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mostly copyright notice adjourned
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g u committed Apr 15, 2020
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113 changes: 113 additions & 0 deletions COMMIT
Original file line number Diff line number Diff line change
@@ -1,5 +1,118 @@
============================================================

Wed Apr 15 23:55:47 CEST 2020

mostly copyright notice adjourned

Rules.make | 2 +-
examples/mar_menor/run.sh | 2 +-
examples/mar_menor/util.sh | 2 +-
fem3d/bin/nemunas-git.sh | 2 +-
fem3d/newclose.f | 18 +-
fembin/CR | 0
fembin/Makefile | 6 +-
fembin/cvs/cvs_utils.sh | 2 +-
fembin/git-automerge.pl | 117 +++++
fembin/git-automerge.sh | 39 ++
fembin/pschange.pl | 8 +
fembin/xfem | 2 +-
femcheck/Makefile | 1 +
femcheck/copyright/check_file.sh | 8 +
femcheck/copyright/check_revision_log.sh | 8 +
femcheck/copyright/copy_stats.pl | 47 ++
femcheck/copyright/copyright.sh | 499 +++++++++++++++++++++
femcheck/copyright/include_copyright.pl | 28 +-
femcheck/copyright/include_copyright.sh | 2 +-
femcheck/copyright/subst_lines.pl | 8 +
femcheck/netcdf/INFO | 8 +
femcheck/netcdf/Makefile | 15 +-
femcheck/netcdf/nc_include.f | 24 +
femcheck/netcdf/nc_mod.f | 24 +
femcheck/netcdf/set_netcdf.sh | 10 +
femcheck/netcdf/test_netcdf.sh | 10 +-
femcheck/rules/Rules.dist | 2 +-
femersem/bfm_env.sh | 0
femersem/src/BFM/Ben/BenBac.nml | 0
femersem/src/BFM/Ben/BenOrganism.nml | 0
femersem/src/BFM/Ben/Bioturbation.nml | 0
femersem/src/BFM/Ben/FilterFeeder.nml | 0
femersem/src/BFM/Bennut/BenAmmonium.nml | 0
femersem/src/BFM/Bennut/BenAnoxic.nml | 0
femersem/src/BFM/Bennut/BenDenitriDepth.nml | 0
femersem/src/BFM/Bennut/BenNitrate.nml | 0
femersem/src/BFM/Bennut/BenOxygen.nml | 0
femersem/src/BFM/Bennut/BenPhosphate.nml | 0
femersem/src/BFM/Bennut/BenQ1Transport.nml | 0
femersem/src/BFM/Bennut/BenSilica.nml | 0
femersem/src/BFM/Bennut/BenthicReturn1.nml | 0
femersem/src/BFM/Bennut/BenthicReturn2.nml | 0
femersem/src/BFM/General/GlobalDefsBFM.model | 0
femersem/src/BFM/General/Param.nml | 0
femersem/src/BFM/Light/LightAdaptation.nml | 0
femersem/src/BFM/Light/PhotoAvailableRadiation.nml | 0
femersem/src/BFM/Oxygen/WindOxReaeration_3.nml | 0
femersem/src/BFM/PelB/MesoZoo.nml | 0
femersem/src/BFM/PelB/MicroZoo.nml | 0
femersem/src/BFM/PelB/PelBac.nml | 0
femersem/src/BFM/PelB/PelChem.nml | 0
femersem/src/BFM/PelB/PelGlobal.nml | 0
femersem/src/BFM/PelB/Phyto.nml | 0
.../BFM/PelBen/ControlBenPartNutrientBuffers.nml | 0
femersem/src/BFM/PelBen/Settling.nml | 0
femersem/src/BFM/proto/AllocateMem.proto | 0
femersem/src/BFM/proto/INCLUDE.proto | 0
femersem/src/BFM/proto/ModuleMem.proto | 0
femersem/src/BFM/proto/set_var_info_bfm.proto | 0
femersem/src/getm/patch_getm_bfm_2.5e | 0
femersem/src/gotm/BFM.make | 0
femersem/src/gotm/Makefile | 0
femersem/src/gotm/patch_gotm_bfm_2.5e | 0
femgotm/Makefile | 16 +-
femgotm/README | 12 +-
femlib/perl/ColorObjetc.pm | 2 +
femlib/perl/ForFile.pm | 0
femlib/perl/GD.pm | 2 +
femlib/perl/GD/Image.pm | 2 +
femlib/perl/GD/Image.pm.PLS | 2 +-
femlib/perl/GD/Polygon.pm | 2 +
femlib/perl/GD/Polyline.pm | 2 +
femlib/perl/GD/Simple.pm | 2 +
femlib/perl/address.pm | 0
femlib/perl/ascii.pm | 0
femlib/perl/bibtex.pm | 0
femlib/perl/csv.pm | 0
femlib/perl/date.pm | 0
femlib/perl/grd.pm | 0
femlib/perl/grdline.pm | 0
femlib/perl/html.pm | 0
femlib/perl/html3.pm | 0
femlib/perl/mail.pm | 0
femlib/perl/message.pm | 0
femlib/perl/missing.pm | 0
femlib/perl/modules/Mail-Sender-0.8.13/test.pl | 2 +
femlib/perl/modules/get.pl | 8 +
femlib/perl/mtree.pm | 0
femlib/perl/spam.pm | 0
femlib/perl/spline.pm | 0
femlib/perl/str.pm | 0
femlib/python/rm.py | 8 +
fempara/README | 9 +
femplot/color/oceanlib/Makefile | 9 +
femplot/color/oceanlib_txt/Makefile | 9 +
femutil/unform/Makefile | 9 +
femutil/unform/test.f | 24 +
femutil/var/femtime.f | 24 +
98 files changed, 1013 insertions(+), 25 deletions(-)
new file:
fembin/git-automerge.pl
fembin/git-automerge.sh
femcheck/copyright/copy_stats.pl
femcheck/copyright/copyright.sh
deleted:
femersem/bfm_env.sh

