Merge remote-tracking branch 'origin/dev' into dev

tests/NILU/basic_tests

+#WORKSPACE=/xnilu_wrk/flexbuild
+#WORKSPACE=/home/ignacio/repos/
+FP_exec=$WORKSPACE/src/FP_ecmwf_gfortran
+path_flextest=$WORKSPACE/flextest/
+declare -a test_names=('1' 'HelloWorld' 'Fwd1' 'Fwd2' 'Bwd1' 'Volc' '2')
+

tests/NILU/run_test

+#!/bin/bash
+
+#input FP exec
+test_dir=$1  # name of dir with pathname and options to be used 
+FP_exec=$2   # path to executable to be run
+base_dir=$3  # base for the output
+options_default=$4
+
+echo run test '>' input
+echo $1
+echo $2
+echo $3
+echo $4
+
+#  echo name= $name
+#  echo working dir= $path_tests/test_$name
+#  echo executable= $FP_exec 
+#  echo default options from $options_default 
+ 
+#echo FP_exec=$FP_exec
+echo env var FLEXOUT_TMP=$FLEXOUT_TP
+
+#suffix=$(date "+%y-%m-%d_%H%M%S")
+test_tmp=${FLEXOUT_TMP}${base_dir}${test_dir}
+#_${suffix}
+
+current_dir=$(pwd)
+#echo test_tmp=$test_tmp
+mkdir $test_tmp
+
+echo run test '>' copy default options to temp dir
+echo from  $options_default  to $test_tmp/options
+cp -r $options_default $test_tmp/options
+#override default options
+echo copy test options files to temp dir
+echo ${test_dir}/options/* $test_tmp/options/
+cp   ${test_dir}/options/* $test_tmp/options/
+echo copy test options/SPECIES to temp dir if needed
+
+if [ -d "${test_dir}/options/SPECIES" ]; then
+echo from ${test_dir}/options/SPECIES/* to $test_tmp/options/SPECIES/
+cp        ${test_dir}/options/SPECIES/*    $test_tmp/options/SPECIES/
+fi
+
+# copy paths form repo source exec tmp dir 
+echo copy test pathnames to temp dir
+cp ${test_dir}/pathnames $test_tmp
+echo create output dir ${test_tmp}/output
+mkdir ${test_tmp}/output
+
+#cp test_1/run $test_tmp
+
+cd $test_tmp
+#echo $(pwd)
+#echo $FP_exec
+#  '&>' o is bash for both out and err
+#echo run $FP_exec   to  out.log #&
+#$FP_exec   &> out.log #&
+echo execute test
+$FP_exec > stdout.log 2> stderr.log #&
+echo flexpart terminated
+
+
+

tests/NILU/run_test_0

+#!/bin/bash
+
+#input 
+# - FP_exec: path to flexpart executable to test 
+
+FP_exec=$1
+
+# diplay path
+echo FP_exec=$FP_exec
+
+# :
+suffix=$(date "+%y-%m-%d_%H%M%S")
+#test_tmp=$FLEXOUT_TMP/test_1_$suffix
+test_tmp=test_0_$suffix
+
+echo test_tmp=$test_tmp
+mkdir $test_tmp
+
+
+#cp -r test_1/options $test_tmp
+cp -r /home/ignacio/repos/flexpart/options $test_tmp
+cp test_1/pathnames $test_tmp
+cp test_1/run $test_tmp
+#echo exit
+#exit
+
+cd $test_tmp
+
+./run $FP_exec
+
+

tests/NILU/run_test_1

+#!/bin/bash
+
+#input FP exec
+FP_exec=$1
+
+echo FP_exec=$FP_exec
+echo $FLEXOUT_TMP
+suffix=$(date "+%y-%m-%d_%H%M%S")
+test_tmp=${FLEXOUT_TMP}test_1_$suffix
+current_dir=$(pwd)
+echo test_tmp=$test_tmp
+mkdir $test_tmp
+
+
+cp -r test_1/options $test_tmp
+cp test_1/pathnames $test_tmp
+cp test_1/run $test_tmp
+
+cd $test_tmp
+
+./run $FP_exec  &> $test_tmp.log #&
+
+
+

