[2696] | 1 | #!/usr/bin/ksh |
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| 2 | |
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[2699] | 3 | # kpp4palm - script for creating gasphase module |
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| 4 | |
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| 5 | #------------------------------------------------------------------------------# |
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| 6 | # This file is part of the PALM model system. |
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[2696] | 7 | # |
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[2699] | 8 | # PALM is free software: you can redistribute it and/or modify it under the terms |
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| 9 | # of the GNU General Public License as published by the Free Software Foundation, |
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| 10 | # either version 3 of the License, or (at your option) any later version. |
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[2696] | 11 | # |
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[2699] | 12 | # PALM is distributed in the hope that it will be useful, but WITHOUT ANY |
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| 13 | # WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR |
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| 14 | # A PARTICULAR PURPOSE. See the GNU General Public License for more details. |
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[2696] | 15 | # |
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[2699] | 16 | # You should have received a copy of the GNU General Public License along with |
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| 17 | # PALM. If not, see <http://www.gnu.org/licenses/>. |
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| 18 | # |
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[2718] | 19 | # Copyright 2017-2018 Klaus Ketelsen and MPI-CH (April 2007) |
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| 20 | # Copyright 2017-2018 Karlsruhe Institute of Technology |
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| 21 | # Copyright 2017-2018 Leibniz Universitaet Hannover |
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[2699] | 22 | #------------------------------------------------------------------------------# |
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[3298] | 23 | # Nov. 2016: Initial Version of KPP chemistry convertor adapted for PALM |
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| 24 | # by Klaus Ketelsen |
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[2699] | 25 | # |
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[3298] | 26 | # This code is a modified version of KP4 (Jöckel, P., Kerkweg, A., Pozzer, A., |
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| 27 | # Sander, R., Tost, H., Riede, H., Baumgaertner, A., Gromov, S., and Kern, B., |
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| 28 | # 2010: Development cycle 2 of the Modular Earth Submodel System (MESSy2), |
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| 29 | # Geosci. Model Dev., 3, 717-752, https://doi.org/10.5194/gmd-3-717-2010). |
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| 30 | # KP4 is part of the Modular Earth Submodel System (MESSy), which is is |
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| 31 | # available under the GNU General Public License (GPL). |
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| 32 | # |
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| 33 | #------------------------------------------------------------------------------# |
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| 34 | # |
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[2696] | 35 | # Current revisions: |
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| 36 | # ------------------ |
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| 37 | # |
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| 38 | # |
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| 39 | # Former revisions: |
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| 40 | # ----------------- |
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[2699] | 41 | # $Id: kpp4palm.ksh 3780 2019-03-05 11:19:45Z forkel $ |
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[3780] | 42 | # forkel 05. March 2019: cs_mech and set_cm |
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[3458] | 43 | # forkel 30. Oktober 2018: Integrating contents of kp4_compress into chem_gasphase_mod.f90 |
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[3298] | 44 | # forkel 25. September 2018: Added cat for $MECH to pass mechanism name to kpp4palm |
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| 45 | # ketelsen 18. September 2018: Added cat for '#INLINE F90_GLOBAL' |
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| 46 | # (moved here from mechanisms/def_MECH/chem_gasphase.kpp |
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| 47 | # |
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| 48 | # forkel: 14. September 2018: WCOPY removed |
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| 49 | # ketelsen: July 2018: Adaptations for vektor mode |
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| 50 | # forkel June 2018: re-established original case of subroutine names |
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| 51 | # forkel May 2018: additional copying of chem_gasphase_mod.f90 into $DEFDIR |
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| 52 | # forkel 20.04.2018: removed wlamch and wlamch_add from $KPP_SUBROUTINE_LIST |
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| 53 | # (epsilon(one) is used now) |
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| 54 | # forkel March 2017 |
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| 55 | # Re-introduced relative path for KPP_HOME |
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| 56 | # Subroutine list adapted to lowercase subroutine names |
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| 57 | # Added arr2, removed update_sun and k_3rd from subroutine list |
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| 58 | # Renamed output file to chem_gasphase_mod |
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| 59 | # Renamed this file from kp4/ksh to kpp4kpp.ksh |
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| 60 | # changed location of def_mechanism directories to gasphase_preproc/mechanisms |
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| 61 | # |
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| 62 | # |
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| 63 | # 2718 2018-01-02 08:49:38Z maronga |
