[2696] | 1 | /****************************************************************************** |
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| 2 | |
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| 3 | KPP - The Kinetic PreProcessor |
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| 4 | Builds simulation code for chemical kinetic systems |
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| 5 | |
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| 6 | Copyright (C) 1995-1996 Valeriu Damian and Adrian Sandu |
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| 7 | Copyright (C) 1997-2005 Adrian Sandu |
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| 8 | |
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| 9 | KPP is free software; you can redistribute it and/or modify it under the |
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| 10 | terms of the GNU General Public License as published by the Free Software |
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| 11 | Foundation (http://www.gnu.org/copyleft/gpl.html); either version 2 of the |
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| 12 | License, or (at your option) any later version. |
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| 13 | |
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| 14 | KPP is distributed in the hope that it will be useful, but WITHOUT ANY |
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| 15 | WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS |
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| 16 | FOR A PARTICULAR PURPOSE. See the GNU General Public License for more |
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| 17 | details. |
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| 18 | |
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| 19 | You should have received a copy of the GNU General Public License along |
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| 20 | with this program; if not, consult http://www.gnu.org/copyleft/gpl.html or |
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| 21 | write to the Free Software Foundation, Inc., 59 Temple Place - Suite 330, |
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| 22 | Boston, MA 02111-1307, USA. |
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| 23 | |
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| 24 | Adrian Sandu |
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| 25 | Computer Science Department |
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| 26 | Virginia Polytechnic Institute and State University |
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| 27 | Blacksburg, VA 24060 |
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| 28 | E-mail: sandu@cs.vt.edu |
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| 29 | |
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| 30 | ******************************************************************************/ |
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| 31 | |
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| 32 | |
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| 33 | #include "gdata.h" |
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| 34 | #include "scan.h" |
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| 35 | #include "y.tab.h" |
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| 36 | #include <stdlib.h> |
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| 37 | #include <string.h> |
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| 38 | #include <math.h> |
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| 39 | |
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| 40 | int AtomNr = 0; |
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| 41 | int SpeciesNr = 0; |
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| 42 | int EqnNr = 0; |
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| 43 | int SpcNr = 0; |
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| 44 | int VarNr = 0; |
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| 45 | int VarActiveNr = 0; |
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| 46 | int FixNr = 0; |
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| 47 | int VarStartNr = 0; |
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| 48 | int FixStartNr = 0; |
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| 49 | |
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| 50 | |
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| 51 | int initNr = -1; |
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| 52 | int xNr = 0; |
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| 53 | int yNr = 0; |
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| 54 | int zNr = 0; |
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| 55 | |
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| 56 | int falseSpcNr = 0; |
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| 57 | |
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| 58 | ATOM_DEF AtomTable[ MAX_ATNR ]; |
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| 59 | SPECIES_DEF SpeciesTable[ MAX_SPECIES ]; |
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| 60 | CODE ReverseCode[ MAX_SPECIES ]; |
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| 61 | CODE Code[ MAX_SPECIES ]; |
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| 62 | KREACT kr[ MAX_EQN ]; |
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| 63 | |
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| 64 | float** Stoich_Left; |
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| 65 | float** Stoich; |
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| 66 | float** Stoich_Right; |
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| 67 | int Reactive[ MAX_SPECIES ]; |
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| 68 | |
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| 69 | INLINE_KEY InlineKeys[] = { { F77_GLOBAL, APPEND, "F77_GLOBAL" }, |
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| 70 | { F77_INIT, APPEND, "F77_INIT" }, |
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| 71 | { F77_DATA, APPEND, "F77_DATA" }, |
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| 72 | { F77_UTIL, APPEND, "F77_UTIL" }, |
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| 73 | { F77_RATES, APPEND, "F77_RATES" }, |
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| 74 | { F77_RCONST, APPEND, "F77_RCONST" }, |
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| 75 | { F90_GLOBAL, APPEND, "F90_GLOBAL" }, |
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| 76 | { F90_INIT, APPEND, "F90_INIT" }, |
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| 77 | { F90_DATA, APPEND, "F90_DATA" }, |
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| 78 | { F90_UTIL, APPEND, "F90_UTIL" }, |