tests/NILU/run_tests

+#!/bin/bash
+
+#input:
+# FP_exec : path to flexpart executable  
+# path_flextest: directory  path to output base directory
+# test_names (bash array): list of tests to be run
+
+# defaults
+#FP_exec=/home/ignacio/repos/flexpart/src/FP_ecmwf_gfortran
+#FP_exec=/xnilu_wrk/flexbuild/tests/NILU/FP_ecmwf_gfortran
+FP_exec=$WORKSPACE/src/FP_ecmwf_gfortran
+#path_flextest=/home/ignacio/repos/flextest/
+#path_flextest=/xnilu_wrk/flexbuild/flextest/
+path_flextest=$WORKSPACE/flextest/
+#options_default=/xnilu_wrk/flexbuild/flexpart/options/
+options_default=$WORKSPACE/options/
+#declare -a test_names=('1' 'HelloWorld' 'Fwd1' 'Fwd2' 'Bwd1' 'Volc' '2')
+#test_names[0]='1' 
+test_names[0]='HelloWorld' 
+
+group_name=tests
+
+source ./$1
+
+
+suffix=$(date "+%y-%m-%d_%H%M%S")
+#tests_dir=tests_${suffix}/
+tests_dir=${group_name}_${suffix}/
+path_tests=${path_flextest}/$tests_dir
+mkdir $path_tests
+
+
+#declare Bash Array
+#declare -a test_names=('1' '2' 'HelloWorld')
+#declare -a test_names=('1' '2' 'HelloWorld' 'Fwd1' 'Fwd2' 'Bwd1' 'Volc')
+#declare -a test_names=('2' 'Volc')
+#declare -a test_names=('1' 'HelloWorld' 'Fwd1' 'Fwd2' 'Bwd1' 'Volc' '2')
+
+#Print the Whole Bash Array
+s_test_names=${test_names[@]}
+# Length of the Bash Array
+n_tests=${#test_names[@]}
+#echo n_tests=$n_tests
+echo run $s_test_names
+echo total $n_tests tests
+#test
+#tests_dir='tests_15-08-19_113139/'
+#path_tests=${path_flextest}/$tests_dir
+
+
+outlog=stdout.log
+i=0
+i_end=$n_tests
+while [ $i -lt $i_end ] ;
+do
+  let j=i+1
+  name=${test_names[i]};
+  echo run test no. $j  
+#  echo name= $name
+#  echo working dir= $path_tests/test_$name
+#  echo executable= $FP_exec 
+#  echo default options from $options_default 
+  ./run_test test_$name  $FP_exec $path_tests $options_default
+  echo test $name terminated
+  success="$(cat $path_tests/test_$name/$outlog  | grep CONGRATULATIONS  | wc -l)"
+  echo success=$success
+let i=i+1;
+done
+ 
+tot_successes="$(cat $path_tests/test_*/$outlog  | grep CONGRATULATIONS  | wc -l)"
+tot_runs="$(ls -1 $path_tests | wc -l)"
+
+echo ' '
+echo finished  $tot_runs tests of $n_tests 
+echo $tot_successes seccessful
+exit
+
+
+
+
+
+
+
+
+
+
+
+
+
+./run_test test_1  $FP_exec $path_tests
+./run_test test_2  $FP_exec $path_tests
+# 6 species
+./run_test test_Volc  $FP_exec $path_tests
+./run_test test_HelloWorld  $FP_exec $path_tests
+./run_test test_Fwd1  $FP_exec $path_tests
+./run_test test_Fwd2  $FP_exec $path_tests
+./run_test test_Bwd1  $FP_exec $path_tests
+
+

tests/NILU/test_1/README

-To run this test, just execute FLEXPART in the current directory. 
-Contains the options directory from relese 9.2 
-The pathfile was modified
+To run this test, execute FLEXPART in the current directory after creating an output directory or
+
+./run path-to-flexpart-executable 
+ 
+This should create a temporary output dir and link output to it.
+Contains the options directory from releiase 9.2.0.2 
 The feature tested are the new SPECIES file.
 
