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RELEASE_NOTES
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25.09.2023 VERS_7_5_84 Pre-community edition
generalized vertical coordinates
many bug fixes for mpi routines
tripple point managing
finished box model
manage nkn==nel bug
worked on closings
24.03.2023 VERS_7_5_83 Pre-Istanbul23 edition
many bug fixes and enhancements for MPI
MPI version generally working
PetSc working
error conditions on boundary relaxed for single domains
horizontal diffusion working (except tripple points)
new format for id_elem(0:3,nel)
ghost_nodes are computed correctly now
sparsekit solver generalized (no dimension error for n2zero,n2max)
mor bug fixes for box model
04.12.2022 VERS_7_5_82 Malta edition bis
04.12.2022 VERS_7_5_81 Malta edition
tons of bug fixes and enhancements for MPI
restart for MPI (bug fix for rhov
shympi_g2l_array() for gathering arrays finished
shympi_gather_root() to gather only to root
flux sections for MPI
boxes for MPI finished
petsc works for some configurations
OBC: condense_valid_coordinates() and recollocate_nodes()
tracer_init_file also working for 2d arrays
sediments: bug fixes, divide by 0
bug fix in init_vertical() - update sigma_info
WW3: final integration and bug fixes for WW3 code
19.05.2022 VERS_7_5_80 Istanbul III edition
petsc fully integrated into shyfem (with howto)
howto files for petsc and mpi in femcheck/info
cpu_time routines introduced
box model reads new version of index file
06.05.2022 VERS_7_5_78 WW3 edition
new wave module WW3 integrated in model
more testing on MPI version
OBC in more than one domain
rain and distributed fluxes now working
new array iboundv to identify real boundary nodes
lagrangian module with density on type post-processing
bug fix in system_solve_global
12.04.2022 VERS_7_5_77 Istanbul II edition bis
This is a second version for MPI shyfem on node partitioning
New things that are working
horizontal diffusivity
regular forcing fem files
regular forcing boundary files
online partitioning - no need to create partition on bas file
routines for partitioning adapted for online use
more adjustments in loop index for mpi (look for ie_mpi)
no need for -mpi switch
zconst was not set correctly
regular interpolation of boundary nodes is correct now
bug fix for INTEL in uvint
12.04.2022 VERS_7_5_76 Istanbul II edition
This is a second version for MPI shyfem on node partitioning
New things that are working
horizontal diffusivity
regular forcing fem files
regular forcing boundary files
online partitioning - no need to create partition on bas file
routines for partitioning adapted for online use
more adjustments in loop index for mpi (look for ie_mpi)
no need for -mpi switch
zconst was not set correctly
regular interpolation of boundary nodes is correct now
bug fix for INTEL in uvint
09.04.2022 VERS_7_5_75 Istanbul I edition
This is a first version for MPI shyfem on node partitioning
The mpi and serial version are bit-to-bit compatible
Most things are now working, including
explicit and isemi-implicit (no PETsC yet)
area code and wetting and drying
advective terms
tracer, T/S, baroclinic
2d, 3d zeta, 3d sigma
gotm turbulence closure
Not working things:
flux sections
no horizontal viscosity and diffusivity
no open boundaries across domains
no WRT
no lagrangian
bug in GOTM fixed (tridiagonal wrong for 2 layers)
new option -mpi_debug in shyfem
new routines for exchanging arrays between domains
adjustments in loop index for mpi (look for ie_mpi)
chezy table adjusted for multi-domain
coupling with WW3 nearly complete
compiler warnings adjusted
compiler bug with PGI (PGI_ggguuu) - no solution
lots of small bug fixes
22.03.2022 VERS_7_5_73 Schnucki edition
This is an intermediate release.