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| 79 | { F90_RATES, APPEND, "F90_RATES" }, |
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| 80 | { F90_RCONST, APPEND, "F90_RCONST" }, |
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| 81 | { C_GLOBAL, APPEND, "C_GLOBAL" }, |
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| 82 | { C_INIT, APPEND, "C_INIT" }, |
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| 83 | { C_DATA, APPEND, "C_DATA" }, |
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| 84 | { C_UTIL, APPEND, "C_UTIL" }, |
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| 85 | { C_RATES, APPEND, "C_RATES" }, |
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| 86 | { C_RCONST, APPEND, "C_RCONST" }, |
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| 87 | { MATLAB_GLOBAL, APPEND, "MATLAB_GLOBAL" }, |
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| 88 | { MATLAB_INIT, APPEND, "MATLAB_INIT" }, |
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| 89 | { MATLAB_DATA, APPEND, "MATLAB_DATA" }, |
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| 90 | { MATLAB_UTIL, APPEND, "MATLAB_UTIL" }, |
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| 91 | { MATLAB_RATES, APPEND, "MATLAB_RATES" }, |
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| 92 | { MATLAB_RCONST, APPEND, "MATLAB_RCONST" } |
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| 93 | }; |
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| 94 | |
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| 95 | int useAggregate = 1; |
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| 96 | int useJacobian = JAC_LU_ROW; |
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| 97 | int useJacSparse = 1; |
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| 98 | int useHessian = 1; |
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| 99 | int useStoicmat = 1; |
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| 100 | int useDouble = 1; |
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| 101 | int useReorder = 1; |
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| 102 | int useMex = 1; |
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| 103 | int useDummyindex = 0; |
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| 104 | int useEqntags = 0; |
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| 105 | int useLang = F77_LANG; |
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| 106 | int useStochastic = 0; |
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| 107 | /* if useValues=1 KPP replaces parameters like NVAR etc. |
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| 108 | by their values in vector/matrix declarations */ |
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| 109 | int useDeclareValues = 0; |
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| 110 | |
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| 111 | char integrator[ MAX_PATH ] = "none"; |
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| 112 | char driver[ MAX_PATH ] = "none"; |
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| 113 | char runArgs[ MAX_PATH ] = ""; |
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| 114 | |
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| 115 | /* mz_rs_20050701+ */ |
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| 116 | /* char varDefault[ MAX_IVAL ] = "1.E-8"; */ |
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| 117 | /* char fixDefault[ MAX_IVAL ] = "1.E-8"; */ |
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| 118 | /* double cfactor = 1.09E+10; */ |
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| 119 | char varDefault[ MAX_IVAL ] = "0."; |
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| 120 | char fixDefault[ MAX_IVAL ] = "0."; |
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| 121 | double cfactor = 1.; |
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| 122 | /* mz_rs_20050701- */ |
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| 123 | |
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| 124 | ATOM crtAtoms[ MAX_ATOMS ]; |
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| 125 | int crtAtomNr = 0; |
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| 126 | |
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| 127 | char *fileList[ MAX_FILES ]; |
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| 128 | int fileNr = 0; |
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| 129 | |
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| 130 | double Abs( double x ) |
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| 131 | { |
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| 132 | return x > 0 ? x : -x; |
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| 133 | } |
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| 134 | |
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| 135 | void DefineInitializeNbr( char *cmd ) |
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| 136 | { |
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| 137 | int n; |
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| 138 | |
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| 139 | n = sscanf( cmd, "%d", &initNr); |
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| 140 | if( n != 1 ) |
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| 141 | ScanError("Bad number of species to initialize <%s>", cmd); |
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| 142 | } |
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| 143 | |
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| 144 | void DefineXGrid( char *cmd ) |
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| 145 | { |
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| 146 | int n; |
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| 147 | |
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| 148 | xNr = 1; |
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| 149 | n = sscanf( cmd, "%d", &xNr); |
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| 150 | if( n != 1 ) |
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| 151 | ScanError("Bad X grid number <%s>", cmd); |
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| 152 | } |
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| 153 | |
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| 154 | void DefineYGrid( char *cmd ) |
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| 155 | { |
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| 156 | int n; |
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| 157 | |
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| 158 | yNr = 1; |
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| 159 | n = sscanf( cmd, "%d", &yNr); |