 2014-10-16, tested on nordre@nilu (Ubuntu 12.04):

tests/NILU/test_1/pathnames

 ./options/
 ./output/
 /
-/flex_wrk/WIND_FIELDS/AVAILABLE_ECMWF_OPER_fields_global
+/xnilu_wrk/flex_wrk/WIND_FIELDS/AVAILABLE_ECMWF_OPER_fields_global
 ============================================
 

tests/NILU/test_1/run

+#!/bin/bash
+
+suffix=$(date "+%y-%m-%d_%H%M%S")
+
+FP_exec=$1 
+output_tmp=output_$suffix
+
+mkdir $output_tmp
+
+rm output
+ln -s $output_tmp output
+
+echo exec $FP_exec
+
+
+$FP_exec

tests/NILU/test_2/options/COMMAND

++++++++++++++ HEADER +++++++++++++++++
++++++++++++++ HEADER +++++++++++++++++
++++++++++++++ HEADER +++++++++++++++++
++++++++++++++ HEADER +++++++++++++++++
++++++++++++++ HEADER +++++++++++++++++
++++++++++++++ HEADER +++++++++++++++++
++++++++++++++ HEADER +++++++++++++++++
+-1
+20140611      0
+20140613      0
+ 86400
+ 86400
+   900
+ 9999999
+900   SYNC
+-5.0  CTL
+4     IFINE
+5     IOUT
+0     IPOUT
+1     LSUBGRID
+0     LCONVECTION
+1     LAGESPECTRA
+0     IPIN
+1     IOFR
+0     IFLUX
+0     MDOMAINFILL
+1     IND_SOURCE
+2     IND_RECEPTOR
+0     MQUASILAG
+1     NESTED_OUTPUT
+2     LINIT_COND
+0     SURF_ONLY

tests/NILU/test_2/options/RELEASES

++++++++++++++ HEADER +++++++++++++++++
++++++++++++++ HEADER +++++++++++++++++
++++++++++++++ HEADER +++++++++++++++++
++++++++++++++ HEADER +++++++++++++++++
++++++++++++++ HEADER +++++++++++++++++
++++++++++++++ HEADER +++++++++++++++++
++++++++++++++ HEADER +++++++++++++++++
++++++++++++++ HEADER +++++++++++++++++
++++++++++++++ HEADER +++++++++++++++++
++++++++++++++ HEADER +++++++++++++++++
++++++++++++++ HEADER +++++++++++++++++
+1
+26
+
+    20140611      180000
+    20140611      210000
+   11.530000    
+   78.540001    
+   11.530000    
+   78.540001    
+           1
+           0
+         100
+        4000
+   1.0000000    
+ZEP_201406_001_087
+
+    20140611      210000
+    20140612           0
+   11.530000    
+   78.540001    
+   11.530000    
+   78.540001    
+           1
+           0
+         100
+        4000
+   1.0000000    
+ZEP_201406_001_088
+

tests/NILU/test_2/options/SPECIES/SPECIES_026

+****************************************************************************
+*                                                                          *
+*     Input file for the Lagrangian particle dispersion model FLEXPART     *
+*               Definition file of chemical species/radionuclides          *
+*                                                                          *
+****************************************************************************
+CH4                Tracer name
+-999.9             Species half life
+-9.9E-09           Wet deposition - A
+                   Wet deposition - B
+-9.9E-09           In-cloud scavenging - Ai (cl=Ai*prec**Bi)
+-9.9               In-cloud scavenging - Bi (cl=Ai*prec**Bi)
+-9.9               In-cloud scavenging - Ci (S_i=Ci/cl)
+-9.9               In-cloud scavenging - Di (wetscav=S_i*prec/3.6E6/clouds_h/Di)
+-9.9               Dry deposition (gases) - D
+                   Dry deposition (gases) - Henrys const.
+                   Dry deposition (gases) - f0 (reactivity)
+-9.9E09            Dry deposition (particles) - rho
+                   Dry deposition (particles) - dquer
+                   Dry deposition (particles) - dsig
+-9.99              Alternative: dry deposition velocity
+16.000             molweight
+ 2.5E-15           OH Reaction rate at 25 deg, [cm^3/sec]
+-9                 number of associated specias (neg. none)
+-99.99             KOA - organic matter air partitioning