output routines upgraded to da_out
averaging routines moved to subconutil.f
changes in lgrelab
new femadd
accept int64 data type for time variable (netcdf.f)
obsolete files moved to new obsolete folder
some code cleaning
15.03.2022 VERS_7_5_72 Ides of March edition
This is a long awaited big release. Main points are:
better handling of box model (with utilities)
new gfortran version warnings fixed
turbines integrated
new age computing added
added Hersbach wind stress formulation
bug fix in iff_init -> BC handling was wrong (subfemintp.f)
lot's of other bug fixes
lot's of small enhancements
27.05.2021 VERS_7_5_71 3rd wave Covid edition
This is a big release. Main points are:
Integration of PETSc for MPI simulations by clr
(some more testing is needed for 3d simulations)
writing shyfiles 2D now working in MPI mode
use metis for partitioning
prepared for new compiler PGI
19.05.2020 VERS_7_5_70 Covid edition
This is a big bug fix release and a pre-release for
the community model
It adds copyright notices to all files
copyright introduced to all files
closure routines adapted (mod_internal,newclose)
new version of femelab (femelab2,elab_resample,elab_check)
new utilities for handling fem files (subfemutil,subfemfile)
worked on BFM
mercury routines debugged, started restart
revisited strings description
offline restructured (suboff,offcat,offinf)
added lagrange_connect for connectivity
cleaned nudging routines in newbcl
06.03.2020 VERS_7_5_69 Vincenzo edition
boxmodel in 3D revisited
better nudging with tau given by external file
closing routines adjourned
documentation upgraded
routines for vorticity
post processing checks for time step
regular output from shybas
31.01.2020 VERS_7_5_68 Brexit edition
lagrangian: integrated some parts of connectivity
shyelab adjourned for computing vorticity in post processing
dummy routines for mercury
netcdf now writes all values as 3d
20.12.2019 VERS_7_5_67
post processing for rain (femelab)
better processing of dated time series
ice cover introduced
25.11.2019 VERS_7_5_66
minor release
femtime eliminated (in some files)
dynamaic implicit setting adapted (setimp)
31.10.2019 VERS_7_5_65
started BFM integration
some update for documentation
elab routines check time step
better checking of grainsize percentage in sedi3d
some enhancements in post-processing routines
better syncronization of time step
condensation of string variables
nc2fem checks for negative dx,dy
bottome stress computation can choose if including dry elements
19.07.2019 VERS_7_5_64
shy_write_scalar_record2d to be used for 2d output
setweg & setznv introduced before make_new_depth
new routines for indirect real sort
bug in rmsdiff (new3di.f)
02.07.2019 VERS_7_5_63
delete use of ishyff in subfvl.f
switched completely to penta solver (new3di.f)
revision log has been completed from git logs
21.05.2019 VERS_7_5_62
various bug fixes in plotting(suplin.f,supiso.f)
output to nc files upgraded
some bug fixes in netcdf.f
in fm_extra_setup() use double precision
in new3di,mod_internal.f introduced rcomputev excluding elements (rcomp)
new application rst2shy
new file newclose.f
in subwrt.f fix problem with too low concentration
13.03.2019 VERS_7_5_61
new routines for tidal potential
added customization for plottinf basin
clean arrays for para array read
bug fix for WRT computation
new friction ireib=10 (quadratic/linear)
various other small stuff
16.02.2019 VERS_7_5_60
This a a first pre-release version for the community model.
All shyfem files now contain copyright notices. Source files
also mention the GPL, script files and other minor files
contain a short version of the copyright notice.
All files now contain a statement like the following:
Copyright (C) 1985-2018 Georg Umgiesser
For many files this is not true, because I am not the only
copyright holder. Therefore this line has to be customized.
I would therefore ask everybody to go through the files and
identify the files where they have contributed. Sometimes
the revision log is a good point to start from.
Please, in case you have contributed, add your name after mine,
or add a new line resembling the line above with your name.
If you are the main author, please put your name first, and if
I have not contributed at all, please delete my name. We can
have as many names as needed in the copyright notice.
Here is a (not complete) list of all the persons I can think
of that have contributed to the code and their contribution:
Andrea: lagrangian, WRT, ERSEM
Christian: sediments, lagrangian, tide, etc.
Michol: lagrangian, connectivity
Debora, William: non-hydrostatic
Francesca: toxi
Petras, Ali: aquabc, box model
Cosimo, Donata: eutro
Eric: OMP implementation
CMCC: MPI implementation
Sorry if I have forgotten someone and some topics. You will
know better, please correct me.
Please send me your input. Deadline is the end of February.
This gives me then time to finalize the version that should
become the starting point of the community model. Either send
me the new files, or do a "pull request" from git-hub.