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| 160 | if( n != 1 ) |
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| 161 | ScanError("Bad Y grid number <%s>", cmd); |
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| 162 | } |
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| 163 | |
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| 164 | void DefineZGrid( char *cmd ) |
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| 165 | { |
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| 166 | int n; |
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| 167 | |
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| 168 | zNr = 1; |
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| 169 | n = sscanf( cmd, "%d", &zNr); |
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| 170 | if( n != 1 ) |
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| 171 | ScanError("Bad Z grid number <%s>", cmd); |
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| 172 | } |
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| 173 | |
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| 174 | void CmdFunction( char *cmd ) |
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| 175 | { |
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| 176 | if( EqNoCase( cmd, "AGGREGATE" ) ) { |
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| 177 | useAggregate = 1; |
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| 178 | return; |
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| 179 | } |
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| 180 | if( EqNoCase( cmd, "SPLIT" ) ) { |
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| 181 | useAggregate = 0; |
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| 182 | return; |
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| 183 | } |
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| 184 | ScanError("'%s': Unknown parameter for #FUNCTION [AGGREGATE|SPLIT]", cmd ); |
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| 185 | } |
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| 186 | |
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| 187 | void CmdDeclareValues( char *cmd ) |
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| 188 | { |
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| 189 | if( EqNoCase( cmd, "SYMBOL" ) ) { |
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| 190 | useDeclareValues = 0; |
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| 191 | return; |
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| 192 | } |
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| 193 | if( EqNoCase( cmd, "VALUE" ) ) { |
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| 194 | useDeclareValues = 1; |
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| 195 | return; |
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| 196 | } |
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| 197 | ScanError("'%s': Unknown parameter for #DECLARE [SYMBOL|VALUE]", cmd ); |
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| 198 | } |
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| 199 | |
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| 200 | void CmdJacobian( char *cmd ) |
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| 201 | { |
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| 202 | if( EqNoCase( cmd, "OFF" ) ) { |
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| 203 | useJacobian = JAC_OFF; |
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| 204 | useJacSparse = 0; |
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| 205 | return; |
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| 206 | } |
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| 207 | if( EqNoCase( cmd, "FULL" ) ) { |
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| 208 | useJacobian = JAC_FULL; |
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| 209 | useJacSparse = 0; |
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| 210 | return; |
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| 211 | } |
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| 212 | if( EqNoCase( cmd, "SPARSE_LU_ROW" ) ) { |
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| 213 | useJacobian = JAC_LU_ROW; |
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| 214 | useJacSparse = 1; |
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| 215 | return; |
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| 216 | } |
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| 217 | if( EqNoCase( cmd, "SPARSE_ROW" ) ) { |
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| 218 | useJacobian = JAC_ROW; |
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| 219 | useJacSparse = 1; |
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| 220 | return; |
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| 221 | } |
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| 222 | ScanError("'%s': Unknown parameter for #JACOBIAN [OFF|FULL|SPARSE_LU_ROW|SPARSE_ROW]", cmd ); |
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| 223 | } |
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| 224 | |
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| 225 | void SparseData( char *cmd ) { |
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| 226 | ScanError("Deprecated use of #SPARSEDATA %s: see #JACOBIAN for equivalent functionality", cmd ); |
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| 227 | } |
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| 228 | |
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| 229 | void CmdHessian( char *cmd ) |
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| 230 | { |
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| 231 | if( EqNoCase( cmd, "OFF" ) ) { |
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| 232 | useHessian = 0; |
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| 233 | return; |
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| 234 | } |
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| 235 | if( EqNoCase( cmd, "ON" ) ) { |
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| 236 | useHessian = 1; |
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| 237 | return; |
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| 238 | } |
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| 239 | ScanError("'%s': Unknown parameter for #HESSIAN [ON|OFF]", cmd ); |
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| 240 | } |
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| 241 | |
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| 242 | void CmdStoicmat( char *cmd ) |
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| 243 | { |
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| 244 | if( EqNoCase( cmd, "OFF" ) ) { |