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[2699] | 64 | # Initial revision |
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| 65 | # |
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| 66 | # |
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[3298] | 67 | ########################################################################## |
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[2696] | 68 | # |
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[2699] | 69 | # |
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| 70 | # Other notes: |
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| 71 | # ------------# |
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[2696] | 72 | # Re-introduced relative path for KPP_HOME |
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| 73 | # Subroutine list adapted to lowercase subroutine names |
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| 74 | # Added arr2, removed update_sun and k_3rd from subroutine list |
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| 75 | # Renamed output file to chem_gasphase_mod |
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| 76 | # Renamed this fikle from kp4/ksh to kpp4kpp.ksh |
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| 77 | # changed location of def_mechanism directories to GASPHASE_PREPROC/mechanisms |
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| 78 | # |
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| 79 | # Nov. 2016: Initial Version of KPP chemistry convertor by Klaus Ketelsen |
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| 80 | # |
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| 81 | # |
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| 82 | |
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| 83 | set -eu |
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| 84 | |
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| 85 | |
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| 86 | ########################### User SetUp #################################### |
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| 87 | |
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| 88 | export KPP_HOME=`pwd`/kpp |
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| 89 | export KPP=$KPP_HOME/bin/kpp |
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| 90 | |
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| 91 | BASE=`pwd`/kpp4palm |
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| 92 | |
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| 93 | ########################## End User Setup ################################ |
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| 94 | |
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| 95 | WORK=tmp_kpp4palm |
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| 96 | |
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| 97 | # Default |
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| 98 | |
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[3298] | 99 | MECH=smog |
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[2699] | 100 | OUTDIR=`pwd`/../../../SOURCE |
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[2696] | 101 | OUTFILE=chem_gasphase_mod |
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| 102 | DEFDIR=`pwd`/mechanisms/def_smog |
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| 103 | PREFIX=chem_gasphase_mod |
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| 104 | MODE="scalar" |
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| 105 | VLEN=1 |
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| 106 | KEEP="NO" |
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[3298] | 107 | UPDT="NO" |
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| 108 | DE_INDEX=0 |
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| 109 | DE_INDEX_FAST="YES" |
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[2696] | 110 | |
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| 111 | export KPP_SOLVER=Rosenbrock |
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| 112 | |
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| 113 | # get Command line option |
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| 114 | |
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[3298] | 115 | while getopts :m:i:fkup:o:s:vl:w: c # get options |
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[2696] | 116 | do case $c in |
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[3298] | 117 | m) MECH=$OPTARG;; # mechanism |
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[2696] | 118 | |
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[3298] | 119 | i) DE_INDEX=$OPTARG;; # if set, deindexing |
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[2696] | 120 | |
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| 121 | f) DE_INDEX_FAST="YES";; # if set, fast deindexing |
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| 122 | |
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| 123 | k) KEEP="YES";; # keep Working directory |
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| 124 | |
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[3458] | 125 | o) OUTDIR=$OPTARG;; # Output directory of Generated Code = |
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| 126 | # SOURCE directory (do not change) |
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[2696] | 127 | |
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[3458] | 128 | p) PREFIX=$OPTARG;; # Name Prefix (chem_gasphase_mod, do not change) |
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[2696] | 129 | |
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[3458] | 130 | s) KPP_SOLVER=$OPTARG;; # Chosen solver (only Rosebrock solvers work for vector mode) |
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[2696] | 131 | |
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[3458] | 132 | u) UPDT="YES";; # update mechanisms/def_$MECH/chem_gasphase_mod.f90 |
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[2696] | 133 | |
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[3298] | 134 | v) MODE="vector";; # Set to vector Mode |
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| 135 | |
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| 136 | l) VLEN=$OPTARG;; # Set vector length |
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| 137 | |
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[2696] | 138 | w) WORK=$OPTARG;; # Working directory |
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| 139 | |
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| 140 | \?) print ${0##*/} "unknown option:" $OPTARG |