14.02.2019 VERS_7_5_56
many bug fixes in sediment transport code (GGUZ0)
bug fix for scalar transport with negative loading and s<0
box model updated
clear handling of bottom shear stress
checks for zero layer case
bug fix for syncronization of last time step
custom reset in WRT computation
waves debuged (GGUZ0)
18.01.2019 VERS_7_5_55
IMPORTANT: the vertical solver has been changed.
This can lead to inconsistencies with existing applications,
but it really should not.
Please try this version and report back any problems.
This version will be slightly slower than the previsous one.
This is only because of the extra testing code inserted.
In the future this testing code will be removed again.
However, I need EVERYBODY to test this new code!!!
solver routines have been ajourned with copyright note
penta solver has been implemented
27.12.2018 VERS_7_5_54
updates in manual
21.12.2018 VERS_7_5_53
Christmas 2018 edition
last minute bug in vertical experimental penta solver
small bug in acquabc
18.12.2018 VERS_7_5_52
nonhydrostatic code added
copyrights added
new routines to read and interpolate time series
linear arrays added to adapt to implicit do compiler error
25.10.2018 VERS_7_5_51
new lagrangian routines with plotting (ccf)
new grid formats gr3 and msh (ccf)
small bug fixes (subrst.f)
examples for tutorial integrated
in femplot eliminate (1) array length
16.10.2018 VERS_7_5_50
various bug fixes
sediment transport - adjust load for deposition
severe bug handled (caux used for different variables)
output of meteo variables
diagnostic tool ts_dia
31.08.2018 VERS_7_5_49
adapted to new gfortran version 8
small bugs with new compiler solved
workaround in subext to avoid warning
06.07.2018 VERS_7_5_48
customization for fonts in shyplot
heavy reworking of nc routines (nc*.f)
single points output (BC) for nc2fem
more on regular interpolation (subreg.f)
shyelab has output option off
bug fix for regular 2d/3d interpolation (2d was wrong) (subfemintp.f)
better handling of line reading routines (subgrd.f)
bug fix for restart file, restart now works with absolute time
scalar transp/diff now also with aa>0, implicit nudging, idtstb/itmstb
(changes in sub time stepping expected)
11.05.2018 VERS_7_5_47
zeta levels now running with mpi
area code working with mpi
wetting and drying working with mpi
26.04.2018 VERS_7_5_46
mpi running with semi-implicit code
new matrix type for multiple matrices (local and global)
istot>1 now solved for mpi
check partition integrity
19.04.2018 VERS_7_5_45
first working version for MPI with partition on nodes
writing shy and ext files under mpi
for shyplot new bkplot
for shybas and shypre new code for partition
stability computation also with gravity wave
wrt made ready for mpi
03.04.2018 VERS_7_5_44
time management now fully in double precision
enhancements for flx handling
new code for optimal interpolation
new parts integrated in bio3d
03.04.2018 VERS_7_5_43 (contains small bug - do not use)
time management now fully in double precision
enhancements for flx handling
new code for optimal interpolation
new parts integrated in bio3d
22.02.2018 VERS_7_5_42
tons of small bug fixes
sediment transport rectified sinking velocity
box fluxes and plotting boxes
use rstol for stability
combine records in fem files (femcombine)
24.01.2018 VERS_7_5_41
more on mpi (not yet finished)
new specific humidity option
some bug fixes
07.12.2017 VERS_7_5_40
first develop version with basic working mpi
all modifications are introduced into develop trunk
partition is only on nodes
partition on elements will follow
automatic partitioning will come soon
05.12.2017 VERS_7_5_39
new implementation in waves and sediments
bug fixes for regular interpolation
start from lgr file with restart
mpi routines started to integrate in develop trunk
17.11.2017 VERS_7_5_38
brown paper bag bug in writing flux section
17.11.2017 VERS_7_5_37
more on output routines
fluxes now also write sediement variables
better time parsing
nc2fem upgraded
14.11.2017 VERS_7_5_36
output routines unified
new functionality tselab
shyplot unified
04.11.2017 VERS_7_5_35
more on consistent output of elab routines
new names for files created with -split and -nodes
time series now written with time as string
for strings short names introduced
new time handling routines
new diagnostic routines for weutro
some updates on manual
sections extra and flux accept now strings for description
new routines to write scalars in shy format
04.11.2017 VERS_7_5_34
...wrong release... updated with next version
09.10.2017 VERS_7_5_33
enhancements in output formats
26.09.2017 VERS_7_5_32
minor enhancements
bug fix in weutro_seed.f (segfault)
for shyfiles limit number of layers to min(nlv,nlvdi)
02.09.2017 VERS_7_5_31
new sediment routines (upgraded to modules)
some enhancements for fem files (subfemutil, femintp)
11.07.2017 VERS_7_5_30
