ | | |
218 jmc 1.2 C/\ | | |-DO_ATMOSPHERIC_PHYS :: Atmospheric physics computation
219 jmc 1.3 C/\ | | | |
220     C/\ | | | |-UPDATE_OCEAN_EXPORTS :: ( see pkg/fizhi )
221     C/\ | | | |-UPDATE_EARTH_EXPORTS :: ( see pkg/fizhi )
222     C/\ | | | |-UPDATE_CHEMISTRY_EXPORTS :: ( see pkg/fizhi )
223     C/\ | | | |-FIZHI_WRAPPER :: ( see pkg/fizhi )
224     C/\ | | | |-STEP_FIZHI_FG :: ( see pkg/fizhi )
225     C/\ | | | |-FIZHI_UPDATE_TIME :: ( see pkg/fizhi )
226     C/\ | | | |
227     C/\ | | | |-ATM_PHYS_DRIVER :: ( see pkg/atm_phys )
228     C/\ | | | |
229     C/\ | | | |-AIM_DO_PHYSICS :: ( see pkg/aim_v23 )
230 jmc 1.2 C/\ | | |
231     C/\ | | |-DO_OCEANIC_PHYS :: Oceanic (& seaice) physics computation
232 jmc 1.3 C/\ | | | |
233 jmc 1.2 C/\ | | | |-OBCS_CALC :: Open boundary. package (see pkg/obcs).
234 jmc 1.3 C/\ | | | |
235     C/\ | | | |-FRAZIL_CALC_RHS :: Compute FRAZIL tendencies ( see pkg/frazil )
236     C/\ | | | |-THSICE_MAIN :: Thermodynamic sea-ice driver (see pkg/thsice)
237     C/\ | | | |-SEAICE_MODEL :: Sea-ice model driver (see pkg/seaice )
238     C/\ | | | |-SEAICE_COST_SENSI :: Sea-ice cost-function (see pkg/seaice )
239     C/\ | | | |-SHELFICE_THERMODYNAMICS :: Compute ShelfIce thermo (pkg/shelfice)
240     C/\ | | | |-ICEFRONT_THERMODYNAMICS :: Compute IceFront thermo (pkg/icefront)
241     C/\ | | | |
242     C/\ | | | |-SALT_PLUME_DO_EXCH :: (see pkg/salt_plume )
243     C/\ | | | |-FREEZE_SURFACE :: Prevent SST to fall below TFreeze
244     C/\ | | | |-OCN_APPLY_IMPORT :: Apply imported fields from coupler
245     C/\ | | | |-EXTERNAL_FORCING_SURF:: Compute appropriately dimensioned
246     C/\ | | | | :: surface forcing terms.
247     C/\ | | | |-FIND_RHO_2D @ p(k) :: Calculate [rho(T,S,p)-Rho_0] of a slice
248     C/\ | | | |-FIND_RHO_2D @ p(k-1) :: Calculate [rho(T,S,p)-Rho_0] of a slice
249     C/\ | | | |-GRAD_SIGMA :: Calculate isoneutral gradients
250     C/\ | | | |-CALC_IVDC :: Set Implicit Vertical Diffusivity for Convection
251     C/\ | | | |-CALC_OCE_MXLAYER :: Diagnose Oceanic Mixed Layer depth
252     C/\ | | | |
253     C/\ | | | |-SALT_PLUME_CALC_DEPTH :: (see pkg/salt_plume )
254     C/\ | | | |-SALT_PLUME_VOLFRAC :: (see pkg/salt_plume )
255     C/\ | | | |-SALT_PLUME_APPLY (Temp) :: (see pkg/salt_plume )
256     C/\ | | | |-SALT_PLUME_APPLY (Salt) :: (see pkg/salt_plume )
257     C/\ | | | |-SALT_PLUME_FORCING_SURF :: (see pkg/salt_plume )