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[3298] | 141 | print "USAGE: ${0##*/} [ -m dir -e -k -u -o dir -p name -s solver -v -l length -w dir ] " |
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[2696] | 142 | exit 1;; |
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| 143 | esac |
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| 144 | done |
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| 145 | shift OPTIND-1 |
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| 146 | |
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[3298] | 147 | echo MECHANISM = $MECH |
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| 148 | echo DE_INDEX = $DE_INDEX |
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| 149 | echo KEEP = $KEEP |
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| 150 | echo UPDT = $UPDT |
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| 151 | echo MODE = $MODE |
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| 152 | echo VLEN = $VLEN |
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[2696] | 153 | |
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| 154 | DEF_PREFIX=${PREFIX}.kpp |
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[3298] | 155 | DEFDIR=`pwd`/mechanisms/def_$MECH |
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| 156 | echo DEFDIR = $DEFDIR |
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[2696] | 157 | |
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| 158 | # Create or clean working directory |
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| 159 | |
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| 160 | MY_PWD=`pwd` |
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| 161 | mkdir -p $WORK |
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| 162 | rm -rf $WORK/* |
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| 163 | cd $WORK |
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| 164 | |
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| 165 | # kpp dependend, may be changed |
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| 166 | |
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| 167 | KPP_FILE_LIST="Initialize Integrator LinearAlgebra Jacobian Function Rates Util" |
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[3458] | 168 | if [[ $MODE = "vector" ]] |
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| 169 | then |
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| 170 | KPP_FILE_LIST="$KPP_FILE_LIST kp4_compress_subroutines" |
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| 171 | fi |
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[2696] | 172 | |
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[3298] | 173 | KPP_SUBROUTINE_LIST="Initialize" |
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| 174 | KPP_SUBROUTINE_LIST="$KPP_SUBROUTINE_LIST INTEGRATE Fun" |
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| 175 | KPP_SUBROUTINE_LIST="$KPP_SUBROUTINE_LIST KppSolve KppDecomp" |
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| 176 | KPP_SUBROUTINE_LIST="$KPP_SUBROUTINE_LIST Jac_SP k_arr " |
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| 177 | KPP_SUBROUTINE_LIST="$KPP_SUBROUTINE_LIST Update_RCONST ARR2" |
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[2696] | 178 | KPP_SUBROUTINE_LIST="$KPP_SUBROUTINE_LIST initialize_kpp_ctrl error_output" |
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| 179 | |
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| 180 | # if [[ $MODE = "vector" && $KPP_SOLVER = "ROS2" ]] |
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| 181 | # then |
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| 182 | # cp $BASE/templates/${KPP_SOLVER}_vec.f90 ${KPP_SOLVER}.f90 # get vector Solver |
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| 183 | # else |
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| 184 | # # KPP_SUBROUTINE_LIST="$KPP_SUBROUTINE_LIST FunTemplate JacTemplate Update_SUN " |
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| 185 | # KPP_SUBROUTINE_LIST="$KPP_SUBROUTINE_LIST WCOPY WSCAL WAXPY" |
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| 186 | # if [[ $MODE = "vector" ]] |
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| 187 | # then |
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| 188 | # cp $BASE/templates/${KPP_SOLVER}_vec.f90 ${KPP_SOLVER}.f90 # get vector Solver |
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| 189 | # else |
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| 190 | # KPP_SUBROUTINE_LIST="$KPP_SUBROUTINE_LIST Rosenbrock FunTemplate JacTemplate Update_SUN" |
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| 191 | # fi |
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| 192 | # fi |
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| 193 | if [[ $MODE = "vector" ]] |
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| 194 | then |
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| 195 | # get vector Solver |
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| 196 | cp $BASE/templates/${KPP_SOLVER}_vec.f90 ${KPP_SOLVER}.f90 |
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[3458] | 197 | cp $BASE/templates/kp4_compress_header ${PREFIX}_kp4_compress_header.f90 |
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| 198 | cp $BASE/templates/kp4_compress_subroutines ${PREFIX}_kp4_compress_subroutines.f90 |
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[2696] | 199 | fi |
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| 200 | |
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| 201 | # Interface ignore list |
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[3298] | 202 | KPP_INTERFACE_IGNORE=" " |
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[2696] | 203 | |
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[3298] | 204 | echo " " |
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| 205 | echo KPP_SOLVER $KPP_SOLVER |
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| 206 | echo " " |
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| 207 | |
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[2696] | 208 | case $KPP_SOLVER in |
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| 209 | ROS2) ;; |
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| 210 | |
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| 211 | Rosenbrock) |
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[3298] | 212 | KPP_SUBROUTINE_LIST="$KPP_SUBROUTINE_LIST WSCAL WAXPY" |
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| 213 | if [[ $MODE != "vector" ]] |
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| 214 | then |
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| 215 | KPP_SUBROUTINE_LIST="$KPP_SUBROUTINE_LIST Rosenbrock FunTemplate JacTemplate" |