tests/NILU/test_2/pathnames

+./options/
+./output/
+/
+/xnilu_wrk/flex_wrk/WIND_FIELDS/AVAILABLE_ECMWF_OPER_fields_global
+============================================
+

tests/NILU/test_Bwd1/options/AGECLASSES

+************************************************
+*                                              *
+*Lagrangian particle dispersion model FLEXPART *
+*         Please select your options           *
+*                                              *
+*This file determines the ageclasses to be used*
+*                                              *
+*Ages are given in seconds. The first class    *
+*starts at age zero and goes up to the first   *
+*age specified. The last age gives the maximum *
+*time a particle is carried in the simulation. *
+*                                              *
+************************************************
+1          Integer        Number of age classes
+1728000 

tests/NILU/test_Bwd1/options/COMMAND

+********************************************************************************
+*                                                                              *
+*      Input file for the Lagrangian particle dispersion model FLEXPART        *
+*                           Please select your options                         *
+*                                                                              *
+********************************************************************************
+
+1. __                3X, I2
+   -1       
+   LDIRECT           1 FOR FORWARD SIMULATION, -1 FOR BACKWARD SIMULATION
+
+2. ________ ______   3X, I8, 1X, I6
+   20070121 090000
+   YYYYMMDD HHMISS   BEGINNING DATE OF SIMULATION
+
+3. ________ ______   3X, I8, 1X, I6
+   20070122 180000
+   YYYYMMDD HHMISS   ENDING DATE OF SIMULATION
+
+4. _____             3X, I5
+    3600 
+   SSSSS             OUTPUT EVERY SSSSS SECONDS
+
+5. _____             3X, I5
+    3600 
+   SSSSS             TIME AVERAGE OF OUTPUT (IN SSSSS SECONDS)
+
+6. _____             3X, I5
+     300 
+   SSSSS             SAMPLING RATE OF OUTPUT (IN SSSSS SECONDS)
+
+7. _________         3X, I9
+   999999999
+   SSSSSSSSS         TIME CONSTANT FOR PARTICLE SPLITTING (IN SECONDS)
+
+8. _____             3X, I5
+     300 
+   SSSSS             SYNCHRONISATION INTERVAL OF FLEXPART (IN SECONDS)
+
+9.  ---.--           4X, F6.4
+      3.0
+    CTL              FACTOR, BY WHICH TIME STEP MUST BE SMALLER THAN TL
+
+10. ---              4X, I3
+      4
+    IFINE            DECREASE OF TIME STEP FOR VERTICAL MOTION BY FACTOR IFINE
+
+11. -                4X, I1
+    1  
+    IOUT             1 CONCENTRATION (RESIDENCE TIME FOR BACKWARD RUNS) OUTPUT, 2 MIXING RATIO OUTPUT, 3 BOTH,4 PLUME TRAJECT., 5=1+4
+
+12. -                4X, I1
+    0  
+    IPOUT            PARTICLE DUMP: 0 NO, 1 EVERY OUTPUT INTERVAL, 2 ONLY AT END
+
+13. _                4X, I1
+    1
+    LSUBGRID         SUBGRID TERRAIN EFFECT PARAMETERIZATION: 1 YES, 0 NO
+
+14. _                4X, I1
+    0
+    LCONVECTION      CONVECTION: 1 YES, 0 NO
+
+15. _                4X, I1
+    0
+    LAGESPECTRA      AGE SPECTRA: 1 YES, 0 NO
+
+16. _                4X, I1
+    0
+    IPIN             CONTINUE SIMULATION WITH DUMPED PARTICLE DATA: 1 YES, 0 NO
+
+17. _                
+    1                4X,I1 
+    IOFR             IOUTPUTFOREACHREL CREATE AN OUPUT FILE FOR EACH RELEASE LOCATION: 1 YES, 0 NO
+
+18. _                4X, I1
+    0
+    IFLUX            CALCULATE FLUXES: 1 YES, 0 NO
+
+19. _                4X, I1
+    0
+    MDOMAINFILL      DOMAIN-FILLING TRAJECTORY OPTION: 1 YES, 0 NO, 2 STRAT. O3 TRACER
+
+20. _                4X, I1
+    1
+    IND_SOURCE       1=MASS UNIT , 2=MASS MIXING RATIO UNIT 
+
+21. _                4X, I1
+    1
+    IND_RECEPTOR     1=MASS UNIT , 2=MASS MIXING RATIO UNIT 
+
+22. _                4X, I1
+    0
+    MQUASILAG        QUASILAGRANGIAN MODE TO TRACK INDIVIDUAL PARTICLES: 1 YES, 0 NO
+
+23. _                4X, I1
+    0
+    NESTED_OUTPUT    SHALL NESTED OUTPUT BE USED? 1 YES, 0 NO
+
+24. _                4X, I1
+    0
+    LINIT_COND       INITIAL COND. FOR BW RUNS: 0=NO,1=MASS UNIT,2=MASS MIXING RATIO UNIT
+
+25. _                4X, I1
+    0
+    SURF_ONLY        IF THIS IS SET TO 1, OUTPUT IS WRITTEN ONLY OUT FOR LOWEST LAYER
+
+
+1. Simulation direction, 1 for forward, -1 for backward in time 
+	(consult Seibert and Frank, 2004 for backward runs)
+
+2. Beginning date and time of simulation. Must be given in format