new projection (Lambert conformal conic)
nc2fem working on 3d (experimental)
more on plotting
13.06.2017 VERS_7_5_29
new tool nc2fem to convert nc files to fem files
works now for 2d files
new default for ishyff is now 1 (no nos or ous files)
25.05.2017 VERS_7_5_28
extract nodes from fem file with femelab
nc2fem improved
subreg split into subreg, submask and subfind
16.05.2017 VERS_7_5_27
new routine nc2fem for preparing fem boundary conditions from nc files
new subiso8601.f for time/date column as string
09.05.2017 VERS_7_5_26
routines for computing bottom stress
default name handling changed
simple sediments debugged
use regular grid for boundary conditions
some changes in netcdf
13.04.2017 VERS_7_5_25
routines to compute bottom stress (current and waves)
new array feature for para (STR)
store cd values of friction coefficient
use array feature for kbound and taupar (decay)
simple_sediment routines finished
31.03.2017 VERS_7_5_24
new box model
fluxes now with variable time step
bug fix in shyelab for min/max/std
afix now working
valmax for plotting
13.02.2017 VERS_7_5_23
new meaning of idecay in newconz.f (incompatible)
in sedi3d read in init data from fem files
bug fix in subgrd: do not allocate at least 1 array element
20.01.2017 VERS_7_5_22
more on manual
shyplot is fixed (vector plot on fem still not working)
12.01.2017 VERS_7_5_21
manual updated
bug fix in determining pressure units
rtauv for differential nudging, set ttauv and stauv
shyplot restructured... directional plot still broken
new output format in rms and wrt files
initialization for tvd made faster
small bug fixes
11.10.2016 VERS_7_5_20
bug fix in interpolation from reg grid
05.10.2016 VERS_7_5_19
expansion of regular grid in shyelab, femelab
clean fem files from NaNs
vertical averaging -> use zeps
for bio3d init conditions from file
29.09.2016 VERS_7_5_18
improvements in regular interpolation
bug fixes in bio3d
some changes in legend reading for plot
09.09.2016 VERS_7_5_17
inprovements in post processing routines
bug fix in newfix.f
new heat formulation in meteo routines (iheat==8)
bug fix in subvintp.f: handel situation with dh == 0
more on bfm
in tracer computation new decay formulation from Chapras
27.06.2016 VERS_7_5_16
weutro and bio3d adjourned (EUTRO)
regular interpolation extended to comprise total basin
in shy files error check for compatibility
bug fix: irho was not saved
17.06.2016 VERS_7_5_15
new color table feature in plotting files
non-hydrostatic version updated
wprv is now running from 1 to nlv
14.06.2016 VERS_7_5_14
shyplot now near feature complete
shydiff included in shyelab
possible to choose between vertical momentum advection schemes
newbcl cleanup (prepared for non-hydrostatic model)
10.06.2016 VERS_7_5_13
shyplot now plots shy and fem files
file interpolate handles nvar==0 and no depth, no integration
tracer write of shy files simplified
mercury framework (really) finished
06.06.2016 VERS_7_5_12
finished framework for mercury routines
file initialization changed
new routines to deal with lines (grd and bnd)
netcdf routines revised
30.05.2016 VERS_7_5_11
code cleaning
output routines and section plot revisted
check STR file for not unique sections
possible bug fix in set_last_layer() for ilytyp==1
25.05.2016 VERS_7_5_10
big changes in post processing routines and plot
read 3d matrices from fem files (still experimental)
format enhancement for fem files
restructured regular file treatment
change albedo treatment (small bug)
exact estimation of ngr
started new eutro and mercury routines
28.04.2016 VERS_7_5_9
nos2nc, ous2nc adapted to new framework
ouselab allows nodes output
more work on shy files
shyelab nearly ready for production
15.04.2016 VERS_7_5_8
shybas has been updated
parametric wave module cleaned
custom reset in WRT
fluxes_template adjourned
new parameter iaicef for ice free areas
big arrays allocatable and not on stack
01.04.2016 VERS_7_5_7
most big arrays moved from stack to allocatable (newcon.f)
sediment transport routine adapted to new model structure
subbnd restructured
bug fix for ets files
22.03.2016 VERS_7_5_6
make scripts executable if downloaded from GitHub
mesh accepts filename w/o .grd extension
exgrd -a changes versus of items (elems/lines)
ouselab writes also with gis format
shybas -depth writes out depth values from basin
11.03.2016 VERS_7_5_5
bug fix in iff_read_header - check for ierr/=0
in parametric wave module fix segfault
check for pressure to be in reasonable bounds
most variables passed in double precision (bug pressure)
22.02.2016 VERS_7_5_4
new bfm implemented
use catmode in noselab
general tracer treatment for initial files
19.02.2016 VERS_7_5_3
bug fix in noselab1.f (sum, bsumvar)
19.02.2016 VERS_7_5_2
handle lagrangian particles on vertical wall gracefully
new lagrangian release type ipvert = -1
some plot params shifted to para section (bbgray, etc.)