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| 245 | useStoicmat = 0; |
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| 246 | return; |
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| 247 | } |
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| 248 | if( EqNoCase( cmd, "ON" ) ) { |
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| 249 | useStoicmat = 1; |
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| 250 | return; |
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| 251 | } |
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| 252 | ScanError("'%s': Unknown parameter for #STOICMAT [ON|OFF]", cmd ); |
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| 253 | } |
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| 254 | |
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| 255 | void CmdDouble( char *cmd ) |
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| 256 | { |
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| 257 | if( EqNoCase( cmd, "OFF" ) ) { |
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| 258 | useDouble = 0; |
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| 259 | return; |
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| 260 | } |
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| 261 | if( EqNoCase( cmd, "ON" ) ) { |
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| 262 | useDouble = 1; |
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| 263 | return; |
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| 264 | } |
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| 265 | ScanError("'%s': Unknown parameter for #DOUBLE [ON|OFF]", cmd ); |
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| 266 | } |
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| 267 | |
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| 268 | void CmdReorder( char *cmd ) |
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| 269 | { |
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| 270 | if( EqNoCase( cmd, "OFF" ) ) { |
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| 271 | useReorder = 0; |
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| 272 | return; |
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| 273 | } |
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| 274 | if( EqNoCase( cmd, "ON" ) ) { |
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| 275 | useReorder = 1; |
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| 276 | return; |
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| 277 | } |
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| 278 | ScanError("'%s': Unknown parameter for #REORDER [ON|OFF]", cmd ); |
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| 279 | } |
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| 280 | |
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| 281 | void CmdMex( char *cmd ) |
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| 282 | { |
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| 283 | if( EqNoCase( cmd, "OFF" ) ) { |
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| 284 | useMex = 0; |
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| 285 | return; |
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| 286 | } |
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| 287 | if( EqNoCase( cmd, "ON" ) ) { |
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| 288 | useMex = 1; |
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| 289 | return; |
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| 290 | } |
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| 291 | ScanError("'%s': Unknown parameter for #MEX [ON|OFF]", cmd ); |
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| 292 | } |
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| 293 | |
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| 294 | void CmdDummyindex( char *cmd ) |
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| 295 | { |
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| 296 | if( EqNoCase( cmd, "OFF" ) ) { |
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| 297 | useDummyindex = 0; |
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| 298 | return; |
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| 299 | } |
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| 300 | if( EqNoCase( cmd, "ON" ) ) { |
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| 301 | useDummyindex = 1; |
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| 302 | return; |
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| 303 | } |
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| 304 | ScanError("'%s': Unknown parameter for #DUMMYINDEX [ON|OFF]", cmd ); |
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| 305 | } |
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| 306 | |
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| 307 | void CmdEqntags( char *cmd ) |
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| 308 | { |
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| 309 | if( EqNoCase( cmd, "OFF" ) ) { |
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| 310 | useEqntags = 0; |
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| 311 | return; |
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| 312 | } |
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| 313 | if( EqNoCase( cmd, "ON" ) ) { |
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| 314 | useEqntags = 1; |
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| 315 | return; |
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| 316 | } |
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| 317 | ScanError("'%s': Unknown parameter for #EQNTAGS [ON|OFF]", cmd ); |
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| 318 | } |
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| 319 | |
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| 320 | void CmdUse( char *cmd ) |
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| 321 | { |
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| 322 | ScanError("Deprecated command '#USE %s';\nReplace with '#LANGUAGE %s'.",cmd,cmd ); |
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| 323 | } |
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| 324 | |
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| 325 | |
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| 326 | void CmdLanguage( char *cmd ) |
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| 327 | { |
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| 328 | if( EqNoCase( cmd, "FORTRAN77" ) ) { |
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| 329 | useLang = F77_LANG; |
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| 330 | return; |
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| 331 | } |