258     C/\ | | | |-KPP_CALC :: Compute KPP vertical mixing ( see pkg/kpp )
259     C/\ | | | |-PP81_CALC :: Compute PP81 vertical mixing ( see pkg/pp81 )
260     C/\ | | | |-KL10_CALC :: Compute KL10 vertical mixing ( see pkg/kl10 )
261     C/\ | | | |-MY82_CALC :: Compute MY82 vertical mixing ( see pkg/kl10 )
262     C/\ | | | |-GGL90_CALC :: Compute GGL90 vertical mixing (see pkg/ggl10)
263     C/\ | | | |-GMREDI_CALC_TENSOR :: Compute GM-Redi tensor ( see pkg/gmredi )
264     C/\ | | | |-DWNSLP_CALC_FLOW :: Compute Down-Slope flow (see pkg/down_slope)
265     C/\ | | | |-BBL_CALC_RHS :: Compute BBL tendencies ( see pkg/bbl )
266     C/\ | | | |-MYPACKAGE_CALC_RHS :: Compute mypackage tendencies (pkg/mypackage)
267     C/\ | | | |
268     C/\ | | | |-GMREDI_DO_EXCH :: ( see pkg/gmredi )
269     C/\ | | | |-KPP_DO_EXCH :: ( see pkg/kpp )
270     C/\ | | | |-DIAGS_RHO_G :: Compute some density related diagnostics
271     C/\ | | | |-DIAGS_OCEANIC_SURF_FLUX :: Diagnose oceanic surface fluxes
272     C/\ | | | |-SALT_PLUME_DIAGNOSTICS_FILL :: (see pkg/salt_plume )
273     C/\ | | | |-ECCO_PHYS :: ( see pkg/ecco )
274     C/\ | | |
275 jmc 1.4 C/\ | | |-STREAMICE_TIMESTEP :: ( see pkg/streamice )
276 jmc 1.3 C/\ | | |
277     C/\ | | |-GCHEM_CALC_TENDENCY :: geochemistry driver routine (see pkg/gchem)
278     C/\ | | |
279     C/\ | | |-LONGSTEP_AVERAGE :: Averaging state vars ( see pkg/longstep )
280     C/\ | | |-LONGSTEP_THERMODYNAMICS :: Step forward tracers ( see pkg/longstep )
281     C/\ | | |
282     C/\ | | |-THERMODYNAMICS :: theta, salt + tracer equations driver.
283     C/\ | | | | (synchronous time-stepping case)
284     C/\ | | | |-CALC_WSURF_TR :: Compute T & S Linear-Free-Surf correction
285     C/\ | | | |-PTRACERS_CALC_WSURF_TR :: Compute Tracers Linear-Free-Surf correct.
286     C/\ | | | |
287     C/\ | | | |-GMREDI_RESIDUAL_FLOW :: Get the flow field used to advect tracers
288 jmc 1.2 C/\ | | | |
289     C/\ | | | |-TEMP_INTEGRATE :: Step forward Prognostic Eq for Temperature.
290 jmc 1.3 C/\ | | | | |
291     C/\ | | | | |-ADAMS_BASHFORTH3 :: Extrapolate tracer forward in time (AB-3)
292     C/\ | | | | |-ADAMS_BASHFORTH2 :: Extrapolate tracer forward in time (AB-2)
293     C/\ | | | | |-CALC_3D_DIFFUSIVITY :: set vertical diffusivity
294     C/\ | | | | |
295     C/\ | | | | |-GAD_SOM_ADVECT :: Second Order Moment (SOM) advection
296 jmc 1.2 C/\ | | | | |-GAD_ADVECTION :: Generalised advection driver (multi-dim
