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Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
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============================== |
============================== |
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o removed gravitySign from PARM04 |
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o switched to g77/ifc from pgf77 in aim experiments |
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checkpoint46l_post |
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o made convective adjustment work with pressure coordinates: |
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- changed the direction of k-loop in convective_adjustment.F for the |
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case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation) |
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- adjusted the reference pressure k-index in convective_adjustment.F |
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- adjusted the convection condition in convect.F (in analogy to |
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calc_ivdc.F) |
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- convective_adjustment no longer computes anything on the halos |
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- removed the warnings about negative salinity from find_rho.F and |
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find_alpha.F; instead the new routine look_for_neg_salinity, called |
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at the beginning of find_rho, find_alpha, and find_beta, does a |
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check of the entire slice, if CPP-option |
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CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined |
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checkpoint46l_pre |
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checkpoint46k_post |
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o fixed the verification/global_ocean.90x40x15 experiment: |
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- new bathymetry (the world according to A., JMC, and M.) |
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- new initial fields and forcing fields (*.bin files) |
28 |
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- new POLY3.COEFFS (for the next release one should switch to a full |
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equation of state: JMD95P or MDJWF) |
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- fixed several errors and redundancies in the data file |
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- experiment uses looped cells |
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- added matlab directory with diagnostic scripts for plotting of output |
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|
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o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F: |
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- read AIM physics parameters from a file (data.aimphys) |
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- set defaults values = F.Molteni paper (Clim.Dyn., 2002) |
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checkpoint46j_post |
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o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH |
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o move wVel computation at the end of the time step, in S/R integr_continuity |
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o create specific S/R to exchange T,S before DYNAMICS (for stagger time step) |
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o update timeave pkg for wVel diagnostic. |
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checkpoint46j_pre |
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checkpoint46i_post |
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o Clean up AIM package (and keep the results unchanged): |
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include CPP_OPTION and use IMPLICT NONE in all routines ; |
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declare all the variables _RL ; use _d 0 for all numerical constants. |
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use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 ! |
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checkpoint46h_post |
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o cleaned up the use of rhoNil and rhoConst. |
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- rhoNil should only appear in the LINEAR equation of state, everywhere |
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else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst |
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and the dynamical equations are all divided by rhoConst |
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o introduced new parameter rhoConstFresh, a reference density of fresh |
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water, to remove the fresh water flux's dependence on rhoNil. The default |
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value is 999.8 kg/m^3 |
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o cleanup up external_forcing.F and external_forcing_surf.F |
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- can now be used by both OCEANIC and OCEANICP |
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checkpoint46h_pre |
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|
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Added code to convert surface volume flux (fresh water) into |
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a mass flux when using P coordinates in the ocean (OCEANICP). |
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Note: It assumes you have set rho0=rhoConst=density of fresh water. |
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checkpoint46g_post |
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o Include a new diagnostic variable phiHydLow for the ocean model |
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- in z-coordinates, it is the bottom pressure anomaly |
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- in p-coordinates, it is the sea surface elevation |
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- in both cases, these variable have global drift, reflecting the mass |
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drift in z-coordinates and the volume drift in p-coordinates |
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- included time averaging for phiHydLow, be aware of the drift! |
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o depth-dependent computation of Bo_surf for pressure coordinates |
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in the ocean (buoyancyRelation='OCEANICP') |
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- requires a new routine (FIND_RHO_SCALAR) to compute density with only |
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Theta, Salinity, and Pressure in the parameter list. This routine is |
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presently contained in find_rho.F. This routine does not give the |
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correct density for 'POLY3', which would be a z-dependent reference |
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density. |
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o cleaned up find_rho |
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- removed obsolete 'eqn' from the parameter list. |
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o added two new verification experiments: gop and goz |
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(4x4 degree global ocean, 15 layers in pressure and height coordinates) |
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checkpoint46g_pre |
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checkpoint46f_post |
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o Enable tangent linear (forward mode) gradient checks: |
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- extended active file handling to g_... files |
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- added TANGENT_SIMULATION to theSimulationMode |