============================================================

Wed Apr 15 23:11:58 CEST 2020

merge conflicts
Expand Down
2 changes: 1 addition & 1 deletion Rules.make
Original file line number Diff line number Diff line change
Expand Up @@ -233,7 +233,7 @@ ECOLOGICAL = NONE
#BFMDIR = /gpfs/work/OGS18_PRACE_P_0/SHYFEM_BFM/bfm
#BFMDIR = /home/georg/appl/donata/bfm/bfmv5
#BFMDIR = /home/georg/appl/donata/bfm/BiogeochemicalFluxModel-5.1.0
#BFMDIR = /home/gumgiesser/bfm/BiogeochemicalFluxModel-5.1.0
#BFMDIR = $(HOME)/BFM

##############################################
# Experimental features
Expand Down
2 changes: 2 additions & 0 deletions VERSION
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,8 @@ version 7_5_69 06-03-2020 VERS_7_5_69 commit_2020-04-15

version 7_5_69 06-03-2020 VERS_7_5_69 commit_2020-04-15

version 7_5_69 06-03-2020 VERS_7_5_69 commit_2020-04-15

version 7_5_69 06-03-2020 VERS_7_5_69 commit_2020-04-14

version 7_5_69 06-03-2020 VERS_7_5_69 commit_2020-04-11
Expand Down
2 changes: 1 addition & 1 deletion examples/mar_menor/run.sh
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
#!/usr/bin/env bash
#!/bin/bash

#------------------------------------------------------------------------
#
Expand Down
2 changes: 1 addition & 1 deletion examples/mar_menor/util.sh
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@

#!/bin/sh

#------------------------------------------------------------------------
#
Expand Down
2 changes: 1 addition & 1 deletion fem3d/bin/nemunas-git.sh
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@

#!/bin/sh

#------------------------------------------------------------------------
#
Expand Down
18 changes: 15 additions & 3 deletions fem3d/newclose.f
Original file line number Diff line number Diff line change
Expand Up @@ -347,7 +347,7 @@ subroutine close_init

write(6,*) 'closing sections initialized: ',nclose

call plot_dist
call check_dist !checks and plots

! -----------------------------------------------
! end of routine
Expand Down Expand Up @@ -468,6 +468,7 @@ subroutine sp136(ic)

use close
use shympi
use mod_internal

implicit none

Expand Down Expand Up @@ -508,6 +509,8 @@ subroutine sp136(ic)
ic=0 !&&&& do not compute new uv-matrix
nsc = nclose

rcomputev = 1 !set all elements to compute

call get_act_dtime(dtime)
call get_act_timeline(aline)

Expand Down Expand Up @@ -1221,6 +1224,7 @@ subroutine set_geyer(id,geyer)

do ie=1,nel
dist = pentry(id)%distfact(ie)
if( dist <= 0. ) cycle
f = 1. + dist*(g-1.)
rcomputev(ie) = f
end do
Expand Down Expand Up @@ -1340,7 +1344,7 @@ subroutine print_closing_info(id,text)

subroutine adjust_distfact(ndist,fact,efact)