297     C/\ | | | | | advection case) (see pkg/gad).
298 jmc 1.3 C/\ | | | | |-CALC_ADV_FLOW :: set 3-D flow field to advect tracer
299     C/\ | | | | |-APPLY_FORCING_T :: Problem specific forcing for temperature.
300 jmc 1.2 C/\ | | | | |-GAD_CALC_RHS :: Calculate Advection-Diffusion tendency terms
301 jmc 1.3 C/\ | | | | |
302     C/\ | | | | |-ADAMS_BASHFORTH3 :: Extrapolate tendency forward in time (AB-3)
303     C/\ | | | | |-ADAMS_BASHFORTH2 :: Extrapolate tendency forward in time (AB-2)
304     C/\ | | | | |-FREESURF_RESCALE_G :: Re-scale Gt for free-surface height.
305     C/\ | | | | |-DWNSLP_APPLY :: Add pkg/down_slope tendency
306     C/\ | | | | |
307 jmc 1.2 C/\ | | | | |-TIMESTEP_TRACER :: Step tracer field forward in time
308 jmc 1.3 C/\ | | | | |
309     C/\ | | | | |-GAD_IMPLICIT_R :: Solve vertical implicit Advect-Diffus. eqn.
310 jmc 1.2 C/\ | | | | |-IMPLDIFF :: Solve vertical implicit diffusion equation.
311     C/\ | | | | |-CYCLE_AB_TRACER :: Cycle time-stepping arrays for tracer field
312 jmc 1.3 C/\ | | | | |-CYCLE_TRACER :: Cycle time-stepping arrays for tracer field
313 jmc 1.2 C/\ | | | |
314     C/\ | | | |-SALT_INTEGRATE :: Step forward Prognostic Eq for Salinity.
315     C/\ | | | | | same sequence of calls as in TEMP_INTEGRATE
316     C/\ | | | |
317     C/\ | | | |-PTRACERS_INTEGRATE :: Integrate other tracer(s) (see pkg/ptracers).
318     C/\ | | | | | same sequence of calls as in TEMP_INTEGRATE
319     C/\ | | | | |-OBCS_APPLY_PTRACER :: Open boundary package for pTracers
320 adcroft 1.1 C/\ | | | |
321 jmc 1.2 C/\ | | | |-OBCS_APPLY_TS :: Open boundary package (see pkg/obcs ).
322 adcroft 1.1 C/\ | | |
323 jmc 1.3 C/\ | | |-LONGSTEP_AVERAGE :: Averaging state vars ( see pkg/longstep )
324     C/\ | | |-LONGSTEP_THERMODYNAMICS :: Step forward tracers ( see pkg/longstep )
325     C/\ | | |
326     C/\ | | |-DO_STAGGER_FIELDS_EXCHANGES :: Update overlap regions of arrays
327     C/\ | | | Theta & Salt (implicit IGW case)
328     C/\ | | |
329 adcroft 1.1 C/\ | | |-DYNAMICS :: Momentum equations driver.
330     C/\ | | | |
331 jmc 1.2 C/\ | | | |-CALC_GRAD_PHI_SURF :: Calculate the gradient of the surface
332 adcroft 1.1 C/\ | | | | Potential anomaly.
333 jmc 1.2 C/\ | | | |-CALC_VISCOSITY :: Calculate net vertical viscosity
334 jmc 1.3 C/\ | | | |-MOM_CALC_3D_STRAIN :: Calculates the strain tensor of 3D flow field
335     C/\ | | | |-OBCS_COPY_UV_N :: for Stevens bndary Conditions (see pkg/obcs)
336     C/\ | | | |
337 jmc 1.2 C/\ | | | |-CALC_PHI_HYD :: Integrate the hydrostatic relation.
338 jmc 1.3 C/\ | | | |-MOM_FLUXFORM :: Flux Form momentum eqn. (pkg/mom_fluxform)
339     C/\ | | | |-MOM_VECINV :: Vector Invariant momentum eqn (pkg/mom_vecinv)
340     C/\ | | | |-MOM_CALC_SMAG_3D :: Calculate Smagorinsky 3D (harmonic) viscosities
341     C/\ | | | |-MOM_UV_SMAG_3D :: Calculate U,V mom. tendency due to Smag 3D Visc
342     C/\ | | | |-TIMESTEP :: Step horizontal momentum fields forward in time
343     C/\ | | | |
344     C/\ | | | |-MOM_U_IMPLICIT_R :: Solve implicitly vertical Adv-Diffus equation.
345 jmc 1.2 C/\ | | | |-IMPLDIFF :: Solve vertical implicit diffusion equation.