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- extended grdchk package accordingly |
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o added tangent linear setup in verification/carbon/code_ftl |
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o added adjoint setup in verification/front_relax/code_ad |
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checkpoint46e_post |
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o Added new equation of state -> MDJWF |
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- EOS of McDougall et al., 2002, JAOT, submitted |
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- caveat: the equation of state is only valid for a smaller (more |
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realistic?) range of values than JMD95P/Z and UNESCO |
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- added masks to the calculation of pressure in store_pressure |
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- added more check values for density in check_eos (ini_eos.F), some of |
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the old check values are out of the range of the MDJWF-eos, so don't |
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expect perfect matches for those |
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checkpoint46e_pre |
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checkpoint46d_post |
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o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and |
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'OCEANICP', also initialised field pressure correctly in ini_eos in the |
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case of pressure coordinates. eosType='JMD95Z' in |
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combination with buoyancyRelation='OCEANICP' now causes an error. |
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o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj) |
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in find_alpha/beta. |
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checkpoint46d_pre |
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|
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o Changed p = pressure(i,j,k,bi,bj) to p = pressure(i,j,kRef,bi,bj) |
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so that JMD95Z and JMD95P give approptiate static stability in find_rho. |
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118 |
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checkpoint46c_post |
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o Changes necessary for ocean in p-coordinates |
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- Added new buoyancy relation = 'OCEANICP' |
121 |
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- Added new parameters = gravitySign (this used to be contained inside |
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the factor dRdZ which I added when we first switched to R coordinates). |
123 |
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X GM/Redi is not compatible (yet) |
124 |
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X bottom drag and no-slip need to be debugged. |
125 |
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checkpoint46c_pre |
126 |
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127 |
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checkpoint46b_post |
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o Added new equation of state -> JMD95Z and JMD95P |
129 |
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- EOS of Jackett and McDougall, 1995, JAOT |
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- moved all EOS parameters into EOS.h |
131 |
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- new routines ini_eos.F, store_pressure.F |
132 |
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o Added UNESCO EOS, but not recommended because it requires |
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in-situ temperature (see JMD95) |
134 |
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o Modified formatting for knudsen2.f in utils/knudsen2 and added |
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unesco.f to be used with POLY3 |
136 |
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checkpoint46b_pre |
137 |
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|
138 |
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checkpoint46a_post |
139 |
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o Added (atmospheric) pressure loading |
140 |
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- new field in FFIELDS.h, etc... |
141 |
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- new cpp flag ATMOSPHERIC_LOADING |
142 |
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o Changed hFacC to _hFacC in calc_phi_hyd.F |
143 |
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o Added SHORTWAVE_HEATING to some files for consistency |
144 |
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checkpoint46a_pre |
145 |
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146 |
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checkpoint46 |
147 |
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further merges from release1_p5 |
148 |
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o new ctrl package |
149 |
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- adopted from ECCO environment to enable optimization |
150 |
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- added Eliassen Palm fluxes to controls |
151 |
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o added Eliassen Palm flux controls to gradient check package |
152 |
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o cost package |
153 |
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- Compatible with new ctrl package |
154 |
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- added Eliassen Palm cost hooks |
155 |
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- modif's of existing cost functions |
156 |
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o Adjoint-related bug fixes in kpp: |
157 |
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- kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix |
158 |
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- kpp_routines: store of Rib avoids partial recomputation bug of TAF. |
159 |
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o autodiff package |
160 |
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- flow directives: |
161 |
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+ new for S/R do_the_model_io |
162 |
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+ enhanced for S/R checkpoint |
163 |
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+ new gmredi.flow |
164 |
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- Introduced CPP option ALLOW_AUTODIFF_MONITOR to |
165 |
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disable adcommon.h/g_common.h by default. |
166 |
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- fixed problem for adjoint of global_max |
167 |
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o modified verification/carbon/ |
168 |
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o New setup for adjoint of global_ocean |
169 |
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o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F) |
170 |
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o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F) |
171 |
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o incorporated hooks for sponge layer code (external_forcing.F) |
172 |
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173 |
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checkpoint45d_post |
174 |
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o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F) |
175 |
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o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S |
176 |
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(affects plume_on_slope "cg2d" output) |
177 |
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o add new parameter deltaTfreesurf for free-surface time stepping |
178 |
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o exchange gT,gS when using staggerTimeStep & GM & Oly<4 |
179 |