22.01.2016 VERS_7_5_1
bug fixes in subspk and COARE heat module
08.01.2016 VERS_7_5_0
new develop version opened
08.01.2016 VERS_7_4_0
new stable major version
08.01.2016 VERS_7_3_18
severe bug fix in meteo_convert_wind_data() - no wind bug
minor enhancements
continued mpi development
18.12.2015 VERS_7_3_17
shybas interpolation is working now
grid can now delete double node in line
distribution prepared for bounds check
changes in compiler options in Rules.make
16.12.2015 VERS_7_3_16
3d matrix solution routines introduced
poisson equation setup
code optimization (newtra.f and subgotm.f)
in restart routines allocate conz data structures
lnk_elems and lnk_nodes eliminated
no open boundaries case is now ok
small bug fixes
mpi project started
16.11.2015 VERS_7_3_15
omp version finalized
some update to lagrangian module
after testing this will become stable 7.4.0 and testing 7.5.0
16.11.2015 VERS_7_3_14
new module for lagrangian (not completely finished)
new routine adjust_xi
09.11.2015 VERS_7_3_13
tracer newly structured
more on omp parallel
05.11.2015 VERS_7_3_12
manual integrated
05.11.2015 VERS_7_3_11
velocity nudging finished
restart revisited
allow for initial output with itm...
offline checked
initializationf from file for u,v,z
26.10.2015 VERS_7_3_10
for parallel version data races eliminated
23.10.2015 VERS_7_3_9
parallel code working (Eric)
22.10.2015 VERS_7_3_8
documentation merged
22.10.2015 VERS_7_3_7
minor improvements
new Eric routines
14.10.2015 VERS_7_3_6
new parts on shy file format introduced
minor modifications
13.10.2015 VERS_7_3_5
Bug fix introduced in 7.3.2 (handle_projection called too early)
12.10.2015 VERS_7_3_4
Pull request Pardiso (Marco Bajo) handled
12.10.2015 VERS_7_3_3
severe bug fix in adjust_bc() (subnev.f)
many fixes for floating point exceptions
fluid mud integrated
new post processing flx files
some bug fix in femadj
10.10.2015 VERS_7_3_2
Pull request from Christian handled:
changes in tidal forcing integrated (tidef)
new module coordinates
new module projection
switched names between subcoord.f and subproj.f
02.10.2015 VERS_7_3_1
this is the first release of the develop branch 7.3
new routine shybas now handling all info/elab on basin
some enhancements in subgrd.f
30.09.2015 VERS_7_2_6
scalar computation now with new OMP code (Eric)
faster domain_clusterization
some fix in optintp.f
allow again for ambient value with scalars
29.09.2015 VERS_7_2_5
nudging of surface velocities finished
bug fix with projection (not using isphe)
bug fix so shyfem can be used with no boundary
output now also double precision
23.09.2015 VERS_7_2_4
in shyelab more files can be given now
time step (idt) can now be fractional
18.09.2015 VERS_7_2_3
new names for hydro routines
more aux variables shifted into routines
advective terms stored in momentx/yv and not in aux arrays
austau() eliminated
code for subset creation integrated (eric)
two bug fixes:
zeqv was not always initialized in tideini
in coo_init n==0 was not checked
14.09.2015 VERS_7_2_2
more options for shyelab, new file formats added
plotting velocities from fem files
31.07.2015 VERS_7_2_1
major release
transition to allocatable objects finished
no need to change Rules.make, model should compile "out of the box"
some routines renamed (shyfem, shypre, shyelab)
routines now want input files on command line
post processing routines are still not completely ready
the following modules still do not work:
waves, sediments, lagrangian
fluidmud, atoxi
biological reactors (bio3d, aquabc, bfm)
boxes
31.07.2015 VERS_7_1_84
minor changes
30.07.2015 VERS_7_1_83
transition to allocatable objects finished
new names for some routines
ht -> shyfem