346 jmc 1.3 C/\ | | | |-OBCS_SAVE_UV_N :: for Stevens bndary Conditions (see pkg/obcs)
347     C/\ | | | |-OBCS_APPLY_UV :: Apply Open bndary Conditions to provisional U,V
348     C/\ | | | |-IMPLDIFF :: (CD-Scheme) Solve vertical impl. diffus. eqn
349     C/\ | | | |
350     C/\ | | | |-CALC_GW :: Vert. momentum tendency terms (Non-Hydrostatic)
351     C/\ | | | | |-MOM_W_SMAG_3D :: Calculate W mom. tendency due to Smag 3D Visc
352     C/\ | | | |-TIMESTEP_WVEL :: Step vert mom forward in time (Non-Hydrostatic)
353 adcroft 1.1 C/\ | | |
354 jmc 1.3 C/\ | | |-MNC_UPDATE_TIME :: Update MNC time record (see pkg/mnc)
355     C/\ | | |
356     C/\ | | |-UPDATE_R_STAR :: Update the level thickness fraction (r* coord).
357     C/\ | | |-UPDATE_SIGMA :: Update the level thickness fraction (sigma-coord).
358     C/\ | | |-UPDATE_R_STAR :: Update the level thickness fraction.
359 adcroft 1.1 C/\ | | |-UPDATE_SURF_DR :: Update the surface-level thickness fraction.
360 jmc 1.3 C/\ | | |-UPDATE_CG2D :: Update 2D conjugate grad. for Free-Surf.
361     C/\ | | |
362     C/\ | | |-SHAP_FILT_APPLY_UV :: Apply Shapiro Filter to provisional velocity
363     C/\ | | |-ZONAL_FILT_APPLY_UV :: Apply Zonal Filter to provisional velocity
364 adcroft 1.1 C/\ | | |
365 jmc 1.2 C/\ | | |-SOLVE_FOR_PRESSURE :: Find surface pressure.
366 jmc 1.3 C/\ | | | |-CALC_DIV_GHAT :: Form the RHS of the surface pressure eqn.
367 adcroft 1.1 C/\ | | | |-CG2D :: Two-dim pre-con. conjugate-gradient.
368 jmc 1.3 C/\ | | | |-PRE_CG3D :: Finish to set the RHS of the 3-D pressure eqn.
369 adcroft 1.1 C/\ | | | |-CG3D :: Three-dim pre-con. conjugate-gradient solver.
370 jmc 1.3 C/\ | | | |-POST_CG3D :: finalise solution of NH and Free-Surf pressure
371 adcroft 1.1 C/\ | | |
372 jmc 1.2 C/\ | | |-MOMENTUM_CORRECTION_STEP :: Finalise momentum stepping
373 jmc 1.3 C/\ | | | |-CALC_GRAD_PHI_SURF :: Return DDx and DDy of surface pressure