! sets up array efact
! sets up array efact - will be between 1 (barriers) and 0 (far field)

use basin

Expand Down Expand Up @@ -1386,7 +1390,7 @@ subroutine adjust_distfact(ndist,fact,efact)

!*****************************************************************

subroutine plot_dist
subroutine check_dist

use basin
use close
Expand All @@ -1395,11 +1399,19 @@ subroutine plot_dist

integer id
real dist(nel)
integer check(nel)

check = 0
do id=1,nclose
dist = dist + pentry(id)%distfact
where( pentry(id)%distfact > 0 ) check = check + 1
end do

if( maxval(check) > 1 ) then
write(6,*) 'barriers are too close for chosen value of ndist'
stop 'error stop check_dist: ndist too big'
end if

call basin_to_grd
call grd_flag_depth
call grd_set_element_depth(dist)
Expand Down
Empty file modified fembin/CR
100755 → 100644
Empty file.
6 changes: 5 additions & 1 deletion fembin/Makefile
100755 → 100644
Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,6 @@
#
#------------------------------------------------------------------------


# makefile for fem/bin

DIR = fembin
Expand All @@ -20,6 +19,8 @@ REMOTEDIR = /net/lagoon/usr/users/georg/fem/$(DIR)
LOCALDIR = $(FEMDIR)/$(DIR)
UPFILES = *

SPECIAL = Makefile CR

#----------------------------------------------------------

all: fem
Expand Down Expand Up @@ -56,6 +57,9 @@ list:

depend: nothing

noexe:
chmod -x $(SPECIAL)

femsave: save
mv $(DIR).zip $(DISTDIR)

Expand Down
2 changes: 1 addition & 1 deletion fembin/cvs/cvs_utils.sh
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
#
#!/bin/sh

#------------------------------------------------------------------------
#
Expand Down
117 changes: 117 additions & 0 deletions fembin/git-automerge.pl
Original file line number Diff line number Diff line change
@@ -0,0 +1,117 @@
#!/usr/bin/perl
#
# automerges merge conflicts
#
#-----------------------------------------------------------

my $file = $ARGV[0];

$debug = 0;

$start="<<<<<<< HEAD";
$end=">>>>>>>";
$mid="=======";

$sep="============================================================";

print STDERR "handling file $file\n" if $debug;

while(<>) {

if( /^$start$/ ) {
$block++;
$in_first = 1;
next;
} elsif( /^$mid$/ ) {
if( not $in_first ) {
die "*** error reading mid but not in first: $_";
}
$in_first = 0;
$in_second = 1;
next;
} elsif( /^$end / ) {
if( not $in_second ) {
die "*** error reading end but not in second: $_";
}
$in_second = 0;
handle_blocks();
next;
}

if( $in_first ) {
push(@first,$_);
} elsif( $in_second ) {
push(@second,$_);
} else {
print;
}
}

print STDERR "finished handling file $file with $block blocks(s)\n" if $debug;

#-----------------------------------------------------------

sub handle_blocks
{
my $ftime = get_time(@first);
my $stime = get_time(@second);

#print STDERR "first: $ftime second: $stime\n";

if( $ftime < $stime ) {
my @aux = @second; @second = @first; @first = @aux;
}

print_block(@first);
print_sep();
print_block(@second);

@first = (); @second = ();
}

sub print_block
{
foreach (@_) {
print;
}
}

sub print_sep
{
if( $file eq "VERSION" ) {
die "*** can handle only one block\n" if( $block > 1 );
print "\n";
} elsif( $file eq "COMMIT" ) {
die "*** can handle only one block\n" if( $block > 1 );
print "\n$sep\n\n";
} elsif( $file eq "fem3d/subver.f" ) {
@second = (); #we only need the first occurrence, no seperator
} else {
die "*** cannot handle file: $file\n";
}
}

sub get_time
{
my $date = shift;

chomp($date);

if( $file eq "VERSION" ) {
$date =~ s/^.*commit_//;
} elsif( $file eq "COMMIT" ) {
;
} elsif( $file eq "fem3d/subver.f" ) {
$date =~ s/^.*(\d{4}-\d{2}-\d{2}).\s*$/$1/;
} else {
die "*** cannot handle file: $file\n";
}

print STDERR "date found: $date\n" if $debug;
my $secs = `date -d "$date" +%s`;

return $secs;
}

#-----------------------------------------------------------

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