vp -> shypre
ousinf -> shyelab
nosinf -> shyelab
routines now want input files on command line
(example: shyfem nador.str)
post processing routines are still not completely ready
please have a look at shyelab for dealing with NOS and OUS files
plotting is still through plots
24.07.2015 VERS_7_1_82
only dependency on fixed dimensions is nbcdim
some auxiliary programs are running
grd treatment has been completely revised
dealt with compilation errors in femadj and femspline
20.07.2015 VERS_7_1_81
no need for setting dimensions anymore
Rules.make file has not to be changed in most cases
files have been cleaned from automatic comments
17.07.2015 VERS_7_1_80
first release based on modules and allocatable arrays
this is still an experimental release
only a limited number of programs are working:
ht, vp, plotsim (plots)
all other programs (mostly post processing) still have to be upgraded
in this case please use an older version
the following modules still do not work in the new version:
waves, sediments, lagrangian
fluidmud, atoxi
biological reactors (bio3d, aquabc, bfm)
boxes
17.07.2015 VERS_7_1_53
new intermediate release ... do not use ...
17.07.2015 VERS_7_1_52
new intermediate release ... do not use ...
13.07.2015 VERS_7_1_51
new intermediate release ... do not use ...
10.07.2015 VERS_7_1_50
this is a big release of changes
nobody should really use this version
this is only used to prepare the new major version with
modules instead of common blocks (inludes)
and arrays allocated on the heap
most of the conversion has been finished, but some points
still have to be done
some files will not be converted before the next major release:
lagrange
box
bfm
05.06.2015 VERS_7_1_12
some more work for transition to module structure
lots of very small changes
21.05.2015 VERS_7_1_11
this is a big and unfocused release...
some central parts rewritten for OMP (new3di.f, newcon.f)
new data structure mklenkii
lagrangian completely rewritten (based on structure)
ext, flx, ets, frcition to modules
plotting with logarithmic scale and color bar
bug fixes in offline
ia_icefree for ice cover implemented
05.05.2015 VERS_7_1_10
ice cover bug eliminated
some adjustments in include files (global arrays)
winkv equivalence eliminated
all param_dummy.h substituted by param.h
compiler bug adjustments:
gfortran: use -O instead of -O3
ifort: remove -check uninit
30.04.2015 VERS_7_1_9
ice cover integrated
czdef default friction for all areas not given
minor changes
post processing - new initialization
23.04.2015 VERS_7_1_8
lagrangian 3d finished !!!!
internal coordinates introduced
should work also for geographical coordinates
works also for zeta (still to be checked)
no diffusion yet
01.04.2015 VERS_7_1_7
intermediate version (3D lagrangian not finished)
27.02.2015 VERS_7_1_6
new version of aquabc_II integrated
26.02.2015 VERS_7_1_5
new calling sequence for BC to avoid parallel bug (bnds_read_new)
subnls.f rewritten
subpar3.f now allows for string of up to 10 chars
optimal interpolation finished (suboi.f, optintp.f)
iapini does not ask for basin/simul anymore
bug fix for waves on lat/lon grid
23.01.2015 VERS_7_1_4
compute fetch also in geo coordinates
handle projection in both directions
19.01.2015 VERS_7_1_3
major changes in code - this is a huge commit
basically all files have been changed
(nearly) all common blocks have been substituted by include files
please base all future changes of the code on this release
the release still has to be thoroughly debugged
19.01.2015 VERS_7_1_2
small bug fixes
consolidation of some features
output for sediment module
15.01.2015 VERS_7_1_1
mostly bug fixes
feminf and femelab are now working as expected