1 | #!/usr/bin/ksh |
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2 | |
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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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7 | # |
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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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11 | # |
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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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15 | # |
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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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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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22 | #------------------------------------------------------------------------------# |
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23 | # Nov. 2016: Initial Version of KPP chemistry convertor adapted for PALM |
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24 | # by Klaus Ketelsen |
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25 | # |
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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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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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41 | # $Id: kpp4palm.ksh 3800 2019-03-15 16:40:25Z maronga $ |
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42 | # Removed edit of phot(nphot) for version edit phot(nphot), now done in fortran_file.C (15.03.2019, forkel) |
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43 | # Editing with sed to add dummy statements toavoud unused variables (15.03.2019, forkel) |
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44 | # |
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45 | # 3780 2019-03-05 11:19:45Z forkel |
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46 | # forkel 05. March 2019: cs_mech and set_cm |
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47 | # forkel 30. Oktober 2018: Integrating contents of kp4_compress into chem_gasphase_mod.f90 |
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48 | # forkel 25. September 2018: Added cat for $MECH to pass mechanism name to kpp4palm |
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49 | # ketelsen 18. September 2018: Added cat for '#INLINE F90_GLOBAL' |
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50 | # (moved here from mechanisms/def_MECH/chem_gasphase.kpp |
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51 | # |
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52 | # forkel: 14. September 2018: WCOPY removed |
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53 | # ketelsen: July 2018: Adaptations for vektor mode |
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54 | # forkel June 2018: re-established original case of subroutine names |
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55 | # forkel May 2018: additional copying of chem_gasphase_mod.f90 into $DEFDIR |
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56 | # forkel 20.04.2018: removed wlamch and wlamch_add from $KPP_SUBROUTINE_LIST |
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57 | # (epsilon(one) is used now) |
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58 | # forkel March 2017 |
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59 | # Re-introduced relative path for KPP_HOME |
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60 | # Subroutine list adapted to lowercase subroutine names |
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61 | # Added arr2, removed update_sun and k_3rd from subroutine list |
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62 | # Renamed output file to chem_gasphase_mod |
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63 | # Renamed this file from kp4/ksh to kpp4kpp.ksh |
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64 | # changed location of def_mechanism directories to gasphase_preproc/mechanisms |
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65 | # |
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66 | # |
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67 | # 2718 2018-01-02 08:49:38Z maronga |
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68 | # Initial revision |
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69 | # |
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70 | # |
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71 | ########################################################################## |
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72 | # |
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73 | # |
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74 | # Other notes: |
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75 | # ------------# |
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76 | # Re-introduced relative path for KPP_HOME |
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77 | # Subroutine list adapted to lowercase subroutine names |
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78 | # Added arr2, removed update_sun and k_3rd from subroutine list |
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79 | # Renamed output file to chem_gasphase_mod |
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80 | # Renamed this fikle from kp4/ksh to kpp4kpp.ksh |
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81 | # changed location of def_mechanism directories to GASPHASE_PREPROC/mechanisms |
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82 | # |
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83 | # Nov. 2016: Initial Version of KPP chemistry convertor by Klaus Ketelsen |
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84 | # |
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85 | # |
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86 | |
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87 | set -eu |
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88 | |
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89 | |
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90 | ########################### User SetUp #################################### |
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91 | |
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92 | export KPP_HOME=`pwd`/kpp |
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93 | export KPP=$KPP_HOME/bin/kpp |
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94 | |
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95 | BASE=`pwd`/kpp4palm |
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96 | |
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97 | ########################## End User Setup ################################ |