+   YYYYMMDD HHMISS, where YYYY is YEAR, MM is MONTH, DD is DAY, HH is HOUR,
+   MI is MINUTE and SS is SECOND. Current version utilizes UTC.
+
+3. Ending date and time of simulation. Same format as 3.
+
+4. Average concentrations are calculated every SSSSS seconds.
+
+5. The average concentrations are time averages of SSSSS seconds
+   duration. If SSSSS is 0, instantaneous concentrations are outputted.
+
+6. The concentrations are sampled every SSSSS seconds to calculate the time
+   average concentration. This period must be shorter than the averaging time.
+
+7. Time constant for particle splitting. Particles are split into two
+   after SSSSS seconds, 2xSSSSS seconds, 4xSSSSS seconds, and so on.
+
+8. All processes are synchronized with this time interval (lsynctime).
+   Therefore, all other time constants must be multiples of this value.
+   Output interval and time average of output must be at least twice lsynctime.
+
+9. CTL must be >1 for time steps shorter than the  Lagrangian time scale
+   If CTL<0, a purely random walk simulation is done
+
+10.IFINE=Reduction factor for time step used for vertical wind
+
+11.IOUT determines how the output shall be made: concentration
+   (ng/m3, Bq/m3), mixing ratio (pptv), or both, or plume trajectory mode,
+   or concentration + plume trajectory mode.
+   In plume trajectory mode, output is in the form of average trajectories.
+
+12.IPOUT determines whether particle positions are outputted (in addition
+   to the gridded concentrations or mixing ratios) or not.
+   0=no output, 1 output every output interval, 2 only at end of the
+   simulation
+
+13.Switch on/off subgridscale terrain parameterization (increase of
+   mixing heights due to subgridscale orographic variations)
+
+14.Switch on/off the convection parameterization
+
+15.Switch on/off the calculation of age spectra: if yes, the file AGECLASSES
+   must be available
+
+16. If IPIN=1, a file "partposit_end" from a previous run must be available in
+    the output directory. Particle positions are read in and previous simulation
+    is continued. If IPIN=0, no particles from a previous run are used
+
+17. IF IOUTPUTFOREACHRELEASE is set to 1, one output field for each location
+    in the RLEASE file is created. For backward calculation this should be
+    set to 1. For forward calculation both possibilities are applicable.
+
+18. If IFLUX is set to 1, fluxes of each species through each of the output
+    boxes are calculated. Six fluxes, corresponding to northward, southward,
+    eastward, westward, upward and downward are calculated for each grid cell of
+    the output grid. The control surfaces are placed in the middle of each
+    output grid cell. If IFLUX is set to 0, no fluxes are determined.
+
+19. If MDOMAINFILL is set to 1, the first box specified in file RELEASES is used
+    as the domain where domain-filling trajectory calculations are to be done.
+    Particles are initialized uniformly distributed (according to the air mass
+    distribution) in that domain at the beginning of the simulation, and are
+    created at the boundaries throughout the simulation period.
+
+20. IND_SOURCE switches between different units for concentrations at the source
+    NOTE that in backward simulations the release of computational particles 
+    takes place at the "receptor" and the sampling of particles at the "source".
+          1=mass units (for bwd-runs = concentration)
+          2=mass mixing ratio units 
+21. IND_RECEPTOR switches between different units for concentrations at the receptor
+          1=mass units (concentrations)
+          2=mass mixing ratio units 
+
+22. MQUASILAG indicates whether particles shall be numbered consecutively (1) or
+    with their release location number (0). The first option allows tracking of
+    individual particles using the partposit output files
+
+23. NESTED_OUTPUT decides whether model output shall be made also for a nested
+    output field (normally with higher resolution)
+
+24. LINIT_COND determines whether, for backward runs only, the sensitivity to initial
+    conditions shall be calculated and written to output files
+    0=no output, 1 or 2 determines in which units the initial conditions are provided.
+
+25. SURF_ONLY: When set to 1, concentration/emission sensitivity is written out only
+    for the surface layer; useful for instance when only footprint emission sensitivity is needed
+    but initial conditions are needed on a full 3-D grid