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| 216 | KPP_INTERFACE_IGNORE="WAXPY" |
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[3458] | 217 | |
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[3298] | 218 | else |
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| 219 | KPP_SUBROUTINE_LIST="$KPP_SUBROUTINE_LIST FunTemplate JacTemplate" |
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[3458] | 220 | KPP_SUBROUTINE_LIST="$KPP_SUBROUTINE_LIST kco_initialize kco_compress kco_finalize" |
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[3298] | 221 | fi;; |
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[2696] | 222 | |
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| 223 | rosenbrock_mz) |
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| 224 | KPP_SUBROUTINE_LIST="$KPP_SUBROUTINE_LIST WCOPY WSCAL WAXPY" |
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| 225 | KPP_SUBROUTINE_LIST="$KPP_SUBROUTINE_LIST Rosenbrock FunTemplate JacTemplate Update_SUN";; |
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| 226 | |
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| 227 | rosenbrock) |
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| 228 | KPP_SUBROUTINE_LIST="$KPP_SUBROUTINE_LIST WCOPY WSCAL WAXPY" |
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[3298] | 229 | KPP_SUBROUTINE_LIST="$KPP_SUBROUTINE_LIST Rosenbrock FunTemplate JacTemplate";; |
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[2696] | 230 | |
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| 231 | kpp_lsode) |
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| 232 | KPP_SUBROUTINE_LIST="$KPP_SUBROUTINE_LIST WCOPY WSCAL WAXPY" |
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| 233 | KPP_SUBROUTINE_LIST="$KPP_SUBROUTINE_LIST KppLsode DLSODE JAC_CHEM FUN_CHEM" |
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| 234 | KPP_INTERFACE_IGNORE="$KPP_INTERFACE_IGNORE JAC_CHEM KppDecomp KppSolve";; |
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| 235 | |
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| 236 | kpp_radau5) |
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| 237 | KPP_SUBROUTINE_LIST="$KPP_SUBROUTINE_LIST WCOPY WSCAL WAXPY FUN_CHEM JAC_CHEM SET2ZERO" |
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| 238 | KPP_SUBROUTINE_LIST="$KPP_SUBROUTINE_LIST RADAU5 Update_SUN" |
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| 239 | KPP_SUBROUTINE_LIST="$KPP_SUBROUTINE_LIST KppSolveCmplx KppDecompCmplx";; |
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| 240 | |
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| 241 | kpp_sdirk) |
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| 242 | KPP_SUBROUTINE_LIST="$KPP_SUBROUTINE_LIST WCOPY WSCAL WAXPY" |
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| 243 | KPP_SUBROUTINE_LIST="$KPP_SUBROUTINE_LIST SDIRK JAC_CHEM SET2ZERO FUN_CHEM" |
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| 244 | KPP_INTERFACE_IGNORE="$KPP_INTERFACE_IGNORE Set2zero SET2ZERO FUN_CHEM";; |
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| 245 | |
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| 246 | kpp_seulex) |
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| 247 | KPP_SUBROUTINE_LIST="$KPP_SUBROUTINE_LIST WCOPY WSCAL WAXPY" |
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| 248 | KPP_SUBROUTINE_LIST="$KPP_SUBROUTINE_LIST ATMSEULEX" |
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| 249 | KPP_SUBROUTINE_LIST="$KPP_SUBROUTINE_LIST SEULEX_ErrorMsg SEULEX_Integrator FUN_CHEM JAC_CHEM SEUL" |
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| 250 | KPP_INTERFACE_IGNORE="$KPP_INTERFACE_IGNORE SEULEX_Integrator SDIRK FUN_CHEM SEUL";; |
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| 251 | |
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| 252 | \?) print "SORRY ONLY ROSENBROCK METHODS WORK AT THE MOMENT:" $KPP_SOLVER |
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| 253 | exit 1;; |
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| 254 | esac |
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| 255 | #mz-ak-20070509+ |
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| 256 | |
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| 257 | KPP_INCLUDE_LIST="Parameters Global JacobianSP Monitor" |
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[3458] | 258 | if [[ $MODE = "vector" ]] |
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| 259 | then |
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| 260 | KPP_INCLUDE_LIST="$KPP_INCLUDE_LIST kp4_compress_header" |
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| 261 | fi |
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[2696] | 262 | |
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| 263 | #Get definition Files |
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| 264 | |
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| 265 | cp $DEFDIR/*.eqn . |
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| 266 | cp $DEFDIR/*.spc . |
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| 267 | cp $DEFDIR/${PREFIX}.kpp . |
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| 268 | |
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[3298] | 269 | # Global variable are defined here |
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| 270 | # This has the advantage that it is not necessary to include these variables in all .kpp definition files |
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| 271 | |
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| 272 | cat >> ${PREFIX}.kpp << EOF |
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| 273 | #INLINE F90_GLOBAL |
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| 274 | ! QVAP - Water vapor |
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| 275 | REAL(kind=dp) :: QVAP |
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| 276 | ! FAKT - Conversion factor |
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| 277 | REAL(kind=dp) :: FAKT |
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| 278 | |
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[3780] | 279 | ! CS_MECH for check of mechanism name with namelist |
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| 280 | CHARACTER(LEN=30) :: CS_MECH |
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[3298] | 281 | #ENDINLINE |
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| 282 | EOF |
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| 283 | |
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| 284 | # Store mechanism name in file mech_list |
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| 285 | cat >> mech_list << EOF |