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| 332 | if( EqNoCase( cmd, "FORTRAN" ) ) { |
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| 333 | ScanWarning("Fortran version not specified in '#LANGUAGE %s'. Will use Fortran 77.", cmd); |
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| 334 | useLang = F77_LANG; |
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| 335 | return; |
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| 336 | } |
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| 337 | if( EqNoCase( cmd, "FORTRAN90" ) ) { |
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| 338 | useLang = F90_LANG; |
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| 339 | return; |
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| 340 | } |
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| 341 | if( EqNoCase( cmd, "MATLAB" ) ) { |
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| 342 | useLang = MATLAB_LANG; |
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| 343 | return; |
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| 344 | } |
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| 345 | if( EqNoCase( cmd, "C" ) ) { |
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| 346 | useLang = C_LANG; |
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| 347 | return; |
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| 348 | } |
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| 349 | ScanError("'%s': Unknown parameter for #LANGUAGE [Fortran77|Fortran90|C|Matlab]", cmd ); |
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| 350 | } |
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| 351 | |
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| 352 | void CmdStochastic( char *cmd ) |
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| 353 | { |
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| 354 | if( EqNoCase( cmd, "ON" ) ) { |
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| 355 | useStochastic = 1; |
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| 356 | return; |
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| 357 | } |
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| 358 | if( EqNoCase( cmd, "OFF" ) ) { |
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| 359 | useStochastic = 0; |
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| 360 | return; |
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| 361 | } |
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| 362 | ScanError("'%s': Unknown parameter for #STOCHASTIC [OFF|ON]", cmd ); |
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| 363 | } |
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| 364 | |
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| 365 | void CmdIntegrator( char *cmd ) |
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| 366 | { |
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| 367 | strcpy( integrator, cmd ); |
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| 368 | } |
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| 369 | |
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| 370 | void CmdDriver( char *cmd ) |
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| 371 | { |
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| 372 | strcpy( driver, cmd ); |
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| 373 | } |
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| 374 | |
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| 375 | void CmdRun( char *cmd ) |
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| 376 | { |
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| 377 | strcpy( runArgs, cmd ); |
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| 378 | } |
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| 379 | |
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| 380 | int FindAtom( char *atname ) |
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| 381 | { |
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| 382 | int i; |
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| 383 | |
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| 384 | for( i=0; i<AtomNr; i++ ) |
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| 385 | if( EqNoCase( AtomTable[ i ].name, atname ) ) { |
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| 386 | return i; |
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| 387 | } |
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| 388 | return -1; |
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| 389 | } |
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| 390 | |
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| 391 | void DeclareAtom( char *atname ) |
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| 392 | { |
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| 393 | int code; |
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| 394 | |
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| 395 | code = FindAtom( atname ); |
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| 396 | if ( code >= 0 ) { |
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| 397 | ScanError("Multiple declaration for atom %s.", atname ); |
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| 398 | return; |
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| 399 | } |
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| 400 | if( AtomNr >= MAX_ATNR ) { |
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| 401 | Error("Too many atoms"); |
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| 402 | return; |
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| 403 | } |
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| 404 | |
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| 405 | strcpy( AtomTable[ AtomNr ].name, atname ); |
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| 406 | AtomTable[ AtomNr ].check = NO_CHECK; |
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| 407 | AtomTable[ AtomNr ].masscheck = 0; |
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| 408 | AtomNr++; |
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| 409 | } |
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| 410 | |
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| 411 | void SetAtomType( char *atname, int type ) |
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| 412 | { |
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| 413 | int code; |
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| 414 | |
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| 415 | code = FindAtom( atname ); |
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| 416 | if ( code < 0 ) { |
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| 417 | ScanError("Undefined atom %s.", atname ); |
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| 418 | return; |
