1 /* Steven Andrews, started 10/22/2001. 2 This is an application programming interface for the Smoldyn program. 3 See documentation called SmoldynManual.pdf and SmoldynCodeDoc.pdf, and the Smoldyn 4 website, which is at www.smoldyn.org. 5 Copyright 2003-2016 by Steven Andrews. This work is distributed under the terms 6 of the Gnu Lesser General Public License (LGPL). */ 7 8 #ifndef __libsmoldyn_h__ 9 #define __libsmoldyn_h__ 10 11 #include "smoldyn.h" 12 13 enum ErrorCode { 14 ECok=0, 15 ECnotify=-1, 16 ECwarning=-2, 17 ECnonexist=-3, 18 ECall=-4, 19 ECmissing=-5, 20 ECbounds=-6, 21 ECsyntax=-7, 22 ECerror=-8, 23 ECmemory=-9, 24 ECbug=-10, 25 ECsame=-11, 26 ECwildcard=-12}; 27 28 #ifdef __cplusplus 29 extern "C" { 30 #endif 31 32 /******************************* Miscellaneous ********************************/ 33 34 double smolGetVersion(void); 35 36 /*********************************** Errors ***********************************/ 37 38 void smolSetLogging(FILE *logfile,void (*logFunction)(simptr,int,const char*,...)); 39 void smolSetThrowing(int corethreshold,int libthreshold); 40 void smolSetError(const char *errorfunction,enum ErrorCode errorcode,const char *errorstring,const char *flags); 41 void smolSetErrorNT(const char *errorfunction,enum ErrorCode errorcode,const char *errorstring); 42 enum ErrorCode smolGetError(char *errorfunction,char *errorstring,int clearerror); 43 void smolClearError(void); 44 void smolSetDebugMode(int debugmode); 45 char* smolErrorCodeToString(enum ErrorCode erc,char *string); 46 47 /******************************** Sim structure *******************************/ 48 49 simptr smolNewSim(int dim,double *lowbounds,double *highbounds); 50 enum ErrorCode smolUpdateSim(simptr sim); 51 enum ErrorCode smolRunTimeStep(simptr sim); 52 enum ErrorCode smolRunSim(simptr sim); 53 enum ErrorCode smolRunSimUntil(simptr sim,double breaktime); 54 enum ErrorCode smolFreeSim(simptr sim); 55 enum ErrorCode smolDisplaySim(simptr sim); 56 57 /************************** Read configuration file ***************************/ 58 59 simptr smolPrepareSimFromFile(const char *filepath,const char *filename,const char *flags); 60 enum ErrorCode smolLoadSimFromFile(const char *filepath,const char *filename,simptr *simpointer,const char *flags); 61 enum ErrorCode smolReadConfigString(simptr sim,const char *statement,char *parameters); 62 63 /***************************** Simulation settings ****************************/ 64 65 enum ErrorCode smolSetSimFlags(simptr sim,const char *flags); 66 enum ErrorCode smolSetSimTimes(simptr sim,double timestart,double timestop,double timestep); 67 enum ErrorCode smolSetTimeStart(simptr sim,double timestart); 68 enum ErrorCode smolSetTimeStop(simptr sim,double timestop); 69 enum ErrorCode smolSetTimeNow(simptr sim,double timenow); 70 enum ErrorCode smolSetTimeStep(simptr sim,double timestep); 71 enum ErrorCode smolSetRandomSeed(simptr sim,long int seed); 72 enum ErrorCode smolSetPartitions(simptr sim,const char *method,double value); 73 74 /********************************** Graphics **********************************/ 75 76 enum ErrorCode smolSetGraphicsParams(simptr sim,const char *method,int timesteps,int delay); 77 enum ErrorCode smolSetTiffParams(simptr sim,int timesteps,const char *tiffname,int lowcount,int highcount); 78 enum ErrorCode smolSetLightParams(simptr sim,int lightindex,double *ambient,double *diffuse,double *specular,double *position); 79 enum ErrorCode smolSetBackgroundStyle(simptr sim,double *color); 80 enum ErrorCode smolSetFrameStyle(simptr sim,double thickness,double *color); 81 enum ErrorCode smolSetGridStyle(simptr sim,double thickness,double *color); 82 enum ErrorCode smolSetTextStyle(simptr sim,double *color); 83 enum ErrorCode smolAddTextDisplay(simptr sim,char *item); 84 85 /***************************** Runtime commands *******************************/ 86 87 enum ErrorCode smolSetOutputPath(simptr sim,const char *path); 