374     C/\ | | | |-CORRECTION_STEP :: Pressure correction to momentum
375     C/\ | | | |-OBCS_APPLY_UV :: Open boundary package (see pkg/obcs).
376     C/\ | | | |-SHAP_FILT_APPLY_UV :: Apply Shapiro Filter to latest velocity
377     C/\ | | | |-ZONAL_FILT_APPLY_UV :: Apply Zonal Filter to latest velocity
378     C/\ | | |
379     C/\ | | |-INTEGR_CONTINUITY :: Integrate continuity equation (see above)
380     C/\ | | |
381     C/\ | | |-CALC_R_STAR :: Calculate the new level thickness factor (r* coord)
382     C/\ | | |-CALC_SURF_DR :: Calculate the new surface level thickness.
383     C/\ | | |
384     C/\ | | |-DO_STAGGER_FIELDS_EXCHANGES :: Update overlap regions of arrays
385     C/\ | | | uVel,vVel & wVel (stagger-time-step case)
386     C/\ | | |
387     C/\ | | |-DO_STATEVARS_DIAGS ( 1 ) :: fill-up state variable diagnostics
388     C/\ | | |
389     C/\ | | |-THERMODYNAMICS :: theta, salt + tracer Eq. driver (see above).
390     C/\ | | | (staggered time-stepping case)
391     C/\ | | |
392     C/\ | | |-TRACERS_CORRECTION_STEP :: Finalise tracer stepping:
393     C/\ | | | | :: apply filter, conv.adjustment
394     C/\ | | | |-TRACERS_IIGW_CORRECTION :: apply Implicit IGW adjustment to T & S
395     C/\ | | | |-SHAP_FILT_APPLY_TS :: Apply Shapiro Filter to latest T & S
396     C/\ | | | |-ZONAL_FILT_APPLY_TS :: Apply Zonal Filter to latest T & S
397     C/\ | | | |-PTRACERS_ZONAL_FILT_APPLY :: Apply Zonal Filter to pTracers
398     C/\ | | | |-SALT_FILL :: Fill up negative Salt
399     C/\ | | | |-OPPS_INTERFACE :: ( see pkg/opps )
400     C/\ | | | |-CONVECTIVE_ADJUSTMENT :: Apply convective adjustment
401     C/\ | | | |-MATRIX_STORE_TENDENCY_IMP :: ( see pkg/matrix )
402     C/\ | | |
403     C/\ | | |-LONGSTEP_AVERAGE :: Averaging state vars ( see pkg/longstep )
404     C/\ | | |-LONGSTEP_THERMODYNAMICS :: Step forward tracers ( see pkg/longstep )
405     C/\ | | |
406     C/\ | | |-GCHEM_FORCING_SEP :: Tracer forcing for gchem pkg (if tracer
407     C/\ | | | :: dependent tendencies calculated separately)
408 jmc 1.2 C/\ | | |
409 jmc 1.3 C/\ | | |-DO_FIELDS_BLOCKING_EXCHANGES :: Sync up overlap regions.
410     C/\ | | |
411     C/\ | | |-DO_STATEVARS_DIAGS ( 2 ) :: fill-up state variable diagnostics
412 adcroft 1.1 C/\ | | |
413 jmc 1.3 C/\ | | |-GRIDALT_UPDATE :: ( see pkg/gridalt )
414     C/\ | | |-STEP_FIZHI_CORR :: ( see pkg/fizhi )
415 jmc 1.2 C/\ | | |
416 jmc 1.3 C/\ | | |-FLT_MAIN :: Step forward Floats (see pkg/flt)
417 adcroft 1.1 C/\ | | |
418 jmc 1.3 C/\ | | |-DO_STATEVARS_TAVE :: Time averaging package (see above)
419 adcroft 1.1 C/\ | | |
420 jmc 1.3 C/\ | | |-NEST_PARENT_IO_2 :: Nesting interface
421     C/\ | | |-NEST_CHILD_TRANSP :: Nesting interface
422 adcroft 1.1 C/\ | | |
423 jmc 1.2 C/\ | | |-MONITOR :: Monitor package (pkg/monitor).