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| 419 | } |
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| 420 | AtomTable[ code ].check = type; |
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| 421 | } |
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| 422 | |
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| 423 | void CheckAll() |
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| 424 | { |
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| 425 | int i; |
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| 426 | |
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| 427 | for( i=0; i<AtomNr; i++ ) { |
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| 428 | if( AtomTable[ i ].check != CANCEL_CHECK ) |
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| 429 | AtomTable[ i ].check = DO_CHECK; |
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| 430 | } |
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| 431 | SetAtomType( "IGNORE", NO_CHECK ); |
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| 432 | } |
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| 433 | |
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| 434 | void AddAtom( char *atname, char *nr ) |
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| 435 | { |
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| 436 | int code; |
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| 437 | |
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| 438 | code = FindAtom( atname ); |
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| 439 | if ( code < 0 ) { |
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| 440 | ScanError("Undefined atom %s.", atname ); |
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| 441 | return; |
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| 442 | } |
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| 443 | crtAtoms[ crtAtomNr ].code = (unsigned char)code; |
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| 444 | crtAtoms[ crtAtomNr ].nr = (unsigned char)atoi(nr); |
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| 445 | crtAtomNr++; |
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| 446 | } |
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| 447 | |
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| 448 | int FindSpecies( char *spname ) |
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| 449 | { |
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| 450 | int i; |
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| 451 | |
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| 452 | for( i=0; i<SpeciesNr; i++ ) |
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| 453 | if( EqNoCase( SpeciesTable[ i ].name, spname ) ) { |
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| 454 | return i; |
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| 455 | } |
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| 456 | for( i=0; i<2; i++ ) |
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| 457 | if( EqNoCase( SpeciesTable[ MAX_SPECIES -1 - i ].name, spname ) ) { |
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| 458 | return MAX_SPECIES -1 - i; |
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| 459 | } |
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| 460 | return -1; |
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| 461 | } |
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| 462 | |
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| 463 | void StoreSpecies( int index, int type, char *spname ) |
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| 464 | { |
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| 465 | int i; |
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| 466 | |
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| 467 | strcpy( SpeciesTable[ index ].name, spname ); |
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| 468 | SpeciesTable[ index ].type = type; |
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| 469 | *SpeciesTable[ index ].ival = '\0'; |
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| 470 | SpeciesTable[ index ].lookat = 0; |
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| 471 | SpeciesTable[ index ].moni = 0; |
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| 472 | SpeciesTable[ index ].trans = 0; |
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| 473 | if( (SpeciesTable[ index ].nratoms == 0) || ( crtAtomNr > 0 ) ) { |
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| 474 | SpeciesTable[ index ].nratoms = crtAtomNr; |
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| 475 | for( i = 0; i < crtAtomNr; i++ ) |
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| 476 | SpeciesTable[ index ].atoms[i] = crtAtoms[i]; |
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| 477 | } |
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| 478 | crtAtomNr = 0; |
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| 479 | } |
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| 480 | |
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| 481 | void DeclareSpecies( int type, char *spname ) |
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| 482 | { |
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| 483 | int code; |
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| 484 | |
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| 485 | code = FindSpecies( spname ); |
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| 486 | if ( code >= 0 ) { |
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| 487 | ScanError("Multiple declaration for species %s.", spname ); |
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| 488 | return; |
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| 489 | } |
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| 490 | if( SpeciesNr >= MAX_SPECIES ) { |
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| 491 | Error("Too many species"); |
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| 492 | return; |
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| 493 | } |
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| 494 | StoreSpecies( SpeciesNr, type, spname ); |
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| 495 | SpeciesNr++; |
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| 496 | } |
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| 497 | |
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| 498 | void SetSpcType( int type, char *spname ) |
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| 499 | { |
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| 500 | int code; |
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| 501 | int i; |
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| 502 | |