88 enum ErrorCode smolAddOutputFile(simptr sim,char *filename,int suffix,int append); 89 enum ErrorCode smolAddOutputData(simptr sim,char *dataname); 90 enum ErrorCode smolOpenOutputFiles(simptr sim, int overwrite); 91 //?? needs function for setting output precision 92 enum ErrorCode smolAddCommand(simptr sim,char type,double on,double off,double step,double multiplier,const char *commandstring); 93 enum ErrorCode smolAddCommandFromString(simptr sim,char *string); 94 enum ErrorCode smolGetOutputData(simptr sim,char *dataname,int *nrow,int *ncol,double **array,int erase); 95 enum ErrorCode smolRunCommand(simptr sim,const char *commandstring); 96 97 /********************************* Molecules **********************************/ 98 99 enum ErrorCode smolAddSpecies(simptr sim,const char *species,const char *mollist); 100 int smolGetSpeciesIndex(simptr sim,const char *species); 101 int smolGetSpeciesIndexNT(simptr sim,const char *species); 102 void smolGetSpeciesName(simptr sim,int speciesindex,char *species); 103 enum ErrorCode smolSetSpeciesMobility(simptr sim,const char *species,enum MolecState state,double difc,double *drift,double *difmatrix); 104 enum ErrorCode smolSetMoleculeColor(simptr sim, const char *species, enum MolecState state, double *color); 105 enum ErrorCode smolSetMoleculeSize(simptr sim, const char *species, enum MolecState state, double size); 106 107 //?? needs function smolSetSpeciesSurfaceDrift 108 enum ErrorCode smolAddMolList(simptr sim,const char *mollist); 109 int smolGetMolListIndex(simptr sim,const char *mollist); 110 int smolGetMolListIndexNT(simptr sim,const char *mollist); 111 char* smolGetMolListName(simptr sim,int mollistindex,char *mollist); 112 enum ErrorCode smolSetMolList(simptr sim,const char *species,enum MolecState state,const char *mollist); 113 enum ErrorCode smolSetMaxMolecules(simptr sim,int maxmolecules); 114 enum ErrorCode smolAddSolutionMolecules(simptr sim,const char *species,int number,double *lowposition,double *highposition); 115 enum ErrorCode smolAddCompartmentMolecules(simptr sim,const char *species,int number,const char *compartment); 116 enum ErrorCode smolAddSurfaceMolecules(simptr sim,const char *species,enum MolecState state,int number,const char *surface,enum PanelShape panelshape,const char *panel,double *position); 117 int smolGetMoleculeCount(simptr sim,const char *species,enum MolecState state); 118 enum ErrorCode smolSetMoleculeStyle(simptr sim,const char *species,enum MolecState state,double size,double *color); 119 120 /********************************** Surfaces **********************************/ 121 122 enum ErrorCode smolSetBoundaryType(simptr sim,int dimension,int highside,char type); 123 enum ErrorCode smolAddSurface(simptr sim,const char *surface); 124 int smolGetSurfaceIndex(simptr sim,const char *surface); 125 int smolGetSurfaceIndexNT(simptr sim,const char *surface); 126 char* smolGetSurfaceName(simptr sim,int surfaceindex,char *surface); 127 enum ErrorCode smolSetReactionIntersurface(simptr sim, const char *reaction, int *rulelist); 128 enum ErrorCode smolSetSurfaceAction(simptr sim,const char *surface,enum PanelFace face,const char *species,enum MolecState state,enum SrfAction action,const char *newspecies); 129 enum ErrorCode smolSetSurfaceRate(simptr sim,const char *surface,const char *species,enum MolecState state,enum MolecState state1,enum MolecState state2,double rate,const char *newspecies,int isinternal); 130 enum ErrorCode smolAddPanel(simptr sim,const char *surface,enum PanelShape panelshape,const char *panel,const char *axisstring,double *params); 131 int smolGetPanelIndex(simptr sim,const char *surface,enum PanelShape *panelshapeptr,const char *panel); 132 int smolGetPanelIndexNT(simptr sim,const char *surface,enum PanelShape *panelshapeptr,const char *panel); 133 char* smolGetPanelName(simptr sim,const char *surface,enum PanelShape panelshape,int panelindex,char *panel); 134 enum ErrorCode