424     C/\ | | |
425 jmc 1.3 C/\ | | |-COST_TILE :: ( see pkg/cost )
426     C/\ | | |
427     C/\ | | |-DO_THE_MODEL_IO :: Controlling routine for IO (see above)
428     C/\ | | |
429     C/\ | | |-PTRACERS_RESET :: Re-initialize PTRACERS ( see pkg/ptracers )
430     C/\ | | |
431     C/\ | | |-DO_WRITE_PICKUP :: Controlling routine for writing files to restart
432     C/\ | | | |-PACKAGES_WRITE_PICKUP :: Write pickup files for each package
433     C/\ | | | | | :: which needs it to restart
434     C/\ | | | | |-GAD_WRITE_PICKUP :: Write Generic AdvDiff pickups for SOM
435     C/\ | | | | | :: advection scheme (pkg/generic_advdiff)
436     C/\ | | | | |-CD_CODE_WRITE_PICKUP :: Write CD-code pickups (see pkg/cd_code)
437     C/\ | | | | |-OBCS_WRITE_PICKUP :: Write OBCS pickups (see pkg/obcs)
438     C/\ | | | | |-GGL90_WRITE_PICKUP :: Write GGL90 pickups (see pkg/ggl90)
439     C/\ | | | | |-BBL_WRITE_PICKUP :: Write BBL pickups (see pkg/bbl)
440     C/\ | | | | |-CHEAPAML_WRITE_PICKUP :: Write CheapAML pickups (pkg/cheapaml)
441     C/\ | | | | |-FLT_WRITE_PICKUP :: Write Floats pickups (see pkg/flt)
442     C/\ | | | | |-PTRACERS_WRITE_PICKUP :: Write pTracers pickups (pkg/ptracers)
443     C/\ | | | | |-GCHEM_WRITE_PICKUP :: Write Geo-Chem pickups (see pkg/gchem)
444     C/\ | | | | |-SEAICE_WRITE_PICKUP :: Write SeaIce pickups (see pkg/seaice)
445     C/\ | | | | |-STREAMICE_WRITE_PICKUP :: Write StreamIce pickups (pkg/streamice)
446     C/\ | | | | |-THSICE_WRITE_PICKUP :: Write ThSIce pickups (see pkg/thsice)
447     C/\ | | | | |-LAND_WRITE_PICKUP :: Write Land pickups (see pkg/land)
448     C/\ | | | | |-ATM_PHYS_WRITE_PICKUP :: Write Atm-Phys pickups (pkg/atm_phys)
449     C/\ | | | | |-FIZHI_WRITE_PICKUP :: Write Fizhi pickups (see pkg/fizhi)
450     C/\ | | | | |-FIZHI_WRITE_VEGTILES :: Write Fizhi VegTiles (see pkg/fizhi)
451     C/\ | | | | |-FIZHI_WRITE_DATETIME :: Write Fizhi DateTime (see pkg/fizhi)
452     C/\ | | | | |-CPL_WRITE_PICKUP :: Write Coupling-Interface pickups
453     C/\ | | | | |-MYPACKAGE_WRITE_PICKUP :: Write pkg/mypackage pickups
454     C/\ | | | |
455     C/\ | | | |-WRITE_PICKUP :: Write main model pickup files.
456     C/\ | | |
457     C/\ | | |-AUTODIFF_INADMODE_SET :: Set/reset some adjoint flags
458 jmc 1.2 C | |
459 adcroft 1.1 C<===|=| **************************
460     C<===|=| END MAIN TIMESTEPPING LOOP
461     C<===|=| **************************
462 jmc 1.2 C | |
463 jmc 1.3 C | |-COST_AVERAGESFIELDS :: Time-averaged Cost function terms (see pkg/cost)
464     C | |-PROFILES_INLOOP :: ( see pkg/profiles )
465     C | |-COST_FINAL :: Cost function package (see pkg/cost)
466 jmc 1.2 C |
467 jmc 1.3 C |-CTRL_PACK :: Control vector support package (see pkg/ctrl)
468 adcroft 1.1 C |
469 jmc 1.3 C |-GRDCHK_MAIN :: Gradient check package (see pkg/grdchk)
470 adcroft 1.1 C |
471 jmc 1.2 C |-TIMER_PRINTALL :: Computational timing summary
472 adcroft 1.1 C |
473 jmc 1.2 C |-COMM_STATS :: Summarise inter-proc and inter-thread communication
474 jmc 1.3 C | :: events.

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