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o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B |
180 |
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o change phiMin in exp1 (to agree with documentation) |
181 |
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o add new flags: |
182 |
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- T,S forcing inside/outside Adams-Bashforth |
183 |
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- turn off temp,salt advection and/or forcing |
184 |
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- for each tracer, define internal flag for multiDimAdvection & A-B |
185 |
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o monitor: change definition of KE to check conservation of Energy |
186 |
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187 |
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checkpoint45c_post |
188 |
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o Removed f90 comments ("!") |
189 |
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o Modified initialisations to enable exf package for MITgcm |
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(without invoking ECCO_PACKAGE). |
191 |
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o modifications to gradient check package (Martin Losch) |
192 |
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- enable centered differences |
193 |
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- modified format of standard output |
194 |
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195 |
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checkpoint45b_post |
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o cleaned exchange calls in cg2d |
197 |
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o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step |
198 |
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o included CPP option SINGLE_LAYER_MODE in thermodynamics |
199 |
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to configure barotropic setup (Martin Losch) |
200 |
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o moved some initialisations within bi,bj loop in dynamics |
201 |
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(TAF flow dependency) |
202 |
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o in initialise_varia, moved call packages_init_variables |
203 |
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before convective_adjustment_init |
204 |
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(corresponding adjustment of TAF tape initialisation). |
205 |
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o in calc_diffusivity/calc_viscosity extended domain to full overlap. |
206 |
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207 |
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checkpoint45a_post |
208 |
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o compute Rho over the whole domain (extend iMin,jMin indices) |
209 |
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o specific exchange for X-slice domain (case Ny=1) |
210 |
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o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code |
211 |
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o solve_for_pressure : set cg2d_x to zero where OBCS are applied |
212 |
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213 |
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checkpoint44h_post = checkpoint45 |
214 |
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o Fix to restore differentiability: |
215 |
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place at which packages_init_variables is called in |
216 |
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initialise_varia is crucial for reverse control flow. |
217 |
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o modifications in GMRedi to enable stable adjoint |
218 |
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(corresponding modif's in thermodynamics, dynamics) |
219 |
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o added missing hook for sponge layer code in external_forcing |
220 |
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o modified test cost functions |
221 |
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o storing in gad_advection (plus removal of write(0,*)! |
222 |
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o missing headers TR1.h added in convective_adjustment routines |
223 |
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o errorMessageUnit set non-equal zero in eeboot |
224 |
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(conflict on some platforms, e.g. IBM SP3) |
225 |
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o modified carbon verif. |
226 |
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227 |
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checkpoint44h_pre |
228 |
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o vertical grid option: allow to put the Interface at the middle between |
229 |
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2 cell-centers ; replace delZ in pkg/kpp by drF. |
230 |
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o GM Advective form: Tracers are advected using the residual transport (= |
231 |
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Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form. |
232 |
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|
233 |
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checkpoint44g_post |
234 |
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o fix surface correction term in multiDimAdvection (affects plume_on_slope |
235 |
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results) ; ifdef missing in thermodynamics.F |
236 |
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237 |
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checkpoint44f_pre,checkpoint44f_post |
238 |
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o added PTRACERS package |
239 |
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This allows an arbitrary number of passive tracers to be integrated |
240 |
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forward simultaneously with the dynamicaly model. |
241 |
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+ Implemented so far: |
242 |
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- basic forward algorithm (time-stepping, advection, diffusion, convection) |
243 |
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- I/O and checkpointing |
244 |
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- GM/Redi *but* using the GM/Redi coefficient of Salt |
245 |
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+ Not implemented so far: |
246 |
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- KPP |
247 |
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- OBCS |
248 |
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+ No specific example supplied (yet) but global_ocean.90x40x15 has the |
249 |
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necessary data.ptracer file. Simply use -enable=ptracers and uncomment |
250 |
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line in data.pkg. |
251 |
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+ This package is disabled by default since it increases storage. |
252 |
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|
253 |
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|
254 |
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o testscript: added -cleanup option |
255 |
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o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter |
256 |
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b) enable to filter 2D fields. |
257 |
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|
258 |
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checkpoint44e_pre,post |
259 |
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o re-wrote convective adjustment to use pre-calculated weights |
260 |
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Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F |
261 |
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Adds: model/src/convective_weights.F, convectively_mixtracer.F |
262 |
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Original calls to convect() still in place. |