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98 | |
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99 | WORK=tmp_kpp4palm |
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100 | |
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101 | # Default |
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102 | |
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103 | MECH=smog |
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104 | OUTDIR=`pwd`/../../../SOURCE |
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105 | OUTFILE=chem_gasphase_mod |
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106 | DEFDIR=`pwd`/mechanisms/def_smog |
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107 | PREFIX=chem_gasphase_mod |
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108 | MODE="scalar" |
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109 | VLEN=1 |
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110 | KEEP="NO" |
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111 | UPDT="NO" |
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112 | DE_INDEX=0 |
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113 | DE_INDEX_FAST="YES" |
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114 | |
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115 | export KPP_SOLVER=Rosenbrock |
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116 | |
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117 | # get Command line option |
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118 | |
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119 | while getopts :m:i:fkup:o:s:vl:w: c # get options |
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120 | do case $c in |
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121 | m) MECH=$OPTARG;; # mechanism |
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122 | |
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123 | i) DE_INDEX=$OPTARG;; # if set, deindexing |
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124 | |
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125 | f) DE_INDEX_FAST="YES";; # if set, fast deindexing |
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126 | |
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127 | k) KEEP="YES";; # keep Working directory |
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128 | |
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129 | o) OUTDIR=$OPTARG;; # Output directory of Generated Code = |
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130 | # SOURCE directory (do not change) |
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131 | |
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132 | p) PREFIX=$OPTARG;; # Name Prefix (chem_gasphase_mod, do not change) |
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133 | |
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134 | s) KPP_SOLVER=$OPTARG;; # Chosen solver (only Rosebrock solvers work for vector mode) |
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135 | |
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136 | u) UPDT="YES";; # update mechanisms/def_$MECH/chem_gasphase_mod.f90 |
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137 | |
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138 | v) MODE="vector";; # Set to vector Mode |
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139 | |
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140 | l) VLEN=$OPTARG;; # Set vector length |
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141 | |
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142 | w) WORK=$OPTARG;; # Working directory |
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143 | |
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144 | \?) print ${0##*/} "unknown option:" $OPTARG |
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145 | print "USAGE: ${0##*/} [ -m dir -e -k -u -o dir -p name -s solver -v -l length -w dir ] " |
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146 | exit 1;; |
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147 | esac |
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148 | done |
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149 | shift OPTIND-1 |
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150 | |
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151 | echo MECHANISM = $MECH |
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152 | echo DE_INDEX = $DE_INDEX |
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153 | echo KEEP = $KEEP |
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154 | echo UPDT = $UPDT |
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155 | echo MODE = $MODE |
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156 | echo VLEN = $VLEN |
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157 | |
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158 | DEF_PREFIX=${PREFIX}.kpp |
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159 | DEFDIR=`pwd`/mechanisms/def_$MECH |
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160 | echo DEFDIR = $DEFDIR |
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161 | |
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162 | # Create or clean working directory |
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163 | |
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164 | MY_PWD=`pwd` |
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165 | mkdir -p $WORK |
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166 | rm -rf $WORK/* |
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167 | cd $WORK |
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168 | |
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169 | # kpp dependend, may be changed |
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170 | |
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171 | KPP_FILE_LIST="Initialize Integrator LinearAlgebra Jacobian Function Rates Util" |
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172 | if [[ $MODE = "vector" ]] |
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173 | then |
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174 | KPP_FILE_LIST="$KPP_FILE_LIST kp4_compress_subroutines" |
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175 | fi |
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176 | |
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177 | KPP_SUBROUTINE_LIST="Initialize" |
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178 | KPP_SUBROUTINE_LIST="$KPP_SUBROUTINE_LIST INTEGRATE Fun" |
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179 | KPP_SUBROUTINE_LIST="$KPP_SUBROUTINE_LIST KppSolve KppDecomp" |
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180 | KPP_SUBROUTINE_LIST="$KPP_SUBROUTINE_LIST Jac_SP k_arr " |
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181 | KPP_SUBROUTINE_LIST="$KPP_SUBROUTINE_LIST Update_RCONST ARR2" |