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| 286 | ! Mechanism: $MECH |
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| 287 | ! |
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| 288 | EOF |
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| 289 | |
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[3780] | 290 | # Store mechanism name for cs_mech |
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| 291 | cat >> set_cm << EOF |
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| 292 | |
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| 293 | ! Set cs_mech for check with mechanism name from namelist |
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| 294 | cs_mech = '$MECH' |
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| 295 | EOF |
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| 296 | |
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[2696] | 297 | # Run kpp |
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| 298 | |
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| 299 | $KPP $DEF_PREFIX |
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| 300 | |
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| 301 | # Get templates for C++ program |
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| 302 | |
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| 303 | cp $BASE/templates/module_header* . # Use fixed Module_header |
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| 304 | cp $BASE/templates/initialize_kpp_ctrl_template.f90 . # CTRL kpp time stepping |
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| 305 | |
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| 306 | # file with subroutine list for c++ program create_kpp_module |
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| 307 | |
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| 308 | for i in $KPP_FILE_LIST |
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| 309 | do |
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| 310 | echo ${PREFIX}_${i} >> file_list |
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| 311 | done |
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| 312 | echo initialize_kpp_ctrl_template >> file_list |
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| 313 | |
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| 314 | # file with subroutine list for c++ program create_kpp_module |
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| 315 | |
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| 316 | for i in $KPP_SUBROUTINE_LIST |
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| 317 | do |
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| 318 | echo $i >> subroutine_list |
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| 319 | done |
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| 320 | |
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| 321 | # file with include list for c++ program create_kpp_module |
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| 322 | |
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| 323 | for i in $KPP_INCLUDE_LIST |
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| 324 | do |
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| 325 | echo ${PREFIX}_${i} >> include_list |
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| 326 | done |
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| 327 | |
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| 328 | touch interface_ignore_list |
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| 329 | for i in $KPP_INTERFACE_IGNORE |
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| 330 | do |
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| 331 | echo $i >> interface_ignore_list |
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| 332 | done |
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| 333 | |
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[3458] | 334 | echo start kpp4palm.exe with arguments |
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[3298] | 335 | echo $PREFIX $MODE $VLEN $DE_INDEX $DE_INDEX_FAST |
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| 336 | |
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[2696] | 337 | $BASE/bin/kpp4palm.exe $PREFIX $MODE $VLEN $DE_INDEX $DE_INDEX_FAST |
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| 338 | |
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[3298] | 339 | #Prelimanary, substitution has to be moved into kpp4palm.exe |
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| 340 | if [[ $MODE = "vector" ]] |
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| 341 | then |
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| 342 | sed -i -e 's/phot(nphot/phot(vl_dim,nphot/g' kk_kpp.f90 |
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| 343 | fi |
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[2696] | 344 | |
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| 345 | if [[ -e $OUTDIR/${OUTFILE}.f90 ]] |
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| 346 | then |
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| 347 | mv $OUTDIR/${OUTFILE}.f90 $OUTDIR/${OUTFILE}.f90.sav |
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| 348 | fi |
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| 349 | cp -p kk_kpp.f90 $OUTDIR/${OUTFILE}.f90 |
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| 350 | echo " " |
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| 351 | echo "Write kpp module -- > " $OUTDIR/${OUTFILE}.f90 |
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| 352 | |
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[3298] | 353 | if [[ $UPDT = "YES" ]] |
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| 354 | then |
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| 355 | cp -p kk_kpp.f90 $DEFDIR/${OUTFILE}.f90 |
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| 356 | echo " " |
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| 357 | echo "Write kpp module -- > " $DEFDIR/${OUTFILE}.f90 |
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| 358 | fi |
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| 359 | |
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[2696] | 360 | if [[ $KEEP = "NO" ]] |
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| 361 | then |
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| 362 | cd $MY_PWD |
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| 363 | rm -rf $WORK |
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| 364 | fi |
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| 365 | exit |
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| 366 | |
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