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| 503 | if( EqNoCase( spname, "VAR_SPEC" ) ) { |
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| 504 | for( i = 0; i < SpeciesNr; i++ ) |
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| 505 | if( SpeciesTable[i].type == VAR_SPC ) |
---|
| 506 | SpeciesTable[i].type = type; |
---|
| 507 | return; |
---|
| 508 | } |
---|
| 509 | if( EqNoCase( spname, "FIX_SPEC" ) ) { |
---|
| 510 | for( i = 0; i < SpeciesNr; i++ ) |
---|
| 511 | if( SpeciesTable[i].type == FIX_SPC ) |
---|
| 512 | SpeciesTable[i].type = type; |
---|
| 513 | return; |
---|
| 514 | } |
---|
| 515 | if( EqNoCase( spname, "ALL_SPEC" ) ) { |
---|
| 516 | for( i = 0; i < SpeciesNr; i++ ) |
---|
| 517 | SpeciesTable[i].type = type; |
---|
| 518 | return; |
---|
| 519 | } |
---|
| 520 | |
---|
| 521 | code = FindSpecies( spname ); |
---|
| 522 | if ( code < 0 ) { |
---|
| 523 | ScanError("Undefined species %s.", spname ); |
---|
| 524 | return; |
---|
| 525 | } |
---|
| 526 | SpeciesTable[ code ].type = type; |
---|
| 527 | } |
---|
| 528 | |
---|
| 529 | void AssignInitialValue( char *spname , char *spval ) |
---|
| 530 | { |
---|
| 531 | int code; |
---|
| 532 | double cf; |
---|
| 533 | |
---|
| 534 | if( EqNoCase( spname, "CFACTOR" ) ) { |
---|
| 535 | code = sscanf( spval, "%lg", &cf ); |
---|
| 536 | if( code != 1 ) { |
---|
| 537 | ScanWarning("Invalid CFACTOR value: %s", spval); |
---|
| 538 | return; |
---|
| 539 | } |
---|
| 540 | cfactor = cf; |
---|
| 541 | return; |
---|
| 542 | } |
---|
| 543 | |
---|
| 544 | if( EqNoCase( spname, "VAR_SPEC" ) ) { |
---|
| 545 | strcpy( varDefault, spval ); |
---|
| 546 | return; |
---|
| 547 | } |
---|
| 548 | |
---|
| 549 | |
---|
| 550 | if( EqNoCase( spname, "FIX_SPEC" ) ) { |
---|
| 551 | strcpy( fixDefault, spval ); |
---|
| 552 | return; |
---|
| 553 | } |
---|
| 554 | |
---|
| 555 | if( EqNoCase( spname, "ALL_SPEC" ) ) { |
---|
| 556 | strcpy( varDefault, spval ); |
---|
| 557 | strcpy( fixDefault, spval ); |
---|
| 558 | return; |
---|
| 559 | } |
---|
| 560 | |
---|
| 561 | code = FindSpecies( spname ); |
---|
| 562 | if ( code < 0 ) { |
---|
| 563 | ScanError("Undefined species %s.", spname ); |
---|
| 564 | return; |
---|
| 565 | } |
---|
| 566 | strcpy( SpeciesTable[ code ].ival, spval ); |
---|
| 567 | } |
---|
| 568 | |
---|
| 569 | void StoreEquationRate( char *rate, char *label ) |
---|
| 570 | { |
---|
| 571 | double f; |
---|
| 572 | char buf[ MAX_K ]; |
---|
| 573 | int n; |
---|
| 574 | KREACT *kreact; |
---|
| 575 | |
---|
| 576 | kreact = &kr[ EqnNr ]; |
---|
| 577 | strcpy( kreact->label, label ); |
---|
| 578 | if( isPhoto ) { |
---|
| 579 | kreact->type = PHOTO; |
---|
| 580 | strcpy( kreact->val.st, rate ); |
---|
| 581 | isPhoto = 0; |
---|
| 582 | return; |
---|
| 583 | } |
---|
| 584 | n = sscanf( rate, "%lf%s", &f, buf ); |
---|
| 585 | if ( n == 1 ) { |
---|
| 586 | kreact->type = NUMBER; |
---|
| 587 | kreact->val.f = f; |
---|
| 588 | return; |
---|
| 589 | } |
---|
| 590 | kreact->type = EXPRESION; |
---|
| 591 | strcpy( kreact->val.st, rate ); |
---|
| 592 | return; |
---|
| 593 | } |
---|
| 594 | |
---|
| 595 | void CheckEquation() |
---|
| 596 | { |
---|
| 597 | int i,j; |
---|
| 598 | int equal, index; |
---|
| 599 | double r1, r2; |
---|
| 600 | float atcnt[ MAX_ATNR ]; |
---|
| 601 | int spc; |
---|
| 602 | SPECIES_DEF *sp; |
---|
| 603 | char errmsg[80]; |
---|
| 604 | int err; |
---|
| 605 | |
---|
| 606 | if( EqnNr >= MAX_EQN ) { |
---|
| 607 | Error("Too many equations"); |
---|
| 608 | return; |
---|
| 609 | } |
---|
| 610 | |
---|
| 611 | for( i = 0; i < AtomNr; i++ ) |
---|
| 612 | atcnt[i] = 0; |
---|
| 613 | |
---|
| 614 | for( spc = 0; spc < SpcNr; spc++ ) { |
---|
| 615 | sp = &SpeciesTable[ Code[spc] ]; |
---|
| 616 | if( Stoich_Left[spc][EqnNr] != 0 ) { |
---|
| 617 | for( i = 0; i < sp->nratoms; i++ ) |
---|
| 618 | atcnt[ sp->atoms[i].code ] += Stoich_Left[spc][EqnNr] * sp->atoms[i].nr; |
---|
| 619 | } |
---|
| 620 | if( Stoich_Right[spc][EqnNr] != 0 ) { |
---|
| 621 | for( i = 0; i < sp->nratoms; i++ ) |
---|
| 622 | atcnt[ sp->atoms[i].code ] -= Stoich_Right[spc][EqnNr] * sp->atoms[i].nr; |
---|
| 623 | } |
---|
| 624 | } |
---|
| 625 | |
---|
| 626 | *errmsg = 0; |
---|
| 627 | err = 0; |
---|
| 628 | |
---|
| 629 | for( i = 0; i < AtomNr; i++ ) { |
---|
| 630 | if ( Abs( atcnt[i] ) > 1e-5 ) { |
---|
| 631 | if ( AtomTable[i].check == CANCEL_CHECK ) { |
---|
| 632 | err = 0; |
---|
| 633 | break; |
---|
| 634 | } |
---|
| 635 | if ( AtomTable[i].check == NO_CHECK ) { |
---|
| 636 | continue; |
---|
| 637 | } |
---|
| 638 | if ( AtomTable[i].check == DO_CHECK ) { |
---|
| 639 | err = 1; |
---|
| 640 | sprintf(errmsg, "%s %s", errmsg, AtomTable[i].name ); |
---|
| 641 | continue; |
---|
| 642 | } |
---|
| 643 | } |
---|
| 644 | } |
---|
| 645 | |
---|
| 646 | if ( err ) |
---|
| 647 | ScanWarning( "(eqn %d) Atom balance mismatch for:%s.", EqnNr+1, errmsg ); |
---|
| 648 | |
---|
| 649 | for( j = 0; j < SpcNr; j++ ) |
---|
| 650 | if( Stoich_Left[j][EqnNr] != 0 ) |
---|
| 651 | { index = j; break; } |
---|
| 652 | for( i = 0; i < EqnNr; i++ ) { |
---|
| 653 | equal = 1; |
---|
| 654 | r1 = Stoich_Left[index][EqnNr]; |
---|
| 655 | r2 = Stoich_Left[index][i]; |
---|
| 656 | for( j = 0; j < SpcNr; j++ ) { |
---|
| 657 | if( r1 * Stoich_Left[j][i] != r2 * Stoich_Left[j][EqnNr] ) |
---|
| 658 | { equal = 0; break; } |
---|
| 659 | if( r1 * Stoich_Right[j][i] != r2 * Stoich_Right[j][EqnNr] ) |
---|
| 660 | { equal = 0; break; } |
---|
| 661 | } |
---|
| 662 | if ( equal ) { |
---|
| 663 | if( r1 == r2 ) |
---|
| 664 | ScanError( "Duplicate equation: " |
---|
| 665 | " (eqn<%d> = eqn<%d> )", i+1, EqnNr+1 ); |
---|
| 666 | else |
---|
| 667 | ScanError( "Linearly dependent equations: " |
---|
| 668 | "( %.0f eqn<%d> = %.0f eqn<%d> )", |
---|
| 669 | r1, i+1, r2, EqnNr+1 ); |
---|
| 670 | break; |
---|
| 671 | } |
---|
| 672 | } |
---|
| 673 | EqnNr++; |
---|
| 674 | } |
---|
| 675 | |
---|
| 676 | void ProcessTerm( int side, char *sign, char *coef, char *spname ) |
---|
| 677 | { |
---|
| 678 | int code; |
---|
| 679 | CODE crtSpec; |
---|
| 680 | double val; |
---|
| 681 | char buf[40]; |
---|
| 682 | |
---|
| 683 | |
---|
| 684 | code = FindSpecies( spname ); |
---|
| 685 | if ( code < 0 ) { |
---|
| 686 | ScanError("Undefined species %s.", spname ); |
---|
| 687 | return; |
---|
| 688 | } |
---|
| 689 | |
---|
| 690 | crtSpec = ReverseCode[ code ]; |
---|
| 691 | |
---|
| 692 | if(EqNoCase(spname,"HV")) isPhoto = 1; |
---|
| 693 | |
---|
| 694 | if ( crtSpec == NO_CODE ) { |
---|
| 695 | if( MAX_SPECIES - code <= 2 ) falseSpcNr++; |
---|
| 696 | crtSpec = SpcNr++; |
---|
| 697 | Code[ crtSpec ] = code; |
---|
| 698 | ReverseCode[ code ] = crtSpec; |
---|
| 699 | } |
---|
| 700 | |
---|
| 701 | strcpy( buf, sign ); |
---|
| 702 | strcat( buf, coef ); |
---|
| 703 | sscanf( buf, "%lf", &val ); |