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182 | KPP_SUBROUTINE_LIST="$KPP_SUBROUTINE_LIST initialize_kpp_ctrl error_output" |
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183 | |
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184 | # if [[ $MODE = "vector" && $KPP_SOLVER = "ROS2" ]] |
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185 | # then |
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186 | # cp $BASE/templates/${KPP_SOLVER}_vec.f90 ${KPP_SOLVER}.f90 # get vector Solver |
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187 | # else |
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188 | # # KPP_SUBROUTINE_LIST="$KPP_SUBROUTINE_LIST FunTemplate JacTemplate Update_SUN " |
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189 | # KPP_SUBROUTINE_LIST="$KPP_SUBROUTINE_LIST WCOPY WSCAL WAXPY" |
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190 | # if [[ $MODE = "vector" ]] |
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191 | # then |
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192 | # cp $BASE/templates/${KPP_SOLVER}_vec.f90 ${KPP_SOLVER}.f90 # get vector Solver |
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193 | # else |
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194 | # KPP_SUBROUTINE_LIST="$KPP_SUBROUTINE_LIST Rosenbrock FunTemplate JacTemplate Update_SUN" |
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195 | # fi |
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196 | # fi |
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197 | if [[ $MODE = "vector" ]] |
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198 | then |
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199 | # get vector Solver |
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200 | cp $BASE/templates/${KPP_SOLVER}_vec.f90 ${KPP_SOLVER}.f90 |
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201 | cp $BASE/templates/kp4_compress_header ${PREFIX}_kp4_compress_header.f90 |
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202 | cp $BASE/templates/kp4_compress_subroutines ${PREFIX}_kp4_compress_subroutines.f90 |
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203 | fi |
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204 | |
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205 | # Interface ignore list |
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206 | KPP_INTERFACE_IGNORE=" " |
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207 | |
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208 | echo " " |
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209 | echo KPP_SOLVER $KPP_SOLVER |
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210 | echo " " |
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211 | |
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212 | case $KPP_SOLVER in |
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213 | ROS2) ;; |
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214 | |
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215 | Rosenbrock) |
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216 | KPP_SUBROUTINE_LIST="$KPP_SUBROUTINE_LIST WSCAL WAXPY" |
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217 | if [[ $MODE != "vector" ]] |
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218 | then |
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219 | KPP_SUBROUTINE_LIST="$KPP_SUBROUTINE_LIST Rosenbrock FunTemplate JacTemplate" |
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220 | KPP_INTERFACE_IGNORE="WAXPY" |
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221 | |
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222 | else |
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223 | KPP_SUBROUTINE_LIST="$KPP_SUBROUTINE_LIST FunTemplate JacTemplate" |
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224 | KPP_SUBROUTINE_LIST="$KPP_SUBROUTINE_LIST kco_initialize kco_compress kco_finalize" |
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225 | fi;; |
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226 | |
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227 | rosenbrock_mz) |
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228 | KPP_SUBROUTINE_LIST="$KPP_SUBROUTINE_LIST WCOPY WSCAL WAXPY" |
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229 | KPP_SUBROUTINE_LIST="$KPP_SUBROUTINE_LIST Rosenbrock FunTemplate JacTemplate Update_SUN";; |
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230 | |
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231 | rosenbrock) |
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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 Rosenbrock FunTemplate JacTemplate";; |
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234 | |
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235 | kpp_lsode) |
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236 | KPP_SUBROUTINE_LIST="$KPP_SUBROUTINE_LIST WCOPY WSCAL WAXPY" |
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237 | KPP_SUBROUTINE_LIST="$KPP_SUBROUTINE_LIST KppLsode DLSODE JAC_CHEM FUN_CHEM" |
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238 | KPP_INTERFACE_IGNORE="$KPP_INTERFACE_IGNORE JAC_CHEM KppDecomp KppSolve";; |
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239 | |
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240 | kpp_radau5) |
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241 | KPP_SUBROUTINE_LIST="$KPP_SUBROUTINE_LIST WCOPY WSCAL WAXPY FUN_CHEM JAC_CHEM SET2ZERO" |
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242 | KPP_SUBROUTINE_LIST="$KPP_SUBROUTINE_LIST RADAU5 Update_SUN" |
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243 | KPP_SUBROUTINE_LIST="$KPP_SUBROUTINE_LIST KppSolveCmplx KppDecompCmplx";; |
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244 | |
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245 | kpp_sdirk) |
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246 | KPP_SUBROUTINE_LIST="$KPP_SUBROUTINE_LIST WCOPY WSCAL WAXPY" |
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247 | KPP_SUBROUTINE_LIST="$KPP_SUBROUTINE_LIST SDIRK JAC_CHEM SET2ZERO FUN_CHEM" |
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248 | KPP_INTERFACE_IGNORE="$KPP_INTERFACE_IGNORE Set2zero SET2ZERO FUN_CHEM";; |
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249 | |
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250 | kpp_seulex) |
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251 | KPP_SUBROUTINE_LIST="$KPP_SUBROUTINE_LIST WCOPY WSCAL WAXPY" |
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252 | KPP_SUBROUTINE_LIST="$KPP_SUBROUTINE_LIST ATMSEULEX" |
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253 | KPP_SUBROUTINE_LIST="$KPP_SUBROUTINE_LIST SEULEX_ErrorMsg SEULEX_Integrator FUN_CHEM JAC_CHEM SEUL" |
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254 | KPP_INTERFACE_IGNORE="$KPP_INTERFACE_IGNORE SEULEX_Integrator SDIRK FUN_CHEM SEUL";; |