tests/NILU/test_Bwd1/options/OUTGRID

+********************************************************************************
+*                                                                              *
+*      Input file for the Lagrangian particle dispersion model FLEXPART        *
+*                       Please specify your output grid                        *
+*                                                                              *
+********************************************************************************
+
+1.  ------.----       4X,F11.4
+       -10.0000       GEOGRAFICAL LONGITUDE OF LOWER LEFT CORNER OF OUTPUT GRID
+    OUTLONLEFT        (left boundary of the first grid cell - not its centre)
+
+2.  ------.----       4X,F11.4
+        35.0000       GEOGRAFICAL LATITUDE OF LOWER LEFT CORNER OF OUTPUT GRID
+    OUTLATLOWER       (lower boundary of the first grid cell - not its centre)
+
+3.  -----             4X,I5
+      60               NUMBER OF GRID POINTS IN X DIRECTION (= No. of cells + 1)
+    NUMXGRID
+
+4.  -----             4X,I5
+      40            NUMBER OF GRID POINTS IN Y DIRECTION (= No. of cells + 1)
+    NUMYGRID
+
+5.  ------.---        4X,F10.3
+         0.5        GRID DISTANCE IN X DIRECTION
+    DXOUTLON
+
+6.  ------.---        4X,F10.3
+        0.5       GRID DISTANCE IN Y DIRECTION
+    DYOUTLAT
+
+10. -----.-           4X, F7.1
+      500.0
+    LEVEL 4           HEIGHT OF LEVEL (UPPER BOUNDARY)
+

tests/NILU/test_Bwd1/options/OUTGRID_NEST

+********************************************************************************
+*                                                                              *
+*      Input file for the Lagrangian particle dispersion model FLEXPART        *
+*                       Please specify your output grid                        *
+*                                                                              *
+********************************************************************************
+
+1.  ------.----       4X,F11.4
+         1.0000       GEOGRAFICAL LONGITUDE OF LOWER LEFT CORNER OF OUTPUT GRID