---|
| 704 | |
---|
| 705 | switch( side ) { |
---|
| 706 | case LHS: Stoich_Left[ crtSpec ][ EqnNr ] += val; |
---|
| 707 | Stoich[ crtSpec ][ EqnNr ] -= val; |
---|
| 708 | Reactive[ crtSpec ] = 1; |
---|
| 709 | break; |
---|
| 710 | case RHS: Stoich_Right[ crtSpec ][ EqnNr ] += val; |
---|
| 711 | Stoich[ crtSpec ][ EqnNr ] += val; |
---|
| 712 | break; |
---|
| 713 | } |
---|
| 714 | } |
---|
| 715 | |
---|
| 716 | void AddLumpSpecies( char *spname ) |
---|
| 717 | { |
---|
| 718 | int code; |
---|
| 719 | |
---|
| 720 | code = FindSpecies( spname ); |
---|
| 721 | if ( code < 0 ) { |
---|
| 722 | ScanError("Undefined species %s.", spname ); |
---|
| 723 | return; |
---|
| 724 | } |
---|
| 725 | |
---|
| 726 | /* ... */ |
---|
| 727 | |
---|
| 728 | } |
---|
| 729 | |
---|
| 730 | void CheckLump( char *spname ) |
---|
| 731 | { |
---|
| 732 | int code; |
---|
| 733 | |
---|
| 734 | code = FindSpecies( spname ); |
---|
| 735 | if ( code < 0 ) { |
---|
| 736 | ScanError("Undefined species %s.", spname ); |
---|
| 737 | return; |
---|
| 738 | } |
---|
| 739 | |
---|
| 740 | /* ... */ |
---|
| 741 | |
---|
| 742 | } |
---|
| 743 | |
---|
| 744 | void AddLookAt( char *spname ) |
---|
| 745 | { |
---|
| 746 | int code; |
---|
| 747 | |
---|
| 748 | code = FindSpecies( spname ); |
---|
| 749 | if ( code < 0 ) { |
---|
| 750 | ScanError("Undefined species %s.", spname ); |
---|
| 751 | return; |
---|
| 752 | } |
---|
| 753 | |
---|
| 754 | SpeciesTable[ code ].lookat = 1; |
---|
| 755 | } |
---|
| 756 | |
---|
| 757 | void LookAtAll() |
---|
| 758 | { |
---|
| 759 | int i; |
---|
| 760 | |
---|
| 761 | for( i=0; i<SpeciesNr; i++ ) |
---|
| 762 | SpeciesTable[ i ].lookat = 1; |
---|
| 763 | } |
---|
| 764 | |
---|
| 765 | void AddMonitor( char *spname ) |
---|
| 766 | { |
---|
| 767 | int code; |
---|
| 768 | |
---|
| 769 | code = FindSpecies( spname ); |
---|
| 770 | if ( code >= 0 ) { |
---|
| 771 | SpeciesTable[ code ].moni = 1; |
---|
| 772 | return; |
---|
| 773 | } |
---|
| 774 | |
---|
| 775 | code = FindAtom( spname ); |
---|
| 776 | if ( code >= 0 ) { |
---|
| 777 | AtomTable[ code ].masscheck = 1; |
---|
| 778 | return; |
---|
| 779 | } |
---|
| 780 | |
---|
| 781 | ScanError("Undefined species or atom %s.", spname ); |
---|
| 782 | } |
---|
| 783 | |
---|
| 784 | void AddTransport( char *spname ) |
---|
| 785 | { |
---|
| 786 | int code; |
---|
| 787 | |
---|
| 788 | code = FindSpecies( spname ); |
---|
| 789 | if ( code < 0 ) { |
---|
| 790 | ScanError("Undefined species %s.", spname ); |
---|
| 791 | return; |
---|
| 792 | } |
---|
| 793 | |
---|
| 794 | SpeciesTable[ code ].trans = 1; |
---|
| 795 | } |
---|
| 796 | |
---|
| 797 | void TransportAll() |
---|
| 798 | { |
---|
| 799 | int i; |
---|
| 800 | |
---|
| 801 | for( i=0; i<SpeciesNr; i++ ) |
---|
| 802 | SpeciesTable[ i ].trans = 1; |
---|
| 803 | } |
---|
| 804 | |
---|
| 805 | void AddUseFile( char *fname ) |
---|
| 806 | { |
---|
| 807 | fileList[fileNr] = (char*)malloc(strlen(fname)+1); |
---|
| 808 | strcpy(fileList[fileNr], fname); |
---|
| 809 | fileNr++; |
---|
| 810 | } |
---|
| 811 | |
---|
| 812 | char * AppendString( char * s1, char * s2, int * maxlen, int addlen ) |
---|
| 813 | { |
---|
| 814 | char * tmp; |
---|
| 815 | |
---|
| 816 | *maxlen += addlen; |
---|
| 817 | |
---|
| 818 | if( !s1 ) { |
---|
| 819 | s1 = (char*)malloc( *maxlen ); |
---|
| 820 | *s1 = 0; |
---|
| 821 | } |
---|
| 822 | |
---|
| 823 | if( strlen( s1 ) + strlen( s2 ) >= *maxlen ) { |
---|
| 824 | s1 = (char*)realloc( (void*)s1, *maxlen ); |
---|
| 825 | } |
---|
| 826 | strcat( s1, s2 ); |
---|
| 827 | return s1; |
---|
| 828 | } |
---|
| 829 | |
---|
| 830 | char * ReplaceString( char * s1, char * s2, int * maxlen, int addlen ) |
---|
| 831 | { |
---|
| 832 | char * tmp; |
---|
| 833 | |
---|
| 834 | if( s1 ) free(s1); |
---|
| 835 | |
---|
| 836 | *maxlen = strlen( s2 ); |
---|
| 837 | s1 = (char*)malloc( 1+*maxlen ); |
---|
| 838 | strcpy( s1, s2 ); |
---|
| 839 | |
---|
| 840 | return s1; |
---|
| 841 | } |
---|
| 842 | |
---|
| 843 | void AddInlineCode( char * ctx, char * s ) |
---|
| 844 | { |
---|
| 845 | ICODE * c; |
---|
| 846 | int i, key, type; |
---|
| 847 | int totallength; /* mz_rs_20050607 */ |
---|
| 848 | |
---|
| 849 | c = NULL; |
---|
| 850 | |
---|
| 851 | for( i = 0; i < INLINE_OPT; i++ ) |
---|
| 852 | if( EqNoCase( ctx, InlineKeys[i].kname ) ) { |
---|
| 853 | key = InlineKeys[i].key; |
---|
| 854 | c = &InlineCode[key]; |
---|
| 855 | type = InlineKeys[i].type; |
---|
| 856 | break; |
---|
| 857 | } |
---|
| 858 | if( !c ) { |
---|
| 859 | printf( "\n'%s': Unknown inline option (ignored)", ctx ); |
---|
| 860 | return; |
---|
| 861 | } |
---|
| 862 | |
---|
| 863 | /* mz_rs_20050607+ */ |
---|
| 864 | if (c->code) |
---|
| 865 | totallength = strlen( c->code )+strlen( s ); |
---|
| 866 | else |
---|
| 867 | totallength = strlen( s ); |
---|
| 868 | if (totallength>MAX_INLINE) |
---|
| 869 | ScanError("\nInline code for %s is too long (%d>%d).\nIncrease MAX_INLINE in scan.h and recompile kpp!", |
---|
| 870 | ctx, totallength, MAX_INLINE); |
---|
| 871 | /* mz_rs_20050607- */ |
---|
| 872 | |
---|
| 873 | switch( type ) { |
---|
| 874 | case APPEND: c->code = AppendString( c->code, s, &c->maxlen, MAX_INLINE ); |
---|
| 875 | break; |
---|
| 876 | case REPLACE: c->code = ReplaceString( c->code, s, &c->maxlen, MAX_INLINE ); |
---|
| 877 | break; |
---|
| 878 | } |
---|
| 879 | } |
---|
| 880 | |
---|
| 881 | int ParseEquationFile( char * filename ) |
---|
| 882 | { |
---|
| 883 | int i,j; |
---|
| 884 | int code; |
---|
| 885 | |
---|
| 886 | for( i = 0; i < MAX_SPECIES; i++ ) { |
---|
| 887 | ReverseCode[i] = NO_CODE; |
---|
| 888 | Reactive[i] = 0; |
---|
| 889 | } |
---|
| 890 | for( i = 0; i < MAX_SPECIES; i++ ) { |
---|
| 891 | for( j = 0; j < MAX_EQN; j++ ) { |
---|
| 892 | Stoich_Left[i][j] = 0; |
---|
| 893 | Stoich[i][j] = 0; |
---|
| 894 | Stoich_Right[i][j] = 0; |
---|
| 895 | } |
---|
| 896 | } |
---|
| 897 | for( i = 0; i < MAX_SPECIES; i++ ) { |
---|
| 898 | SpeciesTable[ i ].nratoms = 0; |
---|
| 899 | } |
---|
| 900 | |
---|
| 901 | for( i = 0; i < INLINE_OPT; i++ ) { |
---|
| 902 | InlineCode[i].code = NULL; |
---|
| 903 | InlineCode[i].maxlen = 0; |
---|
| 904 | } |
---|
| 905 | |
---|
| 906 | EqnNr = 0; |
---|
| 907 | SpcNr = 0; |
---|
| 908 | |
---|
| 909 | DeclareAtom( "CANCEL" ); |
---|
| 910 | SetAtomType( "CANCEL", CANCEL_CHECK ); |
---|
| 911 | DeclareAtom( "IGNORE" ); |
---|
| 912 | SetAtomType( "IGNORE", NO_CHECK ); |
---|
| 913 | DeclareSpecies( DUMMY_SPC, "???" ); |
---|
| 914 | StoreSpecies( MAX_SPECIES-1, DUMMY_SPC, "HV" ); |
---|
| 915 | AddAtom( "CANCEL", "1" ); |
---|
| 916 | StoreSpecies( MAX_SPECIES-2, DUMMY_SPC, "PROD" ); |
---|
| 917 | |
---|
| 918 | code = Parser( filename ); |
---|
| 919 | |
---|
| 920 | return code; |
---|
| 921 | } |
---|
| 922 | |
---|