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255 | |
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256 | \?) print "SORRY ONLY ROSENBROCK METHODS WORK AT THE MOMENT:" $KPP_SOLVER |
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257 | exit 1;; |
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258 | esac |
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259 | #mz-ak-20070509+ |
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260 | |
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261 | KPP_INCLUDE_LIST="Parameters Global JacobianSP Monitor" |
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262 | if [[ $MODE = "vector" ]] |
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263 | then |
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264 | KPP_INCLUDE_LIST="$KPP_INCLUDE_LIST kp4_compress_header" |
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265 | fi |
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266 | |
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267 | #Get definition Files |
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268 | |
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269 | cp $DEFDIR/*.eqn . |
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270 | cp $DEFDIR/*.spc . |
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271 | cp $DEFDIR/${PREFIX}.kpp . |
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272 | |
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273 | # Global variable are defined here |
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274 | # This has the advantage that it is not necessary to include these variables in all .kpp definition files |
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275 | |
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276 | cat >> ${PREFIX}.kpp << EOF |
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277 | #INLINE F90_GLOBAL |
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278 | ! QVAP - Water vapor |
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279 | REAL(kind=dp) :: QVAP |
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280 | ! FAKT - Conversion factor |
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281 | REAL(kind=dp) :: FAKT |
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282 | |
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283 | ! CS_MECH for check of mechanism name with namelist |
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284 | CHARACTER(LEN=30) :: CS_MECH |
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285 | #ENDINLINE |
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286 | EOF |
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287 | |
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288 | # Store mechanism name in file mech_list |
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289 | cat >> mech_list << EOF |
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290 | ! Mechanism: $MECH |
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291 | ! |
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292 | EOF |
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293 | |
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294 | # Store mechanism name for cs_mech |
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295 | cat >> set_cm << EOF |
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296 | |
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297 | ! Set cs_mech for check with mechanism name from namelist |
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298 | cs_mech = '$MECH' |
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299 | EOF |
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300 | |
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301 | # Run kpp |
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302 | |
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303 | $KPP $DEF_PREFIX |
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304 | |
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305 | # Get templates for C++ program |
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306 | |
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307 | cp $BASE/templates/module_header* . # Use fixed Module_header |
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308 | cp $BASE/templates/initialize_kpp_ctrl_template.f90 . # CTRL kpp time stepping |
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309 | |
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310 | # file with subroutine list for c++ program create_kpp_module |
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311 | |
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312 | for i in $KPP_FILE_LIST |
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313 | do |
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314 | echo ${PREFIX}_${i} >> file_list |
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315 | done |
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316 | echo initialize_kpp_ctrl_template >> file_list |
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317 | |
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318 | # file with subroutine list for c++ program create_kpp_module |
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319 | |
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320 | for i in $KPP_SUBROUTINE_LIST |
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321 | do |
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322 | echo $i >> subroutine_list |
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323 | done |
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324 | |
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325 | # file with include list for c++ program create_kpp_module |
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326 | |
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327 | for i in $KPP_INCLUDE_LIST |
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328 | do |
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329 | echo ${PREFIX}_${i} >> include_list |
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330 | done |
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331 | |
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332 | touch interface_ignore_list |
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333 | for i in $KPP_INTERFACE_IGNORE |
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334 | do |
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335 | echo $i >> interface_ignore_list |
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336 | done |
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337 | |
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338 | echo start kpp4palm.exe with arguments |
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339 | echo $PREFIX $MODE $VLEN $DE_INDEX $DE_INDEX_FAST |