263 |
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|
264 |
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chkpt44d_pre,post |
265 |
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o added missing EXCLUDE_MONITOR flags |
266 |
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o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi |
267 |
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(incompatible typ in MIN/MAX expressions caused problems |
268 |
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on IBM SP3) |
269 |
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o in genmake added variable MAKEDEPEND |
270 |
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plus resetting for case SunOS |
271 |
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o added timer_stats.c routine for IBM SP3 |
272 |
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o removed variables in dynamics |
273 |
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!!! I forgot to create tag chkpt44d_pre !!! |
274 |
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!!! But chkpt44d_pre = chkpt44c_post !!! |
275 |
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|
276 |
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o real fresh water flux implemented with non-linear free-surface. |
277 |
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|
278 |
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chkpt44c_pre,post |
279 |
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o few fix (mask in shap_s2, EmPmR in external_field_load, |
280 |
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USE_NATURAL_BCS in solve_for_P); |
281 |
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o add arguments myIter & myTime to S/R obcs_calc & solve_for_P |
282 |
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|
283 |
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checkpoint44b_pre/_post |
284 |
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o merge of relevant stuff from the ecco-branch: |
285 |
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- genmake: removed $S64 overwrite for case SunOS |
286 |
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- pkg/exf: update and corrections for field swapping and obcs |
287 |
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- pkg/ecco: parameter lists for the_model_main, the_main_loop |
288 |
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harmonized between ECCO and MITgcm |
289 |
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- pkg/autodiff: added flow directives for obcs, mdsio_gl_slice |
290 |
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updated checkpointing_lev... lists for obcs |
291 |
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- model/src: minor changes in forward_step, plot_field |
292 |
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added directive for divided adjoint in the_main_loop |
293 |
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- pkg/mdsio: added mdsio_gl_slice |
294 |
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|
295 |
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o check parameters & config (chkpt44a_pre,post) |
296 |
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o OBC and NonLin_FrSurf. |
297 |
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|
298 |
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checkpoint44 |
299 |
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o fix bug in mom_vi_del2uv |
300 |
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o select when filters are applied ; add options to zonal_filter (data.zonfilt) |
301 |
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o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection) |
302 |
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o update AIM experiments (NCEP input files) |
303 |
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o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf) |
304 |
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o added some stuff for AD |
305 |
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|
306 |
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checkpoint43 |
307 |
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o added two new advection tests |
308 |
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o added global 4x4 degree ocean test |
309 |
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o added test of H&S94 with free surface on cube |
310 |
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o some final mods for gradient check, adjoint,... |
311 |
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|
312 |
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checkpoint42 |
313 |
|
Fixed AD-related problems: |
314 |
|
o Store directives up-to-date with re-arranged Adams-Bashforth |
315 |
|
(mainly thermodynamics.F) |
316 |
|
o New store directives for multi-dim. advection schemes |
317 |
|
* new CPP flag ALLOW_MULTI_DIM_ADVECTION |
318 |
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* new common block and key passkey |
319 |
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(mainly gad_advection.F) |
320 |
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o Modified store directives for split of dynamics/thermodynamics |
321 |
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for the case ALLOW_KPP |
322 |
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o Cleaned argument list for timestep_tracer.F |
323 |
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|
324 |
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checkpoint41 |
325 |
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o re-formatted/added comments in prologues of key subroutines |
326 |
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to work with protex |
327 |
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|
328 |
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checkpoint40 |
329 |
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o moved calc_gs, calc_gt and calc_tr1 back to model/src |
330 |
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o added FLT (floats) package from Arne along with demo. experiment |
331 |
|
o re-arranged Adams-Bashforth scheme for tracers to allow easier |
332 |
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implementation of forward-in-time forcing terms |
333 |
|
o more mods for non-linear free-surface including new variable |
334 |
|
o modified multi-dim method to work on cube |
335 |
|
o bug fix in KPP (from DM) |
336 |
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|
337 |
|
checkpoint40pre9 |
338 |
|
o added DST advection schemes |
339 |
|
o fix MPI bug on SGI's |
340 |
|
o modifications for non-linear free-surface |
341 |
|
o fixed conditionals for fixed flow/passive tracer only mode |
342 |
|
o added tension/strain form of stress tensor |
343 |
|
o changes to commenting of arguments for TAF/TAMC |
344 |
|
o added/updated many matlab scripts |
345 |
|
o added multi-dimensional advection method for tracers |
346 |
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|
347 |
|
checkpoint40pre8 |
348 |
|
o new package rw/ |
349 |
|
Added method for dumping intermediate local arrays: |
350 |
|
mdsio_writetile - same as mdsio_writefield except works from inside |
351 |
|
bi,bj loop |
352 |
|
mdsio_writelocal - same as mdsio_writetile except works for local |
353 |
|
arrays |
354 |
|
write_local_r? - higher-level wrapper for mdsio_writelocal |
355 |
|
Controlled by diagFreq. Defaults to zero (ie. no dumps) |
356 |
|
Example given at end of mom_vecinv.F that dumps some local arrays. |
357 |
|
o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to |
358 |
|
control flux-form versus vector invariant code. |
359 |
|
Switch is runtime flag vectorInvariantMomentum (defaults to false) |
360 |
|
or genmake -DISABLE ... |
361 |
|
o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F |
362 |
|
(additional storing is now needed for case vecinv; |
363 |
|
currently nothing implemented to switch this storing off |
364 |
|
in case fluxform is used since no CPP flag available). |
365 |
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|
366 |
checkpoint40pre7 |
checkpoint40pre7 |
367 |
o bug fix in dynamics.F |
o bug fix in dynamics.F |
368 |
calc_viscosity called before k=1,Nr loop. |
calc_viscosity called before k=1,Nr loop. |