smolSetPanelJump(simptr sim,const char *surface,const char *panel1,enum PanelFace face1,const char *panel2,enum PanelFace face2,int isbidirectional); 135 enum ErrorCode smolAddSurfaceUnboundedEmitter(simptr sim,const char *surface,enum PanelFace face,const char *species,double emitamount,double *emitposition); 136 enum ErrorCode smolSetSurfaceSimParams(simptr sim,const char *parameter,double value); 137 enum ErrorCode smolAddPanelNeighbor(simptr sim,const char *surface1,const char *panel1,const char *surface2,const char *panel2,int reciprocal); 138 enum ErrorCode smolSetSurfaceStyle(simptr sim,const char *surface,enum PanelFace face,enum DrawMode mode,double thickness,double *color,int stipplefactor,int stipplepattern,double shininess); 139 140 /********************************* Compartments *******************************/ 141 142 enum ErrorCode smolAddCompartment(simptr sim,const char *compartment); 143 int smolGetCompartmentIndex(simptr sim,const char *compartment); 144 int smolGetCompartmentIndexNT(simptr sim,const char *compartment); 145 char* smolGetCompartmentName(simptr sim,int compartmentindex,char *compartment); 146 enum ErrorCode smolAddCompartmentSurface(simptr sim,const char *compartment,const char *surface); 147 enum ErrorCode smolAddCompartmentPoint(simptr sim,const char *compartment,double *point); 148 enum ErrorCode smolAddCompartmentLogic(simptr sim,const char *compartment,enum CmptLogic logic,const char *compartment2); 149 150 /********************************* Reactions **********************************/ 151 152 enum ErrorCode smolAddReaction(simptr sim,const char *reaction,const char *reactant1,enum MolecState rstate1,const char *reactant2,enum MolecState rstate2,int nproduct,const char **productspecies,enum MolecState *productstates,double rate); 153 int smolGetReactionIndex(simptr sim,int *orderptr,const char *reaction); 154 int smolGetReactionIndexNT(simptr sim,int *orderptr,const char *reaction); 155 char* smolGetReactionName(simptr sim,int order,int reactionindex,char *reaction); 156 enum ErrorCode smolSetReactionRate(simptr sim,const char *reaction,double rate,int type); 157 enum ErrorCode smolSetReactionRegion(simptr sim,const char *reaction,const char *compartment,const char *surface); 158 enum ErrorCode smolSetReactionProducts(simptr sim,const char *reaction,enum RevParam method,double parameter,const char *product,double *position); 159 160 /************************************ Ports ***********************************/ 161 162 enum ErrorCode smolAddPort(simptr sim,const char *port,const char *surface,enum PanelFace face); 163 int smolGetPortIndex(simptr sim,const char *port); 164 int smolGetPortIndexNT(simptr sim,const char *port); 165 char* smolGetPortName(simptr sim,int portindex,char *port); 166 enum ErrorCode smolAddPortMolecules(simptr sim,const char *port,int nmolec,const char *species,double **positions); 167 int smolGetPortMolecules(simptr sim,const char *port,const char *species,enum MolecState state,int remove); 168 169 /************************************ Lattices ***********************************/ 170 171 enum ErrorCode smolAddLattice(simptr sim,const char *lattice,const double *min,const double *max,const double *dx,const char *btype); 172 enum ErrorCode smolAddLatticePort(simptr sim,const char *lattice,const char *port); 173 enum ErrorCode smolAddLatticeSpecies(simptr sim,const char *lattice,const char *species); 174 int smolGetLatticeIndex(simptr sim,const char *lattice); 175 int smolGetLatticeIndexNT(simptr sim,const char *lattice); 176 char* smolGetLatticeName(simptr sim,int latticeindex,char *lattice); 177 enum ErrorCode smolAddLatticeMolecules(simptr sim,const char *lattice, const char *species,int number,double *lowposition,double *highposition); 178 enum ErrorCode smolAddLatticeReaction(simptr sim,const char *lattice,const char *reaction, const int move); 179 180 181 #ifdef __cplusplus 182 } 183 #endif 184 185 186 #endif 187