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340 | |
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341 | $BASE/bin/kpp4palm.exe $PREFIX $MODE $VLEN $DE_INDEX $DE_INDEX_FAST |
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342 | |
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343 | # Add dummy statements in order to prevent warnings due to unused variables |
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344 | # |
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345 | sed -i -e '/cfactor =/a ! ' kk_kpp.f90 |
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346 | sed -i -e '/cfactor =/a BLANKS IF ( lu_crow(1) == 1 .OR. lu_icol(1) == 1 .OR. lu_irow(1) == 1 ) CONTINUE ' kk_kpp.f90 |
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347 | sed -i -e '/cfactor =/a ! Following line is just to avoid compiler message about unused variables' kk_kpp.f90 |
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348 | sed -i -e '/cfactor =/a ! ' kk_kpp.f90 |
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349 | |
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350 | if [[ $MODE = "vector" ]] |
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351 | then |
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352 | sed -i -e '/! Computation of equation rates/i ! Following line is just to avoid compiler message about unused variables' kk_kpp.f90 |
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353 | sed -i -e '/! Computation of equation rates/i BLANKS IF ( f(vl,nfix) > 0.0_dp ) CONTINUE' kk_kpp.f90 |
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354 | sed -i -e '/! Computation of equation rates/i ! ' kk_kpp.f90 |
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355 | else |
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356 | sed -i -e '/! Computation of equation rates/i ! Following line is just to avoid compiler message about unused variables' kk_kpp.f90 |
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357 | sed -i -e '/! Computation of equation rates/i BLANKS IF ( f(nfix) > 0.0_dp ) CONTINUE' kk_kpp.f90 |
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358 | sed -i -e '/! Computation of equation rates/i ! ' kk_kpp.f90 |
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359 | fi |
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360 | |
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361 | if [[ $MODE = "vector" ]] |
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362 | then |
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363 | sed -i -e '/REAL(kind=dp) :: b/a BLANKS IF ( f(vl,nfix) > 0.0_dp ) CONTINUE' kk_kpp.f90 |
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364 | sed -i -e '/REAL(kind=dp) :: b/a ! Following line is just to avoid compiler message about unused variables' kk_kpp.f90 |
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365 | sed -i -e '/REAL(kind=dp):: b/a !' kk_kpp.f90 |
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366 | else |
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367 | sed -i -e '/REAL(kind=dp):: b/a BLANKS IF ( f(nfix) > 0.0_dp ) CONTINUE' kk_kpp.f90 |
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368 | sed -i -e '/REAL(kind=dp):: b/a ! Following line is just to avoid compiler message about unused variables' kk_kpp.f90 |
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369 | sed -i -e '/REAL(kind=dp):: b/a !' kk_kpp.f90 |
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370 | fi |
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371 | |
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372 | sed -i -e '/one=1.0_dp/a BLANKS IF ( incx == 0 ) CONTINUE' kk_kpp.f90 |
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373 | sed -i -e '/one=1.0_dp/a ! Following line is just to avoid compiler message about unused variables' kk_kpp.f90 |
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374 | sed -i -e '/one=1.0_dp/a ! ' kk_kpp.f90 |
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375 | |
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376 | sed -i -e '/IF (alpha .eq. zero)RETURN/i ! ' kk_kpp.f90 |
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377 | sed -i -e '/IF (alpha .eq. zero)RETURN/i ! Following line is just to avoid compiler message about unused variables' kk_kpp.f90 |
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378 | sed -i -e '/IF (alpha .eq. zero)RETURN/i BLANKS IF ( incx == 0 .OR. incy == 0 ) CONTINUE' kk_kpp.f90 |
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379 | |
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380 | sed -i -e '/INTENT(INOUT):: b(n)/a BLANKS IF ( pivot(1) == 0 ) CONTINUE' kk_kpp.f90 |
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381 | sed -i -e '/INTENT(INOUT):: b(n)/a ! Following line is just to avoid compiler message about unused variables' kk_kpp.f90 |
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382 | sed -i -e '/INTENT(INOUT):: b(n)/a ! ' kk_kpp.f90 |
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383 | |
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384 | sed -i -e '1,$s/BLANKS / / ' kk_kpp.f90 |
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385 | |
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386 | if [[ -e $OUTDIR/${OUTFILE}.f90 ]] |
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387 | then |
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388 | mv $OUTDIR/${OUTFILE}.f90 $OUTDIR/${OUTFILE}.f90.sav |
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389 | fi |
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390 | cp -p kk_kpp.f90 $OUTDIR/${OUTFILE}.f90 |
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391 | echo " " |
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392 | echo "Write kpp module -- > " $OUTDIR/${OUTFILE}.f90 |
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393 | |
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394 | if [[ $UPDT = "YES" ]] |
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395 | then |
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396 | cp -p kk_kpp.f90 $DEFDIR/${OUTFILE}.f90 |
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397 | echo " " |
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398 | echo "Write kpp module -- > " $DEFDIR/${OUTFILE}.f90 |
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399 | fi |
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400 | |
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401 | if [[ $KEEP = "NO" ]] |
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402 | then |
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403 | cd $MY_PWD |
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404 | rm -rf $WORK |
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405 | fi |
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406 | exit |
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407 | |
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